Correlation between copy number variation genes (focal) and selected clinical features
PANCANCER cohort with 12 disease types (Primary solid tumor)
22 February 2013 | analyses__2013_02_22
Maintainer Information
Citation Information
doi:10.7908/C190220F
Maintained by TCGA GDAC Team (Broad Institute/MD Anderson Cancer Center/Harvard Medical School)
Cite as Broad Institute TCGA Genome Data Analysis Center (2013): Correlation between copy number variation genes (focal) and selected clinical features. Broad Institute of MIT and Harvard. doi:10.7908/C190220F
Overview
Introduction

This pipeline computes the correlation between significant copy number variation (cnv focal) genes and selected clinical features.

Summary

Testing the association between subtypes identified by 91 different clustering approaches and 21 clinical features across 4563 patients, 527 significant findings detected with Q value < 0.25.

- 2 subtypes identified in current cancer cohort by 'Amp Peak 1(1p34.2) mutation analysis'. These subtypes correlate to 'PRIMARY.SITE.OF.DISEASE', 'GENDER', 'HISTOLOGICAL.TYPE', 'PATHOLOGY.T', and 'TUMOR.STAGE'.

- 2 subtypes identified in current cancer cohort by 'Amp Peak 2(1p22.3) mutation analysis'. These subtypes correlate to 'PRIMARY.SITE.OF.DISEASE', 'GENDER', 'HISTOLOGICAL.TYPE', 'PATHOLOGY.T', and 'TUMOR.STAGE'.

- 2 subtypes identified in current cancer cohort by 'Amp Peak 3(1q21.3) mutation analysis'. These subtypes correlate to 'Time to Death', 'PRIMARY.SITE.OF.DISEASE', 'GENDER', 'HISTOLOGICAL.TYPE', 'PATHOLOGY.T', 'PATHOLOGICSPREAD(M)', and 'TUMOR.STAGE'.

- 2 subtypes identified in current cancer cohort by 'Amp Peak 4(1q32.1) mutation analysis'. These subtypes correlate to 'Time to Death', 'PRIMARY.SITE.OF.DISEASE', 'GENDER', 'HISTOLOGICAL.TYPE', 'PATHOLOGY.T', 'PATHOLOGICSPREAD(M)', 'TOBACCOSMOKINGHISTORYINDICATOR', and 'NEOPLASM.DISEASESTAGE'.

- 2 subtypes identified in current cancer cohort by 'Amp Peak 5(1q44) mutation analysis'. These subtypes correlate to 'Time to Death', 'PRIMARY.SITE.OF.DISEASE', 'GENDER', 'HISTOLOGICAL.TYPE', 'PATHOLOGY.T', 'PATHOLOGICSPREAD(M)', and 'NEOPLASM.DISEASESTAGE'.

- 2 subtypes identified in current cancer cohort by 'Amp Peak 6(2p15) mutation analysis'. These subtypes correlate to 'AGE', 'PRIMARY.SITE.OF.DISEASE', 'KARNOFSKY.PERFORMANCE.SCORE', 'HISTOLOGICAL.TYPE', 'TUMOR.STAGE', 'RADIATIONS.RADIATION.REGIMENINDICATION', and 'NEOPLASM.DISEASESTAGE'.

- 2 subtypes identified in current cancer cohort by 'Amp Peak 7(2q31.2) mutation analysis'. These subtypes correlate to 'AGE', 'PRIMARY.SITE.OF.DISEASE', 'HISTOLOGICAL.TYPE', 'TUMOR.STAGE', 'RADIATIONS.RADIATION.REGIMENINDICATION', and 'TOBACCOSMOKINGHISTORYINDICATOR'.

- 2 subtypes identified in current cancer cohort by 'Amp Peak 8(3q26.2) mutation analysis'. These subtypes correlate to 'PRIMARY.SITE.OF.DISEASE', 'KARNOFSKY.PERFORMANCE.SCORE', 'HISTOLOGICAL.TYPE', 'PATHOLOGY.T', 'PATHOLOGY.N', 'TUMOR.STAGE', 'RADIATIONS.RADIATION.REGIMENINDICATION', and 'NUMBERPACKYEARSSMOKED'.

- 2 subtypes identified in current cancer cohort by 'Amp Peak 9(4p16.3) mutation analysis'. These subtypes correlate to 'PRIMARY.SITE.OF.DISEASE', 'GENDER', 'HISTOLOGICAL.TYPE', 'PATHOLOGY.T', and 'TUMOR.STAGE'.

- 2 subtypes identified in current cancer cohort by 'Amp Peak 10(4q12) mutation analysis'. These subtypes correlate to 'Time to Death', 'PRIMARY.SITE.OF.DISEASE', 'HISTOLOGICAL.TYPE', and 'PATHOLOGY.T'.

- 2 subtypes identified in current cancer cohort by 'Amp Peak 11(5p15.33) mutation analysis'. These subtypes correlate to 'AGE', 'PRIMARY.SITE.OF.DISEASE', 'KARNOFSKY.PERFORMANCE.SCORE', 'HISTOLOGICAL.TYPE', 'PATHOLOGY.T', 'TUMOR.STAGE', 'RADIATIONS.RADIATION.REGIMENINDICATION', and 'TOBACCOSMOKINGHISTORYINDICATOR'.

- 2 subtypes identified in current cancer cohort by 'Amp Peak 12(5q35.3) mutation analysis'. These subtypes correlate to 'Time to Death', 'PRIMARY.SITE.OF.DISEASE', 'HISTOLOGICAL.TYPE', 'PATHOLOGY.T', 'PATHOLOGY.N', 'TUMOR.STAGE', and 'RADIATIONS.RADIATION.REGIMENINDICATION'.

- 2 subtypes identified in current cancer cohort by 'Amp Peak 13(6p22.3) mutation analysis'. These subtypes correlate to 'PRIMARY.SITE.OF.DISEASE', 'GENDER', 'HISTOLOGICAL.TYPE', 'PATHOLOGICSPREAD(M)', 'TUMOR.STAGE', and 'RADIATIONS.RADIATION.REGIMENINDICATION'.

- 2 subtypes identified in current cancer cohort by 'Amp Peak 14(6p21.1) mutation analysis'. These subtypes correlate to 'PRIMARY.SITE.OF.DISEASE', 'GENDER', 'HISTOLOGICAL.TYPE', 'PATHOLOGICSPREAD(M)', 'TUMOR.STAGE', and 'RADIATIONS.RADIATION.REGIMENINDICATION'.

- 2 subtypes identified in current cancer cohort by 'Amp Peak 15(6q21) mutation analysis'. These subtypes correlate to 'PRIMARY.SITE.OF.DISEASE', 'GENDER', 'HISTOLOGICAL.TYPE', and 'PATHOLOGY.T'.

- 2 subtypes identified in current cancer cohort by 'Amp Peak 16(7p11.2) mutation analysis'. These subtypes correlate to 'Time to Death', 'PRIMARY.SITE.OF.DISEASE', 'GENDER', 'HISTOLOGICAL.TYPE', 'PATHOLOGY.T', 'PATHOLOGY.N', and 'RADIATIONS.RADIATION.REGIMENINDICATION'.

- 2 subtypes identified in current cancer cohort by 'Amp Peak 17(7q36.3) mutation analysis'. These subtypes correlate to 'Time to Death', 'PRIMARY.SITE.OF.DISEASE', 'GENDER', 'HISTOLOGICAL.TYPE', 'TUMOR.STAGE', and 'RADIATIONS.RADIATION.REGIMENINDICATION'.

- 2 subtypes identified in current cancer cohort by 'Amp Peak 18(8p11.23) mutation analysis'. These subtypes correlate to 'PRIMARY.SITE.OF.DISEASE', 'HISTOLOGICAL.TYPE', 'PATHOLOGY.T', and 'RADIATIONS.RADIATION.REGIMENINDICATION'.

- 2 subtypes identified in current cancer cohort by 'Amp Peak 19(8p11.21) mutation analysis'. These subtypes correlate to 'AGE', 'PRIMARY.SITE.OF.DISEASE', 'HISTOLOGICAL.TYPE', 'PATHOLOGY.T', 'TUMOR.STAGE', and 'RADIATIONS.RADIATION.REGIMENINDICATION'.

- 2 subtypes identified in current cancer cohort by 'Amp Peak 20(8q24.21) mutation analysis'. These subtypes correlate to 'PRIMARY.SITE.OF.DISEASE', 'GENDER', 'KARNOFSKY.PERFORMANCE.SCORE', 'HISTOLOGICAL.TYPE', 'PATHOLOGY.T', 'PATHOLOGY.N', 'TUMOR.STAGE', and 'RADIATIONS.RADIATION.REGIMENINDICATION'.

- 2 subtypes identified in current cancer cohort by 'Amp Peak 21(9p13.3) mutation analysis'. These subtypes correlate to 'PRIMARY.SITE.OF.DISEASE', 'HISTOLOGICAL.TYPE', and 'PATHOLOGY.T'.

- 2 subtypes identified in current cancer cohort by 'Amp Peak 22(10p15.1) mutation analysis'. These subtypes correlate to 'PRIMARY.SITE.OF.DISEASE', 'GENDER', 'HISTOLOGICAL.TYPE', 'PATHOLOGY.T', 'TUMOR.STAGE', 'RADIATIONS.RADIATION.REGIMENINDICATION', and 'TOBACCOSMOKINGHISTORYINDICATOR'.

- 2 subtypes identified in current cancer cohort by 'Amp Peak 23(10q22.2) mutation analysis'. These subtypes correlate to 'PRIMARY.SITE.OF.DISEASE', 'GENDER', 'HISTOLOGICAL.TYPE', and 'TUMOR.STAGE'.

- 2 subtypes identified in current cancer cohort by 'Amp Peak 24(11q13.3) mutation analysis'. These subtypes correlate to 'PRIMARY.SITE.OF.DISEASE', 'GENDER', 'HISTOLOGICAL.TYPE', 'PATHOLOGY.T', 'PATHOLOGY.N', 'TUMOR.STAGE', and 'RADIATIONS.RADIATION.REGIMENINDICATION'.

- 2 subtypes identified in current cancer cohort by 'Amp Peak 25(12p13.33) mutation analysis'. These subtypes correlate to 'PRIMARY.SITE.OF.DISEASE', 'HISTOLOGICAL.TYPE', 'PATHOLOGY.T', 'TUMOR.STAGE', and 'RADIATIONS.RADIATION.REGIMENINDICATION'.

- 2 subtypes identified in current cancer cohort by 'Amp Peak 26(12p12.1) mutation analysis'. These subtypes correlate to 'PRIMARY.SITE.OF.DISEASE', 'HISTOLOGICAL.TYPE', 'PATHOLOGY.T', 'TUMOR.STAGE', and 'RADIATIONS.RADIATION.REGIMENINDICATION'.

- 2 subtypes identified in current cancer cohort by 'Amp Peak 27(12q14.1) mutation analysis'. These subtypes correlate to 'Time to Death', 'AGE', 'PRIMARY.SITE.OF.DISEASE', and 'HISTOLOGICAL.TYPE'.

- 2 subtypes identified in current cancer cohort by 'Amp Peak 28(12q15) mutation analysis'. These subtypes correlate to 'AGE', 'PRIMARY.SITE.OF.DISEASE', 'HISTOLOGICAL.TYPE', and 'RADIATIONS.RADIATION.REGIMENINDICATION'.

- 2 subtypes identified in current cancer cohort by 'Amp Peak 29(13q34) mutation analysis'. These subtypes correlate to 'AGE', 'PRIMARY.SITE.OF.DISEASE', 'HISTOLOGICAL.TYPE', 'PATHOLOGY.T', 'PATHOLOGY.N', 'PATHOLOGICSPREAD(M)', 'TUMOR.STAGE', 'RADIATIONS.RADIATION.REGIMENINDICATION', and 'TOBACCOSMOKINGHISTORYINDICATOR'.

- 2 subtypes identified in current cancer cohort by 'Amp Peak 30(14q13.3) mutation analysis'. These subtypes correlate to 'PRIMARY.SITE.OF.DISEASE', 'HISTOLOGICAL.TYPE', 'PATHOLOGY.T', 'PATHOLOGICSPREAD(M)', and 'RADIATIONS.RADIATION.REGIMENINDICATION'.

- 2 subtypes identified in current cancer cohort by 'Amp Peak 31(15q26.3) mutation analysis'. These subtypes correlate to 'PRIMARY.SITE.OF.DISEASE', 'HISTOLOGICAL.TYPE', 'PATHOLOGY.T', and 'RADIATIONS.RADIATION.REGIMENINDICATION'.

- 2 subtypes identified in current cancer cohort by 'Amp Peak 32(17q12) mutation analysis'. These subtypes correlate to 'AGE', 'PRIMARY.SITE.OF.DISEASE', 'HISTOLOGICAL.TYPE', 'PATHOLOGY.T', and 'PATHOLOGICSPREAD(M)'.

- 2 subtypes identified in current cancer cohort by 'Amp Peak 33(17q25.3) mutation analysis'. These subtypes correlate to 'PRIMARY.SITE.OF.DISEASE', 'HISTOLOGICAL.TYPE', 'PATHOLOGY.T', 'PATHOLOGICSPREAD(M)', 'RADIATIONS.RADIATION.REGIMENINDICATION', and 'STOPPEDSMOKINGYEAR'.

- 2 subtypes identified in current cancer cohort by 'Amp Peak 34(18q11.2) mutation analysis'. These subtypes correlate to 'PRIMARY.SITE.OF.DISEASE', 'HISTOLOGICAL.TYPE', and 'PATHOLOGY.T'.

- 2 subtypes identified in current cancer cohort by 'Amp Peak 35(19p13.2) mutation analysis'. These subtypes correlate to 'Time to Death', 'PRIMARY.SITE.OF.DISEASE', 'HISTOLOGICAL.TYPE', 'TUMOR.STAGE', and 'RADIATIONS.RADIATION.REGIMENINDICATION'.

- 2 subtypes identified in current cancer cohort by 'Amp Peak 36(19p13.12) mutation analysis'. These subtypes correlate to 'PRIMARY.SITE.OF.DISEASE', 'HISTOLOGICAL.TYPE', 'TUMOR.STAGE', and 'RADIATIONS.RADIATION.REGIMENINDICATION'.

- 2 subtypes identified in current cancer cohort by 'Amp Peak 37(19q12) mutation analysis'. These subtypes correlate to 'Time to Death', 'PRIMARY.SITE.OF.DISEASE', 'HISTOLOGICAL.TYPE', 'PATHOLOGY.T', and 'TUMOR.STAGE'.

- 2 subtypes identified in current cancer cohort by 'Amp Peak 38(20q11.21) mutation analysis'. These subtypes correlate to 'Time to Death', 'AGE', 'PRIMARY.SITE.OF.DISEASE', 'GENDER', 'HISTOLOGICAL.TYPE', 'PATHOLOGY.T', 'PATHOLOGY.N', 'TUMOR.STAGE', and 'RADIATIONS.RADIATION.REGIMENINDICATION'.

- 2 subtypes identified in current cancer cohort by 'Amp Peak 39(20q13.2) mutation analysis'. These subtypes correlate to 'AGE', 'PRIMARY.SITE.OF.DISEASE', 'HISTOLOGICAL.TYPE', 'PATHOLOGY.T', 'TUMOR.STAGE', and 'RADIATIONS.RADIATION.REGIMENINDICATION'.

- 2 subtypes identified in current cancer cohort by 'Amp Peak 40(Xq28) mutation analysis'. These subtypes correlate to 'PRIMARY.SITE.OF.DISEASE', 'HISTOLOGICAL.TYPE', 'PATHOLOGY.T', 'PATHOLOGY.N', and 'TUMOR.STAGE'.

- 2 subtypes identified in current cancer cohort by 'Del Peak 1(1p36.23) mutation analysis'. These subtypes correlate to 'PRIMARY.SITE.OF.DISEASE', 'HISTOLOGICAL.TYPE', and 'NEOPLASM.DISEASESTAGE'.

- 2 subtypes identified in current cancer cohort by 'Del Peak 2(1p36.11) mutation analysis'. These subtypes correlate to 'PRIMARY.SITE.OF.DISEASE', 'HISTOLOGICAL.TYPE', 'TUMOR.STAGE', 'RADIATIONS.RADIATION.REGIMENINDICATION', 'TOBACCOSMOKINGHISTORYINDICATOR', 'NUMBER.OF.LYMPH.NODES', and 'NEOPLASM.DISEASESTAGE'.

- 2 subtypes identified in current cancer cohort by 'Del Peak 3(1p13.2) mutation analysis'. These subtypes correlate to 'AGE', 'PRIMARY.SITE.OF.DISEASE', 'HISTOLOGICAL.TYPE', 'RADIATIONS.RADIATION.REGIMENINDICATION', 'TOBACCOSMOKINGHISTORYINDICATOR', and 'NUMBER.OF.LYMPH.NODES'.

- 2 subtypes identified in current cancer cohort by 'Del Peak 4(2q22.1) mutation analysis'. These subtypes correlate to 'PRIMARY.SITE.OF.DISEASE', 'HISTOLOGICAL.TYPE', 'PATHOLOGY.T', and 'TUMOR.STAGE'.

- 2 subtypes identified in current cancer cohort by 'Del Peak 5(2q37.3) mutation analysis'. These subtypes correlate to 'PRIMARY.SITE.OF.DISEASE', 'HISTOLOGICAL.TYPE', and 'TOBACCOSMOKINGHISTORYINDICATOR'.

- 2 subtypes identified in current cancer cohort by 'Del Peak 6(3p26.2) mutation analysis'. These subtypes correlate to 'PRIMARY.SITE.OF.DISEASE', 'GENDER', 'HISTOLOGICAL.TYPE', 'PATHOLOGY.T', 'TUMOR.STAGE', 'RADIATIONS.RADIATION.REGIMENINDICATION', and 'TOBACCOSMOKINGHISTORYINDICATOR'.

- 2 subtypes identified in current cancer cohort by 'Del Peak 7(3p14.2) mutation analysis'. These subtypes correlate to 'PRIMARY.SITE.OF.DISEASE', 'GENDER', 'KARNOFSKY.PERFORMANCE.SCORE', 'HISTOLOGICAL.TYPE', 'PATHOLOGY.T', 'TUMOR.STAGE', 'RADIATIONS.RADIATION.REGIMENINDICATION', and 'TOBACCOSMOKINGHISTORYINDICATOR'.

- 2 subtypes identified in current cancer cohort by 'Del Peak 8(4p16.3) mutation analysis'. These subtypes correlate to 'PRIMARY.SITE.OF.DISEASE', 'HISTOLOGICAL.TYPE', 'PATHOLOGY.T', 'PATHOLOGY.N', 'TUMOR.STAGE', 'RADIATIONS.RADIATION.REGIMENINDICATION', 'STOPPEDSMOKINGYEAR', and 'TOBACCOSMOKINGHISTORYINDICATOR'.

- 2 subtypes identified in current cancer cohort by 'Del Peak 9(4q22.1) mutation analysis'. These subtypes correlate to 'PRIMARY.SITE.OF.DISEASE', 'HISTOLOGICAL.TYPE', 'PATHOLOGY.T', 'TUMOR.STAGE', and 'RADIATIONS.RADIATION.REGIMENINDICATION'.

- 2 subtypes identified in current cancer cohort by 'Del Peak 10(4q34.3) mutation analysis'. These subtypes correlate to 'PRIMARY.SITE.OF.DISEASE', 'HISTOLOGICAL.TYPE', 'PATHOLOGY.T', 'TUMOR.STAGE', and 'RADIATIONS.RADIATION.REGIMENINDICATION'.

- 2 subtypes identified in current cancer cohort by 'Del Peak 11(5q11.2) mutation analysis'. These subtypes correlate to 'PRIMARY.SITE.OF.DISEASE', 'KARNOFSKY.PERFORMANCE.SCORE', 'HISTOLOGICAL.TYPE', 'PATHOLOGY.T', 'PATHOLOGY.N', 'TUMOR.STAGE', 'RADIATIONS.RADIATION.REGIMENINDICATION', 'NUMBERPACKYEARSSMOKED', 'TOBACCOSMOKINGHISTORYINDICATOR', and 'NEOPLASM.DISEASESTAGE'.

- 2 subtypes identified in current cancer cohort by 'Del Peak 12(5q21.3) mutation analysis'. These subtypes correlate to 'PRIMARY.SITE.OF.DISEASE', 'KARNOFSKY.PERFORMANCE.SCORE', 'HISTOLOGICAL.TYPE', 'PATHOLOGY.T', 'PATHOLOGY.N', 'PATHOLOGICSPREAD(M)', 'RADIATIONS.RADIATION.REGIMENINDICATION', and 'TOBACCOSMOKINGHISTORYINDICATOR'.

- 2 subtypes identified in current cancer cohort by 'Del Peak 13(6p25.3) mutation analysis'. These subtypes correlate to 'PRIMARY.SITE.OF.DISEASE', 'GENDER', and 'HISTOLOGICAL.TYPE'.

- 2 subtypes identified in current cancer cohort by 'Del Peak 14(6q22.31) mutation analysis'. These subtypes correlate to 'PRIMARY.SITE.OF.DISEASE', 'HISTOLOGICAL.TYPE', 'PATHOLOGY.T', and 'TUMOR.STAGE'.

- 2 subtypes identified in current cancer cohort by 'Del Peak 15(6q26) mutation analysis'. These subtypes correlate to 'AGE', 'PRIMARY.SITE.OF.DISEASE', 'HISTOLOGICAL.TYPE', and 'TUMOR.STAGE'.

- 2 subtypes identified in current cancer cohort by 'Del Peak 16(7p22.3) mutation analysis'. These subtypes correlate to 'PRIMARY.SITE.OF.DISEASE', 'GENDER', 'HISTOLOGICAL.TYPE', 'PATHOLOGY.T', and 'TUMOR.STAGE'.

- 2 subtypes identified in current cancer cohort by 'Del Peak 17(7q36.1) mutation analysis'. These subtypes correlate to 'PRIMARY.SITE.OF.DISEASE', 'HISTOLOGICAL.TYPE', and 'PATHOLOGY.T'.

- 2 subtypes identified in current cancer cohort by 'Del Peak 18(8p23.2) mutation analysis'. These subtypes correlate to 'PRIMARY.SITE.OF.DISEASE', 'KARNOFSKY.PERFORMANCE.SCORE', 'HISTOLOGICAL.TYPE', 'PATHOLOGY.T', 'PATHOLOGY.N', 'TUMOR.STAGE', and 'RADIATIONS.RADIATION.REGIMENINDICATION'.

- 2 subtypes identified in current cancer cohort by 'Del Peak 19(8p21.2) mutation analysis'. These subtypes correlate to 'PRIMARY.SITE.OF.DISEASE', 'KARNOFSKY.PERFORMANCE.SCORE', 'HISTOLOGICAL.TYPE', 'PATHOLOGY.N', 'TUMOR.STAGE', and 'RADIATIONS.RADIATION.REGIMENINDICATION'.

- 2 subtypes identified in current cancer cohort by 'Del Peak 20(9p23) mutation analysis'. These subtypes correlate to 'Time to Death', 'PRIMARY.SITE.OF.DISEASE', 'GENDER', 'HISTOLOGICAL.TYPE', and 'PATHOLOGY.T'.

- 2 subtypes identified in current cancer cohort by 'Del Peak 21(9p21.3) mutation analysis'. These subtypes correlate to 'Time to Death', 'PRIMARY.SITE.OF.DISEASE', 'GENDER', 'HISTOLOGICAL.TYPE', 'PATHOLOGY.T', 'RADIATIONS.RADIATION.REGIMENINDICATION', 'LYMPH.NODE.METASTASIS', and 'NEOPLASM.DISEASESTAGE'.

- 2 subtypes identified in current cancer cohort by 'Del Peak 22(9p21.3) mutation analysis'. These subtypes correlate to 'Time to Death', 'PRIMARY.SITE.OF.DISEASE', 'GENDER', 'HISTOLOGICAL.TYPE', 'PATHOLOGY.T', 'RADIATIONS.RADIATION.REGIMENINDICATION', 'LYMPH.NODE.METASTASIS', and 'NEOPLASM.DISEASESTAGE'.

- 2 subtypes identified in current cancer cohort by 'Del Peak 23(9q21.11) mutation analysis'. These subtypes correlate to 'AGE', 'PRIMARY.SITE.OF.DISEASE', 'HISTOLOGICAL.TYPE', 'PATHOLOGY.T', 'TUMOR.STAGE', and 'RADIATIONS.RADIATION.REGIMENINDICATION'.

- 2 subtypes identified in current cancer cohort by 'Del Peak 24(9q34.3) mutation analysis'. These subtypes correlate to 'PRIMARY.SITE.OF.DISEASE', 'HISTOLOGICAL.TYPE', 'PATHOLOGY.T', 'TUMOR.STAGE', and 'RADIATIONS.RADIATION.REGIMENINDICATION'.

- 2 subtypes identified in current cancer cohort by 'Del Peak 25(10p15.3) mutation analysis'. These subtypes correlate to 'Time to Death', 'PRIMARY.SITE.OF.DISEASE', 'GENDER', 'HISTOLOGICAL.TYPE', 'PATHOLOGY.T', and 'RADIATIONS.RADIATION.REGIMENINDICATION'.

- 2 subtypes identified in current cancer cohort by 'Del Peak 26(10q23.31) mutation analysis'. These subtypes correlate to 'Time to Death', 'PRIMARY.SITE.OF.DISEASE', 'GENDER', 'HISTOLOGICAL.TYPE', 'RADIATIONS.RADIATION.REGIMENINDICATION', and 'YEAROFTOBACCOSMOKINGONSET'.

- 2 subtypes identified in current cancer cohort by 'Del Peak 27(10q26.3) mutation analysis'. These subtypes correlate to 'Time to Death', 'PRIMARY.SITE.OF.DISEASE', 'GENDER', 'HISTOLOGICAL.TYPE', and 'RADIATIONS.RADIATION.REGIMENINDICATION'.

- 2 subtypes identified in current cancer cohort by 'Del Peak 28(11p15.5) mutation analysis'. These subtypes correlate to 'PRIMARY.SITE.OF.DISEASE', 'GENDER', 'HISTOLOGICAL.TYPE', 'PATHOLOGY.T', 'TUMOR.STAGE', and 'TOBACCOSMOKINGHISTORYINDICATOR'.

- 2 subtypes identified in current cancer cohort by 'Del Peak 29(11q23.1) mutation analysis'. These subtypes correlate to 'PRIMARY.SITE.OF.DISEASE', 'GENDER', 'HISTOLOGICAL.TYPE', 'PATHOLOGY.T', 'PATHOLOGY.N', and 'TUMOR.STAGE'.

- 2 subtypes identified in current cancer cohort by 'Del Peak 30(11q25) mutation analysis'. These subtypes correlate to 'PRIMARY.SITE.OF.DISEASE', 'GENDER', 'HISTOLOGICAL.TYPE', 'PATHOLOGY.T', 'PATHOLOGY.N', and 'TUMOR.STAGE'.

- 2 subtypes identified in current cancer cohort by 'Del Peak 31(12p13.1) mutation analysis'. These subtypes correlate to 'PRIMARY.SITE.OF.DISEASE', 'GENDER', 'HISTOLOGICAL.TYPE', and 'PATHOLOGICSPREAD(M)'.

- 2 subtypes identified in current cancer cohort by 'Del Peak 32(12q23.1) mutation analysis'. These subtypes correlate to 'PRIMARY.SITE.OF.DISEASE', 'GENDER', 'HISTOLOGICAL.TYPE', 'PATHOLOGY.T', 'PATHOLOGICSPREAD(M)', and 'TUMOR.STAGE'.

- 2 subtypes identified in current cancer cohort by 'Del Peak 33(12q24.33) mutation analysis'. These subtypes correlate to 'PRIMARY.SITE.OF.DISEASE', 'GENDER', 'HISTOLOGICAL.TYPE', 'PATHOLOGY.T', and 'TUMOR.STAGE'.

- 2 subtypes identified in current cancer cohort by 'Del Peak 34(13q11) mutation analysis'. These subtypes correlate to 'PRIMARY.SITE.OF.DISEASE', 'HISTOLOGICAL.TYPE', 'PATHOLOGY.T', 'PATHOLOGICSPREAD(M)', 'TUMOR.STAGE', and 'TOBACCOSMOKINGHISTORYINDICATOR'.

- 2 subtypes identified in current cancer cohort by 'Del Peak 35(13q14.2) mutation analysis'. These subtypes correlate to 'Time to Death', 'PRIMARY.SITE.OF.DISEASE', 'HISTOLOGICAL.TYPE', 'PATHOLOGY.T', 'PATHOLOGICSPREAD(M)', 'TUMOR.STAGE', and 'TOBACCOSMOKINGHISTORYINDICATOR'.

- 2 subtypes identified in current cancer cohort by 'Del Peak 36(14q24.1) mutation analysis'. These subtypes correlate to 'PRIMARY.SITE.OF.DISEASE', 'HISTOLOGICAL.TYPE', 'PATHOLOGY.T', 'PATHOLOGY.N', and 'TUMOR.STAGE'.

- 2 subtypes identified in current cancer cohort by 'Del Peak 37(15q11.2) mutation analysis'. These subtypes correlate to 'PRIMARY.SITE.OF.DISEASE', 'GENDER', 'HISTOLOGICAL.TYPE', 'PATHOLOGY.T', 'PATHOLOGY.N', 'TUMOR.STAGE', and 'RADIATIONS.RADIATION.REGIMENINDICATION'.

- 2 subtypes identified in current cancer cohort by 'Del Peak 38(15q15.1) mutation analysis'. These subtypes correlate to 'PRIMARY.SITE.OF.DISEASE', 'GENDER', 'HISTOLOGICAL.TYPE', 'PATHOLOGY.T', 'PATHOLOGY.N', 'TUMOR.STAGE', and 'RADIATIONS.RADIATION.REGIMENINDICATION'.

- 2 subtypes identified in current cancer cohort by 'Del Peak 39(16p13.3) mutation analysis'. These subtypes correlate to 'Time to Death', 'PRIMARY.SITE.OF.DISEASE', 'HISTOLOGICAL.TYPE', 'TUMOR.STAGE', 'RADIATIONS.RADIATION.REGIMENINDICATION', and 'NEOPLASM.DISEASESTAGE'.

- 2 subtypes identified in current cancer cohort by 'Del Peak 40(16q23.1) mutation analysis'. These subtypes correlate to 'PRIMARY.SITE.OF.DISEASE', 'GENDER', 'HISTOLOGICAL.TYPE', 'PATHOLOGY.T', 'TUMOR.STAGE', 'RADIATIONS.RADIATION.REGIMENINDICATION', and 'NEOPLASM.DISEASESTAGE'.

- 2 subtypes identified in current cancer cohort by 'Del Peak 41(17p12) mutation analysis'. These subtypes correlate to 'PRIMARY.SITE.OF.DISEASE', 'GENDER', 'KARNOFSKY.PERFORMANCE.SCORE', 'HISTOLOGICAL.TYPE', 'PATHOLOGY.T', 'PATHOLOGY.N', 'TUMOR.STAGE', and 'RADIATIONS.RADIATION.REGIMENINDICATION'.

- 2 subtypes identified in current cancer cohort by 'Del Peak 42(17q11.2) mutation analysis'. These subtypes correlate to 'AGE', 'PRIMARY.SITE.OF.DISEASE', 'GENDER', 'HISTOLOGICAL.TYPE', 'TUMOR.STAGE', and 'RADIATIONS.RADIATION.REGIMENINDICATION'.

- 2 subtypes identified in current cancer cohort by 'Del Peak 43(18q21.2) mutation analysis'. These subtypes correlate to 'AGE', 'PRIMARY.SITE.OF.DISEASE', 'HISTOLOGICAL.TYPE', 'PATHOLOGY.T', 'PATHOLOGY.N', 'PATHOLOGICSPREAD(M)', 'TUMOR.STAGE', and 'RADIATIONS.RADIATION.REGIMENINDICATION'.

- 2 subtypes identified in current cancer cohort by 'Del Peak 44(18q23) mutation analysis'. These subtypes correlate to 'PRIMARY.SITE.OF.DISEASE', 'HISTOLOGICAL.TYPE', 'PATHOLOGY.T', 'PATHOLOGY.N', 'PATHOLOGICSPREAD(M)', 'TUMOR.STAGE', and 'RADIATIONS.RADIATION.REGIMENINDICATION'.

- 2 subtypes identified in current cancer cohort by 'Del Peak 45(19p13.3) mutation analysis'. These subtypes correlate to 'PRIMARY.SITE.OF.DISEASE', 'GENDER', 'HISTOLOGICAL.TYPE', 'PATHOLOGY.T', 'PATHOLOGY.N', 'TUMOR.STAGE', and 'RADIATIONS.RADIATION.REGIMENINDICATION'.

- 2 subtypes identified in current cancer cohort by 'Del Peak 46(19q13.32) mutation analysis'. These subtypes correlate to 'PRIMARY.SITE.OF.DISEASE', 'GENDER', 'HISTOLOGICAL.TYPE', 'PATHOLOGY.T', and 'TUMOR.STAGE'.

- 2 subtypes identified in current cancer cohort by 'Del Peak 47(19q13.43) mutation analysis'. These subtypes correlate to 'PRIMARY.SITE.OF.DISEASE', 'GENDER', 'HISTOLOGICAL.TYPE', 'PATHOLOGY.T', and 'TUMOR.STAGE'.

- 2 subtypes identified in current cancer cohort by 'Del Peak 48(20p12.1) mutation analysis'. These subtypes correlate to 'PRIMARY.SITE.OF.DISEASE', 'HISTOLOGICAL.TYPE', and 'RADIATIONS.RADIATION.REGIMENINDICATION'.

- 2 subtypes identified in current cancer cohort by 'Del Peak 49(21q11.2) mutation analysis'. These subtypes correlate to 'PRIMARY.SITE.OF.DISEASE', 'HISTOLOGICAL.TYPE', 'PATHOLOGY.T', 'RADIATIONS.RADIATION.REGIMENINDICATION', and 'TOBACCOSMOKINGHISTORYINDICATOR'.

- 2 subtypes identified in current cancer cohort by 'Del Peak 50(22q13.32) mutation analysis'. These subtypes correlate to 'Time to Death', 'PRIMARY.SITE.OF.DISEASE', 'GENDER', 'HISTOLOGICAL.TYPE', 'PATHOLOGICSPREAD(M)', 'TUMOR.STAGE', and 'COMPLETENESS.OF.RESECTION'.

- 2 subtypes identified in current cancer cohort by 'Del Peak 51(Xp21.1) mutation analysis'. These subtypes correlate to 'Time to Death', 'PRIMARY.SITE.OF.DISEASE', 'HISTOLOGICAL.TYPE', and 'TUMOR.STAGE'.

Results
Overview of the results

Table 1. Get Full Table Overview of the association between subtypes identified by 91 different clustering approaches and 21 clinical features. Shown in the table are P values (Q values). Thresholded by Q value < 0.25, 527 significant findings detected.

Clinical Features | Time to Death | AGE | PRIMARY SITE OF DISEASE | GENDER | KARNOFSKY PERFORMANCE SCORE | HISTOLOGICAL TYPE | PATHOLOGY T | PATHOLOGY N | PATHOLOGICSPREAD(M) | TUMOR STAGE | RADIATIONS RADIATION REGIMENINDICATION | NUMBERPACKYEARSSMOKED | STOPPEDSMOKINGYEAR | TOBACCOSMOKINGHISTORYINDICATOR | YEAROFTOBACCOSMOKINGONSET | DISTANT METASTASIS | LYMPH NODE METASTASIS | COMPLETENESS OF RESECTION | NUMBER OF LYMPH NODES | TUMOR STAGECODE | NEOPLASM DISEASESTAGE
Statistical Tests | logrank test | t-test | Chi-square test | Fisher's exact test | t-test | Chi-square test | Fisher's exact test | Fisher's exact test | Chi-square test | Fisher's exact test | Fisher's exact test | t-test | t-test | Chi-square test | t-test | Fisher's exact test | Chi-square test | Fisher's exact test | t-test | t-test | Chi-square test
Amp Peak 1(1p34 2) | 0.0193 (1.00) | 0.508 (1.00) | 1.57e-118 (2.77e-115) | 2.69e-13 (4.16e-10) | 0.174 (1.00) | 1.32e-115 (2.32e-112) | 1.49e-06 (0.00213) | 0.646 (1.00) | 0.0056 (1.00) | 2.52e-16 (3.94e-13) | 0.0155 (1.00) | 0.999 (1.00) | 0.371 (1.00) | 0.414 (1.00) | 0.586 (1.00) | 0.168 (1.00) | 0.243 (1.00) | 0.0143 (1.00) | 0.979 (1.00) |  | 0.000248 (0.319)
Amp Peak 2(1p22 3) | 0.612 (1.00) | 0.793 (1.00) | 2.49e-44 (4.12e-41) | 8.9e-12 (1.36e-08) | 0.288 (1.00) | 1.9e-41 (3.14e-38) | 5.91e-06 (0.00825) | 0.152 (1.00) | 0.0137 (1.00) | 0.000128 (0.167) | 0.719 (1.00) | 0.293 (1.00) | 0.0428 (1.00) | 0.0304 (1.00) | 0.202 (1.00) | 0.573 (1.00) | 0.68 (1.00) | 0.0808 (1.00) | 0.607 (1.00) |  | 0.391 (1.00)
Amp Peak 3(1q21 3) | 1.78e-06 (0.00254) | 0.00837 (1.00) | 1.2e-202 (2.15e-199) | 1.78e-37 (2.94e-34) | 0.0255 (1.00) | 7.04e-110 (1.23e-106) | 1.13e-15 (1.76e-12) | 0.00784 (1.00) | 1e-05 (0.0139) | 1.62e-06 (0.00231) | 0.0272 (1.00) | 0.497 (1.00) | 0.11 (1.00) | 0.00392 (1.00) | 0.576 (1.00) | 0.369 (1.00) | 0.521 (1.00) | 0.342 (1.00) | 0.0234 (1.00) |  | 0.00826 (1.00)
Amp Peak 4(1q32 1) | 1.36e-05 (0.0187) | 0.09 (1.00) | 3.02e-185 (5.4e-182) | 2.97e-29 (4.81e-26) | 0.0048 (1.00) | 3.76e-84 (6.45e-81) | 1.32e-16 (2.08e-13) | 0.0117 (1.00) | 0.000109 (0.144) | 0.0242 (1.00) | 0.698 (1.00) | 0.474 (1.00) | 0.14 (1.00) | 0.000111 (0.146) | 0.0478 (1.00) | 0.389 (1.00) | 0.0137 (1.00) | 0.433 (1.00) | 0.0201 (1.00) |  | 9.34e-14 (1.45e-10)
Amp Peak 5(1q44) | 7.9e-07 (0.00113) | 0.16 (1.00) | 6.84e-183 (1.23e-179) | 1.15e-31 (1.87e-28) | 0.0146 (1.00) | 1.1e-79 (1.89e-76) | 1.29e-14 (2e-11) | 0.000505 (0.636) | 7.39e-05 (0.0978) | 0.00202 (1.00) | 0.0214 (1.00) | 0.696 (1.00) | 0.0499 (1.00) | 0.000623 (0.776) | 0.231 (1.00) | 0.828 (1.00) | 0.0053 (1.00) | 0.736 (1.00) | 0.0567 (1.00) |  | 1.33e-07 (0.000193)
Amp Peak 6(2p15) | 0.856 (1.00) | 1.12e-06 (0.0016) | 1.81e-77 (3.1e-74) | 0.942 (1.00) | 0.000185 (0.239) | 1.27e-48 (2.11e-45) | 0.000548 (0.688) | 0.0148 (1.00) | 0.0488 (1.00) | 2.63e-05 (0.0356) | 2.25e-13 (3.48e-10) | 0.606 (1.00) | 0.199 (1.00) | 0.00191 (1.00) | 0.744 (1.00) | 0.204 (1.00) | 0.00627 (1.00) | 0.503 (1.00) | 0.0279 (1.00) |  | 3.34e-05 (0.0451)
Amp Peak 7(2q31 2) | 0.225 (1.00) | 3.61e-06 (0.00509) | 5.69e-78 (9.74e-75) | 0.219 (1.00) | 0.2 (1.00) | 4.22e-34 (6.91e-31) | 0.00782 (1.00) | 0.0394 (1.00) | 0.0253 (1.00) | 1.98e-05 (0.0269) | 7.11e-13 (1.09e-09) | 0.328 (1.00) | 0.497 (1.00) | 7.91e-06 (0.011) | 0.499 (1.00) | 0.693 (1.00) | 0.834 (1.00) | 0.478 (1.00) | 0.00414 (1.00) |  | 0.773 (1.00)
Amp Peak 8(3q26 2) | 0.064 (1.00) | 0.0167 (1.00) | 4.38e-244 (7.92e-241) | 0.26 (1.00) | 3.5e-05 (0.0472) | 2.22e-239 (4e-236) | 2.27e-21 (3.61e-18) | 2.73e-10 (4.11e-07) | 0.00604 (1.00) | 1.25e-24 (2.01e-21) | 1.04e-13 (1.62e-10) | 4.66e-06 (0.00655) | 0.00212 (1.00) | 0.0233 (1.00) | 0.533 (1.00) | 0.561 (1.00) | 0.142 (1.00) | 0.018 (1.00) | 0.0162 (1.00) |  | 0.000422 (0.533)
Amp Peak 9(4p16 3) | 0.0235 (1.00) | 0.821 (1.00) | 2.11e-44 (3.5e-41) | 2.63e-05 (0.0357) | 0.256 (1.00) | 2.26e-47 (3.76e-44) | 1.15e-06 (0.00164) | 0.913 (1.00) | 0.063 (1.00) | 4.15e-08 (6.07e-05) | 0.147 (1.00) | 0.66 (1.00) | 0.604 (1.00) | 0.371 (1.00) | 0.331 (1.00) | 0.271 (1.00) | 0.235 (1.00) | 0.00107 (1.00) | 0.655 (1.00) |  | 0.00114 (1.00)
Amp Peak 10(4q12) | 0.000118 (0.155) | 0.146 (1.00) | 7.25e-36 (1.19e-32) | 0.172 (1.00) | 0.4 (1.00) | 1.99e-35 (3.27e-32) | 1e-09 (1.5e-06) | 0.0486 (1.00) | 0.081 (1.00) | 0.127 (1.00) | 0.332 (1.00) | 0.95 (1.00) | 0.209 (1.00) | 0.0242 (1.00) | 0.0392 (1.00) | 0.257 (1.00) | 0.193 (1.00) | 0.321 (1.00) | 0.449 (1.00) |  | 0.0266 (1.00)
Amp Peak 11(5p15 33) | 0.14 (1.00) | 1.15e-05 (0.0159) | 1.11e-158 (1.97e-155) | 0.161 (1.00) | 0.000167 (0.217) | 3.86e-116 (6.77e-113) | 5.27e-21 (8.39e-18) | 0.218 (1.00) | 0.00419 (1.00) | 1.98e-05 (0.027) | 9.74e-15 (1.52e-11) | 0.501 (1.00) | 0.00602 (1.00) | 1.16e-06 (0.00166) | 0.958 (1.00) | 0.845 (1.00) | 0.0415 (1.00) | 0.758 (1.00) | 0.305 (1.00) |  | 0.283 (1.00)
Amp Peak 12(5q35 3) | 1.54e-05 (0.0212) | 0.577 (1.00) | 3.27e-156 (5.82e-153) | 0.761 (1.00) | 0.282 (1.00) | 1.55e-132 (2.74e-129) | 3.57e-17 (5.62e-14) | 3.43e-05 (0.0462) | 0.000235 (0.302) | 1.13e-06 (0.00162) | 2.19e-08 (3.22e-05) | 0.407 (1.00) | 0.262 (1.00) | 0.599 (1.00) | 0.392 (1.00) | 0.152 (1.00) | 0.577 (1.00) | 0.0378 (1.00) | 0.577 (1.00) |  | 0.0393 (1.00)
Amp Peak 13(6p22 3) | 0.0268 (1.00) | 0.161 (1.00) | 2.71e-114 (4.74e-111) | 2.53e-12 (3.88e-09) | 0.403 (1.00) | 1.06e-89 (1.82e-86) | 0.00106 (1.00) | 0.0366 (1.00) | 8.97e-06 (0.0125) | 4.83e-12 (7.4e-09) | 9.67e-11 (1.47e-07) | 0.812 (1.00) | 0.106 (1.00) | 0.0273 (1.00) | 0.173 (1.00) | 0.666 (1.00) | 0.0913 (1.00) | 0.0216 (1.00) | 0.0555 (1.00) |  | 0.135 (1.00)
Amp Peak 14(6p21 1) | 0.0127 (1.00) | 0.000581 (0.726) | 5.45e-75 (9.29e-72) | 4.37e-06 (0.00614) | 0.061 (1.00) | 7.53e-59 (1.27e-55) | 0.0145 (1.00) | 0.0251 (1.00) | 0.000124 (0.162) | 8.33e-07 (0.0012) | 1.41e-08 (2.08e-05) | 0.522 (1.00) | 0.671 (1.00) | 0.334 (1.00) | 0.208 (1.00) | 0.981 (1.00) | 0.379 (1.00) | 0.269 (1.00) | 0.182 (1.00) |  | 0.756 (1.00)
Amp Peak 15(6q21) | 0.22 (1.00) | 0.0723 (1.00) | 5.88e-28 (9.51e-25) | 2.51e-07 (0.000365) | 0.644 (1.00) | 6.14e-24 (9.83e-21) | 0.000172 (0.223) | 0.19 (1.00) | 0.0854 (1.00) | 0.000208 (0.269) | 0.0421 (1.00) | 0.659 (1.00) | 0.462 (1.00) | 0.605 (1.00) | 0.69 (1.00) | 0.791 (1.00) | 0.792 (1.00) | 0.0239 (1.00) | 0.831 (1.00) |  | 0.136 (1.00)
Amp Peak 16(7p11 2) | 0 (0) | 0.00102 (1.00) | 2.02e-154 (3.59e-151) | 1.49e-31 (2.42e-28) | 0.37 (1.00) | 5.96e-51 (9.97e-48) | 3.21e-09 (4.79e-06) | 6.53e-07 (0.000942) | 0.000754 (0.935) | 0.111 (1.00) | 2.81e-13 (4.33e-10) | 0.591 (1.00) | 0.235 (1.00) | 0.055 (1.00) | 0.0571 (1.00) | 0.165 (1.00) | 0.174 (1.00) | 0.0322 (1.00) | 0.112 (1.00) |  | 0.0139 (1.00)
Amp Peak 17(7q36 3) | 0 (0) | 0.952 (1.00) | 8.19e-157 (1.46e-153) | 2.27e-12 (3.48e-09) | 0.0342 (1.00) | 2.41e-50 (4.03e-47) | 0.001 (1.00) | 0.0303 (1.00) | 0.000324 (0.413) | 2.54e-06 (0.00359) | 2.43e-08 (3.57e-05) | 0.781 (1.00) | 0.0144 (1.00) | 0.00655 (1.00) | 0.735 (1.00) | 0.625 (1.00) | 0.962 (1.00) | 0.164 (1.00) | 0.997 (1.00) |  | 0.524 (1.00)
Amp Peak 18(8p11 23) | 0.00596 (1.00) | 0.00092 (1.00) | 2.97e-67 (5.02e-64) | 0.465 (1.00) | 0.000325 (0.414) | 1.66e-37 (2.73e-34) | 2.68e-09 (4e-06) | 0.295 (1.00) | 0.00438 (1.00) | 0.0221 (1.00) | 4.09e-05 (0.055) | 0.0883 (1.00) | 0.0445 (1.00) | 0.00832 (1.00) | 0.188 (1.00) | 0.36 (1.00) | 0.277 (1.00) | 0.525 (1.00) | 0.0852 (1.00) |  | 0.314 (1.00)
Amp Peak 19(8p11 21) | 0.00022 (0.283) | 3.32e-06 (0.00469) | 3.94e-77 (6.74e-74) | 0.00443 (1.00) | 0.00174 (1.00) | 1.92e-46 (3.19e-43) | 6.99e-12 (1.07e-08) | 0.313 (1.00) | 0.0164 (1.00) | 0.000163 (0.212) | 1.77e-08 (2.61e-05) | 0.542 (1.00) | 0.0535 (1.00) | 0.00576 (1.00) | 0.0408 (1.00) | 0.746 (1.00) | 0.744 (1.00) | 0.0425 (1.00) | 0.51 (1.00) |  | 0.71 (1.00)
Amp Peak 20(8q24 21) | 0.00185 (1.00) | 0.612 (1.00) | 2.35e-212 (4.23e-209) | 3.64e-09 (5.42e-06) | 8.85e-06 (0.0123) | 2.77e-129 (4.88e-126) | 1.83e-25 (2.94e-22) | 5.45e-11 (8.29e-08) | 0.00642 (1.00) | 3.83e-18 (6.04e-15) | 7.76e-22 (1.24e-18) | 0.828 (1.00) | 0.144 (1.00) | 0.0126 (1.00) | 0.477 (1.00) | 0.271 (1.00) | 0.0602 (1.00) | 0.0737 (1.00) | 0.0264 (1.00) |  | 0.454 (1.00)
Amp Peak 21(9p13 3) | 0.804 (1.00) | 0.477 (1.00) | 4.48e-35 (7.34e-32) | 0.369 (1.00) | 0.29 (1.00) | 1.12e-32 (1.82e-29) | 1.07e-06 (0.00153) | 0.00316 (1.00) | 0.28 (1.00) | 0.000819 (1.00) | 0.442 (1.00) | 0.298 (1.00) | 0.121 (1.00) | 0.167 (1.00) | 0.547 (1.00) | 0.916 (1.00) | 0.156 (1.00) | 0.0713 (1.00) | 0.0408 (1.00) |  | 0.0526 (1.00)
Amp Peak 22(10p15 1) | 0.014 (1.00) | 0.442 (1.00) | 3.98e-106 (6.93e-103) | 1.31e-23 (2.1e-20) | 0.383 (1.00) | 1.19e-65 (2e-62) | 5.9e-06 (0.00824) | 0.377 (1.00) | 0.101 (1.00) | 6.81e-16 (1.06e-12) | 1.77e-06 (0.00251) | 0.729 (1.00) | 0.169 (1.00) | 1.48e-08 (2.18e-05) | 0.189 (1.00) | 0.455 (1.00) | 0.754 (1.00) | 0.000588 (0.734) | 0.674 (1.00) |  | 0.106 (1.00)
Amp Peak 23(10q22 2) | 0.00619 (1.00) | 0.957 (1.00) | 4.66e-77 (7.95e-74) | 7.43e-21 (1.18e-17) | 0.5 (1.00) | 1.85e-48 (3.09e-45) | 0.00293 (1.00) | 0.0485 (1.00) | 0.581 (1.00) | 1.38e-10 (2.1e-07) | 0.00228 (1.00) | 0.408 (1.00) | 0.135 (1.00) | 0.18 (1.00) | 0.286 (1.00) | 0.582 (1.00) | 0.581 (1.00) | 0.0806 (1.00) | 0.0556 (1.00) |  | 0.225 (1.00)
Amp Peak 24(11q13 3) | 0.0264 (1.00) | 0.221 (1.00) | 1.03e-121 (1.81e-118) | 5.68e-05 (0.0758) | 0.14 (1.00) | 8.78e-67 (1.48e-63) | 1.44e-10 (2.17e-07) | 7.8e-06 (0.0109) | 0.0205 (1.00) | 1.77e-06 (0.00251) | 1.49e-05 (0.0204) | 0.283 (1.00) | 0.0387 (1.00) | 0.000904 (1.00) | 0.0618 (1.00) | 0.947 (1.00) | 0.435 (1.00) | 0.383 (1.00) | 0.0414 (1.00) |  | 0.2 (1.00)
Amp Peak 25(12p13 33) | 0.157 (1.00) | 0.00191 (1.00) | 1.26e-74 (2.14e-71) | 0.866 (1.00) | 0.00106 (1.00) | 2.73e-52 (4.58e-49) | 9.39e-06 (0.013) | 0.635 (1.00) | 0.15 (1.00) | 2.09e-08 (3.07e-05) | 3.93e-13 (6.05e-10) | 0.293 (1.00) | 0.0309 (1.00) | 0.226 (1.00) | 0.773 (1.00) | 1 (1.00) | 0.307 (1.00) | 0.691 (1.00) | 0.353 (1.00) |  | 0.0697 (1.00)
Amp Peak 26(12p12 1) | 0.0226 (1.00) | 0.000347 (0.442) | 1.5e-72 (2.56e-69) | 0.973 (1.00) | 0.00238 (1.00) | 6.28e-48 (1.05e-44) | 6.8e-05 (0.0902) | 0.982 (1.00) | 0.132 (1.00) | 1.25e-07 (0.000182) | 1.77e-10 (2.68e-07) | 0.201 (1.00) | 0.0204 (1.00) | 0.0681 (1.00) | 0.858 (1.00) | 0.974 (1.00) | 0.33 (1.00) | 0.972 (1.00) | 0.248 (1.00) |  | 0.057 (1.00)
Amp Peak 27(12q14 1) | 9.67e-05 (0.128) | 5.92e-05 (0.0788) | 8.12e-23 (1.3e-19) | 0.128 (1.00) | 0.156 (1.00) | 4.4e-17 (6.92e-14) | 0.0794 (1.00) | 0.272 (1.00) | 0.502 (1.00) | 0.000252 (0.323) | 0.00851 (1.00) | 0.866 (1.00) | 0.0412 (1.00) | 0.359 (1.00) | 0.0928 (1.00) | 0.776 (1.00) | 0.0948 (1.00) | 0.732 (1.00) | 0.778 (1.00) |  | 0.0628 (1.00)
Amp Peak 28(12q15) | 0.0125 (1.00) | 3.38e-05 (0.0456) | 5.44e-32 (8.86e-29) | 0.16 (1.00) | 0.0528 (1.00) | 5e-20 (7.94e-17) | 0.0128 (1.00) | 0.185 (1.00) | 0.273 (1.00) | 0.0128 (1.00) | 1.95e-06 (0.00277) | 0.988 (1.00) | 0.0253 (1.00) | 0.372 (1.00) | 0.462 (1.00) | 0.507 (1.00) | 0.0259 (1.00) | 0.802 (1.00) | 0.492 (1.00) |  | 0.0396 (1.00)
Amp Peak 29(13q34) | 0.646 (1.00) | 4.91e-06 (0.00689) | 3.07e-173 (5.49e-170) | 0.0816 (1.00) | 0.195 (1.00) | 8.09e-136 (1.43e-132) | 5.86e-26 (9.45e-23) | 4.2e-08 (6.14e-05) | 3.51e-05 (0.0473) | 2.7e-10 (4.07e-07) | 3.06e-15 (4.76e-12) | 0.351 (1.00) | 0.456 (1.00) | 4.45e-07 (0.000642) | 0.272 (1.00) | 0.682 (1.00) | 0.0707 (1.00) | 0.00184 (1.00) | 0.655 (1.00) |  | 0.000727 (0.903)
Amp Peak 30(14q13 3) | 0.512 (1.00) | 0.587 (1.00) | 5.23e-90 (9e-87) | 0.868 (1.00) | 0.012 (1.00) | 1.47e-72 (2.5e-69) | 2.55e-13 (3.93e-10) | 0.0155 (1.00) | 5.93e-10 (8.9e-07) | 0.666 (1.00) | 3.12e-06 (0.0044) | 0.49 (1.00) | 0.000445 (0.561) | 0.00251 (1.00) | 0.0185 (1.00) | 0.932 (1.00) | 0.273 (1.00) | 0.14 (1.00) | 0.0333 (1.00) |  | 0.0341 (1.00)
Amp Peak 31(15q26 3) | 0.524 (1.00) | 0.448 (1.00) | 7e-52 (1.17e-48) | 0.0644 (1.00) | 0.00476 (1.00) | 2.23e-47 (3.72e-44) | 3.98e-10 (5.99e-07) | 0.0136 (1.00) | 0.131 (1.00) | 0.00626 (1.00) | 8.52e-08 (0.000124) | 0.569 (1.00) | 0.597 (1.00) | 0.000284 (0.362) | 0.661 (1.00) | 0.0584 (1.00) | 0.8 (1.00) | 0.042 (1.00) | 0.899 (1.00) |  | 0.959 (1.00)
Amp Peak 32(17q12) | 0.597 (1.00) | 4.89e-05 (0.0654) | 5.37e-88 (9.22e-85) | 0.0297 (1.00) | 0.0566 (1.00) | 4.32e-70 (7.33e-67) | 4.25e-07 (0.000615) | 0.00142 (1.00) | 2.15e-06 (0.00305) | 0.0014 (1.00) | 0.000997 (1.00) | 0.367 (1.00) | 0.0353 (1.00) | 0.147 (1.00) | 0.692 (1.00) | 0.707 (1.00) | 0.0179 (1.00) | 0.138 (1.00) | 0.0896 (1.00) |  | 0.0998 (1.00)
Amp Peak 33(17q25 3) | 0.601 (1.00) | 0.0591 (1.00) | 1.66e-92 (2.87e-89) | 0.00519 (1.00) | 0.0142 (1.00) | 9.16e-70 (1.55e-66) | 5.96e-08 (8.71e-05) | 0.000763 (0.944) | 2.45e-09 (3.66e-06) | 0.135 (1.00) | 4.41e-07 (0.000638) | 0.389 (1.00) | 6.2e-05 (0.0825) | 0.00881 (1.00) | 0.0665 (1.00) | 0.476 (1.00) | 0.637 (1.00) | 0.141 (1.00) | 0.776 (1.00) |  | 0.17 (1.00)
Amp Peak 34(18q11 2) | 0.925 (1.00) | 0.00571 (1.00) | 2.58e-39 (4.26e-36) | 0.132 (1.00) | 0.00182 (1.00) | 5.99e-48 (9.98e-45) | 7.36e-12 (1.13e-08) | 0.0338 (1.00) | 0.000458 (0.578) | 0.0182 (1.00) | 0.146 (1.00) | 0.0491 (1.00) | 0.0013 (1.00) | 0.143 (1.00) | 0.825 (1.00) | 0.691 (1.00) | 0.0703 (1.00) | 0.625 (1.00) | 0.57 (1.00) |  | 0.442 (1.00)
Amp Peak 35(19p13 2) | 5.21e-10 (7.83e-07) | 0.142 (1.00) | 2.23e-70 (3.79e-67) | 0.00638 (1.00) | 0.982 (1.00) | 2.29e-32 (3.73e-29) | 0.000471 (0.593) | 0.000978 (1.00) | 0.349 (1.00) | 1.83e-09 (2.73e-06) | 2.45e-11 (3.73e-08) | 0.616 (1.00) | 0.0253 (1.00) | 0.25 (1.00) | 0.642 (1.00) | 0.632 (1.00) | 0.952 (1.00) | 0.527 (1.00) | 0.244 (1.00) |  | 0.984 (1.00)
Amp Peak 36(19p13 12) | 0.000609 (0.76) | 0.622 (1.00) | 3.73e-104 (6.49e-101) | 0.000411 (0.521) | 0.41 (1.00) | 9.15e-106 (1.59e-102) | 0.000753 (0.933) | 0.00177 (1.00) | 0.243 (1.00) | 2.83e-29 (4.59e-26) | 0.000105 (0.138) | 0.386 (1.00) | 0.00242 (1.00) | 0.485 (1.00) | 0.939 (1.00) | 0.0838 (1.00) | 0.26 (1.00) | 0.0388 (1.00) | 0.263 (1.00) |  | 0.829 (1.00)
Amp Peak 37(19q12) | 0.000147 (0.192) | 0.0126 (1.00) | 4.38e-77 (7.48e-74) | 0.0952 (1.00) | 0.201 (1.00) | 3.02e-97 (5.23e-94) | 9.09e-06 (0.0126) | 0.00494 (1.00) | 0.158 (1.00) | 1.36e-16 (2.12e-13) | 0.468 (1.00) | 0.149 (1.00) | 0.00112 (1.00) | 0.00222 (1.00) | 0.136 (1.00) | 0.93 (1.00) | 0.416 (1.00) | 0.0884 (1.00) | 0.474 (1.00) |  | 0.0582 (1.00)
Amp Peak 38(20q11 21) | 0.000183 (0.237) | 1.32e-15 (2.06e-12) | 1.59e-101 (2.76e-98) | 0.000106 (0.14) | 0.0748 (1.00) | 3.09e-110 (5.4e-107) | 4.98e-24 (7.98e-21) | 9.07e-06 (0.0126) | 0.00301 (1.00) | 5.57e-10 (8.37e-07) | 2.61e-05 (0.0353) | 0.00475 (1.00) | 0.436 (1.00) | 0.00502 (1.00) | 0.0595 (1.00) | 0.701 (1.00) | 0.338 (1.00) | 0.00117 (1.00) | 0.455 (1.00) |  | 0.000634 (0.789)
Amp Peak 39(20q13 2) | 0.0675 (1.00) | 2.01e-08 (2.96e-05) | 5.34e-112 (9.33e-109) | 0.357 (1.00) | 0.696 (1.00) | 3.57e-118 (6.28e-115) | 3.43e-23 (5.49e-20) | 0.000201 (0.26) | 0.000472 (0.594) | 7.31e-13 (1.12e-09) | 6.59e-06 (0.00918) | 0.704 (1.00) | 0.211 (1.00) | 0.00151 (1.00) | 0.922 (1.00) | 0.477 (1.00) | 0.199 (1.00) | 0.00371 (1.00) | 0.988 (1.00) |  | 0.117 (1.00)
Amp Peak 40(Xq28) | 0.985 (1.00) | 0.845 (1.00) | 2.16e-57 (3.64e-54) | 0.0115 (1.00) | 0.0387 (1.00) | 3.45e-32 (5.62e-29) | 1.11e-08 (1.64e-05) | 0.00012 (0.157) | 0.255 (1.00) | 6.86e-07 (0.000987) | 0.00039 (0.495) | 0.971 (1.00) | 0.382 (1.00) | 0.551 (1.00) | 0.896 (1.00) | 0.0216 (1.00) | 0.703 (1.00) | 0.111 (1.00) | 0.323 (1.00) |  | 0.0366 (1.00)
Del Peak 1(1p36 23) | 0.796 (1.00) | 0.0885 (1.00) | 2.47e-38 (4.07e-35) | 0.438 (1.00) | 0.237 (1.00) | 1.86e-30 (3.03e-27) | 0.00492 (1.00) | 0.00677 (1.00) | 0.026 (1.00) | 0.000952 (1.00) | 0.128 (1.00) | 0.0175 (1.00) | 0.157 (1.00) | 0.00266 (1.00) | 0.356 (1.00) | 0.584 (1.00) | 0.0319 (1.00) | 0.178 (1.00) | 0.000784 (0.969) |  | 2e-05 (0.0272)
Del Peak 2(1p36 11) | 0.0369 (1.00) | 0.00534 (1.00) | 3.87e-76 (6.59e-73) | 0.0267 (1.00) | 0.0176 (1.00) | 1.12e-45 (1.86e-42) | 0.00146 (1.00) | 0.00505 (1.00) | 0.0134 (1.00) | 1.72e-06 (0.00246) | 1.84e-11 (2.81e-08) | 0.00284 (1.00) | 0.234 (1.00) | 1.64e-05 (0.0225) | 0.678 (1.00) | 0.681 (1.00) | 0.00727 (1.00) | 0.00846 (1.00) | 4.47e-05 (0.06) |  | 6.09e-06 (0.00851)
Del Peak 3(1p13 2) | 0.0604 (1.00) | 1.66e-05 (0.0227) | 2.36e-70 (4e-67) | 0.143 (1.00) | 0.00298 (1.00) | 5.09e-41 (8.4e-38) | 0.077 (1.00) | 0.00117 (1.00) | 0.33 (1.00) | 0.613 (1.00) | 9.22e-12 (1.41e-08) | 0.0105 (1.00) | 0.0805 (1.00) | 5.7e-05 (0.076) | 0.946 (1.00) | 0.298 (1.00) | 0.00459 (1.00) | 0.0176 (1.00) | 0.000131 (0.171) |  | 0.00158 (1.00)
Del Peak 4(2q22 1) | 0.164 (1.00) | 0.784 (1.00) | 2.01e-45 (3.34e-42) | 0.000542 (0.681) | 0.042 (1.00) | 1.85e-35 (3.04e-32) | 9.01e-06 (0.0125) | 0.00149 (1.00) | 0.272 (1.00) | 1.02e-05 (0.0141) | 0.0171 (1.00) | 0.216 (1.00) | 0.00213 (1.00) | 0.0171 (1.00) | 0.152 (1.00) | 0.259 (1.00) | 0.687 (1.00) | 0.0827 (1.00) | 0.797 (1.00) |  | 0.356 (1.00)
Del Peak 5(2q37 3) | 0.455 (1.00) | 0.138 (1.00) | 9.98e-68 (1.69e-64) | 0.00143 (1.00) | 0.284 (1.00) | 1.66e-41 (2.74e-38) | 0.00196 (1.00) | 0.068 (1.00) | 0.00508 (1.00) | 0.00173 (1.00) | 0.00284 (1.00) | 0.0378 (1.00) | 0.473 (1.00) | 2.11e-06 (0.00299) | 0.0323 (1.00) | 0.577 (1.00) | 0.233 (1.00) | 0.608 (1.00) | 0.711 (1.00) |  | 0.0191 (1.00)
Del Peak 6(3p26 2) | 0.44 (1.00) | 0.04 (1.00) | 3.1e-311 (5.62e-308) | 3.76e-33 (6.15e-30) | 0.000411 (0.521) | 6.06e-202 (1.09e-198) | 1.2e-19 (1.9e-16) | 0.175 (1.00) | 0.0151 (1.00) | 1.28e-12 (1.96e-09) | 7.96e-25 (1.28e-21) | 0.000429 (0.542) | 0.00112 (1.00) | 2.37e-19 (3.75e-16) | 0.37 (1.00) | 0.0416 (1.00) | 0.999 (1.00) | 0.192 (1.00) | 0.00705 (1.00) |  | 0.385 (1.00)
Del Peak 7(3p14 2) | 0.126 (1.00) | 0.642 (1.00) | 4.18e-251 (7.56e-248) | 4.14e-34 (6.79e-31) | 2.21e-05 (0.03) | 6.91e-199 (1.24e-195) | 1.37e-18 (2.17e-15) | 0.0749 (1.00) | 0.175 (1.00) | 1.18e-16 (1.86e-13) | 2.54e-20 (4.03e-17) | 0.000219 (0.282) | 0.00131 (1.00) | 5.04e-20 (7.99e-17) | 0.623 (1.00) | 0.317 (1.00) | 0.945 (1.00) | 0.0138 (1.00) | 0.0397 (1.00) |  | 0.903 (1.00)
Del Peak 8(4p16 3) | 0.133 (1.00) | 0.207 (1.00) | 2.83e-56 (4.75e-53) | 0.02 (1.00) | 0.000698 (0.866) | 7.22e-60 (1.22e-56) | 7.24e-07 (0.00104) | 7.25e-05 (0.0962) | 0.29 (1.00) | 6.77e-05 (0.0899) | 0.000169 (0.219) | 0.0444 (1.00) | 0.000123 (0.161) | 0.000145 (0.189) | 0.835 (1.00) | 0.823 (1.00) | 0.941 (1.00) | 0.239 (1.00) | 0.0063 (1.00) |  | 0.168 (1.00)
Del Peak 9(4q22 1) | 0.414 (1.00) | 0.0132 (1.00) | 3e-124 (5.28e-121) | 0.00213 (1.00) | 0.00512 (1.00) | 1.81e-107 (3.16e-104) | 3.18e-08 (4.67e-05) | 0.0101 (1.00) | 0.594 (1.00) | 3.84e-22 (6.12e-19) | 1.46e-14 (2.27e-11) | 0.043 (1.00) | 0.0394 (1.00) | 0.0157 (1.00) | 0.0501 (1.00) | 0.7 (1.00) | 0.28 (1.00) | 0.21 (1.00) | 0.0016 (1.00) |  | 0.288 (1.00)
Del Peak 10(4q34 3) | 0.0152 (1.00) | 0.0503 (1.00) | 1.89e-127 (3.34e-124) | 0.0116 (1.00) | 0.0021 (1.00) | 9.53e-120 (1.68e-116) | 1.46e-08 (2.16e-05) | 0.0148 (1.00) | 0.692 (1.00) | 4.37e-16 (6.84e-13) | 4.43e-11 (6.74e-08) | 0.00417 (1.00) | 0.0867 (1.00) | 0.00578 (1.00) | 0.998 (1.00) | 0.635 (1.00) | 0.571 (1.00) | 0.434 (1.00) | 0.0165 (1.00) |  | 0.261 (1.00)
Del Peak 11(5q11 2) | 0.679 (1.00) | 0.0557 (1.00) | 1.28e-171 (2.28e-168) | 0.504 (1.00) | 5.77e-05 (0.0769) | 2.01e-152 (3.57e-149) | 3.08e-17 (4.86e-14) | 6.37e-05 (0.0848) | 0.00178 (1.00) | 9.26e-06 (0.0128) | 9.02e-14 (1.4e-10) | 4.61e-06 (0.00648) | 0.000266 (0.34) | 3.29e-05 (0.0445) | 0.481 (1.00) | 0.303 (1.00) | 0.026 (1.00) | 0.208 (1.00) | 0.0836 (1.00) |  | 1.73e-05 (0.0236)
Del Peak 12(5q21 3) | 0.761 (1.00) | 0.00777 (1.00) | 2.24e-178 (4e-175) | 0.92 (1.00) | 1.22e-05 (0.0168) | 9.1e-152 (1.61e-148) | 7.7e-16 (1.2e-12) | 3.6e-05 (0.0484) | 4.68e-05 (0.0627) | 0.000819 (1.00) | 1.55e-14 (2.41e-11) | 0.000572 (0.717) | 0.00479 (1.00) | 6.54e-06 (0.00913) | 0.1 (1.00) | 0.355 (1.00) | 0.214 (1.00) | 0.57 (1.00) | 0.701 (1.00) |  | 0.000268 (0.342)
Del Peak 13(6p25 3) | 0.018 (1.00) | 0.768 (1.00) | 4.71e-16 (7.37e-13) | 6.41e-05 (0.0852) | 0.0199 (1.00) | 1.37e-13 (2.12e-10) | 0.296 (1.00) | 0.649 (1.00) | 0.675 (1.00) | 0.193 (1.00) | 0.0825 (1.00) | 0.624 (1.00) | 0.745 (1.00) | 0.639 (1.00) | 0.218 (1.00) | 0.877 (1.00) | 0.507 (1.00) | 0.0456 (1.00) | 0.818 (1.00) |  | 0.253 (1.00)
Del Peak 14(6q22 31) | 0.00258 (1.00) | 0.000639 (0.795) | 9.36e-93 (1.62e-89) | 0.0332 (1.00) | 0.183 (1.00) | 6.04e-98 (1.05e-94) | 0.000134 (0.175) | 0.767 (1.00) | 0.0541 (1.00) | 3.25e-09 (4.84e-06) | 0.00302 (1.00) | 0.0954 (1.00) | 0.531 (1.00) | 0.391 (1.00) | 0.0413 (1.00) | 0.524 (1.00) | 0.304 (1.00) | 0.175 (1.00) | 0.0672 (1.00) |  | 0.0506 (1.00)
Del Peak 15(6q26) | 0.0366 (1.00) | 5.89e-06 (0.00823) | 5.42e-104 (9.42e-101) | 0.00239 (1.00) | 0.596 (1.00) | 6.56e-108 (1.14e-104) | 0.000244 (0.314) | 0.743 (1.00) | 0.0906 (1.00) | 1.13e-12 (1.74e-09) | 0.00379 (1.00) | 0.142 (1.00) | 0.773 (1.00) | 0.149 (1.00) | 0.255 (1.00) | 0.974 (1.00) | 0.364 (1.00) | 0.359 (1.00) | 0.218 (1.00) |  | 0.0618 (1.00)
Del Peak 16(7p22 3) | 0.417 (1.00) | 0.00316 (1.00) | 1.43e-143 (2.54e-140) | 1.29e-27 (2.08e-24) | 0.224 (1.00) | 8.12e-127 (1.43e-123) | 3.28e-07 (0.000475) | 0.479 (1.00) | 0.0051 (1.00) | 5.75e-29 (9.32e-26) | 0.000975 (1.00) | 0.0973 (1.00) | 0.0506 (1.00) | 0.292 (1.00) | 0.674 (1.00) | 0.856 (1.00) | 0.703 (1.00) | 0.182 (1.00) | 0.0849 (1.00) |  | 0.00924 (1.00)
Del Peak 17(7q36 1) | 0.654 (1.00) | 0.284 (1.00) | 1.07e-56 (1.8e-53) | 0.00472 (1.00) | 0.00143 (1.00) | 1.29e-52 (2.16e-49) | 8.06e-11 (1.22e-07) | 0.0591 (1.00) | 0.0148 (1.00) | 0.17 (1.00) | 0.254 (1.00) | 0.162 (1.00) | 0.62 (1.00) | 0.463 (1.00) | 0.588 (1.00) | 0.243 (1.00) | 0.924 (1.00) | 0.421 (1.00) | 0.447 (1.00) |  | 0.316 (1.00)
Del Peak 18(8p23 2) | 0.0387 (1.00) | 0.000402 (0.51) | 9.18e-132 (1.62e-128) | 0.0358 (1.00) | 7.72e-05 (0.102) | 6.41e-91 (1.1e-87) | 1.44e-05 (0.0198) | 1.37e-08 (2.03e-05) | 0.791 (1.00) | 6.41e-08 (9.35e-05) | 2.07e-21 (3.29e-18) | 0.00697 (1.00) | 0.525 (1.00) | 0.0421 (1.00) | 0.728 (1.00) | 0.603 (1.00) | 0.0304 (1.00) | 0.0515 (1.00) | 0.00204 (1.00) |  | 0.797 (1.00)
Del Peak 19(8p21 2) | 0.034 (1.00) | 0.000956 (1.00) | 1.38e-135 (2.44e-132) | 0.000212 (0.274) | 1.6e-05 (0.0219) | 1.04e-93 (1.79e-90) | 0.00134 (1.00) | 1.99e-08 (2.94e-05) | 0.29 (1.00) | 1.36e-10 (2.07e-07) | 1.62e-22 (2.59e-19) | 0.142 (1.00) | 0.579 (1.00) | 0.362 (1.00) | 0.845 (1.00) | 0.629 (1.00) | 0.101 (1.00) | 0.219 (1.00) | 0.00114 (1.00) |  | 0.633 (1.00)
Del Peak 20(9p23) | 0 (0) | 0.0108 (1.00) | 2.13e-93 (3.68e-90) | 2.44e-10 (3.68e-07) | 0.0554 (1.00) | 2.4e-86 (4.12e-83) | 2.04e-10 (3.08e-07) | 0.0535 (1.00) | 0.174 (1.00) | 0.00735 (1.00) | 0.445 (1.00) | 0.0903 (1.00) | 0.612 (1.00) | 0.197 (1.00) | 0.0944 (1.00) | 0.0877 (1.00) | 0.000965 (1.00) | 0.627 (1.00) | 0.006 (1.00) |  | 0.000549 (0.689)
Del Peak 21(9p21 3) | 0 (0) | 0.0142 (1.00) | 4.81e-163 (8.59e-160) | 4.97e-22 (7.93e-19) | 0.0171 (1.00) | 4.9e-110 (8.56e-107) | 7.47e-17 (1.17e-13) | 0.0552 (1.00) | 0.295 (1.00) | 0.148 (1.00) | 4.55e-07 (0.000656) | 0.0351 (1.00) | 0.211 (1.00) | 0.138 (1.00) | 0.000374 (0.476) | 0.0828 (1.00) | 4.59e-05 (0.0615) | 0.83 (1.00) | 0.0202 (1.00) |  | 4.69e-06 (0.00658)
Del Peak 22(9p21 3) | 0 (0) | 0.0148 (1.00) | 1.33e-172 (2.37e-169) | 9.41e-26 (1.51e-22) | 0.00513 (1.00) | 1.84e-116 (3.23e-113) | 6.88e-17 (1.08e-13) | 0.00571 (1.00) | 0.366 (1.00) | 0.00882 (1.00) | 3.32e-07 (0.000481) | 0.0662 (1.00) | 0.394 (1.00) | 0.103 (1.00) | 0.00217 (1.00) | 0.0931 (1.00) | 1.99e-05 (0.0271) | 0.893 (1.00) | 0.0179 (1.00) |  | 2.47e-06 (0.00349)
Del Peak 23(9q21 11) | 0.177 (1.00) | 6.47e-07 (0.000932) | 4.31e-84 (7.39e-81) | 0.0617 (1.00) | 0.0286 (1.00) | 2.98e-72 (5.07e-69) | 1.53e-10 (2.31e-07) | 0.012 (1.00) | 0.0197 (1.00) | 6.01e-09 (8.93e-06) | 2.53e-13 (3.92e-10) | 0.106 (1.00) | 0.466 (1.00) | 0.134 (1.00) | 0.0382 (1.00) | 0.269 (1.00) | 0.282 (1.00) | 0.149 (1.00) | 0.259 (1.00) |  | 0.0999 (1.00)
Del Peak 24(9q34 3) | 0.648 (1.00) | 0.000249 (0.319) | 1.7e-96 (2.93e-93) | 0.00058 (0.725) | 0.13 (1.00) | 2.59e-82 (4.43e-79) | 1.11e-09 (1.66e-06) | 0.00119 (1.00) | 0.0397 (1.00) | 5.06e-12 (7.74e-09) | 4.15e-14 (6.44e-11) | 0.0524 (1.00) | 0.41 (1.00) | 0.172 (1.00) | 0.00225 (1.00) | 1 (1.00) | 0.0225 (1.00) | 0.282 (1.00) | 0.438 (1.00) |  | 0.208 (1.00)
Del Peak 25(10p15 3) | 0 (0) | 0.932 (1.00) | 2.23e-243 (4.03e-240) | 5.68e-26 (9.15e-23) | 0.0752 (1.00) | 1.75e-48 (2.92e-45) | 4.88e-08 (7.14e-05) | 0.000858 (1.00) | 0.553 (1.00) | 0.187 (1.00) | 6.01e-35 (9.86e-32) | 0.174 (1.00) | 0.16 (1.00) | 0.00884 (1.00) | 0.0861 (1.00) | 0.361 (1.00) | 0.751 (1.00) | 0.716 (1.00) | 0.0142 (1.00) |  | 0.698 (1.00)
Del Peak 26(10q23 31) | 0 (0) | 0.513 (1.00) | 5.45e-192 (9.79e-189) | 2e-11 (3.05e-08) | 0.241 (1.00) | 2.68e-46 (4.46e-43) | 0.017 (1.00) | 0.0903 (1.00) | 0.833 (1.00) | 0.0111 (1.00) | 7.31e-30 (1.19e-26) | 0.137 (1.00) | 0.828 (1.00) | 0.128 (1.00) | 4.3e-05 (0.0578) | 0.619 (1.00) | 0.184 (1.00) | 0.161 (1.00) | 0.472 (1.00) |  | 0.0446 (1.00)
Del Peak 27(10q26 3) | 0 (0) | 0.488 (1.00) | 1.08e-206 (1.95e-203) | 4.45e-13 (6.85e-10) | 0.525 (1.00) | 1.8e-40 (2.97e-37) | 0.0432 (1.00) | 0.293 (1.00) | 0.658 (1.00) | 0.192 (1.00) | 7.57e-34 (1.24e-30) | 0.171 (1.00) | 0.649 (1.00) | 0.156 (1.00) | 0.0167 (1.00) | 0.336 (1.00) | 0.363 (1.00) | 0.476 (1.00) | 0.144 (1.00) |  | 0.297 (1.00)
Del Peak 28(11p15 5) | 0.00662 (1.00) | 0.666 (1.00) | 1.64e-115 (2.87e-112) | 3.54e-05 (0.0476) | 0.00883 (1.00) | 1.03e-121 (1.82e-118) | 1.72e-10 (2.59e-07) | 0.000578 (0.723) | 0.119 (1.00) | 2.77e-16 (4.33e-13) | 0.00313 (1.00) | 0.0756 (1.00) | 0.274 (1.00) | 0.000141 (0.184) | 0.726 (1.00) | 0.669 (1.00) | 0.14 (1.00) | 0.301 (1.00) | 0.000385 (0.489) |  | 0.0338 (1.00)
Del Peak 29(11q23 1) | 0.556 (1.00) | 0.897 (1.00) | 9.65e-101 (1.67e-97) | 0.000149 (0.193) | 0.0136 (1.00) | 1.38e-53 (2.32e-50) | 8.21e-10 (1.23e-06) | 4.19e-09 (6.23e-06) | 0.509 (1.00) | 4.35e-06 (0.00611) | 0.21 (1.00) | 0.293 (1.00) | 0.438 (1.00) | 0.0967 (1.00) | 0.0788 (1.00) | 0.459 (1.00) | 0.169 (1.00) | 0.943 (1.00) | 0.0142 (1.00) |  | 0.0323 (1.00)
Del Peak 30(11q25) | 0.884 (1.00) | 0.136 (1.00) | 9.57e-91 (1.65e-87) | 8.64e-05 (0.114) | 0.0106 (1.00) | 1.04e-58 (1.74e-55) | 4.93e-11 (7.5e-08) | 1.17e-09 (1.76e-06) | 0.159 (1.00) | 1.55e-05 (0.0213) | 0.281 (1.00) | 0.171 (1.00) | 0.938 (1.00) | 0.0832 (1.00) | 0.274 (1.00) | 0.459 (1.00) | 0.26 (1.00) | 0.516 (1.00) | 0.00461 (1.00) |  | 0.0093 (1.00)
Del Peak 31(12p13 1) | 0.272 (1.00) | 0.213 (1.00) | 1.45e-20 (2.31e-17) | 9.28e-08 (0.000135) | 0.978 (1.00) | 1.21e-35 (1.99e-32) | 0.23 (1.00) | 0.412 (1.00) | 3.65e-06 (0.00514) | 0.135 (1.00) | 0.69 (1.00) | 0.0175 (1.00) | 0.804 (1.00) | 0.579 (1.00) | 0.0274 (1.00) | 0.102 (1.00) | 0.245 (1.00) | 0.117 (1.00) | 0.529 (1.00) |  | 0.231 (1.00)
Del Peak 32(12q23 1) | 0.888 (1.00) | 0.178 (1.00) | 5e-53 (8.38e-50) | 5.49e-09 (8.15e-06) | 0.627 (1.00) | 2.57e-59 (4.32e-56) | 1.75e-05 (0.0239) | 0.0875 (1.00) | 3.07e-05 (0.0415) | 1.69e-05 (0.0232) | 0.00106 (1.00) | 0.116 (1.00) | 0.294 (1.00) | 0.612 (1.00) | 0.523 (1.00) | 0.883 (1.00) | 0.407 (1.00) | 0.529 (1.00) | 0.22 (1.00) |  | 0.166 (1.00)
Del Peak 33(12q24 33) | 0.0548 (1.00) | 0.41 (1.00) | 9.81e-60 (1.66e-56) | 2.37e-08 (3.49e-05) | 0.153 (1.00) | 9.68e-64 (1.64e-60) | 1.21e-06 (0.00173) | 0.0585 (1.00) | 0.00306 (1.00) | 3.32e-07 (0.000481) | 0.00971 (1.00) | 0.692 (1.00) | 0.951 (1.00) | 0.919 (1.00) | 0.185 (1.00) | 0.634 (1.00) | 0.497 (1.00) | 0.203 (1.00) | 0.177 (1.00) |  | 0.726 (1.00)
Del Peak 34(13q11) | 0.000281 (0.359) | 0.811 (1.00) | 1.15e-154 (2.05e-151) | 0.154 (1.00) | 0.000326 (0.415) | 3.77e-153 (6.68e-150) | 2.22e-29 (3.61e-26) | 0.00896 (1.00) | 5.38e-06 (0.00753) | 2.6e-07 (0.000377) | 0.31 (1.00) | 0.00695 (1.00) | 0.00936 (1.00) | 6.36e-09 (9.44e-06) | 0.583 (1.00) | 0.938 (1.00) | 0.945 (1.00) | 0.258 (1.00) | 0.231 (1.00) |  | 0.311 (1.00)
Del Peak 35(13q14 2) | 3.13e-06 (0.00442) | 0.0401 (1.00) | 2.43e-161 (4.33e-158) | 0.0104 (1.00) | 0.0012 (1.00) | 2.68e-158 (4.78e-155) | 1.25e-28 (2.03e-25) | 0.00585 (1.00) | 1.36e-05 (0.0188) | 4.05e-08 (5.94e-05) | 0.781 (1.00) | 0.0185 (1.00) | 0.0139 (1.00) | 0.000134 (0.175) | 0.956 (1.00) | 0.977 (1.00) | 0.658 (1.00) | 0.333 (1.00) | 0.589 (1.00) |  | 0.396 (1.00)
Del Peak 36(14q24 1) | 0.00139 (1.00) | 0.738 (1.00) | 3.5e-50 (5.84e-47) | 0.843 (1.00) | 0.991 (1.00) | 3.47e-53 (5.82e-50) | 3.49e-05 (0.0471) | 8.6e-05 (0.114) | 0.000694 (0.862) | 9.79e-09 (1.45e-05) | 0.000238 (0.306) | 0.625 (1.00) | 0.324 (1.00) | 0.153 (1.00) | 0.678 (1.00) | 0.824 (1.00) | 0.201 (1.00) | 0.356 (1.00) | 0.625 (1.00) |  | 0.369 (1.00)
Del Peak 37(15q11 2) | 0.0667 (1.00) | 0.00127 (1.00) | 6.2e-74 (1.06e-70) | 8.72e-06 (0.0121) | 0.0512 (1.00) | 1.4e-81 (2.39e-78) | 2.02e-07 (0.000294) | 1.56e-06 (0.00222) | 0.00627 (1.00) | 4.36e-09 (6.48e-06) | 2.48e-06 (0.00351) | 0.902 (1.00) | 0.475 (1.00) | 0.174 (1.00) | 0.228 (1.00) | 0.126 (1.00) | 0.655 (1.00) | 0.322 (1.00) | 0.0827 (1.00) |  | 0.394 (1.00)
Del Peak 38(15q15 1) | 0.02 (1.00) | 0.005 (1.00) | 7.53e-92 (1.3e-88) | 5.85e-08 (8.55e-05) | 0.115 (1.00) | 4.97e-103 (8.63e-100) | 3.86e-08 (5.66e-05) | 1.3e-06 (0.00186) | 0.00473 (1.00) | 1.55e-15 (2.41e-12) | 5.22e-05 (0.0698) | 0.759 (1.00) | 0.358 (1.00) | 0.116 (1.00) | 0.528 (1.00) | 0.394 (1.00) | 0.712 (1.00) | 0.696 (1.00) | 0.18 (1.00) |  | 0.806 (1.00)
Del Peak 39(16p13 3) | 1.85e-05 (0.0252) | 0.00806 (1.00) | 8.46e-131 (1.5e-127) | 0.0127 (1.00) | 0.111 (1.00) | 2.73e-96 (4.72e-93) | 0.00125 (1.00) | 0.258 (1.00) | 0.216 (1.00) | 2.9e-13 (4.46e-10) | 2.53e-09 (3.77e-06) | 0.41 (1.00) | 0.314 (1.00) | 0.000897 (1.00) | 0.316 (1.00) | 0.0116 (1.00) | 0.135 (1.00) | 0.416 (1.00) | 0.158 (1.00) |  | 8.49e-09 (1.26e-05)
Del Peak 40(16q23 1) | 0.00572 (1.00) | 0.425 (1.00) | 1.03e-249 (1.85e-246) | 1.35e-71 (2.3e-68) | 0.222 (1.00) | 2e-189 (3.59e-186) | 7.26e-11 (1.1e-07) | 0.049 (1.00) | 0.0292 (1.00) | 4.29e-33 (7.01e-30) | 4.83e-05 (0.0646) | 0.235 (1.00) | 0.354 (1.00) | 0.0022 (1.00) | 0.334 (1.00) | 0.0172 (1.00) | 0.00896 (1.00) | 0.000421 (0.533) | 0.817 (1.00) |  | 1.18e-09 (1.76e-06)
Del Peak 41(17p12) | 0.0431 (1.00) | 0.247 (1.00) | 1.18e-243 (2.13e-240) | 3e-26 (4.84e-23) | 2.4e-05 (0.0326) | 1.94e-191 (3.48e-188) | 2.66e-13 (4.11e-10) | 2.29e-07 (0.000332) | 0.00243 (1.00) | 9.14e-30 (1.48e-26) | 3.15e-28 (5.09e-25) | 0.26 (1.00) | 0.42 (1.00) | 0.443 (1.00) | 0.662 (1.00) | 0.9 (1.00) | 0.0223 (1.00) | 0.189 (1.00) | 0.0113 (1.00) |  | 0.0193 (1.00)
Del Peak 42(17q11 2) | 0.858 (1.00) | 1.08e-05 (0.0149) | 4.51e-260 (8.16e-257) | 2.56e-50 (4.28e-47) | 0.243 (1.00) | 2.51e-232 (4.52e-229) | 0.00096 (1.00) | 0.727 (1.00) | 0.398 (1.00) | 1.47e-59 (2.47e-56) | 1.65e-09 (2.47e-06) | 0.0626 (1.00) | 0.0751 (1.00) | 0.0464 (1.00) | 0.771 (1.00) | 0.115 (1.00) | 0.632 (1.00) | 0.00277 (1.00) | 0.305 (1.00) |  | 0.00344 (1.00)
Del Peak 43(18q21 2) | 0.3 (1.00) | 2.01e-06 (0.00285) | 7.33e-159 (1.31e-155) | 0.0634 (1.00) | 0.00639 (1.00) | 9.15e-112 (1.6e-108) | 3.15e-24 (5.06e-21) | 2.33e-10 (3.52e-07) | 1.36e-06 (0.00195) | 4.15e-17 (6.53e-14) | 3.94e-26 (6.35e-23) | 0.2 (1.00) | 0.413 (1.00) | 0.246 (1.00) | 0.0214 (1.00) | 0.303 (1.00) | 0.0378 (1.00) | 0.00191 (1.00) | 0.00623 (1.00) |  | 0.0469 (1.00)
Del Peak 44(18q23) | 0.405 (1.00) | 0.000287 (0.366) | 3.55e-162 (6.33e-159) | 0.125 (1.00) | 0.0108 (1.00) | 8.86e-116 (1.55e-112) | 4.49e-23 (7.18e-20) | 3.7e-10 (5.57e-07) | 7.29e-05 (0.0966) | 1.51e-19 (2.39e-16) | 9.54e-25 (1.53e-21) | 0.291 (1.00) | 0.0992 (1.00) | 0.126 (1.00) | 0.0102 (1.00) | 0.282 (1.00) | 0.0321 (1.00) | 0.0062 (1.00) | 0.00142 (1.00) |  | 0.182 (1.00)
Del Peak 45(19p13 3) | 0.0982 (1.00) | 0.856 (1.00) | 1.3e-268 (2.35e-265) | 1.38e-24 (2.22e-21) | 0.0652 (1.00) | 4.58e-237 (8.25e-234) | 1.31e-17 (2.07e-14) | 1.11e-05 (0.0153) | 0.000617 (0.769) | 1.59e-41 (2.64e-38) | 6.69e-19 (1.06e-15) | 0.471 (1.00) | 0.38 (1.00) | 0.301 (1.00) | 0.0718 (1.00) | 0.575 (1.00) | 0.752 (1.00) | 0.00209 (1.00) | 0.119 (1.00) |  | 0.754 (1.00)
Del Peak 46(19q13 32) | 0.0052 (1.00) | 0.334 (1.00) | 1.15e-114 (2.02e-111) | 1.42e-07 (0.000206) | 0.717 (1.00) | 3.8e-108 (6.63e-105) | 7.12e-07 (0.00103) | 0.0504 (1.00) | 0.0125 (1.00) | 2.06e-19 (3.27e-16) | 0.0239 (1.00) | 0.489 (1.00) | 0.369 (1.00) | 0.0218 (1.00) | 0.0481 (1.00) | 0.446 (1.00) | 0.294 (1.00) | 0.0083 (1.00) | 0.0854 (1.00) |  | 0.139 (1.00)
Del Peak 47(19q13 43) | 0.00547 (1.00) | 0.622 (1.00) | 1.25e-103 (2.17e-100) | 4.29e-07 (0.000621) | 0.914 (1.00) | 1.91e-95 (3.3e-92) | 2.7e-06 (0.00382) | 0.0171 (1.00) | 0.133 (1.00) | 8.42e-17 (1.32e-13) | 0.0411 (1.00) | 0.0537 (1.00) | 0.307 (1.00) | 0.0146 (1.00) | 0.102 (1.00) | 0.548 (1.00) | 0.691 (1.00) | 0.00182 (1.00) | 0.0446 (1.00) |  | 0.588 (1.00)
Del Peak 48(20p12 1) | 0.332 (1.00) | 0.511 (1.00) | 6.45e-36 (1.06e-32) | 0.264 (1.00) | 0.916 (1.00) | 1.04e-29 (1.69e-26) | 0.000251 (0.321) | 0.000795 (0.983) | 0.028 (1.00) | 0.00895 (1.00) | 2.44e-05 (0.0331) | 0.268 (1.00) | 0.367 (1.00) | 0.21 (1.00) | 0.0293 (1.00) | 0.886 (1.00) | 0.953 (1.00) | 0.213 (1.00) | 0.61 (1.00) |  | 0.211 (1.00)
Del Peak 49(21q11 2) | 0.232 (1.00) | 0.00179 (1.00) | 3.01e-68 (5.09e-65) | 0.02 (1.00) | 0.00565 (1.00) | 5.01e-47 (8.32e-44) | 5.18e-06 (0.00726) | 0.000231 (0.298) | 0.0748 (1.00) | 0.0838 (1.00) | 3.58e-11 (5.45e-08) | 0.0301 (1.00) | 0.00137 (1.00) | 0.000113 (0.149) | 0.373 (1.00) | 0.771 (1.00) | 0.226 (1.00) | 0.46 (1.00) | 0.164 (1.00) |  | 0.0112 (1.00)
Del Peak 50(22q13 32) | 0.000113 (0.149) | 0.301 (1.00) | 3.08e-173 (5.51e-170) | 1.14e-27 (1.84e-24) | 0.136 (1.00) | 1.36e-190 (2.45e-187) | 0.000546 (0.685) | 0.00341 (1.00) | 0.000141 (0.184) | 1.3e-43 (2.15e-40) | 0.0696 (1.00) | 0.0552 (1.00) | 0.748 (1.00) | 0.103 (1.00) | 0.0413 (1.00) | 0.954 (1.00) | 0.171 (1.00) | 8.1e-05 (0.107) | 0.273 (1.00) |  | 0.705 (1.00)
Del Peak 51(Xp21 1) | 1.62e-05 (0.0222) | 0.24 (1.00) | 2.08e-114 (3.65e-111) | 0.0208 (1.00) | 0.14 (1.00) | 2.13e-103 (3.69e-100) | 0.00429 (1.00) | 0.014 (1.00) | 0.963 (1.00) | 1.74e-18 (2.75e-15) | 0.00377 (1.00) | 0.34 (1.00) | 0.319 (1.00) | 0.678 (1.00) | 0.838 (1.00) | 0.776 (1.00) | 0.868 (1.00) | 0.0515 (1.00) | 0.183 (1.00) |  | 0.0262 (1.00)

Clustering Approach #1: 'Amp Peak 1(1p34.2) mutation analysis'

Table S1. Description of clustering approach #1: 'Amp Peak 1(1p34.2) mutation analysis'

Cluster Labels | AMP PEAK 1(1P34.2) MUTATED | AMP PEAK 1(1P34.2) WILD-TYPE
--- | --- | ---
Number of samples | 807 | 3756

'Amp Peak 1(1p34.2) mutation analysis' versus 'PRIMARY.SITE.OF.DISEASE'

P value = 1.57e-118 (Chi-square test), Q value = 2.8e-115

Table S2. Clustering Approach #1: 'Amp Peak 1(1p34.2) mutation analysis' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'

nPatients | BLADDER | BRAIN | BREAST | COLON | ENDOMETRIAL | HEAD/NECK | KIDNEY | LUNG | OMENTUM | OVARY | PERITONEUM (OVARY) | RECTUM
--- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | ---
ALL | 125 | 544 | 846 | 412 | 447 | 319 | 493 | 662 | 2 | 548 | 2 | 159
AMP PEAK 1(1P34.2) MUTATED | 35 | 77 | 123 | 22 | 50 | 46 | 16 | 153 | 1 | 276 | 1 | 7
AMP PEAK 1(1P34.2) WILD-TYPE | 90 | 467 | 723 | 390 | 397 | 273 | 477 | 509 | 1 | 272 | 1 | 152

Figure S1. Get High-res Image Clustering Approach #1: 'Amp Peak 1(1p34.2) mutation analysis' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'

'Amp Peak 1(1p34.2) mutation analysis' versus 'GENDER'

P value = 2.69e-13 (Fisher's exact test), Q value = 4.2e-10

Table S3. Clustering Approach #1: 'Amp Peak 1(1p34.2) mutation analysis' versus Clinical Feature #4: 'GENDER'

nPatients | FEMALE | MALE
--- | --- | ---
ALL | 2881 | 1682
AMP PEAK 1(1P34.2) MUTATED | 599 | 208
AMP PEAK 1(1P34.2) WILD-TYPE | 2282 | 1474

Figure S2. Get High-res Image Clustering Approach #1: 'Amp Peak 1(1p34.2) mutation analysis' versus Clinical Feature #4: 'GENDER'

'Amp Peak 1(1p34.2) mutation analysis' versus 'HISTOLOGICAL.TYPE'

P value = 1.32e-115 (Chi-square test), Q value = 2.3e-112

Table S4. Clustering Approach #1: 'Amp Peak 1(1p34.2) mutation analysis' versus Clinical Feature #6: 'HISTOLOGICAL.TYPE'

nPatients | COLON ADENOCARCINOMA | COLON MUCINOUS ADENOCARCINOMA | ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA | HEAD & NECK SQUAMOUS CELL CARCINOMA | KIDNEY CLEAR CELL RENAL CARCINOMA | LUNG ACINAR ADENOCARCINOMA | LUNG ADENOCARCINOMA MIXED SUBTYPE | LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS) | LUNG BASALOID SQUAMOUS CELL CARCINOMA | LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS | LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS | LUNG CLEAR CELL ADENOCARCINOMA | LUNG MICROPAPILLARY ADENOCARCINOMA | LUNG MUCINOUS ADENOCARCINOMA | LUNG PAPILLARY ADENOCARCINOMA | LUNG PAPILLARY SQUAMOUS CELL CARCINOMA | LUNG PAPILLARY SQUAMOUS CELL CARICNOMA | LUNG SMALL CELL SQUAMOUS CELL CARCINOMA | LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA | LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS) | MIXED SEROUS AND ENDOMETRIOID | MUCINOUS (COLLOID) ADENOCARCINOMA | RECTAL ADENOCARCINOMA | RECTAL MUCINOUS ADENOCARCINOMA | SEROUS CYSTADENOCARCINOMA | SEROUS ENDOMETRIAL ADENOCARCINOMA | TREATED PRIMARY GBM | UNTREATED PRIMARY (DE NOVO) GBM
--- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | ---
ALL | 356 | 54 | 350 | 319 | 493 | 10 | 75 | 205 | 7 | 3 | 15 | 2 | 3 | 2 | 13 | 1 | 1 | 1 | 2 | 315 | 18 | 7 | 143 | 13 | 552 | 79 | 1 | 20
AMP PEAK 1(1P34.2) MUTATED | 20 | 2 | 14 | 46 | 16 | 4 | 15 | 66 | 3 | 0 | 5 | 0 | 1 | 0 | 4 | 0 | 0 | 1 | 1 | 52 | 5 | 1 | 5 | 2 | 278 | 31 | 0 | 2
AMP PEAK 1(1P34.2) WILD-TYPE | 336 | 52 | 336 | 273 | 477 | 6 | 60 | 139 | 4 | 3 | 10 | 2 | 2 | 2 | 9 | 1 | 1 | 0 | 1 | 263 | 13 | 6 | 138 | 11 | 274 | 48 | 1 | 18

Figure S3. Get High-res Image Clustering Approach #1: 'Amp Peak 1(1p34.2) mutation analysis' versus Clinical Feature #6: 'HISTOLOGICAL.TYPE'

'Amp Peak 1(1p34.2) mutation analysis' versus 'PATHOLOGY.T'

P value = 1.49e-06 (Fisher's exact test), Q value = 0.0021

Table S5. Clustering Approach #1: 'Amp Peak 1(1p34.2) mutation analysis' versus Clinical Feature #7: 'PATHOLOGY.T'

nPatients | T0+T1 | T2 | T3 | T4
--- | --- | --- | --- | ---
ALL | 466 | 632 | 694 | 209
AMP PEAK 1(1P34.2) MUTATED | 47 | 105 | 51 | 29
AMP PEAK 1(1P34.2) WILD-TYPE | 419 | 527 | 643 | 180

Figure S4. Get High-res Image Clustering Approach #1: 'Amp Peak 1(1p34.2) mutation analysis' versus Clinical Feature #7: 'PATHOLOGY.T'

'Amp Peak 1(1p34.2) mutation analysis' versus 'TUMOR.STAGE'

P value = 2.52e-16 (Fisher's exact test), Q value = 3.9e-13

Table S6. Clustering Approach #1: 'Amp Peak 1(1p34.2) mutation analysis' versus Clinical Feature #10: 'TUMOR.STAGE'

nPatients | I | II | III | IV
--- | --- | --- | --- | ---
ALL | 712 | 498 | 881 | 423
AMP PEAK 1(1P34.2) MUTATED | 100 | 65 | 257 | 81
AMP PEAK 1(1P34.2) WILD-TYPE | 612 | 433 | 624 | 342

Figure S5. Get High-res Image Clustering Approach #1: 'Amp Peak 1(1p34.2) mutation analysis' versus Clinical Feature #10: 'TUMOR.STAGE'

Clustering Approach #2: 'Amp Peak 2(1p22.3) mutation analysis'

Table S7. Description of clustering approach #2: 'Amp Peak 2(1p22.3) mutation analysis'

Cluster Labels | AMP PEAK 2(1P22.3) MUTATED | AMP PEAK 2(1P22.3) WILD-TYPE
--- | --- | ---
Number of samples | 770 | 3793

'Amp Peak 2(1p22.3) mutation analysis' versus 'PRIMARY.SITE.OF.DISEASE'

P value = 2.49e-44 (Chi-square test), Q value = 4.1e-41

Table S8. Clustering Approach #2: 'Amp Peak 2(1p22.3) mutation analysis' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'

nPatients | BLADDER | BRAIN | BREAST | COLON | ENDOMETRIAL | HEAD/NECK | KIDNEY | LUNG | OMENTUM | OVARY | PERITONEUM (OVARY) | RECTUM
--- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | ---
ALL | 125 | 544 | 846 | 412 | 447 | 319 | 493 | 662 | 2 | 548 | 2 | 159
AMP PEAK 2(1P22.3) MUTATED | 34 | 74 | 186 | 19 | 74 | 38 | 18 | 152 | 1 | 163 | 0 | 11
AMP PEAK 2(1P22.3) WILD-TYPE | 91 | 470 | 660 | 393 | 373 | 281 | 475 | 510 | 1 | 385 | 2 | 148

Figure S6. Get High-res Image Clustering Approach #2: 'Amp Peak 2(1p22.3) mutation analysis' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'

'Amp Peak 2(1p22.3) mutation analysis' versus 'GENDER'

P value = 8.9e-12 (Fisher's exact test), Q value = 1.4e-08

Table S9. Clustering Approach #2: 'Amp Peak 2(1p22.3) mutation analysis' versus Clinical Feature #4: 'GENDER'

nPatients | FEMALE | MALE
--- | --- | ---
ALL | 2881 | 1682
AMP PEAK 2(1P22.3) MUTATED | 568 | 202
AMP PEAK 2(1P22.3) WILD-TYPE | 2313 | 1480

Figure S7. Get High-res Image Clustering Approach #2: 'Amp Peak 2(1p22.3) mutation analysis' versus Clinical Feature #4: 'GENDER'

'Amp Peak 2(1p22.3) mutation analysis' versus 'HISTOLOGICAL.TYPE'

P value = 1.9e-41 (Chi-square test), Q value = 3.1e-38

Table S10. Clustering Approach #2: 'Amp Peak 2(1p22.3) mutation analysis' versus Clinical Feature #6: 'HISTOLOGICAL.TYPE'

nPatients | COLON ADENOCARCINOMA | COLON MUCINOUS ADENOCARCINOMA | ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA | HEAD & NECK SQUAMOUS CELL CARCINOMA | KIDNEY CLEAR CELL RENAL CARCINOMA | LUNG ACINAR ADENOCARCINOMA | LUNG ADENOCARCINOMA MIXED SUBTYPE | LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS) | LUNG BASALOID SQUAMOUS CELL CARCINOMA | LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS | LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS | LUNG CLEAR CELL ADENOCARCINOMA | LUNG MICROPAPILLARY ADENOCARCINOMA | LUNG MUCINOUS ADENOCARCINOMA | LUNG PAPILLARY ADENOCARCINOMA | LUNG PAPILLARY SQUAMOUS CELL CARCINOMA | LUNG PAPILLARY SQUAMOUS CELL CARICNOMA | LUNG SMALL CELL SQUAMOUS CELL CARCINOMA | LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA | LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS) | MIXED SEROUS AND ENDOMETRIOID | MUCINOUS (COLLOID) ADENOCARCINOMA | RECTAL ADENOCARCINOMA | RECTAL MUCINOUS ADENOCARCINOMA | SEROUS CYSTADENOCARCINOMA | SEROUS ENDOMETRIAL ADENOCARCINOMA | TREATED PRIMARY GBM | UNTREATED PRIMARY (DE NOVO) GBM
--- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | ---
ALL | 356 | 54 | 350 | 319 | 493 | 10 | 75 | 205 | 7 | 3 | 15 | 2 | 3 | 2 | 13 | 1 | 1 | 1 | 2 | 315 | 18 | 7 | 143 | 13 | 552 | 79 | 1 | 20
AMP PEAK 2(1P22.3) MUTATED | 17 | 2 | 47 | 38 | 18 | 4 | 18 | 58 | 2 | 0 | 8 | 0 | 2 | 0 | 1 | 1 | 0 | 0 | 1 | 56 | 4 | 1 | 9 | 2 | 164 | 23 | 0 | 2
AMP PEAK 2(1P22.3) WILD-TYPE | 339 | 52 | 303 | 281 | 475 | 6 | 57 | 147 | 5 | 3 | 7 | 2 | 1 | 2 | 12 | 0 | 1 | 1 | 1 | 259 | 14 | 6 | 134 | 11 | 388 | 56 | 1 | 18

Figure S8. Get High-res Image Clustering Approach #2: 'Amp Peak 2(1p22.3) mutation analysis' versus Clinical Feature #6: 'HISTOLOGICAL.TYPE'

'Amp Peak 2(1p22.3) mutation analysis' versus 'PATHOLOGY.T'

P value = 5.91e-06 (Fisher's exact test), Q value = 0.0083

Table S11. Clustering Approach #2: 'Amp Peak 2(1p22.3) mutation analysis' versus Clinical Feature #7: 'PATHOLOGY.T'

nPatients | T0+T1 | T2 | T3 | T4
--- | --- | --- | --- | ---
ALL | 466 | 632 | 694 | 209
AMP PEAK 2(1P22.3) MUTATED | 45 | 103 | 53 | 29
AMP PEAK 2(1P22.3) WILD-TYPE | 421 | 529 | 641 | 180

Figure S9. Get High-res Image Clustering Approach #2: 'Amp Peak 2(1p22.3) mutation analysis' versus Clinical Feature #7: 'PATHOLOGY.T'

'Amp Peak 2(1p22.3) mutation analysis' versus 'TUMOR.STAGE'

P value = 0.000128 (Fisher's exact test), Q value = 0.17

Table S12. Clustering Approach #2: 'Amp Peak 2(1p22.3) mutation analysis' versus Clinical Feature #10: 'TUMOR.STAGE'

nPatients | I | II | III | IV
--- | --- | --- | --- | ---
ALL | 712 | 498 | 881 | 423
AMP PEAK 2(1P22.3) MUTATED | 90 | 62 | 175 | 61
AMP PEAK 2(1P22.3) WILD-TYPE | 622 | 436 | 706 | 362

Figure S10. Get High-res Image Clustering Approach #2: 'Amp Peak 2(1p22.3) mutation analysis' versus Clinical Feature #10: 'TUMOR.STAGE'

Clustering Approach #3: 'Amp Peak 3(1q21.3) mutation analysis'

Table S13. Description of clustering approach #3: 'Amp Peak 3(1q21.3) mutation analysis'

Cluster Labels | AMP PEAK 3(1Q21.3) MUTATED | AMP PEAK 3(1Q21.3) WILD-TYPE
--- | --- | ---
Number of samples | 1998 | 2565

'Amp Peak 3(1q21.3) mutation analysis' versus 'Time to Death'

P value = 1.78e-06 (logrank test), Q value = 0.0025

Table S14. Clustering Approach #3: 'Amp Peak 3(1q21.3) mutation analysis' versus Clinical Feature #1: 'Time to Death'

| nPatients | nDeath | Duration Range (Median), Month
--- | --- | --- | ---
ALL | 4296 | 1401 | 0.0 - 224.0 (14.9)
AMP PEAK 3(1Q21.3) MUTATED | 1897 | 557 | 0.0 - 224.0 (15.3)
AMP PEAK 3(1Q21.3) WILD-TYPE | 2399 | 844 | 0.0 - 210.9 (14.3)

Figure S11. Get High-res Image Clustering Approach #3: 'Amp Peak 3(1q21.3) mutation analysis' versus Clinical Feature #1: 'Time to Death'

'Amp Peak 3(1q21.3) mutation analysis' versus 'PRIMARY.SITE.OF.DISEASE'

P value = 1.2e-202 (Chi-square test), Q value = 2.2e-199

Table S15. Clustering Approach #3: 'Amp Peak 3(1q21.3) mutation analysis' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'

nPatients | BLADDER | BRAIN | BREAST | COLON | ENDOMETRIAL | HEAD/NECK | KIDNEY | LUNG | OMENTUM | OVARY | PERITONEUM (OVARY) | RECTUM
--- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | ---
ALL | 125 | 544 | 846 | 412 | 447 | 319 | 493 | 662 | 2 | 548 | 2 | 159
AMP PEAK 3(1Q21.3) MUTATED | 63 | 92 | 609 | 79 | 193 | 87 | 60 | 421 | 0 | 344 | 2 | 45
AMP PEAK 3(1Q21.3) WILD-TYPE | 62 | 452 | 237 | 333 | 254 | 232 | 433 | 241 | 2 | 204 | 0 | 114

Figure S12. Get High-res Image Clustering Approach #3: 'Amp Peak 3(1q21.3) mutation analysis' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'

'Amp Peak 3(1q21.3) mutation analysis' versus 'GENDER'

P value = 1.78e-37 (Fisher's exact test), Q value = 2.9e-34

Table S16. Clustering Approach #3: 'Amp Peak 3(1q21.3) mutation analysis' versus Clinical Feature #4: 'GENDER'

nPatients | FEMALE | MALE
--- | --- | ---
ALL | 2881 | 1682
AMP PEAK 3(1Q21.3) MUTATED | 1467 | 531
AMP PEAK 3(1Q21.3) WILD-TYPE | 1414 | 1151

Figure S13. Get High-res Image Clustering Approach #3: 'Amp Peak 3(1q21.3) mutation analysis' versus Clinical Feature #4: 'GENDER'

'Amp Peak 3(1q21.3) mutation analysis' versus 'HISTOLOGICAL.TYPE'

P value = 7.04e-110 (Chi-square test), Q value = 1.2e-106

Table S17. Clustering Approach #3: 'Amp Peak 3(1q21.3) mutation analysis' versus Clinical Feature #6: 'HISTOLOGICAL.TYPE'

nPatients | COLON ADENOCARCINOMA | COLON MUCINOUS ADENOCARCINOMA | ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA | HEAD & NECK SQUAMOUS CELL CARCINOMA | KIDNEY CLEAR CELL RENAL CARCINOMA | LUNG ACINAR ADENOCARCINOMA | LUNG ADENOCARCINOMA MIXED SUBTYPE | LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS) | LUNG BASALOID SQUAMOUS CELL CARCINOMA | LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS | LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS | LUNG CLEAR CELL ADENOCARCINOMA | LUNG MICROPAPILLARY ADENOCARCINOMA | LUNG MUCINOUS ADENOCARCINOMA | LUNG PAPILLARY ADENOCARCINOMA | LUNG PAPILLARY SQUAMOUS CELL CARCINOMA | LUNG PAPILLARY SQUAMOUS CELL CARICNOMA | LUNG SMALL CELL SQUAMOUS CELL CARCINOMA | LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA | LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS) | MIXED SEROUS AND ENDOMETRIOID | MUCINOUS (COLLOID) ADENOCARCINOMA | RECTAL ADENOCARCINOMA | RECTAL MUCINOUS ADENOCARCINOMA | SEROUS CYSTADENOCARCINOMA | SEROUS ENDOMETRIAL ADENOCARCINOMA | TREATED PRIMARY GBM | UNTREATED PRIMARY (DE NOVO) GBM
--- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | ---
ALL | 356 | 54 | 350 | 319 | 493 | 10 | 75 | 205 | 7 | 3 | 15 | 2 | 3 | 2 | 13 | 1 | 1 | 1 | 2 | 315 | 18 | 7 | 143 | 13 | 552 | 79 | 1 | 20
AMP PEAK 3(1Q21.3) MUTATED | 72 | 7 | 136 | 87 | 60 | 9 | 58 | 147 | 6 | 0 | 13 | 2 | 2 | 1 | 9 | 1 | 0 | 1 | 1 | 168 | 8 | 3 | 41 | 3 | 346 | 49 | 0 | 2
AMP PEAK 3(1Q21.3) WILD-TYPE | 284 | 47 | 214 | 232 | 433 | 1 | 17 | 58 | 1 | 3 | 2 | 0 | 1 | 1 | 4 | 0 | 1 | 0 | 1 | 147 | 10 | 4 | 102 | 10 | 206 | 30 | 1 | 18

Figure S14. Get High-res Image Clustering Approach #3: 'Amp Peak 3(1q21.3) mutation analysis' versus Clinical Feature #6: 'HISTOLOGICAL.TYPE'

'Amp Peak 3(1q21.3) mutation analysis' versus 'PATHOLOGY.T'

P value = 1.13e-15 (Fisher's exact test), Q value = 1.8e-12

Table S18. Clustering Approach #3: 'Amp Peak 3(1q21.3) mutation analysis' versus Clinical Feature #7: 'PATHOLOGY.T'

nPatients | T0+T1 | T2 | T3 | T4
--- | --- | --- | --- | ---
ALL | 466 | 632 | 694 | 209
AMP PEAK 3(1Q21.3) MUTATED | 135 | 293 | 174 | 75
AMP PEAK 3(1Q21.3) WILD-TYPE | 331 | 339 | 520 | 134

Figure S15. Get High-res Image Clustering Approach #3: 'Amp Peak 3(1q21.3) mutation analysis' versus Clinical Feature #7: 'PATHOLOGY.T'

'Amp Peak 3(1q21.3) mutation analysis' versus 'PATHOLOGICSPREAD(M)'

P value = 1e-05 (Chi-square test), Q value = 0.014

Table S19. Clustering Approach #3: 'Amp Peak 3(1q21.3) mutation analysis' versus Clinical Feature #9: 'PATHOLOGICSPREAD(M)'

nPatients | M0 | M1 | M1A | M1B | MX
--- | --- | --- | --- | --- | ---
ALL | 1424 | 168 | 9 | 3 | 165
AMP PEAK 3(1Q21.3) MUTATED | 469 | 48 | 3 | 0 | 86
AMP PEAK 3(1Q21.3) WILD-TYPE | 955 | 120 | 6 | 3 | 79

Figure S16. Get High-res Image Clustering Approach #3: 'Amp Peak 3(1q21.3) mutation analysis' versus Clinical Feature #9: 'PATHOLOGICSPREAD(M)'

'Amp Peak 3(1q21.3) mutation analysis' versus 'TUMOR.STAGE'

P value = 1.62e-06 (Fisher's exact test), Q value = 0.0023

Table S20. Clustering Approach #3: 'Amp Peak 3(1q21.3) mutation analysis' versus Clinical Feature #10: 'TUMOR.STAGE'

nPatients | I | II | III | IV
--- | --- | --- | --- | ---
ALL | 712 | 498 | 881 | 423
AMP PEAK 3(1Q21.3) MUTATED | 267 | 175 | 418 | 152
AMP PEAK 3(1Q21.3) WILD-TYPE | 445 | 323 | 463 | 271

Figure S17. Get High-res Image Clustering Approach #3: 'Amp Peak 3(1q21.3) mutation analysis' versus Clinical Feature #10: 'TUMOR.STAGE'

Clustering Approach #4: 'Amp Peak 4(1q32.1) mutation analysis'

Table S21. Description of clustering approach #4: 'Amp Peak 4(1q32.1) mutation analysis'

Cluster Labels | AMP PEAK 4(1Q32.1) MUTATED | AMP PEAK 4(1Q32.1) WILD-TYPE
--- | --- | ---
Number of samples | 1998 | 2565

'Amp Peak 4(1q32.1) mutation analysis' versus 'Time to Death'

P value = 1.36e-05 (logrank test), Q value = 0.019

Table S22. Clustering Approach #4: 'Amp Peak 4(1q32.1) mutation analysis' versus Clinical Feature #1: 'Time to Death'

| nPatients | nDeath | Duration Range (Median), Month
--- | --- | --- | ---
ALL | 4296 | 1401 | 0.0 - 224.0 (14.9)
AMP PEAK 4(1Q32.1) MUTATED | 1895 | 553 | 0.0 - 223.4 (15.1)
AMP PEAK 4(1Q32.1) WILD-TYPE | 2401 | 848 | 0.0 - 224.0 (14.6)

Figure S18. Get High-res Image Clustering Approach #4: 'Amp Peak 4(1q32.1) mutation analysis' versus Clinical Feature #1: 'Time to Death'

'Amp Peak 4(1q32.1) mutation analysis' versus 'PRIMARY.SITE.OF.DISEASE'

P value = 3.02e-185 (Chi-square test), Q value = 5.4e-182

Table S23. Clustering Approach #4: 'Amp Peak 4(1q32.1) mutation analysis' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'

nPatients | BLADDER | BRAIN | BREAST | COLON | ENDOMETRIAL | HEAD/NECK | KIDNEY | LUNG | OMENTUM | OVARY | PERITONEUM (OVARY) | RECTUM
--- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | ---
ALL | 125 | 544 | 846 | 412 | 447 | 319 | 493 | 662 | 2 | 548 | 2 | 159
AMP PEAK 4(1Q32.1) MUTATED | 43 | 148 | 652 | 86 | 187 | 87 | 58 | 416 | 0 | 270 | 2 | 47
AMP PEAK 4(1Q32.1) WILD-TYPE | 82 | 396 | 194 | 326 | 260 | 232 | 435 | 246 | 2 | 278 | 0 | 112

Figure S19. Get High-res Image Clustering Approach #4: 'Amp Peak 4(1q32.1) mutation analysis' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'

'Amp Peak 4(1q32.1) mutation analysis' versus 'GENDER'

P value = 2.97e-29 (Fisher's exact test), Q value = 4.8e-26

Table S24. Clustering Approach #4: 'Amp Peak 4(1q32.1) mutation analysis' versus Clinical Feature #4: 'GENDER'

nPatients | FEMALE | MALE
--- | --- | ---
ALL | 2881 | 1682
AMP PEAK 4(1Q32.1) MUTATED | 1442 | 556
AMP PEAK 4(1Q32.1) WILD-TYPE | 1439 | 1126

Figure S20. Get High-res Image Clustering Approach #4: 'Amp Peak 4(1q32.1) mutation analysis' versus Clinical Feature #4: 'GENDER'

'Amp Peak 4(1q32.1) mutation analysis' versus 'HISTOLOGICAL.TYPE'

P value = 3.76e-84 (Chi-square test), Q value = 6.4e-81

Table S25. Clustering Approach #4: 'Amp Peak 4(1q32.1) mutation analysis' versus Clinical Feature #6: 'HISTOLOGICAL.TYPE'

nPatients | COLON ADENOCARCINOMA | COLON MUCINOUS ADENOCARCINOMA | ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA | HEAD & NECK SQUAMOUS CELL CARCINOMA | KIDNEY CLEAR CELL RENAL CARCINOMA | LUNG ACINAR ADENOCARCINOMA | LUNG ADENOCARCINOMA MIXED SUBTYPE | LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS) | LUNG BASALOID SQUAMOUS CELL CARCINOMA | LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS | LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS | LUNG CLEAR CELL ADENOCARCINOMA | LUNG MICROPAPILLARY ADENOCARCINOMA | LUNG MUCINOUS ADENOCARCINOMA | LUNG PAPILLARY ADENOCARCINOMA | LUNG PAPILLARY SQUAMOUS CELL CARCINOMA | LUNG PAPILLARY SQUAMOUS CELL CARICNOMA | LUNG SMALL CELL SQUAMOUS CELL CARCINOMA | LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA | LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS) | MIXED SEROUS AND ENDOMETRIOID | MUCINOUS (COLLOID) ADENOCARCINOMA | RECTAL ADENOCARCINOMA | RECTAL MUCINOUS ADENOCARCINOMA | SEROUS CYSTADENOCARCINOMA | SEROUS ENDOMETRIAL ADENOCARCINOMA | TREATED PRIMARY GBM | UNTREATED PRIMARY (DE NOVO) GBM
--- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | ---
ALL | 356 | 54 | 350 | 319 | 493 | 10 | 75 | 205 | 7 | 3 | 15 | 2 | 3 | 2 | 13 | 1 | 1 | 1 | 2 | 315 | 18 | 7 | 143 | 13 | 552 | 79 | 1 | 20
AMP PEAK 4(1Q32.1) MUTATED | 79 | 7 | 145 | 87 | 58 | 9 | 54 | 150 | 6 | 0 | 13 | 2 | 2 | 0 | 9 | 1 | 0 | 1 | 2 | 164 | 6 | 3 | 42 | 4 | 272 | 36 | 0 | 4
AMP PEAK 4(1Q32.1) WILD-TYPE | 277 | 47 | 205 | 232 | 435 | 1 | 21 | 55 | 1 | 3 | 2 | 0 | 1 | 2 | 4 | 0 | 1 | 0 | 0 | 151 | 12 | 4 | 101 | 9 | 280 | 43 | 1 | 16

Figure S21. Get High-res Image Clustering Approach #4: 'Amp Peak 4(1q32.1) mutation analysis' versus Clinical Feature #6: 'HISTOLOGICAL.TYPE'

'Amp Peak 4(1q32.1) mutation analysis' versus 'PATHOLOGY.T'

P value = 1.32e-16 (Fisher's exact test), Q value = 2.1e-13

Table S26. Clustering Approach #4: 'Amp Peak 4(1q32.1) mutation analysis' versus Clinical Feature #7: 'PATHOLOGY.T'

nPatients | T0+T1 | T2 | T3 | T4
--- | --- | --- | --- | ---
ALL | 466 | 632 | 694 | 209
AMP PEAK 4(1Q32.1) MUTATED | 133 | 296 | 174 | 76
AMP PEAK 4(1Q32.1) WILD-TYPE | 333 | 336 | 520 | 133

Figure S22. Get High-res Image Clustering Approach #4: 'Amp Peak 4(1q32.1) mutation analysis' versus Clinical Feature #7: 'PATHOLOGY.T'

'Amp Peak 4(1q32.1) mutation analysis' versus 'PATHOLOGICSPREAD(M)'

P value = 0.000109 (Chi-square test), Q value = 0.14

Table S27. Clustering Approach #4: 'Amp Peak 4(1q32.1) mutation analysis' versus Clinical Feature #9: 'PATHOLOGICSPREAD(M)'

nPatients | M0 | M1 | M1A | M1B | MX
--- | --- | --- | --- | --- | ---
ALL | 1424 | 168 | 9 | 3 | 165
AMP PEAK 4(1Q32.1) MUTATED | 472 | 52 | 3 | 0 | 84
AMP PEAK 4(1Q32.1) WILD-TYPE | 952 | 116 | 6 | 3 | 81

Figure S23. Get High-res Image Clustering Approach #4: 'Amp Peak 4(1q32.1) mutation analysis' versus Clinical Feature #9: 'PATHOLOGICSPREAD(M)'

'Amp Peak 4(1q32.1) mutation analysis' versus 'TOBACCOSMOKINGHISTORYINDICATOR'

P value = 0.000111 (Chi-square test), Q value = 0.15

Table S28. Clustering Approach #4: 'Amp Peak 4(1q32.1) mutation analysis' versus Clinical Feature #14: 'TOBACCOSMOKINGHISTORYINDICATOR'

nPatients | 1 | 2 | 3 | 4 | 5 | CURRENT REFORMED SMOKER FOR < OR = 15 YEARS | CURRENT REFORMED SMOKER FOR > 15 YEARS | CURRENT SMOKER | LIFELONG NON-SMOKER
--- | --- | --- | --- | --- | --- | --- | --- | --- | ---
ALL | 28 | 23 | 37 | 29 | 2 | 355 | 217 | 250 | 128
AMP PEAK 4(1Q32.1) MUTATED | 6 | 7 | 14 | 13 | 0 | 199 | 114 | 124 | 47
AMP PEAK 4(1Q32.1) WILD-TYPE | 22 | 16 | 23 | 16 | 2 | 156 | 103 | 126 | 81

Figure S24. Get High-res Image Clustering Approach #4: 'Amp Peak 4(1q32.1) mutation analysis' versus Clinical Feature #14: 'TOBACCOSMOKINGHISTORYINDICATOR'

'Amp Peak 4(1q32.1) mutation analysis' versus 'NEOPLASM.DISEASESTAGE'

P value = 9.34e-14 (Chi-square test), Q value = 1.4e-10

Table S29. Clustering Approach #4: 'Amp Peak 4(1q32.1) mutation analysis' versus Clinical Feature #21: 'NEOPLASM.DISEASESTAGE'

nPatients | STAGE I | STAGE IA | STAGE IB | STAGE II | STAGE IIA | STAGE IIB | STAGE III | STAGE IIIA | STAGE IIIB | STAGE IIIC | STAGE IV | STAGE TIS | STAGE X
--- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | ---
ALL | 72 | 62 | 7 | 43 | 287 | 186 | 42 | 124 | 25 | 41 | 59 | 1 | 16
AMP PEAK 4(1Q32.1) MUTATED | 47 | 42 | 6 | 16 | 225 | 147 | 14 | 96 | 21 | 35 | 31 | 1 | 12
AMP PEAK 4(1Q32.1) WILD-TYPE | 25 | 20 | 1 | 27 | 62 | 39 | 28 | 28 | 4 | 6 | 28 | 0 | 4

Figure S25. Get High-res Image Clustering Approach #4: 'Amp Peak 4(1q32.1) mutation analysis' versus Clinical Feature #21: 'NEOPLASM.DISEASESTAGE'

Clustering Approach #5: 'Amp Peak 5(1q44) mutation analysis'

Table S30. Description of clustering approach #5: 'Amp Peak 5(1q44) mutation analysis'

Cluster Labels | AMP PEAK 5(1Q44) MUTATED | AMP PEAK 5(1Q44) WILD-TYPE
--- | --- | ---
Number of samples | 1904 | 2659

'Amp Peak 5(1q44) mutation analysis' versus 'Time to Death'

P value = 7.9e-07 (logrank test), Q value = 0.0011

Table S31. Clustering Approach #5: 'Amp Peak 5(1q44) mutation analysis' versus Clinical Feature #1: 'Time to Death'

| nPatients | nDeath | Duration Range (Median), Month
--- | --- | --- | ---
ALL | 4296 | 1401 | 0.0 - 224.0 (14.9)
AMP PEAK 5(1Q44) MUTATED | 1809 | 524 | 0.0 - 223.4 (15.3)
AMP PEAK 5(1Q44) WILD-TYPE | 2487 | 877 | 0.0 - 224.0 (14.3)

Figure S26. Get High-res Image Clustering Approach #5: 'Amp Peak 5(1q44) mutation analysis' versus Clinical Feature #1: 'Time to Death'

'Amp Peak 5(1q44) mutation analysis' versus 'PRIMARY.SITE.OF.DISEASE'

P value = 6.84e-183 (Chi-square test), Q value = 1.2e-179

Table S32. Clustering Approach #5: 'Amp Peak 5(1q44) mutation analysis' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'

nPatients | BLADDER | BRAIN | BREAST | COLON | ENDOMETRIAL | HEAD/NECK | KIDNEY | LUNG | OMENTUM | OVARY | PERITONEUM (OVARY) | RECTUM
--- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | ---
ALL | 125 | 544 | 846 | 412 | 447 | 319 | 493 | 662 | 2 | 548 | 2 | 159
AMP PEAK 5(1Q44) MUTATED | 48 | 93 | 614 | 85 | 181 | 94 | 55 | 400 | 2 | 283 | 2 | 46
AMP PEAK 5(1Q44) WILD-TYPE | 77 | 451 | 232 | 327 | 266 | 225 | 438 | 262 | 0 | 265 | 0 | 113

Figure S27. Get High-res Image Clustering Approach #5: 'Amp Peak 5(1q44) mutation analysis' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'

'Amp Peak 5(1q44) mutation analysis' versus 'GENDER'

P value = 1.15e-31 (Fisher's exact test), Q value = 1.9e-28

Table S33. Clustering Approach #5: 'Amp Peak 5(1q44) mutation analysis' versus Clinical Feature #4: 'GENDER'

nPatients | FEMALE | MALE
--- | --- | ---
ALL | 2881 | 1682
AMP PEAK 5(1Q44) MUTATED | 1389 | 515
AMP PEAK 5(1Q44) WILD-TYPE | 1492 | 1167

Figure S28. Get High-res Image Clustering Approach #5: 'Amp Peak 5(1q44) mutation analysis' versus Clinical Feature #4: 'GENDER'

'Amp Peak 5(1q44) mutation analysis' versus 'HISTOLOGICAL.TYPE'

P value = 1.1e-79 (Chi-square test), Q value = 1.9e-76

Table S34. Clustering Approach #5: 'Amp Peak 5(1q44) mutation analysis' versus Clinical Feature #6: 'HISTOLOGICAL.TYPE'

nPatients | COLON ADENOCARCINOMA | COLON MUCINOUS ADENOCARCINOMA | ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA | HEAD & NECK SQUAMOUS CELL CARCINOMA | KIDNEY CLEAR CELL RENAL CARCINOMA | LUNG ACINAR ADENOCARCINOMA | LUNG ADENOCARCINOMA MIXED SUBTYPE | LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS) | LUNG BASALOID SQUAMOUS CELL CARCINOMA | LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS | LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS | LUNG CLEAR CELL ADENOCARCINOMA | LUNG MICROPAPILLARY ADENOCARCINOMA | LUNG MUCINOUS ADENOCARCINOMA | LUNG PAPILLARY ADENOCARCINOMA | LUNG PAPILLARY SQUAMOUS CELL CARCINOMA | LUNG PAPILLARY SQUAMOUS CELL CARICNOMA | LUNG SMALL CELL SQUAMOUS CELL CARCINOMA | LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA | LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS) | MIXED SEROUS AND ENDOMETRIOID | MUCINOUS (COLLOID) ADENOCARCINOMA | RECTAL ADENOCARCINOMA | RECTAL MUCINOUS ADENOCARCINOMA | SEROUS CYSTADENOCARCINOMA | SEROUS ENDOMETRIAL ADENOCARCINOMA | TREATED PRIMARY GBM | UNTREATED PRIMARY (DE NOVO) GBM
--- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | ---
ALL | 356 | 54 | 350 | 319 | 493 | 10 | 75 | 205 | 7 | 3 | 15 | 2 | 3 | 2 | 13 | 1 | 1 | 1 | 2 | 315 | 18 | 7 | 143 | 13 | 552 | 79 | 1 | 20
AMP PEAK 5(1Q44) MUTATED | 76 | 9 | 140 | 94 | 55 | 9 | 49 | 142 | 6 | 0 | 12 | 2 | 2 | 0 | 9 | 1 | 0 | 1 | 2 | 162 | 5 | 3 | 41 | 4 | 287 | 36 | 0 | 3
AMP PEAK 5(1Q44) WILD-TYPE | 280 | 45 | 210 | 225 | 438 | 1 | 26 | 63 | 1 | 3 | 3 | 0 | 1 | 2 | 4 | 0 | 1 | 0 | 0 | 153 | 13 | 4 | 102 | 9 | 265 | 43 | 1 | 17

Figure S29. Get High-res Image Clustering Approach #5: 'Amp Peak 5(1q44) mutation analysis' versus Clinical Feature #6: 'HISTOLOGICAL.TYPE'

'Amp Peak 5(1q44) mutation analysis' versus 'PATHOLOGY.T'

P value = 1.29e-14 (Fisher's exact test), Q value = 2e-11

Table S35. Clustering Approach #5: 'Amp Peak 5(1q44) mutation analysis' versus Clinical Feature #7: 'PATHOLOGY.T'

nPatients | T0+T1 | T2 | T3 | T4
--- | --- | --- | --- | ---
ALL | 466 | 632 | 694 | 209
AMP PEAK 5(1Q44) MUTATED | 129 | 281 | 172 | 82
AMP PEAK 5(1Q44) WILD-TYPE | 337 | 351 | 522 | 127

Figure S30. Get High-res Image Clustering Approach #5: 'Amp Peak 5(1q44) mutation analysis' versus Clinical Feature #7: 'PATHOLOGY.T'

'Amp Peak 5(1q44) mutation analysis' versus 'PATHOLOGICSPREAD(M)'

P value = 7.39e-05 (Chi-square test), Q value = 0.098

Table S36. Clustering Approach #5: 'Amp Peak 5(1q44) mutation analysis' versus Clinical Feature #9: 'PATHOLOGICSPREAD(M)'

nPatients | M0 | M1 | M1A | M1B | MX
--- | --- | --- | --- | --- | ---
ALL | 1424 | 168 | 9 | 3 | 165
AMP PEAK 5(1Q44) MUTATED | 448 | 55 | 4 | 0 | 82
AMP PEAK 5(1Q44) WILD-TYPE | 976 | 113 | 5 | 3 | 83

Figure S31. Get High-res Image Clustering Approach #5: 'Amp Peak 5(1q44) mutation analysis' versus Clinical Feature #9: 'PATHOLOGICSPREAD(M)'

'Amp Peak 5(1q44) mutation analysis' versus 'NEOPLASM.DISEASESTAGE'

P value = 1.33e-07 (Chi-square test), Q value = 0.00019

Table S37. Clustering Approach #5: 'Amp Peak 5(1q44) mutation analysis' versus Clinical Feature #21: 'NEOPLASM.DISEASESTAGE'

nPatients | STAGE I | STAGE IA | STAGE IB | STAGE II | STAGE IIA | STAGE IIB | STAGE III | STAGE IIIA | STAGE IIIB | STAGE IIIC | STAGE IV | STAGE TIS | STAGE X
--- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | ---
ALL | 72 | 62 | 7 | 43 | 287 | 186 | 42 | 124 | 25 | 41 | 59 | 1 | 16
AMP PEAK 5(1Q44) MUTATED | 48 | 38 | 6 | 19 | 210 | 140 | 14 | 87 | 21 | 32 | 32 | 1 | 11
AMP PEAK 5(1Q44) WILD-TYPE | 24 | 24 | 1 | 24 | 77 | 46 | 28 | 37 | 4 | 9 | 27 | 0 | 5

Figure S32. Get High-res Image Clustering Approach #5: 'Amp Peak 5(1q44) mutation analysis' versus Clinical Feature #21: 'NEOPLASM.DISEASESTAGE'

Clustering Approach #6: 'Amp Peak 6(2p15) mutation analysis'

Table S38. Description of clustering approach #6: 'Amp Peak 6(2p15) mutation analysis'

Cluster Labels | AMP PEAK 6(2P15) MUTATED | AMP PEAK 6(2P15) WILD-TYPE
--- | --- | ---
Number of samples | 1056 | 3507

'Amp Peak 6(2p15) mutation analysis' versus 'AGE'

P value = 1.12e-06 (t-test), Q value = 0.0016

Table S39. Clustering Approach #6: 'Amp Peak 6(2p15) mutation analysis' versus Clinical Feature #2: 'AGE'

| nPatients | Mean (Std.Dev)
--- | --- | ---
ALL | 4507 | 61.9 (12.6)
AMP PEAK 6(2P15) MUTATED | 1038 | 63.4 (11.8)
AMP PEAK 6(2P15) WILD-TYPE | 3469 | 61.4 (12.9)

Figure S33. Get High-res Image Clustering Approach #6: 'Amp Peak 6(2p15) mutation analysis' versus Clinical Feature #2: 'AGE'

'Amp Peak 6(2p15) mutation analysis' versus 'PRIMARY.SITE.OF.DISEASE'

P value = 1.81e-77 (Chi-square test), Q value = 3.1e-74

Table S40. Clustering Approach #6: 'Amp Peak 6(2p15) mutation analysis' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'

nPatients | BLADDER | BRAIN | BREAST | COLON | ENDOMETRIAL | HEAD/NECK | KIDNEY | LUNG | OMENTUM | OVARY | PERITONEUM (OVARY) | RECTUM
--- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | ---
ALL | 125 | 544 | 846 | 412 | 447 | 319 | 493 | 662 | 2 | 548 | 2 | 159
AMP PEAK 6(2P15) MUTATED | 47 | 30 | 148 | 73 | 81 | 70 | 69 | 284 | 0 | 218 | 0 | 36
AMP PEAK 6(2P15) WILD-TYPE | 78 | 514 | 698 | 339 | 366 | 249 | 424 | 378 | 2 | 330 | 2 | 123

Figure S34. Get High-res Image Clustering Approach #6: 'Amp Peak 6(2p15) mutation analysis' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'

'Amp Peak 6(2p15) mutation analysis' versus 'KARNOFSKY.PERFORMANCE.SCORE'

P value = 0.000185 (t-test), Q value = 0.24

Table S41. Clustering Approach #6: 'Amp Peak 6(2p15) mutation analysis' versus Clinical Feature #5: 'KARNOFSKY.PERFORMANCE.SCORE'

| nPatients | Mean (Std.Dev)
--- | --- | ---
ALL | 640 | 73.6 (23.9)
AMP PEAK 6(2P15) MUTATED | 111 | 62.3 (36.0)
AMP PEAK 6(2P15) WILD-TYPE | 529 | 75.9 (19.8)

Figure S35. Get High-res Image Clustering Approach #6: 'Amp Peak 6(2p15) mutation analysis' versus Clinical Feature #5: 'KARNOFSKY.PERFORMANCE.SCORE'

'Amp Peak 6(2p15) mutation analysis' versus 'HISTOLOGICAL.TYPE'

P value = 1.27e-48 (Chi-square test), Q value = 2.1e-45

Table S42. Clustering Approach #6: 'Amp Peak 6(2p15) mutation analysis' versus Clinical Feature #6: 'HISTOLOGICAL.TYPE'

nPatients | COLON ADENOCARCINOMA | COLON MUCINOUS ADENOCARCINOMA | ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA | HEAD & NECK SQUAMOUS CELL CARCINOMA | KIDNEY CLEAR CELL RENAL CARCINOMA | LUNG ACINAR ADENOCARCINOMA | LUNG ADENOCARCINOMA MIXED SUBTYPE | LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS) | LUNG BASALOID SQUAMOUS CELL CARCINOMA | LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS | LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS | LUNG CLEAR CELL ADENOCARCINOMA | LUNG MICROPAPILLARY ADENOCARCINOMA | LUNG MUCINOUS ADENOCARCINOMA | LUNG PAPILLARY ADENOCARCINOMA | LUNG PAPILLARY SQUAMOUS CELL CARCINOMA | LUNG PAPILLARY SQUAMOUS CELL CARICNOMA | LUNG SMALL CELL SQUAMOUS CELL CARCINOMA | LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA | LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS) | MIXED SEROUS AND ENDOMETRIOID | MUCINOUS (COLLOID) ADENOCARCINOMA | RECTAL ADENOCARCINOMA | RECTAL MUCINOUS ADENOCARCINOMA | SEROUS CYSTADENOCARCINOMA | SEROUS ENDOMETRIAL ADENOCARCINOMA | TREATED PRIMARY GBM | UNTREATED PRIMARY (DE NOVO) GBM
--- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | ---
ALL | 356 | 54 | 350 | 319 | 493 | 10 | 75 | 205 | 7 | 3 | 15 | 2 | 3 | 2 | 13 | 1 | 1 | 1 | 2 | 315 | 18 | 7 | 143 | 13 | 552 | 79 | 1 | 20
AMP PEAK 6(2P15) MUTATED | 67 | 6 | 44 | 70 | 69 | 3 | 27 | 66 | 6 | 0 | 3 | 2 | 1 | 0 | 4 | 1 | 0 | 0 | 0 | 169 | 5 | 2 | 36 | 0 | 218 | 32 | 0 | 2
AMP PEAK 6(2P15) WILD-TYPE | 289 | 48 | 306 | 249 | 424 | 7 | 48 | 139 | 1 | 3 | 12 | 0 | 2 | 2 | 9 | 0 | 1 | 1 | 2 | 146 | 13 | 5 | 107 | 13 | 334 | 47 | 1 | 18

Figure S36. Get High-res Image Clustering Approach #6: 'Amp Peak 6(2p15) mutation analysis' versus Clinical Feature #6: 'HISTOLOGICAL.TYPE'

'Amp Peak 6(2p15) mutation analysis' versus 'TUMOR.STAGE'

P value = 2.63e-05 (Fisher's exact test), Q value = 0.036

Table S43. Clustering Approach #6: 'Amp Peak 6(2p15) mutation analysis' versus Clinical Feature #10: 'TUMOR.STAGE'

nPatients | I | II | III | IV
--- | --- | --- | --- | ---
ALL | 712 | 498 | 881 | 423
AMP PEAK 6(2P15) MUTATED | 178 | 142 | 307 | 104
AMP PEAK 6(2P15) WILD-TYPE | 534 | 356 | 574 | 319

Figure S37. Get High-res Image Clustering Approach #6: 'Amp Peak 6(2p15) mutation analysis' versus Clinical Feature #10: 'TUMOR.STAGE'

'Amp Peak 6(2p15) mutation analysis' versus 'RADIATIONS.RADIATION.REGIMENINDICATION'

P value = 2.25e-13 (Fisher's exact test), Q value = 3.5e-10

Table S44. Clustering Approach #6: 'Amp Peak 6(2p15) mutation analysis' versus Clinical Feature #11: 'RADIATIONS.RADIATION.REGIMENINDICATION'

nPatients | NO | YES
--- | --- | ---
ALL | 826 | 3737
AMP PEAK 6(2P15) MUTATED | 114 | 942
AMP PEAK 6(2P15) WILD-TYPE | 712 | 2795

Figure S38. Get High-res Image Clustering Approach #6: 'Amp Peak 6(2p15) mutation analysis' versus Clinical Feature #11: 'RADIATIONS.RADIATION.REGIMENINDICATION'

'Amp Peak 6(2p15) mutation analysis' versus 'NEOPLASM.DISEASESTAGE'

P value = 3.34e-05 (Chi-square test), Q value = 0.045

Table S45. Clustering Approach #6: 'Amp Peak 6(2p15) mutation analysis' versus Clinical Feature #21: 'NEOPLASM.DISEASESTAGE'

nPatients | STAGE I | STAGE IA | STAGE IB | STAGE II | STAGE IIA | STAGE IIB | STAGE III | STAGE IIIA | STAGE IIIB | STAGE IIIC | STAGE IV | STAGE TIS | STAGE X
--- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | ---
ALL | 72 | 62 | 7 | 43 | 287 | 186 | 42 | 124 | 25 | 41 | 59 | 1 | 16
AMP PEAK 6(2P15) MUTATED | 9 | 8 | 0 | 13 | 52 | 31 | 10 | 25 | 0 | 14 | 25 | 0 | 4
AMP PEAK 6(2P15) WILD-TYPE | 63 | 54 | 7 | 30 | 235 | 155 | 32 | 99 | 25 | 27 | 34 | 1 | 12

Figure S39. Get High-res Image Clustering Approach #6: 'Amp Peak 6(2p15) mutation analysis' versus Clinical Feature #21: 'NEOPLASM.DISEASESTAGE'

Clustering Approach #7: 'Amp Peak 7(2q31.2) mutation analysis'

Table S46. Description of clustering approach #7: 'Amp Peak 7(2q31.2) mutation analysis'

Cluster Labels | AMP PEAK 7(2Q31.2) MUTATED | AMP PEAK 7(2Q31.2) WILD-TYPE
--- | --- | ---
Number of samples | 907 | 3656

'Amp Peak 7(2q31.2) mutation analysis' versus 'AGE'

P value = 3.61e-06 (t-test), Q value = 0.0051

Table S47. Clustering Approach #7: 'Amp Peak 7(2q31.2) mutation analysis' versus Clinical Feature #2: 'AGE'

| nPatients | Mean (Std.Dev)
--- | --- | ---
ALL | 4507 | 61.9 (12.6)
AMP PEAK 7(2Q31.2) MUTATED | 891 | 63.5 (11.6)
AMP PEAK 7(2Q31.2) WILD-TYPE | 3616 | 61.4 (12.8)

Figure S40. Get High-res Image Clustering Approach #7: 'Amp Peak 7(2q31.2) mutation analysis' versus Clinical Feature #2: 'AGE'

'Amp Peak 7(2q31.2) mutation analysis' versus 'PRIMARY.SITE.OF.DISEASE'

P value = 5.69e-78 (Chi-square test), Q value = 9.7e-75

Table S48. Clustering Approach #7: 'Amp Peak 7(2q31.2) mutation analysis' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'

nPatients | BLADDER | BRAIN | BREAST | COLON | ENDOMETRIAL | HEAD/NECK | KIDNEY | LUNG | OMENTUM | OVARY | PERITONEUM (OVARY) | RECTUM
--- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | ---
ALL | 125 | 544 | 846 | 412 | 447 | 319 | 493 | 662 | 2 | 548 | 2 | 159
AMP PEAK 7(2Q31.2) MUTATED | 19 | 28 | 82 | 70 | 72 | 67 | 75 | 223 | 0 | 230 | 1 | 40
AMP PEAK 7(2Q31.2) WILD-TYPE | 106 | 516 | 764 | 342 | 375 | 252 | 418 | 439 | 2 | 318 | 1 | 119

Figure S41. Get High-res Image Clustering Approach #7: 'Amp Peak 7(2q31.2) mutation analysis' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'

'Amp Peak 7(2q31.2) mutation analysis' versus 'HISTOLOGICAL.TYPE'

P value = 4.22e-34 (Chi-square test), Q value = 6.9e-31

Table S49. Clustering Approach #7: 'Amp Peak 7(2q31.2) mutation analysis' versus Clinical Feature #6: 'HISTOLOGICAL.TYPE'

nPatients | COLON ADENOCARCINOMA | COLON MUCINOUS ADENOCARCINOMA | ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA | HEAD & NECK SQUAMOUS CELL CARCINOMA | KIDNEY CLEAR CELL RENAL CARCINOMA | LUNG ACINAR ADENOCARCINOMA | LUNG ADENOCARCINOMA MIXED SUBTYPE | LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS) | LUNG BASALOID SQUAMOUS CELL CARCINOMA | LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS | LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS | LUNG CLEAR CELL ADENOCARCINOMA | LUNG MICROPAPILLARY ADENOCARCINOMA | LUNG MUCINOUS ADENOCARCINOMA | LUNG PAPILLARY ADENOCARCINOMA | LUNG PAPILLARY SQUAMOUS CELL CARCINOMA | LUNG PAPILLARY SQUAMOUS CELL CARICNOMA | LUNG SMALL CELL SQUAMOUS CELL CARCINOMA | LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA | LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS) | MIXED SEROUS AND ENDOMETRIOID | MUCINOUS (COLLOID) ADENOCARCINOMA | RECTAL ADENOCARCINOMA | RECTAL MUCINOUS ADENOCARCINOMA | SEROUS CYSTADENOCARCINOMA | SEROUS ENDOMETRIAL ADENOCARCINOMA | TREATED PRIMARY GBM | UNTREATED PRIMARY (DE NOVO) GBM
--- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | ---
ALL | 356 | 54 | 350 | 319 | 493 | 10 | 75 | 205 | 7 | 3 | 15 | 2 | 3 | 2 | 13 | 1 | 1 | 1 | 2 | 315 | 18 | 7 | 143 | 13 | 552 | 79 | 1 | 20
AMP PEAK 7(2Q31.2) MUTATED | 64 | 6 | 36 | 67 | 75 | 3 | 32 | 64 | 4 | 0 | 3 | 0 | 1 | 0 | 5 | 1 | 0 | 1 | 1 | 106 | 3 | 2 | 40 | 0 | 231 | 33 | 0 | 1
AMP PEAK 7(2Q31.2) WILD-TYPE | 292 | 48 | 314 | 252 | 418 | 7 | 43 | 141 | 3 | 3 | 12 | 2 | 2 | 2 | 8 | 0 | 1 | 0 | 1 | 209 | 15 | 5 | 103 | 13 | 321 | 46 | 1 | 19

Figure S42. Get High-res Image Clustering Approach #7: 'Amp Peak 7(2q31.2) mutation analysis' versus Clinical Feature #6: 'HISTOLOGICAL.TYPE'

'Amp Peak 7(2q31.2) mutation analysis' versus 'TUMOR.STAGE'

P value = 1.98e-05 (Fisher's exact test), Q value = 0.027

Table S50. Clustering Approach #7: 'Amp Peak 7(2q31.2) mutation analysis' versus Clinical Feature #10: 'TUMOR.STAGE'

nPatients | I | II | III | IV
--- | --- | --- | --- | ---
ALL | 712 | 498 | 881 | 423
AMP PEAK 7(2Q31.2) MUTATED | 171 | 122 | 291 | 96
AMP PEAK 7(2Q31.2) WILD-TYPE | 541 | 376 | 590 | 327

Figure S43. Get High-res Image Clustering Approach #7: 'Amp Peak 7(2q31.2) mutation analysis' versus Clinical Feature #10: 'TUMOR.STAGE'

'Amp Peak 7(2q31.2) mutation analysis' versus 'RADIATIONS.RADIATION.REGIMENINDICATION'

P value = 7.11e-13 (Fisher's exact test), Q value = 1.1e-09

Table S51. Clustering Approach #7: 'Amp Peak 7(2q31.2) mutation analysis' versus Clinical Feature #11: 'RADIATIONS.RADIATION.REGIMENINDICATION'

nPatients | NO | YES
--- | --- | ---
ALL | 826 | 3737
AMP PEAK 7(2Q31.2) MUTATED | 93 | 814
AMP PEAK 7(2Q31.2) WILD-TYPE | 733 | 2923

Figure S44. Get High-res Image Clustering Approach #7: 'Amp Peak 7(2q31.2) mutation analysis' versus Clinical Feature #11: 'RADIATIONS.RADIATION.REGIMENINDICATION'

'Amp Peak 7(2q31.2) mutation analysis' versus 'TOBACCOSMOKINGHISTORYINDICATOR'

P value = 7.91e-06 (Chi-square test), Q value = 0.011

Table S52. Clustering Approach #7: 'Amp Peak 7(2q31.2) mutation analysis' versus Clinical Feature #14: 'TOBACCOSMOKINGHISTORYINDICATOR'

nPatients | 1 | 2 | 3 | 4 | 5 | CURRENT REFORMED SMOKER FOR < OR = 15 YEARS | CURRENT REFORMED SMOKER FOR > 15 YEARS | CURRENT SMOKER | LIFELONG NON-SMOKER
--- | --- | --- | --- | --- | --- | --- | --- | --- | ---
ALL | 28 | 23 | 37 | 29 | 2 | 355 | 217 | 250 | 128
AMP PEAK 7(2Q31.2) MUTATED | 2 | 4 | 4 | 8 | 0 | 113 | 71 | 85 | 16
AMP PEAK 7(2Q31.2) WILD-TYPE | 26 | 19 | 33 | 21 | 2 | 242 | 146 | 165 | 112

Figure S45. Get High-res Image Clustering Approach #7: 'Amp Peak 7(2q31.2) mutation analysis' versus Clinical Feature #14: 'TOBACCOSMOKINGHISTORYINDICATOR'

Clustering Approach #8: 'Amp Peak 8(3q26.2) mutation analysis'

Table S53. Description of clustering approach #8: 'Amp Peak 8(3q26.2) mutation analysis'

Cluster Labels | AMP PEAK 8(3Q26.2) MUTATED | AMP PEAK 8(3Q26.2) WILD-TYPE
--- | --- | ---
Number of samples | 1837 | 2726

'Amp Peak 8(3q26.2) mutation analysis' versus 'PRIMARY.SITE.OF.DISEASE'

P value = 4.38e-244 (Chi-square test), Q value = 7.9e-241

Table S54. Clustering Approach #8: 'Amp Peak 8(3q26.2) mutation analysis' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'

nPatients | BLADDER | BRAIN | BREAST | COLON | ENDOMETRIAL | HEAD/NECK | KIDNEY | LUNG | OMENTUM | OVARY | PERITONEUM (OVARY) | RECTUM
--- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | ---
ALL | 125 | 544 | 846 | 412 | 447 | 319 | 493 | 662 | 2 | 548 | 2 | 159
AMP PEAK 8(3Q26.2) MUTATED | 74 | 79 | 273 | 65 | 122 | 236 | 78 | 416 | 1 | 453 | 2 | 37
AMP PEAK 8(3Q26.2) WILD-TYPE | 51 | 465 | 573 | 347 | 325 | 83 | 415 | 246 | 1 | 95 | 0 | 122

Figure S46. Get High-res Image Clustering Approach #8: 'Amp Peak 8(3q26.2) mutation analysis' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'

'Amp Peak 8(3q26.2) mutation analysis' versus 'KARNOFSKY.PERFORMANCE.SCORE'

P value = 3.5e-05 (t-test), Q value = 0.047

Table S55. Clustering Approach #8: 'Amp Peak 8(3q26.2) mutation analysis' versus Clinical Feature #5: 'KARNOFSKY.PERFORMANCE.SCORE'

| nPatients | Mean (Std.Dev)
--- | --- | ---
ALL | 640 | 73.6 (23.9)
AMP PEAK 8(3Q26.2) MUTATED | 214 | 67.2 (30.4)
AMP PEAK 8(3Q26.2) WILD-TYPE | 426 | 76.8 (19.2)

Figure S47. Get High-res Image Clustering Approach #8: 'Amp Peak 8(3q26.2) mutation analysis' versus Clinical Feature #5: 'KARNOFSKY.PERFORMANCE.SCORE'

'Amp Peak 8(3q26.2) mutation analysis' versus 'HISTOLOGICAL.TYPE'

P value = 2.22e-239 (Chi-square test), Q value = 4e-236

Table S56. Clustering Approach #8: 'Amp Peak 8(3q26.2) mutation analysis' versus Clinical Feature #6: 'HISTOLOGICAL.TYPE'

nPatients | COLON ADENOCARCINOMA | COLON MUCINOUS ADENOCARCINOMA | ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA | HEAD & NECK SQUAMOUS CELL CARCINOMA | KIDNEY CLEAR CELL RENAL CARCINOMA | LUNG ACINAR ADENOCARCINOMA | LUNG ADENOCARCINOMA MIXED SUBTYPE | LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS) | LUNG BASALOID SQUAMOUS CELL CARCINOMA | LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS | LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS | LUNG CLEAR CELL ADENOCARCINOMA | LUNG MICROPAPILLARY ADENOCARCINOMA | LUNG MUCINOUS ADENOCARCINOMA | LUNG PAPILLARY ADENOCARCINOMA | LUNG PAPILLARY SQUAMOUS CELL CARCINOMA | LUNG PAPILLARY SQUAMOUS CELL CARICNOMA | LUNG SMALL CELL SQUAMOUS CELL CARCINOMA | LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA | LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS) | MIXED SEROUS AND ENDOMETRIOID | MUCINOUS (COLLOID) ADENOCARCINOMA | RECTAL ADENOCARCINOMA | RECTAL MUCINOUS ADENOCARCINOMA | SEROUS CYSTADENOCARCINOMA | SEROUS ENDOMETRIAL ADENOCARCINOMA | TREATED PRIMARY GBM | UNTREATED PRIMARY (DE NOVO) GBM
--- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | ---
ALL | 356 | 54 | 350 | 319 | 493 | 10 | 75 | 205 | 7 | 3 | 15 | 2 | 3 | 2 | 13 | 1 | 1 | 1 | 2 | 315 | 18 | 7 | 143 | 13 | 552 | 79 | 1 | 20
AMP PEAK 8(3Q26.2) MUTATED | 59 | 6 | 57 | 236 | 78 | 3 | 30 | 74 | 7 | 1 | 4 | 1 | 1 | 0 | 4 | 1 | 0 | 1 | 1 | 288 | 6 | 0 | 36 | 1 | 456 | 59 | 0 | 3
AMP PEAK 8(3Q26.2) WILD-TYPE | 297 | 48 | 293 | 83 | 415 | 7 | 45 | 131 | 0 | 2 | 11 | 1 | 2 | 2 | 9 | 0 | 1 | 0 | 1 | 27 | 12 | 7 | 107 | 12 | 96 | 20 | 1 | 17

Figure S48. Get High-res Image Clustering Approach #8: 'Amp Peak 8(3q26.2) mutation analysis' versus Clinical Feature #6: 'HISTOLOGICAL.TYPE'

'Amp Peak 8(3q26.2) mutation analysis' versus 'PATHOLOGY.T'

P value = 2.27e-21 (Fisher's exact test), Q value = 3.6e-18

Table S57. Clustering Approach #8: 'Amp Peak 8(3q26.2) mutation analysis' versus Clinical Feature #7: 'PATHOLOGY.T'

nPatients | T0+T1 | T2 | T3 | T4
--- | --- | --- | --- | ---
ALL | 466 | 632 | 694 | 209
AMP PEAK 8(3Q26.2) MUTATED | 154 | 325 | 202 | 116
AMP PEAK 8(3Q26.2) WILD-TYPE | 312 | 307 | 492 | 93

Figure S49. Get High-res Image Clustering Approach #8: 'Amp Peak 8(3q26.2) mutation analysis' versus Clinical Feature #7: 'PATHOLOGY.T'

'Amp Peak 8(3q26.2) mutation analysis' versus 'PATHOLOGY.N'

P value = 2.73e-10 (Fisher's exact test), Q value = 4.1e-07

Table S58. Clustering Approach #8: 'Amp Peak 8(3q26.2) mutation analysis' versus Clinical Feature #8: 'PATHOLOGY.N'

nPatients | N0 | N1 | N2 | N3
--- | --- | --- | --- | ---
ALL | 1067 | 353 | 282 | 11
AMP PEAK 8(3Q26.2) MUTATED | 406 | 183 | 146 | 11
AMP PEAK 8(3Q26.2) WILD-TYPE | 661 | 170 | 136 | 0

Figure S50. Get High-res Image Clustering Approach #8: 'Amp Peak 8(3q26.2) mutation analysis' versus Clinical Feature #8: 'PATHOLOGY.N'

'Amp Peak 8(3q26.2) mutation analysis' versus 'TUMOR.STAGE'

P value = 1.25e-24 (Fisher's exact test), Q value = 2e-21

Table S59. Clustering Approach #8: 'Amp Peak 8(3q26.2) mutation analysis' versus Clinical Feature #10: 'TUMOR.STAGE'

nPatients | I | II | III | IV
--- | --- | --- | --- | ---
ALL | 712 | 498 | 881 | 423
AMP PEAK 8(3Q26.2) MUTATED | 265 | 197 | 528 | 246
AMP PEAK 8(3Q26.2) WILD-TYPE | 447 | 301 | 353 | 177

Figure S51. Get High-res Image Clustering Approach #8: 'Amp Peak 8(3q26.2) mutation analysis' versus Clinical Feature #10: 'TUMOR.STAGE'

'Amp Peak 8(3q26.2) mutation analysis' versus 'RADIATIONS.RADIATION.REGIMENINDICATION'

P value = 1.04e-13 (Fisher's exact test), Q value = 1.6e-10

Table S60. Clustering Approach #8: 'Amp Peak 8(3q26.2) mutation analysis' versus Clinical Feature #11: 'RADIATIONS.RADIATION.REGIMENINDICATION'

nPatients | NO | YES
--- | --- | ---
ALL | 826 | 3737
AMP PEAK 8(3Q26.2) MUTATED | 239 | 1598
AMP PEAK 8(3Q26.2) WILD-TYPE | 587 | 2139

Figure S52. Get High-res Image Clustering Approach #8: 'Amp Peak 8(3q26.2) mutation analysis' versus Clinical Feature #11: 'RADIATIONS.RADIATION.REGIMENINDICATION'

'Amp Peak 8(3q26.2) mutation analysis' versus 'NUMBERPACKYEARSSMOKED'

P value = 4.66e-06 (t-test), Q value = 0.0065

Table S61. Clustering Approach #8: 'Amp Peak 8(3q26.2) mutation analysis' versus Clinical Feature #12: 'NUMBERPACKYEARSSMOKED'

| nPatients | Mean (Std.Dev)
--- | --- | ---
ALL | 758 | 46.7 (33.0)
AMP PEAK 8(3Q26.2) MUTATED | 509 | 50.1 (35.1)
AMP PEAK 8(3Q26.2) WILD-TYPE | 249 | 39.5 (26.8)

Figure S53. Get High-res Image Clustering Approach #8: 'Amp Peak 8(3q26.2) mutation analysis' versus Clinical Feature #12: 'NUMBERPACKYEARSSMOKED'

Clustering Approach #9: 'Amp Peak 9(4p16.3) mutation analysis'

Table S62. Description of clustering approach #9: 'Amp Peak 9(4p16.3) mutation analysis'

Cluster Labels | AMP PEAK 9(4P16.3) MUTATED | AMP PEAK 9(4P16.3) WILD-TYPE
--- | --- | ---
Number of samples | 521 | 4042

'Amp Peak 9(4p16.3) mutation analysis' versus 'PRIMARY.SITE.OF.DISEASE'

P value = 2.11e-44 (Chi-square test), Q value = 3.5e-41

Table S63. Clustering Approach #9: 'Amp Peak 9(4p16.3) mutation analysis' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'

nPatients | BLADDER | BRAIN | BREAST | COLON | ENDOMETRIAL | HEAD/NECK | KIDNEY | LUNG | OMENTUM | OVARY | PERITONEUM (OVARY) | RECTUM
--- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | ---
ALL | 125 | 544 | 846 | 412 | 447 | 319 | 493 | 662 | 2 | 548 | 2 | 159
AMP PEAK 9(4P16.3) MUTATED | 26 | 45 | 93 | 12 | 40 | 37 | 13 | 94 | 0 | 150 | 1 | 10
AMP PEAK 9(4P16.3) WILD-TYPE | 99 | 499 | 753 | 400 | 407 | 282 | 480 | 568 | 2 | 398 | 1 | 149

Figure S54. Get High-res Image Clustering Approach #9: 'Amp Peak 9(4p16.3) mutation analysis' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'

'Amp Peak 9(4p16.3) mutation analysis' versus 'GENDER'

P value = 2.63e-05 (Fisher's exact test), Q value = 0.036

Table S64. Clustering Approach #9: 'Amp Peak 9(4p16.3) mutation analysis' versus Clinical Feature #4: 'GENDER'

nPatients | FEMALE | MALE
--- | --- | ---
ALL | 2881 | 1682
AMP PEAK 9(4P16.3) MUTATED | 372 | 149
AMP PEAK 9(4P16.3) WILD-TYPE | 2509 | 1533

Figure S55. Get High-res Image Clustering Approach #9: 'Amp Peak 9(4p16.3) mutation analysis' versus Clinical Feature #4: 'GENDER'

'Amp Peak 9(4p16.3) mutation analysis' versus 'HISTOLOGICAL.TYPE'

P value = 2.26e-47 (Chi-square test), Q value = 3.8e-44

Table S65. Clustering Approach #9: 'Amp Peak 9(4p16.3) mutation analysis' versus Clinical Feature #6: 'HISTOLOGICAL.TYPE'

nPatients | COLON ADENOCARCINOMA | COLON MUCINOUS ADENOCARCINOMA | ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA | HEAD & NECK SQUAMOUS CELL CARCINOMA | KIDNEY CLEAR CELL RENAL CARCINOMA | LUNG ACINAR ADENOCARCINOMA | LUNG ADENOCARCINOMA MIXED SUBTYPE | LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS) | LUNG BASALOID SQUAMOUS CELL CARCINOMA | LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS | LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS | LUNG CLEAR CELL ADENOCARCINOMA | LUNG MICROPAPILLARY ADENOCARCINOMA | LUNG MUCINOUS ADENOCARCINOMA | LUNG PAPILLARY ADENOCARCINOMA | LUNG PAPILLARY SQUAMOUS CELL CARCINOMA | LUNG PAPILLARY SQUAMOUS CELL CARICNOMA | LUNG SMALL CELL SQUAMOUS CELL CARCINOMA | LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA | LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS) | MIXED SEROUS AND ENDOMETRIOID | MUCINOUS (COLLOID) ADENOCARCINOMA | RECTAL ADENOCARCINOMA | RECTAL MUCINOUS ADENOCARCINOMA | SEROUS CYSTADENOCARCINOMA | SEROUS ENDOMETRIAL ADENOCARCINOMA | TREATED PRIMARY GBM | UNTREATED PRIMARY (DE NOVO) GBM
--- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | ---
ALL | 356 | 54 | 350 | 319 | 493 | 10 | 75 | 205 | 7 | 3 | 15 | 2 | 3 | 2 | 13 | 1 | 1 | 1 | 2 | 315 | 18 | 7 | 143 | 13 | 552 | 79 | 1 | 20
AMP PEAK 9(4P16.3) MUTATED | 12 | 0 | 12 | 37 | 13 | 2 | 10 | 43 | 3 | 0 | 3 | 0 | 1 | 0 | 1 | 0 | 0 | 0 | 0 | 30 | 1 | 1 | 10 | 0 | 151 | 27 | 0 | 3
AMP PEAK 9(4P16.3) WILD-TYPE | 344 | 54 | 338 | 282 | 480 | 8 | 65 | 162 | 4 | 3 | 12 | 2 | 2 | 2 | 12 | 1 | 1 | 1 | 2 | 285 | 17 | 6 | 133 | 13 | 401 | 52 | 1 | 17

Figure S56. Get High-res Image Clustering Approach #9: 'Amp Peak 9(4p16.3) mutation analysis' versus Clinical Feature #6: 'HISTOLOGICAL.TYPE'

'Amp Peak 9(4p16.3) mutation analysis' versus 'PATHOLOGY.T'

P value = 1.15e-06 (Fisher's exact test), Q value = 0.0016

Table S66. Clustering Approach #9: 'Amp Peak 9(4p16.3) mutation analysis' versus Clinical Feature #7: 'PATHOLOGY.T'

nPatients | T0+T1 | T2 | T3 | T4
--- | --- | --- | --- | ---
ALL | 466 | 632 | 694 | 209
AMP PEAK 9(4P16.3) MUTATED | 22 | 77 | 36 | 21
AMP PEAK 9(4P16.3) WILD-TYPE | 444 | 555 | 658 | 188

Figure S57. Get High-res Image Clustering Approach #9: 'Amp Peak 9(4p16.3) mutation analysis' versus Clinical Feature #7: 'PATHOLOGY.T'

'Amp Peak 9(4p16.3) mutation analysis' versus 'TUMOR.STAGE'

P value = 4.15e-08 (Fisher's exact test), Q value = 6.1e-05

Table S67. Clustering Approach #9: 'Amp Peak 9(4p16.3) mutation analysis' versus Clinical Feature #10: 'TUMOR.STAGE'

nPatients | I | II | III | IV
--- | --- | --- | --- | ---
ALL | 712 | 498 | 881 | 423
AMP PEAK 9(4P16.3) MUTATED | 60 | 41 | 152 | 51
AMP PEAK 9(4P16.3) WILD-TYPE | 652 | 457 | 729 | 372

Figure S58. Get High-res Image Clustering Approach #9: 'Amp Peak 9(4p16.3) mutation analysis' versus Clinical Feature #10: 'TUMOR.STAGE'

Clustering Approach #10: 'Amp Peak 10(4q12) mutation analysis'

Table S68. Description of clustering approach #10: 'Amp Peak 10(4q12) mutation analysis'

Cluster Labels | AMP PEAK 10(4Q12) MUTATED | AMP PEAK 10(4Q12) WILD-TYPE
--- | --- | ---
Number of samples | 594 | 3969

'Amp Peak 10(4q12) mutation analysis' versus 'Time to Death'

P value = 0.000118 (logrank test), Q value = 0.16

Table S69. Clustering Approach #10: 'Amp Peak 10(4q12) mutation analysis' versus Clinical Feature #1: 'Time to Death'

| nPatients | nDeath | Duration Range (Median), Month
--- | --- | --- | ---
ALL | 4296 | 1401 | 0.0 - 224.0 (14.9)
AMP PEAK 10(4Q12) MUTATED | 567 | 219 | 0.1 - 224.0 (13.1)
AMP PEAK 10(4Q12) WILD-TYPE | 3729 | 1182 | 0.0 - 223.4 (15.0)

Figure S59. Get High-res Image Clustering Approach #10: 'Amp Peak 10(4q12) mutation analysis' versus Clinical Feature #1: 'Time to Death'

'Amp Peak 10(4q12) mutation analysis' versus 'PRIMARY.SITE.OF.DISEASE'

P value = 7.25e-36 (Chi-square test), Q value = 1.2e-32

Table S70. Clustering Approach #10: 'Amp Peak 10(4q12) mutation analysis' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'

nPatients | BLADDER | BRAIN | BREAST | COLON | ENDOMETRIAL | HEAD/NECK | KIDNEY | LUNG | OMENTUM | OVARY | PERITONEUM (OVARY) | RECTUM
--- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | ---
ALL | 125 | 544 | 846 | 412 | 447 | 319 | 493 | 662 | 2 | 548 | 2 | 159
AMP PEAK 10(4Q12) MUTATED | 14 | 101 | 117 | 18 | 19 | 52 | 12 | 140 | 1 | 108 | 1 | 11
AMP PEAK 10(4Q12) WILD-TYPE | 111 | 443 | 729 | 394 | 428 | 267 | 481 | 522 | 1 | 440 | 1 | 148

Figure S60. Get High-res Image Clustering Approach #10: 'Amp Peak 10(4q12) mutation analysis' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'

'Amp Peak 10(4q12) mutation analysis' versus 'HISTOLOGICAL.TYPE'

P value = 1.99e-35 (Chi-square test), Q value = 3.3e-32

Table S71. Clustering Approach #10: 'Amp Peak 10(4q12) mutation analysis' versus Clinical Feature #6: 'HISTOLOGICAL.TYPE'

nPatients | COLON ADENOCARCINOMA | COLON MUCINOUS ADENOCARCINOMA | ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA | HEAD & NECK SQUAMOUS CELL CARCINOMA | KIDNEY CLEAR CELL RENAL CARCINOMA | LUNG ACINAR ADENOCARCINOMA | LUNG ADENOCARCINOMA MIXED SUBTYPE | LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS) | LUNG BASALOID SQUAMOUS CELL CARCINOMA | LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS | LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS | LUNG CLEAR CELL ADENOCARCINOMA | LUNG MICROPAPILLARY ADENOCARCINOMA | LUNG MUCINOUS ADENOCARCINOMA | LUNG PAPILLARY ADENOCARCINOMA | LUNG PAPILLARY SQUAMOUS CELL CARCINOMA | LUNG PAPILLARY SQUAMOUS CELL CARICNOMA | LUNG SMALL CELL SQUAMOUS CELL CARCINOMA | LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA | LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS) | MIXED SEROUS AND ENDOMETRIOID | MUCINOUS (COLLOID) ADENOCARCINOMA | RECTAL ADENOCARCINOMA | RECTAL MUCINOUS ADENOCARCINOMA | SEROUS CYSTADENOCARCINOMA | SEROUS ENDOMETRIAL ADENOCARCINOMA | TREATED PRIMARY GBM | UNTREATED PRIMARY (DE NOVO) GBM
--- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | ---
ALL | 356 | 54 | 350 | 319 | 493 | 10 | 75 | 205 | 7 | 3 | 15 | 2 | 3 | 2 | 13 | 1 | 1 | 1 | 2 | 315 | 18 | 7 | 143 | 13 | 552 | 79 | 1 | 20
AMP PEAK 10(4Q12) MUTATED | 17 | 1 | 6 | 52 | 12 | 4 | 11 | 43 | 3 | 0 | 3 | 1 | 1 | 0 | 0 | 0 | 0 | 0 | 1 | 73 | 1 | 0 | 11 | 0 | 110 | 12 | 0 | 8
AMP PEAK 10(4Q12) WILD-TYPE | 339 | 53 | 344 | 267 | 481 | 6 | 64 | 162 | 4 | 3 | 12 | 1 | 2 | 2 | 13 | 1 | 1 | 1 | 1 | 242 | 17 | 7 | 132 | 13 | 442 | 67 | 1 | 12

Figure S61. Get High-res Image Clustering Approach #10: 'Amp Peak 10(4q12) mutation analysis' versus Clinical Feature #6: 'HISTOLOGICAL.TYPE'

'Amp Peak 10(4q12) mutation analysis' versus 'PATHOLOGY.T'

P value = 1e-09 (Fisher's exact test), Q value = 1.5e-06

Table S72. Clustering Approach #10: 'Amp Peak 10(4q12) mutation analysis' versus Clinical Feature #7: 'PATHOLOGY.T'

nPatients | T0+T1 | T2 | T3 | T4
--- | --- | --- | --- | ---
ALL | 466 | 632 | 694 | 209
AMP PEAK 10(4Q12) MUTATED | 35 | 108 | 49 | 34
AMP PEAK 10(4Q12) WILD-TYPE | 431 | 524 | 645 | 175

Figure S62. Get High-res Image Clustering Approach #10: 'Amp Peak 10(4q12) mutation analysis' versus Clinical Feature #7: 'PATHOLOGY.T'

Clustering Approach #11: 'Amp Peak 11(5p15.33) mutation analysis'

Table S73. Description of clustering approach #11: 'Amp Peak 11(5p15.33) mutation analysis'

Cluster Labels | AMP PEAK 11(5P15.33) MUTATED | AMP PEAK 11(5P15.33) WILD-TYPE
--- | --- | ---
Number of samples | 1663 | 2900

'Amp Peak 11(5p15.33) mutation analysis' versus 'AGE'

P value = 1.15e-05 (t-test), Q value = 0.016

Table S74. Clustering Approach #11: 'Amp Peak 11(5p15.33) mutation analysis' versus Clinical Feature #2: 'AGE'

| nPatients | Mean (Std.Dev)
--- | --- | ---
ALL | 4507 | 61.9 (12.6)
AMP PEAK 11(5P15.33) MUTATED | 1630 | 62.9 (11.8)
AMP PEAK 11(5P15.33) WILD-TYPE | 2877 | 61.2 (13.1)

Figure S63. Get High-res Image Clustering Approach #11: 'Amp Peak 11(5p15.33) mutation analysis' versus Clinical Feature #2: 'AGE'

'Amp Peak 11(5p15.33) mutation analysis' versus 'PRIMARY.SITE.OF.DISEASE'

P value = 1.11e-158 (Chi-square test), Q value = 2e-155

Table S75. Clustering Approach #11: 'Amp Peak 11(5p15.33) mutation analysis' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'

nPatients | BLADDER | BRAIN | BREAST | COLON | ENDOMETRIAL | HEAD/NECK | KIDNEY | LUNG | OMENTUM | OVARY | PERITONEUM (OVARY) | RECTUM
--- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | ---
ALL | 125 | 544 | 846 | 412 | 447 | 319 | 493 | 662 | 2 | 548 | 2 | 159
AMP PEAK 11(5P15.33) MUTATED | 57 | 54 | 303 | 78 | 64 | 143 | 158 | 477 | 1 | 289 | 2 | 37
AMP PEAK 11(5P15.33) WILD-TYPE | 68 | 490 | 543 | 334 | 383 | 176 | 335 | 185 | 1 | 259 | 0 | 122

Figure S64. Get High-res Image Clustering Approach #11: 'Amp Peak 11(5p15.33) mutation analysis' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'

'Amp Peak 11(5p15.33) mutation analysis' versus 'KARNOFSKY.PERFORMANCE.SCORE'

P value = 0.000167 (t-test), Q value = 0.22

Table S76. Clustering Approach #11: 'Amp Peak 11(5p15.33) mutation analysis' versus Clinical Feature #5: 'KARNOFSKY.PERFORMANCE.SCORE'

| nPatients | Mean (Std.Dev)
--- | --- | ---
ALL | 640 | 73.6 (23.9)
AMP PEAK 11(5P15.33) MUTATED | 172 | 66.0 (33.6)
AMP PEAK 11(5P15.33) WILD-TYPE | 468 | 76.3 (18.5)

Figure S65. Get High-res Image Clustering Approach #11: 'Amp Peak 11(5p15.33) mutation analysis' versus Clinical Feature #5: 'KARNOFSKY.PERFORMANCE.SCORE'

'Amp Peak 11(5p15.33) mutation analysis' versus 'HISTOLOGICAL.TYPE'

P value = 3.86e-116 (Chi-square test), Q value = 6.8e-113

Table S77. Clustering Approach #11: 'Amp Peak 11(5p15.33) mutation analysis' versus Clinical Feature #6: 'HISTOLOGICAL.TYPE'

nPatients | COLON ADENOCARCINOMA | COLON MUCINOUS ADENOCARCINOMA | ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA | HEAD & NECK SQUAMOUS CELL CARCINOMA | KIDNEY CLEAR CELL RENAL CARCINOMA | LUNG ACINAR ADENOCARCINOMA | LUNG ADENOCARCINOMA MIXED SUBTYPE | LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS) | LUNG BASALOID SQUAMOUS CELL CARCINOMA | LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS | LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS | LUNG CLEAR CELL ADENOCARCINOMA | LUNG MICROPAPILLARY ADENOCARCINOMA | LUNG MUCINOUS ADENOCARCINOMA | LUNG PAPILLARY ADENOCARCINOMA | LUNG PAPILLARY SQUAMOUS CELL CARCINOMA | LUNG PAPILLARY SQUAMOUS CELL CARICNOMA | LUNG SMALL CELL SQUAMOUS CELL CARCINOMA | LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA | LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS) | MIXED SEROUS AND ENDOMETRIOID | MUCINOUS (COLLOID) ADENOCARCINOMA | RECTAL ADENOCARCINOMA | RECTAL MUCINOUS ADENOCARCINOMA | SEROUS CYSTADENOCARCINOMA | SEROUS ENDOMETRIAL ADENOCARCINOMA | TREATED PRIMARY GBM | UNTREATED PRIMARY (DE NOVO) GBM
--- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | ---
ALL | 356 | 54 | 350 | 319 | 493 | 10 | 75 | 205 | 7 | 3 | 15 | 2 | 3 | 2 | 13 | 1 | 1 | 1 | 2 | 315 | 18 | 7 | 143 | 13 | 552 | 79 | 1 | 20
AMP PEAK 11(5P15.33) MUTATED | 69 | 9 | 24 | 143 | 158 | 7 | 45 | 141 | 5 | 1 | 11 | 2 | 2 | 0 | 9 | 1 | 0 | 1 | 2 | 249 | 3 | 1 | 36 | 1 | 292 | 37 | 1 | 2
AMP PEAK 11(5P15.33) WILD-TYPE | 287 | 45 | 326 | 176 | 335 | 3 | 30 | 64 | 2 | 2 | 4 | 0 | 1 | 2 | 4 | 0 | 1 | 0 | 0 | 66 | 15 | 6 | 107 | 12 | 260 | 42 | 0 | 18

Figure S66. Get High-res Image Clustering Approach #11: 'Amp Peak 11(5p15.33) mutation analysis' versus Clinical Feature #6: 'HISTOLOGICAL.TYPE'

'Amp Peak 11(5p15.33) mutation analysis' versus 'PATHOLOGY.T'

P value = 5.27e-21 (Fisher's exact test), Q value = 8.4e-18

Table S78. Clustering Approach #11: 'Amp Peak 11(5p15.33) mutation analysis' versus Clinical Feature #7: 'PATHOLOGY.T'

nPatients | T0+T1 | T2 | T3 | T4
--- | --- | --- | --- | ---
ALL | 466 | 632 | 694 | 209
AMP PEAK 11(5P15.33) MUTATED | 206 | 361 | 211 | 88
AMP PEAK 11(5P15.33) WILD-TYPE | 260 | 271 | 483 | 121

Figure S67. Get High-res Image Clustering Approach #11: 'Amp Peak 11(5p15.33) mutation analysis' versus Clinical Feature #7: 'PATHOLOGY.T'

'Amp Peak 11(5p15.33) mutation analysis' versus 'TUMOR.STAGE'

P value = 1.98e-05 (Fisher's exact test), Q value = 0.027

Table S79. Clustering Approach #11: 'Amp Peak 11(5p15.33) mutation analysis' versus Clinical Feature #10: 'TUMOR.STAGE'

nPatients | I | II | III | IV
--- | --- | --- | --- | ---
ALL | 712 | 498 | 881 | 423
AMP PEAK 11(5P15.33) MUTATED | 348 | 190 | 434 | 169
AMP PEAK 11(5P15.33) WILD-TYPE | 364 | 308 | 447 | 254

Figure S68. Get High-res Image Clustering Approach #11: 'Amp Peak 11(5p15.33) mutation analysis' versus Clinical Feature #10: 'TUMOR.STAGE'

'Amp Peak 11(5p15.33) mutation analysis' versus 'RADIATIONS.RADIATION.REGIMENINDICATION'

P value = 9.74e-15 (Fisher's exact test), Q value = 1.5e-11

Table S80. Clustering Approach #11: 'Amp Peak 11(5p15.33) mutation analysis' versus Clinical Feature #11: 'RADIATIONS.RADIATION.REGIMENINDICATION'

nPatients | NO | YES
--- | --- | ---
ALL | 826 | 3737
AMP PEAK 11(5P15.33) MUTATED | 206 | 1457
AMP PEAK 11(5P15.33) WILD-TYPE | 620 | 2280

Figure S69. Get High-res Image Clustering Approach #11: 'Amp Peak 11(5p15.33) mutation analysis' versus Clinical Feature #11: 'RADIATIONS.RADIATION.REGIMENINDICATION'

'Amp Peak 11(5p15.33) mutation analysis' versus 'TOBACCOSMOKINGHISTORYINDICATOR'

P value = 1.16e-06 (Chi-square test), Q value = 0.0017

Table S81. Clustering Approach #11: 'Amp Peak 11(5p15.33) mutation analysis' versus Clinical Feature #14: 'TOBACCOSMOKINGHISTORYINDICATOR'

nPatients | 1 | 2 | 3 | 4 | 5 | CURRENT REFORMED SMOKER FOR < OR = 15 YEARS | CURRENT REFORMED SMOKER FOR > 15 YEARS | CURRENT SMOKER | LIFELONG NON-SMOKER
--- | --- | --- | --- | --- | --- | --- | --- | --- | ---
ALL | 28 | 23 | 37 | 29 | 2 | 355 | 217 | 250 | 128
AMP PEAK 11(5P15.33) MUTATED | 9 | 11 | 18 | 14 | 1 | 254 | 134 | 155 | 61
AMP PEAK 11(5P15.33) WILD-TYPE | 19 | 12 | 19 | 15 | 1 | 101 | 83 | 95 | 67

Figure S70. Get High-res Image Clustering Approach #11: 'Amp Peak 11(5p15.33) mutation analysis' versus Clinical Feature #14: 'TOBACCOSMOKINGHISTORYINDICATOR'

Clustering Approach #12: 'Amp Peak 12(5q35.3) mutation analysis'

Table S82. Description of clustering approach #12: 'Amp Peak 12(5q35.3) mutation analysis'

Cluster Labels | AMP PEAK 12(5Q35.3) MUTATED | AMP PEAK 12(5Q35.3) WILD-TYPE
--- | --- | ---
Number of samples | 934 | 3629

'Amp Peak 12(5q35.3) mutation analysis' versus 'Time to Death'

P value = 1.54e-05 (logrank test), Q value = 0.021

Table S83. Clustering Approach #12: 'Amp Peak 12(5q35.3) mutation analysis' versus Clinical Feature #1: 'Time to Death'

| nPatients | nDeath | Duration Range (Median), Month
--- | --- | --- | ---
ALL | 4296 | 1401 | 0.0 - 224.0 (14.9)
AMP PEAK 12(5Q35.3) MUTATED | 893 | 269 | 0.0 - 224.0 (20.0)
AMP PEAK 12(5Q35.3) WILD-TYPE | 3403 | 1132 | 0.0 - 223.4 (13.8)

Figure S71. Get High-res Image Clustering Approach #12: 'Amp Peak 12(5q35.3) mutation analysis' versus Clinical Feature #1: 'Time to Death'

'Amp Peak 12(5q35.3) mutation analysis' versus 'PRIMARY.SITE.OF.DISEASE'

P value = 3.27e-156 (Chi-square test), Q value = 5.8e-153

Table S84. Clustering Approach #12: 'Amp Peak 12(5q35.3) mutation analysis' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'

nPatients | BLADDER | BRAIN | BREAST | COLON | ENDOMETRIAL | HEAD/NECK | KIDNEY | LUNG | OMENTUM | OVARY | PERITONEUM (OVARY) | RECTUM
--- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | ---
ALL | 125 | 544 | 846 | 412 | 447 | 319 | 493 | 662 | 2 | 548 | 2 | 159
AMP PEAK 12(5Q35.3) MUTATED | 11 | 48 | 217 | 37 | 36 | 19 | 311 | 97 | 0 | 136 | 0 | 22
AMP PEAK 12(5Q35.3) WILD-TYPE | 114 | 496 | 629 | 375 | 411 | 300 | 182 | 565 | 2 | 412 | 2 | 137

Figure S72. Get High-res Image Clustering Approach #12: 'Amp Peak 12(5q35.3) mutation analysis' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'

'Amp Peak 12(5q35.3) mutation analysis' versus 'HISTOLOGICAL.TYPE'

P value = 1.55e-132 (Chi-square test), Q value = 2.7e-129

Table S85. Clustering Approach #12: 'Amp Peak 12(5q35.3) mutation analysis' versus Clinical Feature #6: 'HISTOLOGICAL.TYPE'

nPatients | COLON ADENOCARCINOMA | COLON MUCINOUS ADENOCARCINOMA | ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA | HEAD & NECK SQUAMOUS CELL CARCINOMA | KIDNEY CLEAR CELL RENAL CARCINOMA | LUNG ACINAR ADENOCARCINOMA | LUNG ADENOCARCINOMA MIXED SUBTYPE | LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS) | LUNG BASALOID SQUAMOUS CELL CARCINOMA | LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS | LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS | LUNG CLEAR CELL ADENOCARCINOMA | LUNG MICROPAPILLARY ADENOCARCINOMA | LUNG MUCINOUS ADENOCARCINOMA | LUNG PAPILLARY ADENOCARCINOMA | LUNG PAPILLARY SQUAMOUS CELL CARCINOMA | LUNG PAPILLARY SQUAMOUS CELL CARICNOMA | LUNG SMALL CELL SQUAMOUS CELL CARCINOMA | LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA | LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS) | MIXED SEROUS AND ENDOMETRIOID | MUCINOUS (COLLOID) ADENOCARCINOMA | RECTAL ADENOCARCINOMA | RECTAL MUCINOUS ADENOCARCINOMA | SEROUS CYSTADENOCARCINOMA | SEROUS ENDOMETRIAL ADENOCARCINOMA | TREATED PRIMARY GBM | UNTREATED PRIMARY (DE NOVO) GBM
--- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | ---
ALL | 356 | 54 | 350 | 319 | 493 | 10 | 75 | 205 | 7 | 3 | 15 | 2 | 3 | 2 | 13 | 1 | 1 | 1 | 2 | 315 | 18 | 7 | 143 | 13 | 552 | 79 | 1 | 20
AMP PEAK 12(5Q35.3) MUTATED | 33 | 4 | 15 | 19 | 311 | 4 | 13 | 45 | 1 | 1 | 5 | 1 | 0 | 0 | 4 | 0 | 0 | 0 | 0 | 22 | 2 | 1 | 21 | 1 | 136 | 19 | 1 | 2
AMP PEAK 12(5Q35.3) WILD-TYPE | 323 | 50 | 335 | 300 | 182 | 6 | 62 | 160 | 6 | 2 | 10 | 1 | 3 | 2 | 9 | 1 | 1 | 1 | 2 | 293 | 16 | 6 | 122 | 12 | 416 | 60 | 0 | 18

Figure S73. Get High-res Image Clustering Approach #12: 'Amp Peak 12(5q35.3) mutation analysis' versus Clinical Feature #6: 'HISTOLOGICAL.TYPE'

'Amp Peak 12(5q35.3) mutation analysis' versus 'PATHOLOGY.T'

P value = 3.57e-17 (Fisher's exact test), Q value = 5.6e-14

Table S86. Clustering Approach #12: 'Amp Peak 12(5q35.3) mutation analysis' versus Clinical Feature #7: 'PATHOLOGY.T'

nPatients | T0+T1 | T2 | T3 | T4
--- | --- | --- | --- | ---
ALL | 466 | 632 | 694 | 209
AMP PEAK 12(5Q35.3) MUTATED | 176 | 116 | 168 | 22
AMP PEAK 12(5Q35.3) WILD-TYPE | 290 | 516 | 526 | 187

Figure S74. Get High-res Image Clustering Approach #12: 'Amp Peak 12(5q35.3) mutation analysis' versus Clinical Feature #7: 'PATHOLOGY.T'

'Amp Peak 12(5q35.3) mutation analysis' versus 'PATHOLOGY.N'

P value = 3.43e-05 (Fisher's exact test), Q value = 0.046

Table S87. Clustering Approach #12: 'Amp Peak 12(5q35.3) mutation analysis' versus Clinical Feature #8: 'PATHOLOGY.N'

nPatients | N0 | N1 | N2 | N3
--- | --- | --- | --- | ---
ALL | 1067 | 353 | 282 | 11
AMP PEAK 12(5Q35.3) MUTATED | 234 | 49 | 35 | 4
AMP PEAK 12(5Q35.3) WILD-TYPE | 833 | 304 | 247 | 7

Figure S75. Get High-res Image Clustering Approach #12: 'Amp Peak 12(5q35.3) mutation analysis' versus Clinical Feature #8: 'PATHOLOGY.N'

'Amp Peak 12(5q35.3) mutation analysis' versus 'TUMOR.STAGE'

P value = 1.13e-06 (Fisher's exact test), Q value = 0.0016

Table S88. Clustering Approach #12: 'Amp Peak 12(5q35.3) mutation analysis' versus Clinical Feature #10: 'TUMOR.STAGE'

nPatients | I | II | III | IV
--- | --- | --- | --- | ---
ALL | 712 | 498 | 881 | 423
AMP PEAK 12(5Q35.3) MUTATED | 202 | 79 | 235 | 96
AMP PEAK 12(5Q35.3) WILD-TYPE | 510 | 419 | 646 | 327

Figure S76. Get High-res Image Clustering Approach #12: 'Amp Peak 12(5q35.3) mutation analysis' versus Clinical Feature #10: 'TUMOR.STAGE'

'Amp Peak 12(5q35.3) mutation analysis' versus 'RADIATIONS.RADIATION.REGIMENINDICATION'

P value = 2.19e-08 (Fisher's exact test), Q value = 3.2e-05

Table S89. Clustering Approach #12: 'Amp Peak 12(5q35.3) mutation analysis' versus Clinical Feature #11: 'RADIATIONS.RADIATION.REGIMENINDICATION'

nPatients | NO | YES
--- | --- | ---
ALL | 826 | 3737
AMP PEAK 12(5Q35.3) MUTATED | 112 | 822
AMP PEAK 12(5Q35.3) WILD-TYPE | 714 | 2915

Figure S77. Get High-res Image Clustering Approach #12: 'Amp Peak 12(5q35.3) mutation analysis' versus Clinical Feature #11: 'RADIATIONS.RADIATION.REGIMENINDICATION'

Clustering Approach #13: 'Amp Peak 13(6p22.3) mutation analysis'

Table S90. Description of clustering approach #13: 'Amp Peak 13(6p22.3) mutation analysis'

Cluster Labels | AMP PEAK 13(6P22.3) MUTATED | AMP PEAK 13(6P22.3) WILD-TYPE
--- | --- | ---
Number of samples | 1026 | 3537

'Amp Peak 13(6p22.3) mutation analysis' versus 'PRIMARY.SITE.OF.DISEASE'

P value = 2.71e-114 (Chi-square test), Q value = 4.7e-111

Table S91. Clustering Approach #13: 'Amp Peak 13(6p22.3) mutation analysis' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'

nPatients | BLADDER | BRAIN | BREAST | COLON | ENDOMETRIAL | HEAD/NECK | KIDNEY | LUNG | OMENTUM | OVARY | PERITONEUM (OVARY) | RECTUM
--- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | ---
ALL | 125 | 544 | 846 | 412 | 447 | 319 | 493 | 662 | 2 | 548 | 2 | 159
AMP PEAK 13(6P22.3) MUTATED | 48 | 28 | 213 | 74 | 67 | 50 | 8 | 217 | 1 | 280 | 1 | 38
AMP PEAK 13(6P22.3) WILD-TYPE | 77 | 516 | 633 | 338 | 380 | 269 | 485 | 445 | 1 | 268 | 1 | 121

Figure S78. Get High-res Image Clustering Approach #13: 'Amp Peak 13(6p22.3) mutation analysis' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'

'Amp Peak 13(6p22.3) mutation analysis' versus 'GENDER'

P value = 2.53e-12 (Fisher's exact test), Q value = 3.9e-09

Table S92. Clustering Approach #13: 'Amp Peak 13(6p22.3) mutation analysis' versus Clinical Feature #4: 'GENDER'

nPatients | FEMALE | MALE
--- | --- | ---
ALL | 2881 | 1682
AMP PEAK 13(6P22.3) MUTATED | 742 | 284
AMP PEAK 13(6P22.3) WILD-TYPE | 2139 | 1398

Figure S79. Get High-res Image Clustering Approach #13: 'Amp Peak 13(6p22.3) mutation analysis' versus Clinical Feature #4: 'GENDER'

'Amp Peak 13(6p22.3) mutation analysis' versus 'HISTOLOGICAL.TYPE'

P value = 1.06e-89 (Chi-square test), Q value = 1.8e-86

Table S93. Clustering Approach #13: 'Amp Peak 13(6p22.3) mutation analysis' versus Clinical Feature #6: 'HISTOLOGICAL.TYPE'

nPatients | COLON ADENOCARCINOMA | COLON MUCINOUS ADENOCARCINOMA | ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA | HEAD & NECK SQUAMOUS CELL CARCINOMA | KIDNEY CLEAR CELL RENAL CARCINOMA | LUNG ACINAR ADENOCARCINOMA | LUNG ADENOCARCINOMA MIXED SUBTYPE | LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS) | LUNG BASALOID SQUAMOUS CELL CARCINOMA | LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS | LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS | LUNG CLEAR CELL ADENOCARCINOMA | LUNG MICROPAPILLARY ADENOCARCINOMA | LUNG MUCINOUS ADENOCARCINOMA | LUNG PAPILLARY ADENOCARCINOMA | LUNG PAPILLARY SQUAMOUS CELL CARCINOMA | LUNG PAPILLARY SQUAMOUS CELL CARICNOMA | LUNG SMALL CELL SQUAMOUS CELL CARCINOMA | LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA | LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS) | MIXED SEROUS AND ENDOMETRIOID | MUCINOUS (COLLOID) ADENOCARCINOMA | RECTAL ADENOCARCINOMA | RECTAL MUCINOUS ADENOCARCINOMA | SEROUS CYSTADENOCARCINOMA | SEROUS ENDOMETRIAL ADENOCARCINOMA | TREATED PRIMARY GBM | UNTREATED PRIMARY (DE NOVO) GBM
--- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | ---
ALL | 356 | 54 | 350 | 319 | 493 | 10 | 75 | 205 | 7 | 3 | 15 | 2 | 3 | 2 | 13 | 1 | 1 | 1 | 2 | 315 | 18 | 7 | 143 | 13 | 552 | 79 | 1 | 20
AMP PEAK 13(6P22.3) MUTATED | 67 | 7 | 30 | 50 | 8 | 6 | 25 | 77 | 3 | 0 | 8 | 1 | 1 | 0 | 5 | 0 | 0 | 1 | 2 | 87 | 3 | 1 | 36 | 2 | 282 | 34 | 1 | 0
AMP PEAK 13(6P22.3) WILD-TYPE | 289 | 47 | 320 | 269 | 485 | 4 | 50 | 128 | 4 | 3 | 7 | 1 | 2 | 2 | 8 | 1 | 1 | 0 | 0 | 228 | 15 | 6 | 107 | 11 | 270 | 45 | 0 | 20

Figure S80. Get High-res Image Clustering Approach #13: 'Amp Peak 13(6p22.3) mutation analysis' versus Clinical Feature #6: 'HISTOLOGICAL.TYPE'

'Amp Peak 13(6p22.3) mutation analysis' versus 'PATHOLOGICSPREAD(M)'

P value = 8.97e-06 (Chi-square test), Q value = 0.012

Table S94. Clustering Approach #13: 'Amp Peak 13(6p22.3) mutation analysis' versus Clinical Feature #9: 'PATHOLOGICSPREAD(M)'

nPatients | M0 | M1 | M1A | M1B | MX
--- | --- | --- | --- | --- | ---
ALL | 1424 | 168 | 9 | 3 | 165
AMP PEAK 13(6P22.3) MUTATED | 250 | 27 | 3 | 2 | 54
AMP PEAK 13(6P22.3) WILD-TYPE | 1174 | 141 | 6 | 1 | 111

Figure S81. Get High-res Image Clustering Approach #13: 'Amp Peak 13(6p22.3) mutation analysis' versus Clinical Feature #9: 'PATHOLOGICSPREAD(M)'

'Amp Peak 13(6p22.3) mutation analysis' versus 'TUMOR.STAGE'

P value = 4.83e-12 (Fisher's exact test), Q value = 7.4e-09

Table S95. Clustering Approach #13: 'Amp Peak 13(6p22.3) mutation analysis' versus Clinical Feature #10: 'TUMOR.STAGE'

nPatients | I | II | III | IV
--- | --- | --- | --- | ---
ALL | 712 | 498 | 881 | 423
AMP PEAK 13(6P22.3) MUTATED | 146 | 101 | 306 | 96
AMP PEAK 13(6P22.3) WILD-TYPE | 566 | 397 | 575 | 327

Figure S82. Get High-res Image Clustering Approach #13: 'Amp Peak 13(6p22.3) mutation analysis' versus Clinical Feature #10: 'TUMOR.STAGE'

'Amp Peak 13(6p22.3) mutation analysis' versus 'RADIATIONS.RADIATION.REGIMENINDICATION'

P value = 9.67e-11 (Fisher's exact test), Q value = 1.5e-07

Table S96. Clustering Approach #13: 'Amp Peak 13(6p22.3) mutation analysis' versus Clinical Feature #11: 'RADIATIONS.RADIATION.REGIMENINDICATION'

nPatients | NO | YES
--- | --- | ---
ALL | 826 | 3737
AMP PEAK 13(6P22.3) MUTATED | 118 | 908
AMP PEAK 13(6P22.3) WILD-TYPE | 708 | 2829

Figure S83. Get High-res Image Clustering Approach #13: 'Amp Peak 13(6p22.3) mutation analysis' versus Clinical Feature #11: 'RADIATIONS.RADIATION.REGIMENINDICATION'

Clustering Approach #14: 'Amp Peak 14(6p21.1) mutation analysis'

Table S97. Description of clustering approach #14: 'Amp Peak 14(6p21.1) mutation analysis'

Cluster Labels | AMP PEAK 14(6P21.1) MUTATED | AMP PEAK 14(6P21.1) WILD-TYPE
--- | --- | ---
Number of samples | 963 | 3600

'Amp Peak 14(6p21.1) mutation analysis' versus 'PRIMARY.SITE.OF.DISEASE'

P value = 5.45e-75 (Chi-square test), Q value = 9.3e-72

Table S98. Clustering Approach #14: 'Amp Peak 14(6p21.1) mutation analysis' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'

nPatients | BLADDER | BRAIN | BREAST | COLON | ENDOMETRIAL | HEAD/NECK | KIDNEY | LUNG | OMENTUM | OVARY | PERITONEUM (OVARY) | RECTUM
--- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | ---
ALL | 125 | 544 | 846 | 412 | 447 | 319 | 493 | 662 | 2 | 548 | 2 | 159
AMP PEAK 14(6P21.1) MUTATED | 28 | 30 | 195 | 91 | 67 | 52 | 11 | 219 | 0 | 216 | 1 | 50
AMP PEAK 14(6P21.1) WILD-TYPE | 97 | 514 | 651 | 321 | 380 | 267 | 482 | 443 | 2 | 332 | 1 | 109

Figure S84. Get High-res Image Clustering Approach #14: 'Amp Peak 14(6p21.1) mutation analysis' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'

'Amp Peak 14(6p21.1) mutation analysis' versus 'GENDER'

P value = 4.37e-06 (Fisher's exact test), Q value = 0.0061

Table S99. Clustering Approach #14: 'Amp Peak 14(6p21.1) mutation analysis' versus Clinical Feature #4: 'GENDER'

nPatients | FEMALE | MALE
--- | --- | ---
ALL | 2881 | 1682
AMP PEAK 14(6P21.1) MUTATED | 669 | 294
AMP PEAK 14(6P21.1) WILD-TYPE | 2212 | 1388

Figure S85. Get High-res Image Clustering Approach #14: 'Amp Peak 14(6p21.1) mutation analysis' versus Clinical Feature #4: 'GENDER'

'Amp Peak 14(6p21.1) mutation analysis' versus 'HISTOLOGICAL.TYPE'

P value = 7.53e-59 (Chi-square test), Q value = 1.3e-55

Table S100. Clustering Approach #14: 'Amp Peak 14(6p21.1) mutation analysis' versus Clinical Feature #6: 'HISTOLOGICAL.TYPE'

nPatients | COLON ADENOCARCINOMA | COLON MUCINOUS ADENOCARCINOMA | ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA | HEAD & NECK SQUAMOUS CELL CARCINOMA | KIDNEY CLEAR CELL RENAL CARCINOMA | LUNG ACINAR ADENOCARCINOMA | LUNG ADENOCARCINOMA MIXED SUBTYPE | LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS) | LUNG BASALOID SQUAMOUS CELL CARCINOMA | LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS | LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS | LUNG CLEAR CELL ADENOCARCINOMA | LUNG MICROPAPILLARY ADENOCARCINOMA | LUNG MUCINOUS ADENOCARCINOMA | LUNG PAPILLARY ADENOCARCINOMA | LUNG PAPILLARY SQUAMOUS CELL CARCINOMA | LUNG PAPILLARY SQUAMOUS CELL CARICNOMA | LUNG SMALL CELL SQUAMOUS CELL CARCINOMA | LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA | LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS) | MIXED SEROUS AND ENDOMETRIOID | MUCINOUS (COLLOID) ADENOCARCINOMA | RECTAL ADENOCARCINOMA | RECTAL MUCINOUS ADENOCARCINOMA | SEROUS CYSTADENOCARCINOMA | SEROUS ENDOMETRIAL ADENOCARCINOMA | TREATED PRIMARY GBM | UNTREATED PRIMARY (DE NOVO) GBM
--- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | ---
ALL | 356 | 54 | 350 | 319 | 493 | 10 | 75 | 205 | 7 | 3 | 15 | 2 | 3 | 2 | 13 | 1 | 1 | 1 | 2 | 315 | 18 | 7 | 143 | 13 | 552 | 79 | 1 | 20
AMP PEAK 14(6P21.1) MUTATED | 85 | 6 | 33 | 52 | 11 | 5 | 26 | 76 | 2 | 0 | 9 | 1 | 1 | 0 | 5 | 1 | 0 | 1 | 1 | 90 | 0 | 1 | 49 | 1 | 217 | 34 | 0 | 0
AMP PEAK 14(6P21.1) WILD-TYPE | 271 | 48 | 317 | 267 | 482 | 5 | 49 | 129 | 5 | 3 | 6 | 1 | 2 | 2 | 8 | 0 | 1 | 0 | 1 | 225 | 18 | 6 | 94 | 12 | 335 | 45 | 1 | 20

Figure S86. Get High-res Image Clustering Approach #14: 'Amp Peak 14(6p21.1) mutation analysis' versus Clinical Feature #6: 'HISTOLOGICAL.TYPE'

'Amp Peak 14(6p21.1) mutation analysis' versus 'PATHOLOGICSPREAD(M)'

P value = 0.000124 (Chi-square test), Q value = 0.16

Table S101. Clustering Approach #14: 'Amp Peak 14(6p21.1) mutation analysis' versus Clinical Feature #9: 'PATHOLOGICSPREAD(M)'

nPatients | M0 | M1 | M1A | M1B | MX
--- | --- | --- | --- | --- | ---
ALL | 1424 | 168 | 9 | 3 | 165
AMP PEAK 14(6P21.1) MUTATED | 281 | 34 | 4 | 2 | 55
AMP PEAK 14(6P21.1) WILD-TYPE | 1143 | 134 | 5 | 1 | 110

Figure S87. Get High-res Image Clustering Approach #14: 'Amp Peak 14(6p21.1) mutation analysis' versus Clinical Feature #9: 'PATHOLOGICSPREAD(M)'

'Amp Peak 14(6p21.1) mutation analysis' versus 'TUMOR.STAGE'

P value = 8.33e-07 (Fisher's exact test), Q value = 0.0012

Table S102. Clustering Approach #14: 'Amp Peak 14(6p21.1) mutation analysis' versus Clinical Feature #10: 'TUMOR.STAGE'

nPatients | I | II | III | IV
--- | --- | --- | --- | ---
ALL | 712 | 498 | 881 | 423
AMP PEAK 14(6P21.1) MUTATED | 141 | 112 | 276 | 98
AMP PEAK 14(6P21.1) WILD-TYPE | 571 | 386 | 605 | 325

Figure S88. Get High-res Image Clustering Approach #14: 'Amp Peak 14(6p21.1) mutation analysis' versus Clinical Feature #10: 'TUMOR.STAGE'

'Amp Peak 14(6p21.1) mutation analysis' versus 'RADIATIONS.RADIATION.REGIMENINDICATION'

P value = 1.41e-08 (Fisher's exact test), Q value = 2.1e-05

Table S103. Clustering Approach #14: 'Amp Peak 14(6p21.1) mutation analysis' versus Clinical Feature #11: 'RADIATIONS.RADIATION.REGIMENINDICATION'

nPatients | NO | YES
--- | --- | ---
ALL | 826 | 3737
AMP PEAK 14(6P21.1) MUTATED | 116 | 847
AMP PEAK 14(6P21.1) WILD-TYPE | 710 | 2890

Figure S89. Get High-res Image Clustering Approach #14: 'Amp Peak 14(6p21.1) mutation analysis' versus Clinical Feature #11: 'RADIATIONS.RADIATION.REGIMENINDICATION'

Clustering Approach #15: 'Amp Peak 15(6q21) mutation analysis'

Table S104. Description of clustering approach #15: 'Amp Peak 15(6q21) mutation analysis'

Cluster Labels | AMP PEAK 15(6Q21) MUTATED | AMP PEAK 15(6Q21) WILD-TYPE
--- | --- | ---
Number of samples | 572 | 3991

'Amp Peak 15(6q21) mutation analysis' versus 'PRIMARY.SITE.OF.DISEASE'

P value = 5.88e-28 (Chi-square test), Q value = 9.5e-25

Table S105. Clustering Approach #15: 'Amp Peak 15(6q21) mutation analysis' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'

nPatients | BLADDER | BRAIN | BREAST | COLON | ENDOMETRIAL | HEAD/NECK | KIDNEY | LUNG | OMENTUM | OVARY | PERITONEUM (OVARY) | RECTUM
--- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | ---
ALL | 125 | 544 | 846 | 412 | 447 | 319 | 493 | 662 | 2 | 548 | 2 | 159
AMP PEAK 15(6Q21) MUTATED | 12 | 24 | 157 | 59 | 57 | 27 | 9 | 85 | 0 | 106 | 1 | 34
AMP PEAK 15(6Q21) WILD-TYPE | 113 | 520 | 689 | 353 | 390 | 292 | 484 | 577 | 2 | 442 | 1 | 125

Figure S90. Get High-res Image Clustering Approach #15: 'Amp Peak 15(6q21) mutation analysis' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'

'Amp Peak 15(6q21) mutation analysis' versus 'GENDER'

P value = 2.51e-07 (Fisher's exact test), Q value = 0.00037

Table S106. Clustering Approach #15: 'Amp Peak 15(6q21) mutation analysis' versus Clinical Feature #4: 'GENDER'

nPatients | FEMALE | MALE
--- | --- | ---
ALL | 2881 | 1682
AMP PEAK 15(6Q21) MUTATED | 416 | 156
AMP PEAK 15(6Q21) WILD-TYPE | 2465 | 1526

Figure S91. Get High-res Image Clustering Approach #15: 'Amp Peak 15(6q21) mutation analysis' versus Clinical Feature #4: 'GENDER'

'Amp Peak 15(6q21) mutation analysis' versus 'HISTOLOGICAL.TYPE'

P value = 6.14e-24 (Chi-square test), Q value = 9.8e-21

Table S107. Clustering Approach #15: 'Amp Peak 15(6q21) mutation analysis' versus Clinical Feature #6: 'HISTOLOGICAL.TYPE'

nPatients | COLON ADENOCARCINOMA | COLON MUCINOUS ADENOCARCINOMA | ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA | HEAD & NECK SQUAMOUS CELL CARCINOMA | KIDNEY CLEAR CELL RENAL CARCINOMA | LUNG ACINAR ADENOCARCINOMA | LUNG ADENOCARCINOMA MIXED SUBTYPE | LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS) | LUNG BASALOID SQUAMOUS CELL CARCINOMA | LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS | LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS | LUNG CLEAR CELL ADENOCARCINOMA | LUNG MICROPAPILLARY ADENOCARCINOMA | LUNG MUCINOUS ADENOCARCINOMA | LUNG PAPILLARY ADENOCARCINOMA | LUNG PAPILLARY SQUAMOUS CELL CARCINOMA | LUNG PAPILLARY SQUAMOUS CELL CARICNOMA | LUNG SMALL CELL SQUAMOUS CELL CARCINOMA | LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA | LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS) | MIXED SEROUS AND ENDOMETRIOID | MUCINOUS (COLLOID) ADENOCARCINOMA | RECTAL ADENOCARCINOMA | RECTAL MUCINOUS ADENOCARCINOMA | SEROUS CYSTADENOCARCINOMA | SEROUS ENDOMETRIAL ADENOCARCINOMA | TREATED PRIMARY GBM | UNTREATED PRIMARY (DE NOVO) GBM
--- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | ---
ALL | 356 | 54 | 350 | 319 | 493 | 10 | 75 | 205 | 7 | 3 | 15 | 2 | 3 | 2 | 13 | 1 | 1 | 1 | 2 | 315 | 18 | 7 | 143 | 13 | 552 | 79 | 1 | 20
AMP PEAK 15(6Q21) MUTATED | 54 | 5 | 30 | 27 | 9 | 1 | 5 | 15 | 0 | 0 | 1 | 0 | 0 | 0 | 2 | 0 | 0 | 1 | 0 | 59 | 0 | 1 | 34 | 0 | 107 | 27 | 0 | 0
AMP PEAK 15(6Q21) WILD-TYPE | 302 | 49 | 320 | 292 | 484 | 9 | 70 | 190 | 7 | 3 | 14 | 2 | 3 | 2 | 11 | 1 | 1 | 0 | 2 | 256 | 18 | 6 | 109 | 13 | 445 | 52 | 1 | 20

Figure S92. Get High-res Image Clustering Approach #15: 'Amp Peak 15(6q21) mutation analysis' versus Clinical Feature #6: 'HISTOLOGICAL.TYPE'

'Amp Peak 15(6q21) mutation analysis' versus 'PATHOLOGY.T'

P value = 0.000172 (Fisher's exact test), Q value = 0.22

Table S108. Clustering Approach #15: 'Amp Peak 15(6q21) mutation analysis' versus Clinical Feature #7: 'PATHOLOGY.T'

nPatients | T0+T1 | T2 | T3 | T4
--- | --- | --- | --- | ---
ALL | 466 | 632 | 694 | 209
AMP PEAK 15(6Q21) MUTATED | 25 | 76 | 82 | 28
AMP PEAK 15(6Q21) WILD-TYPE | 441 | 556 | 612 | 181

Figure S93. Get High-res Image Clustering Approach #15: 'Amp Peak 15(6q21) mutation analysis' versus Clinical Feature #7: 'PATHOLOGY.T'

Clustering Approach #16: 'Amp Peak 16(7p11.2) mutation analysis'

Table S109. Description of clustering approach #16: 'Amp Peak 16(7p11.2) mutation analysis'

Cluster Labels | AMP PEAK 16(7P11.2) MUTATED | AMP PEAK 16(7P11.2) WILD-TYPE
--- | --- | ---
Number of samples | 2012 | 2551

'Amp Peak 16(7p11.2) mutation analysis' versus 'Time to Death'

P value = 0 (logrank test), Q value = 0

Table S110. Clustering Approach #16: 'Amp Peak 16(7p11.2) mutation analysis' versus Clinical Feature #1: 'Time to Death'

| nPatients | nDeath | Duration Range (Median), Month
--- | --- | --- | ---
ALL | 4296 | 1401 | 0.0 - 224.0 (14.9)
AMP PEAK 16(7P11.2) MUTATED | 1886 | 777 | 0.0 - 224.0 (11.7)
AMP PEAK 16(7P11.2) WILD-TYPE | 2410 | 624 | 0.0 - 220.9 (18.4)

Figure S94. Get High-res Image Clustering Approach #16: 'Amp Peak 16(7p11.2) mutation analysis' versus Clinical Feature #1: 'Time to Death'

'Amp Peak 16(7p11.2) mutation analysis' versus 'PRIMARY.SITE.OF.DISEASE'

P value = 2.02e-154 (Chi-square test), Q value = 3.6e-151

Table S111. Clustering Approach #16: 'Amp Peak 16(7p11.2) mutation analysis' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'

nPatients | BLADDER | BRAIN | BREAST | COLON | ENDOMETRIAL | HEAD/NECK | KIDNEY | LUNG | OMENTUM | OVARY | PERITONEUM (OVARY) | RECTUM
--- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | ---
ALL | 125 | 544 | 846 | 412 | 447 | 319 | 493 | 662 | 2 | 548 | 2 | 159
AMP PEAK 16(7P11.2) MUTATED | 64 | 477 | 261 | 227 | 63 | 136 | 160 | 340 | 1 | 182 | 1 | 98
AMP PEAK 16(7P11.2) WILD-TYPE | 61 | 67 | 585 | 185 | 384 | 183 | 333 | 322 | 1 | 366 | 1 | 61

Figure S95. Get High-res Image Clustering Approach #16: 'Amp Peak 16(7p11.2) mutation analysis' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'

'Amp Peak 16(7p11.2) mutation analysis' versus 'GENDER'

P value = 1.49e-31 (Fisher's exact test), Q value = 2.4e-28

Table S112. Clustering Approach #16: 'Amp Peak 16(7p11.2) mutation analysis' versus Clinical Feature #4: 'GENDER'

nPatients | FEMALE | MALE
--- | --- | ---
ALL | 2881 | 1682
AMP PEAK 16(7P11.2) MUTATED | 1081 | 931
AMP PEAK 16(7P11.2) WILD-TYPE | 1800 | 751

Figure S96. Get High-res Image Clustering Approach #16: 'Amp Peak 16(7p11.2) mutation analysis' versus Clinical Feature #4: 'GENDER'

'Amp Peak 16(7p11.2) mutation analysis' versus 'HISTOLOGICAL.TYPE'

P value = 5.96e-51 (Chi-square test), Q value = 1e-47

Table S113. Clustering Approach #16: 'Amp Peak 16(7p11.2) mutation analysis' versus Clinical Feature #6: 'HISTOLOGICAL.TYPE'

nPatients | COLON ADENOCARCINOMA | COLON MUCINOUS ADENOCARCINOMA | ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA | HEAD & NECK SQUAMOUS CELL CARCINOMA | KIDNEY CLEAR CELL RENAL CARCINOMA | LUNG ACINAR ADENOCARCINOMA | LUNG ADENOCARCINOMA MIXED SUBTYPE | LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS) | LUNG BASALOID SQUAMOUS CELL CARCINOMA | LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS | LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS | LUNG CLEAR CELL ADENOCARCINOMA | LUNG MICROPAPILLARY ADENOCARCINOMA | LUNG MUCINOUS ADENOCARCINOMA | LUNG PAPILLARY ADENOCARCINOMA | LUNG PAPILLARY SQUAMOUS CELL CARCINOMA | LUNG PAPILLARY SQUAMOUS CELL CARICNOMA | LUNG SMALL CELL SQUAMOUS CELL CARCINOMA | LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA | LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS) | MIXED SEROUS AND ENDOMETRIOID | MUCINOUS (COLLOID) ADENOCARCINOMA | RECTAL ADENOCARCINOMA | RECTAL MUCINOUS ADENOCARCINOMA | SEROUS CYSTADENOCARCINOMA | SEROUS ENDOMETRIAL ADENOCARCINOMA | TREATED PRIMARY GBM | UNTREATED PRIMARY (DE NOVO) GBM
--- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | ---
ALL | 356 | 54 | 350 | 319 | 493 | 10 | 75 | 205 | 7 | 3 | 15 | 2 | 3 | 2 | 13 | 1 | 1 | 1 | 2 | 315 | 18 | 7 | 143 | 13 | 552 | 79 | 1 | 20
AMP PEAK 16(7P11.2) MUTATED | 206 | 21 | 38 | 136 | 160 | 5 | 35 | 118 | 5 | 2 | 6 | 0 | 2 | 0 | 6 | 1 | 0 | 0 | 2 | 156 | 4 | 2 | 94 | 3 | 184 | 21 | 1 | 17
AMP PEAK 16(7P11.2) WILD-TYPE | 150 | 33 | 312 | 183 | 333 | 5 | 40 | 87 | 2 | 1 | 9 | 2 | 1 | 2 | 7 | 0 | 1 | 1 | 0 | 159 | 14 | 5 | 49 | 10 | 368 | 58 | 0 | 3

Figure S97. Get High-res Image Clustering Approach #16: 'Amp Peak 16(7p11.2) mutation analysis' versus Clinical Feature #6: 'HISTOLOGICAL.TYPE'

'Amp Peak 16(7p11.2) mutation analysis' versus 'PATHOLOGY.T'

P value = 3.21e-09 (Fisher's exact test), Q value = 4.8e-06

Table S114. Clustering Approach #16: 'Amp Peak 16(7p11.2) mutation analysis' versus Clinical Feature #7: 'PATHOLOGY.T'

nPatients | T0+T1 | T2 | T3 | T4
--- | --- | --- | --- | ---
ALL | 466 | 632 | 694 | 209
AMP PEAK 16(7P11.2) MUTATED | 160 | 322 | 363 | 101
AMP PEAK 16(7P11.2) WILD-TYPE | 306 | 310 | 331 | 108

Figure S98. Get High-res Image Clustering Approach #16: 'Amp Peak 16(7p11.2) mutation analysis' versus Clinical Feature #7: 'PATHOLOGY.T'

'Amp Peak 16(7p11.2) mutation analysis' versus 'PATHOLOGY.N'

P value = 6.53e-07 (Fisher's exact test), Q value = 0.00094

Table S115. Clustering Approach #16: 'Amp Peak 16(7p11.2) mutation analysis' versus Clinical Feature #8: 'PATHOLOGY.N'

nPatients | N0 | N1 | N2 | N3
--- | --- | --- | --- | ---
ALL | 1067 | 353 | 282 | 11
AMP PEAK 16(7P11.2) MUTATED | 476 | 205 | 166 | 6
AMP PEAK 16(7P11.2) WILD-TYPE | 591 | 148 | 116 | 5

Figure S99. Get High-res Image Clustering Approach #16: 'Amp Peak 16(7p11.2) mutation analysis' versus Clinical Feature #8: 'PATHOLOGY.N'

'Amp Peak 16(7p11.2) mutation analysis' versus 'RADIATIONS.RADIATION.REGIMENINDICATION'

P value = 2.81e-13 (Fisher's exact test), Q value = 4.3e-10

Table S116. Clustering Approach #16: 'Amp Peak 16(7p11.2) mutation analysis' versus Clinical Feature #11: 'RADIATIONS.RADIATION.REGIMENINDICATION'

nPatients | NO | YES
--- | --- | ---
ALL | 826 | 3737
AMP PEAK 16(7P11.2) MUTATED | 459 | 1553
AMP PEAK 16(7P11.2) WILD-TYPE | 367 | 2184

Figure S100. Get High-res Image Clustering Approach #16: 'Amp Peak 16(7p11.2) mutation analysis' versus Clinical Feature #11: 'RADIATIONS.RADIATION.REGIMENINDICATION'

Clustering Approach #17: 'Amp Peak 17(7q36.3) mutation analysis'

Table S117. Description of clustering approach #17: 'Amp Peak 17(7q36.3) mutation analysis'

Cluster Labels | AMP PEAK 17(7Q36.3) MUTATED | AMP PEAK 17(7Q36.3) WILD-TYPE
--- | --- | ---
Number of samples | 1835 | 2728

'Amp Peak 17(7q36.3) mutation analysis' versus 'Time to Death'

P value = 0 (logrank test), Q value = 0

Table S118. Clustering Approach #17: 'Amp Peak 17(7q36.3) mutation analysis' versus Clinical Feature #1: 'Time to Death'

| nPatients | nDeath | Duration Range (Median), Month
--- | --- | --- | ---
ALL | 4296 | 1401 | 0.0 - 224.0 (14.9)
AMP PEAK 17(7Q36.3) MUTATED | 1731 | 711 | 0.0 - 223.4 (12.3)
AMP PEAK 17(7Q36.3) WILD-TYPE | 2565 | 690 | 0.0 - 224.0 (16.7)

Figure S101. Get High-res Image Clustering Approach #17: 'Amp Peak 17(7q36.3) mutation analysis' versus Clinical Feature #1: 'Time to Death'

'Amp Peak 17(7q36.3) mutation analysis' versus 'PRIMARY.SITE.OF.DISEASE'

P value = 8.19e-157 (Chi-square test), Q value = 1.5e-153

Table S119. Clustering Approach #17: 'Amp Peak 17(7q36.3) mutation analysis' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'

nPatients | BLADDER | BRAIN | BREAST | COLON | ENDOMETRIAL | HEAD/NECK | KIDNEY | LUNG | OMENTUM | OVARY | PERITONEUM (OVARY) | RECTUM
--- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | ---
ALL | 125 | 544 | 846 | 412 | 447 | 319 | 493 | 662 | 2 | 548 | 2 | 159
AMP PEAK 17(7Q36.3) MUTATED | 39 | 447 | 206 | 201 | 58 | 59 | 164 | 282 | 1 | 293 | 1 | 82
AMP PEAK 17(7Q36.3) WILD-TYPE | 86 | 97 | 640 | 211 | 389 | 260 | 329 | 380 | 1 | 255 | 1 | 77

Figure S102. Get High-res Image Clustering Approach #17: 'Amp Peak 17(7q36.3) mutation analysis' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'

'Amp Peak 17(7q36.3) mutation analysis' versus 'GENDER'

P value = 2.27e-12 (Fisher's exact test), Q value = 3.5e-09

Table S120. Clustering Approach #17: 'Amp Peak 17(7q36.3) mutation analysis' versus Clinical Feature #4: 'GENDER'

nPatients | FEMALE | MALE
--- | --- | ---
ALL | 2881 | 1682
AMP PEAK 17(7Q36.3) MUTATED | 1046 | 789
AMP PEAK 17(7Q36.3) WILD-TYPE | 1835 | 893

Figure S103. Get High-res Image Clustering Approach #17: 'Amp Peak 17(7q36.3) mutation analysis' versus Clinical Feature #4: 'GENDER'

'Amp Peak 17(7q36.3) mutation analysis' versus 'HISTOLOGICAL.TYPE'

P value = 2.41e-50 (Chi-square test), Q value = 4e-47

Table S121. Clustering Approach #17: 'Amp Peak 17(7q36.3) mutation analysis' versus Clinical Feature #6: 'HISTOLOGICAL.TYPE'

nPatients | COLON ADENOCARCINOMA | COLON MUCINOUS ADENOCARCINOMA | ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA | HEAD & NECK SQUAMOUS CELL CARCINOMA | KIDNEY CLEAR CELL RENAL CARCINOMA | LUNG ACINAR ADENOCARCINOMA | LUNG ADENOCARCINOMA MIXED SUBTYPE | LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS) | LUNG BASALOID SQUAMOUS CELL CARCINOMA | LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS | LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS | LUNG CLEAR CELL ADENOCARCINOMA | LUNG MICROPAPILLARY ADENOCARCINOMA | LUNG MUCINOUS ADENOCARCINOMA | LUNG PAPILLARY ADENOCARCINOMA | LUNG PAPILLARY SQUAMOUS CELL CARCINOMA | LUNG PAPILLARY SQUAMOUS CELL CARICNOMA | LUNG SMALL CELL SQUAMOUS CELL CARCINOMA | LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA | LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS) | MIXED SEROUS AND ENDOMETRIOID | MUCINOUS (COLLOID) ADENOCARCINOMA | RECTAL ADENOCARCINOMA | RECTAL MUCINOUS ADENOCARCINOMA | SEROUS CYSTADENOCARCINOMA | SEROUS ENDOMETRIAL ADENOCARCINOMA | TREATED PRIMARY GBM | UNTREATED PRIMARY (DE NOVO) GBM
--- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | ---
ALL | 356 | 54 | 350 | 319 | 493 | 10 | 75 | 205 | 7 | 3 | 15 | 2 | 3 | 2 | 13 | 1 | 1 | 1 | 2 | 315 | 18 | 7 | 143 | 13 | 552 | 79 | 1 | 20
AMP PEAK 17(7Q36.3) MUTATED | 181 | 19 | 38 | 59 | 164 | 4 | 29 | 95 | 2 | 2 | 7 | 0 | 1 | 0 | 5 | 1 | 0 | 1 | 2 | 132 | 3 | 1 | 79 | 2 | 295 | 17 | 1 | 14
AMP PEAK 17(7Q36.3) WILD-TYPE | 175 | 35 | 312 | 260 | 329 | 6 | 46 | 110 | 5 | 1 | 8 | 2 | 2 | 2 | 8 | 0 | 1 | 0 | 0 | 183 | 15 | 6 | 64 | 11 | 257 | 62 | 0 | 6

Figure S104. Get High-res Image Clustering Approach #17: 'Amp Peak 17(7q36.3) mutation analysis' versus Clinical Feature #6: 'HISTOLOGICAL.TYPE'

'Amp Peak 17(7q36.3) mutation analysis' versus 'TUMOR.STAGE'

P value = 2.54e-06 (Fisher's exact test), Q value = 0.0036

Table S122. Clustering Approach #17: 'Amp Peak 17(7q36.3) mutation analysis' versus Clinical Feature #10: 'TUMOR.STAGE'

nPatients | I | II | III | IV
--- | --- | --- | --- | ---
ALL | 712 | 498 | 881 | 423
AMP PEAK 17(7Q36.3) MUTATED | 261 | 194 | 432 | 169
AMP PEAK 17(7Q36.3) WILD-TYPE | 451 | 304 | 449 | 254

Figure S105. Get High-res Image Clustering Approach #17: 'Amp Peak 17(7q36.3) mutation analysis' versus Clinical Feature #10: 'TUMOR.STAGE'

'Amp Peak 17(7q36.3) mutation analysis' versus 'RADIATIONS.RADIATION.REGIMENINDICATION'

P value = 2.43e-08 (Fisher's exact test), Q value = 3.6e-05

Table S123. Clustering Approach #17: 'Amp Peak 17(7q36.3) mutation analysis' versus Clinical Feature #11: 'RADIATIONS.RADIATION.REGIMENINDICATION'

nPatients | NO | YES
--- | --- | ---
ALL | 826 | 3737
AMP PEAK 17(7Q36.3) MUTATED | 404 | 1431
AMP PEAK 17(7Q36.3) WILD-TYPE | 422 | 2306

Figure S106. Get High-res Image Clustering Approach #17: 'Amp Peak 17(7q36.3) mutation analysis' versus Clinical Feature #11: 'RADIATIONS.RADIATION.REGIMENINDICATION'

Clustering Approach #18: 'Amp Peak 18(8p11.23) mutation analysis'

Table S124. Description of clustering approach #18: 'Amp Peak 18(8p11.23) mutation analysis'

Cluster Labels | AMP PEAK 18(8P11.23) MUTATED | AMP PEAK 18(8P11.23) WILD-TYPE
--- | --- | ---
Number of samples | 1207 | 3356

'Amp Peak 18(8p11.23) mutation analysis' versus 'PRIMARY.SITE.OF.DISEASE'

P value = 2.97e-67 (Chi-square test), Q value = 5e-64

Table S125. Clustering Approach #18: 'Amp Peak 18(8p11.23) mutation analysis' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'

nPatients | BLADDER | BRAIN | BREAST | COLON | ENDOMETRIAL | HEAD/NECK | KIDNEY | LUNG | OMENTUM | OVARY | PERITONEUM (OVARY) | RECTUM
--- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | ---
ALL | 125 | 544 | 846 | 412 | 447 | 319 | 493 | 662 | 2 | 548 | 2 | 159
AMP PEAK 18(8P11.23) MUTATED | 44 | 41 | 313 | 143 | 104 | 101 | 27 | 256 | 0 | 125 | 1 | 52
AMP PEAK 18(8P11.23) WILD-TYPE | 81 | 503 | 533 | 269 | 343 | 218 | 466 | 406 | 2 | 423 | 1 | 107

Figure S107. Get High-res Image Clustering Approach #18: 'Amp Peak 18(8p11.23) mutation analysis' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'

'Amp Peak 18(8p11.23) mutation analysis' versus 'HISTOLOGICAL.TYPE'

P value = 1.66e-37 (Chi-square test), Q value = 2.7e-34

Table S126. Clustering Approach #18: 'Amp Peak 18(8p11.23) mutation analysis' versus Clinical Feature #6: 'HISTOLOGICAL.TYPE'

nPatients | COLON ADENOCARCINOMA | COLON MUCINOUS ADENOCARCINOMA | ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA | HEAD & NECK SQUAMOUS CELL CARCINOMA | KIDNEY CLEAR CELL RENAL CARCINOMA | LUNG ACINAR ADENOCARCINOMA | LUNG ADENOCARCINOMA MIXED SUBTYPE | LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS) | LUNG BASALOID SQUAMOUS CELL CARCINOMA | LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS | LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS | LUNG CLEAR CELL ADENOCARCINOMA | LUNG MICROPAPILLARY ADENOCARCINOMA | LUNG MUCINOUS ADENOCARCINOMA | LUNG PAPILLARY ADENOCARCINOMA | LUNG PAPILLARY SQUAMOUS CELL CARCINOMA | LUNG PAPILLARY SQUAMOUS CELL CARICNOMA | LUNG SMALL CELL SQUAMOUS CELL CARCINOMA | LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA | LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS) | MIXED SEROUS AND ENDOMETRIOID | MUCINOUS (COLLOID) ADENOCARCINOMA | RECTAL ADENOCARCINOMA | RECTAL MUCINOUS ADENOCARCINOMA | SEROUS CYSTADENOCARCINOMA | SEROUS ENDOMETRIAL ADENOCARCINOMA | TREATED PRIMARY GBM | UNTREATED PRIMARY (DE NOVO) GBM
--- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | ---
ALL | 356 | 54 | 350 | 319 | 493 | 10 | 75 | 205 | 7 | 3 | 15 | 2 | 3 | 2 | 13 | 1 | 1 | 1 | 2 | 315 | 18 | 7 | 143 | 13 | 552 | 79 | 1 | 20
AMP PEAK 18(8P11.23) MUTATED | 129 | 14 | 79 | 101 | 27 | 4 | 28 | 56 | 3 | 0 | 3 | 0 | 1 | 0 | 3 | 0 | 0 | 1 | 1 | 155 | 6 | 1 | 50 | 2 | 126 | 19 | 0 | 2
AMP PEAK 18(8P11.23) WILD-TYPE | 227 | 40 | 271 | 218 | 466 | 6 | 47 | 149 | 4 | 3 | 12 | 2 | 2 | 2 | 10 | 1 | 1 | 0 | 1 | 160 | 12 | 6 | 93 | 11 | 426 | 60 | 1 | 18

Figure S108. Get High-res Image Clustering Approach #18: 'Amp Peak 18(8p11.23) mutation analysis' versus Clinical Feature #6: 'HISTOLOGICAL.TYPE'

'Amp Peak 18(8p11.23) mutation analysis' versus 'PATHOLOGY.T'

P value = 2.68e-09 (Fisher's exact test), Q value = 4e-06

Table S127. Clustering Approach #18: 'Amp Peak 18(8p11.23) mutation analysis' versus Clinical Feature #7: 'PATHOLOGY.T'

nPatients | T0+T1 | T2 | T3 | T4
--- | --- | --- | --- | ---
ALL | 466 | 632 | 694 | 209
AMP PEAK 18(8P11.23) MUTATED | 85 | 221 | 184 | 71
AMP PEAK 18(8P11.23) WILD-TYPE | 381 | 411 | 510 | 138

Figure S109. Get High-res Image Clustering Approach #18: 'Amp Peak 18(8p11.23) mutation analysis' versus Clinical Feature #7: 'PATHOLOGY.T'

'Amp Peak 18(8p11.23) mutation analysis' versus 'RADIATIONS.RADIATION.REGIMENINDICATION'

P value = 4.09e-05 (Fisher's exact test), Q value = 0.055

Table S128. Clustering Approach #18: 'Amp Peak 18(8p11.23) mutation analysis' versus Clinical Feature #11: 'RADIATIONS.RADIATION.REGIMENINDICATION'

nPatients | NO | YES
--- | --- | ---
ALL | 826 | 3737
AMP PEAK 18(8P11.23) MUTATED | 172 | 1035
AMP PEAK 18(8P11.23) WILD-TYPE | 654 | 2702

Figure S110. Get High-res Image Clustering Approach #18: 'Amp Peak 18(8p11.23) mutation analysis' versus Clinical Feature #11: 'RADIATIONS.RADIATION.REGIMENINDICATION'

Clustering Approach #19: 'Amp Peak 19(8p11.21) mutation analysis'

Table S129. Description of clustering approach #19: 'Amp Peak 19(8p11.21) mutation analysis'

Cluster Labels | AMP PEAK 19(8P11.21) MUTATED | AMP PEAK 19(8P11.21) WILD-TYPE
--- | --- | ---
Number of samples | 1369 | 3194

'Amp Peak 19(8p11.21) mutation analysis' versus 'AGE'

P value = 3.32e-06 (t-test), Q value = 0.0047

Table S130. Clustering Approach #19: 'Amp Peak 19(8p11.21) mutation analysis' versus Clinical Feature #2: 'AGE'

| nPatients | Mean (Std.Dev)
--- | --- | ---
ALL | 4507 | 61.9 (12.6)
AMP PEAK 19(8P11.21) MUTATED | 1350 | 63.2 (12.0)
AMP PEAK 19(8P11.21) WILD-TYPE | 3157 | 61.3 (12.9)

Figure S111. Get High-res Image Clustering Approach #19: 'Amp Peak 19(8p11.21) mutation analysis' versus Clinical Feature #2: 'AGE'

'Amp Peak 19(8p11.21) mutation analysis' versus 'PRIMARY.SITE.OF.DISEASE'

P value = 3.94e-77 (Chi-square test), Q value = 6.7e-74

Table S131. Clustering Approach #19: 'Amp Peak 19(8p11.21) mutation analysis' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'

nPatients | BLADDER | BRAIN | BREAST | COLON | ENDOMETRIAL | HEAD/NECK | KIDNEY | LUNG | OMENTUM | OVARY | PERITONEUM (OVARY) | RECTUM
--- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | ---
ALL | 125 | 544 | 846 | 412 | 447 | 319 | 493 | 662 | 2 | 548 | 2 | 159
AMP PEAK 19(8P11.21) MUTATED | 41 | 42 | 333 | 173 | 131 | 88 | 29 | 264 | 0 | 194 | 2 | 72
AMP PEAK 19(8P11.21) WILD-TYPE | 84 | 502 | 513 | 239 | 316 | 231 | 464 | 398 | 2 | 354 | 0 | 87

Figure S112. Get High-res Image Clustering Approach #19: 'Amp Peak 19(8p11.21) mutation analysis' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'

'Amp Peak 19(8p11.21) mutation analysis' versus 'HISTOLOGICAL.TYPE'

P value = 1.92e-46 (Chi-square test), Q value = 3.2e-43

Table S132. Clustering Approach #19: 'Amp Peak 19(8p11.21) mutation analysis' versus Clinical Feature #6: 'HISTOLOGICAL.TYPE'

nPatients | COLON ADENOCARCINOMA | COLON MUCINOUS ADENOCARCINOMA | ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA | HEAD & NECK SQUAMOUS CELL CARCINOMA | KIDNEY CLEAR CELL RENAL CARCINOMA | LUNG ACINAR ADENOCARCINOMA | LUNG ADENOCARCINOMA MIXED SUBTYPE | LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS) | LUNG BASALOID SQUAMOUS CELL CARCINOMA | LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS | LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS | LUNG CLEAR CELL ADENOCARCINOMA | LUNG MICROPAPILLARY ADENOCARCINOMA | LUNG MUCINOUS ADENOCARCINOMA | LUNG PAPILLARY ADENOCARCINOMA | LUNG PAPILLARY SQUAMOUS CELL CARCINOMA | LUNG PAPILLARY SQUAMOUS CELL CARICNOMA | LUNG SMALL CELL SQUAMOUS CELL CARCINOMA | LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA | LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS) | MIXED SEROUS AND ENDOMETRIOID | MUCINOUS (COLLOID) ADENOCARCINOMA | RECTAL ADENOCARCINOMA | RECTAL MUCINOUS ADENOCARCINOMA | SEROUS CYSTADENOCARCINOMA | SEROUS ENDOMETRIAL ADENOCARCINOMA | TREATED PRIMARY GBM | UNTREATED PRIMARY (DE NOVO) GBM
--- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | ---
ALL | 356 | 54 | 350 | 319 | 493 | 10 | 75 | 205 | 7 | 3 | 15 | 2 | 3 | 2 | 13 | 1 | 1 | 1 | 2 | 315 | 18 | 7 | 143 | 13 | 552 | 79 | 1 | 20
AMP PEAK 19(8P11.21) MUTATED | 155 | 18 | 81 | 88 | 29 | 6 | 30 | 69 | 3 | 0 | 3 | 0 | 0 | 0 | 3 | 0 | 0 | 1 | 2 | 147 | 6 | 0 | 67 | 3 | 196 | 44 | 0 | 2
AMP PEAK 19(8P11.21) WILD-TYPE | 201 | 36 | 269 | 231 | 464 | 4 | 45 | 136 | 4 | 3 | 12 | 2 | 3 | 2 | 10 | 1 | 1 | 0 | 0 | 168 | 12 | 7 | 76 | 10 | 356 | 35 | 1 | 18

Figure S113. Get High-res Image Clustering Approach #19: 'Amp Peak 19(8p11.21) mutation analysis' versus Clinical Feature #6: 'HISTOLOGICAL.TYPE'

'Amp Peak 19(8p11.21) mutation analysis' versus 'PATHOLOGY.T'

P value = 6.99e-12 (Fisher's exact test), Q value = 1.1e-08

Table S133. Clustering Approach #19: 'Amp Peak 19(8p11.21) mutation analysis' versus Clinical Feature #7: 'PATHOLOGY.T'

nPatients | T0+T1 | T2 | T3 | T4
--- | --- | --- | --- | ---
ALL | 466 | 632 | 694 | 209
AMP PEAK 19(8P11.21) MUTATED | 82 | 236 | 223 | 67
AMP PEAK 19(8P11.21) WILD-TYPE | 384 | 396 | 471 | 142

Figure S114. Get High-res Image Clustering Approach #19: 'Amp Peak 19(8p11.21) mutation analysis' versus Clinical Feature #7: 'PATHOLOGY.T'

'Amp Peak 19(8p11.21) mutation analysis' versus 'TUMOR.STAGE'

P value = 0.000163 (Fisher's exact test), Q value = 0.21

Table S134. Clustering Approach #19: 'Amp Peak 19(8p11.21) mutation analysis' versus Clinical Feature #10: 'TUMOR.STAGE'

nPatients | I | II | III | IV
--- | --- | --- | --- | ---
ALL | 712 | 498 | 881 | 423
AMP PEAK 19(8P11.21) MUTATED | 192 | 187 | 293 | 115
AMP PEAK 19(8P11.21) WILD-TYPE | 520 | 311 | 588 | 308

Figure S115. Get High-res Image Clustering Approach #19: 'Amp Peak 19(8p11.21) mutation analysis' versus Clinical Feature #10: 'TUMOR.STAGE'

'Amp Peak 19(8p11.21) mutation analysis' versus 'RADIATIONS.RADIATION.REGIMENINDICATION'

P value = 1.77e-08 (Fisher's exact test), Q value = 2.6e-05

Table S135. Clustering Approach #19: 'Amp Peak 19(8p11.21) mutation analysis' versus Clinical Feature #11: 'RADIATIONS.RADIATION.REGIMENINDICATION'

nPatients | NO | YES
--- | --- | ---
ALL | 826 | 3737
AMP PEAK 19(8P11.21) MUTATED | 182 | 1187
AMP PEAK 19(8P11.21) WILD-TYPE | 644 | 2550

Figure S116. Get High-res Image Clustering Approach #19: 'Amp Peak 19(8p11.21) mutation analysis' versus Clinical Feature #11: 'RADIATIONS.RADIATION.REGIMENINDICATION'

Clustering Approach #20: 'Amp Peak 20(8q24.21) mutation analysis'

Table S136. Description of clustering approach #20: 'Amp Peak 20(8q24.21) mutation analysis'

Cluster Labels | AMP PEAK 20(8Q24.21) MUTATED | AMP PEAK 20(8Q24.21) WILD-TYPE
--- | --- | ---
Number of samples | 2369 | 2194

'Amp Peak 20(8q24.21) mutation analysis' versus 'PRIMARY.SITE.OF.DISEASE'

P value = 2.35e-212 (Chi-square test), Q value = 4.2e-209

Table S137. Clustering Approach #20: 'Amp Peak 20(8q24.21) mutation analysis' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'

nPatients | BLADDER | BRAIN | BREAST | COLON | ENDOMETRIAL | HEAD/NECK | KIDNEY | LUNG | OMENTUM | OVARY | PERITONEUM (OVARY) | RECTUM
--- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | ---
ALL | 125 | 544 | 846 | 412 | 447 | 319 | 493 | 662 | 2 | 548 | 2 | 159
AMP PEAK 20(8Q24.21) MUTATED | 75 | 62 | 550 | 239 | 163 | 229 | 71 | 441 | 2 | 429 | 2 | 105
AMP PEAK 20(8Q24.21) WILD-TYPE | 50 | 482 | 296 | 173 | 284 | 90 | 422 | 221 | 0 | 119 | 0 | 54

Figure S117. Get High-res Image Clustering Approach #20: 'Amp Peak 20(8q24.21) mutation analysis' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'

'Amp Peak 20(8q24.21) mutation analysis' versus 'GENDER'

P value = 3.64e-09 (Fisher's exact test), Q value = 5.4e-06

Table S138. Clustering Approach #20: 'Amp Peak 20(8q24.21) mutation analysis' versus Clinical Feature #4: 'GENDER'

nPatients | FEMALE | MALE
--- | --- | ---
ALL | 2881 | 1682
AMP PEAK 20(8Q24.21) MUTATED | 1592 | 777
AMP PEAK 20(8Q24.21) WILD-TYPE | 1289 | 905

Figure S118. Get High-res Image Clustering Approach #20: 'Amp Peak 20(8q24.21) mutation analysis' versus Clinical Feature #4: 'GENDER'

'Amp Peak 20(8q24.21) mutation analysis' versus 'KARNOFSKY.PERFORMANCE.SCORE'

P value = 8.85e-06 (t-test), Q value = 0.012

Table S139. Clustering Approach #20: 'Amp Peak 20(8q24.21) mutation analysis' versus Clinical Feature #5: 'KARNOFSKY.PERFORMANCE.SCORE'

| nPatients | Mean (Std.Dev)
--- | --- | ---
ALL | 640 | 73.6 (23.9)
AMP PEAK 20(8Q24.21) MUTATED | 192 | 65.9 (30.8)
AMP PEAK 20(8Q24.21) WILD-TYPE | 448 | 76.8 (19.5)

Figure S119. Get High-res Image Clustering Approach #20: 'Amp Peak 20(8q24.21) mutation analysis' versus Clinical Feature #5: 'KARNOFSKY.PERFORMANCE.SCORE'

'Amp Peak 20(8q24.21) mutation analysis' versus 'HISTOLOGICAL.TYPE'

P value = 2.77e-129 (Chi-square test), Q value = 4.9e-126

Table S140. Clustering Approach #20: 'Amp Peak 20(8q24.21) mutation analysis' versus Clinical Feature #6: 'HISTOLOGICAL.TYPE'

nPatients | COLON ADENOCARCINOMA | COLON MUCINOUS ADENOCARCINOMA | ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA | HEAD & NECK SQUAMOUS CELL CARCINOMA | KIDNEY CLEAR CELL RENAL CARCINOMA | LUNG ACINAR ADENOCARCINOMA | LUNG ADENOCARCINOMA MIXED SUBTYPE | LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS) | LUNG BASALOID SQUAMOUS CELL CARCINOMA | LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS | LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS | LUNG CLEAR CELL ADENOCARCINOMA | LUNG MICROPAPILLARY ADENOCARCINOMA | LUNG MUCINOUS ADENOCARCINOMA | LUNG PAPILLARY ADENOCARCINOMA | LUNG PAPILLARY SQUAMOUS CELL CARCINOMA | LUNG PAPILLARY SQUAMOUS CELL CARICNOMA | LUNG SMALL CELL SQUAMOUS CELL CARCINOMA | LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA | LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS) | MIXED SEROUS AND ENDOMETRIOID | MUCINOUS (COLLOID) ADENOCARCINOMA | RECTAL ADENOCARCINOMA | RECTAL MUCINOUS ADENOCARCINOMA | SEROUS CYSTADENOCARCINOMA | SEROUS ENDOMETRIAL ADENOCARCINOMA | TREATED PRIMARY GBM | UNTREATED PRIMARY (DE NOVO) GBM
--- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | ---
ALL | 356 | 54 | 350 | 319 | 493 | 10 | 75 | 205 | 7 | 3 | 15 | 2 | 3 | 2 | 13 | 1 | 1 | 1 | 2 | 315 | 18 | 7 | 143 | 13 | 552 | 79 | 1 | 20
AMP PEAK 20(8Q24.21) MUTATED | 213 | 25 | 98 | 229 | 71 | 7 | 43 | 137 | 6 | 1 | 8 | 1 | 2 | 0 | 9 | 1 | 0 | 1 | 2 | 223 | 8 | 0 | 98 | 5 | 433 | 57 | 0 | 3
AMP PEAK 20(8Q24.21) WILD-TYPE | 143 | 29 | 252 | 90 | 422 | 3 | 32 | 68 | 1 | 2 | 7 | 1 | 1 | 2 | 4 | 0 | 1 | 0 | 0 | 92 | 10 | 7 | 45 | 8 | 119 | 22 | 1 | 17

Figure S120. Get High-res Image Clustering Approach #20: 'Amp Peak 20(8q24.21) mutation analysis' versus Clinical Feature #6: 'HISTOLOGICAL.TYPE'

'Amp Peak 20(8q24.21) mutation analysis' versus 'PATHOLOGY.T'

P value = 1.83e-25 (Fisher's exact test), Q value = 2.9e-22

Table S141. Clustering Approach #20: 'Amp Peak 20(8q24.21) mutation analysis' versus Clinical Feature #7: 'PATHOLOGY.T'

nPatients | T0+T1 | T2 | T3 | T4
--- | --- | --- | --- | ---
ALL | 466 | 632 | 694 | 209
AMP PEAK 20(8Q24.21) MUTATED | 151 | 389 | 373 | 142
AMP PEAK 20(8Q24.21) WILD-TYPE | 315 | 243 | 321 | 67

Figure S121. Get High-res Image Clustering Approach #20: 'Amp Peak 20(8q24.21) mutation analysis' versus Clinical Feature #7: 'PATHOLOGY.T'

'Amp Peak 20(8q24.21) mutation analysis' versus 'PATHOLOGY.N'

P value = 5.45e-11 (Fisher's exact test), Q value = 8.3e-08

Table S142. Clustering Approach #20: 'Amp Peak 20(8q24.21) mutation analysis' versus Clinical Feature #8: 'PATHOLOGY.N'

nPatients | N0 | N1 | N2 | N3
--- | --- | --- | --- | ---
ALL | 1067 | 353 | 282 | 11
AMP PEAK 20(8Q24.21) MUTATED | 551 | 222 | 205 | 9
AMP PEAK 20(8Q24.21) WILD-TYPE | 516 | 131 | 77 | 2

Figure S122. Get High-res Image Clustering Approach #20: 'Amp Peak 20(8q24.21) mutation analysis' versus Clinical Feature #8: 'PATHOLOGY.N'

'Amp Peak 20(8q24.21) mutation analysis' versus 'TUMOR.STAGE'

P value = 3.83e-18 (Fisher's exact test), Q value = 6e-15

Table S143. Clustering Approach #20: 'Amp Peak 20(8q24.21) mutation analysis' versus Clinical Feature #10: 'TUMOR.STAGE'

nPatients | I | II | III | IV
--- | --- | --- | --- | ---
ALL | 712 | 498 | 881 | 423
AMP PEAK 20(8Q24.21) MUTATED | 313 | 298 | 574 | 274
AMP PEAK 20(8Q24.21) WILD-TYPE | 399 | 200 | 307 | 149

Figure S123. Get High-res Image Clustering Approach #20: 'Amp Peak 20(8q24.21) mutation analysis' versus Clinical Feature #10: 'TUMOR.STAGE'

'Amp Peak 20(8q24.21) mutation analysis' versus 'RADIATIONS.RADIATION.REGIMENINDICATION'

P value = 7.76e-22 (Fisher's exact test), Q value = 1.2e-18

Table S144. Clustering Approach #20: 'Amp Peak 20(8q24.21) mutation analysis' versus Clinical Feature #11: 'RADIATIONS.RADIATION.REGIMENINDICATION'

nPatients | NO | YES
--- | --- | ---
ALL | 826 | 3737
AMP PEAK 20(8Q24.21) MUTATED | 304 | 2065
AMP PEAK 20(8Q24.21) WILD-TYPE | 522 | 1672

Figure S124. Get High-res Image Clustering Approach #20: 'Amp Peak 20(8q24.21) mutation analysis' versus Clinical Feature #11: 'RADIATIONS.RADIATION.REGIMENINDICATION'

Clustering Approach #21: 'Amp Peak 21(9p13.3) mutation analysis'

Table S145. Description of clustering approach #21: 'Amp Peak 21(9p13.3) mutation analysis'

Cluster Labels | AMP PEAK 21(9P13.3) MUTATED | AMP PEAK 21(9P13.3) WILD-TYPE
--- | --- | ---
Number of samples | 774 | 3789

'Amp Peak 21(9p13.3) mutation analysis' versus 'PRIMARY.SITE.OF.DISEASE'

P value = 4.48e-35 (Chi-square test), Q value = 7.3e-32

Table S146. Clustering Approach #21: 'Amp Peak 21(9p13.3) mutation analysis' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'

nPatients | BLADDER | BRAIN | BREAST | COLON | ENDOMETRIAL | HEAD/NECK | KIDNEY | LUNG | OMENTUM | OVARY | PERITONEUM (OVARY) | RECTUM
--- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | ---
ALL | 125 | 544 | 846 | 412 | 447 | 319 | 493 | 662 | 2 | 548 | 2 | 159
AMP PEAK 21(9P13.3) MUTATED | 30 | 66 | 152 | 70 | 33 | 90 | 12 | 144 | 0 | 132 | 0 | 45
AMP PEAK 21(9P13.3) WILD-TYPE | 95 | 478 | 694 | 342 | 414 | 229 | 481 | 518 | 2 | 416 | 2 | 114

Figure S125. Get High-res Image Clustering Approach #21: 'Amp Peak 21(9p13.3) mutation analysis' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'

'Amp Peak 21(9p13.3) mutation analysis' versus 'HISTOLOGICAL.TYPE'

P value = 1.12e-32 (Chi-square test), Q value = 1.8e-29

Table S147. Clustering Approach #21: 'Amp Peak 21(9p13.3) mutation analysis' versus Clinical Feature #6: 'HISTOLOGICAL.TYPE'

nPatients | COLON ADENOCARCINOMA | COLON MUCINOUS ADENOCARCINOMA | ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA | HEAD & NECK SQUAMOUS CELL CARCINOMA | KIDNEY CLEAR CELL RENAL CARCINOMA | LUNG ACINAR ADENOCARCINOMA | LUNG ADENOCARCINOMA MIXED SUBTYPE | LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS) | LUNG BASALOID SQUAMOUS CELL CARCINOMA | LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS | LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS | LUNG CLEAR CELL ADENOCARCINOMA | LUNG MICROPAPILLARY ADENOCARCINOMA | LUNG MUCINOUS ADENOCARCINOMA | LUNG PAPILLARY ADENOCARCINOMA | LUNG PAPILLARY SQUAMOUS CELL CARCINOMA | LUNG PAPILLARY SQUAMOUS CELL CARICNOMA | LUNG SMALL CELL SQUAMOUS CELL CARCINOMA | LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA | LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS) | MIXED SEROUS AND ENDOMETRIOID | MUCINOUS (COLLOID) ADENOCARCINOMA | RECTAL ADENOCARCINOMA | RECTAL MUCINOUS ADENOCARCINOMA | SEROUS CYSTADENOCARCINOMA | SEROUS ENDOMETRIAL ADENOCARCINOMA | TREATED PRIMARY GBM | UNTREATED PRIMARY (DE NOVO) GBM
--- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | ---
ALL | 356 | 54 | 350 | 319 | 493 | 10 | 75 | 205 | 7 | 3 | 15 | 2 | 3 | 2 | 13 | 1 | 1 | 1 | 2 | 315 | 18 | 7 | 143 | 13 | 552 | 79 | 1 | 20
AMP PEAK 21(9P13.3) MUTATED | 56 | 14 | 16 | 90 | 12 | 2 | 15 | 31 | 4 | 0 | 3 | 0 | 1 | 0 | 4 | 0 | 0 | 1 | 0 | 83 | 2 | 0 | 39 | 5 | 132 | 15 | 1 | 1
AMP PEAK 21(9P13.3) WILD-TYPE | 300 | 40 | 334 | 229 | 481 | 8 | 60 | 174 | 3 | 3 | 12 | 2 | 2 | 2 | 9 | 1 | 1 | 0 | 2 | 232 | 16 | 7 | 104 | 8 | 420 | 64 | 0 | 19

Figure S126. Get High-res Image Clustering Approach #21: 'Amp Peak 21(9p13.3) mutation analysis' versus Clinical Feature #6: 'HISTOLOGICAL.TYPE'

'Amp Peak 21(9p13.3) mutation analysis' versus 'PATHOLOGY.T'

P value = 1.07e-06 (Fisher's exact test), Q value = 0.0015

Table S148. Clustering Approach #21: 'Amp Peak 21(9p13.3) mutation analysis' versus Clinical Feature #7: 'PATHOLOGY.T'

nPatients | T0+T1 | T2 | T3 | T4
--- | --- | --- | --- | ---
ALL | 466 | 632 | 694 | 209
AMP PEAK 21(9P13.3) MUTATED | 55 | 126 | 114 | 60
AMP PEAK 21(9P13.3) WILD-TYPE | 411 | 506 | 580 | 149

Figure S127. Get High-res Image Clustering Approach #21: 'Amp Peak 21(9p13.3) mutation analysis' versus Clinical Feature #7: 'PATHOLOGY.T'

Clustering Approach #22: 'Amp Peak 22(10p15.1) mutation analysis'

Table S149. Description of clustering approach #22: 'Amp Peak 22(10p15.1) mutation analysis'

Cluster Labels | AMP PEAK 22(10P15.1) MUTATED | AMP PEAK 22(10P15.1) WILD-TYPE
--- | --- | ---
Number of samples | 909 | 3654

'Amp Peak 22(10p15.1) mutation analysis' versus 'PRIMARY.SITE.OF.DISEASE'

P value = 3.98e-106 (Chi-square test), Q value = 6.9e-103

Table S150. Clustering Approach #22: 'Amp Peak 22(10p15.1) mutation analysis' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'

nPatients | BLADDER | BRAIN | BREAST | COLON | ENDOMETRIAL | HEAD/NECK | KIDNEY | LUNG | OMENTUM | OVARY | PERITONEUM (OVARY) | RECTUM
--- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | ---
ALL | 125 | 544 | 846 | 412 | 447 | 319 | 493 | 662 | 2 | 548 | 2 | 159
AMP PEAK 22(10P15.1) MUTATED | 51 | 17 | 238 | 38 | 109 | 29 | 16 | 155 | 0 | 239 | 2 | 15
AMP PEAK 22(10P15.1) WILD-TYPE | 74 | 527 | 608 | 374 | 338 | 290 | 477 | 507 | 2 | 309 | 0 | 144

Figure S128. Get High-res Image Clustering Approach #22: 'Amp Peak 22(10p15.1) mutation analysis' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'

'Amp Peak 22(10p15.1) mutation analysis' versus 'GENDER'

P value = 1.31e-23 (Fisher's exact test), Q value = 2.1e-20

Table S151. Clustering Approach #22: 'Amp Peak 22(10p15.1) mutation analysis' versus Clinical Feature #4: 'GENDER'

nPatients | FEMALE | MALE
--- | --- | ---
ALL | 2881 | 1682
AMP PEAK 22(10P15.1) MUTATED | 701 | 208
AMP PEAK 22(10P15.1) WILD-TYPE | 2180 | 1474

Figure S129. Get High-res Image Clustering Approach #22: 'Amp Peak 22(10p15.1) mutation analysis' versus Clinical Feature #4: 'GENDER'

'Amp Peak 22(10p15.1) mutation analysis' versus 'HISTOLOGICAL.TYPE'

P value = 1.19e-65 (Chi-square test), Q value = 2e-62

Table S152. Clustering Approach #22: 'Amp Peak 22(10p15.1) mutation analysis' versus Clinical Feature #6: 'HISTOLOGICAL.TYPE'

nPatients | COLON ADENOCARCINOMA | COLON MUCINOUS ADENOCARCINOMA | ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA | HEAD & NECK SQUAMOUS CELL CARCINOMA | KIDNEY CLEAR CELL RENAL CARCINOMA | LUNG ACINAR ADENOCARCINOMA | LUNG ADENOCARCINOMA MIXED SUBTYPE | LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS) | LUNG BASALOID SQUAMOUS CELL CARCINOMA | LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS | LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS | LUNG CLEAR CELL ADENOCARCINOMA | LUNG MICROPAPILLARY ADENOCARCINOMA | LUNG MUCINOUS ADENOCARCINOMA | LUNG PAPILLARY ADENOCARCINOMA | LUNG PAPILLARY SQUAMOUS CELL CARCINOMA | LUNG PAPILLARY SQUAMOUS CELL CARICNOMA | LUNG SMALL CELL SQUAMOUS CELL CARCINOMA | LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA | LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS) | MIXED SEROUS AND ENDOMETRIOID | MUCINOUS (COLLOID) ADENOCARCINOMA | RECTAL ADENOCARCINOMA | RECTAL MUCINOUS ADENOCARCINOMA | SEROUS CYSTADENOCARCINOMA | SEROUS ENDOMETRIAL ADENOCARCINOMA | TREATED PRIMARY GBM | UNTREATED PRIMARY (DE NOVO) GBM
--- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | ---
ALL | 356 | 54 | 350 | 319 | 493 | 10 | 75 | 205 | 7 | 3 | 15 | 2 | 3 | 2 | 13 | 1 | 1 | 1 | 2 | 315 | 18 | 7 | 143 | 13 | 552 | 79 | 1 | 20
AMP PEAK 22(10P15.1) MUTATED | 34 | 3 | 84 | 29 | 16 | 3 | 27 | 52 | 2 | 0 | 3 | 0 | 2 | 0 | 5 | 0 | 0 | 0 | 1 | 59 | 4 | 1 | 14 | 1 | 241 | 21 | 0 | 0
AMP PEAK 22(10P15.1) WILD-TYPE | 322 | 51 | 266 | 290 | 477 | 7 | 48 | 153 | 5 | 3 | 12 | 2 | 1 | 2 | 8 | 1 | 1 | 1 | 1 | 256 | 14 | 6 | 129 | 12 | 311 | 58 | 1 | 20

Figure S130. Get High-res Image Clustering Approach #22: 'Amp Peak 22(10p15.1) mutation analysis' versus Clinical Feature #6: 'HISTOLOGICAL.TYPE'

'Amp Peak 22(10p15.1) mutation analysis' versus 'PATHOLOGY.T'

P value = 5.9e-06 (Fisher's exact test), Q value = 0.0082

Table S153. Clustering Approach #22: 'Amp Peak 22(10p15.1) mutation analysis' versus Clinical Feature #7: 'PATHOLOGY.T'

nPatients | T0+T1 | T2 | T3 | T4
--- | --- | --- | --- | ---
ALL | 466 | 632 | 694 | 209
AMP PEAK 22(10P15.1) MUTATED | 41 | 115 | 70 | 25
AMP PEAK 22(10P15.1) WILD-TYPE | 425 | 517 | 624 | 184

Figure S131. Get High-res Image Clustering Approach #22: 'Amp Peak 22(10p15.1) mutation analysis' versus Clinical Feature #7: 'PATHOLOGY.T'

'Amp Peak 22(10p15.1) mutation analysis' versus 'TUMOR.STAGE'

P value = 6.81e-16 (Fisher's exact test), Q value = 1.1e-12

Table S154. Clustering Approach #22: 'Amp Peak 22(10p15.1) mutation analysis' versus Clinical Feature #10: 'TUMOR.STAGE'

nPatients | I | II | III | IV
--- | --- | --- | --- | ---
ALL | 712 | 498 | 881 | 423
AMP PEAK 22(10P15.1) MUTATED | 94 | 77 | 252 | 62
AMP PEAK 22(10P15.1) WILD-TYPE | 618 | 421 | 629 | 361

Figure S132. Get High-res Image Clustering Approach #22: 'Amp Peak 22(10p15.1) mutation analysis' versus Clinical Feature #10: 'TUMOR.STAGE'

'Amp Peak 22(10p15.1) mutation analysis' versus 'RADIATIONS.RADIATION.REGIMENINDICATION'

P value = 1.77e-06 (Fisher's exact test), Q value = 0.0025

Table S155. Clustering Approach #22: 'Amp Peak 22(10p15.1) mutation analysis' versus Clinical Feature #11: 'RADIATIONS.RADIATION.REGIMENINDICATION'

nPatients | NO | YES
--- | --- | ---
ALL | 826 | 3737
AMP PEAK 22(10P15.1) MUTATED | 116 | 793
AMP PEAK 22(10P15.1) WILD-TYPE | 710 | 2944

Figure S133. Get High-res Image Clustering Approach #22: 'Amp Peak 22(10p15.1) mutation analysis' versus Clinical Feature #11: 'RADIATIONS.RADIATION.REGIMENINDICATION'

'Amp Peak 22(10p15.1) mutation analysis' versus 'TOBACCOSMOKINGHISTORYINDICATOR'

P value = 1.48e-08 (Chi-square test), Q value = 2.2e-05

Table S156. Clustering Approach #22: 'Amp Peak 22(10p15.1) mutation analysis' versus Clinical Feature #14: 'TOBACCOSMOKINGHISTORYINDICATOR'

nPatients | 1 | 2 | 3 | 4 | 5 | CURRENT REFORMED SMOKER FOR < OR = 15 YEARS | CURRENT REFORMED SMOKER FOR > 15 YEARS | CURRENT SMOKER | LIFELONG NON-SMOKER
--- | --- | --- | --- | --- | --- | --- | --- | --- | ---
ALL | 28 | 23 | 37 | 29 | 2 | 355 | 217 | 250 | 128
AMP PEAK 22(10P15.1) MUTATED | 9 | 9 | 19 | 11 | 0 | 82 | 37 | 51 | 8
AMP PEAK 22(10P15.1) WILD-TYPE | 19 | 14 | 18 | 18 | 2 | 273 | 180 | 199 | 120

Figure S134. Get High-res Image Clustering Approach #22: 'Amp Peak 22(10p15.1) mutation analysis' versus Clinical Feature #14: 'TOBACCOSMOKINGHISTORYINDICATOR'

Clustering Approach #23: 'Amp Peak 23(10q22.2) mutation analysis'

Table S157. Description of clustering approach #23: 'Amp Peak 23(10q22.2) mutation analysis'

Cluster Labels | AMP PEAK 23(10Q22.2) MUTATED | AMP PEAK 23(10Q22.2) WILD-TYPE
--- | --- | ---
Number of samples | 612 | 3951

'Amp Peak 23(10q22.2) mutation analysis' versus 'PRIMARY.SITE.OF.DISEASE'

P value = 4.66e-77 (Chi-square test), Q value = 7.9e-74

Table S158. Clustering Approach #23: 'Amp Peak 23(10q22.2) mutation analysis' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'

nPatients | BLADDER | BRAIN | BREAST | COLON | ENDOMETRIAL | HEAD/NECK | KIDNEY | LUNG | OMENTUM | OVARY | PERITONEUM (OVARY) | RECTUM
--- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | ---
ALL | 125 | 544 | 846 | 412 | 447 | 319 | 493 | 662 | 2 | 548 | 2 | 159
AMP PEAK 23(10Q22.2) MUTATED | 18 | 2 | 133 | 23 | 121 | 29 | 10 | 94 | 1 | 169 | 1 | 11
AMP PEAK 23(10Q22.2) WILD-TYPE | 107 | 542 | 713 | 389 | 326 | 290 | 483 | 568 | 1 | 379 | 1 | 148

Figure S135. Get High-res Image Clustering Approach #23: 'Amp Peak 23(10q22.2) mutation analysis' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'

'Amp Peak 23(10q22.2) mutation analysis' versus 'GENDER'

P value = 7.43e-21 (Fisher's exact test), Q value = 1.2e-17

Table S159. Clustering Approach #23: 'Amp Peak 23(10q22.2) mutation analysis' versus Clinical Feature #4: 'GENDER'

nPatients | FEMALE | MALE
--- | --- | ---
ALL | 2881 | 1682
AMP PEAK 23(10Q22.2) MUTATED | 487 | 125
AMP PEAK 23(10Q22.2) WILD-TYPE | 2394 | 1557

Figure S136. Get High-res Image Clustering Approach #23: 'Amp Peak 23(10q22.2) mutation analysis' versus Clinical Feature #4: 'GENDER'

'Amp Peak 23(10q22.2) mutation analysis' versus 'HISTOLOGICAL.TYPE'

P value = 1.85e-48 (Chi-square test), Q value = 3.1e-45

Table S160. Clustering Approach #23: 'Amp Peak 23(10q22.2) mutation analysis' versus Clinical Feature #6: 'HISTOLOGICAL.TYPE'

nPatients | COLON ADENOCARCINOMA | COLON MUCINOUS ADENOCARCINOMA | ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA | HEAD & NECK SQUAMOUS CELL CARCINOMA | KIDNEY CLEAR CELL RENAL CARCINOMA | LUNG ACINAR ADENOCARCINOMA | LUNG ADENOCARCINOMA MIXED SUBTYPE | LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS) | LUNG BASALOID SQUAMOUS CELL CARCINOMA | LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS | LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS | LUNG CLEAR CELL ADENOCARCINOMA | LUNG MICROPAPILLARY ADENOCARCINOMA | LUNG MUCINOUS ADENOCARCINOMA | LUNG PAPILLARY ADENOCARCINOMA | LUNG PAPILLARY SQUAMOUS CELL CARCINOMA | LUNG PAPILLARY SQUAMOUS CELL CARICNOMA | LUNG SMALL CELL SQUAMOUS CELL CARCINOMA | LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA | LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS) | MIXED SEROUS AND ENDOMETRIOID | MUCINOUS (COLLOID) ADENOCARCINOMA | RECTAL ADENOCARCINOMA | RECTAL MUCINOUS ADENOCARCINOMA | SEROUS CYSTADENOCARCINOMA | SEROUS ENDOMETRIAL ADENOCARCINOMA | TREATED PRIMARY GBM | UNTREATED PRIMARY (DE NOVO) GBM
--- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | ---
ALL | 356 | 54 | 350 | 319 | 493 | 10 | 75 | 205 | 7 | 3 | 15 | 2 | 3 | 2 | 13 | 1 | 1 | 1 | 2 | 315 | 18 | 7 | 143 | 13 | 552 | 79 | 1 | 20
AMP PEAK 23(10Q22.2) MUTATED | 20 | 3 | 88 | 29 | 10 | 1 | 19 | 32 | 0 | 0 | 1 | 0 | 1 | 0 | 3 | 0 | 0 | 0 | 0 | 37 | 3 | 0 | 9 | 1 | 171 | 30 | 0 | 0
AMP PEAK 23(10Q22.2) WILD-TYPE | 336 | 51 | 262 | 290 | 483 | 9 | 56 | 173 | 7 | 3 | 14 | 2 | 2 | 2 | 10 | 1 | 1 | 1 | 2 | 278 | 15 | 7 | 134 | 12 | 381 | 49 | 1 | 20

Figure S137. Get High-res Image Clustering Approach #23: 'Amp Peak 23(10q22.2) mutation analysis' versus Clinical Feature #6: 'HISTOLOGICAL.TYPE'

'Amp Peak 23(10q22.2) mutation analysis' versus 'TUMOR.STAGE'

P value = 1.38e-10 (Fisher's exact test), Q value = 2.1e-07

Table S161. Clustering Approach #23: 'Amp Peak 23(10q22.2) mutation analysis' versus Clinical Feature #10: 'TUMOR.STAGE'

nPatients | I | II | III | IV
--- | --- | --- | --- | ---
ALL | 712 | 498 | 881 | 423
AMP PEAK 23(10Q22.2) MUTATED | 60 | 47 | 171 | 54
AMP PEAK 23(10Q22.2) WILD-TYPE | 652 | 451 | 710 | 369

Figure S138. Get High-res Image Clustering Approach #23: 'Amp Peak 23(10q22.2) mutation analysis' versus Clinical Feature #10: 'TUMOR.STAGE'

Clustering Approach #24: 'Amp Peak 24(11q13.3) mutation analysis'

Table S162. Description of clustering approach #24: 'Amp Peak 24(11q13.3) mutation analysis'

Cluster Labels | AMP PEAK 24(11Q13.3) MUTATED | AMP PEAK 24(11Q13.3) WILD-TYPE
--- | --- | ---
Number of samples | 1125 | 3438

'Amp Peak 24(11q13.3) mutation analysis' versus 'PRIMARY.SITE.OF.DISEASE'

P value = 1.03e-121 (Chi-square test), Q value = 1.8e-118

Table S163. Clustering Approach #24: 'Amp Peak 24(11q13.3) mutation analysis' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'

nPatients | BLADDER | BRAIN | BREAST | COLON | ENDOMETRIAL | HEAD/NECK | KIDNEY | LUNG | OMENTUM | OVARY | PERITONEUM (OVARY) | RECTUM
--- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | ---
ALL | 125 | 544 | 846 | 412 | 447 | 319 | 493 | 662 | 2 | 548 | 2 | 159
AMP PEAK 24(11Q13.3) MUTATED | 48 | 16 | 328 | 48 | 46 | 145 | 27 | 237 | 0 | 205 | 0 | 25
AMP PEAK 24(11Q13.3) WILD-TYPE | 77 | 528 | 518 | 364 | 401 | 174 | 466 | 425 | 2 | 343 | 2 | 134

Figure S139. Get High-res Image Clustering Approach #24: 'Amp Peak 24(11q13.3) mutation analysis' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'

'Amp Peak 24(11q13.3) mutation analysis' versus 'GENDER'

P value = 5.68e-05 (Fisher's exact test), Q value = 0.076

Table S164. Clustering Approach #24: 'Amp Peak 24(11q13.3) mutation analysis' versus Clinical Feature #4: 'GENDER'

nPatients | FEMALE | MALE
--- | --- | ---
ALL | 2881 | 1682
AMP PEAK 24(11Q13.3) MUTATED | 767 | 358
AMP PEAK 24(11Q13.3) WILD-TYPE | 2114 | 1324

Figure S140. Get High-res Image Clustering Approach #24: 'Amp Peak 24(11q13.3) mutation analysis' versus Clinical Feature #4: 'GENDER'

'Amp Peak 24(11q13.3) mutation analysis' versus 'HISTOLOGICAL.TYPE'

P value = 8.78e-67 (Chi-square test), Q value = 1.5e-63

Table S165. Clustering Approach #24: 'Amp Peak 24(11q13.3) mutation analysis' versus Clinical Feature #6: 'HISTOLOGICAL.TYPE'

nPatients | COLON ADENOCARCINOMA | COLON MUCINOUS ADENOCARCINOMA | ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA | HEAD & NECK SQUAMOUS CELL CARCINOMA | KIDNEY CLEAR CELL RENAL CARCINOMA | LUNG ACINAR ADENOCARCINOMA | LUNG ADENOCARCINOMA MIXED SUBTYPE | LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS) | LUNG BASALOID SQUAMOUS CELL CARCINOMA | LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS | LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS | LUNG CLEAR CELL ADENOCARCINOMA | LUNG MICROPAPILLARY ADENOCARCINOMA | LUNG MUCINOUS ADENOCARCINOMA | LUNG PAPILLARY ADENOCARCINOMA | LUNG PAPILLARY SQUAMOUS CELL CARCINOMA | LUNG PAPILLARY SQUAMOUS CELL CARICNOMA | LUNG SMALL CELL SQUAMOUS CELL CARCINOMA | LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA | LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS) | MIXED SEROUS AND ENDOMETRIOID | MUCINOUS (COLLOID) ADENOCARCINOMA | RECTAL ADENOCARCINOMA | RECTAL MUCINOUS ADENOCARCINOMA | SEROUS CYSTADENOCARCINOMA | SEROUS ENDOMETRIAL ADENOCARCINOMA | TREATED PRIMARY GBM | UNTREATED PRIMARY (DE NOVO) GBM
--- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | ---
ALL | 356 | 54 | 350 | 319 | 493 | 10 | 75 | 205 | 7 | 3 | 15 | 2 | 3 | 2 | 13 | 1 | 1 | 1 | 2 | 315 | 18 | 7 | 143 | 13 | 552 | 79 | 1 | 20
AMP PEAK 24(11Q13.3) MUTATED | 47 | 1 | 29 | 145 | 27 | 3 | 26 | 78 | 2 | 1 | 5 | 1 | 2 | 0 | 2 | 1 | 0 | 0 | 1 | 115 | 1 | 0 | 24 | 1 | 205 | 16 | 0 | 0
AMP PEAK 24(11Q13.3) WILD-TYPE | 309 | 53 | 321 | 174 | 466 | 7 | 49 | 127 | 5 | 2 | 10 | 1 | 1 | 2 | 11 | 0 | 1 | 1 | 1 | 200 | 17 | 7 | 119 | 12 | 347 | 63 | 1 | 20

Figure S141. Get High-res Image Clustering Approach #24: 'Amp Peak 24(11q13.3) mutation analysis' versus Clinical Feature #6: 'HISTOLOGICAL.TYPE'

'Amp Peak 24(11q13.3) mutation analysis' versus 'PATHOLOGY.T'

P value = 1.44e-10 (Fisher's exact test), Q value = 2.2e-07

Table S166. Clustering Approach #24: 'Amp Peak 24(11q13.3) mutation analysis' versus Clinical Feature #7: 'PATHOLOGY.T'

nPatients | T0+T1 | T2 | T3 | T4
--- | --- | --- | --- | ---
ALL | 466 | 632 | 694 | 209
AMP PEAK 24(11Q13.3) MUTATED | 84 | 188 | 120 | 71
AMP PEAK 24(11Q13.3) WILD-TYPE | 382 | 444 | 574 | 138

Figure S142. Get High-res Image Clustering Approach #24: 'Amp Peak 24(11q13.3) mutation analysis' versus Clinical Feature #7: 'PATHOLOGY.T'

'Amp Peak 24(11q13.3) mutation analysis' versus 'PATHOLOGY.N'

P value = 7.8e-06 (Fisher's exact test), Q value = 0.011

Table S167. Clustering Approach #24: 'Amp Peak 24(11q13.3) mutation analysis' versus Clinical Feature #8: 'PATHOLOGY.N'

nPatients | N0 | N1 | N2 | N3
--- | --- | --- | --- | ---
ALL | 1067 | 353 | 282 | 11
AMP PEAK 24(11Q13.3) MUTATED | 239 | 88 | 104 | 5
AMP PEAK 24(11Q13.3) WILD-TYPE | 828 | 265 | 178 | 6

Figure S143. Get High-res Image Clustering Approach #24: 'Amp Peak 24(11q13.3) mutation analysis' versus Clinical Feature #8: 'PATHOLOGY.N'

'Amp Peak 24(11q13.3) mutation analysis' versus 'TUMOR.STAGE'

P value = 1.77e-06 (Fisher's exact test), Q value = 0.0025

Table S168. Clustering Approach #24: 'Amp Peak 24(11q13.3) mutation analysis' versus Clinical Feature #10: 'TUMOR.STAGE'

nPatients | I | II | III | IV
--- | --- | --- | --- | ---
ALL | 712 | 498 | 881 | 423
AMP PEAK 24(11Q13.3) MUTATED | 145 | 126 | 244 | 147
AMP PEAK 24(11Q13.3) WILD-TYPE | 567 | 372 | 637 | 276

Figure S144. Get High-res Image Clustering Approach #24: 'Amp Peak 24(11q13.3) mutation analysis' versus Clinical Feature #10: 'TUMOR.STAGE'

'Amp Peak 24(11q13.3) mutation analysis' versus 'RADIATIONS.RADIATION.REGIMENINDICATION'

P value = 1.49e-05 (Fisher's exact test), Q value = 0.02

Table S169. Clustering Approach #24: 'Amp Peak 24(11q13.3) mutation analysis' versus Clinical Feature #11: 'RADIATIONS.RADIATION.REGIMENINDICATION'

nPatients | NO | YES
--- | --- | ---
ALL | 826 | 3737
AMP PEAK 24(11Q13.3) MUTATED | 156 | 969
AMP PEAK 24(11Q13.3) WILD-TYPE | 670 | 2768

Figure S145. Get High-res Image Clustering Approach #24: 'Amp Peak 24(11q13.3) mutation analysis' versus Clinical Feature #11: 'RADIATIONS.RADIATION.REGIMENINDICATION'

Clustering Approach #25: 'Amp Peak 25(12p13.33) mutation analysis'

Table S170. Description of clustering approach #25: 'Amp Peak 25(12p13.33) mutation analysis'

Cluster Labels | AMP PEAK 25(12P13.33) MUTATED | AMP PEAK 25(12P13.33) WILD-TYPE
--- | --- | ---
Number of samples | 1333 | 3230

'Amp Peak 25(12p13.33) mutation analysis' versus 'PRIMARY.SITE.OF.DISEASE'

P value = 1.26e-74 (Chi-square test), Q value = 2.1e-71

Table S171. Clustering Approach #25: 'Amp Peak 25(12p13.33) mutation analysis' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'

nPatients | BLADDER | BRAIN | BREAST | COLON | ENDOMETRIAL | HEAD/NECK | KIDNEY | LUNG | OMENTUM | OVARY | PERITONEUM (OVARY) | RECTUM
--- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | ---
ALL | 125 | 544 | 846 | 412 | 447 | 319 | 493 | 662 | 2 | 548 | 2 | 159
AMP PEAK 25(12P13.33) MUTATED | 42 | 64 | 220 | 103 | 66 | 108 | 115 | 266 | 2 | 306 | 1 | 38
AMP PEAK 25(12P13.33) WILD-TYPE | 83 | 480 | 626 | 309 | 381 | 211 | 378 | 396 | 0 | 242 | 1 | 121

Figure S146. Get High-res Image Clustering Approach #25: 'Amp Peak 25(12p13.33) mutation analysis' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'

'Amp Peak 25(12p13.33) mutation analysis' versus 'HISTOLOGICAL.TYPE'

P value = 2.73e-52 (Chi-square test), Q value = 4.6e-49

Table S172. Clustering Approach #25: 'Amp Peak 25(12p13.33) mutation analysis' versus Clinical Feature #6: 'HISTOLOGICAL.TYPE'

nPatients | COLON ADENOCARCINOMA | COLON MUCINOUS ADENOCARCINOMA | ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA | HEAD & NECK SQUAMOUS CELL CARCINOMA | KIDNEY CLEAR CELL RENAL CARCINOMA | LUNG ACINAR ADENOCARCINOMA | LUNG ADENOCARCINOMA MIXED SUBTYPE | LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS) | LUNG BASALOID SQUAMOUS CELL CARCINOMA | LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS | LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS | LUNG CLEAR CELL ADENOCARCINOMA | LUNG MICROPAPILLARY ADENOCARCINOMA | LUNG MUCINOUS ADENOCARCINOMA | LUNG PAPILLARY ADENOCARCINOMA | LUNG PAPILLARY SQUAMOUS CELL CARCINOMA | LUNG PAPILLARY SQUAMOUS CELL CARICNOMA | LUNG SMALL CELL SQUAMOUS CELL CARCINOMA | LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA | LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS) | MIXED SEROUS AND ENDOMETRIOID | MUCINOUS (COLLOID) ADENOCARCINOMA | RECTAL ADENOCARCINOMA | RECTAL MUCINOUS ADENOCARCINOMA | SEROUS CYSTADENOCARCINOMA | SEROUS ENDOMETRIAL ADENOCARCINOMA | TREATED PRIMARY GBM | UNTREATED PRIMARY (DE NOVO) GBM
--- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | ---
ALL | 356 | 54 | 350 | 319 | 493 | 10 | 75 | 205 | 7 | 3 | 15 | 2 | 3 | 2 | 13 | 1 | 1 | 1 | 2 | 315 | 18 | 7 | 143 | 13 | 552 | 79 | 1 | 20
AMP PEAK 25(12P13.33) MUTATED | 91 | 11 | 37 | 108 | 115 | 1 | 26 | 65 | 3 | 0 | 4 | 1 | 0 | 0 | 2 | 1 | 0 | 1 | 0 | 160 | 4 | 2 | 32 | 5 | 309 | 25 | 0 | 1
AMP PEAK 25(12P13.33) WILD-TYPE | 265 | 43 | 313 | 211 | 378 | 9 | 49 | 140 | 4 | 3 | 11 | 1 | 3 | 2 | 11 | 0 | 1 | 0 | 2 | 155 | 14 | 5 | 111 | 8 | 243 | 54 | 1 | 19

Figure S147. Get High-res Image Clustering Approach #25: 'Amp Peak 25(12p13.33) mutation analysis' versus Clinical Feature #6: 'HISTOLOGICAL.TYPE'

'Amp Peak 25(12p13.33) mutation analysis' versus 'PATHOLOGY.T'

P value = 9.39e-06 (Fisher's exact test), Q value = 0.013

Table S173. Clustering Approach #25: 'Amp Peak 25(12p13.33) mutation analysis' versus Clinical Feature #7: 'PATHOLOGY.T'

nPatients | T0+T1 | T2 | T3 | T4
--- | --- | --- | --- | ---
ALL | 466 | 632 | 694 | 209
AMP PEAK 25(12P13.33) MUTATED | 107 | 230 | 206 | 75
AMP PEAK 25(12P13.33) WILD-TYPE | 359 | 402 | 488 | 134

Figure S148. Get High-res Image Clustering Approach #25: 'Amp Peak 25(12p13.33) mutation analysis' versus Clinical Feature #7: 'PATHOLOGY.T'

'Amp Peak 25(12p13.33) mutation analysis' versus 'TUMOR.STAGE'

P value = 2.09e-08 (Fisher's exact test), Q value = 3.1e-05

Table S174. Clustering Approach #25: 'Amp Peak 25(12p13.33) mutation analysis' versus Clinical Feature #10: 'TUMOR.STAGE'

nPatients | I | II | III | IV
--- | --- | --- | --- | ---
ALL | 712 | 498 | 881 | 423
AMP PEAK 25(12P13.33) MUTATED | 199 | 184 | 378 | 154
AMP PEAK 25(12P13.33) WILD-TYPE | 513 | 314 | 503 | 269

Figure S149. Get High-res Image Clustering Approach #25: 'Amp Peak 25(12p13.33) mutation analysis' versus Clinical Feature #10: 'TUMOR.STAGE'

'Amp Peak 25(12p13.33) mutation analysis' versus 'RADIATIONS.RADIATION.REGIMENINDICATION'

P value = 3.93e-13 (Fisher's exact test), Q value = 6.1e-10

Table S175. Clustering Approach #25: 'Amp Peak 25(12p13.33) mutation analysis' versus Clinical Feature #11: 'RADIATIONS.RADIATION.REGIMENINDICATION'

nPatients | NO | YES
--- | --- | ---
ALL | 826 | 3737
AMP PEAK 25(12P13.33) MUTATED | 158 | 1175
AMP PEAK 25(12P13.33) WILD-TYPE | 668 | 2562

Figure S150. Get High-res Image Clustering Approach #25: 'Amp Peak 25(12p13.33) mutation analysis' versus Clinical Feature #11: 'RADIATIONS.RADIATION.REGIMENINDICATION'

Clustering Approach #26: 'Amp Peak 26(12p12.1) mutation analysis'

Table S176. Description of clustering approach #26: 'Amp Peak 26(12p12.1) mutation analysis'

Cluster Labels | AMP PEAK 26(12P12.1) MUTATED | AMP PEAK 26(12P12.1) WILD-TYPE
--- | --- | ---
Number of samples | 1293 | 3270

'Amp Peak 26(12p12.1) mutation analysis' versus 'PRIMARY.SITE.OF.DISEASE'

P value = 1.5e-72 (Chi-square test), Q value = 2.6e-69

Table S177. Clustering Approach #26: 'Amp Peak 26(12p12.1) mutation analysis' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'

nPatients | BLADDER | BRAIN | BREAST | COLON | ENDOMETRIAL | HEAD/NECK | KIDNEY | LUNG | OMENTUM | OVARY | PERITONEUM (OVARY) | RECTUM
--- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | ---
ALL | 125 | 544 | 846 | 412 | 447 | 319 | 493 | 662 | 2 | 548 | 2 | 159
AMP PEAK 26(12P12.1) MUTATED | 41 | 62 | 213 | 90 | 67 | 96 | 113 | 279 | 2 | 288 | 2 | 38
AMP PEAK 26(12P12.1) WILD-TYPE | 84 | 482 | 633 | 322 | 380 | 223 | 380 | 383 | 0 | 260 | 0 | 121

Figure S151. Get High-res Image Clustering Approach #26: 'Amp Peak 26(12p12.1) mutation analysis' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'

'Amp Peak 26(12p12.1) mutation analysis' versus 'HISTOLOGICAL.TYPE'

P value = 6.28e-48 (Chi-square test), Q value = 1e-44

Table S178. Clustering Approach #26: 'Amp Peak 26(12p12.1) mutation analysis' versus Clinical Feature #6: 'HISTOLOGICAL.TYPE'

nPatients | COLON ADENOCARCINOMA | COLON MUCINOUS ADENOCARCINOMA | ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA | HEAD & NECK SQUAMOUS CELL CARCINOMA | KIDNEY CLEAR CELL RENAL CARCINOMA | LUNG ACINAR ADENOCARCINOMA | LUNG ADENOCARCINOMA MIXED SUBTYPE | LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS) | LUNG BASALOID SQUAMOUS CELL CARCINOMA | LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS | LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS | LUNG CLEAR CELL ADENOCARCINOMA | LUNG MICROPAPILLARY ADENOCARCINOMA | LUNG MUCINOUS ADENOCARCINOMA | LUNG PAPILLARY ADENOCARCINOMA | LUNG PAPILLARY SQUAMOUS CELL CARCINOMA | LUNG PAPILLARY SQUAMOUS CELL CARICNOMA | LUNG SMALL CELL SQUAMOUS CELL CARCINOMA | LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA | LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS) | MIXED SEROUS AND ENDOMETRIOID | MUCINOUS (COLLOID) ADENOCARCINOMA | RECTAL ADENOCARCINOMA | RECTAL MUCINOUS ADENOCARCINOMA | SEROUS CYSTADENOCARCINOMA | SEROUS ENDOMETRIAL ADENOCARCINOMA | TREATED PRIMARY GBM | UNTREATED PRIMARY (DE NOVO) GBM
--- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | ---
ALL | 356 | 54 | 350 | 319 | 493 | 10 | 75 | 205 | 7 | 3 | 15 | 2 | 3 | 2 | 13 | 1 | 1 | 1 | 2 | 315 | 18 | 7 | 143 | 13 | 552 | 79 | 1 | 20
AMP PEAK 26(12P12.1) MUTATED | 76 | 13 | 36 | 96 | 113 | 2 | 22 | 81 | 3 | 0 | 6 | 1 | 1 | 0 | 3 | 1 | 0 | 0 | 1 | 156 | 2 | 2 | 32 | 5 | 292 | 29 | 0 | 2
AMP PEAK 26(12P12.1) WILD-TYPE | 280 | 41 | 314 | 223 | 380 | 8 | 53 | 124 | 4 | 3 | 9 | 1 | 2 | 2 | 10 | 0 | 1 | 1 | 1 | 159 | 16 | 5 | 111 | 8 | 260 | 50 | 1 | 18

Figure S152. Get High-res Image Clustering Approach #26: 'Amp Peak 26(12p12.1) mutation analysis' versus Clinical Feature #6: 'HISTOLOGICAL.TYPE'

'Amp Peak 26(12p12.1) mutation analysis' versus 'PATHOLOGY.T'

P value = 6.8e-05 (Fisher's exact test), Q value = 0.09

Table S179. Clustering Approach #26: 'Amp Peak 26(12p12.1) mutation analysis' versus Clinical Feature #7: 'PATHOLOGY.T'

nPatients | T0+T1 | T2 | T3 | T4
--- | --- | --- | --- | ---
ALL | 466 | 632 | 694 | 209
AMP PEAK 26(12P12.1) MUTATED | 112 | 232 | 198 | 64
AMP PEAK 26(12P12.1) WILD-TYPE | 354 | 400 | 496 | 145

Figure S153. Get High-res Image Clustering Approach #26: 'Amp Peak 26(12p12.1) mutation analysis' versus Clinical Feature #7: 'PATHOLOGY.T'

'Amp Peak 26(12p12.1) mutation analysis' versus 'TUMOR.STAGE'

P value = 1.25e-07 (Fisher's exact test), Q value = 0.00018

Table S180. Clustering Approach #26: 'Amp Peak 26(12p12.1) mutation analysis' versus Clinical Feature #10: 'TUMOR.STAGE'

nPatients | I | II | III | IV
--- | --- | --- | --- | ---
ALL | 712 | 498 | 881 | 423
AMP PEAK 26(12P12.1) MUTATED | 210 | 167 | 377 | 134
AMP PEAK 26(12P12.1) WILD-TYPE | 502 | 331 | 504 | 289

Figure S154. Get High-res Image Clustering Approach #26: 'Amp Peak 26(12p12.1) mutation analysis' versus Clinical Feature #10: 'TUMOR.STAGE'

'Amp Peak 26(12p12.1) mutation analysis' versus 'RADIATIONS.RADIATION.REGIMENINDICATION'

P value = 1.77e-10 (Fisher's exact test), Q value = 2.7e-07

Table S181. Clustering Approach #26: 'Amp Peak 26(12p12.1) mutation analysis' versus Clinical Feature #11: 'RADIATIONS.RADIATION.REGIMENINDICATION'

nPatients | NO | YES
--- | --- | ---
ALL | 826 | 3737
AMP PEAK 26(12P12.1) MUTATED | 161 | 1132
AMP PEAK 26(12P12.1) WILD-TYPE | 665 | 2605

Figure S155. Get High-res Image Clustering Approach #26: 'Amp Peak 26(12p12.1) mutation analysis' versus Clinical Feature #11: 'RADIATIONS.RADIATION.REGIMENINDICATION'

Clustering Approach #27: 'Amp Peak 27(12q14.1) mutation analysis'

Table S182. Description of clustering approach #27: 'Amp Peak 27(12q14.1) mutation analysis'

Cluster Labels | AMP PEAK 27(12Q14.1) MUTATED | AMP PEAK 27(12Q14.1) WILD-TYPE
--- | --- | ---
Number of samples | 1071 | 3492

'Amp Peak 27(12q14.1) mutation analysis' versus 'Time to Death'

P value = 9.67e-05 (logrank test), Q value = 0.13

Table S183. Clustering Approach #27: 'Amp Peak 27(12q14.1) mutation analysis' versus Clinical Feature #1: 'Time to Death'

| nPatients | nDeath | Duration Range (Median), Month
--- | --- | --- | ---
ALL | 4296 | 1401 | 0.0 - 224.0 (14.9)
AMP PEAK 27(12Q14.1) MUTATED | 1013 | 373 | 0.1 - 180.2 (14.3)
AMP PEAK 27(12Q14.1) WILD-TYPE | 3283 | 1028 | 0.0 - 224.0 (15.0)

Figure S156. Get High-res Image Clustering Approach #27: 'Amp Peak 27(12q14.1) mutation analysis' versus Clinical Feature #1: 'Time to Death'

'Amp Peak 27(12q14.1) mutation analysis' versus 'AGE'

P value = 5.92e-05 (t-test), Q value = 0.079

Table S184. Clustering Approach #27: 'Amp Peak 27(12q14.1) mutation analysis' versus Clinical Feature #2: 'AGE'

| nPatients | Mean (Std.Dev)
--- | --- | ---
ALL | 4507 | 61.9 (12.6)
AMP PEAK 27(12Q14.1) MUTATED | 1052 | 63.2 (12.5)
AMP PEAK 27(12Q14.1) WILD-TYPE | 3455 | 61.4 (12.6)

Figure S157. Get High-res Image Clustering Approach #27: 'Amp Peak 27(12q14.1) mutation analysis' versus Clinical Feature #2: 'AGE'

'Amp Peak 27(12q14.1) mutation analysis' versus 'PRIMARY.SITE.OF.DISEASE'

P value = 8.12e-23 (Chi-square test), Q value = 1.3e-19

Table S185. Clustering Approach #27: 'Amp Peak 27(12q14.1) mutation analysis' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'

nPatients | BLADDER | BRAIN | BREAST | COLON | ENDOMETRIAL | HEAD/NECK | KIDNEY | LUNG | OMENTUM | OVARY | PERITONEUM (OVARY) | RECTUM
--- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | ---
ALL | 125 | 544 | 846 | 412 | 447 | 319 | 493 | 662 | 2 | 548 | 2 | 159
AMP PEAK 27(12Q14.1) MUTATED | 28 | 125 | 187 | 85 | 47 | 56 | 113 | 220 | 1 | 184 | 2 | 23
AMP PEAK 27(12Q14.1) WILD-TYPE | 97 | 419 | 659 | 327 | 400 | 263 | 380 | 442 | 1 | 364 | 0 | 136

Figure S158. Get High-res Image Clustering Approach #27: 'Amp Peak 27(12q14.1) mutation analysis' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'

'Amp Peak 27(12q14.1) mutation analysis' versus 'HISTOLOGICAL.TYPE'

P value = 4.4e-17 (Chi-square test), Q value = 6.9e-14

Table S186. Clustering Approach #27: 'Amp Peak 27(12q14.1) mutation analysis' versus Clinical Feature #6: 'HISTOLOGICAL.TYPE'

nPatients | COLON ADENOCARCINOMA | COLON MUCINOUS ADENOCARCINOMA | ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA | HEAD & NECK SQUAMOUS CELL CARCINOMA | KIDNEY CLEAR CELL RENAL CARCINOMA | LUNG ACINAR ADENOCARCINOMA | LUNG ADENOCARCINOMA MIXED SUBTYPE | LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS) | LUNG BASALOID SQUAMOUS CELL CARCINOMA | LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS | LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS | LUNG CLEAR CELL ADENOCARCINOMA | LUNG MICROPAPILLARY ADENOCARCINOMA | LUNG MUCINOUS ADENOCARCINOMA | LUNG PAPILLARY ADENOCARCINOMA | LUNG PAPILLARY SQUAMOUS CELL CARCINOMA | LUNG PAPILLARY SQUAMOUS CELL CARICNOMA | LUNG SMALL CELL SQUAMOUS CELL CARCINOMA | LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA | LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS) | MIXED SEROUS AND ENDOMETRIOID | MUCINOUS (COLLOID) ADENOCARCINOMA | RECTAL ADENOCARCINOMA | RECTAL MUCINOUS ADENOCARCINOMA | SEROUS CYSTADENOCARCINOMA | SEROUS ENDOMETRIAL ADENOCARCINOMA | TREATED PRIMARY GBM | UNTREATED PRIMARY (DE NOVO) GBM
--- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | ---
ALL | 356 | 54 | 350 | 319 | 493 | 10 | 75 | 205 | 7 | 3 | 15 | 2 | 3 | 2 | 13 | 1 | 1 | 1 | 2 | 315 | 18 | 7 | 143 | 13 | 552 | 79 | 1 | 20
AMP PEAK 27(12Q14.1) MUTATED | 72 | 12 | 30 | 56 | 113 | 3 | 23 | 71 | 2 | 0 | 4 | 1 | 0 | 0 | 3 | 1 | 0 | 0 | 1 | 109 | 2 | 2 | 21 | 2 | 187 | 15 | 0 | 3
AMP PEAK 27(12Q14.1) WILD-TYPE | 284 | 42 | 320 | 263 | 380 | 7 | 52 | 134 | 5 | 3 | 11 | 1 | 3 | 2 | 10 | 0 | 1 | 1 | 1 | 206 | 16 | 5 | 122 | 11 | 365 | 64 | 1 | 17

Figure S159. Get High-res Image Clustering Approach #27: 'Amp Peak 27(12q14.1) mutation analysis' versus Clinical Feature #6: 'HISTOLOGICAL.TYPE'

Clustering Approach #28: 'Amp Peak 28(12q15) mutation analysis'

Table S187. Description of clustering approach #28: 'Amp Peak 28(12q15) mutation analysis'

Cluster Labels | AMP PEAK 28(12Q15) MUTATED | AMP PEAK 28(12Q15) WILD-TYPE
--- | --- | ---
Number of samples | 1081 | 3482

'Amp Peak 28(12q15) mutation analysis' versus 'AGE'

P value = 3.38e-05 (t-test), Q value = 0.046

Table S188. Clustering Approach #28: 'Amp Peak 28(12q15) mutation analysis' versus Clinical Feature #2: 'AGE'

| nPatients | Mean (Std.Dev)
--- | --- | ---
ALL | 4507 | 61.9 (12.6)
AMP PEAK 28(12Q15) MUTATED | 1061 | 63.2 (12.3)
AMP PEAK 28(12Q15) WILD-TYPE | 3446 | 61.4 (12.7)

Figure S160. Get High-res Image Clustering Approach #28: 'Amp Peak 28(12q15) mutation analysis' versus Clinical Feature #2: 'AGE'

'Amp Peak 28(12q15) mutation analysis' versus 'PRIMARY.SITE.OF.DISEASE'

P value = 5.44e-32 (Chi-square test), Q value = 8.9e-29

Table S189. Clustering Approach #28: 'Amp Peak 28(12q15) mutation analysis' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'

nPatients | BLADDER | BRAIN | BREAST | COLON | ENDOMETRIAL | HEAD/NECK | KIDNEY | LUNG | OMENTUM | OVARY | PERITONEUM (OVARY) | RECTUM
--- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | ---
ALL | 125 | 544 | 846 | 412 | 447 | 319 | 493 | 662 | 2 | 548 | 2 | 159
AMP PEAK 28(12Q15) MUTATED | 39 | 87 | 215 | 81 | 45 | 62 | 114 | 231 | 2 | 184 | 2 | 19
AMP PEAK 28(12Q15) WILD-TYPE | 86 | 457 | 631 | 331 | 402 | 257 | 379 | 431 | 0 | 364 | 0 | 140

Figure S161. Get High-res Image Clustering Approach #28: 'Amp Peak 28(12q15) mutation analysis' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'

'Amp Peak 28(12q15) mutation analysis' versus 'HISTOLOGICAL.TYPE'

P value = 5e-20 (Chi-square test), Q value = 7.9e-17

Table S190. Clustering Approach #28: 'Amp Peak 28(12q15) mutation analysis' versus Clinical Feature #6: 'HISTOLOGICAL.TYPE'

nPatients | COLON ADENOCARCINOMA | COLON MUCINOUS ADENOCARCINOMA | ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA | HEAD & NECK SQUAMOUS CELL CARCINOMA | KIDNEY CLEAR CELL RENAL CARCINOMA | LUNG ACINAR ADENOCARCINOMA | LUNG ADENOCARCINOMA MIXED SUBTYPE | LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS) | LUNG BASALOID SQUAMOUS CELL CARCINOMA | LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS | LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS | LUNG CLEAR CELL ADENOCARCINOMA | LUNG MICROPAPILLARY ADENOCARCINOMA | LUNG MUCINOUS ADENOCARCINOMA | LUNG PAPILLARY ADENOCARCINOMA | LUNG PAPILLARY SQUAMOUS CELL CARCINOMA | LUNG PAPILLARY SQUAMOUS CELL CARICNOMA | LUNG SMALL CELL SQUAMOUS CELL CARCINOMA | LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA | LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS) | MIXED SEROUS AND ENDOMETRIOID | MUCINOUS (COLLOID) ADENOCARCINOMA | RECTAL ADENOCARCINOMA | RECTAL MUCINOUS ADENOCARCINOMA | SEROUS CYSTADENOCARCINOMA | SEROUS ENDOMETRIAL ADENOCARCINOMA | TREATED PRIMARY GBM | UNTREATED PRIMARY (DE NOVO) GBM
--- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | ---
ALL | 356 | 54 | 350 | 319 | 493 | 10 | 75 | 205 | 7 | 3 | 15 | 2 | 3 | 2 | 13 | 1 | 1 | 1 | 2 | 315 | 18 | 7 | 143 | 13 | 552 | 79 | 1 | 20
AMP PEAK 28(12Q15) MUTATED | 68 | 12 | 31 | 62 | 114 | 3 | 26 | 70 | 2 | 0 | 3 | 1 | 0 | 0 | 4 | 1 | 0 | 0 | 1 | 118 | 2 | 2 | 17 | 2 | 188 | 12 | 0 | 4
AMP PEAK 28(12Q15) WILD-TYPE | 288 | 42 | 319 | 257 | 379 | 7 | 49 | 135 | 5 | 3 | 12 | 1 | 3 | 2 | 9 | 0 | 1 | 1 | 1 | 197 | 16 | 5 | 126 | 11 | 364 | 67 | 1 | 16

Figure S162. Get High-res Image Clustering Approach #28: 'Amp Peak 28(12q15) mutation analysis' versus Clinical Feature #6: 'HISTOLOGICAL.TYPE'

'Amp Peak 28(12q15) mutation analysis' versus 'RADIATIONS.RADIATION.REGIMENINDICATION'

P value = 1.95e-06 (Fisher's exact test), Q value = 0.0028

Table S191. Clustering Approach #28: 'Amp Peak 28(12q15) mutation analysis' versus Clinical Feature #11: 'RADIATIONS.RADIATION.REGIMENINDICATION'

nPatients | NO | YES
--- | --- | ---
ALL | 826 | 3737
AMP PEAK 28(12Q15) MUTATED | 144 | 937
AMP PEAK 28(12Q15) WILD-TYPE | 682 | 2800

Figure S163. Get High-res Image Clustering Approach #28: 'Amp Peak 28(12q15) mutation analysis' versus Clinical Feature #11: 'RADIATIONS.RADIATION.REGIMENINDICATION'

Clustering Approach #29: 'Amp Peak 29(13q34) mutation analysis'

Table S192. Description of clustering approach #29: 'Amp Peak 29(13q34) mutation analysis'

Cluster Labels | AMP PEAK 29(13Q34) MUTATED | AMP PEAK 29(13Q34) WILD-TYPE
--- | --- | ---
Number of samples | 944 | 3619

'Amp Peak 29(13q34) mutation analysis' versus 'AGE'

P value = 4.91e-06 (t-test), Q value = 0.0069

Table S193. Clustering Approach #29: 'Amp Peak 29(13q34) mutation analysis' versus Clinical Feature #2: 'AGE'

| nPatients | Mean (Std.Dev)
--- | --- | ---
ALL | 4507 | 61.9 (12.6)
AMP PEAK 29(13Q34) MUTATED | 939 | 63.5 (12.4)
AMP PEAK 29(13Q34) WILD-TYPE | 3568 | 61.4 (12.7)

Figure S164. Get High-res Image Clustering Approach #29: 'Amp Peak 29(13q34) mutation analysis' versus Clinical Feature #2: 'AGE'

'Amp Peak 29(13q34) mutation analysis' versus 'PRIMARY.SITE.OF.DISEASE'

P value = 3.07e-173 (Chi-square test), Q value = 5.5e-170

Table S194. Clustering Approach #29: 'Amp Peak 29(13q34) mutation analysis' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'

nPatients | BLADDER | BRAIN | BREAST | COLON | ENDOMETRIAL | HEAD/NECK | KIDNEY | LUNG | OMENTUM | OVARY | PERITONEUM (OVARY) | RECTUM
--- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | ---
ALL | 125 | 544 | 846 | 412 | 447 | 319 | 493 | 662 | 2 | 548 | 2 | 159
AMP PEAK 29(13Q34) MUTATED | 48 | 29 | 142 | 242 | 37 | 58 | 27 | 110 | 1 | 135 | 0 | 112
AMP PEAK 29(13Q34) WILD-TYPE | 77 | 515 | 704 | 170 | 410 | 261 | 466 | 552 | 1 | 413 | 2 | 47

Figure S165. Get High-res Image Clustering Approach #29: 'Amp Peak 29(13q34) mutation analysis' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'

'Amp Peak 29(13q34) mutation analysis' versus 'HISTOLOGICAL.TYPE'

P value = 8.09e-136 (Chi-square test), Q value = 1.4e-132

Table S195. Clustering Approach #29: 'Amp Peak 29(13q34) mutation analysis' versus Clinical Feature #6: 'HISTOLOGICAL.TYPE'

nPatients | COLON ADENOCARCINOMA | COLON MUCINOUS ADENOCARCINOMA | ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA | HEAD & NECK SQUAMOUS CELL CARCINOMA | KIDNEY CLEAR CELL RENAL CARCINOMA | LUNG ACINAR ADENOCARCINOMA | LUNG ADENOCARCINOMA MIXED SUBTYPE | LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS) | LUNG BASALOID SQUAMOUS CELL CARCINOMA | LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS | LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS | LUNG CLEAR CELL ADENOCARCINOMA | LUNG MICROPAPILLARY ADENOCARCINOMA | LUNG MUCINOUS ADENOCARCINOMA | LUNG PAPILLARY ADENOCARCINOMA | LUNG PAPILLARY SQUAMOUS CELL CARCINOMA | LUNG PAPILLARY SQUAMOUS CELL CARICNOMA | LUNG SMALL CELL SQUAMOUS CELL CARCINOMA | LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA | LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS) | MIXED SEROUS AND ENDOMETRIOID | MUCINOUS (COLLOID) ADENOCARCINOMA | RECTAL ADENOCARCINOMA | RECTAL MUCINOUS ADENOCARCINOMA | SEROUS CYSTADENOCARCINOMA | SEROUS ENDOMETRIAL ADENOCARCINOMA | TREATED PRIMARY GBM | UNTREATED PRIMARY (DE NOVO) GBM
--- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | ---
ALL | 356 | 54 | 350 | 319 | 493 | 10 | 75 | 205 | 7 | 3 | 15 | 2 | 3 | 2 | 13 | 1 | 1 | 1 | 2 | 315 | 18 | 7 | 143 | 13 | 552 | 79 | 1 | 20
AMP PEAK 29(13Q34) MUTATED | 224 | 18 | 13 | 58 | 27 | 2 | 12 | 33 | 3 | 0 | 2 | 1 | 0 | 0 | 3 | 1 | 0 | 1 | 0 | 51 | 2 | 1 | 107 | 4 | 136 | 22 | 0 | 1
AMP PEAK 29(13Q34) WILD-TYPE | 132 | 36 | 337 | 261 | 466 | 8 | 63 | 172 | 4 | 3 | 13 | 1 | 3 | 2 | 10 | 0 | 1 | 0 | 2 | 264 | 16 | 6 | 36 | 9 | 416 | 57 | 1 | 19

Figure S166. Get High-res Image Clustering Approach #29: 'Amp Peak 29(13q34) mutation analysis' versus Clinical Feature #6: 'HISTOLOGICAL.TYPE'

'Amp Peak 29(13q34) mutation analysis' versus 'PATHOLOGY.T'

P value = 5.86e-26 (Fisher's exact test), Q value = 9.4e-23

Table S196. Clustering Approach #29: 'Amp Peak 29(13q34) mutation analysis' versus Clinical Feature #7: 'PATHOLOGY.T'

nPatients | T0+T1 | T2 | T3 | T4
--- | --- | --- | --- | ---
ALL | 466 | 632 | 694 | 209
AMP PEAK 29(13Q34) MUTATED | 58 | 147 | 280 | 57
AMP PEAK 29(13Q34) WILD-TYPE | 408 | 485 | 414 | 152

Figure S167. Get High-res Image Clustering Approach #29: 'Amp Peak 29(13q34) mutation analysis' versus Clinical Feature #7: 'PATHOLOGY.T'

'Amp Peak 29(13q34) mutation analysis' versus 'PATHOLOGY.N'

P value = 4.2e-08 (Fisher's exact test), Q value = 6.1e-05

Table S197. Clustering Approach #29: 'Amp Peak 29(13q34) mutation analysis' versus Clinical Feature #8: 'PATHOLOGY.N'

nPatients | N0 | N1 | N2 | N3
--- | --- | --- | --- | ---
ALL | 1067 | 353 | 282 | 11
AMP PEAK 29(13Q34) MUTATED | 266 | 137 | 107 | 1
AMP PEAK 29(13Q34) WILD-TYPE | 801 | 216 | 175 | 10

Figure S168. Get High-res Image Clustering Approach #29: 'Amp Peak 29(13q34) mutation analysis' versus Clinical Feature #8: 'PATHOLOGY.N'

'Amp Peak 29(13q34) mutation analysis' versus 'PATHOLOGICSPREAD(M)'

P value = 3.51e-05 (Chi-square test), Q value = 0.047

Table S198. Clustering Approach #29: 'Amp Peak 29(13q34) mutation analysis' versus Clinical Feature #9: 'PATHOLOGICSPREAD(M)'

nPatients | M0 | M1 | M1A | M1B | MX
--- | --- | --- | --- | --- | ---
ALL | 1424 | 168 | 9 | 3 | 165
AMP PEAK 29(13Q34) MUTATED | 374 | 62 | 8 | 1 | 50
AMP PEAK 29(13Q34) WILD-TYPE | 1050 | 106 | 1 | 2 | 115

Figure S169. Get High-res Image Clustering Approach #29: 'Amp Peak 29(13q34) mutation analysis' versus Clinical Feature #9: 'PATHOLOGICSPREAD(M)'

'Amp Peak 29(13q34) mutation analysis' versus 'TUMOR.STAGE'

P value = 2.7e-10 (Fisher's exact test), Q value = 4.1e-07

Table S199. Clustering Approach #29: 'Amp Peak 29(13q34) mutation analysis' versus Clinical Feature #10: 'TUMOR.STAGE'

nPatients | I | II | III | IV
--- | --- | --- | --- | ---
ALL | 712 | 498 | 881 | 423
AMP PEAK 29(13Q34) MUTATED | 124 | 160 | 268 | 108
AMP PEAK 29(13Q34) WILD-TYPE | 588 | 338 | 613 | 315

Figure S170. Get High-res Image Clustering Approach #29: 'Amp Peak 29(13q34) mutation analysis' versus Clinical Feature #10: 'TUMOR.STAGE'

'Amp Peak 29(13q34) mutation analysis' versus 'RADIATIONS.RADIATION.REGIMENINDICATION'

P value = 3.06e-15 (Fisher's exact test), Q value = 4.8e-12

Table S200. Clustering Approach #29: 'Amp Peak 29(13q34) mutation analysis' versus Clinical Feature #11: 'RADIATIONS.RADIATION.REGIMENINDICATION'

nPatients | NO | YES
--- | --- | ---
ALL | 826 | 3737
AMP PEAK 29(13Q34) MUTATED | 92 | 852
AMP PEAK 29(13Q34) WILD-TYPE | 734 | 2885

Figure S171. Get High-res Image Clustering Approach #29: 'Amp Peak 29(13q34) mutation analysis' versus Clinical Feature #11: 'RADIATIONS.RADIATION.REGIMENINDICATION'

'Amp Peak 29(13q34) mutation analysis' versus 'TOBACCOSMOKINGHISTORYINDICATOR'

P value = 4.45e-07 (Chi-square test), Q value = 0.00064

Table S201. Clustering Approach #29: 'Amp Peak 29(13q34) mutation analysis' versus Clinical Feature #14: 'TOBACCOSMOKINGHISTORYINDICATOR'

nPatients | 1 | 2 | 3 | 4 | 5 | CURRENT REFORMED SMOKER FOR < OR = 15 YEARS | CURRENT REFORMED SMOKER FOR > 15 YEARS | CURRENT SMOKER | LIFELONG NON-SMOKER
--- | --- | --- | --- | --- | --- | --- | --- | --- | ---
ALL | 28 | 23 | 37 | 29 | 2 | 355 | 217 | 250 | 128
AMP PEAK 29(13Q34) MUTATED | 7 | 11 | 13 | 13 | 2 | 54 | 34 | 48 | 28
AMP PEAK 29(13Q34) WILD-TYPE | 21 | 12 | 24 | 16 | 0 | 301 | 183 | 202 | 100

Figure S172. Get High-res Image Clustering Approach #29: 'Amp Peak 29(13q34) mutation analysis' versus Clinical Feature #14: 'TOBACCOSMOKINGHISTORYINDICATOR'

Clustering Approach #30: 'Amp Peak 30(14q13.3) mutation analysis'

Table S202. Description of clustering approach #30: 'Amp Peak 30(14q13.3) mutation analysis'

Cluster Labels | AMP PEAK 30(14Q13.3) MUTATED | AMP PEAK 30(14Q13.3) WILD-TYPE
--- | --- | ---
Number of samples | 738 | 3825

'Amp Peak 30(14q13.3) mutation analysis' versus 'PRIMARY.SITE.OF.DISEASE'

P value = 5.23e-90 (Chi-square test), Q value = 9e-87

Table S203. Clustering Approach #30: 'Amp Peak 30(14q13.3) mutation analysis' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'

nPatients | BLADDER | BRAIN | BREAST | COLON | ENDOMETRIAL | HEAD/NECK | KIDNEY | LUNG | OMENTUM | OVARY | PERITONEUM (OVARY) | RECTUM
--- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | ---
ALL | 125 | 544 | 846 | 412 | 447 | 319 | 493 | 662 | 2 | 548 | 2 | 159
AMP PEAK 30(14Q13.3) MUTATED | 24 | 20 | 165 | 38 | 29 | 91 | 14 | 249 | 1 | 95 | 0 | 12
AMP PEAK 30(14Q13.3) WILD-TYPE | 101 | 524 | 681 | 374 | 418 | 228 | 479 | 413 | 1 | 453 | 2 | 147

Figure S173. Get High-res Image Clustering Approach #30: 'Amp Peak 30(14q13.3) mutation analysis' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'

'Amp Peak 30(14q13.3) mutation analysis' versus 'HISTOLOGICAL.TYPE'

P value = 1.47e-72 (Chi-square test), Q value = 2.5e-69

Table S204. Clustering Approach #30: 'Amp Peak 30(14q13.3) mutation analysis' versus Clinical Feature #6: 'HISTOLOGICAL.TYPE'

nPatients | COLON ADENOCARCINOMA | COLON MUCINOUS ADENOCARCINOMA | ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA | HEAD & NECK SQUAMOUS CELL CARCINOMA | KIDNEY CLEAR CELL RENAL CARCINOMA | LUNG ACINAR ADENOCARCINOMA | LUNG ADENOCARCINOMA MIXED SUBTYPE | LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS) | LUNG BASALOID SQUAMOUS CELL CARCINOMA | LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS | LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS | LUNG CLEAR CELL ADENOCARCINOMA | LUNG MICROPAPILLARY ADENOCARCINOMA | LUNG MUCINOUS ADENOCARCINOMA | LUNG PAPILLARY ADENOCARCINOMA | LUNG PAPILLARY SQUAMOUS CELL CARCINOMA | LUNG PAPILLARY SQUAMOUS CELL CARICNOMA | LUNG SMALL CELL SQUAMOUS CELL CARCINOMA | LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA | LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS) | MIXED SEROUS AND ENDOMETRIOID | MUCINOUS (COLLOID) ADENOCARCINOMA | RECTAL ADENOCARCINOMA | RECTAL MUCINOUS ADENOCARCINOMA | SEROUS CYSTADENOCARCINOMA | SEROUS ENDOMETRIAL ADENOCARCINOMA | TREATED PRIMARY GBM | UNTREATED PRIMARY (DE NOVO) GBM
--- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | ---
ALL | 356 | 54 | 350 | 319 | 493 | 10 | 75 | 205 | 7 | 3 | 15 | 2 | 3 | 2 | 13 | 1 | 1 | 1 | 2 | 315 | 18 | 7 | 143 | 13 | 552 | 79 | 1 | 20
AMP PEAK 30(14Q13.3) MUTATED | 28 | 10 | 14 | 91 | 14 | 6 | 26 | 100 | 1 | 1 | 5 | 1 | 2 | 0 | 5 | 1 | 0 | 0 | 1 | 99 | 1 | 1 | 12 | 0 | 96 | 14 | 1 | 0
AMP PEAK 30(14Q13.3) WILD-TYPE | 328 | 44 | 336 | 228 | 479 | 4 | 49 | 105 | 6 | 2 | 10 | 1 | 1 | 2 | 8 | 0 | 1 | 1 | 1 | 216 | 17 | 6 | 131 | 13 | 456 | 65 | 0 | 20

Figure S174. Get High-res Image Clustering Approach #30: 'Amp Peak 30(14q13.3) mutation analysis' versus Clinical Feature #6: 'HISTOLOGICAL.TYPE'

'Amp Peak 30(14q13.3) mutation analysis' versus 'PATHOLOGY.T'

P value = 2.55e-13 (Fisher's exact test), Q value = 3.9e-10

Table S205. Clustering Approach #30: 'Amp Peak 30(14q13.3) mutation analysis' versus Clinical Feature #7: 'PATHOLOGY.T'

nPatients | T0+T1 | T2 | T3 | T4
--- | --- | --- | --- | ---
ALL | 466 | 632 | 694 | 209
AMP PEAK 30(14Q13.3) MUTATED | 78 | 177 | 84 | 55
AMP PEAK 30(14Q13.3) WILD-TYPE | 388 | 455 | 610 | 154

Figure S175. Get High-res Image Clustering Approach #30: 'Amp Peak 30(14q13.3) mutation analysis' versus Clinical Feature #7: 'PATHOLOGY.T'

'Amp Peak 30(14q13.3) mutation analysis' versus 'PATHOLOGICSPREAD(M)'

P value = 5.93e-10 (Chi-square test), Q value = 8.9e-07

Table S206. Clustering Approach #30: 'Amp Peak 30(14q13.3) mutation analysis' versus Clinical Feature #9: 'PATHOLOGICSPREAD(M)'

nPatients | M0 | M1 | M1A | M1B | MX
--- | --- | --- | --- | --- | ---
ALL | 1424 | 168 | 9 | 3 | 165
AMP PEAK 30(14Q13.3) MUTATED | 244 | 14 | 4 | 0 | 58
AMP PEAK 30(14Q13.3) WILD-TYPE | 1180 | 154 | 5 | 3 | 107

Figure S176. Get High-res Image Clustering Approach #30: 'Amp Peak 30(14q13.3) mutation analysis' versus Clinical Feature #9: 'PATHOLOGICSPREAD(M)'

'Amp Peak 30(14q13.3) mutation analysis' versus 'RADIATIONS.RADIATION.REGIMENINDICATION'

P value = 3.12e-06 (Fisher's exact test), Q value = 0.0044

Table S207. Clustering Approach #30: 'Amp Peak 30(14q13.3) mutation analysis' versus Clinical Feature #11: 'RADIATIONS.RADIATION.REGIMENINDICATION'

nPatients | NO | YES
--- | --- | ---
ALL | 826 | 3737
AMP PEAK 30(14Q13.3) MUTATED | 90 | 648
AMP PEAK 30(14Q13.3) WILD-TYPE | 736 | 3089

Figure S177. Get High-res Image Clustering Approach #30: 'Amp Peak 30(14q13.3) mutation analysis' versus Clinical Feature #11: 'RADIATIONS.RADIATION.REGIMENINDICATION'

Clustering Approach #31: 'Amp Peak 31(15q26.3) mutation analysis'

Table S208. Description of clustering approach #31: 'Amp Peak 31(15q26.3) mutation analysis'

Cluster Labels | AMP PEAK 31(15Q26.3) MUTATED | AMP PEAK 31(15Q26.3) WILD-TYPE
--- | --- | ---
Number of samples | 683 | 3880

'Amp Peak 31(15q26.3) mutation analysis' versus 'PRIMARY.SITE.OF.DISEASE'

P value = 7e-52 (Chi-square test), Q value = 1.2e-48

Table S209. Clustering Approach #31: 'Amp Peak 31(15q26.3) mutation analysis' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'

nPatients | BLADDER | BRAIN | BREAST | COLON | ENDOMETRIAL | HEAD/NECK | KIDNEY | LUNG | OMENTUM | OVARY | PERITONEUM (OVARY) | RECTUM
--- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | ---
ALL | 125 | 544 | 846 | 412 | 447 | 319 | 493 | 662 | 2 | 548 | 2 | 159
AMP PEAK 31(15Q26.3) MUTATED | 19 | 31 | 156 | 26 | 29 | 69 | 24 | 162 | 1 | 153 | 0 | 13
AMP PEAK 31(15Q26.3) WILD-TYPE | 106 | 513 | 690 | 386 | 418 | 250 | 469 | 500 | 1 | 395 | 2 | 146

Figure S178. Get High-res Image Clustering Approach #31: 'Amp Peak 31(15q26.3) mutation analysis' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'

'Amp Peak 31(15q26.3) mutation analysis' versus 'HISTOLOGICAL.TYPE'

P value = 2.23e-47 (Chi-square test), Q value = 3.7e-44

Table S210. Clustering Approach #31: 'Amp Peak 31(15q26.3) mutation analysis' versus Clinical Feature #6: 'HISTOLOGICAL.TYPE'

nPatients | COLON ADENOCARCINOMA | COLON MUCINOUS ADENOCARCINOMA | ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA | HEAD & NECK SQUAMOUS CELL CARCINOMA | KIDNEY CLEAR CELL RENAL CARCINOMA | LUNG ACINAR ADENOCARCINOMA | LUNG ADENOCARCINOMA MIXED SUBTYPE | LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS) | LUNG BASALOID SQUAMOUS CELL CARCINOMA | LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS | LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS | LUNG CLEAR CELL ADENOCARCINOMA | LUNG MICROPAPILLARY ADENOCARCINOMA | LUNG MUCINOUS ADENOCARCINOMA | LUNG PAPILLARY ADENOCARCINOMA | LUNG PAPILLARY SQUAMOUS CELL CARCINOMA | LUNG PAPILLARY SQUAMOUS CELL CARICNOMA | LUNG SMALL CELL SQUAMOUS CELL CARCINOMA | LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA | LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS) | MIXED SEROUS AND ENDOMETRIOID | MUCINOUS (COLLOID) ADENOCARCINOMA | RECTAL ADENOCARCINOMA | RECTAL MUCINOUS ADENOCARCINOMA | SEROUS CYSTADENOCARCINOMA | SEROUS ENDOMETRIAL ADENOCARCINOMA | TREATED PRIMARY GBM | UNTREATED PRIMARY (DE NOVO) GBM
--- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | ---
ALL | 356 | 54 | 350 | 319 | 493 | 10 | 75 | 205 | 7 | 3 | 15 | 2 | 3 | 2 | 13 | 1 | 1 | 1 | 2 | 315 | 18 | 7 | 143 | 13 | 552 | 79 | 1 | 20
AMP PEAK 31(15Q26.3) MUTATED | 22 | 4 | 16 | 69 | 24 | 1 | 15 | 23 | 4 | 1 | 1 | 0 | 0 | 0 | 4 | 0 | 0 | 0 | 1 | 109 | 0 | 3 | 11 | 2 | 154 | 13 | 0 | 1
AMP PEAK 31(15Q26.3) WILD-TYPE | 334 | 50 | 334 | 250 | 469 | 9 | 60 | 182 | 3 | 2 | 14 | 2 | 3 | 2 | 9 | 1 | 1 | 1 | 1 | 206 | 18 | 4 | 132 | 11 | 398 | 66 | 1 | 19

Figure S179. Get High-res Image Clustering Approach #31: 'Amp Peak 31(15q26.3) mutation analysis' versus Clinical Feature #6: 'HISTOLOGICAL.TYPE'

'Amp Peak 31(15q26.3) mutation analysis' versus 'PATHOLOGY.T'

P value = 3.98e-10 (Fisher's exact test), Q value = 6e-07

Table S211. Clustering Approach #31: 'Amp Peak 31(15q26.3) mutation analysis' versus Clinical Feature #7: 'PATHOLOGY.T'

nPatients | T0+T1 | T2 | T3 | T4
--- | --- | --- | --- | ---
ALL | 466 | 632 | 694 | 209
AMP PEAK 31(15Q26.3) MUTATED | 53 | 128 | 60 | 43
AMP PEAK 31(15Q26.3) WILD-TYPE | 413 | 504 | 634 | 166

Figure S180. Get High-res Image Clustering Approach #31: 'Amp Peak 31(15q26.3) mutation analysis' versus Clinical Feature #7: 'PATHOLOGY.T'

'Amp Peak 31(15q26.3) mutation analysis' versus 'RADIATIONS.RADIATION.REGIMENINDICATION'

P value = 8.52e-08 (Fisher's exact test), Q value = 0.00012

Table S212. Clustering Approach #31: 'Amp Peak 31(15q26.3) mutation analysis' versus Clinical Feature #11: 'RADIATIONS.RADIATION.REGIMENINDICATION'

nPatients | NO | YES
--- | --- | ---
ALL | 826 | 3737
AMP PEAK 31(15Q26.3) MUTATED | 76 | 607
AMP PEAK 31(15Q26.3) WILD-TYPE | 750 | 3130

Figure S181. Get High-res Image Clustering Approach #31: 'Amp Peak 31(15q26.3) mutation analysis' versus Clinical Feature #11: 'RADIATIONS.RADIATION.REGIMENINDICATION'

Clustering Approach #32: 'Amp Peak 32(17q12) mutation analysis'

Table S213. Description of clustering approach #32: 'Amp Peak 32(17q12) mutation analysis'

Cluster Labels | AMP PEAK 32(17Q12) MUTATED | AMP PEAK 32(17Q12) WILD-TYPE
--- | --- | ---
Number of samples | 971 | 3592

'Amp Peak 32(17q12) mutation analysis' versus 'AGE'

P value = 4.89e-05 (t-test), Q value = 0.065

Table S214. Clustering Approach #32: 'Amp Peak 32(17q12) mutation analysis' versus Clinical Feature #2: 'AGE'

| nPatients | Mean (Std.Dev)
--- | --- | ---
ALL | 4507 | 61.9 (12.6)
AMP PEAK 32(17Q12) MUTATED | 957 | 63.3 (12.2)
AMP PEAK 32(17Q12) WILD-TYPE | 3550 | 61.5 (12.7)

Figure S182. Get High-res Image Clustering Approach #32: 'Amp Peak 32(17q12) mutation analysis' versus Clinical Feature #2: 'AGE'

'Amp Peak 32(17q12) mutation analysis' versus 'PRIMARY.SITE.OF.DISEASE'

P value = 5.37e-88 (Chi-square test), Q value = 9.2e-85

Table S215. Clustering Approach #32: 'Amp Peak 32(17q12) mutation analysis' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'

nPatients | BLADDER | BRAIN | BREAST | COLON | ENDOMETRIAL | HEAD/NECK | KIDNEY | LUNG | OMENTUM | OVARY | PERITONEUM (OVARY) | RECTUM
--- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | ---
ALL | 125 | 544 | 846 | 412 | 447 | 319 | 493 | 662 | 2 | 548 | 2 | 159
AMP PEAK 32(17Q12) MUTATED | 52 | 48 | 277 | 101 | 53 | 55 | 25 | 265 | 0 | 52 | 0 | 43
AMP PEAK 32(17Q12) WILD-TYPE | 73 | 496 | 569 | 311 | 394 | 264 | 468 | 397 | 2 | 496 | 2 | 116

Figure S183. Get High-res Image Clustering Approach #32: 'Amp Peak 32(17q12) mutation analysis' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'

'Amp Peak 32(17q12) mutation analysis' versus 'HISTOLOGICAL.TYPE'

P value = 4.32e-70 (Chi-square test), Q value = 7.3e-67

Table S216. Clustering Approach #32: 'Amp Peak 32(17q12) mutation analysis' versus Clinical Feature #6: 'HISTOLOGICAL.TYPE'

nPatients | COLON ADENOCARCINOMA | COLON MUCINOUS ADENOCARCINOMA | ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA | HEAD & NECK SQUAMOUS CELL CARCINOMA | KIDNEY CLEAR CELL RENAL CARCINOMA | LUNG ACINAR ADENOCARCINOMA | LUNG ADENOCARCINOMA MIXED SUBTYPE | LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS) | LUNG BASALOID SQUAMOUS CELL CARCINOMA | LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS | LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS | LUNG CLEAR CELL ADENOCARCINOMA | LUNG MICROPAPILLARY ADENOCARCINOMA | LUNG MUCINOUS ADENOCARCINOMA | LUNG PAPILLARY ADENOCARCINOMA | LUNG PAPILLARY SQUAMOUS CELL CARCINOMA | LUNG PAPILLARY SQUAMOUS CELL CARICNOMA | LUNG SMALL CELL SQUAMOUS CELL CARCINOMA | LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA | LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS) | MIXED SEROUS AND ENDOMETRIOID | MUCINOUS (COLLOID) ADENOCARCINOMA | RECTAL ADENOCARCINOMA | RECTAL MUCINOUS ADENOCARCINOMA | SEROUS CYSTADENOCARCINOMA | SEROUS ENDOMETRIAL ADENOCARCINOMA | TREATED PRIMARY GBM | UNTREATED PRIMARY (DE NOVO) GBM
--- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | ---
ALL | 356 | 54 | 350 | 319 | 493 | 10 | 75 | 205 | 7 | 3 | 15 | 2 | 3 | 2 | 13 | 1 | 1 | 1 | 2 | 315 | 18 | 7 | 143 | 13 | 552 | 79 | 1 | 20
AMP PEAK 32(17Q12) MUTATED | 90 | 10 | 16 | 55 | 25 | 4 | 38 | 95 | 2 | 0 | 5 | 2 | 1 | 1 | 5 | 1 | 0 | 0 | 1 | 109 | 3 | 1 | 41 | 2 | 52 | 34 | 0 | 1
AMP PEAK 32(17Q12) WILD-TYPE | 266 | 44 | 334 | 264 | 468 | 6 | 37 | 110 | 5 | 3 | 10 | 0 | 2 | 1 | 8 | 0 | 1 | 1 | 1 | 206 | 15 | 6 | 102 | 11 | 500 | 45 | 1 | 19

Figure S184. Get High-res Image Clustering Approach #32: 'Amp Peak 32(17q12) mutation analysis' versus Clinical Feature #6: 'HISTOLOGICAL.TYPE'

'Amp Peak 32(17q12) mutation analysis' versus 'PATHOLOGY.T'

P value = 4.25e-07 (Fisher's exact test), Q value = 0.00062

Table S217. Clustering Approach #32: 'Amp Peak 32(17q12) mutation analysis' versus Clinical Feature #7: 'PATHOLOGY.T'

nPatients | T0+T1 | T2 | T3 | T4
--- | --- | --- | --- | ---
ALL | 466 | 632 | 694 | 209
AMP PEAK 32(17Q12) MUTATED | 87 | 202 | 144 | 48
AMP PEAK 32(17Q12) WILD-TYPE | 379 | 430 | 550 | 161

Figure S185. Get High-res Image Clustering Approach #32: 'Amp Peak 32(17q12) mutation analysis' versus Clinical Feature #7: 'PATHOLOGY.T'

'Amp Peak 32(17q12) mutation analysis' versus 'PATHOLOGICSPREAD(M)'

P value = 2.15e-06 (Chi-square test), Q value = 0.003

Table S218. Clustering Approach #32: 'Amp Peak 32(17q12) mutation analysis' versus Clinical Feature #9: 'PATHOLOGICSPREAD(M)'

nPatients | M0 | M1 | M1A | M1B | MX
--- | --- | --- | --- | --- | ---
ALL | 1424 | 168 | 9 | 3 | 165
AMP PEAK 32(17Q12) MUTATED | 326 | 38 | 4 | 2 | 68
AMP PEAK 32(17Q12) WILD-TYPE | 1098 | 130 | 5 | 1 | 97

Figure S186. Get High-res Image Clustering Approach #32: 'Amp Peak 32(17q12) mutation analysis' versus Clinical Feature #9: 'PATHOLOGICSPREAD(M)'

Clustering Approach #33: 'Amp Peak 33(17q25.3) mutation analysis'

Table S219. Description of clustering approach #33: 'Amp Peak 33(17q25.3) mutation analysis'

Cluster Labels | AMP PEAK 33(17Q25.3) MUTATED | AMP PEAK 33(17Q25.3) WILD-TYPE
--- | --- | ---
Number of samples | 1289 | 3274

'Amp Peak 33(17q25.3) mutation analysis' versus 'PRIMARY.SITE.OF.DISEASE'

P value = 1.66e-92 (Chi-square test), Q value = 2.9e-89

Table S220. Clustering Approach #33: 'Amp Peak 33(17q25.3) mutation analysis' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'

nPatients | BLADDER | BRAIN | BREAST | COLON | ENDOMETRIAL | HEAD/NECK | KIDNEY | LUNG | OMENTUM | OVARY | PERITONEUM (OVARY) | RECTUM
--- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | ---
ALL | 125 | 544 | 846 | 412 | 447 | 319 | 493 | 662 | 2 | 548 | 2 | 159
AMP PEAK 33(17Q25.3) MUTATED | 65 | 67 | 332 | 95 | 68 | 67 | 38 | 321 | 1 | 200 | 1 | 34
AMP PEAK 33(17Q25.3) WILD-TYPE | 60 | 477 | 514 | 317 | 379 | 252 | 455 | 341 | 1 | 348 | 1 | 125

Figure S187. Get High-res Image Clustering Approach #33: 'Amp Peak 33(17q25.3) mutation analysis' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'

'Amp Peak 33(17q25.3) mutation analysis' versus 'HISTOLOGICAL.TYPE'

P value = 9.16e-70 (Chi-square test), Q value = 1.6e-66

Table S221. Clustering Approach #33: 'Amp Peak 33(17q25.3) mutation analysis' versus Clinical Feature #6: 'HISTOLOGICAL.TYPE'

nPatients | COLON ADENOCARCINOMA | COLON MUCINOUS ADENOCARCINOMA | ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA | HEAD & NECK SQUAMOUS CELL CARCINOMA | KIDNEY CLEAR CELL RENAL CARCINOMA | LUNG ACINAR ADENOCARCINOMA | LUNG ADENOCARCINOMA MIXED SUBTYPE | LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS) | LUNG BASALOID SQUAMOUS CELL CARCINOMA | LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS | LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS | LUNG CLEAR CELL ADENOCARCINOMA | LUNG MICROPAPILLARY ADENOCARCINOMA | LUNG MUCINOUS ADENOCARCINOMA | LUNG PAPILLARY ADENOCARCINOMA | LUNG PAPILLARY SQUAMOUS CELL CARCINOMA | LUNG PAPILLARY SQUAMOUS CELL CARICNOMA | LUNG SMALL CELL SQUAMOUS CELL CARCINOMA | LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA | LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS) | MIXED SEROUS AND ENDOMETRIOID | MUCINOUS (COLLOID) ADENOCARCINOMA | RECTAL ADENOCARCINOMA | RECTAL MUCINOUS ADENOCARCINOMA | SEROUS CYSTADENOCARCINOMA | SEROUS ENDOMETRIAL ADENOCARCINOMA | TREATED PRIMARY GBM | UNTREATED PRIMARY (DE NOVO) GBM
--- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | ---
ALL | 356 | 54 | 350 | 319 | 493 | 10 | 75 | 205 | 7 | 3 | 15 | 2 | 3 | 2 | 13 | 1 | 1 | 1 | 2 | 315 | 18 | 7 | 143 | 13 | 552 | 79 | 1 | 20
AMP PEAK 33(17Q25.3) MUTATED | 88 | 6 | 27 | 67 | 38 | 3 | 40 | 114 | 3 | 0 | 5 | 2 | 2 | 1 | 6 | 1 | 0 | 0 | 2 | 141 | 5 | 1 | 33 | 0 | 202 | 36 | 1 | 2
AMP PEAK 33(17Q25.3) WILD-TYPE | 268 | 48 | 323 | 252 | 455 | 7 | 35 | 91 | 4 | 3 | 10 | 0 | 1 | 1 | 7 | 0 | 1 | 1 | 0 | 174 | 13 | 6 | 110 | 13 | 350 | 43 | 0 | 18

Figure S188. Get High-res Image Clustering Approach #33: 'Amp Peak 33(17q25.3) mutation analysis' versus Clinical Feature #6: 'HISTOLOGICAL.TYPE'

'Amp Peak 33(17q25.3) mutation analysis' versus 'PATHOLOGY.T'

P value = 5.96e-08 (Fisher's exact test), Q value = 8.7e-05

Table S222. Clustering Approach #33: 'Amp Peak 33(17q25.3) mutation analysis' versus Clinical Feature #7: 'PATHOLOGY.T'

nPatients | T0+T1 | T2 | T3 | T4
--- | --- | --- | --- | ---
ALL | 466 | 632 | 694 | 209
AMP PEAK 33(17Q25.3) MUTATED | 105 | 227 | 156 | 54
AMP PEAK 33(17Q25.3) WILD-TYPE | 361 | 405 | 538 | 155

Figure S189. Get High-res Image Clustering Approach #33: 'Amp Peak 33(17q25.3) mutation analysis' versus Clinical Feature #7: 'PATHOLOGY.T'

'Amp Peak 33(17q25.3) mutation analysis' versus 'PATHOLOGICSPREAD(M)'

P value = 2.45e-09 (Chi-square test), Q value = 3.7e-06

Table S223. Clustering Approach #33: 'Amp Peak 33(17q25.3) mutation analysis' versus Clinical Feature #9: 'PATHOLOGICSPREAD(M)'

nPatients | M0 | M1 | M1A | M1B | MX
--- | --- | --- | --- | --- | ---
ALL | 1424 | 168 | 9 | 3 | 165
AMP PEAK 33(17Q25.3) MUTATED | 369 | 37 | 4 | 2 | 81
AMP PEAK 33(17Q25.3) WILD-TYPE | 1055 | 131 | 5 | 1 | 84

Figure S190. Get High-res Image Clustering Approach #33: 'Amp Peak 33(17q25.3) mutation analysis' versus Clinical Feature #9: 'PATHOLOGICSPREAD(M)'

'Amp Peak 33(17q25.3) mutation analysis' versus 'RADIATIONS.RADIATION.REGIMENINDICATION'

P value = 4.41e-07 (Fisher's exact test), Q value = 0.00064

Table S224. Clustering Approach #33: 'Amp Peak 33(17q25.3) mutation analysis' versus Clinical Feature #11: 'RADIATIONS.RADIATION.REGIMENINDICATION'

nPatients | NO | YES
--- | --- | ---
ALL | 826 | 3737
AMP PEAK 33(17Q25.3) MUTATED | 175 | 1114
AMP PEAK 33(17Q25.3) WILD-TYPE | 651 | 2623

Figure S191. Get High-res Image Clustering Approach #33: 'Amp Peak 33(17q25.3) mutation analysis' versus Clinical Feature #11: 'RADIATIONS.RADIATION.REGIMENINDICATION'

'Amp Peak 33(17q25.3) mutation analysis' versus 'STOPPEDSMOKINGYEAR'

P value = 6.2e-05 (t-test), Q value = 0.082

Table S225. Clustering Approach #33: 'Amp Peak 33(17q25.3) mutation analysis' versus Clinical Feature #13: 'STOPPEDSMOKINGYEAR'

| nPatients | Mean (Std.Dev)
--- | --- | ---
ALL | 568 | 1995.2 (13.5)
AMP PEAK 33(17Q25.3) MUTATED | 227 | 1997.9 (12.4)
AMP PEAK 33(17Q25.3) WILD-TYPE | 341 | 1993.4 (13.9)

Figure S192. Get High-res Image Clustering Approach #33: 'Amp Peak 33(17q25.3) mutation analysis' versus Clinical Feature #13: 'STOPPEDSMOKINGYEAR'

Clustering Approach #34: 'Amp Peak 34(18q11.2) mutation analysis'

Table S226. Description of clustering approach #34: 'Amp Peak 34(18q11.2) mutation analysis'

Cluster Labels | AMP PEAK 34(18Q11.2) MUTATED | AMP PEAK 34(18Q11.2) WILD-TYPE
--- | --- | ---
Number of samples | 683 | 3880

'Amp Peak 34(18q11.2) mutation analysis' versus 'PRIMARY.SITE.OF.DISEASE'

P value = 2.58e-39 (Chi-square test), Q value = 4.3e-36

Table S227. Clustering Approach #34: 'Amp Peak 34(18q11.2) mutation analysis' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'

nPatients | BLADDER | BRAIN | BREAST | COLON | ENDOMETRIAL | HEAD/NECK | KIDNEY | LUNG | OMENTUM | OVARY | PERITONEUM (OVARY) | RECTUM
--- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | ---
ALL | 125 | 544 | 846 | 412 | 447 | 319 | 493 | 662 | 2 | 548 | 2 | 159
AMP PEAK 34(18Q11.2) MUTATED | 27 | 54 | 144 | 20 | 51 | 53 | 25 | 168 | 0 | 132 | 2 | 7
AMP PEAK 34(18Q11.2) WILD-TYPE | 98 | 490 | 702 | 392 | 396 | 266 | 468 | 494 | 2 | 416 | 0 | 152

Figure S193. Get High-res Image Clustering Approach #34: 'Amp Peak 34(18q11.2) mutation analysis' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'

'Amp Peak 34(18q11.2) mutation analysis' versus 'HISTOLOGICAL.TYPE'

P value = 5.99e-48 (Chi-square test), Q value = 1e-44

Table S228. Clustering Approach #34: 'Amp Peak 34(18q11.2) mutation analysis' versus Clinical Feature #6: 'HISTOLOGICAL.TYPE'

nPatients | COLON ADENOCARCINOMA | COLON MUCINOUS ADENOCARCINOMA | ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA | HEAD & NECK SQUAMOUS CELL CARCINOMA | KIDNEY CLEAR CELL RENAL CARCINOMA | LUNG ACINAR ADENOCARCINOMA | LUNG ADENOCARCINOMA MIXED SUBTYPE | LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS) | LUNG BASALOID SQUAMOUS CELL CARCINOMA | LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS | LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS | LUNG CLEAR CELL ADENOCARCINOMA | LUNG MICROPAPILLARY ADENOCARCINOMA | LUNG MUCINOUS ADENOCARCINOMA | LUNG PAPILLARY ADENOCARCINOMA | LUNG PAPILLARY SQUAMOUS CELL CARCINOMA | LUNG PAPILLARY SQUAMOUS CELL CARICNOMA | LUNG SMALL CELL SQUAMOUS CELL CARCINOMA | LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA | LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS) | MIXED SEROUS AND ENDOMETRIOID | MUCINOUS (COLLOID) ADENOCARCINOMA | RECTAL ADENOCARCINOMA | RECTAL MUCINOUS ADENOCARCINOMA | SEROUS CYSTADENOCARCINOMA | SEROUS ENDOMETRIAL ADENOCARCINOMA | TREATED PRIMARY GBM | UNTREATED PRIMARY (DE NOVO) GBM
--- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | ---
ALL | 356 | 54 | 350 | 319 | 493 | 10 | 75 | 205 | 7 | 3 | 15 | 2 | 3 | 2 | 13 | 1 | 1 | 1 | 2 | 315 | 18 | 7 | 143 | 13 | 552 | 79 | 1 | 20
AMP PEAK 34(18Q11.2) MUTATED | 13 | 7 | 18 | 53 | 25 | 5 | 12 | 35 | 3 | 0 | 2 | 2 | 1 | 0 | 4 | 1 | 0 | 0 | 0 | 103 | 3 | 0 | 6 | 1 | 134 | 30 | 0 | 2
AMP PEAK 34(18Q11.2) WILD-TYPE | 343 | 47 | 332 | 266 | 468 | 5 | 63 | 170 | 4 | 3 | 13 | 0 | 2 | 2 | 9 | 0 | 1 | 1 | 2 | 212 | 15 | 7 | 137 | 12 | 418 | 49 | 1 | 18

Figure S194. Get High-res Image Clustering Approach #34: 'Amp Peak 34(18q11.2) mutation analysis' versus Clinical Feature #6: 'HISTOLOGICAL.TYPE'

'Amp Peak 34(18q11.2) mutation analysis' versus 'PATHOLOGY.T'

P value = 7.36e-12 (Fisher's exact test), Q value = 1.1e-08

Table S229. Clustering Approach #34: 'Amp Peak 34(18q11.2) mutation analysis' versus Clinical Feature #7: 'PATHOLOGY.T'

nPatients | T0+T1 | T2 | T3 | T4
--- | --- | --- | --- | ---
ALL | 466 | 632 | 694 | 209
AMP PEAK 34(18Q11.2) MUTATED | 64 | 124 | 44 | 30
AMP PEAK 34(18Q11.2) WILD-TYPE | 402 | 508 | 650 | 179

Figure S195. Get High-res Image Clustering Approach #34: 'Amp Peak 34(18q11.2) mutation analysis' versus Clinical Feature #7: 'PATHOLOGY.T'

Clustering Approach #35: 'Amp Peak 35(19p13.2) mutation analysis'

Table S230. Description of clustering approach #35: 'Amp Peak 35(19p13.2) mutation analysis'

Cluster Labels | AMP PEAK 35(19P13.2) MUTATED | AMP PEAK 35(19P13.2) WILD-TYPE
--- | --- | ---
Number of samples | 844 | 3719

'Amp Peak 35(19p13.2) mutation analysis' versus 'Time to Death'

P value = 5.21e-10 (logrank test), Q value = 7.8e-07

Table S231. Clustering Approach #35: 'Amp Peak 35(19p13.2) mutation analysis' versus Clinical Feature #1: 'Time to Death'

| nPatients | nDeath | Duration Range (Median), Month
--- | --- | --- | ---
ALL | 4296 | 1401 | 0.0 - 224.0 (14.9)
AMP PEAK 35(19P13.2) MUTATED | 810 | 338 | 0.1 - 224.0 (14.1)
AMP PEAK 35(19P13.2) WILD-TYPE | 3486 | 1063 | 0.0 - 223.4 (15.0)

Figure S196. Get High-res Image Clustering Approach #35: 'Amp Peak 35(19p13.2) mutation analysis' versus Clinical Feature #1: 'Time to Death'

'Amp Peak 35(19p13.2) mutation analysis' versus 'PRIMARY.SITE.OF.DISEASE'

P value = 2.23e-70 (Chi-square test), Q value = 3.8e-67

Table S232. Clustering Approach #35: 'Amp Peak 35(19p13.2) mutation analysis' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'

nPatients | BLADDER | BRAIN | BREAST | COLON | ENDOMETRIAL | HEAD/NECK | KIDNEY | LUNG | OMENTUM | OVARY | PERITONEUM (OVARY) | RECTUM
--- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | ---
ALL | 125 | 544 | 846 | 412 | 447 | 319 | 493 | 662 | 2 | 548 | 2 | 159
AMP PEAK 35(19P13.2) MUTATED | 18 | 231 | 143 | 65 | 23 | 37 | 43 | 91 | 0 | 160 | 1 | 32
AMP PEAK 35(19P13.2) WILD-TYPE | 107 | 313 | 703 | 347 | 424 | 282 | 450 | 571 | 2 | 388 | 1 | 127

Figure S197. Get High-res Image Clustering Approach #35: 'Amp Peak 35(19p13.2) mutation analysis' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'

'Amp Peak 35(19p13.2) mutation analysis' versus 'HISTOLOGICAL.TYPE'

P value = 2.29e-32 (Chi-square test), Q value = 3.7e-29

Table S233. Clustering Approach #35: 'Amp Peak 35(19p13.2) mutation analysis' versus Clinical Feature #6: 'HISTOLOGICAL.TYPE'

nPatients | COLON ADENOCARCINOMA | COLON MUCINOUS ADENOCARCINOMA | ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA | HEAD & NECK SQUAMOUS CELL CARCINOMA | KIDNEY CLEAR CELL RENAL CARCINOMA | LUNG ACINAR ADENOCARCINOMA | LUNG ADENOCARCINOMA MIXED SUBTYPE | LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS) | LUNG BASALOID SQUAMOUS CELL CARCINOMA | LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS | LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS | LUNG CLEAR CELL ADENOCARCINOMA | LUNG MICROPAPILLARY ADENOCARCINOMA | LUNG MUCINOUS ADENOCARCINOMA | LUNG PAPILLARY ADENOCARCINOMA | LUNG PAPILLARY SQUAMOUS CELL CARCINOMA | LUNG PAPILLARY SQUAMOUS CELL CARICNOMA | LUNG SMALL CELL SQUAMOUS CELL CARCINOMA | LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA | LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS) | MIXED SEROUS AND ENDOMETRIOID | MUCINOUS (COLLOID) ADENOCARCINOMA | RECTAL ADENOCARCINOMA | RECTAL MUCINOUS ADENOCARCINOMA | SEROUS CYSTADENOCARCINOMA | SEROUS ENDOMETRIAL ADENOCARCINOMA | TREATED PRIMARY GBM | UNTREATED PRIMARY (DE NOVO) GBM
--- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | ---
ALL | 356 | 54 | 350 | 319 | 493 | 10 | 75 | 205 | 7 | 3 | 15 | 2 | 3 | 2 | 13 | 1 | 1 | 1 | 2 | 315 | 18 | 7 | 143 | 13 | 552 | 79 | 1 | 20
AMP PEAK 35(19P13.2) MUTATED | 60 | 5 | 11 | 37 | 43 | 0 | 7 | 11 | 3 | 0 | 1 | 0 | 1 | 0 | 1 | 1 | 0 | 0 | 0 | 66 | 3 | 0 | 32 | 0 | 161 | 9 | 1 | 10
AMP PEAK 35(19P13.2) WILD-TYPE | 296 | 49 | 339 | 282 | 450 | 10 | 68 | 194 | 4 | 3 | 14 | 2 | 2 | 2 | 12 | 0 | 1 | 1 | 2 | 249 | 15 | 7 | 111 | 13 | 391 | 70 | 0 | 10

Figure S198. Get High-res Image Clustering Approach #35: 'Amp Peak 35(19p13.2) mutation analysis' versus Clinical Feature #6: 'HISTOLOGICAL.TYPE'

'Amp Peak 35(19p13.2) mutation analysis' versus 'TUMOR.STAGE'

P value = 1.83e-09 (Fisher's exact test), Q value = 2.7e-06

Table S234. Clustering Approach #35: 'Amp Peak 35(19p13.2) mutation analysis' versus Clinical Feature #10: 'TUMOR.STAGE'

nPatients | I | II | III | IV
--- | --- | --- | --- | ---
ALL | 712 | 498 | 881 | 423
AMP PEAK 35(19P13.2) MUTATED | 71 | 80 | 195 | 69
AMP PEAK 35(19P13.2) WILD-TYPE | 641 | 418 | 686 | 354

Figure S199. Get High-res Image Clustering Approach #35: 'Amp Peak 35(19p13.2) mutation analysis' versus Clinical Feature #10: 'TUMOR.STAGE'

'Amp Peak 35(19p13.2) mutation analysis' versus 'RADIATIONS.RADIATION.REGIMENINDICATION'

P value = 2.45e-11 (Fisher's exact test), Q value = 3.7e-08

Table S235. Clustering Approach #35: 'Amp Peak 35(19p13.2) mutation analysis' versus Clinical Feature #11: 'RADIATIONS.RADIATION.REGIMENINDICATION'

nPatients | NO | YES
--- | --- | ---
ALL | 826 | 3737
AMP PEAK 35(19P13.2) MUTATED | 223 | 621
AMP PEAK 35(19P13.2) WILD-TYPE | 603 | 3116

Figure S200. Get High-res Image Clustering Approach #35: 'Amp Peak 35(19p13.2) mutation analysis' versus Clinical Feature #11: 'RADIATIONS.RADIATION.REGIMENINDICATION'

Clustering Approach #36: 'Amp Peak 36(19p13.12) mutation analysis'

Table S236. Description of clustering approach #36: 'Amp Peak 36(19p13.12) mutation analysis'

Cluster Labels | AMP PEAK 36(19P13.12) MUTATED | AMP PEAK 36(19P13.12) WILD-TYPE
--- | --- | ---
Number of samples | 1054 | 3509

'Amp Peak 36(19p13.12) mutation analysis' versus 'PRIMARY.SITE.OF.DISEASE'

P value = 3.73e-104 (Chi-square test), Q value = 6.5e-101

Table S237. Clustering Approach #36: 'Amp Peak 36(19p13.12) mutation analysis' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'

nPatients | BLADDER | BRAIN | BREAST | COLON | ENDOMETRIAL | HEAD/NECK | KIDNEY | LUNG | OMENTUM | OVARY | PERITONEUM (OVARY) | RECTUM
--- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | ---
ALL | 125 | 544 | 846 | 412 | 447 | 319 | 493 | 662 | 2 | 548 | 2 | 159
AMP PEAK 36(19P13.12) MUTATED | 19 | 210 | 181 | 65 | 70 | 42 | 43 | 94 | 0 | 299 | 1 | 30
AMP PEAK 36(19P13.12) WILD-TYPE | 106 | 334 | 665 | 347 | 377 | 277 | 450 | 568 | 2 | 249 | 1 | 129

Figure S201. Get High-res Image Clustering Approach #36: 'Amp Peak 36(19p13.12) mutation analysis' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'

'Amp Peak 36(19p13.12) mutation analysis' versus 'HISTOLOGICAL.TYPE'

P value = 9.15e-106 (Chi-square test), Q value = 1.6e-102

Table S238. Clustering Approach #36: 'Amp Peak 36(19p13.12) mutation analysis' versus Clinical Feature #6: 'HISTOLOGICAL.TYPE'

nPatients | COLON ADENOCARCINOMA | COLON MUCINOUS ADENOCARCINOMA | ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA | HEAD & NECK SQUAMOUS CELL CARCINOMA | KIDNEY CLEAR CELL RENAL CARCINOMA | LUNG ACINAR ADENOCARCINOMA | LUNG ADENOCARCINOMA MIXED SUBTYPE | LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS) | LUNG BASALOID SQUAMOUS CELL CARCINOMA | LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS | LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS | LUNG CLEAR CELL ADENOCARCINOMA | LUNG MICROPAPILLARY ADENOCARCINOMA | LUNG MUCINOUS ADENOCARCINOMA | LUNG PAPILLARY ADENOCARCINOMA | LUNG PAPILLARY SQUAMOUS CELL CARCINOMA | LUNG PAPILLARY SQUAMOUS CELL CARICNOMA | LUNG SMALL CELL SQUAMOUS CELL CARCINOMA | LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA | LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS) | MIXED SEROUS AND ENDOMETRIOID | MUCINOUS (COLLOID) ADENOCARCINOMA | RECTAL ADENOCARCINOMA | RECTAL MUCINOUS ADENOCARCINOMA | SEROUS CYSTADENOCARCINOMA | SEROUS ENDOMETRIAL ADENOCARCINOMA | TREATED PRIMARY GBM | UNTREATED PRIMARY (DE NOVO) GBM
--- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | ---
ALL | 356 | 54 | 350 | 319 | 493 | 10 | 75 | 205 | 7 | 3 | 15 | 2 | 3 | 2 | 13 | 1 | 1 | 1 | 2 | 315 | 18 | 7 | 143 | 13 | 552 | 79 | 1 | 20
AMP PEAK 36(19P13.12) MUTATED | 59 | 6 | 24 | 42 | 43 | 0 | 5 | 11 | 3 | 0 | 0 | 0 | 1 | 0 | 1 | 1 | 0 | 0 | 0 | 71 | 6 | 1 | 30 | 0 | 300 | 40 | 1 | 9
AMP PEAK 36(19P13.12) WILD-TYPE | 297 | 48 | 326 | 277 | 450 | 10 | 70 | 194 | 4 | 3 | 15 | 2 | 2 | 2 | 12 | 0 | 1 | 1 | 2 | 244 | 12 | 6 | 113 | 13 | 252 | 39 | 0 | 11

Figure S202. Get High-res Image Clustering Approach #36: 'Amp Peak 36(19p13.12) mutation analysis' versus Clinical Feature #6: 'HISTOLOGICAL.TYPE'

'Amp Peak 36(19p13.12) mutation analysis' versus 'TUMOR.STAGE'

P value = 2.83e-29 (Fisher's exact test), Q value = 4.6e-26

Table S239. Clustering Approach #36: 'Amp Peak 36(19p13.12) mutation analysis' versus Clinical Feature #10: 'TUMOR.STAGE'

nPatients | I | II | III | IV
--- | --- | --- | --- | ---
ALL | 712 | 498 | 881 | 423
AMP PEAK 36(19P13.12) MUTATED | 78 | 94 | 305 | 84
AMP PEAK 36(19P13.12) WILD-TYPE | 634 | 404 | 576 | 339

Figure S203. Get High-res Image Clustering Approach #36: 'Amp Peak 36(19p13.12) mutation analysis' versus Clinical Feature #10: 'TUMOR.STAGE'

'Amp Peak 36(19p13.12) mutation analysis' versus 'RADIATIONS.RADIATION.REGIMENINDICATION'

P value = 0.000105 (Fisher's exact test), Q value = 0.14

Table S240. Clustering Approach #36: 'Amp Peak 36(19p13.12) mutation analysis' versus Clinical Feature #11: 'RADIATIONS.RADIATION.REGIMENINDICATION'

nPatients | NO | YES
--- | --- | ---
ALL | 826 | 3737
AMP PEAK 36(19P13.12) MUTATED | 234 | 820
AMP PEAK 36(19P13.12) WILD-TYPE | 592 | 2917

Figure S204. Get High-res Image Clustering Approach #36: 'Amp Peak 36(19p13.12) mutation analysis' versus Clinical Feature #11: 'RADIATIONS.RADIATION.REGIMENINDICATION'

Clustering Approach #37: 'Amp Peak 37(19q12) mutation analysis'

Table S241. Description of clustering approach #37: 'Amp Peak 37(19q12) mutation analysis'

Cluster Labels | AMP PEAK 37(19Q12) MUTATED | AMP PEAK 37(19Q12) WILD-TYPE
--- | --- | ---
Number of samples | 1290 | 3273

'Amp Peak 37(19q12) mutation analysis' versus 'Time to Death'

P value = 0.000147 (logrank test), Q value = 0.19

Table S242. Clustering Approach #37: 'Amp Peak 37(19q12) mutation analysis' versus Clinical Feature #1: 'Time to Death'

| nPatients | nDeath | Duration Range (Median), Month
--- | --- | --- | ---
ALL | 4296 | 1401 | 0.0 - 224.0 (14.9)
AMP PEAK 37(19Q12) MUTATED | 1236 | 466 | 0.0 - 186.4 (15.8)
AMP PEAK 37(19Q12) WILD-TYPE | 3060 | 935 | 0.0 - 224.0 (14.3)

Figure S205. Get High-res Image Clustering Approach #37: 'Amp Peak 37(19q12) mutation analysis' versus Clinical Feature #1: 'Time to Death'

'Amp Peak 37(19q12) mutation analysis' versus 'PRIMARY.SITE.OF.DISEASE'

P value = 4.38e-77 (Chi-square test), Q value = 7.5e-74

Table S243. Clustering Approach #37: 'Amp Peak 37(19q12) mutation analysis' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'

nPatients | BLADDER | BRAIN | BREAST | COLON | ENDOMETRIAL | HEAD/NECK | KIDNEY | LUNG | OMENTUM | OVARY | PERITONEUM (OVARY) | RECTUM
--- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | ---
ALL | 125 | 544 | 846 | 412 | 447 | 319 | 493 | 662 | 2 | 548 | 2 | 159
AMP PEAK 37(19Q12) MUTATED | 50 | 195 | 217 | 83 | 80 | 44 | 51 | 227 | 0 | 303 | 2 | 38
AMP PEAK 37(19Q12) WILD-TYPE | 75 | 349 | 629 | 329 | 367 | 275 | 442 | 435 | 2 | 245 | 0 | 121

Figure S206. Get High-res Image Clustering Approach #37: 'Amp Peak 37(19q12) mutation analysis' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'

'Amp Peak 37(19q12) mutation analysis' versus 'HISTOLOGICAL.TYPE'

P value = 3.02e-97 (Chi-square test), Q value = 5.2e-94

Table S244. Clustering Approach #37: 'Amp Peak 37(19q12) mutation analysis' versus Clinical Feature #6: 'HISTOLOGICAL.TYPE'

nPatients | COLON ADENOCARCINOMA | COLON MUCINOUS ADENOCARCINOMA | ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA | HEAD & NECK SQUAMOUS CELL CARCINOMA | KIDNEY CLEAR CELL RENAL CARCINOMA | LUNG ACINAR ADENOCARCINOMA | LUNG ADENOCARCINOMA MIXED SUBTYPE | LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS) | LUNG BASALOID SQUAMOUS CELL CARCINOMA | LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS | LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS | LUNG CLEAR CELL ADENOCARCINOMA | LUNG MICROPAPILLARY ADENOCARCINOMA | LUNG MUCINOUS ADENOCARCINOMA | LUNG PAPILLARY ADENOCARCINOMA | LUNG PAPILLARY SQUAMOUS CELL CARCINOMA | LUNG PAPILLARY SQUAMOUS CELL CARICNOMA | LUNG SMALL CELL SQUAMOUS CELL CARCINOMA | LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA | LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS) | MIXED SEROUS AND ENDOMETRIOID | MUCINOUS (COLLOID) ADENOCARCINOMA | RECTAL ADENOCARCINOMA | RECTAL MUCINOUS ADENOCARCINOMA | SEROUS CYSTADENOCARCINOMA | SEROUS ENDOMETRIAL ADENOCARCINOMA | TREATED PRIMARY GBM | UNTREATED PRIMARY (DE NOVO) GBM
--- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | ---
ALL | 356 | 54 | 350 | 319 | 493 | 10 | 75 | 205 | 7 | 3 | 15 | 2 | 3 | 2 | 13 | 1 | 1 | 1 | 2 | 315 | 18 | 7 | 143 | 13 | 552 | 79 | 1 | 20
AMP PEAK 37(19Q12) MUTATED | 76 | 7 | 18 | 44 | 51 | 5 | 23 | 50 | 5 | 0 | 4 | 1 | 1 | 0 | 6 | 1 | 0 | 0 | 0 | 129 | 9 | 2 | 38 | 0 | 305 | 53 | 1 | 8
AMP PEAK 37(19Q12) WILD-TYPE | 280 | 47 | 332 | 275 | 442 | 5 | 52 | 155 | 2 | 3 | 11 | 1 | 2 | 2 | 7 | 0 | 1 | 1 | 2 | 186 | 9 | 5 | 105 | 13 | 247 | 26 | 0 | 12

Figure S207. Get High-res Image Clustering Approach #37: 'Amp Peak 37(19q12) mutation analysis' versus Clinical Feature #6: 'HISTOLOGICAL.TYPE'

'Amp Peak 37(19q12) mutation analysis' versus 'PATHOLOGY.T'

P value = 9.09e-06 (Fisher's exact test), Q value = 0.013

Table S245. Clustering Approach #37: 'Amp Peak 37(19q12) mutation analysis' versus Clinical Feature #7: 'PATHOLOGY.T'

nPatients | T0+T1 | T2 | T3 | T4
--- | --- | --- | --- | ---
ALL | 466 | 632 | 694 | 209
AMP PEAK 37(19Q12) MUTATED | 75 | 179 | 139 | 41
AMP PEAK 37(19Q12) WILD-TYPE | 391 | 453 | 555 | 168

Figure S208. Get High-res Image Clustering Approach #37: 'Amp Peak 37(19q12) mutation analysis' versus Clinical Feature #7: 'PATHOLOGY.T'

'Amp Peak 37(19q12) mutation analysis' versus 'TUMOR.STAGE'

P value = 1.36e-16 (Fisher's exact test), Q value = 2.1e-13

Table S246. Clustering Approach #37: 'Amp Peak 37(19q12) mutation analysis' versus Clinical Feature #10: 'TUMOR.STAGE'

nPatients | I | II | III | IV
--- | --- | --- | --- | ---
ALL | 712 | 498 | 881 | 423
AMP PEAK 37(19Q12) MUTATED | 150 | 130 | 350 | 101
AMP PEAK 37(19Q12) WILD-TYPE | 562 | 368 | 531 | 322

Figure S209. Get High-res Image Clustering Approach #37: 'Amp Peak 37(19q12) mutation analysis' versus Clinical Feature #10: 'TUMOR.STAGE'

Clustering Approach #38: 'Amp Peak 38(20q11.21) mutation analysis'

Table S247. Description of clustering approach #38: 'Amp Peak 38(20q11.21) mutation analysis'

Cluster Labels | AMP PEAK 38(20Q11.21) MUTATED | AMP PEAK 38(20Q11.21) WILD-TYPE
--- | --- | ---
Number of samples | 2126 | 2437

'Amp Peak 38(20q11.21) mutation analysis' versus 'Time to Death'

P value = 0.000183 (logrank test), Q value = 0.24

Table S248. Clustering Approach #38: 'Amp Peak 38(20q11.21) mutation analysis' versus Clinical Feature #1: 'Time to Death'

| nPatients | nDeath | Duration Range (Median), Month
--- | --- | --- | ---
ALL | 4296 | 1401 | 0.0 - 224.0 (14.9)
AMP PEAK 38(20Q11.21) MUTATED | 1962 | 664 | 0.0 - 224.0 (13.0)
AMP PEAK 38(20Q11.21) WILD-TYPE | 2334 | 737 | 0.0 - 223.4 (15.9)

Figure S210. Get High-res Image Clustering Approach #38: 'Amp Peak 38(20q11.21) mutation analysis' versus Clinical Feature #1: 'Time to Death'

'Amp Peak 38(20q11.21) mutation analysis' versus 'AGE'

P value = 1.32e-15 (t-test), Q value = 2.1e-12

Table S249. Clustering Approach #38: 'Amp Peak 38(20q11.21) mutation analysis' versus Clinical Feature #2: 'AGE'

| nPatients | Mean (Std.Dev)
--- | --- | ---
ALL | 4507 | 61.9 (12.6)
AMP PEAK 38(20Q11.21) MUTATED | 2104 | 63.4 (12.1)
AMP PEAK 38(20Q11.21) WILD-TYPE | 2403 | 60.5 (12.9)

Figure S211. Get High-res Image Clustering Approach #38: 'Amp Peak 38(20q11.21) mutation analysis' versus Clinical Feature #2: 'AGE'

'Amp Peak 38(20q11.21) mutation analysis' versus 'PRIMARY.SITE.OF.DISEASE'

P value = 1.59e-101 (Chi-square test), Q value = 2.8e-98

Table S250. Clustering Approach #38: 'Amp Peak 38(20q11.21) mutation analysis' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'

nPatients | BLADDER | BRAIN | BREAST | COLON | ENDOMETRIAL | HEAD/NECK | KIDNEY | LUNG | OMENTUM | OVARY | PERITONEUM (OVARY) | RECTUM
--- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | ---
ALL | 125 | 544 | 846 | 412 | 447 | 319 | 493 | 662 | 2 | 548 | 2 | 159
AMP PEAK 38(20Q11.21) MUTATED | 87 | 210 | 366 | 295 | 108 | 146 | 109 | 340 | 1 | 319 | 1 | 141
AMP PEAK 38(20Q11.21) WILD-TYPE | 38 | 334 | 480 | 117 | 339 | 173 | 384 | 322 | 1 | 229 | 1 | 18

Figure S212. Get High-res Image Clustering Approach #38: 'Amp Peak 38(20q11.21) mutation analysis' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'

'Amp Peak 38(20q11.21) mutation analysis' versus 'GENDER'

P value = 0.000106 (Fisher's exact test), Q value = 0.14

Table S251. Clustering Approach #38: 'Amp Peak 38(20q11.21) mutation analysis' versus Clinical Feature #4: 'GENDER'

nPatients | FEMALE | MALE
--- | --- | ---
ALL | 2881 | 1682
AMP PEAK 38(20Q11.21) MUTATED | 1279 | 847
AMP PEAK 38(20Q11.21) WILD-TYPE | 1602 | 835

Figure S213. Get High-res Image Clustering Approach #38: 'Amp Peak 38(20q11.21) mutation analysis' versus Clinical Feature #4: 'GENDER'

'Amp Peak 38(20q11.21) mutation analysis' versus 'HISTOLOGICAL.TYPE'

P value = 3.09e-110 (Chi-square test), Q value = 5.4e-107

Table S252. Clustering Approach #38: 'Amp Peak 38(20q11.21) mutation analysis' versus Clinical Feature #6: 'HISTOLOGICAL.TYPE'

nPatients | COLON ADENOCARCINOMA | COLON MUCINOUS ADENOCARCINOMA | ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA | HEAD & NECK SQUAMOUS CELL CARCINOMA | KIDNEY CLEAR CELL RENAL CARCINOMA | LUNG ACINAR ADENOCARCINOMA | LUNG ADENOCARCINOMA MIXED SUBTYPE | LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS) | LUNG BASALOID SQUAMOUS CELL CARCINOMA | LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS | LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS | LUNG CLEAR CELL ADENOCARCINOMA | LUNG MICROPAPILLARY ADENOCARCINOMA | LUNG MUCINOUS ADENOCARCINOMA | LUNG PAPILLARY ADENOCARCINOMA | LUNG PAPILLARY SQUAMOUS CELL CARCINOMA | LUNG PAPILLARY SQUAMOUS CELL CARICNOMA | LUNG SMALL CELL SQUAMOUS CELL CARCINOMA | LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA | LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS) | MIXED SEROUS AND ENDOMETRIOID | MUCINOUS (COLLOID) ADENOCARCINOMA | RECTAL ADENOCARCINOMA | RECTAL MUCINOUS ADENOCARCINOMA | SEROUS CYSTADENOCARCINOMA | SEROUS ENDOMETRIAL ADENOCARCINOMA | TREATED PRIMARY GBM | UNTREATED PRIMARY (DE NOVO) GBM
--- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | ---
ALL | 356 | 54 | 350 | 319 | 493 | 10 | 75 | 205 | 7 | 3 | 15 | 2 | 3 | 2 | 13 | 1 | 1 | 1 | 2 | 315 | 18 | 7 | 143 | 13 | 552 | 79 | 1 | 20
AMP PEAK 38(20Q11.21) MUTATED | 269 | 24 | 47 | 146 | 109 | 5 | 26 | 101 | 6 | 1 | 5 | 0 | 2 | 0 | 5 | 0 | 0 | 0 | 1 | 187 | 5 | 1 | 132 | 7 | 321 | 56 | 1 | 7
AMP PEAK 38(20Q11.21) WILD-TYPE | 87 | 30 | 303 | 173 | 384 | 5 | 49 | 104 | 1 | 2 | 10 | 2 | 1 | 2 | 8 | 1 | 1 | 1 | 1 | 128 | 13 | 6 | 11 | 6 | 231 | 23 | 0 | 13

Figure S214. Get High-res Image Clustering Approach #38: 'Amp Peak 38(20q11.21) mutation analysis' versus Clinical Feature #6: 'HISTOLOGICAL.TYPE'

'Amp Peak 38(20q11.21) mutation analysis' versus 'PATHOLOGY.T'

P value = 4.98e-24 (Fisher's exact test), Q value = 8e-21

Table S253. Clustering Approach #38: 'Amp Peak 38(20q11.21) mutation analysis' versus Clinical Feature #7: 'PATHOLOGY.T'

nPatients | T0+T1 | T2 | T3 | T4
--- | --- | --- | --- | ---
ALL | 466 | 632 | 694 | 209
AMP PEAK 38(20Q11.21) MUTATED | 139 | 341 | 418 | 110
AMP PEAK 38(20Q11.21) WILD-TYPE | 327 | 291 | 276 | 99

Figure S215. Get High-res Image Clustering Approach #38: 'Amp Peak 38(20q11.21) mutation analysis' versus Clinical Feature #7: 'PATHOLOGY.T'

'Amp Peak 38(20q11.21) mutation analysis' versus 'PATHOLOGY.N'

P value = 9.07e-06 (Fisher's exact test), Q value = 0.013

Table S254. Clustering Approach #38: 'Amp Peak 38(20q11.21) mutation analysis' versus Clinical Feature #8: 'PATHOLOGY.N'

nPatients | N0 | N1 | N2 | N3
--- | --- | --- | --- | ---
ALL | 1067 | 353 | 282 | 11
AMP PEAK 38(20Q11.21) MUTATED | 538 | 229 | 163 | 4
AMP PEAK 38(20Q11.21) WILD-TYPE | 529 | 124 | 119 | 7

Figure S216. Get High-res Image Clustering Approach #38: 'Amp Peak 38(20q11.21) mutation analysis' versus Clinical Feature #8: 'PATHOLOGY.N'

'Amp Peak 38(20q11.21) mutation analysis' versus 'TUMOR.STAGE'

P value = 5.57e-10 (Fisher's exact test), Q value = 8.4e-07

Table S255. Clustering Approach #38: 'Amp Peak 38(20q11.21) mutation analysis' versus Clinical Feature #10: 'TUMOR.STAGE'

nPatients | I | II | III | IV
--- | --- | --- | --- | ---
ALL | 712 | 498 | 881 | 423
AMP PEAK 38(20Q11.21) MUTATED | 297 | 276 | 512 | 214
AMP PEAK 38(20Q11.21) WILD-TYPE | 415 | 222 | 369 | 209

Figure S217. Get High-res Image Clustering Approach #38: 'Amp Peak 38(20q11.21) mutation analysis' versus Clinical Feature #10: 'TUMOR.STAGE'

'Amp Peak 38(20q11.21) mutation analysis' versus 'RADIATIONS.RADIATION.REGIMENINDICATION'

P value = 2.61e-05 (Fisher's exact test), Q value = 0.035

Table S256. Clustering Approach #38: 'Amp Peak 38(20q11.21) mutation analysis' versus Clinical Feature #11: 'RADIATIONS.RADIATION.REGIMENINDICATION'

nPatients | NO | YES
--- | --- | ---
ALL | 826 | 3737
AMP PEAK 38(20Q11.21) MUTATED | 330 | 1796
AMP PEAK 38(20Q11.21) WILD-TYPE | 496 | 1941

Figure S218. Get High-res Image Clustering Approach #38: 'Amp Peak 38(20q11.21) mutation analysis' versus Clinical Feature #11: 'RADIATIONS.RADIATION.REGIMENINDICATION'

Clustering Approach #39: 'Amp Peak 39(20q13.2) mutation analysis'

Table S257. Description of clustering approach #39: 'Amp Peak 39(20q13.2) mutation analysis'

Cluster Labels | AMP PEAK 39(20Q13.2) MUTATED | AMP PEAK 39(20Q13.2) WILD-TYPE
--- | --- | ---
Number of samples | 2209 | 2354

'Amp Peak 39(20q13.2) mutation analysis' versus 'AGE'

P value = 2.01e-08 (t-test), Q value = 3e-05

Table S258. Clustering Approach #39: 'Amp Peak 39(20q13.2) mutation analysis' versus Clinical Feature #2: 'AGE'

| nPatients | Mean (Std.Dev)
--- | --- | ---
ALL | 4507 | 61.9 (12.6)
AMP PEAK 39(20Q13.2) MUTATED | 2186 | 62.9 (12.3)
AMP PEAK 39(20Q13.2) WILD-TYPE | 2321 | 60.8 (12.9)

Figure S219. Get High-res Image Clustering Approach #39: 'Amp Peak 39(20q13.2) mutation analysis' versus Clinical Feature #2: 'AGE'

'Amp Peak 39(20q13.2) mutation analysis' versus 'PRIMARY.SITE.OF.DISEASE'

P value = 5.34e-112 (Chi-square test), Q value = 9.3e-109

Table S259. Clustering Approach #39: 'Amp Peak 39(20q13.2) mutation analysis' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'

nPatients | BLADDER | BRAIN | BREAST | COLON | ENDOMETRIAL | HEAD/NECK | KIDNEY | LUNG | OMENTUM | OVARY | PERITONEUM (OVARY) | RECTUM
--- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | ---
ALL | 125 | 544 | 846 | 412 | 447 | 319 | 493 | 662 | 2 | 548 | 2 | 159
AMP PEAK 39(20Q13.2) MUTATED | 81 | 206 | 440 | 299 | 116 | 122 | 111 | 320 | 1 | 367 | 2 | 141
AMP PEAK 39(20Q13.2) WILD-TYPE | 44 | 338 | 406 | 113 | 331 | 197 | 382 | 342 | 1 | 181 | 0 | 18

Figure S220. Get High-res Image Clustering Approach #39: 'Amp Peak 39(20q13.2) mutation analysis' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'

'Amp Peak 39(20q13.2) mutation analysis' versus 'HISTOLOGICAL.TYPE'

P value = 3.57e-118 (Chi-square test), Q value = 6.3e-115

Table S260. Clustering Approach #39: 'Amp Peak 39(20q13.2) mutation analysis' versus Clinical Feature #6: 'HISTOLOGICAL.TYPE'

nPatients | COLON ADENOCARCINOMA | COLON MUCINOUS ADENOCARCINOMA | ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA | HEAD & NECK SQUAMOUS CELL CARCINOMA | KIDNEY CLEAR CELL RENAL CARCINOMA | LUNG ACINAR ADENOCARCINOMA | LUNG ADENOCARCINOMA MIXED SUBTYPE | LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS) | LUNG BASALOID SQUAMOUS CELL CARCINOMA | LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS | LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS | LUNG CLEAR CELL ADENOCARCINOMA | LUNG MICROPAPILLARY ADENOCARCINOMA | LUNG MUCINOUS ADENOCARCINOMA | LUNG PAPILLARY ADENOCARCINOMA | LUNG PAPILLARY SQUAMOUS CELL CARCINOMA | LUNG PAPILLARY SQUAMOUS CELL CARICNOMA | LUNG SMALL CELL SQUAMOUS CELL CARCINOMA | LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA | LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS) | MIXED SEROUS AND ENDOMETRIOID | MUCINOUS (COLLOID) ADENOCARCINOMA | RECTAL ADENOCARCINOMA | RECTAL MUCINOUS ADENOCARCINOMA | SEROUS CYSTADENOCARCINOMA | SEROUS ENDOMETRIAL ADENOCARCINOMA | TREATED PRIMARY GBM | UNTREATED PRIMARY (DE NOVO) GBM
--- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | ---
ALL | 356 | 54 | 350 | 319 | 493 | 10 | 75 | 205 | 7 | 3 | 15 | 2 | 3 | 2 | 13 | 1 | 1 | 1 | 2 | 315 | 18 | 7 | 143 | 13 | 552 | 79 | 1 | 20
AMP PEAK 39(20Q13.2) MUTATED | 273 | 24 | 54 | 122 | 111 | 8 | 31 | 103 | 5 | 1 | 6 | 1 | 2 | 0 | 6 | 0 | 0 | 1 | 2 | 154 | 6 | 0 | 132 | 7 | 370 | 56 | 1 | 6
AMP PEAK 39(20Q13.2) WILD-TYPE | 83 | 30 | 296 | 197 | 382 | 2 | 44 | 102 | 2 | 2 | 9 | 1 | 1 | 2 | 7 | 1 | 1 | 0 | 0 | 161 | 12 | 7 | 11 | 6 | 182 | 23 | 0 | 14

Figure S221. Get High-res Image Clustering Approach #39: 'Amp Peak 39(20q13.2) mutation analysis' versus Clinical Feature #6: 'HISTOLOGICAL.TYPE'

'Amp Peak 39(20q13.2) mutation analysis' versus 'PATHOLOGY.T'

P value = 3.43e-23 (Fisher's exact test), Q value = 5.5e-20

Table S261. Clustering Approach #39: 'Amp Peak 39(20q13.2) mutation analysis' versus Clinical Feature #7: 'PATHOLOGY.T'

nPatients | T0+T1 | T2 | T3 | T4
--- | --- | --- | --- | ---
ALL | 466 | 632 | 694 | 209
AMP PEAK 39(20Q13.2) MUTATED | 138 | 317 | 417 | 109
AMP PEAK 39(20Q13.2) WILD-TYPE | 328 | 315 | 277 | 100

Figure S222. Get High-res Image Clustering Approach #39: 'Amp Peak 39(20q13.2) mutation analysis' versus Clinical Feature #7: 'PATHOLOGY.T'

'Amp Peak 39(20q13.2) mutation analysis' versus 'TUMOR.STAGE'

P value = 7.31e-13 (Fisher's exact test), Q value = 1.1e-09

Table S262. Clustering Approach #39: 'Amp Peak 39(20q13.2) mutation analysis' versus Clinical Feature #10: 'TUMOR.STAGE'

nPatients | I | II | III | IV
--- | --- | --- | --- | ---
ALL | 712 | 498 | 881 | 423
AMP PEAK 39(20Q13.2) MUTATED | 295 | 269 | 535 | 222
AMP PEAK 39(20Q13.2) WILD-TYPE | 417 | 229 | 346 | 201

Figure S223. Get High-res Image Clustering Approach #39: 'Amp Peak 39(20q13.2) mutation analysis' versus Clinical Feature #10: 'TUMOR.STAGE'

'Amp Peak 39(20q13.2) mutation analysis' versus 'RADIATIONS.RADIATION.REGIMENINDICATION'

P value = 6.59e-06 (Fisher's exact test), Q value = 0.0092

Table S263. Clustering Approach #39: 'Amp Peak 39(20q13.2) mutation analysis' versus Clinical Feature #11: 'RADIATIONS.RADIATION.REGIMENINDICATION'

nPatients | NO | YES
--- | --- | ---
ALL | 826 | 3737
AMP PEAK 39(20Q13.2) MUTATED | 341 | 1868
AMP PEAK 39(20Q13.2) WILD-TYPE | 485 | 1869

Figure S224. Get High-res Image Clustering Approach #39: 'Amp Peak 39(20q13.2) mutation analysis' versus Clinical Feature #11: 'RADIATIONS.RADIATION.REGIMENINDICATION'

Clustering Approach #40: 'Amp Peak 40(Xq28) mutation analysis'

Table S264. Description of clustering approach #40: 'Amp Peak 40(Xq28) mutation analysis'

Cluster Labels | AMP PEAK 40(XQ28) MUTATED | AMP PEAK 40(XQ28) WILD-TYPE
--- | --- | ---
Number of samples | 957 | 3606

'Amp Peak 40(Xq28) mutation analysis' versus 'PRIMARY.SITE.OF.DISEASE'

P value = 2.16e-57 (Chi-square test), Q value = 3.6e-54

Table S265. Clustering Approach #40: 'Amp Peak 40(Xq28) mutation analysis' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'

nPatients | BLADDER | BRAIN | BREAST | COLON | ENDOMETRIAL | HEAD/NECK | KIDNEY | LUNG | OMENTUM | OVARY | PERITONEUM (OVARY) | RECTUM
--- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | ---
ALL | 125 | 544 | 846 | 412 | 447 | 319 | 493 | 662 | 2 | 548 | 2 | 159
AMP PEAK 40(XQ28) MUTATED | 25 | 30 | 165 | 82 | 72 | 96 | 38 | 193 | 0 | 217 | 1 | 36
AMP PEAK 40(XQ28) WILD-TYPE | 100 | 514 | 681 | 330 | 375 | 223 | 455 | 469 | 2 | 331 | 1 | 123

Figure S225. Get High-res Image Clustering Approach #40: 'Amp Peak 40(Xq28) mutation analysis' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'

'Amp Peak 40(Xq28) mutation analysis' versus 'HISTOLOGICAL.TYPE'

P value = 3.45e-32 (Chi-square test), Q value = 5.6e-29

Table S266. Clustering Approach #40: 'Amp Peak 40(Xq28) mutation analysis' versus Clinical Feature #6: 'HISTOLOGICAL.TYPE'

nPatients | COLON ADENOCARCINOMA | COLON MUCINOUS ADENOCARCINOMA | ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA | HEAD & NECK SQUAMOUS CELL CARCINOMA | KIDNEY CLEAR CELL RENAL CARCINOMA | LUNG ACINAR ADENOCARCINOMA | LUNG ADENOCARCINOMA MIXED SUBTYPE | LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS) | LUNG BASALOID SQUAMOUS CELL CARCINOMA | LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS | LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS | LUNG CLEAR CELL ADENOCARCINOMA | LUNG MICROPAPILLARY ADENOCARCINOMA | LUNG MUCINOUS ADENOCARCINOMA | LUNG PAPILLARY ADENOCARCINOMA | LUNG PAPILLARY SQUAMOUS CELL CARCINOMA | LUNG PAPILLARY SQUAMOUS CELL CARICNOMA | LUNG SMALL CELL SQUAMOUS CELL CARCINOMA | LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA | LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS) | MIXED SEROUS AND ENDOMETRIOID | MUCINOUS (COLLOID) ADENOCARCINOMA | RECTAL ADENOCARCINOMA | RECTAL MUCINOUS ADENOCARCINOMA | SEROUS CYSTADENOCARCINOMA | SEROUS ENDOMETRIAL ADENOCARCINOMA | TREATED PRIMARY GBM | UNTREATED PRIMARY (DE NOVO) GBM
--- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | ---
ALL | 356 | 54 | 350 | 319 | 493 | 10 | 75 | 205 | 7 | 3 | 15 | 2 | 3 | 2 | 13 | 1 | 1 | 1 | 2 | 315 | 18 | 7 | 143 | 13 | 552 | 79 | 1 | 20
AMP PEAK 40(XQ28) MUTATED | 77 | 5 | 46 | 96 | 38 | 4 | 23 | 74 | 2 | 1 | 2 | 1 | 1 | 0 | 4 | 1 | 0 | 0 | 0 | 80 | 2 | 0 | 34 | 1 | 218 | 24 | 0 | 1
AMP PEAK 40(XQ28) WILD-TYPE | 279 | 49 | 304 | 223 | 455 | 6 | 52 | 131 | 5 | 2 | 13 | 1 | 2 | 2 | 9 | 0 | 1 | 1 | 2 | 235 | 16 | 7 | 109 | 12 | 334 | 55 | 1 | 19

Figure S226. Get High-res Image Clustering Approach #40: 'Amp Peak 40(Xq28) mutation analysis' versus Clinical Feature #6: 'HISTOLOGICAL.TYPE'

'Amp Peak 40(Xq28) mutation analysis' versus 'PATHOLOGY.T'

P value = 1.11e-08 (Fisher's exact test), Q value = 1.6e-05

Table S267. Clustering Approach #40: 'Amp Peak 40(Xq28) mutation analysis' versus Clinical Feature #7: 'PATHOLOGY.T'

nPatients | T0+T1 | T2 | T3 | T4
--- | --- | --- | --- | ---
ALL | 466 | 632 | 694 | 209
AMP PEAK 40(XQ28) MUTATED | 60 | 174 | 144 | 57
AMP PEAK 40(XQ28) WILD-TYPE | 406 | 458 | 550 | 152

Figure S227. Get High-res Image Clustering Approach #40: 'Amp Peak 40(Xq28) mutation analysis' versus Clinical Feature #7: 'PATHOLOGY.T'

'Amp Peak 40(Xq28) mutation analysis' versus 'PATHOLOGY.N'

P value = 0.00012 (Fisher's exact test), Q value = 0.16

Table S268. Clustering Approach #40: 'Amp Peak 40(Xq28) mutation analysis' versus Clinical Feature #8: 'PATHOLOGY.N'

nPatients | N0 | N1 | N2 | N3
--- | --- | --- | --- | ---
ALL | 1067 | 353 | 282 | 11
AMP PEAK 40(XQ28) MUTATED | 219 | 96 | 92 | 2
AMP PEAK 40(XQ28) WILD-TYPE | 848 | 257 | 190 | 9

Figure S228. Get High-res Image Clustering Approach #40: 'Amp Peak 40(Xq28) mutation analysis' versus Clinical Feature #8: 'PATHOLOGY.N'

'Amp Peak 40(Xq28) mutation analysis' versus 'TUMOR.STAGE'

P value = 6.86e-07 (Fisher's exact test), Q value = 0.00099

Table S269. Clustering Approach #40: 'Amp Peak 40(Xq28) mutation analysis' versus Clinical Feature #10: 'TUMOR.STAGE'

nPatients | I | II | III | IV
--- | --- | --- | --- | ---
ALL | 712 | 498 | 881 | 423
AMP PEAK 40(XQ28) MUTATED | 133 | 121 | 257 | 131
AMP PEAK 40(XQ28) WILD-TYPE | 579 | 377 | 624 | 292

Figure S229. Get High-res Image Clustering Approach #40: 'Amp Peak 40(Xq28) mutation analysis' versus Clinical Feature #10: 'TUMOR.STAGE'

Clustering Approach #41: 'Del Peak 1(1p36.23) mutation analysis'

Table S270. Description of clustering approach #41: 'Del Peak 1(1p36.23) mutation analysis'

Cluster Labels | DEL PEAK 1(1P36.23) MUTATED | DEL PEAK 1(1P36.23) WILD-TYPE
--- | --- | ---
Number of samples | 1333 | 3230

'Del Peak 1(1p36.23) mutation analysis' versus 'PRIMARY.SITE.OF.DISEASE'

P value = 2.47e-38 (Chi-square test), Q value = 4.1e-35

Table S271. Clustering Approach #41: 'Del Peak 1(1p36.23) mutation analysis' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'

nPatients | BLADDER | BRAIN | BREAST | COLON | ENDOMETRIAL | HEAD/NECK | KIDNEY | LUNG | OMENTUM | OVARY | PERITONEUM (OVARY) | RECTUM
--- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | ---
ALL | 125 | 544 | 846 | 412 | 447 | 319 | 493 | 662 | 2 | 548 | 2 | 159
DEL PEAK 1(1P36.23) MUTATED | 22 | 129 | 348 | 135 | 54 | 65 | 97 | 213 | 2 | 200 | 0 | 65
DEL PEAK 1(1P36.23) WILD-TYPE | 103 | 415 | 498 | 277 | 393 | 254 | 396 | 449 | 0 | 348 | 2 | 94

Figure S230. Get High-res Image Clustering Approach #41: 'Del Peak 1(1p36.23) mutation analysis' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'

'Del Peak 1(1p36.23) mutation analysis' versus 'HISTOLOGICAL.TYPE'

P value = 1.86e-30 (Chi-square test), Q value = 3e-27

Table S272. Clustering Approach #41: 'Del Peak 1(1p36.23) mutation analysis' versus Clinical Feature #6: 'HISTOLOGICAL.TYPE'

nPatients | COLON ADENOCARCINOMA | COLON MUCINOUS ADENOCARCINOMA | ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA | HEAD & NECK SQUAMOUS CELL CARCINOMA | KIDNEY CLEAR CELL RENAL CARCINOMA | LUNG ACINAR ADENOCARCINOMA | LUNG ADENOCARCINOMA MIXED SUBTYPE | LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS) | LUNG BASALOID SQUAMOUS CELL CARCINOMA | LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS | LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS | LUNG CLEAR CELL ADENOCARCINOMA | LUNG MICROPAPILLARY ADENOCARCINOMA | LUNG MUCINOUS ADENOCARCINOMA | LUNG PAPILLARY ADENOCARCINOMA | LUNG PAPILLARY SQUAMOUS CELL CARCINOMA | LUNG PAPILLARY SQUAMOUS CELL CARICNOMA | LUNG SMALL CELL SQUAMOUS CELL CARCINOMA | LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA | LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS) | MIXED SEROUS AND ENDOMETRIOID | MUCINOUS (COLLOID) ADENOCARCINOMA | RECTAL ADENOCARCINOMA | RECTAL MUCINOUS ADENOCARCINOMA | SEROUS CYSTADENOCARCINOMA | SEROUS ENDOMETRIAL ADENOCARCINOMA | TREATED PRIMARY GBM | UNTREATED PRIMARY (DE NOVO) GBM
--- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | ---
ALL | 356 | 54 | 350 | 319 | 493 | 10 | 75 | 205 | 7 | 3 | 15 | 2 | 3 | 2 | 13 | 1 | 1 | 1 | 2 | 315 | 18 | 7 | 143 | 13 | 552 | 79 | 1 | 20
DEL PEAK 1(1P36.23) MUTATED | 125 | 10 | 23 | 65 | 97 | 3 | 21 | 43 | 4 | 0 | 3 | 1 | 0 | 0 | 1 | 1 | 0 | 1 | 0 | 134 | 4 | 1 | 57 | 7 | 202 | 27 | 0 | 6
DEL PEAK 1(1P36.23) WILD-TYPE | 231 | 44 | 327 | 254 | 396 | 7 | 54 | 162 | 3 | 3 | 12 | 1 | 3 | 2 | 12 | 0 | 1 | 0 | 2 | 181 | 14 | 6 | 86 | 6 | 350 | 52 | 1 | 14

Figure S231. Get High-res Image Clustering Approach #41: 'Del Peak 1(1p36.23) mutation analysis' versus Clinical Feature #6: 'HISTOLOGICAL.TYPE'

'Del Peak 1(1p36.23) mutation analysis' versus 'NEOPLASM.DISEASESTAGE'

P value = 2e-05 (Chi-square test), Q value = 0.027

Table S273. Clustering Approach #41: 'Del Peak 1(1p36.23) mutation analysis' versus Clinical Feature #21: 'NEOPLASM.DISEASESTAGE'

nPatients | STAGE I | STAGE IA | STAGE IB | STAGE II | STAGE IIA | STAGE IIB | STAGE III | STAGE IIIA | STAGE IIIB | STAGE IIIC | STAGE IV | STAGE TIS | STAGE X
--- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | ---
ALL | 72 | 62 | 7 | 43 | 287 | 186 | 42 | 124 | 25 | 41 | 59 | 1 | 16
DEL PEAK 1(1P36.23) MUTATED | 20 | 18 | 3 | 4 | 117 | 79 | 8 | 61 | 15 | 17 | 18 | 0 | 6
DEL PEAK 1(1P36.23) WILD-TYPE | 52 | 44 | 4 | 39 | 170 | 107 | 34 | 63 | 10 | 24 | 41 | 1 | 10

Figure S232. Get High-res Image Clustering Approach #41: 'Del Peak 1(1p36.23) mutation analysis' versus Clinical Feature #21: 'NEOPLASM.DISEASESTAGE'

Clustering Approach #42: 'Del Peak 2(1p36.11) mutation analysis'

Table S274. Description of clustering approach #42: 'Del Peak 2(1p36.11) mutation analysis'

Cluster Labels | DEL PEAK 2(1P36.11) MUTATED | DEL PEAK 2(1P36.11) WILD-TYPE
--- | --- | ---
Number of samples | 1354 | 3209

'Del Peak 2(1p36.11) mutation analysis' versus 'PRIMARY.SITE.OF.DISEASE'

P value = 3.87e-76 (Chi-square test), Q value = 6.6e-73

Table S275. Clustering Approach #42: 'Del Peak 2(1p36.11) mutation analysis' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'

nPatients | BLADDER | BRAIN | BREAST | COLON | ENDOMETRIAL | HEAD/NECK | KIDNEY | LUNG | OMENTUM | OVARY | PERITONEUM (OVARY) | RECTUM
--- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | ---
ALL | 125 | 544 | 846 | 412 | 447 | 319 | 493 | 662 | 2 | 548 | 2 | 159
DEL PEAK 2(1P36.11) MUTATED | 25 | 47 | 353 | 150 | 59 | 64 | 95 | 233 | 1 | 255 | 0 | 69
DEL PEAK 2(1P36.11) WILD-TYPE | 100 | 497 | 493 | 262 | 388 | 255 | 398 | 429 | 1 | 293 | 2 | 90

Figure S233. Get High-res Image Clustering Approach #42: 'Del Peak 2(1p36.11) mutation analysis' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'

'Del Peak 2(1p36.11) mutation analysis' versus 'HISTOLOGICAL.TYPE'

P value = 1.12e-45 (Chi-square test), Q value = 1.9e-42

Table S276. Clustering Approach #42: 'Del Peak 2(1p36.11) mutation analysis' versus Clinical Feature #6: 'HISTOLOGICAL.TYPE'

nPatients | COLON ADENOCARCINOMA | COLON MUCINOUS ADENOCARCINOMA | ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA | HEAD & NECK SQUAMOUS CELL CARCINOMA | KIDNEY CLEAR CELL RENAL CARCINOMA | LUNG ACINAR ADENOCARCINOMA | LUNG ADENOCARCINOMA MIXED SUBTYPE | LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS) | LUNG BASALOID SQUAMOUS CELL CARCINOMA | LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS | LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS | LUNG CLEAR CELL ADENOCARCINOMA | LUNG MICROPAPILLARY ADENOCARCINOMA | LUNG MUCINOUS ADENOCARCINOMA | LUNG PAPILLARY ADENOCARCINOMA | LUNG PAPILLARY SQUAMOUS CELL CARCINOMA | LUNG PAPILLARY SQUAMOUS CELL CARICNOMA | LUNG SMALL CELL SQUAMOUS CELL CARCINOMA | LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA | LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS) | MIXED SEROUS AND ENDOMETRIOID | MUCINOUS (COLLOID) ADENOCARCINOMA | RECTAL ADENOCARCINOMA | RECTAL MUCINOUS ADENOCARCINOMA | SEROUS CYSTADENOCARCINOMA | SEROUS ENDOMETRIAL ADENOCARCINOMA | TREATED PRIMARY GBM | UNTREATED PRIMARY (DE NOVO) GBM
--- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | ---
ALL | 356 | 54 | 350 | 319 | 493 | 10 | 75 | 205 | 7 | 3 | 15 | 2 | 3 | 2 | 13 | 1 | 1 | 1 | 2 | 315 | 18 | 7 | 143 | 13 | 552 | 79 | 1 | 20
DEL PEAK 2(1P36.11) MUTATED | 139 | 10 | 24 | 64 | 95 | 5 | 21 | 52 | 3 | 0 | 3 | 1 | 0 | 0 | 2 | 1 | 0 | 1 | 1 | 142 | 4 | 1 | 61 | 7 | 256 | 31 | 0 | 3
DEL PEAK 2(1P36.11) WILD-TYPE | 217 | 44 | 326 | 255 | 398 | 5 | 54 | 153 | 4 | 3 | 12 | 1 | 3 | 2 | 11 | 0 | 1 | 0 | 1 | 173 | 14 | 6 | 82 | 6 | 296 | 48 | 1 | 17

Figure S234. Get High-res Image Clustering Approach #42: 'Del Peak 2(1p36.11) mutation analysis' versus Clinical Feature #6: 'HISTOLOGICAL.TYPE'

'Del Peak 2(1p36.11) mutation analysis' versus 'TUMOR.STAGE'

P value = 1.72e-06 (Fisher's exact test), Q value = 0.0025

Table S277. Clustering Approach #42: 'Del Peak 2(1p36.11) mutation analysis' versus Clinical Feature #10: 'TUMOR.STAGE'

nPatients | I | II | III | IV
--- | --- | --- | --- | ---
ALL | 712 | 498 | 881 | 423
DEL PEAK 2(1P36.11) MUTATED | 196 | 150 | 350 | 147
DEL PEAK 2(1P36.11) WILD-TYPE | 516 | 348 | 531 | 276

Figure S235. Get High-res Image Clustering Approach #42: 'Del Peak 2(1p36.11) mutation analysis' versus Clinical Feature #10: 'TUMOR.STAGE'

'Del Peak 2(1p36.11) mutation analysis' versus 'RADIATIONS.RADIATION.REGIMENINDICATION'

P value = 1.84e-11 (Fisher's exact test), Q value = 2.8e-08

Table S278. Clustering Approach #42: 'Del Peak 2(1p36.11) mutation analysis' versus Clinical Feature #11: 'RADIATIONS.RADIATION.REGIMENINDICATION'

nPatients | NO | YES
--- | --- | ---
ALL | 826 | 3737
DEL PEAK 2(1P36.11) MUTATED | 167 | 1187
DEL PEAK 2(1P36.11) WILD-TYPE | 659 | 2550

Figure S236. Get High-res Image Clustering Approach #42: 'Del Peak 2(1p36.11) mutation analysis' versus Clinical Feature #11: 'RADIATIONS.RADIATION.REGIMENINDICATION'

'Del Peak 2(1p36.11) mutation analysis' versus 'TOBACCOSMOKINGHISTORYINDICATOR'

P value = 1.64e-05 (Chi-square test), Q value = 0.022

Table S279. Clustering Approach #42: 'Del Peak 2(1p36.11) mutation analysis' versus Clinical Feature #14: 'TOBACCOSMOKINGHISTORYINDICATOR'

nPatients | 1 | 2 | 3 | 4 | 5 | CURRENT REFORMED SMOKER FOR < OR = 15 YEARS | CURRENT REFORMED SMOKER FOR > 15 YEARS | CURRENT SMOKER | LIFELONG NON-SMOKER
--- | --- | --- | --- | --- | --- | --- | --- | --- | ---
ALL | 28 | 23 | 37 | 29 | 2 | 355 | 217 | 250 | 128
DEL PEAK 2(1P36.11) MUTATED | 4 | 3 | 13 | 4 | 0 | 123 | 58 | 90 | 18
DEL PEAK 2(1P36.11) WILD-TYPE | 24 | 20 | 24 | 25 | 2 | 232 | 159 | 160 | 110

Figure S237. Get High-res Image Clustering Approach #42: 'Del Peak 2(1p36.11) mutation analysis' versus Clinical Feature #14: 'TOBACCOSMOKINGHISTORYINDICATOR'

'Del Peak 2(1p36.11) mutation analysis' versus 'NUMBER.OF.LYMPH.NODES'

P value = 4.47e-05 (t-test), Q value = 0.06

Table S280. Clustering Approach #42: 'Del Peak 2(1p36.11) mutation analysis' versus Clinical Feature #19: 'NUMBER.OF.LYMPH.NODES'

| nPatients | Mean (Std.Dev)
--- | --- | ---
ALL | 1576 | 2.3 (4.6)
DEL PEAK 2(1P36.11) MUTATED | 569 | 3.0 (5.8)
DEL PEAK 2(1P36.11) WILD-TYPE | 1007 | 1.9 (3.7)

Figure S238. Get High-res Image Clustering Approach #42: 'Del Peak 2(1p36.11) mutation analysis' versus Clinical Feature #19: 'NUMBER.OF.LYMPH.NODES'

'Del Peak 2(1p36.11) mutation analysis' versus 'NEOPLASM.DISEASESTAGE'

P value = 6.09e-06 (Chi-square test), Q value = 0.0085

Table S281. Clustering Approach #42: 'Del Peak 2(1p36.11) mutation analysis' versus Clinical Feature #21: 'NEOPLASM.DISEASESTAGE'

nPatients | STAGE I | STAGE IA | STAGE IB | STAGE II | STAGE IIA | STAGE IIB | STAGE III | STAGE IIIA | STAGE IIIB | STAGE IIIC | STAGE IV | STAGE TIS | STAGE X
--- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | ---
ALL | 72 | 62 | 7 | 43 | 287 | 186 | 42 | 124 | 25 | 41 | 59 | 1 | 16
DEL PEAK 2(1P36.11) MUTATED | 17 | 17 | 3 | 7 | 124 | 81 | 9 | 60 | 17 | 18 | 17 | 0 | 6
DEL PEAK 2(1P36.11) WILD-TYPE | 55 | 45 | 4 | 36 | 163 | 105 | 33 | 64 | 8 | 23 | 42 | 1 | 10

Figure S239. Get High-res Image Clustering Approach #42: 'Del Peak 2(1p36.11) mutation analysis' versus Clinical Feature #21: 'NEOPLASM.DISEASESTAGE'

Clustering Approach #43: 'Del Peak 3(1p13.2) mutation analysis'

Table S282. Description of clustering approach #43: 'Del Peak 3(1p13.2) mutation analysis'

Cluster Labels | DEL PEAK 3(1P13.2) MUTATED | DEL PEAK 3(1P13.2) WILD-TYPE
--- | --- | ---
Number of samples | 964 | 3599

'Del Peak 3(1p13.2) mutation analysis' versus 'AGE'

P value = 1.66e-05 (t-test), Q value = 0.023

Table S283. Clustering Approach #43: 'Del Peak 3(1p13.2) mutation analysis' versus Clinical Feature #2: 'AGE'

| nPatients | Mean (Std.Dev)
--- | --- | ---
ALL | 4507 | 61.9 (12.6)
DEL PEAK 3(1P13.2) MUTATED | 953 | 63.4 (12.1)
DEL PEAK 3(1P13.2) WILD-TYPE | 3554 | 61.4 (12.8)

Figure S240. Get High-res Image Clustering Approach #43: 'Del Peak 3(1p13.2) mutation analysis' versus Clinical Feature #2: 'AGE'

'Del Peak 3(1p13.2) mutation analysis' versus 'PRIMARY.SITE.OF.DISEASE'

P value = 2.36e-70 (Chi-square test), Q value = 4e-67

Table S284. Clustering Approach #43: 'Del Peak 3(1p13.2) mutation analysis' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'

nPatients | BLADDER | BRAIN | BREAST | COLON | ENDOMETRIAL | HEAD/NECK | KIDNEY | LUNG | OMENTUM | OVARY | PERITONEUM (OVARY) | RECTUM
--- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | ---
ALL | 125 | 544 | 846 | 412 | 447 | 319 | 493 | 662 | 2 | 548 | 2 | 159
DEL PEAK 3(1P13.2) MUTATED | 19 | 23 | 251 | 107 | 25 | 78 | 59 | 251 | 0 | 97 | 1 | 51
DEL PEAK 3(1P13.2) WILD-TYPE | 106 | 521 | 595 | 305 | 422 | 241 | 434 | 411 | 2 | 451 | 1 | 108

Figure S241. Get High-res Image Clustering Approach #43: 'Del Peak 3(1p13.2) mutation analysis' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'

'Del Peak 3(1p13.2) mutation analysis' versus 'HISTOLOGICAL.TYPE'

P value = 5.09e-41 (Chi-square test), Q value = 8.4e-38

Table S285. Clustering Approach #43: 'Del Peak 3(1p13.2) mutation analysis' versus Clinical Feature #6: 'HISTOLOGICAL.TYPE'

nPatients | COLON ADENOCARCINOMA | COLON MUCINOUS ADENOCARCINOMA | ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA | HEAD & NECK SQUAMOUS CELL CARCINOMA | KIDNEY CLEAR CELL RENAL CARCINOMA | LUNG ACINAR ADENOCARCINOMA | LUNG ADENOCARCINOMA MIXED SUBTYPE | LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS) | LUNG BASALOID SQUAMOUS CELL CARCINOMA | LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS | LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS | LUNG CLEAR CELL ADENOCARCINOMA | LUNG MICROPAPILLARY ADENOCARCINOMA | LUNG MUCINOUS ADENOCARCINOMA | LUNG PAPILLARY ADENOCARCINOMA | LUNG PAPILLARY SQUAMOUS CELL CARCINOMA | LUNG PAPILLARY SQUAMOUS CELL CARICNOMA | LUNG SMALL CELL SQUAMOUS CELL CARCINOMA | LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA | LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS) | MIXED SEROUS AND ENDOMETRIOID | MUCINOUS (COLLOID) ADENOCARCINOMA | RECTAL ADENOCARCINOMA | RECTAL MUCINOUS ADENOCARCINOMA | SEROUS CYSTADENOCARCINOMA | SEROUS ENDOMETRIAL ADENOCARCINOMA | TREATED PRIMARY GBM | UNTREATED PRIMARY (DE NOVO) GBM
--- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | ---
ALL | 356 | 54 | 350 | 319 | 493 | 10 | 75 | 205 | 7 | 3 | 15 | 2 | 3 | 2 | 13 | 1 | 1 | 1 | 2 | 315 | 18 | 7 | 143 | 13 | 552 | 79 | 1 | 20
DEL PEAK 3(1P13.2) MUTATED | 98 | 9 | 11 | 78 | 59 | 4 | 26 | 60 | 3 | 0 | 6 | 1 | 0 | 0 | 6 | 1 | 0 | 0 | 1 | 141 | 3 | 2 | 48 | 2 | 98 | 11 | 0 | 0
DEL PEAK 3(1P13.2) WILD-TYPE | 258 | 45 | 339 | 241 | 434 | 6 | 49 | 145 | 4 | 3 | 9 | 1 | 3 | 2 | 7 | 0 | 1 | 1 | 1 | 174 | 15 | 5 | 95 | 11 | 454 | 68 | 1 | 20

Figure S242. Get High-res Image Clustering Approach #43: 'Del Peak 3(1p13.2) mutation analysis' versus Clinical Feature #6: 'HISTOLOGICAL.TYPE'

'Del Peak 3(1p13.2) mutation analysis' versus 'RADIATIONS.RADIATION.REGIMENINDICATION'

P value = 9.22e-12 (Fisher's exact test), Q value = 1.4e-08

Table S286. Clustering Approach #43: 'Del Peak 3(1p13.2) mutation analysis' versus Clinical Feature #11: 'RADIATIONS.RADIATION.REGIMENINDICATION'

nPatients | NO | YES
--- | --- | ---
ALL | 826 | 3737
DEL PEAK 3(1P13.2) MUTATED | 105 | 859
DEL PEAK 3(1P13.2) WILD-TYPE | 721 | 2878

Figure S243. Get High-res Image Clustering Approach #43: 'Del Peak 3(1p13.2) mutation analysis' versus Clinical Feature #11: 'RADIATIONS.RADIATION.REGIMENINDICATION'

'Del Peak 3(1p13.2) mutation analysis' versus 'TOBACCOSMOKINGHISTORYINDICATOR'

P value = 5.7e-05 (Chi-square test), Q value = 0.076

Table S287. Clustering Approach #43: 'Del Peak 3(1p13.2) mutation analysis' versus Clinical Feature #14: 'TOBACCOSMOKINGHISTORYINDICATOR'

nPatients | 1 | 2 | 3 | 4 | 5 | CURRENT REFORMED SMOKER FOR < OR = 15 YEARS | CURRENT REFORMED SMOKER FOR > 15 YEARS | CURRENT SMOKER | LIFELONG NON-SMOKER
--- | --- | --- | --- | --- | --- | --- | --- | --- | ---
ALL | 28 | 23 | 37 | 29 | 2 | 355 | 217 | 250 | 128
DEL PEAK 3(1P13.2) MUTATED | 3 | 4 | 7 | 5 | 0 | 138 | 63 | 92 | 27
DEL PEAK 3(1P13.2) WILD-TYPE | 25 | 19 | 30 | 24 | 2 | 217 | 154 | 158 | 101

Figure S244. Get High-res Image Clustering Approach #43: 'Del Peak 3(1p13.2) mutation analysis' versus Clinical Feature #14: 'TOBACCOSMOKINGHISTORYINDICATOR'

'Del Peak 3(1p13.2) mutation analysis' versus 'NUMBER.OF.LYMPH.NODES'

P value = 0.000131 (t-test), Q value = 0.17

Table S288. Clustering Approach #43: 'Del Peak 3(1p13.2) mutation analysis' versus Clinical Feature #19: 'NUMBER.OF.LYMPH.NODES'

| nPatients | Mean (Std.Dev)
--- | --- | ---
ALL | 1576 | 2.3 (4.6)
DEL PEAK 3(1P13.2) MUTATED | 425 | 3.1 (5.5)
DEL PEAK 3(1P13.2) WILD-TYPE | 1151 | 2.0 (4.3)

Figure S245. Get High-res Image Clustering Approach #43: 'Del Peak 3(1p13.2) mutation analysis' versus Clinical Feature #19: 'NUMBER.OF.LYMPH.NODES'

Clustering Approach #44: 'Del Peak 4(2q22.1) mutation analysis'

Table S289. Description of clustering approach #44: 'Del Peak 4(2q22.1) mutation analysis'

Cluster Labels | DEL PEAK 4(2Q22.1) MUTATED | DEL PEAK 4(2Q22.1) WILD-TYPE
--- | --- | ---
Number of samples | 675 | 3888

'Del Peak 4(2q22.1) mutation analysis' versus 'PRIMARY.SITE.OF.DISEASE'

P value = 2.01e-45 (Chi-square test), Q value = 3.3e-42

Table S290. Clustering Approach #44: 'Del Peak 4(2q22.1) mutation analysis' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'

nPatients | BLADDER | BRAIN | BREAST | COLON | ENDOMETRIAL | HEAD/NECK | KIDNEY | LUNG | OMENTUM | OVARY | PERITONEUM (OVARY) | RECTUM
--- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | ---
ALL | 125 | 544 | 846 | 412 | 447 | 319 | 493 | 662 | 2 | 548 | 2 | 159
DEL PEAK 4(2Q22.1) MUTATED | 38 | 43 | 193 | 24 | 31 | 64 | 19 | 124 | 0 | 128 | 1 | 10
DEL PEAK 4(2Q22.1) WILD-TYPE | 87 | 501 | 653 | 388 | 416 | 255 | 474 | 538 | 2 | 420 | 1 | 149

Figure S246. Get High-res Image Clustering Approach #44: 'Del Peak 4(2q22.1) mutation analysis' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'

'Del Peak 4(2q22.1) mutation analysis' versus 'HISTOLOGICAL.TYPE'

P value = 1.85e-35 (Chi-square test), Q value = 3e-32

Table S291. Clustering Approach #44: 'Del Peak 4(2q22.1) mutation analysis' versus Clinical Feature #6: 'HISTOLOGICAL.TYPE'

nPatients | COLON ADENOCARCINOMA | COLON MUCINOUS ADENOCARCINOMA | ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA | HEAD & NECK SQUAMOUS CELL CARCINOMA | KIDNEY CLEAR CELL RENAL CARCINOMA | LUNG ACINAR ADENOCARCINOMA | LUNG ADENOCARCINOMA MIXED SUBTYPE | LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS) | LUNG BASALOID SQUAMOUS CELL CARCINOMA | LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS | LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS | LUNG CLEAR CELL ADENOCARCINOMA | LUNG MICROPAPILLARY ADENOCARCINOMA | LUNG MUCINOUS ADENOCARCINOMA | LUNG PAPILLARY ADENOCARCINOMA | LUNG PAPILLARY SQUAMOUS CELL CARCINOMA | LUNG PAPILLARY SQUAMOUS CELL CARICNOMA | LUNG SMALL CELL SQUAMOUS CELL CARCINOMA | LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA | LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS) | MIXED SEROUS AND ENDOMETRIOID | MUCINOUS (COLLOID) ADENOCARCINOMA | RECTAL ADENOCARCINOMA | RECTAL MUCINOUS ADENOCARCINOMA | SEROUS CYSTADENOCARCINOMA | SEROUS ENDOMETRIAL ADENOCARCINOMA | TREATED PRIMARY GBM | UNTREATED PRIMARY (DE NOVO) GBM
--- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | ---
ALL | 356 | 54 | 350 | 319 | 493 | 10 | 75 | 205 | 7 | 3 | 15 | 2 | 3 | 2 | 13 | 1 | 1 | 1 | 2 | 315 | 18 | 7 | 143 | 13 | 552 | 79 | 1 | 20
DEL PEAK 4(2Q22.1) MUTATED | 22 | 2 | 15 | 64 | 19 | 3 | 7 | 19 | 0 | 0 | 3 | 0 | 0 | 0 | 4 | 1 | 0 | 1 | 0 | 85 | 1 | 1 | 9 | 0 | 129 | 15 | 0 | 1
DEL PEAK 4(2Q22.1) WILD-TYPE | 334 | 52 | 335 | 255 | 474 | 7 | 68 | 186 | 7 | 3 | 12 | 2 | 3 | 2 | 9 | 0 | 1 | 0 | 2 | 230 | 17 | 6 | 134 | 13 | 423 | 64 | 1 | 19

Figure S247. Get High-res Image Clustering Approach #44: 'Del Peak 4(2q22.1) mutation analysis' versus Clinical Feature #6: 'HISTOLOGICAL.TYPE'

'Del Peak 4(2q22.1) mutation analysis' versus 'PATHOLOGY.T'

P value = 9.01e-06 (Fisher's exact test), Q value = 0.013

Table S292. Clustering Approach #44: 'Del Peak 4(2q22.1) mutation analysis' versus Clinical Feature #7: 'PATHOLOGY.T'

nPatients | T0+T1 | T2 | T3 | T4
--- | --- | --- | --- | ---
ALL | 466 | 632 | 694 | 209
DEL PEAK 4(2Q22.1) MUTATED | 40 | 95 | 59 | 38
DEL PEAK 4(2Q22.1) WILD-TYPE | 426 | 537 | 635 | 171

Figure S248. Get High-res Image Clustering Approach #44: 'Del Peak 4(2q22.1) mutation analysis' versus Clinical Feature #7: 'PATHOLOGY.T'

'Del Peak 4(2q22.1) mutation analysis' versus 'TUMOR.STAGE'

P value = 1.02e-05 (Fisher's exact test), Q value = 0.014

Table S293. Clustering Approach #44: 'Del Peak 4(2q22.1) mutation analysis' versus Clinical Feature #10: 'TUMOR.STAGE'

nPatients | I | II | III | IV
--- | --- | --- | --- | ---
ALL | 712 | 498 | 881 | 423
DEL PEAK 4(2Q22.1) MUTATED | 65 | 73 | 156 | 66
DEL PEAK 4(2Q22.1) WILD-TYPE | 647 | 425 | 725 | 357

Figure S249. Get High-res Image Clustering Approach #44: 'Del Peak 4(2q22.1) mutation analysis' versus Clinical Feature #10: 'TUMOR.STAGE'

Clustering Approach #45: 'Del Peak 5(2q37.3) mutation analysis'

Table S294. Description of clustering approach #45: 'Del Peak 5(2q37.3) mutation analysis'

Cluster Labels | DEL PEAK 5(2Q37.3) MUTATED | DEL PEAK 5(2Q37.3) WILD-TYPE
--- | --- | ---
Number of samples | 910 | 3653

'Del Peak 5(2q37.3) mutation analysis' versus 'PRIMARY.SITE.OF.DISEASE'

P value = 9.98e-68 (Chi-square test), Q value = 1.7e-64

Table S295. Clustering Approach #45: 'Del Peak 5(2q37.3) mutation analysis' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'

nPatients | BLADDER | BRAIN | BREAST | COLON | ENDOMETRIAL | HEAD/NECK | KIDNEY | LUNG | OMENTUM | OVARY | PERITONEUM (OVARY) | RECTUM
--- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | ---
ALL | 125 | 544 | 846 | 412 | 447 | 319 | 493 | 662 | 2 | 548 | 2 | 159
DEL PEAK 5(2Q37.3) MUTATED | 60 | 58 | 253 | 21 | 40 | 92 | 47 | 156 | 1 | 169 | 1 | 12
DEL PEAK 5(2Q37.3) WILD-TYPE | 65 | 486 | 593 | 391 | 407 | 227 | 446 | 506 | 1 | 379 | 1 | 147

Figure S250. Get High-res Image Clustering Approach #45: 'Del Peak 5(2q37.3) mutation analysis' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'

'Del Peak 5(2q37.3) mutation analysis' versus 'HISTOLOGICAL.TYPE'

P value = 1.66e-41 (Chi-square test), Q value = 2.7e-38

Table S296. Clustering Approach #45: 'Del Peak 5(2q37.3) mutation analysis' versus Clinical Feature #6: 'HISTOLOGICAL.TYPE'

nPatients | COLON ADENOCARCINOMA | COLON MUCINOUS ADENOCARCINOMA | ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA | HEAD & NECK SQUAMOUS CELL CARCINOMA | KIDNEY CLEAR CELL RENAL CARCINOMA | LUNG ACINAR ADENOCARCINOMA | LUNG ADENOCARCINOMA MIXED SUBTYPE | LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS) | LUNG BASALOID SQUAMOUS CELL CARCINOMA | LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS | LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS | LUNG CLEAR CELL ADENOCARCINOMA | LUNG MICROPAPILLARY ADENOCARCINOMA | LUNG MUCINOUS ADENOCARCINOMA | LUNG PAPILLARY ADENOCARCINOMA | LUNG PAPILLARY SQUAMOUS CELL CARCINOMA | LUNG PAPILLARY SQUAMOUS CELL CARICNOMA | LUNG SMALL CELL SQUAMOUS CELL CARCINOMA | LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA | LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS) | MIXED SEROUS AND ENDOMETRIOID | MUCINOUS (COLLOID) ADENOCARCINOMA | RECTAL ADENOCARCINOMA | RECTAL MUCINOUS ADENOCARCINOMA | SEROUS CYSTADENOCARCINOMA | SEROUS ENDOMETRIAL ADENOCARCINOMA | TREATED PRIMARY GBM | UNTREATED PRIMARY (DE NOVO) GBM
--- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | ---
ALL | 356 | 54 | 350 | 319 | 493 | 10 | 75 | 205 | 7 | 3 | 15 | 2 | 3 | 2 | 13 | 1 | 1 | 1 | 2 | 315 | 18 | 7 | 143 | 13 | 552 | 79 | 1 | 20
DEL PEAK 5(2Q37.3) MUTATED | 19 | 1 | 24 | 92 | 47 | 3 | 7 | 32 | 2 | 0 | 5 | 1 | 0 | 0 | 4 | 1 | 0 | 0 | 0 | 100 | 2 | 1 | 11 | 0 | 171 | 14 | 0 | 2
DEL PEAK 5(2Q37.3) WILD-TYPE | 337 | 53 | 326 | 227 | 446 | 7 | 68 | 173 | 5 | 3 | 10 | 1 | 3 | 2 | 9 | 0 | 1 | 1 | 2 | 215 | 16 | 6 | 132 | 13 | 381 | 65 | 1 | 18

Figure S251. Get High-res Image Clustering Approach #45: 'Del Peak 5(2q37.3) mutation analysis' versus Clinical Feature #6: 'HISTOLOGICAL.TYPE'

'Del Peak 5(2q37.3) mutation analysis' versus 'TOBACCOSMOKINGHISTORYINDICATOR'

P value = 2.11e-06 (Chi-square test), Q value = 0.003

Table S297. Clustering Approach #45: 'Del Peak 5(2q37.3) mutation analysis' versus Clinical Feature #14: 'TOBACCOSMOKINGHISTORYINDICATOR'

nPatients | 1 | 2 | 3 | 4 | 5 | CURRENT REFORMED SMOKER FOR < OR = 15 YEARS | CURRENT REFORMED SMOKER FOR > 15 YEARS | CURRENT SMOKER | LIFELONG NON-SMOKER
--- | --- | --- | --- | --- | --- | --- | --- | --- | ---
ALL | 28 | 23 | 37 | 29 | 2 | 355 | 217 | 250 | 128
DEL PEAK 5(2Q37.3) MUTATED | 13 | 6 | 19 | 15 | 2 | 89 | 42 | 81 | 31
DEL PEAK 5(2Q37.3) WILD-TYPE | 15 | 17 | 18 | 14 | 0 | 266 | 175 | 169 | 97

Figure S252. Get High-res Image Clustering Approach #45: 'Del Peak 5(2q37.3) mutation analysis' versus Clinical Feature #14: 'TOBACCOSMOKINGHISTORYINDICATOR'

Clustering Approach #46: 'Del Peak 6(3p26.2) mutation analysis'

Table S298. Description of clustering approach #46: 'Del Peak 6(3p26.2) mutation analysis'

Cluster Labels | DEL PEAK 6(3P26.2) MUTATED | DEL PEAK 6(3P26.2) WILD-TYPE
--- | --- | ---
Number of samples | 1593 | 2970

'Del Peak 6(3p26.2) mutation analysis' versus 'PRIMARY.SITE.OF.DISEASE'

P value = 3.10000000000018e-311 (Chi-square test), Q value = 5.6e-308

Table S299. Clustering Approach #46: 'Del Peak 6(3p26.2) mutation analysis' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'

nPatients | BLADDER | BRAIN | BREAST | COLON | ENDOMETRIAL | HEAD/NECK | KIDNEY | LUNG | OMENTUM | OVARY | PERITONEUM (OVARY) | RECTUM
--- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | ---
ALL | 125 | 544 | 846 | 412 | 447 | 319 | 493 | 662 | 2 | 548 | 2 | 159
DEL PEAK 6(3P26.2) MUTATED | 25 | 42 | 140 | 61 | 49 | 221 | 426 | 404 | 2 | 201 | 0 | 20
DEL PEAK 6(3P26.2) WILD-TYPE | 100 | 502 | 706 | 351 | 398 | 98 | 67 | 258 | 0 | 347 | 2 | 139

Figure S253. Get High-res Image Clustering Approach #46: 'Del Peak 6(3p26.2) mutation analysis' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'

'Del Peak 6(3p26.2) mutation analysis' versus 'GENDER'

P value = 3.76e-33 (Fisher's exact test), Q value = 6.1e-30

Table S300. Clustering Approach #46: 'Del Peak 6(3p26.2) mutation analysis' versus Clinical Feature #4: 'GENDER'

nPatients | FEMALE | MALE
--- | --- | ---
ALL | 2881 | 1682
DEL PEAK 6(3P26.2) MUTATED | 818 | 775
DEL PEAK 6(3P26.2) WILD-TYPE | 2063 | 907

Figure S254. Get High-res Image Clustering Approach #46: 'Del Peak 6(3p26.2) mutation analysis' versus Clinical Feature #4: 'GENDER'

'Del Peak 6(3p26.2) mutation analysis' versus 'HISTOLOGICAL.TYPE'

P value = 6.06e-202 (Chi-square test), Q value = 1.1e-198

Table S301. Clustering Approach #46: 'Del Peak 6(3p26.2) mutation analysis' versus Clinical Feature #6: 'HISTOLOGICAL.TYPE'

nPatients | COLON ADENOCARCINOMA | COLON MUCINOUS ADENOCARCINOMA | ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA | HEAD & NECK SQUAMOUS CELL CARCINOMA | KIDNEY CLEAR CELL RENAL CARCINOMA | LUNG ACINAR ADENOCARCINOMA | LUNG ADENOCARCINOMA MIXED SUBTYPE | LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS) | LUNG BASALOID SQUAMOUS CELL CARCINOMA | LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS | LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS | LUNG CLEAR CELL ADENOCARCINOMA | LUNG MICROPAPILLARY ADENOCARCINOMA | LUNG MUCINOUS ADENOCARCINOMA | LUNG PAPILLARY ADENOCARCINOMA | LUNG PAPILLARY SQUAMOUS CELL CARCINOMA | LUNG PAPILLARY SQUAMOUS CELL CARICNOMA | LUNG SMALL CELL SQUAMOUS CELL CARCINOMA | LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA | LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS) | MIXED SEROUS AND ENDOMETRIOID | MUCINOUS (COLLOID) ADENOCARCINOMA | RECTAL ADENOCARCINOMA | RECTAL MUCINOUS ADENOCARCINOMA | SEROUS CYSTADENOCARCINOMA | SEROUS ENDOMETRIAL ADENOCARCINOMA | TREATED PRIMARY GBM | UNTREATED PRIMARY (DE NOVO) GBM
--- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | ---
ALL | 356 | 54 | 350 | 319 | 493 | 10 | 75 | 205 | 7 | 3 | 15 | 2 | 3 | 2 | 13 | 1 | 1 | 1 | 2 | 315 | 18 | 7 | 143 | 13 | 552 | 79 | 1 | 20
DEL PEAK 6(3P26.2) MUTATED | 57 | 4 | 16 | 221 | 426 | 5 | 35 | 96 | 6 | 0 | 6 | 1 | 2 | 0 | 7 | 1 | 0 | 1 | 0 | 242 | 6 | 2 | 16 | 3 | 203 | 27 | 0 | 3
DEL PEAK 6(3P26.2) WILD-TYPE | 299 | 50 | 334 | 98 | 67 | 5 | 40 | 109 | 1 | 3 | 9 | 1 | 1 | 2 | 6 | 0 | 1 | 0 | 2 | 73 | 12 | 5 | 127 | 10 | 349 | 52 | 1 | 17

Figure S255. Get High-res Image Clustering Approach #46: 'Del Peak 6(3p26.2) mutation analysis' versus Clinical Feature #6: 'HISTOLOGICAL.TYPE'

'Del Peak 6(3p26.2) mutation analysis' versus 'PATHOLOGY.T'

P value = 1.2e-19 (Fisher's exact test), Q value = 1.9e-16

Table S302. Clustering Approach #46: 'Del Peak 6(3p26.2) mutation analysis' versus Clinical Feature #7: 'PATHOLOGY.T'

nPatients | T0+T1 | T2 | T3 | T4
--- | --- | --- | --- | ---
ALL | 466 | 632 | 694 | 209
DEL PEAK 6(3P26.2) MUTATED | 337 | 347 | 307 | 115
DEL PEAK 6(3P26.2) WILD-TYPE | 129 | 285 | 387 | 94

Figure S256. Get High-res Image Clustering Approach #46: 'Del Peak 6(3p26.2) mutation analysis' versus Clinical Feature #7: 'PATHOLOGY.T'

'Del Peak 6(3p26.2) mutation analysis' versus 'TUMOR.STAGE'

P value = 1.28e-12 (Fisher's exact test), Q value = 2e-09

Table S303. Clustering Approach #46: 'Del Peak 6(3p26.2) mutation analysis' versus Clinical Feature #10: 'TUMOR.STAGE'

nPatients | I | II | III | IV
--- | --- | --- | --- | ---
ALL | 712 | 498 | 881 | 423
DEL PEAK 6(3P26.2) MUTATED | 432 | 210 | 411 | 248
DEL PEAK 6(3P26.2) WILD-TYPE | 280 | 288 | 470 | 175

Figure S257. Get High-res Image Clustering Approach #46: 'Del Peak 6(3p26.2) mutation analysis' versus Clinical Feature #10: 'TUMOR.STAGE'

'Del Peak 6(3p26.2) mutation analysis' versus 'RADIATIONS.RADIATION.REGIMENINDICATION'

P value = 7.96e-25 (Fisher's exact test), Q value = 1.3e-21

Table S304. Clustering Approach #46: 'Del Peak 6(3p26.2) mutation analysis' versus Clinical Feature #11: 'RADIATIONS.RADIATION.REGIMENINDICATION'

nPatients | NO | YES
--- | --- | ---
ALL | 826 | 3737
DEL PEAK 6(3P26.2) MUTATED | 165 | 1428
DEL PEAK 6(3P26.2) WILD-TYPE | 661 | 2309

Figure S258. Get High-res Image Clustering Approach #46: 'Del Peak 6(3p26.2) mutation analysis' versus Clinical Feature #11: 'RADIATIONS.RADIATION.REGIMENINDICATION'

'Del Peak 6(3p26.2) mutation analysis' versus 'TOBACCOSMOKINGHISTORYINDICATOR'

P value = 2.37e-19 (Chi-square test), Q value = 3.7e-16

Table S305. Clustering Approach #46: 'Del Peak 6(3p26.2) mutation analysis' versus Clinical Feature #14: 'TOBACCOSMOKINGHISTORYINDICATOR'

nPatients | 1 | 2 | 3 | 4 | 5 | CURRENT REFORMED SMOKER FOR < OR = 15 YEARS | CURRENT REFORMED SMOKER FOR > 15 YEARS | CURRENT SMOKER | LIFELONG NON-SMOKER
--- | --- | --- | --- | --- | --- | --- | --- | --- | ---
ALL | 28 | 23 | 37 | 29 | 2 | 355 | 217 | 250 | 128
DEL PEAK 6(3P26.2) MUTATED | 2 | 7 | 8 | 6 | 0 | 237 | 120 | 177 | 69
DEL PEAK 6(3P26.2) WILD-TYPE | 26 | 16 | 29 | 23 | 2 | 118 | 97 | 73 | 59

Figure S259. Get High-res Image Clustering Approach #46: 'Del Peak 6(3p26.2) mutation analysis' versus Clinical Feature #14: 'TOBACCOSMOKINGHISTORYINDICATOR'

Clustering Approach #47: 'Del Peak 7(3p14.2) mutation analysis'

Table S306. Description of clustering approach #47: 'Del Peak 7(3p14.2) mutation analysis'

Cluster Labels | DEL PEAK 7(3P14.2) MUTATED | DEL PEAK 7(3P14.2) WILD-TYPE
--- | --- | ---
Number of samples | 1740 | 2823

'Del Peak 7(3p14.2) mutation analysis' versus 'PRIMARY.SITE.OF.DISEASE'

P value = 4.18e-251 (Chi-square test), Q value = 7.6e-248

Table S307. Clustering Approach #47: 'Del Peak 7(3p14.2) mutation analysis' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'

nPatients | BLADDER | BRAIN | BREAST | COLON | ENDOMETRIAL | HEAD/NECK | KIDNEY | LUNG | OMENTUM | OVARY | PERITONEUM (OVARY) | RECTUM
--- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | ---
ALL | 125 | 544 | 846 | 412 | 447 | 319 | 493 | 662 | 2 | 548 | 2 | 159
DEL PEAK 7(3P14.2) MUTATED | 41 | 51 | 258 | 75 | 57 | 240 | 387 | 439 | 1 | 162 | 0 | 27
DEL PEAK 7(3P14.2) WILD-TYPE | 84 | 493 | 588 | 337 | 390 | 79 | 106 | 223 | 1 | 386 | 2 | 132

Figure S260. Get High-res Image Clustering Approach #47: 'Del Peak 7(3p14.2) mutation analysis' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'

'Del Peak 7(3p14.2) mutation analysis' versus 'GENDER'

P value = 4.14e-34 (Fisher's exact test), Q value = 6.8e-31

Table S308. Clustering Approach #47: 'Del Peak 7(3p14.2) mutation analysis' versus Clinical Feature #4: 'GENDER'

nPatients | FEMALE | MALE
--- | --- | ---
ALL | 2881 | 1682
DEL PEAK 7(3P14.2) MUTATED | 905 | 835
DEL PEAK 7(3P14.2) WILD-TYPE | 1976 | 847

Figure S261. Get High-res Image Clustering Approach #47: 'Del Peak 7(3p14.2) mutation analysis' versus Clinical Feature #4: 'GENDER'

'Del Peak 7(3p14.2) mutation analysis' versus 'KARNOFSKY.PERFORMANCE.SCORE'

P value = 2.21e-05 (t-test), Q value = 0.03

Table S309. Clustering Approach #47: 'Del Peak 7(3p14.2) mutation analysis' versus Clinical Feature #5: 'KARNOFSKY.PERFORMANCE.SCORE'

| nPatients | Mean (Std.Dev)
--- | --- | ---
ALL | 640 | 73.6 (23.9)
DEL PEAK 7(3P14.2) MUTATED | 161 | 64.1 (35.4)
DEL PEAK 7(3P14.2) WILD-TYPE | 479 | 76.7 (17.5)

Figure S262. Get High-res Image Clustering Approach #47: 'Del Peak 7(3p14.2) mutation analysis' versus Clinical Feature #5: 'KARNOFSKY.PERFORMANCE.SCORE'

'Del Peak 7(3p14.2) mutation analysis' versus 'HISTOLOGICAL.TYPE'

P value = 6.91e-199 (Chi-square test), Q value = 1.2e-195

Table S310. Clustering Approach #47: 'Del Peak 7(3p14.2) mutation analysis' versus Clinical Feature #6: 'HISTOLOGICAL.TYPE'

nPatients | COLON ADENOCARCINOMA | COLON MUCINOUS ADENOCARCINOMA | ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA | HEAD & NECK SQUAMOUS CELL CARCINOMA | KIDNEY CLEAR CELL RENAL CARCINOMA | LUNG ACINAR ADENOCARCINOMA | LUNG ADENOCARCINOMA MIXED SUBTYPE | LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS) | LUNG BASALOID SQUAMOUS CELL CARCINOMA | LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS | LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS | LUNG CLEAR CELL ADENOCARCINOMA | LUNG MICROPAPILLARY ADENOCARCINOMA | LUNG MUCINOUS ADENOCARCINOMA | LUNG PAPILLARY ADENOCARCINOMA | LUNG PAPILLARY SQUAMOUS CELL CARCINOMA | LUNG PAPILLARY SQUAMOUS CELL CARICNOMA | LUNG SMALL CELL SQUAMOUS CELL CARCINOMA | LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA | LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS) | MIXED SEROUS AND ENDOMETRIOID | MUCINOUS (COLLOID) ADENOCARCINOMA | RECTAL ADENOCARCINOMA | RECTAL MUCINOUS ADENOCARCINOMA | SEROUS CYSTADENOCARCINOMA | SEROUS ENDOMETRIAL ADENOCARCINOMA | TREATED PRIMARY GBM | UNTREATED PRIMARY (DE NOVO) GBM
--- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | ---
ALL | 356 | 54 | 350 | 319 | 493 | 10 | 75 | 205 | 7 | 3 | 15 | 2 | 3 | 2 | 13 | 1 | 1 | 1 | 2 | 315 | 18 | 7 | 143 | 13 | 552 | 79 | 1 | 20
DEL PEAK 7(3P14.2) MUTATED | 69 | 6 | 19 | 240 | 387 | 4 | 38 | 102 | 6 | 0 | 5 | 1 | 1 | 0 | 6 | 1 | 0 | 1 | 0 | 270 | 6 | 4 | 23 | 3 | 163 | 32 | 0 | 2
DEL PEAK 7(3P14.2) WILD-TYPE | 287 | 48 | 331 | 79 | 106 | 6 | 37 | 103 | 1 | 3 | 10 | 1 | 2 | 2 | 7 | 0 | 1 | 0 | 2 | 45 | 12 | 3 | 120 | 10 | 389 | 47 | 1 | 18

Figure S263. Get High-res Image Clustering Approach #47: 'Del Peak 7(3p14.2) mutation analysis' versus Clinical Feature #6: 'HISTOLOGICAL.TYPE'

'Del Peak 7(3p14.2) mutation analysis' versus 'PATHOLOGY.T'

P value = 1.37e-18 (Fisher's exact test), Q value = 2.2e-15

Table S311. Clustering Approach #47: 'Del Peak 7(3p14.2) mutation analysis' versus Clinical Feature #7: 'PATHOLOGY.T'

nPatients | T0+T1 | T2 | T3 | T4
--- | --- | --- | --- | ---
ALL | 466 | 632 | 694 | 209
DEL PEAK 7(3P14.2) MUTATED | 330 | 375 | 306 | 125
DEL PEAK 7(3P14.2) WILD-TYPE | 136 | 257 | 388 | 84

Figure S264. Get High-res Image Clustering Approach #47: 'Del Peak 7(3p14.2) mutation analysis' versus Clinical Feature #7: 'PATHOLOGY.T'

'Del Peak 7(3p14.2) mutation analysis' versus 'TUMOR.STAGE'

P value = 1.18e-16 (Fisher's exact test), Q value = 1.9e-13

Table S312. Clustering Approach #47: 'Del Peak 7(3p14.2) mutation analysis' versus Clinical Feature #10: 'TUMOR.STAGE'

nPatients | I | II | III | IV
--- | --- | --- | --- | ---
ALL | 712 | 498 | 881 | 423
DEL PEAK 7(3P14.2) MUTATED | 439 | 214 | 382 | 250
DEL PEAK 7(3P14.2) WILD-TYPE | 273 | 284 | 499 | 173

Figure S265. Get High-res Image Clustering Approach #47: 'Del Peak 7(3p14.2) mutation analysis' versus Clinical Feature #10: 'TUMOR.STAGE'

'Del Peak 7(3p14.2) mutation analysis' versus 'RADIATIONS.RADIATION.REGIMENINDICATION'

P value = 2.54e-20 (Fisher's exact test), Q value = 4e-17

Table S313. Clustering Approach #47: 'Del Peak 7(3p14.2) mutation analysis' versus Clinical Feature #11: 'RADIATIONS.RADIATION.REGIMENINDICATION'

nPatients | NO | YES
--- | --- | ---
ALL | 826 | 3737
DEL PEAK 7(3P14.2) MUTATED | 201 | 1539
DEL PEAK 7(3P14.2) WILD-TYPE | 625 | 2198

Figure S266. Get High-res Image Clustering Approach #47: 'Del Peak 7(3p14.2) mutation analysis' versus Clinical Feature #11: 'RADIATIONS.RADIATION.REGIMENINDICATION'

'Del Peak 7(3p14.2) mutation analysis' versus 'TOBACCOSMOKINGHISTORYINDICATOR'

P value = 5.04e-20 (Chi-square test), Q value = 8e-17

Table S314. Clustering Approach #47: 'Del Peak 7(3p14.2) mutation analysis' versus Clinical Feature #14: 'TOBACCOSMOKINGHISTORYINDICATOR'

nPatients | 1 | 2 | 3 | 4 | 5 | CURRENT REFORMED SMOKER FOR < OR = 15 YEARS | CURRENT REFORMED SMOKER FOR > 15 YEARS | CURRENT SMOKER | LIFELONG NON-SMOKER
--- | --- | --- | --- | --- | --- | --- | --- | --- | ---
ALL | 28 | 23 | 37 | 29 | 2 | 355 | 217 | 250 | 128
DEL PEAK 7(3P14.2) MUTATED | 2 | 12 | 14 | 8 | 2 | 262 | 131 | 193 | 71
DEL PEAK 7(3P14.2) WILD-TYPE | 26 | 11 | 23 | 21 | 0 | 93 | 86 | 57 | 57

Figure S267. Get High-res Image Clustering Approach #47: 'Del Peak 7(3p14.2) mutation analysis' versus Clinical Feature #14: 'TOBACCOSMOKINGHISTORYINDICATOR'

Clustering Approach #48: 'Del Peak 8(4p16.3) mutation analysis'

Table S315. Description of clustering approach #48: 'Del Peak 8(4p16.3) mutation analysis'

Cluster Labels | DEL PEAK 8(4P16.3) MUTATED | DEL PEAK 8(4P16.3) WILD-TYPE
--- | --- | ---
Number of samples | 1338 | 3225

'Del Peak 8(4p16.3) mutation analysis' versus 'PRIMARY.SITE.OF.DISEASE'

P value = 2.83e-56 (Chi-square test), Q value = 4.8e-53

Table S316. Clustering Approach #48: 'Del Peak 8(4p16.3) mutation analysis' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'

nPatients | BLADDER | BRAIN | BREAST | COLON | ENDOMETRIAL | HEAD/NECK | KIDNEY | LUNG | OMENTUM | OVARY | PERITONEUM (OVARY) | RECTUM
--- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | ---
ALL | 125 | 544 | 846 | 412 | 447 | 319 | 493 | 662 | 2 | 548 | 2 | 159
DEL PEAK 8(4P16.3) MUTATED | 42 | 78 | 267 | 117 | 65 | 137 | 67 | 278 | 2 | 223 | 0 | 59
DEL PEAK 8(4P16.3) WILD-TYPE | 83 | 466 | 579 | 295 | 382 | 182 | 426 | 384 | 0 | 325 | 2 | 100

Figure S268. Get High-res Image Clustering Approach #48: 'Del Peak 8(4p16.3) mutation analysis' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'

'Del Peak 8(4p16.3) mutation analysis' versus 'HISTOLOGICAL.TYPE'

P value = 7.22e-60 (Chi-square test), Q value = 1.2e-56

Table S317. Clustering Approach #48: 'Del Peak 8(4p16.3) mutation analysis' versus Clinical Feature #6: 'HISTOLOGICAL.TYPE'

nPatients | COLON ADENOCARCINOMA | COLON MUCINOUS ADENOCARCINOMA | ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA | HEAD & NECK SQUAMOUS CELL CARCINOMA | KIDNEY CLEAR CELL RENAL CARCINOMA | LUNG ACINAR ADENOCARCINOMA | LUNG ADENOCARCINOMA MIXED SUBTYPE | LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS) | LUNG BASALOID SQUAMOUS CELL CARCINOMA | LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS | LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS | LUNG CLEAR CELL ADENOCARCINOMA | LUNG MICROPAPILLARY ADENOCARCINOMA | LUNG MUCINOUS ADENOCARCINOMA | LUNG PAPILLARY ADENOCARCINOMA | LUNG PAPILLARY SQUAMOUS CELL CARCINOMA | LUNG PAPILLARY SQUAMOUS CELL CARICNOMA | LUNG SMALL CELL SQUAMOUS CELL CARCINOMA | LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA | LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS) | MIXED SEROUS AND ENDOMETRIOID | MUCINOUS (COLLOID) ADENOCARCINOMA | RECTAL ADENOCARCINOMA | RECTAL MUCINOUS ADENOCARCINOMA | SEROUS CYSTADENOCARCINOMA | SEROUS ENDOMETRIAL ADENOCARCINOMA | TREATED PRIMARY GBM | UNTREATED PRIMARY (DE NOVO) GBM
--- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | ---
ALL | 356 | 54 | 350 | 319 | 493 | 10 | 75 | 205 | 7 | 3 | 15 | 2 | 3 | 2 | 13 | 1 | 1 | 1 | 2 | 315 | 18 | 7 | 143 | 13 | 552 | 79 | 1 | 20
DEL PEAK 8(4P16.3) MUTATED | 108 | 9 | 27 | 137 | 67 | 3 | 18 | 58 | 3 | 0 | 1 | 1 | 0 | 1 | 2 | 1 | 0 | 1 | 1 | 187 | 4 | 1 | 54 | 4 | 225 | 34 | 0 | 2
DEL PEAK 8(4P16.3) WILD-TYPE | 248 | 45 | 323 | 182 | 426 | 7 | 57 | 147 | 4 | 3 | 14 | 1 | 3 | 1 | 11 | 0 | 1 | 0 | 1 | 128 | 14 | 6 | 89 | 9 | 327 | 45 | 1 | 18

Figure S269. Get High-res Image Clustering Approach #48: 'Del Peak 8(4p16.3) mutation analysis' versus Clinical Feature #6: 'HISTOLOGICAL.TYPE'

'Del Peak 8(4p16.3) mutation analysis' versus 'PATHOLOGY.T'

P value = 7.24e-07 (Fisher's exact test), Q value = 0.001

Table S318. Clustering Approach #48: 'Del Peak 8(4p16.3) mutation analysis' versus Clinical Feature #7: 'PATHOLOGY.T'

nPatients | T0+T1 | T2 | T3 | T4
--- | --- | --- | --- | ---
ALL | 466 | 632 | 694 | 209
DEL PEAK 8(4P16.3) MUTATED | 108 | 231 | 218 | 86
DEL PEAK 8(4P16.3) WILD-TYPE | 358 | 401 | 476 | 123

Figure S270. Get High-res Image Clustering Approach #48: 'Del Peak 8(4p16.3) mutation analysis' versus Clinical Feature #7: 'PATHOLOGY.T'

'Del Peak 8(4p16.3) mutation analysis' versus 'PATHOLOGY.N'

P value = 7.25e-05 (Fisher's exact test), Q value = 0.096

Table S319. Clustering Approach #48: 'Del Peak 8(4p16.3) mutation analysis' versus Clinical Feature #8: 'PATHOLOGY.N'

nPatients | N0 | N1 | N2 | N3
--- | --- | --- | --- | ---
ALL | 1067 | 353 | 282 | 11
DEL PEAK 8(4P16.3) MUTATED | 329 | 133 | 122 | 7
DEL PEAK 8(4P16.3) WILD-TYPE | 738 | 220 | 160 | 4

Figure S271. Get High-res Image Clustering Approach #48: 'Del Peak 8(4p16.3) mutation analysis' versus Clinical Feature #8: 'PATHOLOGY.N'

'Del Peak 8(4p16.3) mutation analysis' versus 'TUMOR.STAGE'

P value = 6.77e-05 (Fisher's exact test), Q value = 0.09

Table S320. Clustering Approach #48: 'Del Peak 8(4p16.3) mutation analysis' versus Clinical Feature #10: 'TUMOR.STAGE'

nPatients | I | II | III | IV
--- | --- | --- | --- | ---
ALL | 712 | 498 | 881 | 423
DEL PEAK 8(4P16.3) MUTATED | 210 | 147 | 327 | 170
DEL PEAK 8(4P16.3) WILD-TYPE | 502 | 351 | 554 | 253

Figure S272. Get High-res Image Clustering Approach #48: 'Del Peak 8(4p16.3) mutation analysis' versus Clinical Feature #10: 'TUMOR.STAGE'

'Del Peak 8(4p16.3) mutation analysis' versus 'RADIATIONS.RADIATION.REGIMENINDICATION'

P value = 0.000169 (Fisher's exact test), Q value = 0.22

Table S321. Clustering Approach #48: 'Del Peak 8(4p16.3) mutation analysis' versus Clinical Feature #11: 'RADIATIONS.RADIATION.REGIMENINDICATION'

nPatients | NO | YES
--- | --- | ---
ALL | 826 | 3737
DEL PEAK 8(4P16.3) MUTATED | 198 | 1140
DEL PEAK 8(4P16.3) WILD-TYPE | 628 | 2597

Figure S273. Get High-res Image Clustering Approach #48: 'Del Peak 8(4p16.3) mutation analysis' versus Clinical Feature #11: 'RADIATIONS.RADIATION.REGIMENINDICATION'

'Del Peak 8(4p16.3) mutation analysis' versus 'STOPPEDSMOKINGYEAR'

P value = 0.000123 (t-test), Q value = 0.16

Table S322. Clustering Approach #48: 'Del Peak 8(4p16.3) mutation analysis' versus Clinical Feature #13: 'STOPPEDSMOKINGYEAR'

| nPatients | Mean (Std.Dev)
--- | --- | ---
ALL | 568 | 1995.2 (13.5)
DEL PEAK 8(4P16.3) MUTATED | 241 | 1997.6 (11.9)
DEL PEAK 8(4P16.3) WILD-TYPE | 327 | 1993.4 (14.3)

Figure S274. Get High-res Image Clustering Approach #48: 'Del Peak 8(4p16.3) mutation analysis' versus Clinical Feature #13: 'STOPPEDSMOKINGYEAR'

'Del Peak 8(4p16.3) mutation analysis' versus 'TOBACCOSMOKINGHISTORYINDICATOR'

P value = 0.000145 (Chi-square test), Q value = 0.19

Table S323. Clustering Approach #48: 'Del Peak 8(4p16.3) mutation analysis' versus Clinical Feature #14: 'TOBACCOSMOKINGHISTORYINDICATOR'

nPatients | 1 | 2 | 3 | 4 | 5 | CURRENT REFORMED SMOKER FOR < OR = 15 YEARS | CURRENT REFORMED SMOKER FOR > 15 YEARS | CURRENT SMOKER | LIFELONG NON-SMOKER
--- | --- | --- | --- | --- | --- | --- | --- | --- | ---
ALL | 28 | 23 | 37 | 29 | 2 | 355 | 217 | 250 | 128
DEL PEAK 8(4P16.3) MUTATED | 9 | 8 | 12 | 9 | 0 | 171 | 73 | 123 | 38
DEL PEAK 8(4P16.3) WILD-TYPE | 19 | 15 | 25 | 20 | 2 | 184 | 144 | 127 | 90

Figure S275. Get High-res Image Clustering Approach #48: 'Del Peak 8(4p16.3) mutation analysis' versus Clinical Feature #14: 'TOBACCOSMOKINGHISTORYINDICATOR'

Clustering Approach #49: 'Del Peak 9(4q22.1) mutation analysis'

Table S324. Description of clustering approach #49: 'Del Peak 9(4q22.1) mutation analysis'

Cluster Labels | DEL PEAK 9(4Q22.1) MUTATED | DEL PEAK 9(4Q22.1) WILD-TYPE
--- | --- | ---
Number of samples | 1440 | 3123

'Del Peak 9(4q22.1) mutation analysis' versus 'PRIMARY.SITE.OF.DISEASE'

P value = 3e-124 (Chi-square test), Q value = 5.3e-121

Table S325. Clustering Approach #49: 'Del Peak 9(4q22.1) mutation analysis' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'

nPatients | BLADDER | BRAIN | BREAST | COLON | ENDOMETRIAL | HEAD/NECK | KIDNEY | LUNG | OMENTUM | OVARY | PERITONEUM (OVARY) | RECTUM
--- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | ---
ALL | 125 | 544 | 846 | 412 | 447 | 319 | 493 | 662 | 2 | 548 | 2 | 159
DEL PEAK 9(4Q22.1) MUTATED | 49 | 58 | 234 | 125 | 76 | 102 | 67 | 286 | 2 | 367 | 1 | 69
DEL PEAK 9(4Q22.1) WILD-TYPE | 76 | 486 | 612 | 287 | 371 | 217 | 426 | 376 | 0 | 181 | 1 | 90

Figure S276. Get High-res Image Clustering Approach #49: 'Del Peak 9(4q22.1) mutation analysis' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'

'Del Peak 9(4q22.1) mutation analysis' versus 'HISTOLOGICAL.TYPE'

P value = 1.81e-107 (Chi-square test), Q value = 3.2e-104

Table S326. Clustering Approach #49: 'Del Peak 9(4q22.1) mutation analysis' versus Clinical Feature #6: 'HISTOLOGICAL.TYPE'

nPatients | COLON ADENOCARCINOMA | COLON MUCINOUS ADENOCARCINOMA | ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA | HEAD & NECK SQUAMOUS CELL CARCINOMA | KIDNEY CLEAR CELL RENAL CARCINOMA | LUNG ACINAR ADENOCARCINOMA | LUNG ADENOCARCINOMA MIXED SUBTYPE | LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS) | LUNG BASALOID SQUAMOUS CELL CARCINOMA | LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS | LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS | LUNG CLEAR CELL ADENOCARCINOMA | LUNG MICROPAPILLARY ADENOCARCINOMA | LUNG MUCINOUS ADENOCARCINOMA | LUNG PAPILLARY ADENOCARCINOMA | LUNG PAPILLARY SQUAMOUS CELL CARCINOMA | LUNG PAPILLARY SQUAMOUS CELL CARICNOMA | LUNG SMALL CELL SQUAMOUS CELL CARCINOMA | LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA | LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS) | MIXED SEROUS AND ENDOMETRIOID | MUCINOUS (COLLOID) ADENOCARCINOMA | RECTAL ADENOCARCINOMA | RECTAL MUCINOUS ADENOCARCINOMA | SEROUS CYSTADENOCARCINOMA | SEROUS ENDOMETRIAL ADENOCARCINOMA | TREATED PRIMARY GBM | UNTREATED PRIMARY (DE NOVO) GBM
--- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | ---
ALL | 356 | 54 | 350 | 319 | 493 | 10 | 75 | 205 | 7 | 3 | 15 | 2 | 3 | 2 | 13 | 1 | 1 | 1 | 2 | 315 | 18 | 7 | 143 | 13 | 552 | 79 | 1 | 20
DEL PEAK 9(4Q22.1) MUTATED | 116 | 9 | 25 | 102 | 67 | 2 | 20 | 68 | 3 | 0 | 3 | 2 | 1 | 0 | 4 | 1 | 0 | 1 | 1 | 179 | 5 | 1 | 64 | 4 | 370 | 46 | 0 | 0
DEL PEAK 9(4Q22.1) WILD-TYPE | 240 | 45 | 325 | 217 | 426 | 8 | 55 | 137 | 4 | 3 | 12 | 0 | 2 | 2 | 9 | 0 | 1 | 0 | 1 | 136 | 13 | 6 | 79 | 9 | 182 | 33 | 1 | 20

Figure S277. Get High-res Image Clustering Approach #49: 'Del Peak 9(4q22.1) mutation analysis' versus Clinical Feature #6: 'HISTOLOGICAL.TYPE'

'Del Peak 9(4q22.1) mutation analysis' versus 'PATHOLOGY.T'

P value = 3.18e-08 (Fisher's exact test), Q value = 4.7e-05

Table S327. Clustering Approach #49: 'Del Peak 9(4q22.1) mutation analysis' versus Clinical Feature #7: 'PATHOLOGY.T'

nPatients | T0+T1 | T2 | T3 | T4
--- | --- | --- | --- | ---
ALL | 466 | 632 | 694 | 209
DEL PEAK 9(4Q22.1) MUTATED | 98 | 235 | 232 | 76
DEL PEAK 9(4Q22.1) WILD-TYPE | 368 | 397 | 462 | 133

Figure S278. Get High-res Image Clustering Approach #49: 'Del Peak 9(4q22.1) mutation analysis' versus Clinical Feature #7: 'PATHOLOGY.T'

'Del Peak 9(4q22.1) mutation analysis' versus 'TUMOR.STAGE'

P value = 3.84e-22 (Fisher's exact test), Q value = 6.1e-19

Table S328. Clustering Approach #49: 'Del Peak 9(4q22.1) mutation analysis' versus Clinical Feature #10: 'TUMOR.STAGE'

nPatients | I | II | III | IV
--- | --- | --- | --- | ---
ALL | 712 | 498 | 881 | 423
DEL PEAK 9(4Q22.1) MUTATED | 216 | 156 | 464 | 160
DEL PEAK 9(4Q22.1) WILD-TYPE | 496 | 342 | 417 | 263

Figure S279. Get High-res Image Clustering Approach #49: 'Del Peak 9(4q22.1) mutation analysis' versus Clinical Feature #10: 'TUMOR.STAGE'

'Del Peak 9(4q22.1) mutation analysis' versus 'RADIATIONS.RADIATION.REGIMENINDICATION'

P value = 1.46e-14 (Fisher's exact test), Q value = 2.3e-11

Table S329. Clustering Approach #49: 'Del Peak 9(4q22.1) mutation analysis' versus Clinical Feature #11: 'RADIATIONS.RADIATION.REGIMENINDICATION'

nPatients | NO | YES
--- | --- | ---
ALL | 826 | 3737
DEL PEAK 9(4Q22.1) MUTATED | 170 | 1270
DEL PEAK 9(4Q22.1) WILD-TYPE | 656 | 2467

Figure S280. Get High-res Image Clustering Approach #49: 'Del Peak 9(4q22.1) mutation analysis' versus Clinical Feature #11: 'RADIATIONS.RADIATION.REGIMENINDICATION'

Clustering Approach #50: 'Del Peak 10(4q34.3) mutation analysis'

Table S330. Description of clustering approach #50: 'Del Peak 10(4q34.3) mutation analysis'

Cluster Labels | DEL PEAK 10(4Q34.3) MUTATED | DEL PEAK 10(4Q34.3) WILD-TYPE
--- | --- | ---
Number of samples | 1640 | 2923

'Del Peak 10(4q34.3) mutation analysis' versus 'PRIMARY.SITE.OF.DISEASE'

P value = 1.89e-127 (Chi-square test), Q value = 3.3e-124

Table S331. Clustering Approach #50: 'Del Peak 10(4q34.3) mutation analysis' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'

nPatients | BLADDER | BRAIN | BREAST | COLON | ENDOMETRIAL | HEAD/NECK | KIDNEY | LUNG | OMENTUM | OVARY | PERITONEUM (OVARY) | RECTUM
--- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | ---
ALL | 125 | 544 | 846 | 412 | 447 | 319 | 493 | 662 | 2 | 548 | 2 | 159
DEL PEAK 10(4Q34.3) MUTATED | 53 | 89 | 270 | 132 | 91 | 118 | 76 | 338 | 2 | 396 | 1 | 70
DEL PEAK 10(4Q34.3) WILD-TYPE | 72 | 455 | 576 | 280 | 356 | 201 | 417 | 324 | 0 | 152 | 1 | 89

Figure S281. Get High-res Image Clustering Approach #50: 'Del Peak 10(4q34.3) mutation analysis' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'

'Del Peak 10(4q34.3) mutation analysis' versus 'HISTOLOGICAL.TYPE'

P value = 9.53e-120 (Chi-square test), Q value = 1.7e-116

Table S332. Clustering Approach #50: 'Del Peak 10(4q34.3) mutation analysis' versus Clinical Feature #6: 'HISTOLOGICAL.TYPE'

nPatients | COLON ADENOCARCINOMA | COLON MUCINOUS ADENOCARCINOMA | ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA | HEAD & NECK SQUAMOUS CELL CARCINOMA | KIDNEY CLEAR CELL RENAL CARCINOMA | LUNG ACINAR ADENOCARCINOMA | LUNG ADENOCARCINOMA MIXED SUBTYPE | LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS) | LUNG BASALOID SQUAMOUS CELL CARCINOMA | LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS | LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS | LUNG CLEAR CELL ADENOCARCINOMA | LUNG MICROPAPILLARY ADENOCARCINOMA | LUNG MUCINOUS ADENOCARCINOMA | LUNG PAPILLARY ADENOCARCINOMA | LUNG PAPILLARY SQUAMOUS CELL CARCINOMA | LUNG PAPILLARY SQUAMOUS CELL CARICNOMA | LUNG SMALL CELL SQUAMOUS CELL CARCINOMA | LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA | LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS) | MIXED SEROUS AND ENDOMETRIOID | MUCINOUS (COLLOID) ADENOCARCINOMA | RECTAL ADENOCARCINOMA | RECTAL MUCINOUS ADENOCARCINOMA | SEROUS CYSTADENOCARCINOMA | SEROUS ENDOMETRIAL ADENOCARCINOMA | TREATED PRIMARY GBM | UNTREATED PRIMARY (DE NOVO) GBM
--- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | ---
ALL | 356 | 54 | 350 | 319 | 493 | 10 | 75 | 205 | 7 | 3 | 15 | 2 | 3 | 2 | 13 | 1 | 1 | 1 | 2 | 315 | 18 | 7 | 143 | 13 | 552 | 79 | 1 | 20
DEL PEAK 10(4Q34.3) MUTATED | 121 | 11 | 35 | 118 | 76 | 2 | 31 | 79 | 3 | 0 | 4 | 2 | 1 | 0 | 2 | 1 | 0 | 1 | 2 | 209 | 6 | 1 | 66 | 3 | 399 | 50 | 0 | 3
DEL PEAK 10(4Q34.3) WILD-TYPE | 235 | 43 | 315 | 201 | 417 | 8 | 44 | 126 | 4 | 3 | 11 | 0 | 2 | 2 | 11 | 0 | 1 | 0 | 0 | 106 | 12 | 6 | 77 | 10 | 153 | 29 | 1 | 17

Figure S282. Get High-res Image Clustering Approach #50: 'Del Peak 10(4q34.3) mutation analysis' versus Clinical Feature #6: 'HISTOLOGICAL.TYPE'

'Del Peak 10(4q34.3) mutation analysis' versus 'PATHOLOGY.T'

P value = 1.46e-08 (Fisher's exact test), Q value = 2.2e-05

Table S333. Clustering Approach #50: 'Del Peak 10(4q34.3) mutation analysis' versus Clinical Feature #7: 'PATHOLOGY.T'

nPatients | T0+T1 | T2 | T3 | T4
--- | --- | --- | --- | ---
ALL | 466 | 632 | 694 | 209
DEL PEAK 10(4Q34.3) MUTATED | 119 | 275 | 247 | 82
DEL PEAK 10(4Q34.3) WILD-TYPE | 347 | 357 | 447 | 127

Figure S283. Get High-res Image Clustering Approach #50: 'Del Peak 10(4q34.3) mutation analysis' versus Clinical Feature #7: 'PATHOLOGY.T'

'Del Peak 10(4q34.3) mutation analysis' versus 'TUMOR.STAGE'

P value = 4.37e-16 (Fisher's exact test), Q value = 6.8e-13

Table S334. Clustering Approach #50: 'Del Peak 10(4q34.3) mutation analysis' versus Clinical Feature #10: 'TUMOR.STAGE'

nPatients | I | II | III | IV
--- | --- | --- | --- | ---
ALL | 712 | 498 | 881 | 423
DEL PEAK 10(4Q34.3) MUTATED | 253 | 184 | 485 | 182
DEL PEAK 10(4Q34.3) WILD-TYPE | 459 | 314 | 396 | 241

Figure S284. Get High-res Image Clustering Approach #50: 'Del Peak 10(4q34.3) mutation analysis' versus Clinical Feature #10: 'TUMOR.STAGE'

'Del Peak 10(4q34.3) mutation analysis' versus 'RADIATIONS.RADIATION.REGIMENINDICATION'

P value = 4.43e-11 (Fisher's exact test), Q value = 6.7e-08

Table S335. Clustering Approach #50: 'Del Peak 10(4q34.3) mutation analysis' versus Clinical Feature #11: 'RADIATIONS.RADIATION.REGIMENINDICATION'

nPatients | NO | YES
--- | --- | ---
ALL | 826 | 3737
DEL PEAK 10(4Q34.3) MUTATED | 216 | 1424
DEL PEAK 10(4Q34.3) WILD-TYPE | 610 | 2313

Figure S285. Get High-res Image Clustering Approach #50: 'Del Peak 10(4q34.3) mutation analysis' versus Clinical Feature #11: 'RADIATIONS.RADIATION.REGIMENINDICATION'

Clustering Approach #51: 'Del Peak 11(5q11.2) mutation analysis'

Table S336. Description of clustering approach #51: 'Del Peak 11(5q11.2) mutation analysis'

Cluster Labels | DEL PEAK 11(5Q11.2) MUTATED | DEL PEAK 11(5Q11.2) WILD-TYPE
--- | --- | ---
Number of samples | 1373 | 3190

'Del Peak 11(5q11.2) mutation analysis' versus 'PRIMARY.SITE.OF.DISEASE'

P value = 1.28e-171 (Chi-square test), Q value = 2.3e-168

Table S337. Clustering Approach #51: 'Del Peak 11(5q11.2) mutation analysis' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'

nPatients | BLADDER | BRAIN | BREAST | COLON | ENDOMETRIAL | HEAD/NECK | KIDNEY | LUNG | OMENTUM | OVARY | PERITONEUM (OVARY) | RECTUM
--- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | ---
ALL | 125 | 544 | 846 | 412 | 447 | 319 | 493 | 662 | 2 | 548 | 2 | 159
DEL PEAK 11(5Q11.2) MUTATED | 64 | 43 | 214 | 91 | 78 | 134 | 10 | 361 | 2 | 326 | 1 | 49
DEL PEAK 11(5Q11.2) WILD-TYPE | 61 | 501 | 632 | 321 | 369 | 185 | 483 | 301 | 0 | 222 | 1 | 110

Figure S286. Get High-res Image Clustering Approach #51: 'Del Peak 11(5q11.2) mutation analysis' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'

'Del Peak 11(5q11.2) mutation analysis' versus 'KARNOFSKY.PERFORMANCE.SCORE'

P value = 5.77e-05 (t-test), Q value = 0.077

Table S338. Clustering Approach #51: 'Del Peak 11(5q11.2) mutation analysis' versus Clinical Feature #5: 'KARNOFSKY.PERFORMANCE.SCORE'

| nPatients | Mean (Std.Dev)
--- | --- | ---
ALL | 640 | 73.6 (23.9)
DEL PEAK 11(5Q11.2) MUTATED | 152 | 65.1 (31.1)
DEL PEAK 11(5Q11.2) WILD-TYPE | 488 | 76.2 (20.6)

Figure S287. Get High-res Image Clustering Approach #51: 'Del Peak 11(5q11.2) mutation analysis' versus Clinical Feature #5: 'KARNOFSKY.PERFORMANCE.SCORE'

'Del Peak 11(5q11.2) mutation analysis' versus 'HISTOLOGICAL.TYPE'

P value = 2.01e-152 (Chi-square test), Q value = 3.6e-149

Table S339. Clustering Approach #51: 'Del Peak 11(5q11.2) mutation analysis' versus Clinical Feature #6: 'HISTOLOGICAL.TYPE'

nPatients | COLON ADENOCARCINOMA | COLON MUCINOUS ADENOCARCINOMA | ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA | HEAD & NECK SQUAMOUS CELL CARCINOMA | KIDNEY CLEAR CELL RENAL CARCINOMA | LUNG ACINAR ADENOCARCINOMA | LUNG ADENOCARCINOMA MIXED SUBTYPE | LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS) | LUNG BASALOID SQUAMOUS CELL CARCINOMA | LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS | LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS | LUNG CLEAR CELL ADENOCARCINOMA | LUNG MICROPAPILLARY ADENOCARCINOMA | LUNG MUCINOUS ADENOCARCINOMA | LUNG PAPILLARY ADENOCARCINOMA | LUNG PAPILLARY SQUAMOUS CELL CARCINOMA | LUNG PAPILLARY SQUAMOUS CELL CARICNOMA | LUNG SMALL CELL SQUAMOUS CELL CARCINOMA | LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA | LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS) | MIXED SEROUS AND ENDOMETRIOID | MUCINOUS (COLLOID) ADENOCARCINOMA | RECTAL ADENOCARCINOMA | RECTAL MUCINOUS ADENOCARCINOMA | SEROUS CYSTADENOCARCINOMA | SEROUS ENDOMETRIAL ADENOCARCINOMA | TREATED PRIMARY GBM | UNTREATED PRIMARY (DE NOVO) GBM
--- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | ---
ALL | 356 | 54 | 350 | 319 | 493 | 10 | 75 | 205 | 7 | 3 | 15 | 2 | 3 | 2 | 13 | 1 | 1 | 1 | 2 | 315 | 18 | 7 | 143 | 13 | 552 | 79 | 1 | 20
DEL PEAK 11(5Q11.2) MUTATED | 84 | 7 | 29 | 134 | 10 | 3 | 28 | 78 | 5 | 0 | 3 | 0 | 2 | 1 | 4 | 1 | 0 | 0 | 2 | 233 | 2 | 1 | 46 | 2 | 329 | 47 | 0 | 0
DEL PEAK 11(5Q11.2) WILD-TYPE | 272 | 47 | 321 | 185 | 483 | 7 | 47 | 127 | 2 | 3 | 12 | 2 | 1 | 1 | 9 | 0 | 1 | 1 | 0 | 82 | 16 | 6 | 97 | 11 | 223 | 32 | 1 | 20

Figure S288. Get High-res Image Clustering Approach #51: 'Del Peak 11(5q11.2) mutation analysis' versus Clinical Feature #6: 'HISTOLOGICAL.TYPE'

'Del Peak 11(5q11.2) mutation analysis' versus 'PATHOLOGY.T'

P value = 3.08e-17 (Fisher's exact test), Q value = 4.9e-14

Table S340. Clustering Approach #51: 'Del Peak 11(5q11.2) mutation analysis' versus Clinical Feature #7: 'PATHOLOGY.T'

nPatients | T0+T1 | T2 | T3 | T4
--- | --- | --- | --- | ---
ALL | 466 | 632 | 694 | 209
DEL PEAK 11(5Q11.2) MUTATED | 114 | 270 | 158 | 85
DEL PEAK 11(5Q11.2) WILD-TYPE | 352 | 362 | 536 | 124

Figure S289. Get High-res Image Clustering Approach #51: 'Del Peak 11(5q11.2) mutation analysis' versus Clinical Feature #7: 'PATHOLOGY.T'

'Del Peak 11(5q11.2) mutation analysis' versus 'PATHOLOGY.N'

P value = 6.37e-05 (Fisher's exact test), Q value = 0.085

Table S341. Clustering Approach #51: 'Del Peak 11(5q11.2) mutation analysis' versus Clinical Feature #8: 'PATHOLOGY.N'

nPatients | N0 | N1 | N2 | N3
--- | --- | --- | --- | ---
ALL | 1067 | 353 | 282 | 11
DEL PEAK 11(5Q11.2) MUTATED | 333 | 153 | 114 | 5
DEL PEAK 11(5Q11.2) WILD-TYPE | 734 | 200 | 168 | 6

Figure S290. Get High-res Image Clustering Approach #51: 'Del Peak 11(5q11.2) mutation analysis' versus Clinical Feature #8: 'PATHOLOGY.N'

'Del Peak 11(5q11.2) mutation analysis' versus 'TUMOR.STAGE'

P value = 9.26e-06 (Fisher's exact test), Q value = 0.013

Table S342. Clustering Approach #51: 'Del Peak 11(5q11.2) mutation analysis' versus Clinical Feature #10: 'TUMOR.STAGE'

nPatients | I | II | III | IV
--- | --- | --- | --- | ---
ALL | 712 | 498 | 881 | 423
DEL PEAK 11(5Q11.2) MUTATED | 227 | 166 | 379 | 170
DEL PEAK 11(5Q11.2) WILD-TYPE | 485 | 332 | 502 | 253

Figure S291. Get High-res Image Clustering Approach #51: 'Del Peak 11(5q11.2) mutation analysis' versus Clinical Feature #10: 'TUMOR.STAGE'

'Del Peak 11(5q11.2) mutation analysis' versus 'RADIATIONS.RADIATION.REGIMENINDICATION'

P value = 9.02e-14 (Fisher's exact test), Q value = 1.4e-10

Table S343. Clustering Approach #51: 'Del Peak 11(5q11.2) mutation analysis' versus Clinical Feature #11: 'RADIATIONS.RADIATION.REGIMENINDICATION'

nPatients | NO | YES
--- | --- | ---
ALL | 826 | 3737
DEL PEAK 11(5Q11.2) MUTATED | 162 | 1211
DEL PEAK 11(5Q11.2) WILD-TYPE | 664 | 2526

Figure S292. Get High-res Image Clustering Approach #51: 'Del Peak 11(5q11.2) mutation analysis' versus Clinical Feature #11: 'RADIATIONS.RADIATION.REGIMENINDICATION'

'Del Peak 11(5q11.2) mutation analysis' versus 'NUMBERPACKYEARSSMOKED'

P value = 4.61e-06 (t-test), Q value = 0.0065

Table S344. Clustering Approach #51: 'Del Peak 11(5q11.2) mutation analysis' versus Clinical Feature #12: 'NUMBERPACKYEARSSMOKED'

| nPatients | Mean (Std.Dev)
--- | --- | ---
ALL | 758 | 46.7 (33.0)
DEL PEAK 11(5Q11.2) MUTATED | 400 | 51.8 (34.8)
DEL PEAK 11(5Q11.2) WILD-TYPE | 358 | 40.9 (29.9)

Figure S293. Get High-res Image Clustering Approach #51: 'Del Peak 11(5q11.2) mutation analysis' versus Clinical Feature #12: 'NUMBERPACKYEARSSMOKED'

'Del Peak 11(5q11.2) mutation analysis' versus 'TOBACCOSMOKINGHISTORYINDICATOR'

P value = 3.29e-05 (Chi-square test), Q value = 0.045

Table S345. Clustering Approach #51: 'Del Peak 11(5q11.2) mutation analysis' versus Clinical Feature #14: 'TOBACCOSMOKINGHISTORYINDICATOR'

nPatients | 1 | 2 | 3 | 4 | 5 | CURRENT REFORMED SMOKER FOR < OR = 15 YEARS | CURRENT REFORMED SMOKER FOR > 15 YEARS | CURRENT SMOKER | LIFELONG NON-SMOKER
--- | --- | --- | --- | --- | --- | --- | --- | --- | ---
ALL | 28 | 23 | 37 | 29 | 2 | 355 | 217 | 250 | 128
DEL PEAK 11(5Q11.2) MUTATED | 13 | 8 | 22 | 17 | 0 | 206 | 98 | 136 | 42
DEL PEAK 11(5Q11.2) WILD-TYPE | 15 | 15 | 15 | 12 | 2 | 149 | 119 | 114 | 86

Figure S294. Get High-res Image Clustering Approach #51: 'Del Peak 11(5q11.2) mutation analysis' versus Clinical Feature #14: 'TOBACCOSMOKINGHISTORYINDICATOR'

'Del Peak 11(5q11.2) mutation analysis' versus 'NEOPLASM.DISEASESTAGE'

P value = 1.73e-05 (Chi-square test), Q value = 0.024

Table S346. Clustering Approach #51: 'Del Peak 11(5q11.2) mutation analysis' versus Clinical Feature #21: 'NEOPLASM.DISEASESTAGE'

nPatients | STAGE I | STAGE IA | STAGE IB | STAGE II | STAGE IIA | STAGE IIB | STAGE III | STAGE IIIA | STAGE IIIB | STAGE IIIC | STAGE IV | STAGE TIS | STAGE X
--- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | ---
ALL | 72 | 62 | 7 | 43 | 287 | 186 | 42 | 124 | 25 | 41 | 59 | 1 | 16
DEL PEAK 11(5Q11.2) MUTATED | 19 | 10 | 3 | 24 | 79 | 51 | 11 | 31 | 5 | 7 | 30 | 1 | 3
DEL PEAK 11(5Q11.2) WILD-TYPE | 53 | 52 | 4 | 19 | 208 | 135 | 31 | 93 | 20 | 34 | 29 | 0 | 13

Figure S295. Get High-res Image Clustering Approach #51: 'Del Peak 11(5q11.2) mutation analysis' versus Clinical Feature #21: 'NEOPLASM.DISEASESTAGE'

Clustering Approach #52: 'Del Peak 12(5q21.3) mutation analysis'

Table S347. Description of clustering approach #52: 'Del Peak 12(5q21.3) mutation analysis'

Cluster Labels | DEL PEAK 12(5Q21.3) MUTATED | DEL PEAK 12(5Q21.3) WILD-TYPE
--- | --- | ---
Number of samples | 1388 | 3175

'Del Peak 12(5q21.3) mutation analysis' versus 'PRIMARY.SITE.OF.DISEASE'

P value = 2.24e-178 (Chi-square test), Q value = 4e-175

Table S348. Clustering Approach #52: 'Del Peak 12(5q21.3) mutation analysis' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'

nPatients | BLADDER | BRAIN | BREAST | COLON | ENDOMETRIAL | HEAD/NECK | KIDNEY | LUNG | OMENTUM | OVARY | PERITONEUM (OVARY) | RECTUM
--- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | ---
ALL | 125 | 544 | 846 | 412 | 447 | 319 | 493 | 662 | 2 | 548 | 2 | 159
DEL PEAK 12(5Q21.3) MUTATED | 63 | 43 | 212 | 117 | 67 | 128 | 5 | 388 | 2 | 311 | 1 | 51
DEL PEAK 12(5Q21.3) WILD-TYPE | 62 | 501 | 634 | 295 | 380 | 191 | 488 | 274 | 0 | 237 | 1 | 108

Figure S296. Get High-res Image Clustering Approach #52: 'Del Peak 12(5q21.3) mutation analysis' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'

'Del Peak 12(5q21.3) mutation analysis' versus 'KARNOFSKY.PERFORMANCE.SCORE'

P value = 1.22e-05 (t-test), Q value = 0.017

Table S349. Clustering Approach #52: 'Del Peak 12(5q21.3) mutation analysis' versus Clinical Feature #5: 'KARNOFSKY.PERFORMANCE.SCORE'

| nPatients | Mean (Std.Dev)
--- | --- | ---
ALL | 640 | 73.6 (23.9)
DEL PEAK 12(5Q21.3) MUTATED | 149 | 64.0 (32.1)
DEL PEAK 12(5Q21.3) WILD-TYPE | 491 | 76.5 (20.0)

Figure S297. Get High-res Image Clustering Approach #52: 'Del Peak 12(5q21.3) mutation analysis' versus Clinical Feature #5: 'KARNOFSKY.PERFORMANCE.SCORE'

'Del Peak 12(5q21.3) mutation analysis' versus 'HISTOLOGICAL.TYPE'

P value = 9.1e-152 (Chi-square test), Q value = 1.6e-148

Table S350. Clustering Approach #52: 'Del Peak 12(5q21.3) mutation analysis' versus Clinical Feature #6: 'HISTOLOGICAL.TYPE'

nPatients | COLON ADENOCARCINOMA | COLON MUCINOUS ADENOCARCINOMA | ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA | HEAD & NECK SQUAMOUS CELL CARCINOMA | KIDNEY CLEAR CELL RENAL CARCINOMA | LUNG ACINAR ADENOCARCINOMA | LUNG ADENOCARCINOMA MIXED SUBTYPE | LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS) | LUNG BASALOID SQUAMOUS CELL CARCINOMA | LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS | LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS | LUNG CLEAR CELL ADENOCARCINOMA | LUNG MICROPAPILLARY ADENOCARCINOMA | LUNG MUCINOUS ADENOCARCINOMA | LUNG PAPILLARY ADENOCARCINOMA | LUNG PAPILLARY SQUAMOUS CELL CARCINOMA | LUNG PAPILLARY SQUAMOUS CELL CARICNOMA | LUNG SMALL CELL SQUAMOUS CELL CARCINOMA | LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA | LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS) | MIXED SEROUS AND ENDOMETRIOID | MUCINOUS (COLLOID) ADENOCARCINOMA | RECTAL ADENOCARCINOMA | RECTAL MUCINOUS ADENOCARCINOMA | SEROUS CYSTADENOCARCINOMA | SEROUS ENDOMETRIAL ADENOCARCINOMA | TREATED PRIMARY GBM | UNTREATED PRIMARY (DE NOVO) GBM
--- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | ---
ALL | 356 | 54 | 350 | 319 | 493 | 10 | 75 | 205 | 7 | 3 | 15 | 2 | 3 | 2 | 13 | 1 | 1 | 1 | 2 | 315 | 18 | 7 | 143 | 13 | 552 | 79 | 1 | 20
DEL PEAK 12(5Q21.3) MUTATED | 107 | 10 | 23 | 128 | 5 | 4 | 33 | 86 | 5 | 0 | 3 | 1 | 2 | 1 | 5 | 1 | 0 | 1 | 2 | 243 | 3 | 1 | 48 | 2 | 314 | 41 | 0 | 0
DEL PEAK 12(5Q21.3) WILD-TYPE | 249 | 44 | 327 | 191 | 488 | 6 | 42 | 119 | 2 | 3 | 12 | 1 | 1 | 1 | 8 | 0 | 1 | 0 | 0 | 72 | 15 | 6 | 95 | 11 | 238 | 38 | 1 | 20

Figure S298. Get High-res Image Clustering Approach #52: 'Del Peak 12(5q21.3) mutation analysis' versus Clinical Feature #6: 'HISTOLOGICAL.TYPE'

'Del Peak 12(5q21.3) mutation analysis' versus 'PATHOLOGY.T'

P value = 7.7e-16 (Fisher's exact test), Q value = 1.2e-12

Table S351. Clustering Approach #52: 'Del Peak 12(5q21.3) mutation analysis' versus Clinical Feature #7: 'PATHOLOGY.T'

nPatients | T0+T1 | T2 | T3 | T4
--- | --- | --- | --- | ---
ALL | 466 | 632 | 694 | 209
DEL PEAK 12(5Q21.3) MUTATED | 121 | 285 | 179 | 86
DEL PEAK 12(5Q21.3) WILD-TYPE | 345 | 347 | 515 | 123

Figure S299. Get High-res Image Clustering Approach #52: 'Del Peak 12(5q21.3) mutation analysis' versus Clinical Feature #7: 'PATHOLOGY.T'

'Del Peak 12(5q21.3) mutation analysis' versus 'PATHOLOGY.N'

P value = 3.6e-05 (Fisher's exact test), Q value = 0.048

Table S352. Clustering Approach #52: 'Del Peak 12(5q21.3) mutation analysis' versus Clinical Feature #8: 'PATHOLOGY.N'

nPatients | N0 | N1 | N2 | N3
--- | --- | --- | --- | ---
ALL | 1067 | 353 | 282 | 11
DEL PEAK 12(5Q21.3) MUTATED | 360 | 165 | 118 | 6
DEL PEAK 12(5Q21.3) WILD-TYPE | 707 | 188 | 164 | 5

Figure S300. Get High-res Image Clustering Approach #52: 'Del Peak 12(5q21.3) mutation analysis' versus Clinical Feature #8: 'PATHOLOGY.N'

'Del Peak 12(5q21.3) mutation analysis' versus 'PATHOLOGICSPREAD(M)'

P value = 4.68e-05 (Chi-square test), Q value = 0.063

Table S353. Clustering Approach #52: 'Del Peak 12(5q21.3) mutation analysis' versus Clinical Feature #9: 'PATHOLOGICSPREAD(M)'

nPatients | M0 | M1 | M1A | M1B | MX
--- | --- | --- | --- | --- | ---
ALL | 1424 | 168 | 9 | 3 | 165
DEL PEAK 12(5Q21.3) MUTATED | 448 | 40 | 6 | 1 | 76
DEL PEAK 12(5Q21.3) WILD-TYPE | 976 | 128 | 3 | 2 | 89

Figure S301. Get High-res Image Clustering Approach #52: 'Del Peak 12(5q21.3) mutation analysis' versus Clinical Feature #9: 'PATHOLOGICSPREAD(M)'

'Del Peak 12(5q21.3) mutation analysis' versus 'RADIATIONS.RADIATION.REGIMENINDICATION'

P value = 1.55e-14 (Fisher's exact test), Q value = 2.4e-11

Table S354. Clustering Approach #52: 'Del Peak 12(5q21.3) mutation analysis' versus Clinical Feature #11: 'RADIATIONS.RADIATION.REGIMENINDICATION'

nPatients | NO | YES
--- | --- | ---
ALL | 826 | 3737
DEL PEAK 12(5Q21.3) MUTATED | 162 | 1226
DEL PEAK 12(5Q21.3) WILD-TYPE | 664 | 2511

Figure S302. Get High-res Image Clustering Approach #52: 'Del Peak 12(5q21.3) mutation analysis' versus Clinical Feature #11: 'RADIATIONS.RADIATION.REGIMENINDICATION'

'Del Peak 12(5q21.3) mutation analysis' versus 'TOBACCOSMOKINGHISTORYINDICATOR'

P value = 6.54e-06 (Chi-square test), Q value = 0.0091

Table S355. Clustering Approach #52: 'Del Peak 12(5q21.3) mutation analysis' versus Clinical Feature #14: 'TOBACCOSMOKINGHISTORYINDICATOR'

nPatients | 1 | 2 | 3 | 4 | 5 | CURRENT REFORMED SMOKER FOR < OR = 15 YEARS | CURRENT REFORMED SMOKER FOR > 15 YEARS | CURRENT SMOKER | LIFELONG NON-SMOKER
--- | --- | --- | --- | --- | --- | --- | --- | --- | ---
ALL | 28 | 23 | 37 | 29 | 2 | 355 | 217 | 250 | 128
DEL PEAK 12(5Q21.3) MUTATED | 13 | 10 | 21 | 15 | 1 | 213 | 103 | 146 | 40
DEL PEAK 12(5Q21.3) WILD-TYPE | 15 | 13 | 16 | 14 | 1 | 142 | 114 | 104 | 88

Figure S303. Get High-res Image Clustering Approach #52: 'Del Peak 12(5q21.3) mutation analysis' versus Clinical Feature #14: 'TOBACCOSMOKINGHISTORYINDICATOR'

Clustering Approach #53: 'Del Peak 13(6p25.3) mutation analysis'

Table S356. Description of clustering approach #53: 'Del Peak 13(6p25.3) mutation analysis'

Cluster Labels | DEL PEAK 13(6P25.3) MUTATED | DEL PEAK 13(6P25.3) WILD-TYPE
--- | --- | ---
Number of samples | 780 | 3783

'Del Peak 13(6p25.3) mutation analysis' versus 'PRIMARY.SITE.OF.DISEASE'

P value = 4.71e-16 (Chi-square test), Q value = 7.4e-13

Table S357. Clustering Approach #53: 'Del Peak 13(6p25.3) mutation analysis' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'

nPatients | BLADDER | BRAIN | BREAST | COLON | ENDOMETRIAL | HEAD/NECK | KIDNEY | LUNG | OMENTUM | OVARY | PERITONEUM (OVARY) | RECTUM
--- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | ---
ALL | 125 | 544 | 846 | 412 | 447 | 319 | 493 | 662 | 2 | 548 | 2 | 159
DEL PEAK 13(6P25.3) MUTATED | 32 | 84 | 157 | 54 | 14 | 64 | 93 | 132 | 0 | 126 | 0 | 21
DEL PEAK 13(6P25.3) WILD-TYPE | 93 | 460 | 689 | 358 | 433 | 255 | 400 | 530 | 2 | 422 | 2 | 138

Figure S304. Get High-res Image Clustering Approach #53: 'Del Peak 13(6p25.3) mutation analysis' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'

'Del Peak 13(6p25.3) mutation analysis' versus 'GENDER'

P value = 6.41e-05 (Fisher's exact test), Q value = 0.085

Table S358. Clustering Approach #53: 'Del Peak 13(6p25.3) mutation analysis' versus Clinical Feature #4: 'GENDER'

nPatients | FEMALE | MALE
--- | --- | ---
ALL | 2881 | 1682
DEL PEAK 13(6P25.3) MUTATED | 443 | 337
DEL PEAK 13(6P25.3) WILD-TYPE | 2438 | 1345

Figure S305. Get High-res Image Clustering Approach #53: 'Del Peak 13(6p25.3) mutation analysis' versus Clinical Feature #4: 'GENDER'

'Del Peak 13(6p25.3) mutation analysis' versus 'HISTOLOGICAL.TYPE'

P value = 1.37e-13 (Chi-square test), Q value = 2.1e-10

Table S359. Clustering Approach #53: 'Del Peak 13(6p25.3) mutation analysis' versus Clinical Feature #6: 'HISTOLOGICAL.TYPE'

nPatients | COLON ADENOCARCINOMA | COLON MUCINOUS ADENOCARCINOMA | ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA | HEAD & NECK SQUAMOUS CELL CARCINOMA | KIDNEY CLEAR CELL RENAL CARCINOMA | LUNG ACINAR ADENOCARCINOMA | LUNG ADENOCARCINOMA MIXED SUBTYPE | LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS) | LUNG BASALOID SQUAMOUS CELL CARCINOMA | LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS | LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS | LUNG CLEAR CELL ADENOCARCINOMA | LUNG MICROPAPILLARY ADENOCARCINOMA | LUNG MUCINOUS ADENOCARCINOMA | LUNG PAPILLARY ADENOCARCINOMA | LUNG PAPILLARY SQUAMOUS CELL CARCINOMA | LUNG PAPILLARY SQUAMOUS CELL CARICNOMA | LUNG SMALL CELL SQUAMOUS CELL CARCINOMA | LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA | LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS) | MIXED SEROUS AND ENDOMETRIOID | MUCINOUS (COLLOID) ADENOCARCINOMA | RECTAL ADENOCARCINOMA | RECTAL MUCINOUS ADENOCARCINOMA | SEROUS CYSTADENOCARCINOMA | SEROUS ENDOMETRIAL ADENOCARCINOMA | TREATED PRIMARY GBM | UNTREATED PRIMARY (DE NOVO) GBM
--- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | ---
ALL | 356 | 54 | 350 | 319 | 493 | 10 | 75 | 205 | 7 | 3 | 15 | 2 | 3 | 2 | 13 | 1 | 1 | 1 | 2 | 315 | 18 | 7 | 143 | 13 | 552 | 79 | 1 | 20
DEL PEAK 13(6P25.3) MUTATED | 49 | 5 | 6 | 64 | 93 | 1 | 9 | 31 | 2 | 0 | 2 | 0 | 0 | 0 | 3 | 1 | 0 | 0 | 0 | 82 | 1 | 1 | 18 | 3 | 126 | 7 | 0 | 5
DEL PEAK 13(6P25.3) WILD-TYPE | 307 | 49 | 344 | 255 | 400 | 9 | 66 | 174 | 5 | 3 | 13 | 2 | 3 | 2 | 10 | 0 | 1 | 1 | 2 | 233 | 17 | 6 | 125 | 10 | 426 | 72 | 1 | 15

Figure S306. Get High-res Image Clustering Approach #53: 'Del Peak 13(6p25.3) mutation analysis' versus Clinical Feature #6: 'HISTOLOGICAL.TYPE'

Clustering Approach #54: 'Del Peak 14(6q22.31) mutation analysis'

Table S360. Description of clustering approach #54: 'Del Peak 14(6q22.31) mutation analysis'

Cluster Labels | DEL PEAK 14(6Q22.31) MUTATED | DEL PEAK 14(6Q22.31) WILD-TYPE
--- | --- | ---
Number of samples | 1326 | 3237

'Del Peak 14(6q22.31) mutation analysis' versus 'PRIMARY.SITE.OF.DISEASE'

P value = 9.36e-93 (Chi-square test), Q value = 1.6e-89

Table S361. Clustering Approach #54: 'Del Peak 14(6q22.31) mutation analysis' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'

nPatients | BLADDER | BRAIN | BREAST | COLON | ENDOMETRIAL | HEAD/NECK | KIDNEY | LUNG | OMENTUM | OVARY | PERITONEUM (OVARY) | RECTUM
--- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | ---
ALL | 125 | 544 | 846 | 412 | 447 | 319 | 493 | 662 | 2 | 548 | 2 | 159
DEL PEAK 14(6Q22.31) MUTATED | 49 | 152 | 254 | 57 | 23 | 54 | 138 | 252 | 2 | 315 | 2 | 25
DEL PEAK 14(6Q22.31) WILD-TYPE | 76 | 392 | 592 | 355 | 424 | 265 | 355 | 410 | 0 | 233 | 0 | 134

Figure S307. Get High-res Image Clustering Approach #54: 'Del Peak 14(6q22.31) mutation analysis' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'

'Del Peak 14(6q22.31) mutation analysis' versus 'HISTOLOGICAL.TYPE'

P value = 6.04e-98 (Chi-square test), Q value = 1e-94

Table S362. Clustering Approach #54: 'Del Peak 14(6q22.31) mutation analysis' versus Clinical Feature #6: 'HISTOLOGICAL.TYPE'

nPatients | COLON ADENOCARCINOMA | COLON MUCINOUS ADENOCARCINOMA | ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA | HEAD & NECK SQUAMOUS CELL CARCINOMA | KIDNEY CLEAR CELL RENAL CARCINOMA | LUNG ACINAR ADENOCARCINOMA | LUNG ADENOCARCINOMA MIXED SUBTYPE | LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS) | LUNG BASALOID SQUAMOUS CELL CARCINOMA | LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS | LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS | LUNG CLEAR CELL ADENOCARCINOMA | LUNG MICROPAPILLARY ADENOCARCINOMA | LUNG MUCINOUS ADENOCARCINOMA | LUNG PAPILLARY ADENOCARCINOMA | LUNG PAPILLARY SQUAMOUS CELL CARCINOMA | LUNG PAPILLARY SQUAMOUS CELL CARICNOMA | LUNG SMALL CELL SQUAMOUS CELL CARCINOMA | LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA | LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS) | MIXED SEROUS AND ENDOMETRIOID | MUCINOUS (COLLOID) ADENOCARCINOMA | RECTAL ADENOCARCINOMA | RECTAL MUCINOUS ADENOCARCINOMA | SEROUS CYSTADENOCARCINOMA | SEROUS ENDOMETRIAL ADENOCARCINOMA | TREATED PRIMARY GBM | UNTREATED PRIMARY (DE NOVO) GBM
--- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | ---
ALL | 356 | 54 | 350 | 319 | 493 | 10 | 75 | 205 | 7 | 3 | 15 | 2 | 3 | 2 | 13 | 1 | 1 | 1 | 2 | 315 | 18 | 7 | 143 | 13 | 552 | 79 | 1 | 20
DEL PEAK 14(6Q22.31) MUTATED | 49 | 8 | 5 | 54 | 138 | 4 | 43 | 102 | 2 | 2 | 9 | 1 | 1 | 0 | 7 | 1 | 0 | 0 | 1 | 77 | 2 | 2 | 19 | 6 | 319 | 16 | 1 | 8
DEL PEAK 14(6Q22.31) WILD-TYPE | 307 | 46 | 345 | 265 | 355 | 6 | 32 | 103 | 5 | 1 | 6 | 1 | 2 | 2 | 6 | 0 | 1 | 1 | 1 | 238 | 16 | 5 | 124 | 7 | 233 | 63 | 0 | 12

Figure S308. Get High-res Image Clustering Approach #54: 'Del Peak 14(6q22.31) mutation analysis' versus Clinical Feature #6: 'HISTOLOGICAL.TYPE'

'Del Peak 14(6q22.31) mutation analysis' versus 'PATHOLOGY.T'

P value = 0.000134 (Fisher's exact test), Q value = 0.17

Table S363. Clustering Approach #54: 'Del Peak 14(6q22.31) mutation analysis' versus Clinical Feature #7: 'PATHOLOGY.T'

nPatients | T0+T1 | T2 | T3 | T4
--- | --- | --- | --- | ---
ALL | 466 | 632 | 694 | 209
DEL PEAK 14(6Q22.31) MUTATED | 132 | 193 | 141 | 50
DEL PEAK 14(6Q22.31) WILD-TYPE | 334 | 439 | 553 | 159

Figure S309. Get High-res Image Clustering Approach #54: 'Del Peak 14(6q22.31) mutation analysis' versus Clinical Feature #7: 'PATHOLOGY.T'

'Del Peak 14(6q22.31) mutation analysis' versus 'TUMOR.STAGE'

P value = 3.25e-09 (Fisher's exact test), Q value = 4.8e-06

Table S364. Clustering Approach #54: 'Del Peak 14(6q22.31) mutation analysis' versus Clinical Feature #10: 'TUMOR.STAGE'

nPatients | I | II | III | IV
--- | --- | --- | --- | ---
ALL | 712 | 498 | 881 | 423
DEL PEAK 14(6Q22.31) MUTATED | 215 | 127 | 360 | 123
DEL PEAK 14(6Q22.31) WILD-TYPE | 497 | 371 | 521 | 300

Figure S310. Get High-res Image Clustering Approach #54: 'Del Peak 14(6q22.31) mutation analysis' versus Clinical Feature #10: 'TUMOR.STAGE'

Clustering Approach #55: 'Del Peak 15(6q26) mutation analysis'

Table S365. Description of clustering approach #55: 'Del Peak 15(6q26) mutation analysis'

Cluster Labels | DEL PEAK 15(6Q26) MUTATED | DEL PEAK 15(6Q26) WILD-TYPE
--- | --- | ---
Number of samples | 1441 | 3122

'Del Peak 15(6q26) mutation analysis' versus 'AGE'

P value = 5.89e-06 (t-test), Q value = 0.0082

Table S366. Clustering Approach #55: 'Del Peak 15(6q26) mutation analysis' versus Clinical Feature #2: 'AGE'

| nPatients | Mean (Std.Dev)
--- | --- | ---
ALL | 4507 | 61.9 (12.6)
DEL PEAK 15(6Q26) MUTATED | 1416 | 60.6 (12.4)
DEL PEAK 15(6Q26) WILD-TYPE | 3091 | 62.4 (12.7)

Figure S311. Get High-res Image Clustering Approach #55: 'Del Peak 15(6q26) mutation analysis' versus Clinical Feature #2: 'AGE'

'Del Peak 15(6q26) mutation analysis' versus 'PRIMARY.SITE.OF.DISEASE'

P value = 5.42e-104 (Chi-square test), Q value = 9.4e-101

Table S367. Clustering Approach #55: 'Del Peak 15(6q26) mutation analysis' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'

nPatients | BLADDER | BRAIN | BREAST | COLON | ENDOMETRIAL | HEAD/NECK | KIDNEY | LUNG | OMENTUM | OVARY | PERITONEUM (OVARY) | RECTUM
--- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | ---
ALL | 125 | 544 | 846 | 412 | 447 | 319 | 493 | 662 | 2 | 548 | 2 | 159
DEL PEAK 15(6Q26) MUTATED | 54 | 162 | 287 | 60 | 35 | 55 | 142 | 263 | 1 | 351 | 1 | 28
DEL PEAK 15(6Q26) WILD-TYPE | 71 | 382 | 559 | 352 | 412 | 264 | 351 | 399 | 1 | 197 | 1 | 131

Figure S312. Get High-res Image Clustering Approach #55: 'Del Peak 15(6q26) mutation analysis' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'

'Del Peak 15(6q26) mutation analysis' versus 'HISTOLOGICAL.TYPE'

P value = 6.56e-108 (Chi-square test), Q value = 1.1e-104

Table S368. Clustering Approach #55: 'Del Peak 15(6q26) mutation analysis' versus Clinical Feature #6: 'HISTOLOGICAL.TYPE'

nPatients | COLON ADENOCARCINOMA | COLON MUCINOUS ADENOCARCINOMA | ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA | HEAD & NECK SQUAMOUS CELL CARCINOMA | KIDNEY CLEAR CELL RENAL CARCINOMA | LUNG ACINAR ADENOCARCINOMA | LUNG ADENOCARCINOMA MIXED SUBTYPE | LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS) | LUNG BASALOID SQUAMOUS CELL CARCINOMA | LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS | LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS | LUNG CLEAR CELL ADENOCARCINOMA | LUNG MICROPAPILLARY ADENOCARCINOMA | LUNG MUCINOUS ADENOCARCINOMA | LUNG PAPILLARY ADENOCARCINOMA | LUNG PAPILLARY SQUAMOUS CELL CARCINOMA | LUNG PAPILLARY SQUAMOUS CELL CARICNOMA | LUNG SMALL CELL SQUAMOUS CELL CARCINOMA | LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA | LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS) | MIXED SEROUS AND ENDOMETRIOID | MUCINOUS (COLLOID) ADENOCARCINOMA | RECTAL ADENOCARCINOMA | RECTAL MUCINOUS ADENOCARCINOMA | SEROUS CYSTADENOCARCINOMA | SEROUS ENDOMETRIAL ADENOCARCINOMA | TREATED PRIMARY GBM | UNTREATED PRIMARY (DE NOVO) GBM
--- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | ---
ALL | 356 | 54 | 350 | 319 | 493 | 10 | 75 | 205 | 7 | 3 | 15 | 2 | 3 | 2 | 13 | 1 | 1 | 1 | 2 | 315 | 18 | 7 | 143 | 13 | 552 | 79 | 1 | 20
DEL PEAK 15(6Q26) MUTATED | 52 | 8 | 12 | 55 | 142 | 4 | 43 | 105 | 2 | 2 | 7 | 1 | 1 | 0 | 8 | 1 | 0 | 0 | 1 | 86 | 3 | 2 | 22 | 6 | 353 | 20 | 1 | 11
DEL PEAK 15(6Q26) WILD-TYPE | 304 | 46 | 338 | 264 | 351 | 6 | 32 | 100 | 5 | 1 | 8 | 1 | 2 | 2 | 5 | 0 | 1 | 1 | 1 | 229 | 15 | 5 | 121 | 7 | 199 | 59 | 0 | 9

Figure S313. Get High-res Image Clustering Approach #55: 'Del Peak 15(6q26) mutation analysis' versus Clinical Feature #6: 'HISTOLOGICAL.TYPE'

'Del Peak 15(6q26) mutation analysis' versus 'TUMOR.STAGE'

P value = 1.13e-12 (Fisher's exact test), Q value = 1.7e-09

Table S369. Clustering Approach #55: 'Del Peak 15(6q26) mutation analysis' versus Clinical Feature #10: 'TUMOR.STAGE'

nPatients | I | II | III | IV
--- | --- | --- | --- | ---
ALL | 712 | 498 | 881 | 423
DEL PEAK 15(6Q26) MUTATED | 221 | 129 | 392 | 138
DEL PEAK 15(6Q26) WILD-TYPE | 491 | 369 | 489 | 285

Figure S314. Get High-res Image Clustering Approach #55: 'Del Peak 15(6q26) mutation analysis' versus Clinical Feature #10: 'TUMOR.STAGE'

Clustering Approach #56: 'Del Peak 16(7p22.3) mutation analysis'

Table S370. Description of clustering approach #56: 'Del Peak 16(7p22.3) mutation analysis'

Cluster Labels | DEL PEAK 16(7P22.3) MUTATED | DEL PEAK 16(7P22.3) WILD-TYPE
--- | --- | ---
Number of samples | 511 | 4052

'Del Peak 16(7p22.3) mutation analysis' versus 'PRIMARY.SITE.OF.DISEASE'

P value = 1.43e-143 (Chi-square test), Q value = 2.5e-140

Table S371. Clustering Approach #56: 'Del Peak 16(7p22.3) mutation analysis' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'

nPatients | BLADDER | BRAIN | BREAST | COLON | ENDOMETRIAL | HEAD/NECK | KIDNEY | LUNG | OMENTUM | OVARY | PERITONEUM (OVARY) | RECTUM
--- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | ---
ALL | 125 | 544 | 846 | 412 | 447 | 319 | 493 | 662 | 2 | 548 | 2 | 159
DEL PEAK 16(7P22.3) MUTATED | 7 | 13 | 114 | 2 | 56 | 17 | 2 | 68 | 0 | 229 | 1 | 2
DEL PEAK 16(7P22.3) WILD-TYPE | 118 | 531 | 732 | 410 | 391 | 302 | 491 | 594 | 2 | 319 | 1 | 157

Figure S315. Get High-res Image Clustering Approach #56: 'Del Peak 16(7p22.3) mutation analysis' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'

'Del Peak 16(7p22.3) mutation analysis' versus 'GENDER'

P value = 1.29e-27 (Fisher's exact test), Q value = 2.1e-24

Table S372. Clustering Approach #56: 'Del Peak 16(7p22.3) mutation analysis' versus Clinical Feature #4: 'GENDER'

nPatients | FEMALE | MALE
--- | --- | ---
ALL | 2881 | 1682
DEL PEAK 16(7P22.3) MUTATED | 429 | 82
DEL PEAK 16(7P22.3) WILD-TYPE | 2452 | 1600

Figure S316. Get High-res Image Clustering Approach #56: 'Del Peak 16(7p22.3) mutation analysis' versus Clinical Feature #4: 'GENDER'

'Del Peak 16(7p22.3) mutation analysis' versus 'HISTOLOGICAL.TYPE'

P value = 8.12e-127 (Chi-square test), Q value = 1.4e-123

Table S373. Clustering Approach #56: 'Del Peak 16(7p22.3) mutation analysis' versus Clinical Feature #6: 'HISTOLOGICAL.TYPE'

nPatients | COLON ADENOCARCINOMA | COLON MUCINOUS ADENOCARCINOMA | ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA | HEAD & NECK SQUAMOUS CELL CARCINOMA | KIDNEY CLEAR CELL RENAL CARCINOMA | LUNG ACINAR ADENOCARCINOMA | LUNG ADENOCARCINOMA MIXED SUBTYPE | LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS) | LUNG BASALOID SQUAMOUS CELL CARCINOMA | LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS | LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS | LUNG CLEAR CELL ADENOCARCINOMA | LUNG MICROPAPILLARY ADENOCARCINOMA | LUNG MUCINOUS ADENOCARCINOMA | LUNG PAPILLARY ADENOCARCINOMA | LUNG PAPILLARY SQUAMOUS CELL CARCINOMA | LUNG PAPILLARY SQUAMOUS CELL CARICNOMA | LUNG SMALL CELL SQUAMOUS CELL CARCINOMA | LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA | LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS) | MIXED SEROUS AND ENDOMETRIOID | MUCINOUS (COLLOID) ADENOCARCINOMA | RECTAL ADENOCARCINOMA | RECTAL MUCINOUS ADENOCARCINOMA | SEROUS CYSTADENOCARCINOMA | SEROUS ENDOMETRIAL ADENOCARCINOMA | TREATED PRIMARY GBM | UNTREATED PRIMARY (DE NOVO) GBM
--- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | ---
ALL | 356 | 54 | 350 | 319 | 493 | 10 | 75 | 205 | 7 | 3 | 15 | 2 | 3 | 2 | 13 | 1 | 1 | 1 | 2 | 315 | 18 | 7 | 143 | 13 | 552 | 79 | 1 | 20
DEL PEAK 16(7P22.3) MUTATED | 2 | 0 | 21 | 17 | 2 | 0 | 4 | 15 | 1 | 0 | 0 | 0 | 0 | 0 | 2 | 1 | 0 | 0 | 0 | 45 | 4 | 0 | 1 | 1 | 230 | 31 | 0 | 0
DEL PEAK 16(7P22.3) WILD-TYPE | 354 | 54 | 329 | 302 | 491 | 10 | 71 | 190 | 6 | 3 | 15 | 2 | 3 | 2 | 11 | 0 | 1 | 1 | 2 | 270 | 14 | 7 | 142 | 12 | 322 | 48 | 1 | 20

Figure S317. Get High-res Image Clustering Approach #56: 'Del Peak 16(7p22.3) mutation analysis' versus Clinical Feature #6: 'HISTOLOGICAL.TYPE'

'Del Peak 16(7p22.3) mutation analysis' versus 'PATHOLOGY.T'

P value = 3.28e-07 (Fisher's exact test), Q value = 0.00048

Table S374. Clustering Approach #56: 'Del Peak 16(7p22.3) mutation analysis' versus Clinical Feature #7: 'PATHOLOGY.T'

nPatients | T0+T1 | T2 | T3 | T4
--- | --- | --- | --- | ---
ALL | 466 | 632 | 694 | 209
DEL PEAK 16(7P22.3) MUTATED | 16 | 49 | 11 | 12
DEL PEAK 16(7P22.3) WILD-TYPE | 450 | 583 | 683 | 197

Figure S318. Get High-res Image Clustering Approach #56: 'Del Peak 16(7p22.3) mutation analysis' versus Clinical Feature #7: 'PATHOLOGY.T'

'Del Peak 16(7p22.3) mutation analysis' versus 'TUMOR.STAGE'

P value = 5.75e-29 (Fisher's exact test), Q value = 9.3e-26

Table S375. Clustering Approach #56: 'Del Peak 16(7p22.3) mutation analysis' versus Clinical Feature #10: 'TUMOR.STAGE'

nPatients | I | II | III | IV
--- | --- | --- | --- | ---
ALL | 712 | 498 | 881 | 423
DEL PEAK 16(7P22.3) MUTATED | 38 | 30 | 200 | 46
DEL PEAK 16(7P22.3) WILD-TYPE | 674 | 468 | 681 | 377

Figure S319. Get High-res Image Clustering Approach #56: 'Del Peak 16(7p22.3) mutation analysis' versus Clinical Feature #10: 'TUMOR.STAGE'

Clustering Approach #57: 'Del Peak 17(7q36.1) mutation analysis'

Table S376. Description of clustering approach #57: 'Del Peak 17(7q36.1) mutation analysis'

Cluster Labels | DEL PEAK 17(7Q36.1) MUTATED | DEL PEAK 17(7Q36.1) WILD-TYPE
--- | --- | ---
Number of samples | 530 | 4033

'Del Peak 17(7q36.1) mutation analysis' versus 'PRIMARY.SITE.OF.DISEASE'

P value = 1.07e-56 (Chi-square test), Q value = 1.8e-53

Table S377. Clustering Approach #57: 'Del Peak 17(7q36.1) mutation analysis' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'

nPatients | BLADDER | BRAIN | BREAST | COLON | ENDOMETRIAL | HEAD/NECK | KIDNEY | LUNG | OMENTUM | OVARY | PERITONEUM (OVARY) | RECTUM
--- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | ---
ALL | 125 | 544 | 846 | 412 | 447 | 319 | 493 | 662 | 2 | 548 | 2 | 159
DEL PEAK 17(7Q36.1) MUTATED | 14 | 8 | 171 | 8 | 50 | 80 | 6 | 117 | 0 | 67 | 1 | 8
DEL PEAK 17(7Q36.1) WILD-TYPE | 111 | 536 | 675 | 404 | 397 | 239 | 487 | 545 | 2 | 481 | 1 | 151

Figure S320. Get High-res Image Clustering Approach #57: 'Del Peak 17(7q36.1) mutation analysis' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'

'Del Peak 17(7q36.1) mutation analysis' versus 'HISTOLOGICAL.TYPE'

P value = 1.29e-52 (Chi-square test), Q value = 2.2e-49

Table S378. Clustering Approach #57: 'Del Peak 17(7q36.1) mutation analysis' versus Clinical Feature #6: 'HISTOLOGICAL.TYPE'

nPatients | COLON ADENOCARCINOMA | COLON MUCINOUS ADENOCARCINOMA | ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA | HEAD & NECK SQUAMOUS CELL CARCINOMA | KIDNEY CLEAR CELL RENAL CARCINOMA | LUNG ACINAR ADENOCARCINOMA | LUNG ADENOCARCINOMA MIXED SUBTYPE | LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS) | LUNG BASALOID SQUAMOUS CELL CARCINOMA | LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS | LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS | LUNG CLEAR CELL ADENOCARCINOMA | LUNG MICROPAPILLARY ADENOCARCINOMA | LUNG MUCINOUS ADENOCARCINOMA | LUNG PAPILLARY ADENOCARCINOMA | LUNG PAPILLARY SQUAMOUS CELL CARCINOMA | LUNG PAPILLARY SQUAMOUS CELL CARICNOMA | LUNG SMALL CELL SQUAMOUS CELL CARCINOMA | LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA | LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS) | MIXED SEROUS AND ENDOMETRIOID | MUCINOUS (COLLOID) ADENOCARCINOMA | RECTAL ADENOCARCINOMA | RECTAL MUCINOUS ADENOCARCINOMA | SEROUS CYSTADENOCARCINOMA | SEROUS ENDOMETRIAL ADENOCARCINOMA | TREATED PRIMARY GBM | UNTREATED PRIMARY (DE NOVO) GBM
--- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | ---
ALL | 356 | 54 | 350 | 319 | 493 | 10 | 75 | 205 | 7 | 3 | 15 | 2 | 3 | 2 | 13 | 1 | 1 | 1 | 2 | 315 | 18 | 7 | 143 | 13 | 552 | 79 | 1 | 20
DEL PEAK 17(7Q36.1) MUTATED | 7 | 1 | 12 | 80 | 6 | 0 | 6 | 32 | 2 | 0 | 2 | 1 | 1 | 0 | 3 | 0 | 0 | 0 | 0 | 67 | 4 | 3 | 5 | 3 | 68 | 34 | 0 | 0
DEL PEAK 17(7Q36.1) WILD-TYPE | 349 | 53 | 338 | 239 | 487 | 10 | 69 | 173 | 5 | 3 | 13 | 1 | 2 | 2 | 10 | 1 | 1 | 1 | 2 | 248 | 14 | 4 | 138 | 10 | 484 | 45 | 1 | 20

Figure S321. Get High-res Image Clustering Approach #57: 'Del Peak 17(7q36.1) mutation analysis' versus Clinical Feature #6: 'HISTOLOGICAL.TYPE'

'Del Peak 17(7q36.1) mutation analysis' versus 'PATHOLOGY.T'

P value = 8.06e-11 (Fisher's exact test), Q value = 1.2e-07

Table S379. Clustering Approach #57: 'Del Peak 17(7q36.1) mutation analysis' versus Clinical Feature #7: 'PATHOLOGY.T'

nPatients | T0+T1 | T2 | T3 | T4
--- | --- | --- | --- | ---
ALL | 466 | 632 | 694 | 209
DEL PEAK 17(7Q36.1) MUTATED | 36 | 98 | 38 | 36
DEL PEAK 17(7Q36.1) WILD-TYPE | 430 | 534 | 656 | 173

Figure S322. Get High-res Image Clustering Approach #57: 'Del Peak 17(7q36.1) mutation analysis' versus Clinical Feature #7: 'PATHOLOGY.T'

Clustering Approach #58: 'Del Peak 18(8p23.2) mutation analysis'

Table S380. Description of clustering approach #58: 'Del Peak 18(8p23.2) mutation analysis'

Cluster Labels | DEL PEAK 18(8P23.2) MUTATED | DEL PEAK 18(8P23.2) WILD-TYPE
--- | --- | ---
Number of samples | 2024 | 2539

'Del Peak 18(8p23.2) mutation analysis' versus 'PRIMARY.SITE.OF.DISEASE'

P value = 9.18e-132 (Chi-square test), Q value = 1.6e-128

Table S381. Clustering Approach #58: 'Del Peak 18(8p23.2) mutation analysis' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'

nPatients | BLADDER | BRAIN | BREAST | COLON | ENDOMETRIAL | HEAD/NECK | KIDNEY | LUNG | OMENTUM | OVARY | PERITONEUM (OVARY) | RECTUM
--- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | ---
ALL | 125 | 544 | 846 | 412 | 447 | 319 | 493 | 662 | 2 | 548 | 2 | 159
DEL PEAK 18(8P23.2) MUTATED | 67 | 65 | 449 | 172 | 81 | 183 | 146 | 390 | 2 | 367 | 2 | 98
DEL PEAK 18(8P23.2) WILD-TYPE | 58 | 479 | 397 | 240 | 366 | 136 | 347 | 272 | 0 | 181 | 0 | 61

Figure S323. Get High-res Image Clustering Approach #58: 'Del Peak 18(8p23.2) mutation analysis' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'

'Del Peak 18(8p23.2) mutation analysis' versus 'KARNOFSKY.PERFORMANCE.SCORE'

P value = 7.72e-05 (t-test), Q value = 0.1

Table S382. Clustering Approach #58: 'Del Peak 18(8p23.2) mutation analysis' versus Clinical Feature #5: 'KARNOFSKY.PERFORMANCE.SCORE'

| nPatients | Mean (Std.Dev)
--- | --- | ---
ALL | 640 | 73.6 (23.9)
DEL PEAK 18(8P23.2) MUTATED | 183 | 66.2 (32.4)
DEL PEAK 18(8P23.2) WILD-TYPE | 457 | 76.5 (18.8)

Figure S324. Get High-res Image Clustering Approach #58: 'Del Peak 18(8p23.2) mutation analysis' versus Clinical Feature #5: 'KARNOFSKY.PERFORMANCE.SCORE'

'Del Peak 18(8p23.2) mutation analysis' versus 'HISTOLOGICAL.TYPE'

P value = 6.41e-91 (Chi-square test), Q value = 1.1e-87

Table S383. Clustering Approach #58: 'Del Peak 18(8p23.2) mutation analysis' versus Clinical Feature #6: 'HISTOLOGICAL.TYPE'

nPatients | COLON ADENOCARCINOMA | COLON MUCINOUS ADENOCARCINOMA | ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA | HEAD & NECK SQUAMOUS CELL CARCINOMA | KIDNEY CLEAR CELL RENAL CARCINOMA | LUNG ACINAR ADENOCARCINOMA | LUNG ADENOCARCINOMA MIXED SUBTYPE | LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS) | LUNG BASALOID SQUAMOUS CELL CARCINOMA | LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS | LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS | LUNG CLEAR CELL ADENOCARCINOMA | LUNG MICROPAPILLARY ADENOCARCINOMA | LUNG MUCINOUS ADENOCARCINOMA | LUNG PAPILLARY ADENOCARCINOMA | LUNG PAPILLARY SQUAMOUS CELL CARCINOMA | LUNG PAPILLARY SQUAMOUS CELL CARICNOMA | LUNG SMALL CELL SQUAMOUS CELL CARCINOMA | LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA | LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS) | MIXED SEROUS AND ENDOMETRIOID | MUCINOUS (COLLOID) ADENOCARCINOMA | RECTAL ADENOCARCINOMA | RECTAL MUCINOUS ADENOCARCINOMA | SEROUS CYSTADENOCARCINOMA | SEROUS ENDOMETRIAL ADENOCARCINOMA | TREATED PRIMARY GBM | UNTREATED PRIMARY (DE NOVO) GBM
--- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | ---
ALL | 356 | 54 | 350 | 319 | 493 | 10 | 75 | 205 | 7 | 3 | 15 | 2 | 3 | 2 | 13 | 1 | 1 | 1 | 2 | 315 | 18 | 7 | 143 | 13 | 552 | 79 | 1 | 20
DEL PEAK 18(8P23.2) MUTATED | 156 | 15 | 28 | 183 | 146 | 4 | 31 | 108 | 4 | 0 | 9 | 2 | 3 | 0 | 6 | 1 | 0 | 0 | 2 | 220 | 4 | 0 | 89 | 7 | 371 | 49 | 0 | 4
DEL PEAK 18(8P23.2) WILD-TYPE | 200 | 39 | 322 | 136 | 347 | 6 | 44 | 97 | 3 | 3 | 6 | 0 | 0 | 2 | 7 | 0 | 1 | 1 | 0 | 95 | 14 | 7 | 54 | 6 | 181 | 30 | 1 | 16

Figure S325. Get High-res Image Clustering Approach #58: 'Del Peak 18(8p23.2) mutation analysis' versus Clinical Feature #6: 'HISTOLOGICAL.TYPE'

'Del Peak 18(8p23.2) mutation analysis' versus 'PATHOLOGY.T'

P value = 1.44e-05 (Fisher's exact test), Q value = 0.02

Table S384. Clustering Approach #58: 'Del Peak 18(8p23.2) mutation analysis' versus Clinical Feature #7: 'PATHOLOGY.T'

nPatients | T0+T1 | T2 | T3 | T4
--- | --- | --- | --- | ---
ALL | 466 | 632 | 694 | 209
DEL PEAK 18(8P23.2) MUTATED | 189 | 341 | 327 | 118
DEL PEAK 18(8P23.2) WILD-TYPE | 277 | 291 | 367 | 91

Figure S326. Get High-res Image Clustering Approach #58: 'Del Peak 18(8p23.2) mutation analysis' versus Clinical Feature #7: 'PATHOLOGY.T'

'Del Peak 18(8p23.2) mutation analysis' versus 'PATHOLOGY.N'

P value = 1.37e-08 (Fisher's exact test), Q value = 2e-05

Table S385. Clustering Approach #58: 'Del Peak 18(8p23.2) mutation analysis' versus Clinical Feature #8: 'PATHOLOGY.N'

nPatients | N0 | N1 | N2 | N3
--- | --- | --- | --- | ---
ALL | 1067 | 353 | 282 | 11
DEL PEAK 18(8P23.2) MUTATED | 480 | 205 | 175 | 8
DEL PEAK 18(8P23.2) WILD-TYPE | 587 | 148 | 107 | 3

Figure S327. Get High-res Image Clustering Approach #58: 'Del Peak 18(8p23.2) mutation analysis' versus Clinical Feature #8: 'PATHOLOGY.N'

'Del Peak 18(8p23.2) mutation analysis' versus 'TUMOR.STAGE'

P value = 6.41e-08 (Fisher's exact test), Q value = 9.4e-05

Table S386. Clustering Approach #58: 'Del Peak 18(8p23.2) mutation analysis' versus Clinical Feature #10: 'TUMOR.STAGE'

nPatients | I | II | III | IV
--- | --- | --- | --- | ---
ALL | 712 | 498 | 881 | 423
DEL PEAK 18(8P23.2) MUTATED | 321 | 245 | 517 | 245
DEL PEAK 18(8P23.2) WILD-TYPE | 391 | 253 | 364 | 178

Figure S328. Get High-res Image Clustering Approach #58: 'Del Peak 18(8p23.2) mutation analysis' versus Clinical Feature #10: 'TUMOR.STAGE'

'Del Peak 18(8p23.2) mutation analysis' versus 'RADIATIONS.RADIATION.REGIMENINDICATION'

P value = 2.07e-21 (Fisher's exact test), Q value = 3.3e-18

Table S387. Clustering Approach #58: 'Del Peak 18(8p23.2) mutation analysis' versus Clinical Feature #11: 'RADIATIONS.RADIATION.REGIMENINDICATION'

nPatients | NO | YES
--- | --- | ---
ALL | 826 | 3737
DEL PEAK 18(8P23.2) MUTATED | 245 | 1779
DEL PEAK 18(8P23.2) WILD-TYPE | 581 | 1958

Figure S329. Get High-res Image Clustering Approach #58: 'Del Peak 18(8p23.2) mutation analysis' versus Clinical Feature #11: 'RADIATIONS.RADIATION.REGIMENINDICATION'

Clustering Approach #59: 'Del Peak 19(8p21.2) mutation analysis'

Table S388. Description of clustering approach #59: 'Del Peak 19(8p21.2) mutation analysis'

Cluster Labels | DEL PEAK 19(8P21.2) MUTATED | DEL PEAK 19(8P21.2) WILD-TYPE
--- | --- | ---
Number of samples | 2041 | 2522

'Del Peak 19(8p21.2) mutation analysis' versus 'PRIMARY.SITE.OF.DISEASE'

P value = 1.38e-135 (Chi-square test), Q value = 2.4e-132

Table S389. Clustering Approach #59: 'Del Peak 19(8p21.2) mutation analysis' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'

nPatients | BLADDER | BRAIN | BREAST | COLON | ENDOMETRIAL | HEAD/NECK | KIDNEY | LUNG | OMENTUM | OVARY | PERITONEUM (OVARY) | RECTUM
--- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | ---
ALL | 125 | 544 | 846 | 412 | 447 | 319 | 493 | 662 | 2 | 548 | 2 | 159
DEL PEAK 19(8P21.2) MUTATED | 70 | 66 | 462 | 179 | 80 | 161 | 148 | 393 | 2 | 382 | 2 | 94
DEL PEAK 19(8P21.2) WILD-TYPE | 55 | 478 | 384 | 233 | 367 | 158 | 345 | 269 | 0 | 166 | 0 | 65

Figure S330. Get High-res Image Clustering Approach #59: 'Del Peak 19(8p21.2) mutation analysis' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'

'Del Peak 19(8p21.2) mutation analysis' versus 'KARNOFSKY.PERFORMANCE.SCORE'

P value = 1.6e-05 (t-test), Q value = 0.022

Table S390. Clustering Approach #59: 'Del Peak 19(8p21.2) mutation analysis' versus Clinical Feature #5: 'KARNOFSKY.PERFORMANCE.SCORE'

| nPatients | Mean (Std.Dev)
--- | --- | ---
ALL | 640 | 73.6 (23.9)
DEL PEAK 19(8P21.2) MUTATED | 188 | 65.7 (32.3)
DEL PEAK 19(8P21.2) WILD-TYPE | 452 | 76.8 (18.5)

Figure S331. Get High-res Image Clustering Approach #59: 'Del Peak 19(8p21.2) mutation analysis' versus Clinical Feature #5: 'KARNOFSKY.PERFORMANCE.SCORE'

'Del Peak 19(8p21.2) mutation analysis' versus 'HISTOLOGICAL.TYPE'

P value = 1.04e-93 (Chi-square test), Q value = 1.8e-90

Table S391. Clustering Approach #59: 'Del Peak 19(8p21.2) mutation analysis' versus Clinical Feature #6: 'HISTOLOGICAL.TYPE'

nPatients | COLON ADENOCARCINOMA | COLON MUCINOUS ADENOCARCINOMA | ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA | HEAD & NECK SQUAMOUS CELL CARCINOMA | KIDNEY CLEAR CELL RENAL CARCINOMA | LUNG ACINAR ADENOCARCINOMA | LUNG ADENOCARCINOMA MIXED SUBTYPE | LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS) | LUNG BASALOID SQUAMOUS CELL CARCINOMA | LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS | LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS | LUNG CLEAR CELL ADENOCARCINOMA | LUNG MICROPAPILLARY ADENOCARCINOMA | LUNG MUCINOUS ADENOCARCINOMA | LUNG PAPILLARY ADENOCARCINOMA | LUNG PAPILLARY SQUAMOUS CELL CARCINOMA | LUNG PAPILLARY SQUAMOUS CELL CARICNOMA | LUNG SMALL CELL SQUAMOUS CELL CARCINOMA | LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA | LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS) | MIXED SEROUS AND ENDOMETRIOID | MUCINOUS (COLLOID) ADENOCARCINOMA | RECTAL ADENOCARCINOMA | RECTAL MUCINOUS ADENOCARCINOMA | SEROUS CYSTADENOCARCINOMA | SEROUS ENDOMETRIAL ADENOCARCINOMA | TREATED PRIMARY GBM | UNTREATED PRIMARY (DE NOVO) GBM
--- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | ---
ALL | 356 | 54 | 350 | 319 | 493 | 10 | 75 | 205 | 7 | 3 | 15 | 2 | 3 | 2 | 13 | 1 | 1 | 1 | 2 | 315 | 18 | 7 | 143 | 13 | 552 | 79 | 1 | 20
DEL PEAK 19(8P21.2) MUTATED | 163 | 15 | 22 | 161 | 148 | 4 | 35 | 115 | 4 | 0 | 9 | 2 | 3 | 0 | 9 | 1 | 0 | 0 | 2 | 209 | 5 | 0 | 85 | 7 | 386 | 53 | 0 | 5
DEL PEAK 19(8P21.2) WILD-TYPE | 193 | 39 | 328 | 158 | 345 | 6 | 40 | 90 | 3 | 3 | 6 | 0 | 0 | 2 | 4 | 0 | 1 | 1 | 0 | 106 | 13 | 7 | 58 | 6 | 166 | 26 | 1 | 15

Figure S332. Get High-res Image Clustering Approach #59: 'Del Peak 19(8p21.2) mutation analysis' versus Clinical Feature #6: 'HISTOLOGICAL.TYPE'

'Del Peak 19(8p21.2) mutation analysis' versus 'PATHOLOGY.N'

P value = 1.99e-08 (Fisher's exact test), Q value = 2.9e-05

Table S392. Clustering Approach #59: 'Del Peak 19(8p21.2) mutation analysis' versus Clinical Feature #8: 'PATHOLOGY.N'

nPatients | N0 | N1 | N2 | N3
--- | --- | --- | --- | ---
ALL | 1067 | 353 | 282 | 11
DEL PEAK 19(8P21.2) MUTATED | 473 | 203 | 172 | 8
DEL PEAK 19(8P21.2) WILD-TYPE | 594 | 150 | 110 | 3

Figure S333. Get High-res Image Clustering Approach #59: 'Del Peak 19(8p21.2) mutation analysis' versus Clinical Feature #8: 'PATHOLOGY.N'

'Del Peak 19(8p21.2) mutation analysis' versus 'TUMOR.STAGE'

P value = 1.36e-10 (Fisher's exact test), Q value = 2.1e-07

Table S393. Clustering Approach #59: 'Del Peak 19(8p21.2) mutation analysis' versus Clinical Feature #10: 'TUMOR.STAGE'

nPatients | I | II | III | IV
--- | --- | --- | --- | ---
ALL | 712 | 498 | 881 | 423
DEL PEAK 19(8P21.2) MUTATED | 319 | 235 | 534 | 240
DEL PEAK 19(8P21.2) WILD-TYPE | 393 | 263 | 347 | 183

Figure S334. Get High-res Image Clustering Approach #59: 'Del Peak 19(8p21.2) mutation analysis' versus Clinical Feature #10: 'TUMOR.STAGE'

'Del Peak 19(8p21.2) mutation analysis' versus 'RADIATIONS.RADIATION.REGIMENINDICATION'

P value = 1.62e-22 (Fisher's exact test), Q value = 2.6e-19

Table S394. Clustering Approach #59: 'Del Peak 19(8p21.2) mutation analysis' versus Clinical Feature #11: 'RADIATIONS.RADIATION.REGIMENINDICATION'

nPatients | NO | YES
--- | --- | ---
ALL | 826 | 3737
DEL PEAK 19(8P21.2) MUTATED | 245 | 1796
DEL PEAK 19(8P21.2) WILD-TYPE | 581 | 1941

Figure S335. Get High-res Image Clustering Approach #59: 'Del Peak 19(8p21.2) mutation analysis' versus Clinical Feature #11: 'RADIATIONS.RADIATION.REGIMENINDICATION'

Clustering Approach #60: 'Del Peak 20(9p23) mutation analysis'

Table S395. Description of clustering approach #60: 'Del Peak 20(9p23) mutation analysis'

Cluster Labels | DEL PEAK 20(9P23) MUTATED | DEL PEAK 20(9P23) WILD-TYPE
--- | --- | ---
Number of samples | 1611 | 2952

'Del Peak 20(9p23) mutation analysis' versus 'Time to Death'

P value = 0 (logrank test), Q value = 0

Table S396. Clustering Approach #60: 'Del Peak 20(9p23) mutation analysis' versus Clinical Feature #1: 'Time to Death'

| nPatients | nDeath | Duration Range (Median), Month
--- | --- | --- | ---
ALL | 4296 | 1401 | 0.0 - 224.0 (14.9)
DEL PEAK 20(9P23) MUTATED | 1530 | 623 | 0.0 - 163.1 (14.2)
DEL PEAK 20(9P23) WILD-TYPE | 2766 | 778 | 0.0 - 224.0 (15.0)

Figure S336. Get High-res Image Clustering Approach #60: 'Del Peak 20(9p23) mutation analysis' versus Clinical Feature #1: 'Time to Death'

'Del Peak 20(9p23) mutation analysis' versus 'PRIMARY.SITE.OF.DISEASE'

P value = 2.13e-93 (Chi-square test), Q value = 3.7e-90

Table S397. Clustering Approach #60: 'Del Peak 20(9p23) mutation analysis' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'

nPatients | BLADDER | BRAIN | BREAST | COLON | ENDOMETRIAL | HEAD/NECK | KIDNEY | LUNG | OMENTUM | OVARY | PERITONEUM (OVARY) | RECTUM
--- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | ---
ALL | 125 | 544 | 846 | 412 | 447 | 319 | 493 | 662 | 2 | 548 | 2 | 159
DEL PEAK 20(9P23) MUTATED | 57 | 232 | 261 | 53 | 51 | 149 | 144 | 390 | 1 | 245 | 2 | 25
DEL PEAK 20(9P23) WILD-TYPE | 68 | 312 | 585 | 359 | 396 | 170 | 349 | 272 | 1 | 303 | 0 | 134

Figure S337. Get High-res Image Clustering Approach #60: 'Del Peak 20(9p23) mutation analysis' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'

'Del Peak 20(9p23) mutation analysis' versus 'GENDER'

P value = 2.44e-10 (Fisher's exact test), Q value = 3.7e-07

Table S398. Clustering Approach #60: 'Del Peak 20(9p23) mutation analysis' versus Clinical Feature #4: 'GENDER'

nPatients | FEMALE | MALE
--- | --- | ---
ALL | 2881 | 1682
DEL PEAK 20(9P23) MUTATED | 918 | 693
DEL PEAK 20(9P23) WILD-TYPE | 1963 | 989

Figure S338. Get High-res Image Clustering Approach #60: 'Del Peak 20(9p23) mutation analysis' versus Clinical Feature #4: 'GENDER'

'Del Peak 20(9p23) mutation analysis' versus 'HISTOLOGICAL.TYPE'

P value = 2.4e-86 (Chi-square test), Q value = 4.1e-83

Table S399. Clustering Approach #60: 'Del Peak 20(9p23) mutation analysis' versus Clinical Feature #6: 'HISTOLOGICAL.TYPE'

nPatients | COLON ADENOCARCINOMA | COLON MUCINOUS ADENOCARCINOMA | ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA | HEAD & NECK SQUAMOUS CELL CARCINOMA | KIDNEY CLEAR CELL RENAL CARCINOMA | LUNG ACINAR ADENOCARCINOMA | LUNG ADENOCARCINOMA MIXED SUBTYPE | LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS) | LUNG BASALOID SQUAMOUS CELL CARCINOMA | LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS | LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS | LUNG CLEAR CELL ADENOCARCINOMA | LUNG MICROPAPILLARY ADENOCARCINOMA | LUNG MUCINOUS ADENOCARCINOMA | LUNG PAPILLARY ADENOCARCINOMA | LUNG PAPILLARY SQUAMOUS CELL CARCINOMA | LUNG PAPILLARY SQUAMOUS CELL CARICNOMA | LUNG SMALL CELL SQUAMOUS CELL CARCINOMA | LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA | LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS) | MIXED SEROUS AND ENDOMETRIOID | MUCINOUS (COLLOID) ADENOCARCINOMA | RECTAL ADENOCARCINOMA | RECTAL MUCINOUS ADENOCARCINOMA | SEROUS CYSTADENOCARCINOMA | SEROUS ENDOMETRIAL ADENOCARCINOMA | TREATED PRIMARY GBM | UNTREATED PRIMARY (DE NOVO) GBM
--- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | ---
ALL | 356 | 54 | 350 | 319 | 493 | 10 | 75 | 205 | 7 | 3 | 15 | 2 | 3 | 2 | 13 | 1 | 1 | 1 | 2 | 315 | 18 | 7 | 143 | 13 | 552 | 79 | 1 | 20
DEL PEAK 20(9P23) MUTATED | 49 | 4 | 20 | 149 | 144 | 6 | 42 | 110 | 3 | 1 | 11 | 1 | 3 | 1 | 5 | 1 | 0 | 0 | 1 | 203 | 3 | 2 | 24 | 1 | 248 | 28 | 0 | 10
DEL PEAK 20(9P23) WILD-TYPE | 307 | 50 | 330 | 170 | 349 | 4 | 33 | 95 | 4 | 2 | 4 | 1 | 0 | 1 | 8 | 0 | 1 | 1 | 1 | 112 | 15 | 5 | 119 | 12 | 304 | 51 | 1 | 10

Figure S339. Get High-res Image Clustering Approach #60: 'Del Peak 20(9p23) mutation analysis' versus Clinical Feature #6: 'HISTOLOGICAL.TYPE'

'Del Peak 20(9p23) mutation analysis' versus 'PATHOLOGY.T'

P value = 2.04e-10 (Fisher's exact test), Q value = 3.1e-07

Table S400. Clustering Approach #60: 'Del Peak 20(9p23) mutation analysis' versus Clinical Feature #7: 'PATHOLOGY.T'

nPatients | T0+T1 | T2 | T3 | T4
--- | --- | --- | --- | ---
ALL | 466 | 632 | 694 | 209
DEL PEAK 20(9P23) MUTATED | 171 | 292 | 195 | 85
DEL PEAK 20(9P23) WILD-TYPE | 295 | 340 | 499 | 124

Figure S340. Get High-res Image Clustering Approach #60: 'Del Peak 20(9p23) mutation analysis' versus Clinical Feature #7: 'PATHOLOGY.T'

Clustering Approach #61: 'Del Peak 21(9p21.3) mutation analysis'

Table S401. Description of clustering approach #61: 'Del Peak 21(9p21.3) mutation analysis'

Cluster Labels | DEL PEAK 21(9P21.3) MUTATED | DEL PEAK 21(9P21.3) WILD-TYPE
--- | --- | ---
Number of samples | 1887 | 2676

'Del Peak 21(9p21.3) mutation analysis' versus 'Time to Death'

P value = 0 (logrank test), Q value = 0

Table S402. Clustering Approach #61: 'Del Peak 21(9p21.3) mutation analysis' versus Clinical Feature #1: 'Time to Death'

| nPatients | nDeath | Duration Range (Median), Month
--- | --- | --- | ---
ALL | 4296 | 1401 | 0.0 - 224.0 (14.9)
DEL PEAK 21(9P21.3) MUTATED | 1795 | 790 | 0.0 - 177.0 (13.3)
DEL PEAK 21(9P21.3) WILD-TYPE | 2501 | 611 | 0.0 - 224.0 (15.9)

Figure S341. Get High-res Image Clustering Approach #61: 'Del Peak 21(9p21.3) mutation analysis' versus Clinical Feature #1: 'Time to Death'

'Del Peak 21(9p21.3) mutation analysis' versus 'PRIMARY.SITE.OF.DISEASE'

P value = 4.81e-163 (Chi-square test), Q value = 8.6e-160

Table S403. Clustering Approach #61: 'Del Peak 21(9p21.3) mutation analysis' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'

nPatients | BLADDER | BRAIN | BREAST | COLON | ENDOMETRIAL | HEAD/NECK | KIDNEY | LUNG | OMENTUM | OVARY | PERITONEUM (OVARY) | RECTUM
--- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | ---
ALL | 125 | 544 | 846 | 412 | 447 | 319 | 493 | 662 | 2 | 548 | 2 | 159
DEL PEAK 21(9P21.3) MUTATED | 70 | 405 | 289 | 56 | 57 | 160 | 148 | 429 | 1 | 245 | 2 | 24
DEL PEAK 21(9P21.3) WILD-TYPE | 55 | 139 | 557 | 356 | 390 | 159 | 345 | 233 | 1 | 303 | 0 | 135

Figure S342. Get High-res Image Clustering Approach #61: 'Del Peak 21(9p21.3) mutation analysis' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'

'Del Peak 21(9p21.3) mutation analysis' versus 'GENDER'

P value = 4.97e-22 (Fisher's exact test), Q value = 7.9e-19

Table S404. Clustering Approach #61: 'Del Peak 21(9p21.3) mutation analysis' versus Clinical Feature #4: 'GENDER'

nPatients | FEMALE | MALE
--- | --- | ---
ALL | 2881 | 1682
DEL PEAK 21(9P21.3) MUTATED | 1036 | 851
DEL PEAK 21(9P21.3) WILD-TYPE | 1845 | 831

Figure S343. Get High-res Image Clustering Approach #61: 'Del Peak 21(9p21.3) mutation analysis' versus Clinical Feature #4: 'GENDER'

'Del Peak 21(9p21.3) mutation analysis' versus 'HISTOLOGICAL.TYPE'

P value = 4.9e-110 (Chi-square test), Q value = 8.6e-107

Table S405. Clustering Approach #61: 'Del Peak 21(9p21.3) mutation analysis' versus Clinical Feature #6: 'HISTOLOGICAL.TYPE'

nPatients | COLON ADENOCARCINOMA | COLON MUCINOUS ADENOCARCINOMA | ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA | HEAD & NECK SQUAMOUS CELL CARCINOMA | KIDNEY CLEAR CELL RENAL CARCINOMA | LUNG ACINAR ADENOCARCINOMA | LUNG ADENOCARCINOMA MIXED SUBTYPE | LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS) | LUNG BASALOID SQUAMOUS CELL CARCINOMA | LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS | LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS | LUNG CLEAR CELL ADENOCARCINOMA | LUNG MICROPAPILLARY ADENOCARCINOMA | LUNG MUCINOUS ADENOCARCINOMA | LUNG PAPILLARY ADENOCARCINOMA | LUNG PAPILLARY SQUAMOUS CELL CARCINOMA | LUNG PAPILLARY SQUAMOUS CELL CARICNOMA | LUNG SMALL CELL SQUAMOUS CELL CARCINOMA | LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA | LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS) | MIXED SEROUS AND ENDOMETRIOID | MUCINOUS (COLLOID) ADENOCARCINOMA | RECTAL ADENOCARCINOMA | RECTAL MUCINOUS ADENOCARCINOMA | SEROUS CYSTADENOCARCINOMA | SEROUS ENDOMETRIAL ADENOCARCINOMA | TREATED PRIMARY GBM | UNTREATED PRIMARY (DE NOVO) GBM
--- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | ---
ALL | 356 | 54 | 350 | 319 | 493 | 10 | 75 | 205 | 7 | 3 | 15 | 2 | 3 | 2 | 13 | 1 | 1 | 1 | 2 | 315 | 18 | 7 | 143 | 13 | 552 | 79 | 1 | 20
DEL PEAK 21(9P21.3) MUTATED | 52 | 4 | 21 | 160 | 148 | 5 | 41 | 114 | 3 | 3 | 10 | 1 | 3 | 1 | 6 | 1 | 0 | 0 | 2 | 237 | 3 | 2 | 23 | 1 | 248 | 33 | 1 | 16
DEL PEAK 21(9P21.3) WILD-TYPE | 304 | 50 | 329 | 159 | 345 | 5 | 34 | 91 | 4 | 0 | 5 | 1 | 0 | 1 | 7 | 0 | 1 | 1 | 0 | 78 | 15 | 5 | 120 | 12 | 304 | 46 | 0 | 4

Figure S344. Get High-res Image Clustering Approach #61: 'Del Peak 21(9p21.3) mutation analysis' versus Clinical Feature #6: 'HISTOLOGICAL.TYPE'

'Del Peak 21(9p21.3) mutation analysis' versus 'PATHOLOGY.T'

P value = 7.47e-17 (Fisher's exact test), Q value = 1.2e-13

Table S406. Clustering Approach #61: 'Del Peak 21(9p21.3) mutation analysis' versus Clinical Feature #7: 'PATHOLOGY.T'

nPatients | T0+T1 | T2 | T3 | T4
--- | --- | --- | --- | ---
ALL | 466 | 632 | 694 | 209
DEL PEAK 21(9P21.3) MUTATED | 184 | 331 | 199 | 86
DEL PEAK 21(9P21.3) WILD-TYPE | 282 | 301 | 495 | 123

Figure S345. Get High-res Image Clustering Approach #61: 'Del Peak 21(9p21.3) mutation analysis' versus Clinical Feature #7: 'PATHOLOGY.T'

'Del Peak 21(9p21.3) mutation analysis' versus 'RADIATIONS.RADIATION.REGIMENINDICATION'

P value = 4.55e-07 (Fisher's exact test), Q value = 0.00066

Table S407. Clustering Approach #61: 'Del Peak 21(9p21.3) mutation analysis' versus Clinical Feature #11: 'RADIATIONS.RADIATION.REGIMENINDICATION'

nPatients | NO | YES
--- | --- | ---
ALL | 826 | 3737
DEL PEAK 21(9P21.3) MUTATED | 407 | 1480
DEL PEAK 21(9P21.3) WILD-TYPE | 419 | 2257

Figure S346. Get High-res Image Clustering Approach #61: 'Del Peak 21(9p21.3) mutation analysis' versus Clinical Feature #11: 'RADIATIONS.RADIATION.REGIMENINDICATION'

'Del Peak 21(9p21.3) mutation analysis' versus 'LYMPH.NODE.METASTASIS'

P value = 4.59e-05 (Chi-square test), Q value = 0.062

Table S408. Clustering Approach #61: 'Del Peak 21(9p21.3) mutation analysis' versus Clinical Feature #17: 'LYMPH.NODE.METASTASIS'

nPatients | N0 | N0 (I+) | N0 (I-) | N0 (MOL+) | N1 | N1A | N1B | N1C | N1MI | N2 | N2A | N3 | N3A | N3B | N3C | NX
--- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | ---
ALL | 316 | 22 | 127 | 1 | 115 | 124 | 32 | 2 | 22 | 75 | 53 | 23 | 30 | 2 | 1 | 24
DEL PEAK 21(9P21.3) MUTATED | 131 | 3 | 29 | 0 | 38 | 38 | 8 | 0 | 7 | 42 | 23 | 9 | 16 | 0 | 1 | 12
DEL PEAK 21(9P21.3) WILD-TYPE | 185 | 19 | 98 | 1 | 77 | 86 | 24 | 2 | 15 | 33 | 30 | 14 | 14 | 2 | 0 | 12

Figure S347. Get High-res Image Clustering Approach #61: 'Del Peak 21(9p21.3) mutation analysis' versus Clinical Feature #17: 'LYMPH.NODE.METASTASIS'

'Del Peak 21(9p21.3) mutation analysis' versus 'NEOPLASM.DISEASESTAGE'

P value = 4.69e-06 (Chi-square test), Q value = 0.0066

Table S409. Clustering Approach #61: 'Del Peak 21(9p21.3) mutation analysis' versus Clinical Feature #21: 'NEOPLASM.DISEASESTAGE'

nPatients | STAGE I | STAGE IA | STAGE IB | STAGE II | STAGE IIA | STAGE IIB | STAGE III | STAGE IIIA | STAGE IIIB | STAGE IIIC | STAGE IV | STAGE TIS | STAGE X
--- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | ---
ALL | 72 | 62 | 7 | 43 | 287 | 186 | 42 | 124 | 25 | 41 | 59 | 1 | 16
DEL PEAK 21(9P21.3) MUTATED | 22 | 15 | 2 | 22 | 87 | 56 | 24 | 55 | 17 | 18 | 31 | 0 | 6
DEL PEAK 21(9P21.3) WILD-TYPE | 50 | 47 | 5 | 21 | 200 | 130 | 18 | 69 | 8 | 23 | 28 | 1 | 10

Figure S348. Get High-res Image Clustering Approach #61: 'Del Peak 21(9p21.3) mutation analysis' versus Clinical Feature #21: 'NEOPLASM.DISEASESTAGE'

Clustering Approach #62: 'Del Peak 22(9p21.3) mutation analysis'

Table S410. Description of clustering approach #62: 'Del Peak 22(9p21.3) mutation analysis'

Cluster Labels | DEL PEAK 22(9P21.3) MUTATED | DEL PEAK 22(9P21.3) WILD-TYPE
--- | --- | ---
Number of samples | 1933 | 2630

'Del Peak 22(9p21.3) mutation analysis' versus 'Time to Death'

P value = 0 (logrank test), Q value = 0

Table S411. Clustering Approach #62: 'Del Peak 22(9p21.3) mutation analysis' versus Clinical Feature #1: 'Time to Death'

| nPatients | nDeath | Duration Range (Median), Month
--- | --- | --- | ---
ALL | 4296 | 1401 | 0.0 - 224.0 (14.9)
DEL PEAK 22(9P21.3) MUTATED | 1837 | 812 | 0.0 - 177.0 (13.3)
DEL PEAK 22(9P21.3) WILD-TYPE | 2459 | 589 | 0.0 - 224.0 (15.9)

Figure S349. Get High-res Image Clustering Approach #62: 'Del Peak 22(9p21.3) mutation analysis' versus Clinical Feature #1: 'Time to Death'

'Del Peak 22(9p21.3) mutation analysis' versus 'PRIMARY.SITE.OF.DISEASE'

P value = 1.33e-172 (Chi-square test), Q value = 2.4e-169

Table S412. Clustering Approach #62: 'Del Peak 22(9p21.3) mutation analysis' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'

nPatients | BLADDER | BRAIN | BREAST | COLON | ENDOMETRIAL | HEAD/NECK | KIDNEY | LUNG | OMENTUM | OVARY | PERITONEUM (OVARY) | RECTUM
--- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | ---
ALL | 125 | 544 | 846 | 412 | 447 | 319 | 493 | 662 | 2 | 548 | 2 | 159
DEL PEAK 22(9P21.3) MUTATED | 73 | 413 | 293 | 56 | 57 | 185 | 152 | 432 | 1 | 244 | 2 | 24
DEL PEAK 22(9P21.3) WILD-TYPE | 52 | 131 | 553 | 356 | 390 | 134 | 341 | 230 | 1 | 304 | 0 | 135

Figure S350. Get High-res Image Clustering Approach #62: 'Del Peak 22(9p21.3) mutation analysis' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'

'Del Peak 22(9p21.3) mutation analysis' versus 'GENDER'

P value = 9.41e-26 (Fisher's exact test), Q value = 1.5e-22

Table S413. Clustering Approach #62: 'Del Peak 22(9p21.3) mutation analysis' versus Clinical Feature #4: 'GENDER'

nPatients | FEMALE | MALE
--- | --- | ---
ALL | 2881 | 1682
DEL PEAK 22(9P21.3) MUTATED | 1051 | 882
DEL PEAK 22(9P21.3) WILD-TYPE | 1830 | 800

Figure S351. Get High-res Image Clustering Approach #62: 'Del Peak 22(9p21.3) mutation analysis' versus Clinical Feature #4: 'GENDER'

'Del Peak 22(9p21.3) mutation analysis' versus 'HISTOLOGICAL.TYPE'

P value = 1.84e-116 (Chi-square test), Q value = 3.2e-113

Table S414. Clustering Approach #62: 'Del Peak 22(9p21.3) mutation analysis' versus Clinical Feature #6: 'HISTOLOGICAL.TYPE'

nPatients | COLON ADENOCARCINOMA | COLON MUCINOUS ADENOCARCINOMA | ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA | HEAD & NECK SQUAMOUS CELL CARCINOMA | KIDNEY CLEAR CELL RENAL CARCINOMA | LUNG ACINAR ADENOCARCINOMA | LUNG ADENOCARCINOMA MIXED SUBTYPE | LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS) | LUNG BASALOID SQUAMOUS CELL CARCINOMA | LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS | LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS | LUNG CLEAR CELL ADENOCARCINOMA | LUNG MICROPAPILLARY ADENOCARCINOMA | LUNG MUCINOUS ADENOCARCINOMA | LUNG PAPILLARY ADENOCARCINOMA | LUNG PAPILLARY SQUAMOUS CELL CARCINOMA | LUNG PAPILLARY SQUAMOUS CELL CARICNOMA | LUNG SMALL CELL SQUAMOUS CELL CARCINOMA | LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA | LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS) | MIXED SEROUS AND ENDOMETRIOID | MUCINOUS (COLLOID) ADENOCARCINOMA | RECTAL ADENOCARCINOMA | RECTAL MUCINOUS ADENOCARCINOMA | SEROUS CYSTADENOCARCINOMA | SEROUS ENDOMETRIAL ADENOCARCINOMA | TREATED PRIMARY GBM | UNTREATED PRIMARY (DE NOVO) GBM
--- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | ---
ALL | 356 | 54 | 350 | 319 | 493 | 10 | 75 | 205 | 7 | 3 | 15 | 2 | 3 | 2 | 13 | 1 | 1 | 1 | 2 | 315 | 18 | 7 | 143 | 13 | 552 | 79 | 1 | 20
DEL PEAK 22(9P21.3) MUTATED | 52 | 4 | 21 | 185 | 152 | 5 | 41 | 116 | 3 | 2 | 10 | 1 | 3 | 1 | 6 | 1 | 0 | 0 | 2 | 239 | 3 | 2 | 23 | 1 | 247 | 33 | 1 | 16
DEL PEAK 22(9P21.3) WILD-TYPE | 304 | 50 | 329 | 134 | 341 | 5 | 34 | 89 | 4 | 1 | 5 | 1 | 0 | 1 | 7 | 0 | 1 | 1 | 0 | 76 | 15 | 5 | 120 | 12 | 305 | 46 | 0 | 4

Figure S352. Get High-res Image Clustering Approach #62: 'Del Peak 22(9p21.3) mutation analysis' versus Clinical Feature #6: 'HISTOLOGICAL.TYPE'

'Del Peak 22(9p21.3) mutation analysis' versus 'PATHOLOGY.T'

P value = 6.88e-17 (Fisher's exact test), Q value = 1.1e-13

Table S415. Clustering Approach #62: 'Del Peak 22(9p21.3) mutation analysis' versus Clinical Feature #7: 'PATHOLOGY.T'

nPatients | T0+T1 | T2 | T3 | T4
--- | --- | --- | --- | ---
ALL | 466 | 632 | 694 | 209
DEL PEAK 22(9P21.3) MUTATED | 184 | 337 | 209 | 100
DEL PEAK 22(9P21.3) WILD-TYPE | 282 | 295 | 485 | 109

Figure S353. Get High-res Image Clustering Approach #62: 'Del Peak 22(9p21.3) mutation analysis' versus Clinical Feature #7: 'PATHOLOGY.T'

'Del Peak 22(9p21.3) mutation analysis' versus 'RADIATIONS.RADIATION.REGIMENINDICATION'

P value = 3.32e-07 (Fisher's exact test), Q value = 0.00048

Table S416. Clustering Approach #62: 'Del Peak 22(9p21.3) mutation analysis' versus Clinical Feature #11: 'RADIATIONS.RADIATION.REGIMENINDICATION'

nPatients | NO | YES
--- | --- | ---
ALL | 826 | 3737
DEL PEAK 22(9P21.3) MUTATED | 416 | 1517
DEL PEAK 22(9P21.3) WILD-TYPE | 410 | 2220

Figure S354. Get High-res Image Clustering Approach #62: 'Del Peak 22(9p21.3) mutation analysis' versus Clinical Feature #11: 'RADIATIONS.RADIATION.REGIMENINDICATION'

'Del Peak 22(9p21.3) mutation analysis' versus 'LYMPH.NODE.METASTASIS'

P value = 1.99e-05 (Chi-square test), Q value = 0.027

Table S417. Clustering Approach #62: 'Del Peak 22(9p21.3) mutation analysis' versus Clinical Feature #17: 'LYMPH.NODE.METASTASIS'

nPatients | N0 | N0 (I+) | N0 (I-) | N0 (MOL+) | N1 | N1A | N1B | N1C | N1MI | N2 | N2A | N3 | N3A | N3B | N3C | NX
--- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | ---
ALL | 316 | 22 | 127 | 1 | 115 | 124 | 32 | 2 | 22 | 75 | 53 | 23 | 30 | 2 | 1 | 24
DEL PEAK 22(9P21.3) MUTATED | 136 | 3 | 30 | 0 | 38 | 38 | 8 | 0 | 7 | 43 | 23 | 9 | 16 | 0 | 1 | 12
DEL PEAK 22(9P21.3) WILD-TYPE | 180 | 19 | 97 | 1 | 77 | 86 | 24 | 2 | 15 | 32 | 30 | 14 | 14 | 2 | 0 | 12

Figure S355. Get High-res Image Clustering Approach #62: 'Del Peak 22(9p21.3) mutation analysis' versus Clinical Feature #17: 'LYMPH.NODE.METASTASIS'

'Del Peak 22(9p21.3) mutation analysis' versus 'NEOPLASM.DISEASESTAGE'

P value = 2.47e-06 (Chi-square test), Q value = 0.0035

Table S418. Clustering Approach #62: 'Del Peak 22(9p21.3) mutation analysis' versus Clinical Feature #21: 'NEOPLASM.DISEASESTAGE'

nPatients | STAGE I | STAGE IA | STAGE IB | STAGE II | STAGE IIA | STAGE IIB | STAGE III | STAGE IIIA | STAGE IIIB | STAGE IIIC | STAGE IV | STAGE TIS | STAGE X
--- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | ---
ALL | 72 | 62 | 7 | 43 | 287 | 186 | 42 | 124 | 25 | 41 | 59 | 1 | 16
DEL PEAK 22(9P21.3) MUTATED | 22 | 15 | 2 | 24 | 90 | 57 | 24 | 55 | 17 | 18 | 32 | 0 | 6
DEL PEAK 22(9P21.3) WILD-TYPE | 50 | 47 | 5 | 19 | 197 | 129 | 18 | 69 | 8 | 23 | 27 | 1 | 10

Figure S356. Get High-res Image Clustering Approach #62: 'Del Peak 22(9p21.3) mutation analysis' versus Clinical Feature #21: 'NEOPLASM.DISEASESTAGE'

Clustering Approach #63: 'Del Peak 23(9q21.11) mutation analysis'

Table S419. Description of clustering approach #63: 'Del Peak 23(9q21.11) mutation analysis'

Cluster Labels | DEL PEAK 23(9Q21.11) MUTATED | DEL PEAK 23(9Q21.11) WILD-TYPE
--- | --- | ---
Number of samples | 1301 | 3262

'Del Peak 23(9q21.11) mutation analysis' versus 'AGE'

P value = 6.47e-07 (t-test), Q value = 0.00093

Table S420. Clustering Approach #63: 'Del Peak 23(9q21.11) mutation analysis' versus Clinical Feature #2: 'AGE'

| nPatients | Mean (Std.Dev)
--- | --- | ---
ALL | 4507 | 61.9 (12.6)
DEL PEAK 23(9Q21.11) MUTATED | 1273 | 63.3 (11.9)
DEL PEAK 23(9Q21.11) WILD-TYPE | 3234 | 61.3 (12.9)

Figure S357. Get High-res Image Clustering Approach #63: 'Del Peak 23(9q21.11) mutation analysis' versus Clinical Feature #2: 'AGE'

'Del Peak 23(9q21.11) mutation analysis' versus 'PRIMARY.SITE.OF.DISEASE'

P value = 4.31e-84 (Chi-square test), Q value = 7.4e-81

Table S421. Clustering Approach #63: 'Del Peak 23(9q21.11) mutation analysis' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'

nPatients | BLADDER | BRAIN | BREAST | COLON | ENDOMETRIAL | HEAD/NECK | KIDNEY | LUNG | OMENTUM | OVARY | PERITONEUM (OVARY) | RECTUM
--- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | ---
ALL | 125 | 544 | 846 | 412 | 447 | 319 | 493 | 662 | 2 | 548 | 2 | 159
DEL PEAK 23(9Q21.11) MUTATED | 53 | 72 | 232 | 49 | 91 | 50 | 143 | 320 | 2 | 262 | 2 | 23
DEL PEAK 23(9Q21.11) WILD-TYPE | 72 | 472 | 614 | 363 | 356 | 269 | 350 | 342 | 0 | 286 | 0 | 136

Figure S358. Get High-res Image Clustering Approach #63: 'Del Peak 23(9q21.11) mutation analysis' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'

'Del Peak 23(9q21.11) mutation analysis' versus 'HISTOLOGICAL.TYPE'

P value = 2.98e-72 (Chi-square test), Q value = 5.1e-69

Table S422. Clustering Approach #63: 'Del Peak 23(9q21.11) mutation analysis' versus Clinical Feature #6: 'HISTOLOGICAL.TYPE'

nPatients | COLON ADENOCARCINOMA | COLON MUCINOUS ADENOCARCINOMA | ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA | HEAD & NECK SQUAMOUS CELL CARCINOMA | KIDNEY CLEAR CELL RENAL CARCINOMA | LUNG ACINAR ADENOCARCINOMA | LUNG ADENOCARCINOMA MIXED SUBTYPE | LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS) | LUNG BASALOID SQUAMOUS CELL CARCINOMA | LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS | LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS | LUNG CLEAR CELL ADENOCARCINOMA | LUNG MICROPAPILLARY ADENOCARCINOMA | LUNG MUCINOUS ADENOCARCINOMA | LUNG PAPILLARY ADENOCARCINOMA | LUNG PAPILLARY SQUAMOUS CELL CARCINOMA | LUNG PAPILLARY SQUAMOUS CELL CARICNOMA | LUNG SMALL CELL SQUAMOUS CELL CARCINOMA | LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA | LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS) | MIXED SEROUS AND ENDOMETRIOID | MUCINOUS (COLLOID) ADENOCARCINOMA | RECTAL ADENOCARCINOMA | RECTAL MUCINOUS ADENOCARCINOMA | SEROUS CYSTADENOCARCINOMA | SEROUS ENDOMETRIAL ADENOCARCINOMA | TREATED PRIMARY GBM | UNTREATED PRIMARY (DE NOVO) GBM
--- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | ---
ALL | 356 | 54 | 350 | 319 | 493 | 10 | 75 | 205 | 7 | 3 | 15 | 2 | 3 | 2 | 13 | 1 | 1 | 1 | 2 | 315 | 18 | 7 | 143 | 13 | 552 | 79 | 1 | 20
DEL PEAK 23(9Q21.11) MUTATED | 47 | 2 | 38 | 50 | 143 | 4 | 28 | 111 | 3 | 0 | 9 | 1 | 3 | 0 | 4 | 0 | 0 | 1 | 2 | 152 | 7 | 2 | 21 | 1 | 266 | 46 | 0 | 5
DEL PEAK 23(9Q21.11) WILD-TYPE | 309 | 52 | 312 | 269 | 350 | 6 | 47 | 94 | 4 | 3 | 6 | 1 | 0 | 2 | 9 | 1 | 1 | 0 | 0 | 163 | 11 | 5 | 122 | 12 | 286 | 33 | 1 | 15

Figure S359. Get High-res Image Clustering Approach #63: 'Del Peak 23(9q21.11) mutation analysis' versus Clinical Feature #6: 'HISTOLOGICAL.TYPE'

'Del Peak 23(9q21.11) mutation analysis' versus 'PATHOLOGY.T'

P value = 1.53e-10 (Fisher's exact test), Q value = 2.3e-07

Table S423. Clustering Approach #63: 'Del Peak 23(9q21.11) mutation analysis' versus Clinical Feature #7: 'PATHOLOGY.T'

nPatients | T0+T1 | T2 | T3 | T4
--- | --- | --- | --- | ---
ALL | 466 | 632 | 694 | 209
DEL PEAK 23(9Q21.11) MUTATED | 148 | 236 | 153 | 41
DEL PEAK 23(9Q21.11) WILD-TYPE | 318 | 396 | 541 | 168

Figure S360. Get High-res Image Clustering Approach #63: 'Del Peak 23(9q21.11) mutation analysis' versus Clinical Feature #7: 'PATHOLOGY.T'

'Del Peak 23(9q21.11) mutation analysis' versus 'TUMOR.STAGE'

P value = 6.01e-09 (Fisher's exact test), Q value = 8.9e-06

Table S424. Clustering Approach #63: 'Del Peak 23(9q21.11) mutation analysis' versus Clinical Feature #10: 'TUMOR.STAGE'

nPatients | I | II | III | IV
--- | --- | --- | --- | ---
ALL | 712 | 498 | 881 | 423
DEL PEAK 23(9Q21.11) MUTATED | 240 | 134 | 354 | 106
DEL PEAK 23(9Q21.11) WILD-TYPE | 472 | 364 | 527 | 317

Figure S361. Get High-res Image Clustering Approach #63: 'Del Peak 23(9q21.11) mutation analysis' versus Clinical Feature #10: 'TUMOR.STAGE'

'Del Peak 23(9q21.11) mutation analysis' versus 'RADIATIONS.RADIATION.REGIMENINDICATION'

P value = 2.53e-13 (Fisher's exact test), Q value = 3.9e-10

Table S425. Clustering Approach #63: 'Del Peak 23(9q21.11) mutation analysis' versus Clinical Feature #11: 'RADIATIONS.RADIATION.REGIMENINDICATION'

nPatients | NO | YES
--- | --- | ---
ALL | 826 | 3737
DEL PEAK 23(9Q21.11) MUTATED | 152 | 1149
DEL PEAK 23(9Q21.11) WILD-TYPE | 674 | 2588

Figure S362. Get High-res Image Clustering Approach #63: 'Del Peak 23(9q21.11) mutation analysis' versus Clinical Feature #11: 'RADIATIONS.RADIATION.REGIMENINDICATION'

Clustering Approach #64: 'Del Peak 24(9q34.3) mutation analysis'

Table S426. Description of clustering approach #64: 'Del Peak 24(9q34.3) mutation analysis'

Cluster Labels | DEL PEAK 24(9Q34.3) MUTATED | DEL PEAK 24(9Q34.3) WILD-TYPE
--- | --- | ---
Number of samples | 1335 | 3228

'Del Peak 24(9q34.3) mutation analysis' versus 'PRIMARY.SITE.OF.DISEASE'

P value = 1.7e-96 (Chi-square test), Q value = 2.9e-93

Table S427. Clustering Approach #64: 'Del Peak 24(9q34.3) mutation analysis' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'

nPatients | BLADDER | BRAIN | BREAST | COLON | ENDOMETRIAL | HEAD/NECK | KIDNEY | LUNG | OMENTUM | OVARY | PERITONEUM (OVARY) | RECTUM
--- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | ---
ALL | 125 | 544 | 846 | 412 | 447 | 319 | 493 | 662 | 2 | 548 | 2 | 159
DEL PEAK 24(9Q34.3) MUTATED | 45 | 73 | 230 | 49 | 100 | 45 | 149 | 288 | 1 | 321 | 2 | 30
DEL PEAK 24(9Q34.3) WILD-TYPE | 80 | 471 | 616 | 363 | 347 | 274 | 344 | 374 | 1 | 227 | 0 | 129

Figure S363. Get High-res Image Clustering Approach #64: 'Del Peak 24(9q34.3) mutation analysis' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'

'Del Peak 24(9q34.3) mutation analysis' versus 'HISTOLOGICAL.TYPE'

P value = 2.59e-82 (Chi-square test), Q value = 4.4e-79

Table S428. Clustering Approach #64: 'Del Peak 24(9q34.3) mutation analysis' versus Clinical Feature #6: 'HISTOLOGICAL.TYPE'

nPatients | COLON ADENOCARCINOMA | COLON MUCINOUS ADENOCARCINOMA | ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA | HEAD & NECK SQUAMOUS CELL CARCINOMA | KIDNEY CLEAR CELL RENAL CARCINOMA | LUNG ACINAR ADENOCARCINOMA | LUNG ADENOCARCINOMA MIXED SUBTYPE | LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS) | LUNG BASALOID SQUAMOUS CELL CARCINOMA | LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS | LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS | LUNG CLEAR CELL ADENOCARCINOMA | LUNG MICROPAPILLARY ADENOCARCINOMA | LUNG MUCINOUS ADENOCARCINOMA | LUNG PAPILLARY ADENOCARCINOMA | LUNG PAPILLARY SQUAMOUS CELL CARCINOMA | LUNG PAPILLARY SQUAMOUS CELL CARICNOMA | LUNG SMALL CELL SQUAMOUS CELL CARCINOMA | LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA | LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS) | MIXED SEROUS AND ENDOMETRIOID | MUCINOUS (COLLOID) ADENOCARCINOMA | RECTAL ADENOCARCINOMA | RECTAL MUCINOUS ADENOCARCINOMA | SEROUS CYSTADENOCARCINOMA | SEROUS ENDOMETRIAL ADENOCARCINOMA | TREATED PRIMARY GBM | UNTREATED PRIMARY (DE NOVO) GBM
--- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | ---
ALL | 356 | 54 | 350 | 319 | 493 | 10 | 75 | 205 | 7 | 3 | 15 | 2 | 3 | 2 | 13 | 1 | 1 | 1 | 2 | 315 | 18 | 7 | 143 | 13 | 552 | 79 | 1 | 20
DEL PEAK 24(9Q34.3) MUTATED | 47 | 2 | 45 | 45 | 149 | 3 | 24 | 87 | 3 | 0 | 9 | 1 | 3 | 0 | 4 | 0 | 0 | 0 | 2 | 150 | 8 | 2 | 29 | 1 | 324 | 47 | 0 | 6
DEL PEAK 24(9Q34.3) WILD-TYPE | 309 | 52 | 305 | 274 | 344 | 7 | 51 | 118 | 4 | 3 | 6 | 1 | 0 | 2 | 9 | 1 | 1 | 1 | 0 | 165 | 10 | 5 | 114 | 12 | 228 | 32 | 1 | 14

Figure S364. Get High-res Image Clustering Approach #64: 'Del Peak 24(9q34.3) mutation analysis' versus Clinical Feature #6: 'HISTOLOGICAL.TYPE'

'Del Peak 24(9q34.3) mutation analysis' versus 'PATHOLOGY.T'

P value = 1.11e-09 (Fisher's exact test), Q value = 1.7e-06

Table S429. Clustering Approach #64: 'Del Peak 24(9q34.3) mutation analysis' versus Clinical Feature #7: 'PATHOLOGY.T'

nPatients | T0+T1 | T2 | T3 | T4
--- | --- | --- | --- | ---
ALL | 466 | 632 | 694 | 209
DEL PEAK 24(9Q34.3) MUTATED | 136 | 228 | 159 | 34
DEL PEAK 24(9Q34.3) WILD-TYPE | 330 | 404 | 535 | 175

Figure S365. Get High-res Image Clustering Approach #64: 'Del Peak 24(9q34.3) mutation analysis' versus Clinical Feature #7: 'PATHOLOGY.T'

'Del Peak 24(9q34.3) mutation analysis' versus 'TUMOR.STAGE'

P value = 5.06e-12 (Fisher's exact test), Q value = 7.7e-09

Table S430. Clustering Approach #64: 'Del Peak 24(9q34.3) mutation analysis' versus Clinical Feature #10: 'TUMOR.STAGE'

nPatients | I | II | III | IV
--- | --- | --- | --- | ---
ALL | 712 | 498 | 881 | 423
DEL PEAK 24(9Q34.3) MUTATED | 222 | 135 | 389 | 125
DEL PEAK 24(9Q34.3) WILD-TYPE | 490 | 363 | 492 | 298

Figure S366. Get High-res Image Clustering Approach #64: 'Del Peak 24(9q34.3) mutation analysis' versus Clinical Feature #10: 'TUMOR.STAGE'

'Del Peak 24(9q34.3) mutation analysis' versus 'RADIATIONS.RADIATION.REGIMENINDICATION'

P value = 4.15e-14 (Fisher's exact test), Q value = 6.4e-11

Table S431. Clustering Approach #64: 'Del Peak 24(9q34.3) mutation analysis' versus Clinical Feature #11: 'RADIATIONS.RADIATION.REGIMENINDICATION'

nPatients | NO | YES
--- | --- | ---
ALL | 826 | 3737
DEL PEAK 24(9Q34.3) MUTATED | 155 | 1180
DEL PEAK 24(9Q34.3) WILD-TYPE | 671 | 2557

Figure S367. Get High-res Image Clustering Approach #64: 'Del Peak 24(9q34.3) mutation analysis' versus Clinical Feature #11: 'RADIATIONS.RADIATION.REGIMENINDICATION'

Clustering Approach #65: 'Del Peak 25(10p15.3) mutation analysis'

Table S432. Description of clustering approach #65: 'Del Peak 25(10p15.3) mutation analysis'

Cluster Labels | DEL PEAK 25(10P15.3) MUTATED | DEL PEAK 25(10P15.3) WILD-TYPE
--- | --- | ---
Number of samples | 1226 | 3337

'Del Peak 25(10p15.3) mutation analysis' versus 'Time to Death'

P value = 0 (logrank test), Q value = 0

Table S433. Clustering Approach #65: 'Del Peak 25(10p15.3) mutation analysis' versus Clinical Feature #1: 'Time to Death'

| nPatients | nDeath | Duration Range (Median), Month
--- | --- | --- | ---
ALL | 4296 | 1401 | 0.0 - 224.0 (14.9)
DEL PEAK 25(10P15.3) MUTATED | 1184 | 570 | 0.0 - 177.4 (11.7)
DEL PEAK 25(10P15.3) WILD-TYPE | 3112 | 831 | 0.0 - 224.0 (16.7)

Figure S368. Get High-res Image Clustering Approach #65: 'Del Peak 25(10p15.3) mutation analysis' versus Clinical Feature #1: 'Time to Death'

'Del Peak 25(10p15.3) mutation analysis' versus 'PRIMARY.SITE.OF.DISEASE'

P value = 2.23e-243 (Chi-square test), Q value = 4e-240

Table S434. Clustering Approach #65: 'Del Peak 25(10p15.3) mutation analysis' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'

nPatients | BLADDER | BRAIN | BREAST | COLON | ENDOMETRIAL | HEAD/NECK | KIDNEY | LUNG | OMENTUM | OVARY | PERITONEUM (OVARY) | RECTUM
--- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | ---
ALL | 125 | 544 | 846 | 412 | 447 | 319 | 493 | 662 | 2 | 548 | 2 | 159
DEL PEAK 25(10P15.3) MUTATED | 20 | 449 | 106 | 68 | 30 | 108 | 62 | 234 | 1 | 114 | 0 | 33
DEL PEAK 25(10P15.3) WILD-TYPE | 105 | 95 | 740 | 344 | 417 | 211 | 431 | 428 | 1 | 434 | 2 | 126

Figure S369. Get High-res Image Clustering Approach #65: 'Del Peak 25(10p15.3) mutation analysis' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'

'Del Peak 25(10p15.3) mutation analysis' versus 'GENDER'

P value = 5.68e-26 (Fisher's exact test), Q value = 9.2e-23

Table S435. Clustering Approach #65: 'Del Peak 25(10p15.3) mutation analysis' versus Clinical Feature #4: 'GENDER'

nPatients | FEMALE | MALE
--- | --- | ---
ALL | 2881 | 1682
DEL PEAK 25(10P15.3) MUTATED | 620 | 606
DEL PEAK 25(10P15.3) WILD-TYPE | 2261 | 1076

Figure S370. Get High-res Image Clustering Approach #65: 'Del Peak 25(10p15.3) mutation analysis' versus Clinical Feature #4: 'GENDER'

'Del Peak 25(10p15.3) mutation analysis' versus 'HISTOLOGICAL.TYPE'

P value = 1.75e-48 (Chi-square test), Q value = 2.9e-45

Table S436. Clustering Approach #65: 'Del Peak 25(10p15.3) mutation analysis' versus Clinical Feature #6: 'HISTOLOGICAL.TYPE'

nPatients | COLON ADENOCARCINOMA | COLON MUCINOUS ADENOCARCINOMA | ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA | HEAD & NECK SQUAMOUS CELL CARCINOMA | KIDNEY CLEAR CELL RENAL CARCINOMA | LUNG ACINAR ADENOCARCINOMA | LUNG ADENOCARCINOMA MIXED SUBTYPE | LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS) | LUNG BASALOID SQUAMOUS CELL CARCINOMA | LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS | LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS | LUNG CLEAR CELL ADENOCARCINOMA | LUNG MICROPAPILLARY ADENOCARCINOMA | LUNG MUCINOUS ADENOCARCINOMA | LUNG PAPILLARY ADENOCARCINOMA | LUNG PAPILLARY SQUAMOUS CELL CARCINOMA | LUNG PAPILLARY SQUAMOUS CELL CARICNOMA | LUNG SMALL CELL SQUAMOUS CELL CARCINOMA | LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA | LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS) | MIXED SEROUS AND ENDOMETRIOID | MUCINOUS (COLLOID) ADENOCARCINOMA | RECTAL ADENOCARCINOMA | RECTAL MUCINOUS ADENOCARCINOMA | SEROUS CYSTADENOCARCINOMA | SEROUS ENDOMETRIAL ADENOCARCINOMA | TREATED PRIMARY GBM | UNTREATED PRIMARY (DE NOVO) GBM
--- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | ---
ALL | 356 | 54 | 350 | 319 | 493 | 10 | 75 | 205 | 7 | 3 | 15 | 2 | 3 | 2 | 13 | 1 | 1 | 1 | 2 | 315 | 18 | 7 | 143 | 13 | 552 | 79 | 1 | 20
DEL PEAK 25(10P15.3) MUTATED | 61 | 7 | 11 | 108 | 62 | 3 | 12 | 60 | 5 | 1 | 4 | 0 | 1 | 0 | 3 | 1 | 0 | 0 | 0 | 142 | 1 | 2 | 29 | 4 | 115 | 18 | 1 | 16
DEL PEAK 25(10P15.3) WILD-TYPE | 295 | 47 | 339 | 211 | 431 | 7 | 63 | 145 | 2 | 2 | 11 | 2 | 2 | 2 | 10 | 0 | 1 | 1 | 2 | 173 | 17 | 5 | 114 | 9 | 437 | 61 | 0 | 4

Figure S371. Get High-res Image Clustering Approach #65: 'Del Peak 25(10p15.3) mutation analysis' versus Clinical Feature #6: 'HISTOLOGICAL.TYPE'

'Del Peak 25(10p15.3) mutation analysis' versus 'PATHOLOGY.T'

P value = 4.88e-08 (Fisher's exact test), Q value = 7.1e-05

Table S437. Clustering Approach #65: 'Del Peak 25(10p15.3) mutation analysis' versus Clinical Feature #7: 'PATHOLOGY.T'

nPatients | T0+T1 | T2 | T3 | T4
--- | --- | --- | --- | ---
ALL | 466 | 632 | 694 | 209
DEL PEAK 25(10P15.3) MUTATED | 97 | 196 | 132 | 69
DEL PEAK 25(10P15.3) WILD-TYPE | 369 | 436 | 562 | 140

Figure S372. Get High-res Image Clustering Approach #65: 'Del Peak 25(10p15.3) mutation analysis' versus Clinical Feature #7: 'PATHOLOGY.T'

'Del Peak 25(10p15.3) mutation analysis' versus 'RADIATIONS.RADIATION.REGIMENINDICATION'

P value = 6.01e-35 (Fisher's exact test), Q value = 9.9e-32

Table S438. Clustering Approach #65: 'Del Peak 25(10p15.3) mutation analysis' versus Clinical Feature #11: 'RADIATIONS.RADIATION.REGIMENINDICATION'

nPatients | NO | YES
--- | --- | ---
ALL | 826 | 3737
DEL PEAK 25(10P15.3) MUTATED | 370 | 856
DEL PEAK 25(10P15.3) WILD-TYPE | 456 | 2881

Figure S373. Get High-res Image Clustering Approach #65: 'Del Peak 25(10p15.3) mutation analysis' versus Clinical Feature #11: 'RADIATIONS.RADIATION.REGIMENINDICATION'

Clustering Approach #66: 'Del Peak 26(10q23.31) mutation analysis'

Table S439. Description of clustering approach #66: 'Del Peak 26(10q23.31) mutation analysis'

Cluster Labels | DEL PEAK 26(10Q23.31) MUTATED | DEL PEAK 26(10Q23.31) WILD-TYPE
--- | --- | ---
Number of samples | 1624 | 2939

'Del Peak 26(10q23.31) mutation analysis' versus 'Time to Death'

P value = 0 (logrank test), Q value = 0

Table S440. Clustering Approach #66: 'Del Peak 26(10q23.31) mutation analysis' versus Clinical Feature #1: 'Time to Death'

| nPatients | nDeath | Duration Range (Median), Month
--- | --- | --- | ---
ALL | 4296 | 1401 | 0.0 - 224.0 (14.9)
DEL PEAK 26(10Q23.31) MUTATED | 1549 | 687 | 0.0 - 211.5 (12.1)
DEL PEAK 26(10Q23.31) WILD-TYPE | 2747 | 714 | 0.0 - 224.0 (16.8)

Figure S374. Get High-res Image Clustering Approach #66: 'Del Peak 26(10q23.31) mutation analysis' versus Clinical Feature #1: 'Time to Death'

'Del Peak 26(10q23.31) mutation analysis' versus 'PRIMARY.SITE.OF.DISEASE'

P value = 5.45e-192 (Chi-square test), Q value = 9.8e-189

Table S441. Clustering Approach #66: 'Del Peak 26(10q23.31) mutation analysis' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'

nPatients | BLADDER | BRAIN | BREAST | COLON | ENDOMETRIAL | HEAD/NECK | KIDNEY | LUNG | OMENTUM | OVARY | PERITONEUM (OVARY) | RECTUM
--- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | ---
ALL | 125 | 544 | 846 | 412 | 447 | 319 | 493 | 662 | 2 | 548 | 2 | 159
DEL PEAK 26(10Q23.31) MUTATED | 53 | 486 | 245 | 94 | 53 | 82 | 90 | 256 | 1 | 212 | 1 | 50
DEL PEAK 26(10Q23.31) WILD-TYPE | 72 | 58 | 601 | 318 | 394 | 237 | 403 | 406 | 1 | 336 | 1 | 109

Figure S375. Get High-res Image Clustering Approach #66: 'Del Peak 26(10q23.31) mutation analysis' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'

'Del Peak 26(10q23.31) mutation analysis' versus 'GENDER'

P value = 2e-11 (Fisher's exact test), Q value = 3e-08

Table S442. Clustering Approach #66: 'Del Peak 26(10q23.31) mutation analysis' versus Clinical Feature #4: 'GENDER'

nPatients | FEMALE | MALE
--- | --- | ---
ALL | 2881 | 1682
DEL PEAK 26(10Q23.31) MUTATED | 920 | 704
DEL PEAK 26(10Q23.31) WILD-TYPE | 1961 | 978

Figure S376. Get High-res Image Clustering Approach #66: 'Del Peak 26(10q23.31) mutation analysis' versus Clinical Feature #4: 'GENDER'

'Del Peak 26(10q23.31) mutation analysis' versus 'HISTOLOGICAL.TYPE'

P value = 2.68e-46 (Chi-square test), Q value = 4.5e-43

Table S443. Clustering Approach #66: 'Del Peak 26(10q23.31) mutation analysis' versus Clinical Feature #6: 'HISTOLOGICAL.TYPE'

nPatients | COLON ADENOCARCINOMA | COLON MUCINOUS ADENOCARCINOMA | ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA | HEAD & NECK SQUAMOUS CELL CARCINOMA | KIDNEY CLEAR CELL RENAL CARCINOMA | LUNG ACINAR ADENOCARCINOMA | LUNG ADENOCARCINOMA MIXED SUBTYPE | LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS) | LUNG BASALOID SQUAMOUS CELL CARCINOMA | LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS | LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS | LUNG CLEAR CELL ADENOCARCINOMA | LUNG MICROPAPILLARY ADENOCARCINOMA | LUNG MUCINOUS ADENOCARCINOMA | LUNG PAPILLARY ADENOCARCINOMA | LUNG PAPILLARY SQUAMOUS CELL CARCINOMA | LUNG PAPILLARY SQUAMOUS CELL CARICNOMA | LUNG SMALL CELL SQUAMOUS CELL CARCINOMA | LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA | LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS) | MIXED SEROUS AND ENDOMETRIOID | MUCINOUS (COLLOID) ADENOCARCINOMA | RECTAL ADENOCARCINOMA | RECTAL MUCINOUS ADENOCARCINOMA | SEROUS CYSTADENOCARCINOMA | SEROUS ENDOMETRIAL ADENOCARCINOMA | TREATED PRIMARY GBM | UNTREATED PRIMARY (DE NOVO) GBM
--- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | ---
ALL | 356 | 54 | 350 | 319 | 493 | 10 | 75 | 205 | 7 | 3 | 15 | 2 | 3 | 2 | 13 | 1 | 1 | 1 | 2 | 315 | 18 | 7 | 143 | 13 | 552 | 79 | 1 | 20
DEL PEAK 26(10Q23.31) MUTATED | 85 | 8 | 28 | 82 | 90 | 3 | 13 | 60 | 4 | 1 | 4 | 0 | 3 | 0 | 3 | 1 | 0 | 1 | 2 | 159 | 3 | 2 | 41 | 7 | 214 | 22 | 1 | 19
DEL PEAK 26(10Q23.31) WILD-TYPE | 271 | 46 | 322 | 237 | 403 | 7 | 62 | 145 | 3 | 2 | 11 | 2 | 0 | 2 | 10 | 0 | 1 | 0 | 0 | 156 | 15 | 5 | 102 | 6 | 338 | 57 | 0 | 1

Figure S377. Get High-res Image Clustering Approach #66: 'Del Peak 26(10q23.31) mutation analysis' versus Clinical Feature #6: 'HISTOLOGICAL.TYPE'

'Del Peak 26(10q23.31) mutation analysis' versus 'RADIATIONS.RADIATION.REGIMENINDICATION'

P value = 7.31e-30 (Fisher's exact test), Q value = 1.2e-26

Table S444. Clustering Approach #66: 'Del Peak 26(10q23.31) mutation analysis' versus Clinical Feature #11: 'RADIATIONS.RADIATION.REGIMENINDICATION'

nPatients | NO | YES
--- | --- | ---
ALL | 826 | 3737
DEL PEAK 26(10Q23.31) MUTATED | 438 | 1186
DEL PEAK 26(10Q23.31) WILD-TYPE | 388 | 2551

Figure S378. Get High-res Image Clustering Approach #66: 'Del Peak 26(10q23.31) mutation analysis' versus Clinical Feature #11: 'RADIATIONS.RADIATION.REGIMENINDICATION'

'Del Peak 26(10q23.31) mutation analysis' versus 'YEAROFTOBACCOSMOKINGONSET'

P value = 4.3e-05 (t-test), Q value = 0.058

Table S445. Clustering Approach #66: 'Del Peak 26(10q23.31) mutation analysis' versus Clinical Feature #15: 'YEAROFTOBACCOSMOKINGONSET'

| nPatients | Mean (Std.Dev)
--- | --- | ---
ALL | 566 | 1962.6 (12.7)
DEL PEAK 26(10Q23.31) MUTATED | 193 | 1959.7 (10.7)
DEL PEAK 26(10Q23.31) WILD-TYPE | 373 | 1964.0 (13.3)

Figure S379. Get High-res Image Clustering Approach #66: 'Del Peak 26(10q23.31) mutation analysis' versus Clinical Feature #15: 'YEAROFTOBACCOSMOKINGONSET'

Clustering Approach #67: 'Del Peak 27(10q26.3) mutation analysis'

Table S446. Description of clustering approach #67: 'Del Peak 27(10q26.3) mutation analysis'

Cluster Labels | DEL PEAK 27(10Q26.3) MUTATED | DEL PEAK 27(10Q26.3) WILD-TYPE
--- | --- | ---
Number of samples | 1543 | 3020

'Del Peak 27(10q26.3) mutation analysis' versus 'Time to Death'

P value = 0 (logrank test), Q value = 0

Table S447. Clustering Approach #67: 'Del Peak 27(10q26.3) mutation analysis' versus Clinical Feature #1: 'Time to Death'

| nPatients | nDeath | Duration Range (Median), Month
--- | --- | --- | ---
ALL | 4296 | 1401 | 0.0 - 224.0 (14.9)
DEL PEAK 27(10Q26.3) MUTATED | 1471 | 675 | 0.0 - 211.5 (12.0)
DEL PEAK 27(10Q26.3) WILD-TYPE | 2825 | 726 | 0.0 - 224.0 (16.9)

Figure S380. Get High-res Image Clustering Approach #67: 'Del Peak 27(10q26.3) mutation analysis' versus Clinical Feature #1: 'Time to Death'

'Del Peak 27(10q26.3) mutation analysis' versus 'PRIMARY.SITE.OF.DISEASE'

P value = 1.08e-206 (Chi-square test), Q value = 1.9e-203

Table S448. Clustering Approach #67: 'Del Peak 27(10q26.3) mutation analysis' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'

nPatients | BLADDER | BRAIN | BREAST | COLON | ENDOMETRIAL | HEAD/NECK | KIDNEY | LUNG | OMENTUM | OVARY | PERITONEUM (OVARY) | RECTUM
--- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | ---
ALL | 125 | 544 | 846 | 412 | 447 | 319 | 493 | 662 | 2 | 548 | 2 | 159
DEL PEAK 27(10Q26.3) MUTATED | 45 | 487 | 246 | 89 | 34 | 74 | 94 | 241 | 0 | 185 | 1 | 46
DEL PEAK 27(10Q26.3) WILD-TYPE | 80 | 57 | 600 | 323 | 413 | 245 | 399 | 421 | 2 | 363 | 1 | 113

Figure S381. Get High-res Image Clustering Approach #67: 'Del Peak 27(10q26.3) mutation analysis' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'

'Del Peak 27(10q26.3) mutation analysis' versus 'GENDER'

P value = 4.45e-13 (Fisher's exact test), Q value = 6.9e-10

Table S449. Clustering Approach #67: 'Del Peak 27(10q26.3) mutation analysis' versus Clinical Feature #4: 'GENDER'

nPatients | FEMALE | MALE
--- | --- | ---
ALL | 2881 | 1682
DEL PEAK 27(10Q26.3) MUTATED | 862 | 681
DEL PEAK 27(10Q26.3) WILD-TYPE | 2019 | 1001

Figure S382. Get High-res Image Clustering Approach #67: 'Del Peak 27(10q26.3) mutation analysis' versus Clinical Feature #4: 'GENDER'

'Del Peak 27(10q26.3) mutation analysis' versus 'HISTOLOGICAL.TYPE'

P value = 1.8e-40 (Chi-square test), Q value = 3e-37

Table S450. Clustering Approach #67: 'Del Peak 27(10q26.3) mutation analysis' versus Clinical Feature #6: 'HISTOLOGICAL.TYPE'

nPatients | COLON ADENOCARCINOMA | COLON MUCINOUS ADENOCARCINOMA | ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA | HEAD & NECK SQUAMOUS CELL CARCINOMA | KIDNEY CLEAR CELL RENAL CARCINOMA | LUNG ACINAR ADENOCARCINOMA | LUNG ADENOCARCINOMA MIXED SUBTYPE | LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS) | LUNG BASALOID SQUAMOUS CELL CARCINOMA | LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS | LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS | LUNG CLEAR CELL ADENOCARCINOMA | LUNG MICROPAPILLARY ADENOCARCINOMA | LUNG MUCINOUS ADENOCARCINOMA | LUNG PAPILLARY ADENOCARCINOMA | LUNG PAPILLARY SQUAMOUS CELL CARCINOMA | LUNG PAPILLARY SQUAMOUS CELL CARICNOMA | LUNG SMALL CELL SQUAMOUS CELL CARCINOMA | LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA | LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS) | MIXED SEROUS AND ENDOMETRIOID | MUCINOUS (COLLOID) ADENOCARCINOMA | RECTAL ADENOCARCINOMA | RECTAL MUCINOUS ADENOCARCINOMA | SEROUS CYSTADENOCARCINOMA | SEROUS ENDOMETRIAL ADENOCARCINOMA | TREATED PRIMARY GBM | UNTREATED PRIMARY (DE NOVO) GBM
--- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | ---
ALL | 356 | 54 | 350 | 319 | 493 | 10 | 75 | 205 | 7 | 3 | 15 | 2 | 3 | 2 | 13 | 1 | 1 | 1 | 2 | 315 | 18 | 7 | 143 | 13 | 552 | 79 | 1 | 20
DEL PEAK 27(10Q26.3) MUTATED | 81 | 8 | 20 | 74 | 94 | 3 | 15 | 59 | 3 | 1 | 5 | 0 | 2 | 0 | 3 | 0 | 0 | 1 | 1 | 146 | 2 | 2 | 38 | 6 | 186 | 12 | 1 | 20
DEL PEAK 27(10Q26.3) WILD-TYPE | 275 | 46 | 330 | 245 | 399 | 7 | 60 | 146 | 4 | 2 | 10 | 2 | 1 | 2 | 10 | 1 | 1 | 0 | 1 | 169 | 16 | 5 | 105 | 7 | 366 | 67 | 0 | 0

Figure S383. Get High-res Image Clustering Approach #67: 'Del Peak 27(10q26.3) mutation analysis' versus Clinical Feature #6: 'HISTOLOGICAL.TYPE'

'Del Peak 27(10q26.3) mutation analysis' versus 'RADIATIONS.RADIATION.REGIMENINDICATION'

P value = 7.57e-34 (Fisher's exact test), Q value = 1.2e-30

Table S451. Clustering Approach #67: 'Del Peak 27(10q26.3) mutation analysis' versus Clinical Feature #11: 'RADIATIONS.RADIATION.REGIMENINDICATION'

nPatients | NO | YES
--- | --- | ---
ALL | 826 | 3737
DEL PEAK 27(10Q26.3) MUTATED | 432 | 1111
DEL PEAK 27(10Q26.3) WILD-TYPE | 394 | 2626

Figure S384. Get High-res Image Clustering Approach #67: 'Del Peak 27(10q26.3) mutation analysis' versus Clinical Feature #11: 'RADIATIONS.RADIATION.REGIMENINDICATION'

Clustering Approach #68: 'Del Peak 28(11p15.5) mutation analysis'

Table S452. Description of clustering approach #68: 'Del Peak 28(11p15.5) mutation analysis'

Cluster Labels | DEL PEAK 28(11P15.5) MUTATED | DEL PEAK 28(11P15.5) WILD-TYPE
--- | --- | ---
Number of samples | 1279 | 3284

'Del Peak 28(11p15.5) mutation analysis' versus 'PRIMARY.SITE.OF.DISEASE'

P value = 1.64e-115 (Chi-square test), Q value = 2.9e-112

Table S453. Clustering Approach #68: 'Del Peak 28(11p15.5) mutation analysis' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'

nPatients | BLADDER | BRAIN | BREAST | COLON | ENDOMETRIAL | HEAD/NECK | KIDNEY | LUNG | OMENTUM | OVARY | PERITONEUM (OVARY) | RECTUM
--- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | ---
ALL | 125 | 544 | 846 | 412 | 447 | 319 | 493 | 662 | 2 | 548 | 2 | 159
DEL PEAK 28(11P15.5) MUTATED | 62 | 125 | 248 | 54 | 77 | 100 | 17 | 245 | 0 | 327 | 0 | 23
DEL PEAK 28(11P15.5) WILD-TYPE | 63 | 419 | 598 | 358 | 370 | 219 | 476 | 417 | 2 | 221 | 2 | 136

Figure S385. Get High-res Image Clustering Approach #68: 'Del Peak 28(11p15.5) mutation analysis' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'

'Del Peak 28(11p15.5) mutation analysis' versus 'GENDER'

P value = 3.54e-05 (Fisher's exact test), Q value = 0.048

Table S454. Clustering Approach #68: 'Del Peak 28(11p15.5) mutation analysis' versus Clinical Feature #4: 'GENDER'

nPatients | FEMALE | MALE
--- | --- | ---
ALL | 2881 | 1682
DEL PEAK 28(11P15.5) MUTATED | 868 | 411
DEL PEAK 28(11P15.5) WILD-TYPE | 2013 | 1271

Figure S386. Get High-res Image Clustering Approach #68: 'Del Peak 28(11p15.5) mutation analysis' versus Clinical Feature #4: 'GENDER'

'Del Peak 28(11p15.5) mutation analysis' versus 'HISTOLOGICAL.TYPE'

P value = 1.03e-121 (Chi-square test), Q value = 1.8e-118

Table S455. Clustering Approach #68: 'Del Peak 28(11p15.5) mutation analysis' versus Clinical Feature #6: 'HISTOLOGICAL.TYPE'

nPatients | COLON ADENOCARCINOMA | COLON MUCINOUS ADENOCARCINOMA | ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA | HEAD & NECK SQUAMOUS CELL CARCINOMA | KIDNEY CLEAR CELL RENAL CARCINOMA | LUNG ACINAR ADENOCARCINOMA | LUNG ADENOCARCINOMA MIXED SUBTYPE | LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS) | LUNG BASALOID SQUAMOUS CELL CARCINOMA | LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS | LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS | LUNG CLEAR CELL ADENOCARCINOMA | LUNG MICROPAPILLARY ADENOCARCINOMA | LUNG MUCINOUS ADENOCARCINOMA | LUNG PAPILLARY ADENOCARCINOMA | LUNG PAPILLARY SQUAMOUS CELL CARCINOMA | LUNG PAPILLARY SQUAMOUS CELL CARICNOMA | LUNG SMALL CELL SQUAMOUS CELL CARCINOMA | LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA | LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS) | MIXED SEROUS AND ENDOMETRIOID | MUCINOUS (COLLOID) ADENOCARCINOMA | RECTAL ADENOCARCINOMA | RECTAL MUCINOUS ADENOCARCINOMA | SEROUS CYSTADENOCARCINOMA | SEROUS ENDOMETRIAL ADENOCARCINOMA | TREATED PRIMARY GBM | UNTREATED PRIMARY (DE NOVO) GBM
--- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | ---
ALL | 356 | 54 | 350 | 319 | 493 | 10 | 75 | 205 | 7 | 3 | 15 | 2 | 3 | 2 | 13 | 1 | 1 | 1 | 2 | 315 | 18 | 7 | 143 | 13 | 552 | 79 | 1 | 20
DEL PEAK 28(11P15.5) MUTATED | 47 | 7 | 28 | 100 | 17 | 1 | 21 | 59 | 4 | 0 | 4 | 2 | 0 | 0 | 2 | 1 | 0 | 1 | 0 | 149 | 5 | 1 | 19 | 3 | 327 | 44 | 0 | 6
DEL PEAK 28(11P15.5) WILD-TYPE | 309 | 47 | 322 | 219 | 476 | 9 | 54 | 146 | 3 | 3 | 11 | 0 | 3 | 2 | 11 | 0 | 1 | 0 | 2 | 166 | 13 | 6 | 124 | 10 | 225 | 35 | 1 | 14

Figure S387. Get High-res Image Clustering Approach #68: 'Del Peak 28(11p15.5) mutation analysis' versus Clinical Feature #6: 'HISTOLOGICAL.TYPE'

'Del Peak 28(11p15.5) mutation analysis' versus 'PATHOLOGY.T'

P value = 1.72e-10 (Fisher's exact test), Q value = 2.6e-07

Table S456. Clustering Approach #68: 'Del Peak 28(11p15.5) mutation analysis' versus Clinical Feature #7: 'PATHOLOGY.T'

nPatients | T0+T1 | T2 | T3 | T4
--- | --- | --- | --- | ---
ALL | 466 | 632 | 694 | 209
DEL PEAK 28(11P15.5) MUTATED | 73 | 179 | 106 | 59
DEL PEAK 28(11P15.5) WILD-TYPE | 393 | 453 | 588 | 150

Figure S388. Get High-res Image Clustering Approach #68: 'Del Peak 28(11p15.5) mutation analysis' versus Clinical Feature #7: 'PATHOLOGY.T'

'Del Peak 28(11p15.5) mutation analysis' versus 'TUMOR.STAGE'

P value = 2.77e-16 (Fisher's exact test), Q value = 4.3e-13

Table S457. Clustering Approach #68: 'Del Peak 28(11p15.5) mutation analysis' versus Clinical Feature #10: 'TUMOR.STAGE'

nPatients | I | II | III | IV
--- | --- | --- | --- | ---
ALL | 712 | 498 | 881 | 423
DEL PEAK 28(11P15.5) MUTATED | 157 | 106 | 346 | 128
DEL PEAK 28(11P15.5) WILD-TYPE | 555 | 392 | 535 | 295

Figure S389. Get High-res Image Clustering Approach #68: 'Del Peak 28(11p15.5) mutation analysis' versus Clinical Feature #10: 'TUMOR.STAGE'

'Del Peak 28(11p15.5) mutation analysis' versus 'TOBACCOSMOKINGHISTORYINDICATOR'

P value = 0.000141 (Chi-square test), Q value = 0.18

Table S458. Clustering Approach #68: 'Del Peak 28(11p15.5) mutation analysis' versus Clinical Feature #14: 'TOBACCOSMOKINGHISTORYINDICATOR'

nPatients | 1 | 2 | 3 | 4 | 5 | CURRENT REFORMED SMOKER FOR < OR = 15 YEARS | CURRENT REFORMED SMOKER FOR > 15 YEARS | CURRENT SMOKER | LIFELONG NON-SMOKER
--- | --- | --- | --- | --- | --- | --- | --- | --- | ---
ALL | 28 | 23 | 37 | 29 | 2 | 355 | 217 | 250 | 128
DEL PEAK 28(11P15.5) MUTATED | 16 | 11 | 19 | 11 | 1 | 147 | 63 | 94 | 28
DEL PEAK 28(11P15.5) WILD-TYPE | 12 | 12 | 18 | 18 | 1 | 208 | 154 | 156 | 100

Figure S390. Get High-res Image Clustering Approach #68: 'Del Peak 28(11p15.5) mutation analysis' versus Clinical Feature #14: 'TOBACCOSMOKINGHISTORYINDICATOR'

Clustering Approach #69: 'Del Peak 29(11q23.1) mutation analysis'

Table S459. Description of clustering approach #69: 'Del Peak 29(11q23.1) mutation analysis'

Cluster Labels | DEL PEAK 29(11Q23.1) MUTATED | DEL PEAK 29(11Q23.1) WILD-TYPE
--- | --- | ---
Number of samples | 1243 | 3320

'Del Peak 29(11q23.1) mutation analysis' versus 'PRIMARY.SITE.OF.DISEASE'

P value = 9.65e-101 (Chi-square test), Q value = 1.7e-97

Table S460. Clustering Approach #69: 'Del Peak 29(11q23.1) mutation analysis' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'

nPatients | BLADDER | BRAIN | BREAST | COLON | ENDOMETRIAL | HEAD/NECK | KIDNEY | LUNG | OMENTUM | OVARY | PERITONEUM (OVARY) | RECTUM
--- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | ---
ALL | 125 | 544 | 846 | 412 | 447 | 319 | 493 | 662 | 2 | 548 | 2 | 159
DEL PEAK 29(11Q23.1) MUTATED | 44 | 89 | 412 | 62 | 66 | 152 | 27 | 178 | 2 | 171 | 2 | 34
DEL PEAK 29(11Q23.1) WILD-TYPE | 81 | 455 | 434 | 350 | 381 | 167 | 466 | 484 | 0 | 377 | 0 | 125

Figure S391. Get High-res Image Clustering Approach #69: 'Del Peak 29(11q23.1) mutation analysis' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'

'Del Peak 29(11q23.1) mutation analysis' versus 'GENDER'

P value = 0.000149 (Fisher's exact test), Q value = 0.19

Table S461. Clustering Approach #69: 'Del Peak 29(11q23.1) mutation analysis' versus Clinical Feature #4: 'GENDER'

nPatients | FEMALE | MALE
--- | --- | ---
ALL | 2881 | 1682
DEL PEAK 29(11Q23.1) MUTATED | 840 | 403
DEL PEAK 29(11Q23.1) WILD-TYPE | 2041 | 1279

Figure S392. Get High-res Image Clustering Approach #69: 'Del Peak 29(11q23.1) mutation analysis' versus Clinical Feature #4: 'GENDER'

'Del Peak 29(11q23.1) mutation analysis' versus 'HISTOLOGICAL.TYPE'

P value = 1.38e-53 (Chi-square test), Q value = 2.3e-50

Table S462. Clustering Approach #69: 'Del Peak 29(11q23.1) mutation analysis' versus Clinical Feature #6: 'HISTOLOGICAL.TYPE'

nPatients | COLON ADENOCARCINOMA | COLON MUCINOUS ADENOCARCINOMA | ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA | HEAD & NECK SQUAMOUS CELL CARCINOMA | KIDNEY CLEAR CELL RENAL CARCINOMA | LUNG ACINAR ADENOCARCINOMA | LUNG ADENOCARCINOMA MIXED SUBTYPE | LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS) | LUNG BASALOID SQUAMOUS CELL CARCINOMA | LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS | LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS | LUNG CLEAR CELL ADENOCARCINOMA | LUNG MICROPAPILLARY ADENOCARCINOMA | LUNG MUCINOUS ADENOCARCINOMA | LUNG PAPILLARY ADENOCARCINOMA | LUNG PAPILLARY SQUAMOUS CELL CARCINOMA | LUNG PAPILLARY SQUAMOUS CELL CARICNOMA | LUNG SMALL CELL SQUAMOUS CELL CARCINOMA | LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA | LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS) | MIXED SEROUS AND ENDOMETRIOID | MUCINOUS (COLLOID) ADENOCARCINOMA | RECTAL ADENOCARCINOMA | RECTAL MUCINOUS ADENOCARCINOMA | SEROUS CYSTADENOCARCINOMA | SEROUS ENDOMETRIAL ADENOCARCINOMA | TREATED PRIMARY GBM | UNTREATED PRIMARY (DE NOVO) GBM
--- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | ---
ALL | 356 | 54 | 350 | 319 | 493 | 10 | 75 | 205 | 7 | 3 | 15 | 2 | 3 | 2 | 13 | 1 | 1 | 1 | 2 | 315 | 18 | 7 | 143 | 13 | 552 | 79 | 1 | 20
DEL PEAK 29(11Q23.1) MUTATED | 55 | 7 | 27 | 152 | 27 | 1 | 21 | 43 | 4 | 0 | 3 | 1 | 0 | 0 | 4 | 0 | 0 | 0 | 0 | 99 | 6 | 2 | 27 | 6 | 175 | 33 | 0 | 5
DEL PEAK 29(11Q23.1) WILD-TYPE | 301 | 47 | 323 | 167 | 466 | 9 | 54 | 162 | 3 | 3 | 12 | 1 | 3 | 2 | 9 | 1 | 1 | 1 | 2 | 216 | 12 | 5 | 116 | 7 | 377 | 46 | 1 | 15

Figure S393. Get High-res Image Clustering Approach #69: 'Del Peak 29(11q23.1) mutation analysis' versus Clinical Feature #6: 'HISTOLOGICAL.TYPE'

'Del Peak 29(11q23.1) mutation analysis' versus 'PATHOLOGY.T'

P value = 8.21e-10 (Fisher's exact test), Q value = 1.2e-06

Table S463. Clustering Approach #69: 'Del Peak 29(11q23.1) mutation analysis' versus Clinical Feature #7: 'PATHOLOGY.T'

nPatients | T0+T1 | T2 | T3 | T4
--- | --- | --- | --- | ---
ALL | 466 | 632 | 694 | 209
DEL PEAK 29(11Q23.1) MUTATED | 70 | 159 | 122 | 74
DEL PEAK 29(11Q23.1) WILD-TYPE | 396 | 473 | 572 | 135

Figure S394. Get High-res Image Clustering Approach #69: 'Del Peak 29(11q23.1) mutation analysis' versus Clinical Feature #7: 'PATHOLOGY.T'

'Del Peak 29(11q23.1) mutation analysis' versus 'PATHOLOGY.N'

P value = 4.19e-09 (Fisher's exact test), Q value = 6.2e-06

Table S464. Clustering Approach #69: 'Del Peak 29(11q23.1) mutation analysis' versus Clinical Feature #8: 'PATHOLOGY.N'

nPatients | N0 | N1 | N2 | N3
--- | --- | --- | --- | ---
ALL | 1067 | 353 | 282 | 11
DEL PEAK 29(11Q23.1) MUTATED | 194 | 101 | 97 | 4
DEL PEAK 29(11Q23.1) WILD-TYPE | 873 | 252 | 185 | 7

Figure S395. Get High-res Image Clustering Approach #69: 'Del Peak 29(11q23.1) mutation analysis' versus Clinical Feature #8: 'PATHOLOGY.N'

'Del Peak 29(11q23.1) mutation analysis' versus 'TUMOR.STAGE'

P value = 4.35e-06 (Fisher's exact test), Q value = 0.0061

Table S465. Clustering Approach #69: 'Del Peak 29(11q23.1) mutation analysis' versus Clinical Feature #10: 'TUMOR.STAGE'

nPatients | I | II | III | IV
--- | --- | --- | --- | ---
ALL | 712 | 498 | 881 | 423
DEL PEAK 29(11Q23.1) MUTATED | 128 | 103 | 227 | 128
DEL PEAK 29(11Q23.1) WILD-TYPE | 584 | 395 | 654 | 295

Figure S396. Get High-res Image Clustering Approach #69: 'Del Peak 29(11q23.1) mutation analysis' versus Clinical Feature #10: 'TUMOR.STAGE'

Clustering Approach #70: 'Del Peak 30(11q25) mutation analysis'

Table S466. Description of clustering approach #70: 'Del Peak 30(11q25) mutation analysis'

Cluster Labels | DEL PEAK 30(11Q25) MUTATED | DEL PEAK 30(11Q25) WILD-TYPE
--- | --- | ---
Number of samples | 1248 | 3315

'Del Peak 30(11q25) mutation analysis' versus 'PRIMARY.SITE.OF.DISEASE'

P value = 9.57e-91 (Chi-square test), Q value = 1.6e-87

Table S467. Clustering Approach #70: 'Del Peak 30(11q25) mutation analysis' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'

nPatients | BLADDER | BRAIN | BREAST | COLON | ENDOMETRIAL | HEAD/NECK | KIDNEY | LUNG | OMENTUM | OVARY | PERITONEUM (OVARY) | RECTUM
--- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | ---
ALL | 125 | 544 | 846 | 412 | 447 | 319 | 493 | 662 | 2 | 548 | 2 | 159
DEL PEAK 30(11Q25) MUTATED | 39 | 91 | 397 | 59 | 69 | 141 | 26 | 198 | 1 | 189 | 2 | 32
DEL PEAK 30(11Q25) WILD-TYPE | 86 | 453 | 449 | 353 | 378 | 178 | 467 | 464 | 1 | 359 | 0 | 127

Figure S397. Get High-res Image Clustering Approach #70: 'Del Peak 30(11q25) mutation analysis' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'

'Del Peak 30(11q25) mutation analysis' versus 'GENDER'

P value = 8.64e-05 (Fisher's exact test), Q value = 0.11

Table S468. Clustering Approach #70: 'Del Peak 30(11q25) mutation analysis' versus Clinical Feature #4: 'GENDER'

nPatients | FEMALE | MALE
--- | --- | ---
ALL | 2881 | 1682
DEL PEAK 30(11Q25) MUTATED | 845 | 403
DEL PEAK 30(11Q25) WILD-TYPE | 2036 | 1279

Figure S398. Get High-res Image Clustering Approach #70: 'Del Peak 30(11q25) mutation analysis' versus Clinical Feature #4: 'GENDER'

'Del Peak 30(11q25) mutation analysis' versus 'HISTOLOGICAL.TYPE'

P value = 1.04e-58 (Chi-square test), Q value = 1.7e-55

Table S469. Clustering Approach #70: 'Del Peak 30(11q25) mutation analysis' versus Clinical Feature #6: 'HISTOLOGICAL.TYPE'

nPatients | COLON ADENOCARCINOMA | COLON MUCINOUS ADENOCARCINOMA | ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA | HEAD & NECK SQUAMOUS CELL CARCINOMA | KIDNEY CLEAR CELL RENAL CARCINOMA | LUNG ACINAR ADENOCARCINOMA | LUNG ADENOCARCINOMA MIXED SUBTYPE | LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS) | LUNG BASALOID SQUAMOUS CELL CARCINOMA | LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS | LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS | LUNG CLEAR CELL ADENOCARCINOMA | LUNG MICROPAPILLARY ADENOCARCINOMA | LUNG MUCINOUS ADENOCARCINOMA | LUNG PAPILLARY ADENOCARCINOMA | LUNG PAPILLARY SQUAMOUS CELL CARCINOMA | LUNG PAPILLARY SQUAMOUS CELL CARICNOMA | LUNG SMALL CELL SQUAMOUS CELL CARCINOMA | LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA | LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS) | MIXED SEROUS AND ENDOMETRIOID | MUCINOUS (COLLOID) ADENOCARCINOMA | RECTAL ADENOCARCINOMA | RECTAL MUCINOUS ADENOCARCINOMA | SEROUS CYSTADENOCARCINOMA | SEROUS ENDOMETRIAL ADENOCARCINOMA | TREATED PRIMARY GBM | UNTREATED PRIMARY (DE NOVO) GBM
--- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | ---
ALL | 356 | 54 | 350 | 319 | 493 | 10 | 75 | 205 | 7 | 3 | 15 | 2 | 3 | 2 | 13 | 1 | 1 | 1 | 2 | 315 | 18 | 7 | 143 | 13 | 552 | 79 | 1 | 20
DEL PEAK 30(11Q25) MUTATED | 53 | 6 | 27 | 141 | 26 | 1 | 20 | 43 | 4 | 0 | 3 | 1 | 0 | 0 | 4 | 0 | 0 | 1 | 1 | 118 | 5 | 2 | 25 | 6 | 192 | 37 | 0 | 4
DEL PEAK 30(11Q25) WILD-TYPE | 303 | 48 | 323 | 178 | 467 | 9 | 55 | 162 | 3 | 3 | 12 | 1 | 3 | 2 | 9 | 1 | 1 | 0 | 1 | 197 | 13 | 5 | 118 | 7 | 360 | 42 | 1 | 16

Figure S399. Get High-res Image Clustering Approach #70: 'Del Peak 30(11q25) mutation analysis' versus Clinical Feature #6: 'HISTOLOGICAL.TYPE'

'Del Peak 30(11q25) mutation analysis' versus 'PATHOLOGY.T'

P value = 4.93e-11 (Fisher's exact test), Q value = 7.5e-08

Table S470. Clustering Approach #70: 'Del Peak 30(11q25) mutation analysis' versus Clinical Feature #7: 'PATHOLOGY.T'

nPatients | T0+T1 | T2 | T3 | T4
--- | --- | --- | --- | ---
ALL | 466 | 632 | 694 | 209
DEL PEAK 30(11Q25) MUTATED | 72 | 174 | 118 | 72
DEL PEAK 30(11Q25) WILD-TYPE | 394 | 458 | 576 | 137

Figure S400. Get High-res Image Clustering Approach #70: 'Del Peak 30(11q25) mutation analysis' versus Clinical Feature #7: 'PATHOLOGY.T'

'Del Peak 30(11q25) mutation analysis' versus 'PATHOLOGY.N'

P value = 1.17e-09 (Fisher's exact test), Q value = 1.8e-06

Table S471. Clustering Approach #70: 'Del Peak 30(11q25) mutation analysis' versus Clinical Feature #8: 'PATHOLOGY.N'

nPatients | N0 | N1 | N2 | N3
--- | --- | --- | --- | ---
ALL | 1067 | 353 | 282 | 11
DEL PEAK 30(11Q25) MUTATED | 199 | 108 | 99 | 3
DEL PEAK 30(11Q25) WILD-TYPE | 868 | 245 | 183 | 8

Figure S401. Get High-res Image Clustering Approach #70: 'Del Peak 30(11q25) mutation analysis' versus Clinical Feature #8: 'PATHOLOGY.N'

'Del Peak 30(11q25) mutation analysis' versus 'TUMOR.STAGE'

P value = 1.55e-05 (Fisher's exact test), Q value = 0.021

Table S472. Clustering Approach #70: 'Del Peak 30(11q25) mutation analysis' versus Clinical Feature #10: 'TUMOR.STAGE'

nPatients | I | II | III | IV
--- | --- | --- | --- | ---
ALL | 712 | 498 | 881 | 423
DEL PEAK 30(11Q25) MUTATED | 139 | 105 | 237 | 131
DEL PEAK 30(11Q25) WILD-TYPE | 573 | 393 | 644 | 292

Figure S402. Get High-res Image Clustering Approach #70: 'Del Peak 30(11q25) mutation analysis' versus Clinical Feature #10: 'TUMOR.STAGE'

Clustering Approach #71: 'Del Peak 31(12p13.1) mutation analysis'

Table S473. Description of clustering approach #71: 'Del Peak 31(12p13.1) mutation analysis'

Cluster Labels | DEL PEAK 31(12P13.1) MUTATED | DEL PEAK 31(12P13.1) WILD-TYPE
--- | --- | ---
Number of samples | 597 | 3966

'Del Peak 31(12p13.1) mutation analysis' versus 'PRIMARY.SITE.OF.DISEASE'

P value = 1.45e-20 (Chi-square test), Q value = 2.3e-17

Table S474. Clustering Approach #71: 'Del Peak 31(12p13.1) mutation analysis' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'

nPatients | BLADDER | BRAIN | BREAST | COLON | ENDOMETRIAL | HEAD/NECK | KIDNEY | LUNG | OMENTUM | OVARY | PERITONEUM (OVARY) | RECTUM
--- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | ---
ALL | 125 | 544 | 846 | 412 | 447 | 319 | 493 | 662 | 2 | 548 | 2 | 159
DEL PEAK 31(12P13.1) MUTATED | 16 | 72 | 150 | 45 | 35 | 30 | 6 | 120 | 0 | 90 | 1 | 29
DEL PEAK 31(12P13.1) WILD-TYPE | 109 | 472 | 696 | 367 | 412 | 289 | 487 | 542 | 2 | 458 | 1 | 130

Figure S403. Get High-res Image Clustering Approach #71: 'Del Peak 31(12p13.1) mutation analysis' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'

'Del Peak 31(12p13.1) mutation analysis' versus 'GENDER'

P value = 9.28e-08 (Fisher's exact test), Q value = 0.00014

Table S475. Clustering Approach #71: 'Del Peak 31(12p13.1) mutation analysis' versus Clinical Feature #4: 'GENDER'

nPatients | FEMALE | MALE
--- | --- | ---
ALL | 2881 | 1682
DEL PEAK 31(12P13.1) MUTATED | 435 | 162
DEL PEAK 31(12P13.1) WILD-TYPE | 2446 | 1520

Figure S404. Get High-res Image Clustering Approach #71: 'Del Peak 31(12p13.1) mutation analysis' versus Clinical Feature #4: 'GENDER'

'Del Peak 31(12p13.1) mutation analysis' versus 'HISTOLOGICAL.TYPE'

P value = 1.21e-35 (Chi-square test), Q value = 2e-32

Table S476. Clustering Approach #71: 'Del Peak 31(12p13.1) mutation analysis' versus Clinical Feature #6: 'HISTOLOGICAL.TYPE'

nPatients | COLON ADENOCARCINOMA | COLON MUCINOUS ADENOCARCINOMA | ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA | HEAD & NECK SQUAMOUS CELL CARCINOMA | KIDNEY CLEAR CELL RENAL CARCINOMA | LUNG ACINAR ADENOCARCINOMA | LUNG ADENOCARCINOMA MIXED SUBTYPE | LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS) | LUNG BASALOID SQUAMOUS CELL CARCINOMA | LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS | LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS | LUNG CLEAR CELL ADENOCARCINOMA | LUNG MICROPAPILLARY ADENOCARCINOMA | LUNG MUCINOUS ADENOCARCINOMA | LUNG PAPILLARY ADENOCARCINOMA | LUNG PAPILLARY SQUAMOUS CELL CARCINOMA | LUNG PAPILLARY SQUAMOUS CELL CARICNOMA | LUNG SMALL CELL SQUAMOUS CELL CARCINOMA | LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA | LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS) | MIXED SEROUS AND ENDOMETRIOID | MUCINOUS (COLLOID) ADENOCARCINOMA | RECTAL ADENOCARCINOMA | RECTAL MUCINOUS ADENOCARCINOMA | SEROUS CYSTADENOCARCINOMA | SEROUS ENDOMETRIAL ADENOCARCINOMA | TREATED PRIMARY GBM | UNTREATED PRIMARY (DE NOVO) GBM
--- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | ---
ALL | 356 | 54 | 350 | 319 | 493 | 10 | 75 | 205 | 7 | 3 | 15 | 2 | 3 | 2 | 13 | 1 | 1 | 1 | 2 | 315 | 18 | 7 | 143 | 13 | 552 | 79 | 1 | 20
DEL PEAK 31(12P13.1) MUTATED | 45 | 0 | 13 | 30 | 6 | 1 | 24 | 57 | 1 | 0 | 6 | 1 | 1 | 0 | 5 | 0 | 0 | 0 | 1 | 21 | 2 | 2 | 28 | 1 | 91 | 20 | 0 | 3
DEL PEAK 31(12P13.1) WILD-TYPE | 311 | 54 | 337 | 289 | 487 | 9 | 51 | 148 | 6 | 3 | 9 | 1 | 2 | 2 | 8 | 1 | 1 | 1 | 1 | 294 | 16 | 5 | 115 | 12 | 461 | 59 | 1 | 17

Figure S405. Get High-res Image Clustering Approach #71: 'Del Peak 31(12p13.1) mutation analysis' versus Clinical Feature #6: 'HISTOLOGICAL.TYPE'

'Del Peak 31(12p13.1) mutation analysis' versus 'PATHOLOGICSPREAD(M)'

P value = 3.65e-06 (Chi-square test), Q value = 0.0051

Table S477. Clustering Approach #71: 'Del Peak 31(12p13.1) mutation analysis' versus Clinical Feature #9: 'PATHOLOGICSPREAD(M)'

nPatients | M0 | M1 | M1A | M1B | MX
--- | --- | --- | --- | --- | ---
ALL | 1424 | 168 | 9 | 3 | 165
DEL PEAK 31(12P13.1) MUTATED | 144 | 22 | 0 | 0 | 40
DEL PEAK 31(12P13.1) WILD-TYPE | 1280 | 146 | 9 | 3 | 125

Figure S406. Get High-res Image Clustering Approach #71: 'Del Peak 31(12p13.1) mutation analysis' versus Clinical Feature #9: 'PATHOLOGICSPREAD(M)'

Clustering Approach #72: 'Del Peak 32(12q23.1) mutation analysis'

Table S478. Description of clustering approach #72: 'Del Peak 32(12q23.1) mutation analysis'

Cluster Labels | DEL PEAK 32(12Q23.1) MUTATED | DEL PEAK 32(12Q23.1) WILD-TYPE
--- | --- | ---
Number of samples | 692 | 3871

'Del Peak 32(12q23.1) mutation analysis' versus 'PRIMARY.SITE.OF.DISEASE'

P value = 5e-53 (Chi-square test), Q value = 8.4e-50

Table S479. Clustering Approach #72: 'Del Peak 32(12q23.1) mutation analysis' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'

nPatients | BLADDER | BRAIN | BREAST | COLON | ENDOMETRIAL | HEAD/NECK | KIDNEY | LUNG | OMENTUM | OVARY | PERITONEUM (OVARY) | RECTUM
--- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | ---
ALL | 125 | 544 | 846 | 412 | 447 | 319 | 493 | 662 | 2 | 548 | 2 | 159
DEL PEAK 32(12Q23.1) MUTATED | 18 | 61 | 146 | 48 | 34 | 36 | 6 | 130 | 1 | 187 | 0 | 24
DEL PEAK 32(12Q23.1) WILD-TYPE | 107 | 483 | 700 | 364 | 413 | 283 | 487 | 532 | 1 | 361 | 2 | 135

Figure S407. Get High-res Image Clustering Approach #72: 'Del Peak 32(12q23.1) mutation analysis' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'

'Del Peak 32(12q23.1) mutation analysis' versus 'GENDER'

P value = 5.49e-09 (Fisher's exact test), Q value = 8.1e-06

Table S480. Clustering Approach #72: 'Del Peak 32(12q23.1) mutation analysis' versus Clinical Feature #4: 'GENDER'

nPatients | FEMALE | MALE
--- | --- | ---
ALL | 2881 | 1682
DEL PEAK 32(12Q23.1) MUTATED | 504 | 188
DEL PEAK 32(12Q23.1) WILD-TYPE | 2377 | 1494

Figure S408. Get High-res Image Clustering Approach #72: 'Del Peak 32(12q23.1) mutation analysis' versus Clinical Feature #4: 'GENDER'

'Del Peak 32(12q23.1) mutation analysis' versus 'HISTOLOGICAL.TYPE'

P value = 2.57e-59 (Chi-square test), Q value = 4.3e-56

Table S481. Clustering Approach #72: 'Del Peak 32(12q23.1) mutation analysis' versus Clinical Feature #6: 'HISTOLOGICAL.TYPE'

nPatients | COLON ADENOCARCINOMA | COLON MUCINOUS ADENOCARCINOMA | ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA | HEAD & NECK SQUAMOUS CELL CARCINOMA | KIDNEY CLEAR CELL RENAL CARCINOMA | LUNG ACINAR ADENOCARCINOMA | LUNG ADENOCARCINOMA MIXED SUBTYPE | LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS) | LUNG BASALOID SQUAMOUS CELL CARCINOMA | LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS | LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS | LUNG CLEAR CELL ADENOCARCINOMA | LUNG MICROPAPILLARY ADENOCARCINOMA | LUNG MUCINOUS ADENOCARCINOMA | LUNG PAPILLARY ADENOCARCINOMA | LUNG PAPILLARY SQUAMOUS CELL CARCINOMA | LUNG PAPILLARY SQUAMOUS CELL CARICNOMA | LUNG SMALL CELL SQUAMOUS CELL CARCINOMA | LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA | LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS) | MIXED SEROUS AND ENDOMETRIOID | MUCINOUS (COLLOID) ADENOCARCINOMA | RECTAL ADENOCARCINOMA | RECTAL MUCINOUS ADENOCARCINOMA | SEROUS CYSTADENOCARCINOMA | SEROUS ENDOMETRIAL ADENOCARCINOMA | TREATED PRIMARY GBM | UNTREATED PRIMARY (DE NOVO) GBM
--- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | ---
ALL | 356 | 54 | 350 | 319 | 493 | 10 | 75 | 205 | 7 | 3 | 15 | 2 | 3 | 2 | 13 | 1 | 1 | 1 | 2 | 315 | 18 | 7 | 143 | 13 | 552 | 79 | 1 | 20
DEL PEAK 32(12Q23.1) MUTATED | 44 | 3 | 10 | 36 | 6 | 0 | 16 | 47 | 2 | 0 | 9 | 1 | 0 | 0 | 8 | 0 | 0 | 0 | 1 | 44 | 1 | 2 | 23 | 1 | 188 | 23 | 0 | 3
DEL PEAK 32(12Q23.1) WILD-TYPE | 312 | 51 | 340 | 283 | 487 | 10 | 59 | 158 | 5 | 3 | 6 | 1 | 3 | 2 | 5 | 1 | 1 | 1 | 1 | 271 | 17 | 5 | 120 | 12 | 364 | 56 | 1 | 17

Figure S409. Get High-res Image Clustering Approach #72: 'Del Peak 32(12q23.1) mutation analysis' versus Clinical Feature #6: 'HISTOLOGICAL.TYPE'

'Del Peak 32(12q23.1) mutation analysis' versus 'PATHOLOGY.T'

P value = 1.75e-05 (Fisher's exact test), Q value = 0.024

Table S482. Clustering Approach #72: 'Del Peak 32(12q23.1) mutation analysis' versus Clinical Feature #7: 'PATHOLOGY.T'

nPatients | T0+T1 | T2 | T3 | T4
--- | --- | --- | --- | ---
ALL | 466 | 632 | 694 | 209
DEL PEAK 32(12Q23.1) MUTATED | 33 | 105 | 84 | 20
DEL PEAK 32(12Q23.1) WILD-TYPE | 433 | 527 | 610 | 189

Figure S410. Get High-res Image Clustering Approach #72: 'Del Peak 32(12q23.1) mutation analysis' versus Clinical Feature #7: 'PATHOLOGY.T'

'Del Peak 32(12q23.1) mutation analysis' versus 'PATHOLOGICSPREAD(M)'

P value = 3.07e-05 (Chi-square test), Q value = 0.042

Table S483. Clustering Approach #72: 'Del Peak 32(12q23.1) mutation analysis' versus Clinical Feature #9: 'PATHOLOGICSPREAD(M)'

nPatients | M0 | M1 | M1A | M1B | MX
--- | --- | --- | --- | --- | ---
ALL | 1424 | 168 | 9 | 3 | 165
DEL PEAK 32(12Q23.1) MUTATED | 154 | 15 | 1 | 1 | 39
DEL PEAK 32(12Q23.1) WILD-TYPE | 1270 | 153 | 8 | 2 | 126

Figure S411. Get High-res Image Clustering Approach #72: 'Del Peak 32(12q23.1) mutation analysis' versus Clinical Feature #9: 'PATHOLOGICSPREAD(M)'

'Del Peak 32(12q23.1) mutation analysis' versus 'TUMOR.STAGE'

P value = 1.69e-05 (Fisher's exact test), Q value = 0.023

Table S484. Clustering Approach #72: 'Del Peak 32(12q23.1) mutation analysis' versus Clinical Feature #10: 'TUMOR.STAGE'

nPatients | I | II | III | IV
--- | --- | --- | --- | ---
ALL | 712 | 498 | 881 | 423
DEL PEAK 32(12Q23.1) MUTATED | 92 | 69 | 190 | 74
DEL PEAK 32(12Q23.1) WILD-TYPE | 620 | 429 | 691 | 349

Figure S412. Get High-res Image Clustering Approach #72: 'Del Peak 32(12q23.1) mutation analysis' versus Clinical Feature #10: 'TUMOR.STAGE'

Clustering Approach #73: 'Del Peak 33(12q24.33) mutation analysis'

Table S485. Description of clustering approach #73: 'Del Peak 33(12q24.33) mutation analysis'

Cluster Labels | DEL PEAK 33(12Q24.33) MUTATED | DEL PEAK 33(12Q24.33) WILD-TYPE
--- | --- | ---
Number of samples | 757 | 3806

'Del Peak 33(12q24.33) mutation analysis' versus 'PRIMARY.SITE.OF.DISEASE'

P value = 9.81e-60 (Chi-square test), Q value = 1.7e-56

Table S486. Clustering Approach #73: 'Del Peak 33(12q24.33) mutation analysis' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'

nPatients | BLADDER | BRAIN | BREAST | COLON | ENDOMETRIAL | HEAD/NECK | KIDNEY | LUNG | OMENTUM | OVARY | PERITONEUM (OVARY) | RECTUM
--- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | ---
ALL | 125 | 544 | 846 | 412 | 447 | 319 | 493 | 662 | 2 | 548 | 2 | 159
DEL PEAK 33(12Q24.33) MUTATED | 23 | 68 | 149 | 45 | 44 | 42 | 8 | 144 | 2 | 205 | 0 | 26
DEL PEAK 33(12Q24.33) WILD-TYPE | 102 | 476 | 697 | 367 | 403 | 277 | 485 | 518 | 0 | 343 | 2 | 133

Figure S413. Get High-res Image Clustering Approach #73: 'Del Peak 33(12q24.33) mutation analysis' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'

'Del Peak 33(12q24.33) mutation analysis' versus 'GENDER'

P value = 2.37e-08 (Fisher's exact test), Q value = 3.5e-05

Table S487. Clustering Approach #73: 'Del Peak 33(12q24.33) mutation analysis' versus Clinical Feature #4: 'GENDER'

nPatients | FEMALE | MALE
--- | --- | ---
ALL | 2881 | 1682
DEL PEAK 33(12Q24.33) MUTATED | 545 | 212
DEL PEAK 33(12Q24.33) WILD-TYPE | 2336 | 1470

Figure S414. Get High-res Image Clustering Approach #73: 'Del Peak 33(12q24.33) mutation analysis' versus Clinical Feature #4: 'GENDER'

'Del Peak 33(12q24.33) mutation analysis' versus 'HISTOLOGICAL.TYPE'

P value = 9.68e-64 (Chi-square test), Q value = 1.6e-60

Table S488. Clustering Approach #73: 'Del Peak 33(12q24.33) mutation analysis' versus Clinical Feature #6: 'HISTOLOGICAL.TYPE'

nPatients | COLON ADENOCARCINOMA | COLON MUCINOUS ADENOCARCINOMA | ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA | HEAD & NECK SQUAMOUS CELL CARCINOMA | KIDNEY CLEAR CELL RENAL CARCINOMA | LUNG ACINAR ADENOCARCINOMA | LUNG ADENOCARCINOMA MIXED SUBTYPE | LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS) | LUNG BASALOID SQUAMOUS CELL CARCINOMA | LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS | LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS | LUNG CLEAR CELL ADENOCARCINOMA | LUNG MICROPAPILLARY ADENOCARCINOMA | LUNG MUCINOUS ADENOCARCINOMA | LUNG PAPILLARY ADENOCARCINOMA | LUNG PAPILLARY SQUAMOUS CELL CARCINOMA | LUNG PAPILLARY SQUAMOUS CELL CARICNOMA | LUNG SMALL CELL SQUAMOUS CELL CARCINOMA | LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA | LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS) | MIXED SEROUS AND ENDOMETRIOID | MUCINOUS (COLLOID) ADENOCARCINOMA | RECTAL ADENOCARCINOMA | RECTAL MUCINOUS ADENOCARCINOMA | SEROUS CYSTADENOCARCINOMA | SEROUS ENDOMETRIAL ADENOCARCINOMA | TREATED PRIMARY GBM | UNTREATED PRIMARY (DE NOVO) GBM
--- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | ---
ALL | 356 | 54 | 350 | 319 | 493 | 10 | 75 | 205 | 7 | 3 | 15 | 2 | 3 | 2 | 13 | 1 | 1 | 1 | 2 | 315 | 18 | 7 | 143 | 13 | 552 | 79 | 1 | 20
DEL PEAK 33(12Q24.33) MUTATED | 42 | 2 | 14 | 42 | 8 | 2 | 16 | 53 | 4 | 0 | 7 | 0 | 1 | 0 | 7 | 0 | 0 | 0 | 1 | 51 | 1 | 2 | 25 | 1 | 207 | 29 | 0 | 3
DEL PEAK 33(12Q24.33) WILD-TYPE | 314 | 52 | 336 | 277 | 485 | 8 | 59 | 152 | 3 | 3 | 8 | 2 | 2 | 2 | 6 | 1 | 1 | 1 | 1 | 264 | 17 | 5 | 118 | 12 | 345 | 50 | 1 | 17

Figure S415. Get High-res Image Clustering Approach #73: 'Del Peak 33(12q24.33) mutation analysis' versus Clinical Feature #6: 'HISTOLOGICAL.TYPE'

'Del Peak 33(12q24.33) mutation analysis' versus 'PATHOLOGY.T'

P value = 1.21e-06 (Fisher's exact test), Q value = 0.0017

Table S489. Clustering Approach #73: 'Del Peak 33(12q24.33) mutation analysis' versus Clinical Feature #7: 'PATHOLOGY.T'

nPatients | T0+T1 | T2 | T3 | T4
--- | --- | --- | --- | ---
ALL | 466 | 632 | 694 | 209
DEL PEAK 33(12Q24.33) MUTATED | 36 | 117 | 79 | 30
DEL PEAK 33(12Q24.33) WILD-TYPE | 430 | 515 | 615 | 179

Figure S416. Get High-res Image Clustering Approach #73: 'Del Peak 33(12q24.33) mutation analysis' versus Clinical Feature #7: 'PATHOLOGY.T'

'Del Peak 33(12q24.33) mutation analysis' versus 'TUMOR.STAGE'

P value = 3.32e-07 (Fisher's exact test), Q value = 0.00048

Table S490. Clustering Approach #73: 'Del Peak 33(12q24.33) mutation analysis' versus Clinical Feature #10: 'TUMOR.STAGE'

nPatients | I | II | III | IV
--- | --- | --- | --- | ---
ALL | 712 | 498 | 881 | 423
DEL PEAK 33(12Q24.33) MUTATED | 102 | 67 | 209 | 83
DEL PEAK 33(12Q24.33) WILD-TYPE | 610 | 431 | 672 | 340

Figure S417. Get High-res Image Clustering Approach #73: 'Del Peak 33(12q24.33) mutation analysis' versus Clinical Feature #10: 'TUMOR.STAGE'

Clustering Approach #74: 'Del Peak 34(13q11) mutation analysis'

Table S491. Description of clustering approach #74: 'Del Peak 34(13q11) mutation analysis'

Cluster Labels | DEL PEAK 34(13Q11) MUTATED | DEL PEAK 34(13Q11) WILD-TYPE
--- | --- | ---
Number of samples | 1547 | 3016

'Del Peak 34(13q11) mutation analysis' versus 'PRIMARY.SITE.OF.DISEASE'

P value = 1.15e-154 (Chi-square test), Q value = 2e-151

Table S492. Clustering Approach #74: 'Del Peak 34(13q11) mutation analysis' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'

nPatients | BLADDER | BRAIN | BREAST | COLON | ENDOMETRIAL | HEAD/NECK | KIDNEY | LUNG | OMENTUM | OVARY | PERITONEUM (OVARY) | RECTUM
--- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | ---
ALL | 125 | 544 | 846 | 412 | 447 | 319 | 493 | 662 | 2 | 548 | 2 | 159
DEL PEAK 34(13Q11) MUTATED | 29 | 177 | 339 | 10 | 67 | 131 | 73 | 401 | 1 | 308 | 2 | 9
DEL PEAK 34(13Q11) WILD-TYPE | 96 | 367 | 507 | 402 | 380 | 188 | 420 | 261 | 1 | 240 | 0 | 150

Figure S418. Get High-res Image Clustering Approach #74: 'Del Peak 34(13q11) mutation analysis' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'

'Del Peak 34(13q11) mutation analysis' versus 'HISTOLOGICAL.TYPE'

P value = 3.77e-153 (Chi-square test), Q value = 6.7e-150

Table S493. Clustering Approach #74: 'Del Peak 34(13q11) mutation analysis' versus Clinical Feature #6: 'HISTOLOGICAL.TYPE'

nPatients | COLON ADENOCARCINOMA | COLON MUCINOUS ADENOCARCINOMA | ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA | HEAD & NECK SQUAMOUS CELL CARCINOMA | KIDNEY CLEAR CELL RENAL CARCINOMA | LUNG ACINAR ADENOCARCINOMA | LUNG ADENOCARCINOMA MIXED SUBTYPE | LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS) | LUNG BASALOID SQUAMOUS CELL CARCINOMA | LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS | LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS | LUNG CLEAR CELL ADENOCARCINOMA | LUNG MICROPAPILLARY ADENOCARCINOMA | LUNG MUCINOUS ADENOCARCINOMA | LUNG PAPILLARY ADENOCARCINOMA | LUNG PAPILLARY SQUAMOUS CELL CARCINOMA | LUNG PAPILLARY SQUAMOUS CELL CARICNOMA | LUNG SMALL CELL SQUAMOUS CELL CARCINOMA | LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA | LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS) | MIXED SEROUS AND ENDOMETRIOID | MUCINOUS (COLLOID) ADENOCARCINOMA | RECTAL ADENOCARCINOMA | RECTAL MUCINOUS ADENOCARCINOMA | SEROUS CYSTADENOCARCINOMA | SEROUS ENDOMETRIAL ADENOCARCINOMA | TREATED PRIMARY GBM | UNTREATED PRIMARY (DE NOVO) GBM
--- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | ---
ALL | 356 | 54 | 350 | 319 | 493 | 10 | 75 | 205 | 7 | 3 | 15 | 2 | 3 | 2 | 13 | 1 | 1 | 1 | 2 | 315 | 18 | 7 | 143 | 13 | 552 | 79 | 1 | 20
DEL PEAK 34(13Q11) MUTATED | 8 | 2 | 32 | 131 | 73 | 6 | 41 | 117 | 4 | 0 | 11 | 2 | 0 | 0 | 5 | 1 | 0 | 1 | 2 | 210 | 3 | 1 | 5 | 4 | 311 | 32 | 0 | 9
DEL PEAK 34(13Q11) WILD-TYPE | 348 | 52 | 318 | 188 | 420 | 4 | 34 | 88 | 3 | 3 | 4 | 0 | 3 | 2 | 8 | 0 | 1 | 0 | 0 | 105 | 15 | 6 | 138 | 9 | 241 | 47 | 1 | 11

Figure S419. Get High-res Image Clustering Approach #74: 'Del Peak 34(13q11) mutation analysis' versus Clinical Feature #6: 'HISTOLOGICAL.TYPE'

'Del Peak 34(13q11) mutation analysis' versus 'PATHOLOGY.T'

P value = 2.22e-29 (Fisher's exact test), Q value = 3.6e-26

Table S494. Clustering Approach #74: 'Del Peak 34(13q11) mutation analysis' versus Clinical Feature #7: 'PATHOLOGY.T'

nPatients | T0+T1 | T2 | T3 | T4
--- | --- | --- | --- | ---
ALL | 466 | 632 | 694 | 209
DEL PEAK 34(13Q11) MUTATED | 131 | 281 | 113 | 81
DEL PEAK 34(13Q11) WILD-TYPE | 335 | 351 | 581 | 128

Figure S420. Get High-res Image Clustering Approach #74: 'Del Peak 34(13q11) mutation analysis' versus Clinical Feature #7: 'PATHOLOGY.T'

'Del Peak 34(13q11) mutation analysis' versus 'PATHOLOGICSPREAD(M)'

P value = 5.38e-06 (Chi-square test), Q value = 0.0075

Table S495. Clustering Approach #74: 'Del Peak 34(13q11) mutation analysis' versus Clinical Feature #9: 'PATHOLOGICSPREAD(M)'

nPatients | M0 | M1 | M1A | M1B | MX
--- | --- | --- | --- | --- | ---
ALL | 1424 | 168 | 9 | 3 | 165
DEL PEAK 34(13Q11) MUTATED | 404 | 33 | 0 | 1 | 73
DEL PEAK 34(13Q11) WILD-TYPE | 1020 | 135 | 9 | 2 | 92

Figure S421. Get High-res Image Clustering Approach #74: 'Del Peak 34(13q11) mutation analysis' versus Clinical Feature #9: 'PATHOLOGICSPREAD(M)'

'Del Peak 34(13q11) mutation analysis' versus 'TUMOR.STAGE'

P value = 2.6e-07 (Fisher's exact test), Q value = 0.00038

Table S496. Clustering Approach #74: 'Del Peak 34(13q11) mutation analysis' versus Clinical Feature #10: 'TUMOR.STAGE'

nPatients | I | II | III | IV
--- | --- | --- | --- | ---
ALL | 712 | 498 | 881 | 423
DEL PEAK 34(13Q11) MUTATED | 252 | 132 | 368 | 160
DEL PEAK 34(13Q11) WILD-TYPE | 460 | 366 | 513 | 263

Figure S422. Get High-res Image Clustering Approach #74: 'Del Peak 34(13q11) mutation analysis' versus Clinical Feature #10: 'TUMOR.STAGE'

'Del Peak 34(13q11) mutation analysis' versus 'TOBACCOSMOKINGHISTORYINDICATOR'

P value = 6.36e-09 (Chi-square test), Q value = 9.4e-06

Table S497. Clustering Approach #74: 'Del Peak 34(13q11) mutation analysis' versus Clinical Feature #14: 'TOBACCOSMOKINGHISTORYINDICATOR'

nPatients | 1 | 2 | 3 | 4 | 5 | CURRENT REFORMED SMOKER FOR < OR = 15 YEARS | CURRENT REFORMED SMOKER FOR > 15 YEARS | CURRENT SMOKER | LIFELONG NON-SMOKER
--- | --- | --- | --- | --- | --- | --- | --- | --- | ---
ALL | 28 | 23 | 37 | 29 | 2 | 355 | 217 | 250 | 128
DEL PEAK 34(13Q11) MUTATED | 6 | 4 | 9 | 7 | 1 | 213 | 105 | 139 | 60
DEL PEAK 34(13Q11) WILD-TYPE | 22 | 19 | 28 | 22 | 1 | 142 | 112 | 111 | 68

Figure S423. Get High-res Image Clustering Approach #74: 'Del Peak 34(13q11) mutation analysis' versus Clinical Feature #14: 'TOBACCOSMOKINGHISTORYINDICATOR'

Clustering Approach #75: 'Del Peak 35(13q14.2) mutation analysis'

Table S498. Description of clustering approach #75: 'Del Peak 35(13q14.2) mutation analysis'

Cluster Labels | DEL PEAK 35(13Q14.2) MUTATED | DEL PEAK 35(13Q14.2) WILD-TYPE
--- | --- | ---
Number of samples | 1724 | 2839

'Del Peak 35(13q14.2) mutation analysis' versus 'Time to Death'

P value = 3.13e-06 (logrank test), Q value = 0.0044

Table S499. Clustering Approach #75: 'Del Peak 35(13q14.2) mutation analysis' versus Clinical Feature #1: 'Time to Death'

| nPatients | nDeath | Duration Range (Median), Month
--- | --- | --- | ---
ALL | 4296 | 1401 | 0.0 - 224.0 (14.9)
DEL PEAK 35(13Q14.2) MUTATED | 1648 | 632 | 0.0 - 211.5 (15.4)
DEL PEAK 35(13Q14.2) WILD-TYPE | 2648 | 769 | 0.0 - 224.0 (14.3)

Figure S424. Get High-res Image Clustering Approach #75: 'Del Peak 35(13q14.2) mutation analysis' versus Clinical Feature #1: 'Time to Death'

'Del Peak 35(13q14.2) mutation analysis' versus 'PRIMARY.SITE.OF.DISEASE'

P value = 2.43e-161 (Chi-square test), Q value = 4.3e-158

Table S500. Clustering Approach #75: 'Del Peak 35(13q14.2) mutation analysis' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'

nPatients | BLADDER | BRAIN | BREAST | COLON | ENDOMETRIAL | HEAD/NECK | KIDNEY | LUNG | OMENTUM | OVARY | PERITONEUM (OVARY) | RECTUM
--- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | ---
ALL | 125 | 544 | 846 | 412 | 447 | 319 | 493 | 662 | 2 | 548 | 2 | 159
DEL PEAK 35(13Q14.2) MUTATED | 48 | 230 | 391 | 15 | 72 | 135 | 77 | 403 | 1 | 339 | 2 | 10
DEL PEAK 35(13Q14.2) WILD-TYPE | 77 | 314 | 455 | 397 | 375 | 184 | 416 | 259 | 1 | 209 | 0 | 149

Figure S425. Get High-res Image Clustering Approach #75: 'Del Peak 35(13q14.2) mutation analysis' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'

'Del Peak 35(13q14.2) mutation analysis' versus 'HISTOLOGICAL.TYPE'

P value = 2.68e-158 (Chi-square test), Q value = 4.8e-155

Table S501. Clustering Approach #75: 'Del Peak 35(13q14.2) mutation analysis' versus Clinical Feature #6: 'HISTOLOGICAL.TYPE'

nPatients | COLON ADENOCARCINOMA | COLON MUCINOUS ADENOCARCINOMA | ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA | HEAD & NECK SQUAMOUS CELL CARCINOMA | KIDNEY CLEAR CELL RENAL CARCINOMA | LUNG ACINAR ADENOCARCINOMA | LUNG ADENOCARCINOMA MIXED SUBTYPE | LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS) | LUNG BASALOID SQUAMOUS CELL CARCINOMA | LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS | LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS | LUNG CLEAR CELL ADENOCARCINOMA | LUNG MICROPAPILLARY ADENOCARCINOMA | LUNG MUCINOUS ADENOCARCINOMA | LUNG PAPILLARY ADENOCARCINOMA | LUNG PAPILLARY SQUAMOUS CELL CARCINOMA | LUNG PAPILLARY SQUAMOUS CELL CARICNOMA | LUNG SMALL CELL SQUAMOUS CELL CARCINOMA | LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA | LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS) | MIXED SEROUS AND ENDOMETRIOID | MUCINOUS (COLLOID) ADENOCARCINOMA | RECTAL ADENOCARCINOMA | RECTAL MUCINOUS ADENOCARCINOMA | SEROUS CYSTADENOCARCINOMA | SEROUS ENDOMETRIAL ADENOCARCINOMA | TREATED PRIMARY GBM | UNTREATED PRIMARY (DE NOVO) GBM
--- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | ---
ALL | 356 | 54 | 350 | 319 | 493 | 10 | 75 | 205 | 7 | 3 | 15 | 2 | 3 | 2 | 13 | 1 | 1 | 1 | 2 | 315 | 18 | 7 | 143 | 13 | 552 | 79 | 1 | 20
DEL PEAK 35(13Q14.2) MUTATED | 12 | 2 | 42 | 135 | 77 | 7 | 39 | 112 | 3 | 0 | 10 | 2 | 1 | 0 | 4 | 1 | 0 | 1 | 1 | 221 | 4 | 1 | 6 | 4 | 342 | 26 | 0 | 11
DEL PEAK 35(13Q14.2) WILD-TYPE | 344 | 52 | 308 | 184 | 416 | 3 | 36 | 93 | 4 | 3 | 5 | 0 | 2 | 2 | 9 | 0 | 1 | 0 | 1 | 94 | 14 | 6 | 137 | 9 | 210 | 53 | 1 | 9

Figure S426. Get High-res Image Clustering Approach #75: 'Del Peak 35(13q14.2) mutation analysis' versus Clinical Feature #6: 'HISTOLOGICAL.TYPE'

'Del Peak 35(13q14.2) mutation analysis' versus 'PATHOLOGY.T'

P value = 1.25e-28 (Fisher's exact test), Q value = 2e-25

Table S502. Clustering Approach #75: 'Del Peak 35(13q14.2) mutation analysis' versus Clinical Feature #7: 'PATHOLOGY.T'

nPatients | T0+T1 | T2 | T3 | T4
--- | --- | --- | --- | ---
ALL | 466 | 632 | 694 | 209
DEL PEAK 35(13Q14.2) MUTATED | 148 | 282 | 113 | 75
DEL PEAK 35(13Q14.2) WILD-TYPE | 318 | 350 | 581 | 134

Figure S427. Get High-res Image Clustering Approach #75: 'Del Peak 35(13q14.2) mutation analysis' versus Clinical Feature #7: 'PATHOLOGY.T'

'Del Peak 35(13q14.2) mutation analysis' versus 'PATHOLOGICSPREAD(M)'

P value = 1.36e-05 (Chi-square test), Q value = 0.019

Table S503. Clustering Approach #75: 'Del Peak 35(13q14.2) mutation analysis' versus Clinical Feature #9: 'PATHOLOGICSPREAD(M)'

nPatients | M0 | M1 | M1A | M1B | MX
--- | --- | --- | --- | --- | ---
ALL | 1424 | 168 | 9 | 3 | 165
DEL PEAK 35(13Q14.2) MUTATED | 418 | 33 | 1 | 1 | 74
DEL PEAK 35(13Q14.2) WILD-TYPE | 1006 | 135 | 8 | 2 | 91

Figure S428. Get High-res Image Clustering Approach #75: 'Del Peak 35(13q14.2) mutation analysis' versus Clinical Feature #9: 'PATHOLOGICSPREAD(M)'

'Del Peak 35(13q14.2) mutation analysis' versus 'TUMOR.STAGE'

P value = 4.05e-08 (Fisher's exact test), Q value = 5.9e-05

Table S504. Clustering Approach #75: 'Del Peak 35(13q14.2) mutation analysis' versus Clinical Feature #10: 'TUMOR.STAGE'

nPatients | I | II | III | IV
--- | --- | --- | --- | ---
ALL | 712 | 498 | 881 | 423
DEL PEAK 35(13Q14.2) MUTATED | 265 | 140 | 392 | 157
DEL PEAK 35(13Q14.2) WILD-TYPE | 447 | 358 | 489 | 266

Figure S429. Get High-res Image Clustering Approach #75: 'Del Peak 35(13q14.2) mutation analysis' versus Clinical Feature #10: 'TUMOR.STAGE'

'Del Peak 35(13q14.2) mutation analysis' versus 'TOBACCOSMOKINGHISTORYINDICATOR'

P value = 0.000134 (Chi-square test), Q value = 0.17

Table S505. Clustering Approach #75: 'Del Peak 35(13q14.2) mutation analysis' versus Clinical Feature #14: 'TOBACCOSMOKINGHISTORYINDICATOR'

nPatients | 1 | 2 | 3 | 4 | 5 | CURRENT REFORMED SMOKER FOR < OR = 15 YEARS | CURRENT REFORMED SMOKER FOR > 15 YEARS | CURRENT SMOKER | LIFELONG NON-SMOKER
--- | --- | --- | --- | --- | --- | --- | --- | --- | ---
ALL | 28 | 23 | 37 | 29 | 2 | 355 | 217 | 250 | 128
DEL PEAK 35(13Q14.2) MUTATED | 7 | 7 | 14 | 15 | 1 | 217 | 101 | 139 | 64
DEL PEAK 35(13Q14.2) WILD-TYPE | 21 | 16 | 23 | 14 | 1 | 138 | 116 | 111 | 64

Figure S430. Get High-res Image Clustering Approach #75: 'Del Peak 35(13q14.2) mutation analysis' versus Clinical Feature #14: 'TOBACCOSMOKINGHISTORYINDICATOR'

Clustering Approach #76: 'Del Peak 36(14q24.1) mutation analysis'

Table S506. Description of clustering approach #76: 'Del Peak 36(14q24.1) mutation analysis'

Cluster Labels | DEL PEAK 36(14Q24.1) MUTATED | DEL PEAK 36(14Q24.1) WILD-TYPE
--- | --- | ---
Number of samples | 1456 | 3107

'Del Peak 36(14q24.1) mutation analysis' versus 'PRIMARY.SITE.OF.DISEASE'

P value = 3.5e-50 (Chi-square test), Q value = 5.8e-47

Table S507. Clustering Approach #76: 'Del Peak 36(14q24.1) mutation analysis' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'

nPatients | BLADDER | BRAIN | BREAST | COLON | ENDOMETRIAL | HEAD/NECK | KIDNEY | LUNG | OMENTUM | OVARY | PERITONEUM (OVARY) | RECTUM
--- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | ---
ALL | 125 | 544 | 846 | 412 | 447 | 319 | 493 | 662 | 2 | 548 | 2 | 159
DEL PEAK 36(14Q24.1) MUTATED | 36 | 168 | 263 | 125 | 53 | 39 | 218 | 211 | 1 | 273 | 1 | 66
DEL PEAK 36(14Q24.1) WILD-TYPE | 89 | 376 | 583 | 287 | 394 | 280 | 275 | 451 | 1 | 275 | 1 | 93

Figure S431. Get High-res Image Clustering Approach #76: 'Del Peak 36(14q24.1) mutation analysis' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'

'Del Peak 36(14q24.1) mutation analysis' versus 'HISTOLOGICAL.TYPE'

P value = 3.47e-53 (Chi-square test), Q value = 5.8e-50

Table S508. Clustering Approach #76: 'Del Peak 36(14q24.1) mutation analysis' versus Clinical Feature #6: 'HISTOLOGICAL.TYPE'

nPatients | COLON ADENOCARCINOMA | COLON MUCINOUS ADENOCARCINOMA | ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA | HEAD & NECK SQUAMOUS CELL CARCINOMA | KIDNEY CLEAR CELL RENAL CARCINOMA | LUNG ACINAR ADENOCARCINOMA | LUNG ADENOCARCINOMA MIXED SUBTYPE | LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS) | LUNG BASALOID SQUAMOUS CELL CARCINOMA | LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS | LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS | LUNG CLEAR CELL ADENOCARCINOMA | LUNG MICROPAPILLARY ADENOCARCINOMA | LUNG MUCINOUS ADENOCARCINOMA | LUNG PAPILLARY ADENOCARCINOMA | LUNG PAPILLARY SQUAMOUS CELL CARCINOMA | LUNG PAPILLARY SQUAMOUS CELL CARICNOMA | LUNG SMALL CELL SQUAMOUS CELL CARCINOMA | LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA | LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS) | MIXED SEROUS AND ENDOMETRIOID | MUCINOUS (COLLOID) ADENOCARCINOMA | RECTAL ADENOCARCINOMA | RECTAL MUCINOUS ADENOCARCINOMA | SEROUS CYSTADENOCARCINOMA | SEROUS ENDOMETRIAL ADENOCARCINOMA | TREATED PRIMARY GBM | UNTREATED PRIMARY (DE NOVO) GBM
--- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | ---
ALL | 356 | 54 | 350 | 319 | 493 | 10 | 75 | 205 | 7 | 3 | 15 | 2 | 3 | 2 | 13 | 1 | 1 | 1 | 2 | 315 | 18 | 7 | 143 | 13 | 552 | 79 | 1 | 20
DEL PEAK 36(14Q24.1) MUTATED | 119 | 5 | 21 | 39 | 218 | 5 | 19 | 54 | 3 | 0 | 4 | 1 | 0 | 1 | 3 | 0 | 0 | 1 | 0 | 117 | 4 | 3 | 64 | 1 | 275 | 28 | 0 | 5
DEL PEAK 36(14Q24.1) WILD-TYPE | 237 | 49 | 329 | 280 | 275 | 5 | 56 | 151 | 4 | 3 | 11 | 1 | 3 | 1 | 10 | 1 | 1 | 0 | 2 | 198 | 14 | 4 | 79 | 12 | 277 | 51 | 1 | 15

Figure S432. Get High-res Image Clustering Approach #76: 'Del Peak 36(14q24.1) mutation analysis' versus Clinical Feature #6: 'HISTOLOGICAL.TYPE'

'Del Peak 36(14q24.1) mutation analysis' versus 'PATHOLOGY.T'

P value = 3.49e-05 (Fisher's exact test), Q value = 0.047

Table S509. Clustering Approach #76: 'Del Peak 36(14q24.1) mutation analysis' versus Clinical Feature #7: 'PATHOLOGY.T'

nPatients | T0+T1 | T2 | T3 | T4
--- | --- | --- | --- | ---
ALL | 466 | 632 | 694 | 209
DEL PEAK 36(14Q24.1) MUTATED | 151 | 198 | 259 | 42
DEL PEAK 36(14Q24.1) WILD-TYPE | 315 | 434 | 435 | 167

Figure S433. Get High-res Image Clustering Approach #76: 'Del Peak 36(14q24.1) mutation analysis' versus Clinical Feature #7: 'PATHOLOGY.T'

'Del Peak 36(14q24.1) mutation analysis' versus 'PATHOLOGY.N'

P value = 8.6e-05 (Fisher's exact test), Q value = 0.11

Table S510. Clustering Approach #76: 'Del Peak 36(14q24.1) mutation analysis' versus Clinical Feature #8: 'PATHOLOGY.N'

nPatients | N0 | N1 | N2 | N3
--- | --- | --- | --- | ---
ALL | 1067 | 353 | 282 | 11
DEL PEAK 36(14Q24.1) MUTATED | 335 | 135 | 61 | 4
DEL PEAK 36(14Q24.1) WILD-TYPE | 732 | 218 | 221 | 7

Figure S434. Get High-res Image Clustering Approach #76: 'Del Peak 36(14q24.1) mutation analysis' versus Clinical Feature #8: 'PATHOLOGY.N'

'Del Peak 36(14q24.1) mutation analysis' versus 'TUMOR.STAGE'

P value = 9.79e-09 (Fisher's exact test), Q value = 1.5e-05

Table S511. Clustering Approach #76: 'Del Peak 36(14q24.1) mutation analysis' versus Clinical Feature #10: 'TUMOR.STAGE'

nPatients | I | II | III | IV
--- | --- | --- | --- | ---
ALL | 712 | 498 | 881 | 423
DEL PEAK 36(14Q24.1) MUTATED | 234 | 154 | 392 | 131
DEL PEAK 36(14Q24.1) WILD-TYPE | 478 | 344 | 489 | 292

Figure S435. Get High-res Image Clustering Approach #76: 'Del Peak 36(14q24.1) mutation analysis' versus Clinical Feature #10: 'TUMOR.STAGE'

Clustering Approach #77: 'Del Peak 37(15q11.2) mutation analysis'

Table S512. Description of clustering approach #77: 'Del Peak 37(15q11.2) mutation analysis'

Cluster Labels | DEL PEAK 37(15Q11.2) MUTATED | DEL PEAK 37(15Q11.2) WILD-TYPE
--- | --- | ---
Number of samples | 1456 | 3107

'Del Peak 37(15q11.2) mutation analysis' versus 'PRIMARY.SITE.OF.DISEASE'

P value = 6.2e-74 (Chi-square test), Q value = 1.1e-70

Table S513. Clustering Approach #77: 'Del Peak 37(15q11.2) mutation analysis' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'

nPatients | BLADDER | BRAIN | BREAST | COLON | ENDOMETRIAL | HEAD/NECK | KIDNEY | LUNG | OMENTUM | OVARY | PERITONEUM (OVARY) | RECTUM
--- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | ---
ALL | 125 | 544 | 846 | 412 | 447 | 319 | 493 | 662 | 2 | 548 | 2 | 159
DEL PEAK 37(15Q11.2) MUTATED | 44 | 116 | 292 | 159 | 89 | 68 | 39 | 288 | 2 | 283 | 2 | 71
DEL PEAK 37(15Q11.2) WILD-TYPE | 81 | 428 | 554 | 253 | 358 | 251 | 454 | 374 | 0 | 265 | 0 | 88

Figure S436. Get High-res Image Clustering Approach #77: 'Del Peak 37(15q11.2) mutation analysis' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'

'Del Peak 37(15q11.2) mutation analysis' versus 'GENDER'

P value = 8.72e-06 (Fisher's exact test), Q value = 0.012

Table S514. Clustering Approach #77: 'Del Peak 37(15q11.2) mutation analysis' versus Clinical Feature #4: 'GENDER'

nPatients | FEMALE | MALE
--- | --- | ---
ALL | 2881 | 1682
DEL PEAK 37(15Q11.2) MUTATED | 987 | 469
DEL PEAK 37(15Q11.2) WILD-TYPE | 1894 | 1213

Figure S437. Get High-res Image Clustering Approach #77: 'Del Peak 37(15q11.2) mutation analysis' versus Clinical Feature #4: 'GENDER'

'Del Peak 37(15q11.2) mutation analysis' versus 'HISTOLOGICAL.TYPE'

P value = 1.4e-81 (Chi-square test), Q value = 2.4e-78

Table S515. Clustering Approach #77: 'Del Peak 37(15q11.2) mutation analysis' versus Clinical Feature #6: 'HISTOLOGICAL.TYPE'

nPatients | COLON ADENOCARCINOMA | COLON MUCINOUS ADENOCARCINOMA | ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA | HEAD & NECK SQUAMOUS CELL CARCINOMA | KIDNEY CLEAR CELL RENAL CARCINOMA | LUNG ACINAR ADENOCARCINOMA | LUNG ADENOCARCINOMA MIXED SUBTYPE | LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS) | LUNG BASALOID SQUAMOUS CELL CARCINOMA | LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS | LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS | LUNG CLEAR CELL ADENOCARCINOMA | LUNG MICROPAPILLARY ADENOCARCINOMA | LUNG MUCINOUS ADENOCARCINOMA | LUNG PAPILLARY ADENOCARCINOMA | LUNG PAPILLARY SQUAMOUS CELL CARCINOMA | LUNG PAPILLARY SQUAMOUS CELL CARICNOMA | LUNG SMALL CELL SQUAMOUS CELL CARCINOMA | LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA | LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS) | MIXED SEROUS AND ENDOMETRIOID | MUCINOUS (COLLOID) ADENOCARCINOMA | RECTAL ADENOCARCINOMA | RECTAL MUCINOUS ADENOCARCINOMA | SEROUS CYSTADENOCARCINOMA | SEROUS ENDOMETRIAL ADENOCARCINOMA | TREATED PRIMARY GBM | UNTREATED PRIMARY (DE NOVO) GBM
--- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | ---
ALL | 356 | 54 | 350 | 319 | 493 | 10 | 75 | 205 | 7 | 3 | 15 | 2 | 3 | 2 | 13 | 1 | 1 | 1 | 2 | 315 | 18 | 7 | 143 | 13 | 552 | 79 | 1 | 20
DEL PEAK 37(15Q11.2) MUTATED | 145 | 13 | 38 | 68 | 39 | 4 | 32 | 122 | 2 | 0 | 8 | 1 | 3 | 0 | 9 | 0 | 0 | 1 | 1 | 104 | 5 | 1 | 64 | 6 | 287 | 46 | 0 | 6
DEL PEAK 37(15Q11.2) WILD-TYPE | 211 | 41 | 312 | 251 | 454 | 6 | 43 | 83 | 5 | 3 | 7 | 1 | 0 | 2 | 4 | 1 | 1 | 0 | 1 | 211 | 13 | 6 | 79 | 7 | 265 | 33 | 1 | 14

Figure S438. Get High-res Image Clustering Approach #77: 'Del Peak 37(15q11.2) mutation analysis' versus Clinical Feature #6: 'HISTOLOGICAL.TYPE'

'Del Peak 37(15q11.2) mutation analysis' versus 'PATHOLOGY.T'

P value = 2.02e-07 (Fisher's exact test), Q value = 0.00029

Table S516. Clustering Approach #77: 'Del Peak 37(15q11.2) mutation analysis' versus Clinical Feature #7: 'PATHOLOGY.T'

nPatients | T0+T1 | T2 | T3 | T4
--- | --- | --- | --- | ---
ALL | 466 | 632 | 694 | 209
DEL PEAK 37(15Q11.2) MUTATED | 98 | 231 | 230 | 60
DEL PEAK 37(15Q11.2) WILD-TYPE | 368 | 401 | 464 | 149

Figure S439. Get High-res Image Clustering Approach #77: 'Del Peak 37(15q11.2) mutation analysis' versus Clinical Feature #7: 'PATHOLOGY.T'

'Del Peak 37(15q11.2) mutation analysis' versus 'PATHOLOGY.N'

P value = 1.56e-06 (Fisher's exact test), Q value = 0.0022

Table S517. Clustering Approach #77: 'Del Peak 37(15q11.2) mutation analysis' versus Clinical Feature #8: 'PATHOLOGY.N'

nPatients | N0 | N1 | N2 | N3
--- | --- | --- | --- | ---
ALL | 1067 | 353 | 282 | 11
DEL PEAK 37(15Q11.2) MUTATED | 315 | 150 | 118 | 5
DEL PEAK 37(15Q11.2) WILD-TYPE | 752 | 203 | 164 | 6

Figure S440. Get High-res Image Clustering Approach #77: 'Del Peak 37(15q11.2) mutation analysis' versus Clinical Feature #8: 'PATHOLOGY.N'

'Del Peak 37(15q11.2) mutation analysis' versus 'TUMOR.STAGE'

P value = 4.36e-09 (Fisher's exact test), Q value = 6.5e-06

Table S518. Clustering Approach #77: 'Del Peak 37(15q11.2) mutation analysis' versus Clinical Feature #10: 'TUMOR.STAGE'

nPatients | I | II | III | IV
--- | --- | --- | --- | ---
ALL | 712 | 498 | 881 | 423
DEL PEAK 37(15Q11.2) MUTATED | 197 | 175 | 379 | 141
DEL PEAK 37(15Q11.2) WILD-TYPE | 515 | 323 | 502 | 282

Figure S441. Get High-res Image Clustering Approach #77: 'Del Peak 37(15q11.2) mutation analysis' versus Clinical Feature #10: 'TUMOR.STAGE'

'Del Peak 37(15q11.2) mutation analysis' versus 'RADIATIONS.RADIATION.REGIMENINDICATION'

P value = 2.48e-06 (Fisher's exact test), Q value = 0.0035

Table S519. Clustering Approach #77: 'Del Peak 37(15q11.2) mutation analysis' versus Clinical Feature #11: 'RADIATIONS.RADIATION.REGIMENINDICATION'

nPatients | NO | YES
--- | --- | ---
ALL | 826 | 3737
DEL PEAK 37(15Q11.2) MUTATED | 207 | 1249
DEL PEAK 37(15Q11.2) WILD-TYPE | 619 | 2488

Figure S442. Get High-res Image Clustering Approach #77: 'Del Peak 37(15q11.2) mutation analysis' versus Clinical Feature #11: 'RADIATIONS.RADIATION.REGIMENINDICATION'

Clustering Approach #78: 'Del Peak 38(15q15.1) mutation analysis'

Table S520. Description of clustering approach #78: 'Del Peak 38(15q15.1) mutation analysis'

Cluster Labels | DEL PEAK 38(15Q15.1) MUTATED | DEL PEAK 38(15Q15.1) WILD-TYPE
--- | --- | ---
Number of samples | 1579 | 2984

'Del Peak 38(15q15.1) mutation analysis' versus 'PRIMARY.SITE.OF.DISEASE'

P value = 7.53e-92 (Chi-square test), Q value = 1.3e-88

Table S521. Clustering Approach #78: 'Del Peak 38(15q15.1) mutation analysis' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'

nPatients | BLADDER | BRAIN | BREAST | COLON | ENDOMETRIAL | HEAD/NECK | KIDNEY | LUNG | OMENTUM | OVARY | PERITONEUM (OVARY) | RECTUM
--- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | ---
ALL | 125 | 544 | 846 | 412 | 447 | 319 | 493 | 662 | 2 | 548 | 2 | 159
DEL PEAK 38(15Q15.1) MUTATED | 45 | 140 | 310 | 149 | 103 | 74 | 38 | 296 | 2 | 343 | 2 | 74
DEL PEAK 38(15Q15.1) WILD-TYPE | 80 | 404 | 536 | 263 | 344 | 245 | 455 | 366 | 0 | 205 | 0 | 85

Figure S443. Get High-res Image Clustering Approach #78: 'Del Peak 38(15q15.1) mutation analysis' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'

'Del Peak 38(15q15.1) mutation analysis' versus 'GENDER'

P value = 5.85e-08 (Fisher's exact test), Q value = 8.6e-05

Table S522. Clustering Approach #78: 'Del Peak 38(15q15.1) mutation analysis' versus Clinical Feature #4: 'GENDER'

nPatients | FEMALE | MALE
--- | --- | ---
ALL | 2881 | 1682
DEL PEAK 38(15Q15.1) MUTATED | 1081 | 498
DEL PEAK 38(15Q15.1) WILD-TYPE | 1800 | 1184

Figure S444. Get High-res Image Clustering Approach #78: 'Del Peak 38(15q15.1) mutation analysis' versus Clinical Feature #4: 'GENDER'

'Del Peak 38(15q15.1) mutation analysis' versus 'HISTOLOGICAL.TYPE'

P value = 4.97e-103 (Chi-square test), Q value = 8.6e-100

Table S523. Clustering Approach #78: 'Del Peak 38(15q15.1) mutation analysis' versus Clinical Feature #6: 'HISTOLOGICAL.TYPE'

nPatients | COLON ADENOCARCINOMA | COLON MUCINOUS ADENOCARCINOMA | ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA | HEAD & NECK SQUAMOUS CELL CARCINOMA | KIDNEY CLEAR CELL RENAL CARCINOMA | LUNG ACINAR ADENOCARCINOMA | LUNG ADENOCARCINOMA MIXED SUBTYPE | LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS) | LUNG BASALOID SQUAMOUS CELL CARCINOMA | LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS | LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS | LUNG CLEAR CELL ADENOCARCINOMA | LUNG MICROPAPILLARY ADENOCARCINOMA | LUNG MUCINOUS ADENOCARCINOMA | LUNG PAPILLARY ADENOCARCINOMA | LUNG PAPILLARY SQUAMOUS CELL CARCINOMA | LUNG PAPILLARY SQUAMOUS CELL CARICNOMA | LUNG SMALL CELL SQUAMOUS CELL CARCINOMA | LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA | LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS) | MIXED SEROUS AND ENDOMETRIOID | MUCINOUS (COLLOID) ADENOCARCINOMA | RECTAL ADENOCARCINOMA | RECTAL MUCINOUS ADENOCARCINOMA | SEROUS CYSTADENOCARCINOMA | SEROUS ENDOMETRIAL ADENOCARCINOMA | TREATED PRIMARY GBM | UNTREATED PRIMARY (DE NOVO) GBM
--- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | ---
ALL | 356 | 54 | 350 | 319 | 493 | 10 | 75 | 205 | 7 | 3 | 15 | 2 | 3 | 2 | 13 | 1 | 1 | 1 | 2 | 315 | 18 | 7 | 143 | 13 | 552 | 79 | 1 | 20
DEL PEAK 38(15Q15.1) MUTATED | 136 | 12 | 46 | 74 | 38 | 4 | 32 | 126 | 2 | 0 | 8 | 1 | 3 | 0 | 9 | 0 | 0 | 1 | 1 | 108 | 7 | 1 | 67 | 6 | 347 | 50 | 0 | 6
DEL PEAK 38(15Q15.1) WILD-TYPE | 220 | 42 | 304 | 245 | 455 | 6 | 43 | 79 | 5 | 3 | 7 | 1 | 0 | 2 | 4 | 1 | 1 | 0 | 1 | 207 | 11 | 6 | 76 | 7 | 205 | 29 | 1 | 14

Figure S445. Get High-res Image Clustering Approach #78: 'Del Peak 38(15q15.1) mutation analysis' versus Clinical Feature #6: 'HISTOLOGICAL.TYPE'

'Del Peak 38(15q15.1) mutation analysis' versus 'PATHOLOGY.T'

P value = 3.86e-08 (Fisher's exact test), Q value = 5.7e-05

Table S524. Clustering Approach #78: 'Del Peak 38(15q15.1) mutation analysis' versus Clinical Feature #7: 'PATHOLOGY.T'

nPatients | T0+T1 | T2 | T3 | T4
--- | --- | --- | --- | ---
ALL | 466 | 632 | 694 | 209
DEL PEAK 38(15Q15.1) MUTATED | 97 | 237 | 227 | 62
DEL PEAK 38(15Q15.1) WILD-TYPE | 369 | 395 | 467 | 147

Figure S446. Get High-res Image Clustering Approach #78: 'Del Peak 38(15q15.1) mutation analysis' versus Clinical Feature #7: 'PATHOLOGY.T'

'Del Peak 38(15q15.1) mutation analysis' versus 'PATHOLOGY.N'

P value = 1.3e-06 (Fisher's exact test), Q value = 0.0019

Table S525. Clustering Approach #78: 'Del Peak 38(15q15.1) mutation analysis' versus Clinical Feature #8: 'PATHOLOGY.N'

nPatients | N0 | N1 | N2 | N3
--- | --- | --- | --- | ---
ALL | 1067 | 353 | 282 | 11
DEL PEAK 38(15Q15.1) MUTATED | 316 | 152 | 117 | 5
DEL PEAK 38(15Q15.1) WILD-TYPE | 751 | 201 | 165 | 6

Figure S447. Get High-res Image Clustering Approach #78: 'Del Peak 38(15q15.1) mutation analysis' versus Clinical Feature #8: 'PATHOLOGY.N'

'Del Peak 38(15q15.1) mutation analysis' versus 'TUMOR.STAGE'

P value = 1.55e-15 (Fisher's exact test), Q value = 2.4e-12

Table S526. Clustering Approach #78: 'Del Peak 38(15q15.1) mutation analysis' versus Clinical Feature #10: 'TUMOR.STAGE'

nPatients | I | II | III | IV
--- | --- | --- | --- | ---
ALL | 712 | 498 | 881 | 423
DEL PEAK 38(15Q15.1) MUTATED | 202 | 179 | 427 | 146
DEL PEAK 38(15Q15.1) WILD-TYPE | 510 | 319 | 454 | 277

Figure S448. Get High-res Image Clustering Approach #78: 'Del Peak 38(15q15.1) mutation analysis' versus Clinical Feature #10: 'TUMOR.STAGE'

'Del Peak 38(15q15.1) mutation analysis' versus 'RADIATIONS.RADIATION.REGIMENINDICATION'

P value = 5.22e-05 (Fisher's exact test), Q value = 0.07

Table S527. Clustering Approach #78: 'Del Peak 38(15q15.1) mutation analysis' versus Clinical Feature #11: 'RADIATIONS.RADIATION.REGIMENINDICATION'

nPatients | NO | YES
--- | --- | ---
ALL | 826 | 3737
DEL PEAK 38(15Q15.1) MUTATED | 236 | 1343
DEL PEAK 38(15Q15.1) WILD-TYPE | 590 | 2394

Figure S449. Get High-res Image Clustering Approach #78: 'Del Peak 38(15q15.1) mutation analysis' versus Clinical Feature #11: 'RADIATIONS.RADIATION.REGIMENINDICATION'

Clustering Approach #79: 'Del Peak 39(16p13.3) mutation analysis'

Table S528. Description of clustering approach #79: 'Del Peak 39(16p13.3) mutation analysis'

Cluster Labels | DEL PEAK 39(16P13.3) MUTATED | DEL PEAK 39(16P13.3) WILD-TYPE
--- | --- | ---
Number of samples | 744 | 3819

'Del Peak 39(16p13.3) mutation analysis' versus 'Time to Death'

P value = 1.85e-05 (logrank test), Q value = 0.025

Table S529. Clustering Approach #79: 'Del Peak 39(16p13.3) mutation analysis' versus Clinical Feature #1: 'Time to Death'

| nPatients | nDeath | Duration Range (Median), Month
--- | --- | --- | ---
ALL | 4296 | 1401 | 0.0 - 224.0 (14.9)
DEL PEAK 39(16P13.3) MUTATED | 708 | 290 | 0.0 - 211.5 (16.0)
DEL PEAK 39(16P13.3) WILD-TYPE | 3588 | 1111 | 0.0 - 224.0 (14.7)

Figure S450. Get High-res Image Clustering Approach #79: 'Del Peak 39(16p13.3) mutation analysis' versus Clinical Feature #1: 'Time to Death'

'Del Peak 39(16p13.3) mutation analysis' versus 'PRIMARY.SITE.OF.DISEASE'

P value = 8.46e-131 (Chi-square test), Q value = 1.5e-127

Table S530. Clustering Approach #79: 'Del Peak 39(16p13.3) mutation analysis' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'

nPatients | BLADDER | BRAIN | BREAST | COLON | ENDOMETRIAL | HEAD/NECK | KIDNEY | LUNG | OMENTUM | OVARY | PERITONEUM (OVARY) | RECTUM
--- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | ---
ALL | 125 | 544 | 846 | 412 | 447 | 319 | 493 | 662 | 2 | 548 | 2 | 159
DEL PEAK 39(16P13.3) MUTATED | 36 | 66 | 48 | 45 | 55 | 37 | 12 | 165 | 2 | 264 | 1 | 13
DEL PEAK 39(16P13.3) WILD-TYPE | 89 | 478 | 798 | 367 | 392 | 282 | 481 | 497 | 0 | 284 | 1 | 146

Figure S451. Get High-res Image Clustering Approach #79: 'Del Peak 39(16p13.3) mutation analysis' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'

'Del Peak 39(16p13.3) mutation analysis' versus 'HISTOLOGICAL.TYPE'

P value = 2.73e-96 (Chi-square test), Q value = 4.7e-93

Table S531. Clustering Approach #79: 'Del Peak 39(16p13.3) mutation analysis' versus Clinical Feature #6: 'HISTOLOGICAL.TYPE'

nPatients | COLON ADENOCARCINOMA | COLON MUCINOUS ADENOCARCINOMA | ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA | HEAD & NECK SQUAMOUS CELL CARCINOMA | KIDNEY CLEAR CELL RENAL CARCINOMA | LUNG ACINAR ADENOCARCINOMA | LUNG ADENOCARCINOMA MIXED SUBTYPE | LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS) | LUNG BASALOID SQUAMOUS CELL CARCINOMA | LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS | LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS | LUNG CLEAR CELL ADENOCARCINOMA | LUNG MICROPAPILLARY ADENOCARCINOMA | LUNG MUCINOUS ADENOCARCINOMA | LUNG PAPILLARY ADENOCARCINOMA | LUNG PAPILLARY SQUAMOUS CELL CARCINOMA | LUNG PAPILLARY SQUAMOUS CELL CARICNOMA | LUNG SMALL CELL SQUAMOUS CELL CARCINOMA | LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA | LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS) | MIXED SEROUS AND ENDOMETRIOID | MUCINOUS (COLLOID) ADENOCARCINOMA | RECTAL ADENOCARCINOMA | RECTAL MUCINOUS ADENOCARCINOMA | SEROUS CYSTADENOCARCINOMA | SEROUS ENDOMETRIAL ADENOCARCINOMA | TREATED PRIMARY GBM | UNTREATED PRIMARY (DE NOVO) GBM
--- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | ---
ALL | 356 | 54 | 350 | 319 | 493 | 10 | 75 | 205 | 7 | 3 | 15 | 2 | 3 | 2 | 13 | 1 | 1 | 1 | 2 | 315 | 18 | 7 | 143 | 13 | 552 | 79 | 1 | 20
DEL PEAK 39(16P13.3) MUTATED | 39 | 6 | 20 | 37 | 12 | 2 | 15 | 38 | 4 | 0 | 2 | 0 | 0 | 0 | 2 | 1 | 0 | 0 | 1 | 99 | 4 | 1 | 10 | 2 | 267 | 31 | 0 | 3
DEL PEAK 39(16P13.3) WILD-TYPE | 317 | 48 | 330 | 282 | 481 | 8 | 60 | 167 | 3 | 3 | 13 | 2 | 3 | 2 | 11 | 0 | 1 | 1 | 1 | 216 | 14 | 6 | 133 | 11 | 285 | 48 | 1 | 17

Figure S452. Get High-res Image Clustering Approach #79: 'Del Peak 39(16p13.3) mutation analysis' versus Clinical Feature #6: 'HISTOLOGICAL.TYPE'

'Del Peak 39(16p13.3) mutation analysis' versus 'TUMOR.STAGE'

P value = 2.9e-13 (Fisher's exact test), Q value = 4.5e-10

Table S532. Clustering Approach #79: 'Del Peak 39(16p13.3) mutation analysis' versus Clinical Feature #10: 'TUMOR.STAGE'

nPatients | I | II | III | IV
--- | --- | --- | --- | ---
ALL | 712 | 498 | 881 | 423
DEL PEAK 39(16P13.3) MUTATED | 107 | 82 | 262 | 79
DEL PEAK 39(16P13.3) WILD-TYPE | 605 | 416 | 619 | 344

Figure S453. Get High-res Image Clustering Approach #79: 'Del Peak 39(16p13.3) mutation analysis' versus Clinical Feature #10: 'TUMOR.STAGE'

'Del Peak 39(16p13.3) mutation analysis' versus 'RADIATIONS.RADIATION.REGIMENINDICATION'

P value = 2.53e-09 (Fisher's exact test), Q value = 3.8e-06

Table S533. Clustering Approach #79: 'Del Peak 39(16p13.3) mutation analysis' versus Clinical Feature #11: 'RADIATIONS.RADIATION.REGIMENINDICATION'

nPatients | NO | YES
--- | --- | ---
ALL | 826 | 3737
DEL PEAK 39(16P13.3) MUTATED | 80 | 664
DEL PEAK 39(16P13.3) WILD-TYPE | 746 | 3073

Figure S454. Get High-res Image Clustering Approach #79: 'Del Peak 39(16p13.3) mutation analysis' versus Clinical Feature #11: 'RADIATIONS.RADIATION.REGIMENINDICATION'

'Del Peak 39(16p13.3) mutation analysis' versus 'NEOPLASM.DISEASESTAGE'

P value = 8.49e-09 (Chi-square test), Q value = 1.3e-05

Table S534. Clustering Approach #79: 'Del Peak 39(16p13.3) mutation analysis' versus Clinical Feature #21: 'NEOPLASM.DISEASESTAGE'

nPatients | STAGE I | STAGE IA | STAGE IB | STAGE II | STAGE IIA | STAGE IIB | STAGE III | STAGE IIIA | STAGE IIIB | STAGE IIIC | STAGE IV | STAGE TIS | STAGE X
--- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | ---
ALL | 72 | 62 | 7 | 43 | 287 | 186 | 42 | 124 | 25 | 41 | 59 | 1 | 16
DEL PEAK 39(16P13.3) MUTATED | 5 | 2 | 1 | 7 | 19 | 10 | 13 | 5 | 1 | 3 | 15 | 0 | 2
DEL PEAK 39(16P13.3) WILD-TYPE | 67 | 60 | 6 | 36 | 268 | 176 | 29 | 119 | 24 | 38 | 44 | 1 | 14

Figure S455. Get High-res Image Clustering Approach #79: 'Del Peak 39(16p13.3) mutation analysis' versus Clinical Feature #21: 'NEOPLASM.DISEASESTAGE'

Clustering Approach #80: 'Del Peak 40(16q23.1) mutation analysis'

Table S535. Description of clustering approach #80: 'Del Peak 40(16q23.1) mutation analysis'

Cluster Labels | DEL PEAK 40(16Q23.1) MUTATED | DEL PEAK 40(16Q23.1) WILD-TYPE
--- | --- | ---
Number of samples | 1614 | 2949

'Del Peak 40(16q23.1) mutation analysis' versus 'PRIMARY.SITE.OF.DISEASE'

P value = 1.03e-249 (Chi-square test), Q value = 1.9e-246

Table S536. Clustering Approach #80: 'Del Peak 40(16q23.1) mutation analysis' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'

nPatients | BLADDER | BRAIN | BREAST | COLON | ENDOMETRIAL | HEAD/NECK | KIDNEY | LUNG | OMENTUM | OVARY | PERITONEUM (OVARY) | RECTUM
--- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | ---
ALL | 125 | 544 | 846 | 412 | 447 | 319 | 493 | 662 | 2 | 548 | 2 | 159
DEL PEAK 40(16Q23.1) MUTATED | 34 | 96 | 537 | 49 | 127 | 60 | 19 | 240 | 1 | 426 | 2 | 23
DEL PEAK 40(16Q23.1) WILD-TYPE | 91 | 448 | 309 | 363 | 320 | 259 | 474 | 422 | 1 | 122 | 0 | 136

Figure S456. Get High-res Image Clustering Approach #80: 'Del Peak 40(16q23.1) mutation analysis' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'

'Del Peak 40(16q23.1) mutation analysis' versus 'GENDER'

P value = 1.35e-71 (Fisher's exact test), Q value = 2.3e-68

Table S537. Clustering Approach #80: 'Del Peak 40(16q23.1) mutation analysis' versus Clinical Feature #4: 'GENDER'

nPatients | FEMALE | MALE
--- | --- | ---
ALL | 2881 | 1682
DEL PEAK 40(16Q23.1) MUTATED | 1291 | 323
DEL PEAK 40(16Q23.1) WILD-TYPE | 1590 | 1359

Figure S457. Get High-res Image Clustering Approach #80: 'Del Peak 40(16q23.1) mutation analysis' versus Clinical Feature #4: 'GENDER'

'Del Peak 40(16q23.1) mutation analysis' versus 'HISTOLOGICAL.TYPE'

P value = 2e-189 (Chi-square test), Q value = 3.6e-186

Table S538. Clustering Approach #80: 'Del Peak 40(16q23.1) mutation analysis' versus Clinical Feature #6: 'HISTOLOGICAL.TYPE'

nPatients | COLON ADENOCARCINOMA | COLON MUCINOUS ADENOCARCINOMA | ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA | HEAD & NECK SQUAMOUS CELL CARCINOMA | KIDNEY CLEAR CELL RENAL CARCINOMA | LUNG ACINAR ADENOCARCINOMA | LUNG ADENOCARCINOMA MIXED SUBTYPE | LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS) | LUNG BASALOID SQUAMOUS CELL CARCINOMA | LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS | LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS | LUNG CLEAR CELL ADENOCARCINOMA | LUNG MICROPAPILLARY ADENOCARCINOMA | LUNG MUCINOUS ADENOCARCINOMA | LUNG PAPILLARY ADENOCARCINOMA | LUNG PAPILLARY SQUAMOUS CELL CARCINOMA | LUNG PAPILLARY SQUAMOUS CELL CARICNOMA | LUNG SMALL CELL SQUAMOUS CELL CARCINOMA | LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA | LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS) | MIXED SEROUS AND ENDOMETRIOID | MUCINOUS (COLLOID) ADENOCARCINOMA | RECTAL ADENOCARCINOMA | RECTAL MUCINOUS ADENOCARCINOMA | SEROUS CYSTADENOCARCINOMA | SEROUS ENDOMETRIAL ADENOCARCINOMA | TREATED PRIMARY GBM | UNTREATED PRIMARY (DE NOVO) GBM
--- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | ---
ALL | 356 | 54 | 350 | 319 | 493 | 10 | 75 | 205 | 7 | 3 | 15 | 2 | 3 | 2 | 13 | 1 | 1 | 1 | 2 | 315 | 18 | 7 | 143 | 13 | 552 | 79 | 1 | 20
DEL PEAK 40(16Q23.1) MUTATED | 40 | 9 | 59 | 60 | 19 | 4 | 25 | 67 | 3 | 0 | 6 | 2 | 1 | 0 | 5 | 0 | 0 | 0 | 1 | 123 | 6 | 3 | 20 | 2 | 429 | 62 | 0 | 6
DEL PEAK 40(16Q23.1) WILD-TYPE | 316 | 45 | 291 | 259 | 474 | 6 | 50 | 138 | 4 | 3 | 9 | 0 | 2 | 2 | 8 | 1 | 1 | 1 | 1 | 192 | 12 | 4 | 123 | 11 | 123 | 17 | 1 | 14

Figure S458. Get High-res Image Clustering Approach #80: 'Del Peak 40(16q23.1) mutation analysis' versus Clinical Feature #6: 'HISTOLOGICAL.TYPE'

'Del Peak 40(16q23.1) mutation analysis' versus 'PATHOLOGY.T'

P value = 7.26e-11 (Fisher's exact test), Q value = 1.1e-07

Table S539. Clustering Approach #80: 'Del Peak 40(16q23.1) mutation analysis' versus Clinical Feature #7: 'PATHOLOGY.T'

nPatients | T0+T1 | T2 | T3 | T4
--- | --- | --- | --- | ---
ALL | 466 | 632 | 694 | 209
DEL PEAK 40(16Q23.1) MUTATED | 67 | 170 | 89 | 46
DEL PEAK 40(16Q23.1) WILD-TYPE | 399 | 462 | 605 | 163

Figure S459. Get High-res Image Clustering Approach #80: 'Del Peak 40(16q23.1) mutation analysis' versus Clinical Feature #7: 'PATHOLOGY.T'

'Del Peak 40(16q23.1) mutation analysis' versus 'TUMOR.STAGE'

P value = 4.29e-33 (Fisher's exact test), Q value = 7e-30

Table S540. Clustering Approach #80: 'Del Peak 40(16q23.1) mutation analysis' versus Clinical Feature #10: 'TUMOR.STAGE'

nPatients | I | II | III | IV
--- | --- | --- | --- | ---
ALL | 712 | 498 | 881 | 423
DEL PEAK 40(16Q23.1) MUTATED | 149 | 111 | 413 | 117
DEL PEAK 40(16Q23.1) WILD-TYPE | 563 | 387 | 468 | 306

Figure S460. Get High-res Image Clustering Approach #80: 'Del Peak 40(16q23.1) mutation analysis' versus Clinical Feature #10: 'TUMOR.STAGE'

'Del Peak 40(16q23.1) mutation analysis' versus 'RADIATIONS.RADIATION.REGIMENINDICATION'

P value = 4.83e-05 (Fisher's exact test), Q value = 0.065

Table S541. Clustering Approach #80: 'Del Peak 40(16q23.1) mutation analysis' versus Clinical Feature #11: 'RADIATIONS.RADIATION.REGIMENINDICATION'

nPatients | NO | YES
--- | --- | ---
ALL | 826 | 3737
DEL PEAK 40(16Q23.1) MUTATED | 242 | 1372
DEL PEAK 40(16Q23.1) WILD-TYPE | 584 | 2365

Figure S461. Get High-res Image Clustering Approach #80: 'Del Peak 40(16q23.1) mutation analysis' versus Clinical Feature #11: 'RADIATIONS.RADIATION.REGIMENINDICATION'

'Del Peak 40(16q23.1) mutation analysis' versus 'NEOPLASM.DISEASESTAGE'

P value = 1.18e-09 (Chi-square test), Q value = 1.8e-06

Table S542. Clustering Approach #80: 'Del Peak 40(16q23.1) mutation analysis' versus Clinical Feature #21: 'NEOPLASM.DISEASESTAGE'

nPatients | STAGE I | STAGE IA | STAGE IB | STAGE II | STAGE IIA | STAGE IIB | STAGE III | STAGE IIIA | STAGE IIIB | STAGE IIIC | STAGE IV | STAGE TIS | STAGE X
--- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | ---
ALL | 72 | 62 | 7 | 43 | 287 | 186 | 42 | 124 | 25 | 41 | 59 | 1 | 16
DEL PEAK 40(16Q23.1) MUTATED | 55 | 40 | 4 | 16 | 186 | 112 | 9 | 74 | 14 | 28 | 20 | 0 | 12
DEL PEAK 40(16Q23.1) WILD-TYPE | 17 | 22 | 3 | 27 | 101 | 74 | 33 | 50 | 11 | 13 | 39 | 1 | 4

Figure S462. Get High-res Image Clustering Approach #80: 'Del Peak 40(16q23.1) mutation analysis' versus Clinical Feature #21: 'NEOPLASM.DISEASESTAGE'

Clustering Approach #81: 'Del Peak 41(17p12) mutation analysis'

Table S543. Description of clustering approach #81: 'Del Peak 41(17p12) mutation analysis'

Cluster Labels | DEL PEAK 41(17P12) MUTATED | DEL PEAK 41(17P12) WILD-TYPE
--- | --- | ---
Number of samples | 2062 | 2501

'Del Peak 41(17p12) mutation analysis' versus 'PRIMARY.SITE.OF.DISEASE'

P value = 1.18e-243 (Chi-square test), Q value = 2.1e-240

Table S544. Clustering Approach #81: 'Del Peak 41(17p12) mutation analysis' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'

nPatients | BLADDER | BRAIN | BREAST | COLON | ENDOMETRIAL | HEAD/NECK | KIDNEY | LUNG | OMENTUM | OVARY | PERITONEUM (OVARY) | RECTUM
--- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | ---
ALL | 125 | 544 | 846 | 412 | 447 | 319 | 493 | 662 | 2 | 548 | 2 | 159
DEL PEAK 41(17P12) MUTATED | 64 | 68 | 513 | 228 | 97 | 75 | 50 | 387 | 2 | 463 | 1 | 110
DEL PEAK 41(17P12) WILD-TYPE | 61 | 476 | 333 | 184 | 350 | 244 | 443 | 275 | 0 | 85 | 1 | 49

Figure S463. Get High-res Image Clustering Approach #81: 'Del Peak 41(17p12) mutation analysis' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'

'Del Peak 41(17p12) mutation analysis' versus 'GENDER'

P value = 3e-26 (Fisher's exact test), Q value = 4.8e-23

Table S545. Clustering Approach #81: 'Del Peak 41(17p12) mutation analysis' versus Clinical Feature #4: 'GENDER'

nPatients | FEMALE | MALE
--- | --- | ---
ALL | 2881 | 1682
DEL PEAK 41(17P12) MUTATED | 1473 | 589
DEL PEAK 41(17P12) WILD-TYPE | 1408 | 1093

Figure S464. Get High-res Image Clustering Approach #81: 'Del Peak 41(17p12) mutation analysis' versus Clinical Feature #4: 'GENDER'

'Del Peak 41(17p12) mutation analysis' versus 'KARNOFSKY.PERFORMANCE.SCORE'

P value = 2.4e-05 (t-test), Q value = 0.033

Table S546. Clustering Approach #81: 'Del Peak 41(17p12) mutation analysis' versus Clinical Feature #5: 'KARNOFSKY.PERFORMANCE.SCORE'

| nPatients | Mean (Std.Dev)
--- | --- | ---
ALL | 640 | 73.6 (23.9)
DEL PEAK 41(17P12) MUTATED | 198 | 66.6 (30.5)
DEL PEAK 41(17P12) WILD-TYPE | 442 | 76.7 (19.6)

Figure S465. Get High-res Image Clustering Approach #81: 'Del Peak 41(17p12) mutation analysis' versus Clinical Feature #5: 'KARNOFSKY.PERFORMANCE.SCORE'

'Del Peak 41(17p12) mutation analysis' versus 'HISTOLOGICAL.TYPE'

P value = 1.94e-191 (Chi-square test), Q value = 3.5e-188

Table S547. Clustering Approach #81: 'Del Peak 41(17p12) mutation analysis' versus Clinical Feature #6: 'HISTOLOGICAL.TYPE'

nPatients | COLON ADENOCARCINOMA | COLON MUCINOUS ADENOCARCINOMA | ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA | HEAD & NECK SQUAMOUS CELL CARCINOMA | KIDNEY CLEAR CELL RENAL CARCINOMA | LUNG ACINAR ADENOCARCINOMA | LUNG ADENOCARCINOMA MIXED SUBTYPE | LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS) | LUNG BASALOID SQUAMOUS CELL CARCINOMA | LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS | LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS | LUNG CLEAR CELL ADENOCARCINOMA | LUNG MICROPAPILLARY ADENOCARCINOMA | LUNG MUCINOUS ADENOCARCINOMA | LUNG PAPILLARY ADENOCARCINOMA | LUNG PAPILLARY SQUAMOUS CELL CARCINOMA | LUNG PAPILLARY SQUAMOUS CELL CARICNOMA | LUNG SMALL CELL SQUAMOUS CELL CARCINOMA | LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA | LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS) | MIXED SEROUS AND ENDOMETRIOID | MUCINOUS (COLLOID) ADENOCARCINOMA | RECTAL ADENOCARCINOMA | RECTAL MUCINOUS ADENOCARCINOMA | SEROUS CYSTADENOCARCINOMA | SEROUS ENDOMETRIAL ADENOCARCINOMA | TREATED PRIMARY GBM | UNTREATED PRIMARY (DE NOVO) GBM
--- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | ---
ALL | 356 | 54 | 350 | 319 | 493 | 10 | 75 | 205 | 7 | 3 | 15 | 2 | 3 | 2 | 13 | 1 | 1 | 1 | 2 | 315 | 18 | 7 | 143 | 13 | 552 | 79 | 1 | 20
DEL PEAK 41(17P12) MUTATED | 213 | 14 | 36 | 75 | 50 | 6 | 33 | 126 | 5 | 1 | 8 | 2 | 3 | 0 | 5 | 0 | 0 | 1 | 2 | 193 | 9 | 2 | 102 | 6 | 466 | 52 | 0 | 2
DEL PEAK 41(17P12) WILD-TYPE | 143 | 40 | 314 | 244 | 443 | 4 | 42 | 79 | 2 | 2 | 7 | 0 | 0 | 2 | 8 | 1 | 1 | 0 | 0 | 122 | 9 | 5 | 41 | 7 | 86 | 27 | 1 | 18

Figure S466. Get High-res Image Clustering Approach #81: 'Del Peak 41(17p12) mutation analysis' versus Clinical Feature #6: 'HISTOLOGICAL.TYPE'

'Del Peak 41(17p12) mutation analysis' versus 'PATHOLOGY.T'

P value = 2.66e-13 (Fisher's exact test), Q value = 4.1e-10

Table S548. Clustering Approach #81: 'Del Peak 41(17p12) mutation analysis' versus Clinical Feature #7: 'PATHOLOGY.T'

nPatients | T0+T1 | T2 | T3 | T4
--- | --- | --- | --- | ---
ALL | 466 | 632 | 694 | 209
DEL PEAK 41(17P12) MUTATED | 133 | 317 | 318 | 73
DEL PEAK 41(17P12) WILD-TYPE | 333 | 315 | 376 | 136

Figure S467. Get High-res Image Clustering Approach #81: 'Del Peak 41(17p12) mutation analysis' versus Clinical Feature #7: 'PATHOLOGY.T'

'Del Peak 41(17p12) mutation analysis' versus 'PATHOLOGY.N'

P value = 2.29e-07 (Fisher's exact test), Q value = 0.00033

Table S549. Clustering Approach #81: 'Del Peak 41(17p12) mutation analysis' versus Clinical Feature #8: 'PATHOLOGY.N'

nPatients | N0 | N1 | N2 | N3
--- | --- | --- | --- | ---
ALL | 1067 | 353 | 282 | 11
DEL PEAK 41(17P12) MUTATED | 439 | 202 | 148 | 5
DEL PEAK 41(17P12) WILD-TYPE | 628 | 151 | 134 | 6

Figure S468. Get High-res Image Clustering Approach #81: 'Del Peak 41(17p12) mutation analysis' versus Clinical Feature #8: 'PATHOLOGY.N'

'Del Peak 41(17p12) mutation analysis' versus 'TUMOR.STAGE'

P value = 9.14e-30 (Fisher's exact test), Q value = 1.5e-26

Table S550. Clustering Approach #81: 'Del Peak 41(17p12) mutation analysis' versus Clinical Feature #10: 'TUMOR.STAGE'

nPatients | I | II | III | IV
--- | --- | --- | --- | ---
ALL | 712 | 498 | 881 | 423
DEL PEAK 41(17P12) MUTATED | 274 | 239 | 585 | 190
DEL PEAK 41(17P12) WILD-TYPE | 438 | 259 | 296 | 233

Figure S469. Get High-res Image Clustering Approach #81: 'Del Peak 41(17p12) mutation analysis' versus Clinical Feature #10: 'TUMOR.STAGE'

'Del Peak 41(17p12) mutation analysis' versus 'RADIATIONS.RADIATION.REGIMENINDICATION'

P value = 3.15e-28 (Fisher's exact test), Q value = 5.1e-25

Table S551. Clustering Approach #81: 'Del Peak 41(17p12) mutation analysis' versus Clinical Feature #11: 'RADIATIONS.RADIATION.REGIMENINDICATION'

nPatients | NO | YES
--- | --- | ---
ALL | 826 | 3737
DEL PEAK 41(17P12) MUTATED | 233 | 1829
DEL PEAK 41(17P12) WILD-TYPE | 593 | 1908

Figure S470. Get High-res Image Clustering Approach #81: 'Del Peak 41(17p12) mutation analysis' versus Clinical Feature #11: 'RADIATIONS.RADIATION.REGIMENINDICATION'

Clustering Approach #82: 'Del Peak 42(17q11.2) mutation analysis'

Table S552. Description of clustering approach #82: 'Del Peak 42(17q11.2) mutation analysis'

Cluster Labels | DEL PEAK 42(17Q11.2) MUTATED | DEL PEAK 42(17Q11.2) WILD-TYPE
--- | --- | ---
Number of samples | 1131 | 3432

'Del Peak 42(17q11.2) mutation analysis' versus 'AGE'

P value = 1.08e-05 (t-test), Q value = 0.015

Table S553. Clustering Approach #82: 'Del Peak 42(17q11.2) mutation analysis' versus Clinical Feature #2: 'AGE'

| nPatients | Mean (Std.Dev)
--- | --- | ---
ALL | 4507 | 61.9 (12.6)
DEL PEAK 42(17Q11.2) MUTATED | 1117 | 60.4 (12.2)
DEL PEAK 42(17Q11.2) WILD-TYPE | 3390 | 62.3 (12.7)

Figure S471. Get High-res Image Clustering Approach #82: 'Del Peak 42(17q11.2) mutation analysis' versus Clinical Feature #2: 'AGE'

'Del Peak 42(17q11.2) mutation analysis' versus 'PRIMARY.SITE.OF.DISEASE'

P value = 4.51e-260 (Chi-square test), Q value = 8.2e-257

Table S554. Clustering Approach #82: 'Del Peak 42(17q11.2) mutation analysis' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'

nPatients | BLADDER | BRAIN | BREAST | COLON | ENDOMETRIAL | HEAD/NECK | KIDNEY | LUNG | OMENTUM | OVARY | PERITONEUM (OVARY) | RECTUM
--- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | ---
ALL | 125 | 544 | 846 | 412 | 447 | 319 | 493 | 662 | 2 | 548 | 2 | 159
DEL PEAK 42(17Q11.2) MUTATED | 12 | 67 | 264 | 47 | 78 | 30 | 33 | 126 | 2 | 448 | 0 | 21
DEL PEAK 42(17Q11.2) WILD-TYPE | 113 | 477 | 582 | 365 | 369 | 289 | 460 | 536 | 0 | 100 | 2 | 138

Figure S472. Get High-res Image Clustering Approach #82: 'Del Peak 42(17q11.2) mutation analysis' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'

'Del Peak 42(17q11.2) mutation analysis' versus 'GENDER'

P value = 2.56e-50 (Fisher's exact test), Q value = 4.3e-47

Table S555. Clustering Approach #82: 'Del Peak 42(17q11.2) mutation analysis' versus Clinical Feature #4: 'GENDER'

nPatients | FEMALE | MALE
--- | --- | ---
ALL | 2881 | 1682
DEL PEAK 42(17Q11.2) MUTATED | 917 | 214
DEL PEAK 42(17Q11.2) WILD-TYPE | 1964 | 1468

Figure S473. Get High-res Image Clustering Approach #82: 'Del Peak 42(17q11.2) mutation analysis' versus Clinical Feature #4: 'GENDER'

'Del Peak 42(17q11.2) mutation analysis' versus 'HISTOLOGICAL.TYPE'

P value = 2.51e-232 (Chi-square test), Q value = 4.5e-229

Table S556. Clustering Approach #82: 'Del Peak 42(17q11.2) mutation analysis' versus Clinical Feature #6: 'HISTOLOGICAL.TYPE'

nPatients | COLON ADENOCARCINOMA | COLON MUCINOUS ADENOCARCINOMA | ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA | HEAD & NECK SQUAMOUS CELL CARCINOMA | KIDNEY CLEAR CELL RENAL CARCINOMA | LUNG ACINAR ADENOCARCINOMA | LUNG ADENOCARCINOMA MIXED SUBTYPE | LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS) | LUNG BASALOID SQUAMOUS CELL CARCINOMA | LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS | LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS | LUNG CLEAR CELL ADENOCARCINOMA | LUNG MICROPAPILLARY ADENOCARCINOMA | LUNG MUCINOUS ADENOCARCINOMA | LUNG PAPILLARY ADENOCARCINOMA | LUNG PAPILLARY SQUAMOUS CELL CARCINOMA | LUNG PAPILLARY SQUAMOUS CELL CARICNOMA | LUNG SMALL CELL SQUAMOUS CELL CARCINOMA | LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA | LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS) | MIXED SEROUS AND ENDOMETRIOID | MUCINOUS (COLLOID) ADENOCARCINOMA | RECTAL ADENOCARCINOMA | RECTAL MUCINOUS ADENOCARCINOMA | SEROUS CYSTADENOCARCINOMA | SEROUS ENDOMETRIAL ADENOCARCINOMA | TREATED PRIMARY GBM | UNTREATED PRIMARY (DE NOVO) GBM
--- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | ---
ALL | 356 | 54 | 350 | 319 | 493 | 10 | 75 | 205 | 7 | 3 | 15 | 2 | 3 | 2 | 13 | 1 | 1 | 1 | 2 | 315 | 18 | 7 | 143 | 13 | 552 | 79 | 1 | 20
DEL PEAK 42(17Q11.2) MUTATED | 41 | 6 | 38 | 30 | 33 | 0 | 9 | 33 | 1 | 0 | 2 | 0 | 1 | 0 | 1 | 0 | 0 | 1 | 0 | 77 | 5 | 1 | 20 | 1 | 450 | 35 | 0 | 2
DEL PEAK 42(17Q11.2) WILD-TYPE | 315 | 48 | 312 | 289 | 460 | 10 | 66 | 172 | 6 | 3 | 13 | 2 | 2 | 2 | 12 | 1 | 1 | 0 | 2 | 238 | 13 | 6 | 123 | 12 | 102 | 44 | 1 | 18

Figure S474. Get High-res Image Clustering Approach #82: 'Del Peak 42(17q11.2) mutation analysis' versus Clinical Feature #6: 'HISTOLOGICAL.TYPE'

'Del Peak 42(17q11.2) mutation analysis' versus 'TUMOR.STAGE'

P value = 1.47e-59 (Fisher's exact test), Q value = 2.5e-56

Table S557. Clustering Approach #82: 'Del Peak 42(17q11.2) mutation analysis' versus Clinical Feature #10: 'TUMOR.STAGE'

nPatients | I | II | III | IV
--- | --- | --- | --- | ---
ALL | 712 | 498 | 881 | 423
DEL PEAK 42(17Q11.2) MUTATED | 104 | 73 | 419 | 101
DEL PEAK 42(17Q11.2) WILD-TYPE | 608 | 425 | 462 | 322

Figure S475. Get High-res Image Clustering Approach #82: 'Del Peak 42(17q11.2) mutation analysis' versus Clinical Feature #10: 'TUMOR.STAGE'

'Del Peak 42(17q11.2) mutation analysis' versus 'RADIATIONS.RADIATION.REGIMENINDICATION'

P value = 1.65e-09 (Fisher's exact test), Q value = 2.5e-06

Table S558. Clustering Approach #82: 'Del Peak 42(17q11.2) mutation analysis' versus Clinical Feature #11: 'RADIATIONS.RADIATION.REGIMENINDICATION'

nPatients | NO | YES
--- | --- | ---
ALL | 826 | 3737
DEL PEAK 42(17Q11.2) MUTATED | 139 | 992
DEL PEAK 42(17Q11.2) WILD-TYPE | 687 | 2745

Figure S476. Get High-res Image Clustering Approach #82: 'Del Peak 42(17q11.2) mutation analysis' versus Clinical Feature #11: 'RADIATIONS.RADIATION.REGIMENINDICATION'

Clustering Approach #83: 'Del Peak 43(18q21.2) mutation analysis'

Table S559. Description of clustering approach #83: 'Del Peak 43(18q21.2) mutation analysis'

Cluster Labels | DEL PEAK 43(18Q21.2) MUTATED | DEL PEAK 43(18Q21.2) WILD-TYPE
--- | --- | ---
Number of samples | 1777 | 2786

'Del Peak 43(18q21.2) mutation analysis' versus 'AGE'

P value = 2.01e-06 (t-test), Q value = 0.0028

Table S560. Clustering Approach #83: 'Del Peak 43(18q21.2) mutation analysis' versus Clinical Feature #2: 'AGE'

| nPatients | Mean (Std.Dev)
--- | --- | ---
ALL | 4507 | 61.9 (12.6)
DEL PEAK 43(18Q21.2) MUTATED | 1749 | 63.0 (12.1)
DEL PEAK 43(18Q21.2) WILD-TYPE | 2758 | 61.1 (12.9)

Figure S477. Get High-res Image Clustering Approach #83: 'Del Peak 43(18q21.2) mutation analysis' versus Clinical Feature #2: 'AGE'

'Del Peak 43(18q21.2) mutation analysis' versus 'PRIMARY.SITE.OF.DISEASE'

P value = 7.33e-159 (Chi-square test), Q value = 1.3e-155

Table S561. Clustering Approach #83: 'Del Peak 43(18q21.2) mutation analysis' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'

nPatients | BLADDER | BRAIN | BREAST | COLON | ENDOMETRIAL | HEAD/NECK | KIDNEY | LUNG | OMENTUM | OVARY | PERITONEUM (OVARY) | RECTUM
--- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | ---
ALL | 125 | 544 | 846 | 412 | 447 | 319 | 493 | 662 | 2 | 548 | 2 | 159
DEL PEAK 43(18Q21.2) MUTATED | 59 | 67 | 278 | 260 | 67 | 168 | 97 | 306 | 1 | 331 | 0 | 140
DEL PEAK 43(18Q21.2) WILD-TYPE | 66 | 477 | 568 | 152 | 380 | 151 | 396 | 356 | 1 | 217 | 2 | 19

Figure S478. Get High-res Image Clustering Approach #83: 'Del Peak 43(18q21.2) mutation analysis' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'

'Del Peak 43(18q21.2) mutation analysis' versus 'HISTOLOGICAL.TYPE'

P value = 9.15e-112 (Chi-square test), Q value = 1.6e-108

Table S562. Clustering Approach #83: 'Del Peak 43(18q21.2) mutation analysis' versus Clinical Feature #6: 'HISTOLOGICAL.TYPE'

nPatients | COLON ADENOCARCINOMA | COLON MUCINOUS ADENOCARCINOMA | ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA | HEAD & NECK SQUAMOUS CELL CARCINOMA | KIDNEY CLEAR CELL RENAL CARCINOMA | LUNG ACINAR ADENOCARCINOMA | LUNG ADENOCARCINOMA MIXED SUBTYPE | LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS) | LUNG BASALOID SQUAMOUS CELL CARCINOMA | LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS | LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS | LUNG CLEAR CELL ADENOCARCINOMA | LUNG MICROPAPILLARY ADENOCARCINOMA | LUNG MUCINOUS ADENOCARCINOMA | LUNG PAPILLARY ADENOCARCINOMA | LUNG PAPILLARY SQUAMOUS CELL CARCINOMA | LUNG PAPILLARY SQUAMOUS CELL CARICNOMA | LUNG SMALL CELL SQUAMOUS CELL CARCINOMA | LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA | LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS) | MIXED SEROUS AND ENDOMETRIOID | MUCINOUS (COLLOID) ADENOCARCINOMA | RECTAL ADENOCARCINOMA | RECTAL MUCINOUS ADENOCARCINOMA | SEROUS CYSTADENOCARCINOMA | SEROUS ENDOMETRIAL ADENOCARCINOMA | TREATED PRIMARY GBM | UNTREATED PRIMARY (DE NOVO) GBM
--- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | ---
ALL | 356 | 54 | 350 | 319 | 493 | 10 | 75 | 205 | 7 | 3 | 15 | 2 | 3 | 2 | 13 | 1 | 1 | 1 | 2 | 315 | 18 | 7 | 143 | 13 | 552 | 79 | 1 | 20
DEL PEAK 43(18Q21.2) MUTATED | 245 | 14 | 29 | 168 | 97 | 4 | 38 | 110 | 1 | 1 | 7 | 2 | 2 | 1 | 4 | 1 | 0 | 0 | 1 | 130 | 5 | 4 | 126 | 12 | 332 | 33 | 0 | 5
DEL PEAK 43(18Q21.2) WILD-TYPE | 111 | 40 | 321 | 151 | 396 | 6 | 37 | 95 | 6 | 2 | 8 | 0 | 1 | 1 | 9 | 0 | 1 | 1 | 1 | 185 | 13 | 3 | 17 | 1 | 220 | 46 | 1 | 15

Figure S479. Get High-res Image Clustering Approach #83: 'Del Peak 43(18q21.2) mutation analysis' versus Clinical Feature #6: 'HISTOLOGICAL.TYPE'

'Del Peak 43(18q21.2) mutation analysis' versus 'PATHOLOGY.T'

P value = 3.15e-24 (Fisher's exact test), Q value = 5.1e-21

Table S563. Clustering Approach #83: 'Del Peak 43(18q21.2) mutation analysis' versus Clinical Feature #7: 'PATHOLOGY.T'

nPatients | T0+T1 | T2 | T3 | T4
--- | --- | --- | --- | ---
ALL | 466 | 632 | 694 | 209
DEL PEAK 43(18Q21.2) MUTATED | 128 | 310 | 394 | 122
DEL PEAK 43(18Q21.2) WILD-TYPE | 338 | 322 | 300 | 87

Figure S480. Get High-res Image Clustering Approach #83: 'Del Peak 43(18q21.2) mutation analysis' versus Clinical Feature #7: 'PATHOLOGY.T'

'Del Peak 43(18q21.2) mutation analysis' versus 'PATHOLOGY.N'

P value = 2.33e-10 (Fisher's exact test), Q value = 3.5e-07

Table S564. Clustering Approach #83: 'Del Peak 43(18q21.2) mutation analysis' versus Clinical Feature #8: 'PATHOLOGY.N'

nPatients | N0 | N1 | N2 | N3
--- | --- | --- | --- | ---
ALL | 1067 | 353 | 282 | 11
DEL PEAK 43(18Q21.2) MUTATED | 485 | 216 | 180 | 5
DEL PEAK 43(18Q21.2) WILD-TYPE | 582 | 137 | 102 | 6

Figure S481. Get High-res Image Clustering Approach #83: 'Del Peak 43(18q21.2) mutation analysis' versus Clinical Feature #8: 'PATHOLOGY.N'

'Del Peak 43(18q21.2) mutation analysis' versus 'PATHOLOGICSPREAD(M)'

P value = 1.36e-06 (Chi-square test), Q value = 0.0019

Table S565. Clustering Approach #83: 'Del Peak 43(18q21.2) mutation analysis' versus Clinical Feature #9: 'PATHOLOGICSPREAD(M)'

nPatients | M0 | M1 | M1A | M1B | MX
--- | --- | --- | --- | --- | ---
ALL | 1424 | 168 | 9 | 3 | 165
DEL PEAK 43(18Q21.2) MUTATED | 618 | 100 | 8 | 1 | 96
DEL PEAK 43(18Q21.2) WILD-TYPE | 806 | 68 | 1 | 2 | 69

Figure S482. Get High-res Image Clustering Approach #83: 'Del Peak 43(18q21.2) mutation analysis' versus Clinical Feature #9: 'PATHOLOGICSPREAD(M)'

'Del Peak 43(18q21.2) mutation analysis' versus 'TUMOR.STAGE'

P value = 4.15e-17 (Fisher's exact test), Q value = 6.5e-14

Table S566. Clustering Approach #83: 'Del Peak 43(18q21.2) mutation analysis' versus Clinical Feature #10: 'TUMOR.STAGE'

nPatients | I | II | III | IV
--- | --- | --- | --- | ---
ALL | 712 | 498 | 881 | 423
DEL PEAK 43(18Q21.2) MUTATED | 260 | 266 | 479 | 255
DEL PEAK 43(18Q21.2) WILD-TYPE | 452 | 232 | 402 | 168

Figure S483. Get High-res Image Clustering Approach #83: 'Del Peak 43(18q21.2) mutation analysis' versus Clinical Feature #10: 'TUMOR.STAGE'

'Del Peak 43(18q21.2) mutation analysis' versus 'RADIATIONS.RADIATION.REGIMENINDICATION'

P value = 3.94e-26 (Fisher's exact test), Q value = 6.4e-23

Table S567. Clustering Approach #83: 'Del Peak 43(18q21.2) mutation analysis' versus Clinical Feature #11: 'RADIATIONS.RADIATION.REGIMENINDICATION'

nPatients | NO | YES
--- | --- | ---
ALL | 826 | 3737
DEL PEAK 43(18Q21.2) MUTATED | 191 | 1586
DEL PEAK 43(18Q21.2) WILD-TYPE | 635 | 2151

Figure S484. Get High-res Image Clustering Approach #83: 'Del Peak 43(18q21.2) mutation analysis' versus Clinical Feature #11: 'RADIATIONS.RADIATION.REGIMENINDICATION'

Clustering Approach #84: 'Del Peak 44(18q23) mutation analysis'

Table S568. Description of clustering approach #84: 'Del Peak 44(18q23) mutation analysis'

Cluster Labels | DEL PEAK 44(18Q23) MUTATED | DEL PEAK 44(18Q23) WILD-TYPE
--- | --- | ---
Number of samples | 1834 | 2729

'Del Peak 44(18q23) mutation analysis' versus 'PRIMARY.SITE.OF.DISEASE'

P value = 3.55e-162 (Chi-square test), Q value = 6.3e-159

Table S569. Clustering Approach #84: 'Del Peak 44(18q23) mutation analysis' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'

nPatients | BLADDER | BRAIN | BREAST | COLON | ENDOMETRIAL | HEAD/NECK | KIDNEY | LUNG | OMENTUM | OVARY | PERITONEUM (OVARY) | RECTUM
--- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | ---
ALL | 125 | 544 | 846 | 412 | 447 | 319 | 493 | 662 | 2 | 548 | 2 | 159
DEL PEAK 44(18Q23) MUTATED | 55 | 73 | 278 | 258 | 73 | 179 | 101 | 317 | 1 | 360 | 0 | 136
DEL PEAK 44(18Q23) WILD-TYPE | 70 | 471 | 568 | 154 | 374 | 140 | 392 | 345 | 1 | 188 | 2 | 23

Figure S485. Get High-res Image Clustering Approach #84: 'Del Peak 44(18q23) mutation analysis' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'

'Del Peak 44(18q23) mutation analysis' versus 'HISTOLOGICAL.TYPE'

P value = 8.86e-116 (Chi-square test), Q value = 1.6e-112

Table S570. Clustering Approach #84: 'Del Peak 44(18q23) mutation analysis' versus Clinical Feature #6: 'HISTOLOGICAL.TYPE'

nPatients | COLON ADENOCARCINOMA | COLON MUCINOUS ADENOCARCINOMA | ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA | HEAD & NECK SQUAMOUS CELL CARCINOMA | KIDNEY CLEAR CELL RENAL CARCINOMA | LUNG ACINAR ADENOCARCINOMA | LUNG ADENOCARCINOMA MIXED SUBTYPE | LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS) | LUNG BASALOID SQUAMOUS CELL CARCINOMA | LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS | LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS | LUNG CLEAR CELL ADENOCARCINOMA | LUNG MICROPAPILLARY ADENOCARCINOMA | LUNG MUCINOUS ADENOCARCINOMA | LUNG PAPILLARY ADENOCARCINOMA | LUNG PAPILLARY SQUAMOUS CELL CARCINOMA | LUNG PAPILLARY SQUAMOUS CELL CARICNOMA | LUNG SMALL CELL SQUAMOUS CELL CARCINOMA | LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA | LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS) | MIXED SEROUS AND ENDOMETRIOID | MUCINOUS (COLLOID) ADENOCARCINOMA | RECTAL ADENOCARCINOMA | RECTAL MUCINOUS ADENOCARCINOMA | SEROUS CYSTADENOCARCINOMA | SEROUS ENDOMETRIAL ADENOCARCINOMA | TREATED PRIMARY GBM | UNTREATED PRIMARY (DE NOVO) GBM
--- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | ---
ALL | 356 | 54 | 350 | 319 | 493 | 10 | 75 | 205 | 7 | 3 | 15 | 2 | 3 | 2 | 13 | 1 | 1 | 1 | 2 | 315 | 18 | 7 | 143 | 13 | 552 | 79 | 1 | 20
DEL PEAK 44(18Q23) MUTATED | 244 | 13 | 30 | 179 | 101 | 5 | 38 | 104 | 1 | 1 | 7 | 2 | 2 | 1 | 3 | 1 | 0 | 0 | 0 | 148 | 5 | 4 | 124 | 11 | 361 | 38 | 0 | 5
DEL PEAK 44(18Q23) WILD-TYPE | 112 | 41 | 320 | 140 | 392 | 5 | 37 | 101 | 6 | 2 | 8 | 0 | 1 | 1 | 10 | 0 | 1 | 1 | 2 | 167 | 13 | 3 | 19 | 2 | 191 | 41 | 1 | 15

Figure S486. Get High-res Image Clustering Approach #84: 'Del Peak 44(18q23) mutation analysis' versus Clinical Feature #6: 'HISTOLOGICAL.TYPE'

'Del Peak 44(18q23) mutation analysis' versus 'PATHOLOGY.T'

P value = 4.49e-23 (Fisher's exact test), Q value = 7.2e-20

Table S571. Clustering Approach #84: 'Del Peak 44(18q23) mutation analysis' versus Clinical Feature #7: 'PATHOLOGY.T'

nPatients | T0+T1 | T2 | T3 | T4
--- | --- | --- | --- | ---
ALL | 466 | 632 | 694 | 209
DEL PEAK 44(18Q23) MUTATED | 136 | 311 | 399 | 127
DEL PEAK 44(18Q23) WILD-TYPE | 330 | 321 | 295 | 82

Figure S487. Get High-res Image Clustering Approach #84: 'Del Peak 44(18q23) mutation analysis' versus Clinical Feature #7: 'PATHOLOGY.T'

'Del Peak 44(18q23) mutation analysis' versus 'PATHOLOGY.N'

P value = 3.7e-10 (Fisher's exact test), Q value = 5.6e-07

Table S572. Clustering Approach #84: 'Del Peak 44(18q23) mutation analysis' versus Clinical Feature #8: 'PATHOLOGY.N'

nPatients | N0 | N1 | N2 | N3
--- | --- | --- | --- | ---
ALL | 1067 | 353 | 282 | 11
DEL PEAK 44(18Q23) MUTATED | 495 | 213 | 186 | 6
DEL PEAK 44(18Q23) WILD-TYPE | 572 | 140 | 96 | 5

Figure S488. Get High-res Image Clustering Approach #84: 'Del Peak 44(18q23) mutation analysis' versus Clinical Feature #8: 'PATHOLOGY.N'

'Del Peak 44(18q23) mutation analysis' versus 'PATHOLOGICSPREAD(M)'

P value = 7.29e-05 (Chi-square test), Q value = 0.097

Table S573. Clustering Approach #84: 'Del Peak 44(18q23) mutation analysis' versus Clinical Feature #9: 'PATHOLOGICSPREAD(M)'

nPatients | M0 | M1 | M1A | M1B | MX
--- | --- | --- | --- | --- | ---
ALL | 1424 | 168 | 9 | 3 | 165
DEL PEAK 44(18Q23) MUTATED | 635 | 97 | 8 | 1 | 94
DEL PEAK 44(18Q23) WILD-TYPE | 789 | 71 | 1 | 2 | 71

Figure S489. Get High-res Image Clustering Approach #84: 'Del Peak 44(18q23) mutation analysis' versus Clinical Feature #9: 'PATHOLOGICSPREAD(M)'

'Del Peak 44(18q23) mutation analysis' versus 'TUMOR.STAGE'

P value = 1.51e-19 (Fisher's exact test), Q value = 2.4e-16

Table S574. Clustering Approach #84: 'Del Peak 44(18q23) mutation analysis' versus Clinical Feature #10: 'TUMOR.STAGE'

nPatients | I | II | III | IV
--- | --- | --- | --- | ---
ALL | 712 | 498 | 881 | 423
DEL PEAK 44(18Q23) MUTATED | 266 | 268 | 515 | 258
DEL PEAK 44(18Q23) WILD-TYPE | 446 | 230 | 366 | 165

Figure S490. Get High-res Image Clustering Approach #84: 'Del Peak 44(18q23) mutation analysis' versus Clinical Feature #10: 'TUMOR.STAGE'

'Del Peak 44(18q23) mutation analysis' versus 'RADIATIONS.RADIATION.REGIMENINDICATION'

P value = 9.54e-25 (Fisher's exact test), Q value = 1.5e-21

Table S575. Clustering Approach #84: 'Del Peak 44(18q23) mutation analysis' versus Clinical Feature #11: 'RADIATIONS.RADIATION.REGIMENINDICATION'

nPatients | NO | YES
--- | --- | ---
ALL | 826 | 3737
DEL PEAK 44(18Q23) MUTATED | 204 | 1630
DEL PEAK 44(18Q23) WILD-TYPE | 622 | 2107

Figure S491. Get High-res Image Clustering Approach #84: 'Del Peak 44(18q23) mutation analysis' versus Clinical Feature #11: 'RADIATIONS.RADIATION.REGIMENINDICATION'

Clustering Approach #85: 'Del Peak 45(19p13.3) mutation analysis'

Table S576. Description of clustering approach #85: 'Del Peak 45(19p13.3) mutation analysis'

Cluster Labels | DEL PEAK 45(19P13.3) MUTATED | DEL PEAK 45(19P13.3) WILD-TYPE
--- | --- | ---
Number of samples | 1511 | 3052

'Del Peak 45(19p13.3) mutation analysis' versus 'PRIMARY.SITE.OF.DISEASE'

P value = 1.3e-268 (Chi-square test), Q value = 2.4e-265

Table S577. Clustering Approach #85: 'Del Peak 45(19p13.3) mutation analysis' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'

nPatients | BLADDER | BRAIN | BREAST | COLON | ENDOMETRIAL | HEAD/NECK | KIDNEY | LUNG | OMENTUM | OVARY | PERITONEUM (OVARY) | RECTUM
--- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | ---
ALL | 125 | 544 | 846 | 412 | 447 | 319 | 493 | 662 | 2 | 548 | 2 | 159
DEL PEAK 45(19P13.3) MUTATED | 47 | 36 | 293 | 56 | 106 | 107 | 18 | 331 | 2 | 478 | 2 | 34
DEL PEAK 45(19P13.3) WILD-TYPE | 78 | 508 | 553 | 356 | 341 | 212 | 475 | 331 | 0 | 70 | 0 | 125

Figure S492. Get High-res Image Clustering Approach #85: 'Del Peak 45(19p13.3) mutation analysis' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'

'Del Peak 45(19p13.3) mutation analysis' versus 'GENDER'

P value = 1.38e-24 (Fisher's exact test), Q value = 2.2e-21

Table S578. Clustering Approach #85: 'Del Peak 45(19p13.3) mutation analysis' versus Clinical Feature #4: 'GENDER'

nPatients | FEMALE | MALE
--- | --- | ---
ALL | 2881 | 1682
DEL PEAK 45(19P13.3) MUTATED | 1109 | 402
DEL PEAK 45(19P13.3) WILD-TYPE | 1772 | 1280

Figure S493. Get High-res Image Clustering Approach #85: 'Del Peak 45(19p13.3) mutation analysis' versus Clinical Feature #4: 'GENDER'

'Del Peak 45(19p13.3) mutation analysis' versus 'HISTOLOGICAL.TYPE'

P value = 4.58e-237 (Chi-square test), Q value = 8.3e-234

Table S579. Clustering Approach #85: 'Del Peak 45(19p13.3) mutation analysis' versus Clinical Feature #6: 'HISTOLOGICAL.TYPE'

nPatients | COLON ADENOCARCINOMA | COLON MUCINOUS ADENOCARCINOMA | ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA | HEAD & NECK SQUAMOUS CELL CARCINOMA | KIDNEY CLEAR CELL RENAL CARCINOMA | LUNG ACINAR ADENOCARCINOMA | LUNG ADENOCARCINOMA MIXED SUBTYPE | LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS) | LUNG BASALOID SQUAMOUS CELL CARCINOMA | LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS | LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS | LUNG CLEAR CELL ADENOCARCINOMA | LUNG MICROPAPILLARY ADENOCARCINOMA | LUNG MUCINOUS ADENOCARCINOMA | LUNG PAPILLARY ADENOCARCINOMA | LUNG PAPILLARY SQUAMOUS CELL CARCINOMA | LUNG PAPILLARY SQUAMOUS CELL CARICNOMA | LUNG SMALL CELL SQUAMOUS CELL CARCINOMA | LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA | LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS) | MIXED SEROUS AND ENDOMETRIOID | MUCINOUS (COLLOID) ADENOCARCINOMA | RECTAL ADENOCARCINOMA | RECTAL MUCINOUS ADENOCARCINOMA | SEROUS CYSTADENOCARCINOMA | SEROUS ENDOMETRIAL ADENOCARCINOMA | TREATED PRIMARY GBM | UNTREATED PRIMARY (DE NOVO) GBM
--- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | ---
ALL | 356 | 54 | 350 | 319 | 493 | 10 | 75 | 205 | 7 | 3 | 15 | 2 | 3 | 2 | 13 | 1 | 1 | 1 | 2 | 315 | 18 | 7 | 143 | 13 | 552 | 79 | 1 | 20
DEL PEAK 45(19P13.3) MUTATED | 51 | 4 | 35 | 107 | 18 | 4 | 45 | 109 | 3 | 0 | 8 | 1 | 3 | 1 | 8 | 1 | 0 | 1 | 2 | 143 | 7 | 2 | 31 | 2 | 482 | 64 | 0 | 1
DEL PEAK 45(19P13.3) WILD-TYPE | 305 | 50 | 315 | 212 | 475 | 6 | 30 | 96 | 4 | 3 | 7 | 1 | 0 | 1 | 5 | 0 | 1 | 0 | 0 | 172 | 11 | 5 | 112 | 11 | 70 | 15 | 1 | 19

Figure S494. Get High-res Image Clustering Approach #85: 'Del Peak 45(19p13.3) mutation analysis' versus Clinical Feature #6: 'HISTOLOGICAL.TYPE'

'Del Peak 45(19p13.3) mutation analysis' versus 'PATHOLOGY.T'

P value = 1.31e-17 (Fisher's exact test), Q value = 2.1e-14

Table S580. Clustering Approach #85: 'Del Peak 45(19p13.3) mutation analysis' versus Clinical Feature #7: 'PATHOLOGY.T'

nPatients | T0+T1 | T2 | T3 | T4
--- | --- | --- | --- | ---
ALL | 466 | 632 | 694 | 209
DEL PEAK 45(19P13.3) MUTATED | 93 | 243 | 130 | 70
DEL PEAK 45(19P13.3) WILD-TYPE | 373 | 389 | 564 | 139

Figure S495. Get High-res Image Clustering Approach #85: 'Del Peak 45(19p13.3) mutation analysis' versus Clinical Feature #7: 'PATHOLOGY.T'

'Del Peak 45(19p13.3) mutation analysis' versus 'PATHOLOGY.N'

P value = 1.11e-05 (Fisher's exact test), Q value = 0.015

Table S581. Clustering Approach #85: 'Del Peak 45(19p13.3) mutation analysis' versus Clinical Feature #8: 'PATHOLOGY.N'

nPatients | N0 | N1 | N2 | N3
--- | --- | --- | --- | ---
ALL | 1067 | 353 | 282 | 11
DEL PEAK 45(19P13.3) MUTATED | 275 | 119 | 112 | 5
DEL PEAK 45(19P13.3) WILD-TYPE | 792 | 234 | 170 | 6

Figure S496. Get High-res Image Clustering Approach #85: 'Del Peak 45(19p13.3) mutation analysis' versus Clinical Feature #8: 'PATHOLOGY.N'

'Del Peak 45(19p13.3) mutation analysis' versus 'TUMOR.STAGE'

P value = 1.59e-41 (Fisher's exact test), Q value = 2.6e-38

Table S582. Clustering Approach #85: 'Del Peak 45(19p13.3) mutation analysis' versus Clinical Feature #10: 'TUMOR.STAGE'

nPatients | I | II | III | IV
--- | --- | --- | --- | ---
ALL | 712 | 498 | 881 | 423
DEL PEAK 45(19P13.3) MUTATED | 193 | 141 | 508 | 167
DEL PEAK 45(19P13.3) WILD-TYPE | 519 | 357 | 373 | 256

Figure S497. Get High-res Image Clustering Approach #85: 'Del Peak 45(19p13.3) mutation analysis' versus Clinical Feature #10: 'TUMOR.STAGE'

'Del Peak 45(19p13.3) mutation analysis' versus 'RADIATIONS.RADIATION.REGIMENINDICATION'

P value = 6.69e-19 (Fisher's exact test), Q value = 1.1e-15

Table S583. Clustering Approach #85: 'Del Peak 45(19p13.3) mutation analysis' versus Clinical Feature #11: 'RADIATIONS.RADIATION.REGIMENINDICATION'

nPatients | NO | YES
--- | --- | ---
ALL | 826 | 3737
DEL PEAK 45(19P13.3) MUTATED | 168 | 1343
DEL PEAK 45(19P13.3) WILD-TYPE | 658 | 2394

Figure S498. Get High-res Image Clustering Approach #85: 'Del Peak 45(19p13.3) mutation analysis' versus Clinical Feature #11: 'RADIATIONS.RADIATION.REGIMENINDICATION'

Clustering Approach #86: 'Del Peak 46(19q13.32) mutation analysis'

Table S584. Description of clustering approach #86: 'Del Peak 46(19q13.32) mutation analysis'

Cluster Labels | DEL PEAK 46(19Q13.32) MUTATED | DEL PEAK 46(19Q13.32) WILD-TYPE
--- | --- | ---
Number of samples | 968 | 3595

'Del Peak 46(19q13.32) mutation analysis' versus 'PRIMARY.SITE.OF.DISEASE'

P value = 1.15e-114 (Chi-square test), Q value = 2e-111

Table S585. Clustering Approach #86: 'Del Peak 46(19q13.32) mutation analysis' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'

nPatients | BLADDER | BRAIN | BREAST | COLON | ENDOMETRIAL | HEAD/NECK | KIDNEY | LUNG | OMENTUM | OVARY | PERITONEUM (OVARY) | RECTUM
--- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | ---
ALL | 125 | 544 | 846 | 412 | 447 | 319 | 493 | 662 | 2 | 548 | 2 | 159
DEL PEAK 46(19Q13.32) MUTATED | 14 | 96 | 174 | 43 | 44 | 61 | 7 | 218 | 1 | 286 | 1 | 22
DEL PEAK 46(19Q13.32) WILD-TYPE | 111 | 448 | 672 | 369 | 403 | 258 | 486 | 444 | 1 | 262 | 1 | 137

Figure S499. Get High-res Image Clustering Approach #86: 'Del Peak 46(19q13.32) mutation analysis' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'

'Del Peak 46(19q13.32) mutation analysis' versus 'GENDER'

P value = 1.42e-07 (Fisher's exact test), Q value = 0.00021

Table S586. Clustering Approach #86: 'Del Peak 46(19q13.32) mutation analysis' versus Clinical Feature #4: 'GENDER'

nPatients | FEMALE | MALE
--- | --- | ---
ALL | 2881 | 1682
DEL PEAK 46(19Q13.32) MUTATED | 681 | 287
DEL PEAK 46(19Q13.32) WILD-TYPE | 2200 | 1395

Figure S500. Get High-res Image Clustering Approach #86: 'Del Peak 46(19q13.32) mutation analysis' versus Clinical Feature #4: 'GENDER'

'Del Peak 46(19q13.32) mutation analysis' versus 'HISTOLOGICAL.TYPE'

P value = 3.8e-108 (Chi-square test), Q value = 6.6e-105

Table S587. Clustering Approach #86: 'Del Peak 46(19q13.32) mutation analysis' versus Clinical Feature #6: 'HISTOLOGICAL.TYPE'

nPatients | COLON ADENOCARCINOMA | COLON MUCINOUS ADENOCARCINOMA | ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA | HEAD & NECK SQUAMOUS CELL CARCINOMA | KIDNEY CLEAR CELL RENAL CARCINOMA | LUNG ACINAR ADENOCARCINOMA | LUNG ADENOCARCINOMA MIXED SUBTYPE | LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS) | LUNG BASALOID SQUAMOUS CELL CARCINOMA | LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS | LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS | LUNG CLEAR CELL ADENOCARCINOMA | LUNG MICROPAPILLARY ADENOCARCINOMA | LUNG MUCINOUS ADENOCARCINOMA | LUNG PAPILLARY ADENOCARCINOMA | LUNG PAPILLARY SQUAMOUS CELL CARCINOMA | LUNG PAPILLARY SQUAMOUS CELL CARICNOMA | LUNG SMALL CELL SQUAMOUS CELL CARCINOMA | LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA | LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS) | MIXED SEROUS AND ENDOMETRIOID | MUCINOUS (COLLOID) ADENOCARCINOMA | RECTAL ADENOCARCINOMA | RECTAL MUCINOUS ADENOCARCINOMA | SEROUS CYSTADENOCARCINOMA | SEROUS ENDOMETRIAL ADENOCARCINOMA | TREATED PRIMARY GBM | UNTREATED PRIMARY (DE NOVO) GBM
--- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | ---
ALL | 356 | 54 | 350 | 319 | 493 | 10 | 75 | 205 | 7 | 3 | 15 | 2 | 3 | 2 | 13 | 1 | 1 | 1 | 2 | 315 | 18 | 7 | 143 | 13 | 552 | 79 | 1 | 20
DEL PEAK 46(19Q13.32) MUTATED | 37 | 5 | 15 | 61 | 7 | 3 | 32 | 73 | 4 | 0 | 5 | 1 | 1 | 0 | 8 | 1 | 0 | 0 | 2 | 87 | 5 | 1 | 20 | 1 | 288 | 24 | 0 | 5
DEL PEAK 46(19Q13.32) WILD-TYPE | 319 | 49 | 335 | 258 | 486 | 7 | 43 | 132 | 3 | 3 | 10 | 1 | 2 | 2 | 5 | 0 | 1 | 1 | 0 | 228 | 13 | 6 | 123 | 12 | 264 | 55 | 1 | 15

Figure S501. Get High-res Image Clustering Approach #86: 'Del Peak 46(19q13.32) mutation analysis' versus Clinical Feature #6: 'HISTOLOGICAL.TYPE'

'Del Peak 46(19q13.32) mutation analysis' versus 'PATHOLOGY.T'

P value = 7.12e-07 (Fisher's exact test), Q value = 0.001

Table S588. Clustering Approach #86: 'Del Peak 46(19q13.32) mutation analysis' versus Clinical Feature #7: 'PATHOLOGY.T'

nPatients | T0+T1 | T2 | T3 | T4
--- | --- | --- | --- | ---
ALL | 466 | 632 | 694 | 209
DEL PEAK 46(19Q13.32) MUTATED | 59 | 151 | 96 | 38
DEL PEAK 46(19Q13.32) WILD-TYPE | 407 | 481 | 598 | 171

Figure S502. Get High-res Image Clustering Approach #86: 'Del Peak 46(19q13.32) mutation analysis' versus Clinical Feature #7: 'PATHOLOGY.T'

'Del Peak 46(19q13.32) mutation analysis' versus 'TUMOR.STAGE'

P value = 2.06e-19 (Fisher's exact test), Q value = 3.3e-16

Table S589. Clustering Approach #86: 'Del Peak 46(19q13.32) mutation analysis' versus Clinical Feature #10: 'TUMOR.STAGE'

nPatients | I | II | III | IV
--- | --- | --- | --- | ---
ALL | 712 | 498 | 881 | 423
DEL PEAK 46(19Q13.32) MUTATED | 128 | 91 | 318 | 88
DEL PEAK 46(19Q13.32) WILD-TYPE | 584 | 407 | 563 | 335

Figure S503. Get High-res Image Clustering Approach #86: 'Del Peak 46(19q13.32) mutation analysis' versus Clinical Feature #10: 'TUMOR.STAGE'

Clustering Approach #87: 'Del Peak 47(19q13.43) mutation analysis'

Table S590. Description of clustering approach #87: 'Del Peak 47(19q13.43) mutation analysis'

Cluster Labels | DEL PEAK 47(19Q13.43) MUTATED | DEL PEAK 47(19Q13.43) WILD-TYPE
--- | --- | ---
Number of samples | 884 | 3679

'Del Peak 47(19q13.43) mutation analysis' versus 'PRIMARY.SITE.OF.DISEASE'

P value = 1.25e-103 (Chi-square test), Q value = 2.2e-100

Table S591. Clustering Approach #87: 'Del Peak 47(19q13.43) mutation analysis' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'

nPatients | BLADDER | BRAIN | BREAST | COLON | ENDOMETRIAL | HEAD/NECK | KIDNEY | LUNG | OMENTUM | OVARY | PERITONEUM (OVARY) | RECTUM
--- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | ---
ALL | 125 | 544 | 846 | 412 | 447 | 319 | 493 | 662 | 2 | 548 | 2 | 159
DEL PEAK 47(19Q13.43) MUTATED | 13 | 82 | 144 | 42 | 46 | 63 | 5 | 194 | 1 | 267 | 1 | 25
DEL PEAK 47(19Q13.43) WILD-TYPE | 112 | 462 | 702 | 370 | 401 | 256 | 488 | 468 | 1 | 281 | 1 | 134

Figure S504. Get High-res Image Clustering Approach #87: 'Del Peak 47(19q13.43) mutation analysis' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'

'Del Peak 47(19q13.43) mutation analysis' versus 'GENDER'

P value = 4.29e-07 (Fisher's exact test), Q value = 0.00062

Table S592. Clustering Approach #87: 'Del Peak 47(19q13.43) mutation analysis' versus Clinical Feature #4: 'GENDER'

nPatients | FEMALE | MALE
--- | --- | ---
ALL | 2881 | 1682
DEL PEAK 47(19Q13.43) MUTATED | 623 | 261
DEL PEAK 47(19Q13.43) WILD-TYPE | 2258 | 1421

Figure S505. Get High-res Image Clustering Approach #87: 'Del Peak 47(19q13.43) mutation analysis' versus Clinical Feature #4: 'GENDER'

'Del Peak 47(19q13.43) mutation analysis' versus 'HISTOLOGICAL.TYPE'

P value = 1.91e-95 (Chi-square test), Q value = 3.3e-92

Table S593. Clustering Approach #87: 'Del Peak 47(19q13.43) mutation analysis' versus Clinical Feature #6: 'HISTOLOGICAL.TYPE'

nPatients | COLON ADENOCARCINOMA | COLON MUCINOUS ADENOCARCINOMA | ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA | HEAD & NECK SQUAMOUS CELL CARCINOMA | KIDNEY CLEAR CELL RENAL CARCINOMA | LUNG ACINAR ADENOCARCINOMA | LUNG ADENOCARCINOMA MIXED SUBTYPE | LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS) | LUNG BASALOID SQUAMOUS CELL CARCINOMA | LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS | LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS | LUNG CLEAR CELL ADENOCARCINOMA | LUNG MICROPAPILLARY ADENOCARCINOMA | LUNG MUCINOUS ADENOCARCINOMA | LUNG PAPILLARY ADENOCARCINOMA | LUNG PAPILLARY SQUAMOUS CELL CARCINOMA | LUNG PAPILLARY SQUAMOUS CELL CARICNOMA | LUNG SMALL CELL SQUAMOUS CELL CARCINOMA | LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA | LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS) | MIXED SEROUS AND ENDOMETRIOID | MUCINOUS (COLLOID) ADENOCARCINOMA | RECTAL ADENOCARCINOMA | RECTAL MUCINOUS ADENOCARCINOMA | SEROUS CYSTADENOCARCINOMA | SEROUS ENDOMETRIAL ADENOCARCINOMA | TREATED PRIMARY GBM | UNTREATED PRIMARY (DE NOVO) GBM
--- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | ---
ALL | 356 | 54 | 350 | 319 | 493 | 10 | 75 | 205 | 7 | 3 | 15 | 2 | 3 | 2 | 13 | 1 | 1 | 1 | 2 | 315 | 18 | 7 | 143 | 13 | 552 | 79 | 1 | 20
DEL PEAK 47(19Q13.43) MUTATED | 36 | 5 | 13 | 63 | 5 | 3 | 29 | 63 | 4 | 0 | 5 | 0 | 2 | 0 | 6 | 1 | 0 | 0 | 1 | 79 | 4 | 1 | 23 | 1 | 269 | 29 | 0 | 6
DEL PEAK 47(19Q13.43) WILD-TYPE | 320 | 49 | 337 | 256 | 488 | 7 | 46 | 142 | 3 | 3 | 10 | 2 | 1 | 2 | 7 | 0 | 1 | 1 | 1 | 236 | 14 | 6 | 120 | 12 | 283 | 50 | 1 | 14

Figure S506. Get High-res Image Clustering Approach #87: 'Del Peak 47(19q13.43) mutation analysis' versus Clinical Feature #6: 'HISTOLOGICAL.TYPE'

'Del Peak 47(19q13.43) mutation analysis' versus 'PATHOLOGY.T'

P value = 2.7e-06 (Fisher's exact test), Q value = 0.0038

Table S594. Clustering Approach #87: 'Del Peak 47(19q13.43) mutation analysis' versus Clinical Feature #7: 'PATHOLOGY.T'

nPatients | T0+T1 | T2 | T3 | T4
--- | --- | --- | --- | ---
ALL | 466 | 632 | 694 | 209
DEL PEAK 47(19Q13.43) MUTATED | 50 | 136 | 95 | 41
DEL PEAK 47(19Q13.43) WILD-TYPE | 416 | 496 | 599 | 168

Figure S507. Get High-res Image Clustering Approach #87: 'Del Peak 47(19q13.43) mutation analysis' versus Clinical Feature #7: 'PATHOLOGY.T'

'Del Peak 47(19q13.43) mutation analysis' versus 'TUMOR.STAGE'

P value = 8.42e-17 (Fisher's exact test), Q value = 1.3e-13

Table S595. Clustering Approach #87: 'Del Peak 47(19q13.43) mutation analysis' versus Clinical Feature #10: 'TUMOR.STAGE'

nPatients | I | II | III | IV
--- | --- | --- | --- | ---
ALL | 712 | 498 | 881 | 423
DEL PEAK 47(19Q13.43) MUTATED | 112 | 90 | 292 | 89
DEL PEAK 47(19Q13.43) WILD-TYPE | 600 | 408 | 589 | 334

Figure S508. Get High-res Image Clustering Approach #87: 'Del Peak 47(19q13.43) mutation analysis' versus Clinical Feature #10: 'TUMOR.STAGE'

Clustering Approach #88: 'Del Peak 48(20p12.1) mutation analysis'

Table S596. Description of clustering approach #88: 'Del Peak 48(20p12.1) mutation analysis'

Cluster Labels | DEL PEAK 48(20P12.1) MUTATED | DEL PEAK 48(20P12.1) WILD-TYPE
--- | --- | ---
Number of samples | 512 | 4051

'Del Peak 48(20p12.1) mutation analysis' versus 'PRIMARY.SITE.OF.DISEASE'

P value = 6.45e-36 (Chi-square test), Q value = 1.1e-32

Table S597. Clustering Approach #88: 'Del Peak 48(20p12.1) mutation analysis' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'

nPatients | BLADDER | BRAIN | BREAST | COLON | ENDOMETRIAL | HEAD/NECK | KIDNEY | LUNG | OMENTUM | OVARY | PERITONEUM (OVARY) | RECTUM
--- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | ---
ALL | 125 | 544 | 846 | 412 | 447 | 319 | 493 | 662 | 2 | 548 | 2 | 159
DEL PEAK 48(20P12.1) MUTATED | 8 | 18 | 103 | 79 | 25 | 45 | 9 | 110 | 0 | 68 | 0 | 46
DEL PEAK 48(20P12.1) WILD-TYPE | 117 | 526 | 743 | 333 | 422 | 274 | 484 | 552 | 2 | 480 | 2 | 113

Figure S509. Get High-res Image Clustering Approach #88: 'Del Peak 48(20p12.1) mutation analysis' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'

'Del Peak 48(20p12.1) mutation analysis' versus 'HISTOLOGICAL.TYPE'

P value = 1.04e-29 (Chi-square test), Q value = 1.7e-26

Table S598. Clustering Approach #88: 'Del Peak 48(20p12.1) mutation analysis' versus Clinical Feature #6: 'HISTOLOGICAL.TYPE'

nPatients | COLON ADENOCARCINOMA | COLON MUCINOUS ADENOCARCINOMA | ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA | HEAD & NECK SQUAMOUS CELL CARCINOMA | KIDNEY CLEAR CELL RENAL CARCINOMA | LUNG ACINAR ADENOCARCINOMA | LUNG ADENOCARCINOMA MIXED SUBTYPE | LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS) | LUNG BASALOID SQUAMOUS CELL CARCINOMA | LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS | LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS | LUNG CLEAR CELL ADENOCARCINOMA | LUNG MICROPAPILLARY ADENOCARCINOMA | LUNG MUCINOUS ADENOCARCINOMA | LUNG PAPILLARY ADENOCARCINOMA | LUNG PAPILLARY SQUAMOUS CELL CARCINOMA | LUNG PAPILLARY SQUAMOUS CELL CARICNOMA | LUNG SMALL CELL SQUAMOUS CELL CARCINOMA | LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA | LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS) | MIXED SEROUS AND ENDOMETRIOID | MUCINOUS (COLLOID) ADENOCARCINOMA | RECTAL ADENOCARCINOMA | RECTAL MUCINOUS ADENOCARCINOMA | SEROUS CYSTADENOCARCINOMA | SEROUS ENDOMETRIAL ADENOCARCINOMA | TREATED PRIMARY GBM | UNTREATED PRIMARY (DE NOVO) GBM
--- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | ---
ALL | 356 | 54 | 350 | 319 | 493 | 10 | 75 | 205 | 7 | 3 | 15 | 2 | 3 | 2 | 13 | 1 | 1 | 1 | 2 | 315 | 18 | 7 | 143 | 13 | 552 | 79 | 1 | 20
DEL PEAK 48(20P12.1) MUTATED | 73 | 6 | 12 | 45 | 9 | 2 | 20 | 47 | 0 | 0 | 4 | 2 | 1 | 0 | 2 | 0 | 0 | 0 | 1 | 29 | 2 | 2 | 41 | 5 | 68 | 11 | 0 | 0
DEL PEAK 48(20P12.1) WILD-TYPE | 283 | 48 | 338 | 274 | 484 | 8 | 55 | 158 | 7 | 3 | 11 | 0 | 2 | 2 | 11 | 1 | 1 | 1 | 1 | 286 | 16 | 5 | 102 | 8 | 484 | 68 | 1 | 20

Figure S510. Get High-res Image Clustering Approach #88: 'Del Peak 48(20p12.1) mutation analysis' versus Clinical Feature #6: 'HISTOLOGICAL.TYPE'

'Del Peak 48(20p12.1) mutation analysis' versus 'RADIATIONS.RADIATION.REGIMENINDICATION'

P value = 2.44e-05 (Fisher's exact test), Q value = 0.033

Table S599. Clustering Approach #88: 'Del Peak 48(20p12.1) mutation analysis' versus Clinical Feature #11: 'RADIATIONS.RADIATION.REGIMENINDICATION'

nPatients | NO | YES
--- | --- | ---
ALL | 826 | 3737
DEL PEAK 48(20P12.1) MUTATED | 59 | 453
DEL PEAK 48(20P12.1) WILD-TYPE | 767 | 3284

Figure S511. Get High-res Image Clustering Approach #88: 'Del Peak 48(20p12.1) mutation analysis' versus Clinical Feature #11: 'RADIATIONS.RADIATION.REGIMENINDICATION'

Clustering Approach #89: 'Del Peak 49(21q11.2) mutation analysis'

Table S600. Description of clustering approach #89: 'Del Peak 49(21q11.2) mutation analysis'

Cluster Labels | DEL PEAK 49(21Q11.2) MUTATED | DEL PEAK 49(21Q11.2) WILD-TYPE
--- | --- | ---
Number of samples | 1107 | 3456

'Del Peak 49(21q11.2) mutation analysis' versus 'PRIMARY.SITE.OF.DISEASE'

P value = 3.01e-68 (Chi-square test), Q value = 5.1e-65

Table S601. Clustering Approach #89: 'Del Peak 49(21q11.2) mutation analysis' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'

nPatients | BLADDER | BRAIN | BREAST | COLON | ENDOMETRIAL | HEAD/NECK | KIDNEY | LUNG | OMENTUM | OVARY | PERITONEUM (OVARY) | RECTUM
--- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | ---
ALL | 125 | 544 | 846 | 412 | 447 | 319 | 493 | 662 | 2 | 548 | 2 | 159
DEL PEAK 49(21Q11.2) MUTATED | 21 | 53 | 172 | 124 | 50 | 105 | 54 | 275 | 2 | 180 | 0 | 68
DEL PEAK 49(21Q11.2) WILD-TYPE | 104 | 491 | 674 | 288 | 397 | 214 | 439 | 387 | 0 | 368 | 2 | 91

Figure S512. Get High-res Image Clustering Approach #89: 'Del Peak 49(21q11.2) mutation analysis' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'

'Del Peak 49(21q11.2) mutation analysis' versus 'HISTOLOGICAL.TYPE'

P value = 5.01e-47 (Chi-square test), Q value = 8.3e-44

Table S602. Clustering Approach #89: 'Del Peak 49(21q11.2) mutation analysis' versus Clinical Feature #6: 'HISTOLOGICAL.TYPE'

nPatients | COLON ADENOCARCINOMA | COLON MUCINOUS ADENOCARCINOMA | ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA | HEAD & NECK SQUAMOUS CELL CARCINOMA | KIDNEY CLEAR CELL RENAL CARCINOMA | LUNG ACINAR ADENOCARCINOMA | LUNG ADENOCARCINOMA MIXED SUBTYPE | LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS) | LUNG BASALOID SQUAMOUS CELL CARCINOMA | LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS | LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS | LUNG CLEAR CELL ADENOCARCINOMA | LUNG MICROPAPILLARY ADENOCARCINOMA | LUNG MUCINOUS ADENOCARCINOMA | LUNG PAPILLARY ADENOCARCINOMA | LUNG PAPILLARY SQUAMOUS CELL CARCINOMA | LUNG PAPILLARY SQUAMOUS CELL CARICNOMA | LUNG SMALL CELL SQUAMOUS CELL CARCINOMA | LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA | LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS) | MIXED SEROUS AND ENDOMETRIOID | MUCINOUS (COLLOID) ADENOCARCINOMA | RECTAL ADENOCARCINOMA | RECTAL MUCINOUS ADENOCARCINOMA | SEROUS CYSTADENOCARCINOMA | SEROUS ENDOMETRIAL ADENOCARCINOMA | TREATED PRIMARY GBM | UNTREATED PRIMARY (DE NOVO) GBM
--- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | ---
ALL | 356 | 54 | 350 | 319 | 493 | 10 | 75 | 205 | 7 | 3 | 15 | 2 | 3 | 2 | 13 | 1 | 1 | 1 | 2 | 315 | 18 | 7 | 143 | 13 | 552 | 79 | 1 | 20
DEL PEAK 49(21Q11.2) MUTATED | 115 | 8 | 17 | 105 | 54 | 6 | 23 | 74 | 3 | 0 | 5 | 0 | 1 | 0 | 6 | 1 | 0 | 1 | 0 | 152 | 5 | 3 | 63 | 3 | 182 | 28 | 0 | 2
DEL PEAK 49(21Q11.2) WILD-TYPE | 241 | 46 | 333 | 214 | 439 | 4 | 52 | 131 | 4 | 3 | 10 | 2 | 2 | 2 | 7 | 0 | 1 | 0 | 2 | 163 | 13 | 4 | 80 | 10 | 370 | 51 | 1 | 18

Figure S513. Get High-res Image Clustering Approach #89: 'Del Peak 49(21q11.2) mutation analysis' versus Clinical Feature #6: 'HISTOLOGICAL.TYPE'

'Del Peak 49(21q11.2) mutation analysis' versus 'PATHOLOGY.T'

P value = 5.18e-06 (Fisher's exact test), Q value = 0.0073

Table S603. Clustering Approach #89: 'Del Peak 49(21q11.2) mutation analysis' versus Clinical Feature #7: 'PATHOLOGY.T'

nPatients | T0+T1 | T2 | T3 | T4
--- | --- | --- | --- | ---
ALL | 466 | 632 | 694 | 209
DEL PEAK 49(21Q11.2) MUTATED | 107 | 231 | 204 | 76
DEL PEAK 49(21Q11.2) WILD-TYPE | 359 | 401 | 490 | 133

Figure S514. Get High-res Image Clustering Approach #89: 'Del Peak 49(21q11.2) mutation analysis' versus Clinical Feature #7: 'PATHOLOGY.T'

'Del Peak 49(21q11.2) mutation analysis' versus 'RADIATIONS.RADIATION.REGIMENINDICATION'

P value = 3.58e-11 (Fisher's exact test), Q value = 5.5e-08

Table S604. Clustering Approach #89: 'Del Peak 49(21q11.2) mutation analysis' versus Clinical Feature #11: 'RADIATIONS.RADIATION.REGIMENINDICATION'

nPatients | NO | YES
--- | --- | ---
ALL | 826 | 3737
DEL PEAK 49(21Q11.2) MUTATED | 129 | 978
DEL PEAK 49(21Q11.2) WILD-TYPE | 697 | 2759

Figure S515. Get High-res Image Clustering Approach #89: 'Del Peak 49(21q11.2) mutation analysis' versus Clinical Feature #11: 'RADIATIONS.RADIATION.REGIMENINDICATION'

'Del Peak 49(21q11.2) mutation analysis' versus 'TOBACCOSMOKINGHISTORYINDICATOR'

P value = 0.000113 (Chi-square test), Q value = 0.15

Table S605. Clustering Approach #89: 'Del Peak 49(21q11.2) mutation analysis' versus Clinical Feature #14: 'TOBACCOSMOKINGHISTORYINDICATOR'

nPatients | 1 | 2 | 3 | 4 | 5 | CURRENT REFORMED SMOKER FOR < OR = 15 YEARS | CURRENT REFORMED SMOKER FOR > 15 YEARS | CURRENT SMOKER | LIFELONG NON-SMOKER
--- | --- | --- | --- | --- | --- | --- | --- | --- | ---
ALL | 28 | 23 | 37 | 29 | 2 | 355 | 217 | 250 | 128
DEL PEAK 49(21Q11.2) MUTATED | 2 | 2 | 8 | 7 | 0 | 150 | 76 | 99 | 43
DEL PEAK 49(21Q11.2) WILD-TYPE | 26 | 21 | 29 | 22 | 2 | 205 | 141 | 151 | 85

Figure S516. Get High-res Image Clustering Approach #89: 'Del Peak 49(21q11.2) mutation analysis' versus Clinical Feature #14: 'TOBACCOSMOKINGHISTORYINDICATOR'

Clustering Approach #90: 'Del Peak 50(22q13.32) mutation analysis'

Table S606. Description of clustering approach #90: 'Del Peak 50(22q13.32) mutation analysis'

Cluster Labels | DEL PEAK 50(22Q13.32) MUTATED | DEL PEAK 50(22Q13.32) WILD-TYPE
--- | --- | ---
Number of samples | 1768 | 2795

'Del Peak 50(22q13.32) mutation analysis' versus 'Time to Death'

P value = 0.000113 (logrank test), Q value = 0.15

Table S607. Clustering Approach #90: 'Del Peak 50(22q13.32) mutation analysis' versus Clinical Feature #1: 'Time to Death'

| nPatients | nDeath | Duration Range (Median), Month
--- | --- | --- | ---
ALL | 4296 | 1401 | 0.0 - 224.0 (14.9)
DEL PEAK 50(22Q13.32) MUTATED | 1652 | 604 | 0.0 - 224.0 (15.1)
DEL PEAK 50(22Q13.32) WILD-TYPE | 2644 | 797 | 0.0 - 223.4 (14.4)

Figure S517. Get High-res Image Clustering Approach #90: 'Del Peak 50(22q13.32) mutation analysis' versus Clinical Feature #1: 'Time to Death'

'Del Peak 50(22q13.32) mutation analysis' versus 'PRIMARY.SITE.OF.DISEASE'

P value = 3.08e-173 (Chi-square test), Q value = 5.5e-170

Table S608. Clustering Approach #90: 'Del Peak 50(22q13.32) mutation analysis' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'

nPatients | BLADDER | BRAIN | BREAST | COLON | ENDOMETRIAL | HEAD/NECK | KIDNEY | LUNG | OMENTUM | OVARY | PERITONEUM (OVARY) | RECTUM
--- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | ---
ALL | 125 | 544 | 846 | 412 | 447 | 319 | 493 | 662 | 2 | 548 | 2 | 159
DEL PEAK 50(22Q13.32) MUTATED | 49 | 206 | 378 | 143 | 106 | 63 | 37 | 242 | 2 | 474 | 1 | 63
DEL PEAK 50(22Q13.32) WILD-TYPE | 76 | 338 | 468 | 269 | 341 | 256 | 456 | 420 | 0 | 74 | 1 | 96

Figure S518. Get High-res Image Clustering Approach #90: 'Del Peak 50(22q13.32) mutation analysis' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'

'Del Peak 50(22q13.32) mutation analysis' versus 'GENDER'

P value = 1.14e-27 (Fisher's exact test), Q value = 1.8e-24

Table S609. Clustering Approach #90: 'Del Peak 50(22q13.32) mutation analysis' versus Clinical Feature #4: 'GENDER'

nPatients | FEMALE | MALE
--- | --- | ---
ALL | 2881 | 1682
DEL PEAK 50(22Q13.32) MUTATED | 1288 | 480
DEL PEAK 50(22Q13.32) WILD-TYPE | 1593 | 1202

Figure S519. Get High-res Image Clustering Approach #90: 'Del Peak 50(22q13.32) mutation analysis' versus Clinical Feature #4: 'GENDER'

'Del Peak 50(22q13.32) mutation analysis' versus 'HISTOLOGICAL.TYPE'

P value = 1.36e-190 (Chi-square test), Q value = 2.4e-187

Table S610. Clustering Approach #90: 'Del Peak 50(22q13.32) mutation analysis' versus Clinical Feature #6: 'HISTOLOGICAL.TYPE'

nPatients | COLON ADENOCARCINOMA | COLON MUCINOUS ADENOCARCINOMA | ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA | HEAD & NECK SQUAMOUS CELL CARCINOMA | KIDNEY CLEAR CELL RENAL CARCINOMA | LUNG ACINAR ADENOCARCINOMA | LUNG ADENOCARCINOMA MIXED SUBTYPE | LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS) | LUNG BASALOID SQUAMOUS CELL CARCINOMA | LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS | LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS | LUNG CLEAR CELL ADENOCARCINOMA | LUNG MICROPAPILLARY ADENOCARCINOMA | LUNG MUCINOUS ADENOCARCINOMA | LUNG PAPILLARY ADENOCARCINOMA | LUNG PAPILLARY SQUAMOUS CELL CARCINOMA | LUNG PAPILLARY SQUAMOUS CELL CARICNOMA | LUNG SMALL CELL SQUAMOUS CELL CARCINOMA | LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA | LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS) | MIXED SEROUS AND ENDOMETRIOID | MUCINOUS (COLLOID) ADENOCARCINOMA | RECTAL ADENOCARCINOMA | RECTAL MUCINOUS ADENOCARCINOMA | SEROUS CYSTADENOCARCINOMA | SEROUS ENDOMETRIAL ADENOCARCINOMA | TREATED PRIMARY GBM | UNTREATED PRIMARY (DE NOVO) GBM
--- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | ---
ALL | 356 | 54 | 350 | 319 | 493 | 10 | 75 | 205 | 7 | 3 | 15 | 2 | 3 | 2 | 13 | 1 | 1 | 1 | 2 | 315 | 18 | 7 | 143 | 13 | 552 | 79 | 1 | 20
DEL PEAK 50(22Q13.32) MUTATED | 133 | 10 | 48 | 63 | 37 | 5 | 32 | 106 | 4 | 1 | 10 | 0 | 2 | 0 | 7 | 1 | 0 | 1 | 2 | 70 | 8 | 1 | 59 | 4 | 477 | 50 | 0 | 9
DEL PEAK 50(22Q13.32) WILD-TYPE | 223 | 44 | 302 | 256 | 456 | 5 | 43 | 99 | 3 | 2 | 5 | 2 | 1 | 2 | 6 | 0 | 1 | 0 | 0 | 245 | 10 | 6 | 84 | 9 | 75 | 29 | 1 | 11

Figure S520. Get High-res Image Clustering Approach #90: 'Del Peak 50(22q13.32) mutation analysis' versus Clinical Feature #6: 'HISTOLOGICAL.TYPE'

'Del Peak 50(22q13.32) mutation analysis' versus 'PATHOLOGICSPREAD(M)'

P value = 0.000141 (Chi-square test), Q value = 0.18

Table S611. Clustering Approach #90: 'Del Peak 50(22q13.32) mutation analysis' versus Clinical Feature #9: 'PATHOLOGICSPREAD(M)'

nPatients | M0 | M1 | M1A | M1B | MX
--- | --- | --- | --- | --- | ---
ALL | 1424 | 168 | 9 | 3 | 165
DEL PEAK 50(22Q13.32) MUTATED | 361 | 59 | 2 | 3 | 60
DEL PEAK 50(22Q13.32) WILD-TYPE | 1063 | 109 | 7 | 0 | 105

Figure S521. Get High-res Image Clustering Approach #90: 'Del Peak 50(22q13.32) mutation analysis' versus Clinical Feature #9: 'PATHOLOGICSPREAD(M)'

'Del Peak 50(22q13.32) mutation analysis' versus 'TUMOR.STAGE'

P value = 1.3e-43 (Fisher's exact test), Q value = 2.2e-40

Table S612. Clustering Approach #90: 'Del Peak 50(22q13.32) mutation analysis' versus Clinical Feature #10: 'TUMOR.STAGE'

nPatients | I | II | III | IV
--- | --- | --- | --- | ---
ALL | 712 | 498 | 881 | 423
DEL PEAK 50(22Q13.32) MUTATED | 179 | 150 | 508 | 161
DEL PEAK 50(22Q13.32) WILD-TYPE | 533 | 348 | 373 | 262

Figure S522. Get High-res Image Clustering Approach #90: 'Del Peak 50(22q13.32) mutation analysis' versus Clinical Feature #10: 'TUMOR.STAGE'

'Del Peak 50(22q13.32) mutation analysis' versus 'COMPLETENESS.OF.RESECTION'

P value = 8.1e-05 (Fisher's exact test), Q value = 0.11

Table S613. Clustering Approach #90: 'Del Peak 50(22q13.32) mutation analysis' versus Clinical Feature #18: 'COMPLETENESS.OF.RESECTION'

nPatients | R0 | R1 | R2 | RX
--- | --- | --- | --- | ---
ALL | 1171 | 69 | 59 | 77
DEL PEAK 50(22Q13.32) MUTATED | 377 | 41 | 23 | 29
DEL PEAK 50(22Q13.32) WILD-TYPE | 794 | 28 | 36 | 48

Figure S523. Get High-res Image Clustering Approach #90: 'Del Peak 50(22q13.32) mutation analysis' versus Clinical Feature #18: 'COMPLETENESS.OF.RESECTION'

Clustering Approach #91: 'Del Peak 51(Xp21.1) mutation analysis'

Table S614. Description of clustering approach #91: 'Del Peak 51(Xp21.1) mutation analysis'

Cluster Labels | DEL PEAK 51(XP21.1) MUTATED | DEL PEAK 51(XP21.1) WILD-TYPE
--- | --- | ---
Number of samples | 1181 | 3382

'Del Peak 51(Xp21.1) mutation analysis' versus 'Time to Death'

P value = 1.62e-05 (logrank test), Q value = 0.022

Table S615. Clustering Approach #91: 'Del Peak 51(Xp21.1) mutation analysis' versus Clinical Feature #1: 'Time to Death'

| nPatients | nDeath | Duration Range (Median), Month
--- | --- | --- | ---
ALL | 4296 | 1401 | 0.0 - 224.0 (14.9)
DEL PEAK 51(XP21.1) MUTATED | 1112 | 439 | 0.0 - 173.8 (17.0)
DEL PEAK 51(XP21.1) WILD-TYPE | 3184 | 962 | 0.0 - 224.0 (14.1)

Figure S524. Get High-res Image Clustering Approach #91: 'Del Peak 51(Xp21.1) mutation analysis' versus Clinical Feature #1: 'Time to Death'

'Del Peak 51(Xp21.1) mutation analysis' versus 'PRIMARY.SITE.OF.DISEASE'

P value = 2.08e-114 (Chi-square test), Q value = 3.6e-111

Table S616. Clustering Approach #91: 'Del Peak 51(Xp21.1) mutation analysis' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'

nPatients | BLADDER | BRAIN | BREAST | COLON | ENDOMETRIAL | HEAD/NECK | KIDNEY | LUNG | OMENTUM | OVARY | PERITONEUM (OVARY) | RECTUM
--- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | ---
ALL | 125 | 544 | 846 | 412 | 447 | 319 | 493 | 662 | 2 | 548 | 2 | 159
DEL PEAK 51(XP21.1) MUTATED | 33 | 121 | 173 | 63 | 62 | 103 | 51 | 193 | 1 | 350 | 1 | 28
DEL PEAK 51(XP21.1) WILD-TYPE | 92 | 423 | 673 | 349 | 385 | 216 | 442 | 469 | 1 | 198 | 1 | 131

Figure S525. Get High-res Image Clustering Approach #91: 'Del Peak 51(Xp21.1) mutation analysis' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'

'Del Peak 51(Xp21.1) mutation analysis' versus 'HISTOLOGICAL.TYPE'

P value = 2.13e-103 (Chi-square test), Q value = 3.7e-100

Table S617. Clustering Approach #91: 'Del Peak 51(Xp21.1) mutation analysis' versus Clinical Feature #6: 'HISTOLOGICAL.TYPE'

nPatients | COLON ADENOCARCINOMA | COLON MUCINOUS ADENOCARCINOMA | ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA | HEAD & NECK SQUAMOUS CELL CARCINOMA | KIDNEY CLEAR CELL RENAL CARCINOMA | LUNG ACINAR ADENOCARCINOMA | LUNG ADENOCARCINOMA MIXED SUBTYPE | LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS) | LUNG BASALOID SQUAMOUS CELL CARCINOMA | LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS | LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS | LUNG CLEAR CELL ADENOCARCINOMA | LUNG MICROPAPILLARY ADENOCARCINOMA | LUNG MUCINOUS ADENOCARCINOMA | LUNG PAPILLARY ADENOCARCINOMA | LUNG PAPILLARY SQUAMOUS CELL CARCINOMA | LUNG PAPILLARY SQUAMOUS CELL CARICNOMA | LUNG SMALL CELL SQUAMOUS CELL CARCINOMA | LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA | LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS) | MIXED SEROUS AND ENDOMETRIOID | MUCINOUS (COLLOID) ADENOCARCINOMA | RECTAL ADENOCARCINOMA | RECTAL MUCINOUS ADENOCARCINOMA | SEROUS CYSTADENOCARCINOMA | SEROUS ENDOMETRIAL ADENOCARCINOMA | TREATED PRIMARY GBM | UNTREATED PRIMARY (DE NOVO) GBM
--- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | ---
ALL | 356 | 54 | 350 | 319 | 493 | 10 | 75 | 205 | 7 | 3 | 15 | 2 | 3 | 2 | 13 | 1 | 1 | 1 | 2 | 315 | 18 | 7 | 143 | 13 | 552 | 79 | 1 | 20
DEL PEAK 51(XP21.1) MUTATED | 59 | 4 | 26 | 103 | 51 | 3 | 19 | 58 | 1 | 1 | 2 | 0 | 2 | 1 | 3 | 1 | 0 | 0 | 0 | 100 | 2 | 2 | 23 | 4 | 352 | 34 | 0 | 7
DEL PEAK 51(XP21.1) WILD-TYPE | 297 | 50 | 324 | 216 | 442 | 7 | 56 | 147 | 6 | 2 | 13 | 2 | 1 | 1 | 10 | 0 | 1 | 1 | 2 | 215 | 16 | 5 | 120 | 9 | 200 | 45 | 1 | 13

Figure S526. Get High-res Image Clustering Approach #91: 'Del Peak 51(Xp21.1) mutation analysis' versus Clinical Feature #6: 'HISTOLOGICAL.TYPE'

'Del Peak 51(Xp21.1) mutation analysis' versus 'TUMOR.STAGE'

P value = 1.74e-18 (Fisher's exact test), Q value = 2.7e-15

Table S618. Clustering Approach #91: 'Del Peak 51(Xp21.1) mutation analysis' versus Clinical Feature #10: 'TUMOR.STAGE'

nPatients | I | II | III | IV
--- | --- | --- | --- | ---
ALL | 712 | 498 | 881 | 423
DEL PEAK 51(XP21.1) MUTATED | 152 | 115 | 359 | 138
DEL PEAK 51(XP21.1) WILD-TYPE | 560 | 383 | 522 | 285

Figure S527. Get High-res Image Clustering Approach #91: 'Del Peak 51(Xp21.1) mutation analysis' versus Clinical Feature #10: 'TUMOR.STAGE'

Methods & Data
Input

- Cluster data file = all_lesions.conf_99.cnv.cluster.txt

- Clinical data file = PANCAN12-TP.clin.merged.picked.txt

- Number of patients = 4563

- Number of clustering approaches = 91

- Number of selected clinical features = 21

- Exclude small clusters that include fewer than K patients, K = 3

Survival analysis

For survival clinical features, the Kaplan-Meier survival curves of tumors with and without gene mutations were plotted and the statistical significance P values were estimated by logrank test (Bland and Altman 2004) using the 'survdiff' function in R

Student's t-test analysis

For continuous numerical clinical features, two-tailed Student's t test with unequal variance (Lehmann and Romano 2005) was applied to compare the clinical values between two tumor subtypes using 't.test' function in R

Chi-square test

For multi-class clinical features (nominal or ordinal), Chi-square tests (Greenwood and Nikulin 1996) were used to estimate the P values using the 'chisq.test' function in R

Fisher's exact test

For binary clinical features, two-tailed Fisher's exact tests (Fisher 1922) were used to estimate the P values using the 'fisher.test' function in R

Q value calculation

For multiple hypothesis correction, Q value is the False Discovery Rate (FDR) analogue of the P value (Benjamini and Hochberg 1995), defined as the minimum FDR at which the test may be called significant. We used the 'Benjamini and Hochberg' method of 'p.adjust' function in R to convert P values into Q values.

Download Results

This is an experimental feature. The full results of the analysis summarized in this report can be downloaded from the TCGA Data Coordination Center.

- Analysis Results (MD5 checksum)

- Auxiliary Data (MD5 checksum)

- MAGE-TAB File (MD5 checksum)

References
[1] Bland and Altman, Statistics notes: The logrank test, BMJ 328(7447):1073 (2004)
[2] Lehmann and Romano, Testing Statistical Hypotheses (3E ed.), New York: Springer. ISBN 0387988645 (2005)
[3] Greenwood and Nikulin, A guide to chi-squared testing, Wiley, New York. ISBN 047155779X (1996)
[4] Fisher, R.A., On the interpretation of chi-square from contingency tables, and the calculation of P, Journal of the Royal Statistical Society 85(1):87-94 (1922)
[5] Benjamini and Hochberg, Controlling the false discovery rate: a practical and powerful approach to multiple testing, Journal of the Royal Statistical Society Series B 59:289-300 (1995)
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