Correlation between copy number variation genes (focal) and selected clinical features
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.

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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