Correlation between copy number variation genes (focal) and selected clinical features
PANCANCER cohort with 12 disease types (Primary solid tumor)
21 April 2013 | analyses__2013_04_21
Maintainer Information
Citation Information
doi:10.7908/C13B5X49
Maintained by TCGA GDAC Team (Broad Institute/MD Anderson Cancer Center/Harvard Medical School)
Cite as Broad Institute TCGA Genome Data Analysis Center (2013): PANCANCER cohort with 12 disease types (Primary solid tumor cohort) - 21 April 2013: Correlation between copy number variation genes (focal) and selected clinical features. Broad Institute of MIT and Harvard. doi:10.7908/C13B5X49
Overview
Introduction

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

Summary

Testing the association between copy number variation 92 arm-level results and 20 clinical features across 4651 patients, 515 significant findings detected with Q value < 0.25.

- Amp Peak 1(1p34.2) cnv correlated to 'PRIMARY.SITE.OF.DISEASE', 'GENDER', 'HISTOLOGICAL.TYPE', 'PATHOLOGY.T', and 'TUMOR.STAGE'.

- Amp Peak 2(1p22.3) cnv correlated to 'PRIMARY.SITE.OF.DISEASE', 'GENDER', 'HISTOLOGICAL.TYPE', 'PATHOLOGY.T', and 'TUMOR.STAGE'.

- Amp Peak 3(1q21.3) cnv correlated to 'Time to Death', 'PRIMARY.SITE.OF.DISEASE', 'GENDER', 'HISTOLOGICAL.TYPE', 'PATHOLOGY.T', 'PATHOLOGICSPREAD(M)', and 'TUMOR.STAGE'.

- Amp Peak 4(1q32.1) cnv correlated to 'Time to Death', 'PRIMARY.SITE.OF.DISEASE', 'GENDER', 'HISTOLOGICAL.TYPE', 'PATHOLOGY.T', and 'NEOPLASM.DISEASESTAGE'.

- Amp Peak 5(1q44) cnv correlated to 'Time to Death', 'PRIMARY.SITE.OF.DISEASE', 'GENDER', 'HISTOLOGICAL.TYPE', 'PATHOLOGY.T', and 'PATHOLOGY.N'.

- Amp Peak 6(2p15) cnv correlated to 'AGE', 'PRIMARY.SITE.OF.DISEASE', 'HISTOLOGICAL.TYPE', 'TUMOR.STAGE', and 'RADIATIONS.RADIATION.REGIMENINDICATION'.

- Amp Peak 7(2q31.2) cnv correlated to 'AGE', 'PRIMARY.SITE.OF.DISEASE', 'HISTOLOGICAL.TYPE', 'TUMOR.STAGE', and 'RADIATIONS.RADIATION.REGIMENINDICATION'.

- Amp Peak 8(3q26.2) cnv correlated to 'PRIMARY.SITE.OF.DISEASE', 'KARNOFSKY.PERFORMANCE.SCORE', 'HISTOLOGICAL.TYPE', 'PATHOLOGY.T', 'PATHOLOGY.N', 'TUMOR.STAGE', 'RADIATIONS.RADIATION.REGIMENINDICATION', and 'NUMBERPACKYEARSSMOKED'.

- Amp Peak 9(4p16.3) cnv correlated to 'PRIMARY.SITE.OF.DISEASE', 'GENDER', 'HISTOLOGICAL.TYPE', 'PATHOLOGY.T', 'TUMOR.STAGE', and 'NEOPLASM.DISEASESTAGE'.

- Amp Peak 10(4q12) cnv correlated to 'Time to Death', 'PRIMARY.SITE.OF.DISEASE', 'HISTOLOGICAL.TYPE', and 'PATHOLOGY.T'.

- Amp Peak 11(5p15.33) cnv correlated to 'AGE', 'PRIMARY.SITE.OF.DISEASE', 'KARNOFSKY.PERFORMANCE.SCORE', 'HISTOLOGICAL.TYPE', 'PATHOLOGY.T', 'TUMOR.STAGE', and 'RADIATIONS.RADIATION.REGIMENINDICATION'.

- Amp Peak 12(5q35.3) cnv correlated to 'Time to Death', 'PRIMARY.SITE.OF.DISEASE', 'HISTOLOGICAL.TYPE', 'PATHOLOGY.T', 'PATHOLOGY.N', 'TUMOR.STAGE', and 'RADIATIONS.RADIATION.REGIMENINDICATION'.

- Amp Peak 13(6p22.3) cnv correlated to 'PRIMARY.SITE.OF.DISEASE', 'GENDER', 'HISTOLOGICAL.TYPE', 'PATHOLOGICSPREAD(M)', 'TUMOR.STAGE', and 'RADIATIONS.RADIATION.REGIMENINDICATION'.

- Amp Peak 14(6p21.1) cnv correlated to 'PRIMARY.SITE.OF.DISEASE', 'GENDER', 'HISTOLOGICAL.TYPE', 'TUMOR.STAGE', and 'RADIATIONS.RADIATION.REGIMENINDICATION'.

- Amp Peak 15(6q21) cnv correlated to 'PRIMARY.SITE.OF.DISEASE', 'GENDER', and 'HISTOLOGICAL.TYPE'.

- Amp Peak 16(7p11.2) cnv correlated to 'Time to Death', 'PRIMARY.SITE.OF.DISEASE', 'GENDER', 'HISTOLOGICAL.TYPE', 'PATHOLOGY.T', 'PATHOLOGY.N', and 'RADIATIONS.RADIATION.REGIMENINDICATION'.

- Amp Peak 17(7q21.2) cnv correlated to 'Time to Death', 'PRIMARY.SITE.OF.DISEASE', 'GENDER', 'HISTOLOGICAL.TYPE', and 'RADIATIONS.RADIATION.REGIMENINDICATION'.

- Amp Peak 18(7q36.3) cnv correlated to 'Time to Death', 'PRIMARY.SITE.OF.DISEASE', 'GENDER', 'HISTOLOGICAL.TYPE', 'TUMOR.STAGE', and 'RADIATIONS.RADIATION.REGIMENINDICATION'.

- Amp Peak 19(8p11.23) cnv correlated to 'PRIMARY.SITE.OF.DISEASE', 'HISTOLOGICAL.TYPE', 'PATHOLOGY.T', and 'RADIATIONS.RADIATION.REGIMENINDICATION'.

- Amp Peak 20(8p11.21) cnv correlated to 'AGE', 'PRIMARY.SITE.OF.DISEASE', 'HISTOLOGICAL.TYPE', 'PATHOLOGY.T', 'TUMOR.STAGE', and 'RADIATIONS.RADIATION.REGIMENINDICATION'.

- Amp Peak 21(8q24.21) cnv correlated to 'PRIMARY.SITE.OF.DISEASE', 'GENDER', 'KARNOFSKY.PERFORMANCE.SCORE', 'HISTOLOGICAL.TYPE', 'PATHOLOGY.T', 'PATHOLOGY.N', 'TUMOR.STAGE', and 'RADIATIONS.RADIATION.REGIMENINDICATION'.

- Amp Peak 22(9p13.3) cnv correlated to 'PRIMARY.SITE.OF.DISEASE', 'HISTOLOGICAL.TYPE', and 'PATHOLOGY.T'.

- Amp Peak 23(10p15.1) cnv correlated to 'PRIMARY.SITE.OF.DISEASE', 'GENDER', 'HISTOLOGICAL.TYPE', 'PATHOLOGY.T', 'TUMOR.STAGE', 'RADIATIONS.RADIATION.REGIMENINDICATION', and 'TOBACCOSMOKINGHISTORYINDICATOR'.

- Amp Peak 24(10q22.2) cnv correlated to 'PRIMARY.SITE.OF.DISEASE', 'GENDER', 'HISTOLOGICAL.TYPE', and 'TUMOR.STAGE'.

- Amp Peak 25(11q13.3) cnv correlated to 'PRIMARY.SITE.OF.DISEASE', 'GENDER', 'HISTOLOGICAL.TYPE', 'PATHOLOGY.T', 'PATHOLOGY.N', 'TUMOR.STAGE', and 'RADIATIONS.RADIATION.REGIMENINDICATION'.

- Amp Peak 26(12p13.33) cnv correlated to 'PRIMARY.SITE.OF.DISEASE', 'HISTOLOGICAL.TYPE', 'PATHOLOGY.T', 'TUMOR.STAGE', and 'RADIATIONS.RADIATION.REGIMENINDICATION'.

- Amp Peak 27(12p12.1) cnv correlated to 'PRIMARY.SITE.OF.DISEASE', 'HISTOLOGICAL.TYPE', 'PATHOLOGY.T', 'TUMOR.STAGE', and 'RADIATIONS.RADIATION.REGIMENINDICATION'.

- Amp Peak 28(12q14.1) cnv correlated to 'Time to Death', 'AGE', 'PRIMARY.SITE.OF.DISEASE', 'HISTOLOGICAL.TYPE', and 'TUMOR.STAGE'.

- Amp Peak 29(12q15) cnv correlated to 'AGE', 'PRIMARY.SITE.OF.DISEASE', 'HISTOLOGICAL.TYPE', and 'RADIATIONS.RADIATION.REGIMENINDICATION'.

- Amp Peak 30(13q34) cnv correlated to 'AGE', 'PRIMARY.SITE.OF.DISEASE', 'HISTOLOGICAL.TYPE', 'PATHOLOGY.T', 'PATHOLOGY.N', 'PATHOLOGICSPREAD(M)', 'TUMOR.STAGE', 'RADIATIONS.RADIATION.REGIMENINDICATION', 'TOBACCOSMOKINGHISTORYINDICATOR', and 'NEOPLASM.DISEASESTAGE'.

- Amp Peak 31(14q13.3) cnv correlated to 'PRIMARY.SITE.OF.DISEASE', 'HISTOLOGICAL.TYPE', 'PATHOLOGY.T', 'PATHOLOGICSPREAD(M)', and 'RADIATIONS.RADIATION.REGIMENINDICATION'.

- Amp Peak 32(15q26.3) cnv correlated to 'PRIMARY.SITE.OF.DISEASE', 'HISTOLOGICAL.TYPE', 'PATHOLOGY.T', and 'RADIATIONS.RADIATION.REGIMENINDICATION'.

- Amp Peak 33(17q12) cnv correlated to 'AGE', 'PRIMARY.SITE.OF.DISEASE', 'HISTOLOGICAL.TYPE', 'PATHOLOGY.T', and 'PATHOLOGICSPREAD(M)'.

- Amp Peak 34(17q25.3) cnv correlated to 'PRIMARY.SITE.OF.DISEASE', 'HISTOLOGICAL.TYPE', 'PATHOLOGY.T', 'PATHOLOGICSPREAD(M)', and 'RADIATIONS.RADIATION.REGIMENINDICATION'.

- Amp Peak 35(18q11.2) cnv correlated to 'PRIMARY.SITE.OF.DISEASE', 'HISTOLOGICAL.TYPE', and 'PATHOLOGY.T'.

- Amp Peak 36(19p13.2) cnv correlated to 'Time to Death', 'PRIMARY.SITE.OF.DISEASE', 'HISTOLOGICAL.TYPE', 'TUMOR.STAGE', and 'RADIATIONS.RADIATION.REGIMENINDICATION'.

- Amp Peak 37(19p13.12) cnv correlated to 'PRIMARY.SITE.OF.DISEASE', 'HISTOLOGICAL.TYPE', 'TUMOR.STAGE', and 'RADIATIONS.RADIATION.REGIMENINDICATION'.

- Amp Peak 38(19q12) cnv correlated to 'PRIMARY.SITE.OF.DISEASE', 'HISTOLOGICAL.TYPE', 'PATHOLOGY.T', and 'TUMOR.STAGE'.

- Amp Peak 39(20q11.21) cnv correlated to 'Time to Death', 'AGE', 'PRIMARY.SITE.OF.DISEASE', 'GENDER', 'HISTOLOGICAL.TYPE', 'PATHOLOGY.T', 'PATHOLOGY.N', 'TUMOR.STAGE', and 'RADIATIONS.RADIATION.REGIMENINDICATION'.

- Amp Peak 40(20q13.2) cnv correlated to 'AGE', 'PRIMARY.SITE.OF.DISEASE', 'HISTOLOGICAL.TYPE', 'PATHOLOGY.T', 'PATHOLOGICSPREAD(M)', 'TUMOR.STAGE', and 'RADIATIONS.RADIATION.REGIMENINDICATION'.

- Amp Peak 41(Xq28) cnv correlated to 'PRIMARY.SITE.OF.DISEASE', 'HISTOLOGICAL.TYPE', 'PATHOLOGY.T', 'PATHOLOGY.N', and 'TUMOR.STAGE'.

- Del Peak 1(1p36.23) cnv correlated to 'PRIMARY.SITE.OF.DISEASE' and 'HISTOLOGICAL.TYPE'.

- Del Peak 2(1p36.11) cnv correlated to 'PRIMARY.SITE.OF.DISEASE', 'HISTOLOGICAL.TYPE', 'TUMOR.STAGE', 'RADIATIONS.RADIATION.REGIMENINDICATION', 'TOBACCOSMOKINGHISTORYINDICATOR', 'NUMBER.OF.LYMPH.NODES', and 'NEOPLASM.DISEASESTAGE'.

- Del Peak 3(1p13.2) cnv correlated to 'AGE', 'PRIMARY.SITE.OF.DISEASE', 'HISTOLOGICAL.TYPE', 'RADIATIONS.RADIATION.REGIMENINDICATION', 'TOBACCOSMOKINGHISTORYINDICATOR', and 'NUMBER.OF.LYMPH.NODES'.

- Del Peak 4(2q22.1) cnv correlated to 'PRIMARY.SITE.OF.DISEASE', 'HISTOLOGICAL.TYPE', 'PATHOLOGY.T', and 'TUMOR.STAGE'.

- Del Peak 5(2q37.3) cnv correlated to 'PRIMARY.SITE.OF.DISEASE', 'HISTOLOGICAL.TYPE', and 'TOBACCOSMOKINGHISTORYINDICATOR'.

- Del Peak 6(3p25.3) cnv correlated to 'PRIMARY.SITE.OF.DISEASE', 'GENDER', 'HISTOLOGICAL.TYPE', 'PATHOLOGY.T', 'TUMOR.STAGE', 'RADIATIONS.RADIATION.REGIMENINDICATION', and 'TOBACCOSMOKINGHISTORYINDICATOR'.

- Del Peak 7(3p14.2) cnv correlated to 'PRIMARY.SITE.OF.DISEASE', 'GENDER', 'KARNOFSKY.PERFORMANCE.SCORE', 'HISTOLOGICAL.TYPE', 'PATHOLOGY.T', 'TUMOR.STAGE', 'RADIATIONS.RADIATION.REGIMENINDICATION', and 'TOBACCOSMOKINGHISTORYINDICATOR'.

- Del Peak 8(4p16.3) cnv correlated to 'PRIMARY.SITE.OF.DISEASE', 'HISTOLOGICAL.TYPE', 'PATHOLOGY.T', 'PATHOLOGY.N', 'TUMOR.STAGE', and 'RADIATIONS.RADIATION.REGIMENINDICATION'.

- Del Peak 9(4q22.1) cnv correlated to 'PRIMARY.SITE.OF.DISEASE', 'HISTOLOGICAL.TYPE', 'PATHOLOGY.T', 'TUMOR.STAGE', and 'RADIATIONS.RADIATION.REGIMENINDICATION'.

- Del Peak 10(4q34.3) cnv correlated to 'PRIMARY.SITE.OF.DISEASE', 'HISTOLOGICAL.TYPE', 'PATHOLOGY.T', 'TUMOR.STAGE', and 'RADIATIONS.RADIATION.REGIMENINDICATION'.

- Del Peak 11(5q11.2) cnv correlated to 'PRIMARY.SITE.OF.DISEASE', 'KARNOFSKY.PERFORMANCE.SCORE', 'HISTOLOGICAL.TYPE', 'PATHOLOGY.T', 'PATHOLOGY.N', 'TUMOR.STAGE', 'RADIATIONS.RADIATION.REGIMENINDICATION', 'NUMBERPACKYEARSSMOKED', 'TOBACCOSMOKINGHISTORYINDICATOR', and 'NEOPLASM.DISEASESTAGE'.

- Del Peak 12(5q21.3) cnv correlated to 'PRIMARY.SITE.OF.DISEASE', 'KARNOFSKY.PERFORMANCE.SCORE', 'HISTOLOGICAL.TYPE', 'PATHOLOGY.T', 'PATHOLOGY.N', 'PATHOLOGICSPREAD(M)', 'RADIATIONS.RADIATION.REGIMENINDICATION', 'TOBACCOSMOKINGHISTORYINDICATOR', and 'NEOPLASM.DISEASESTAGE'.

- Del Peak 13(6p25.3) cnv correlated to 'PRIMARY.SITE.OF.DISEASE', 'GENDER', and 'HISTOLOGICAL.TYPE'.

- Del Peak 14(6q22.31) cnv correlated to 'PRIMARY.SITE.OF.DISEASE', 'HISTOLOGICAL.TYPE', and 'TUMOR.STAGE'.

- Del Peak 15(6q26) cnv correlated to 'AGE', 'PRIMARY.SITE.OF.DISEASE', 'HISTOLOGICAL.TYPE', and 'TUMOR.STAGE'.

- Del Peak 16(7p22.3) cnv correlated to 'PRIMARY.SITE.OF.DISEASE', 'GENDER', 'HISTOLOGICAL.TYPE', 'PATHOLOGY.T', and 'TUMOR.STAGE'.

- Del Peak 17(7q36.1) cnv correlated to 'PRIMARY.SITE.OF.DISEASE', 'HISTOLOGICAL.TYPE', 'PATHOLOGY.T', and 'PATHOLOGICSPREAD(M)'.

- Del Peak 18(8p23.2) cnv correlated to 'PRIMARY.SITE.OF.DISEASE', 'KARNOFSKY.PERFORMANCE.SCORE', 'HISTOLOGICAL.TYPE', 'PATHOLOGY.T', 'PATHOLOGY.N', 'TUMOR.STAGE', and 'RADIATIONS.RADIATION.REGIMENINDICATION'.

- Del Peak 19(8p21.2) cnv correlated to 'PRIMARY.SITE.OF.DISEASE', 'GENDER', 'KARNOFSKY.PERFORMANCE.SCORE', 'HISTOLOGICAL.TYPE', 'PATHOLOGY.N', 'TUMOR.STAGE', and 'RADIATIONS.RADIATION.REGIMENINDICATION'.

- Del Peak 20(9p23) cnv correlated to 'Time to Death', 'PRIMARY.SITE.OF.DISEASE', 'GENDER', 'HISTOLOGICAL.TYPE', and 'PATHOLOGY.T'.

- Del Peak 21(9p21.3) cnv correlated to 'Time to Death', 'PRIMARY.SITE.OF.DISEASE', 'GENDER', 'HISTOLOGICAL.TYPE', 'PATHOLOGY.T', and 'RADIATIONS.RADIATION.REGIMENINDICATION'.

- Del Peak 22(9q21.11) cnv correlated to 'AGE', 'PRIMARY.SITE.OF.DISEASE', 'HISTOLOGICAL.TYPE', 'PATHOLOGY.T', 'TUMOR.STAGE', and 'RADIATIONS.RADIATION.REGIMENINDICATION'.

- Del Peak 23(9q34.13) cnv correlated to 'AGE', 'PRIMARY.SITE.OF.DISEASE', 'HISTOLOGICAL.TYPE', 'PATHOLOGY.T', 'TUMOR.STAGE', and 'RADIATIONS.RADIATION.REGIMENINDICATION'.

- Del Peak 24(9q34.3) cnv correlated to 'AGE', 'PRIMARY.SITE.OF.DISEASE', 'HISTOLOGICAL.TYPE', 'PATHOLOGY.T', 'TUMOR.STAGE', and 'RADIATIONS.RADIATION.REGIMENINDICATION'.

- Del Peak 25(10p15.3) cnv correlated to 'Time to Death', 'PRIMARY.SITE.OF.DISEASE', 'GENDER', 'HISTOLOGICAL.TYPE', 'PATHOLOGY.T', and 'RADIATIONS.RADIATION.REGIMENINDICATION'.

- Del Peak 26(10q23.31) cnv correlated to 'Time to Death', 'PRIMARY.SITE.OF.DISEASE', 'GENDER', 'HISTOLOGICAL.TYPE', 'RADIATIONS.RADIATION.REGIMENINDICATION', and 'YEAROFTOBACCOSMOKINGONSET'.

- Del Peak 27(10q26.3) cnv correlated to 'Time to Death', 'PRIMARY.SITE.OF.DISEASE', 'GENDER', 'HISTOLOGICAL.TYPE', and 'RADIATIONS.RADIATION.REGIMENINDICATION'.

- Del Peak 28(11p15.5) cnv correlated to 'PRIMARY.SITE.OF.DISEASE', 'HISTOLOGICAL.TYPE', 'PATHOLOGY.T', 'PATHOLOGY.N', and 'TUMOR.STAGE'.

- Del Peak 29(11q22.3) cnv correlated to 'PRIMARY.SITE.OF.DISEASE', 'HISTOLOGICAL.TYPE', 'PATHOLOGY.T', 'PATHOLOGY.N', and 'TUMOR.STAGE'.

- Del Peak 30(11q25) cnv correlated to 'PRIMARY.SITE.OF.DISEASE', 'GENDER', 'HISTOLOGICAL.TYPE', 'PATHOLOGY.T', 'PATHOLOGY.N', and 'TUMOR.STAGE'.

- Del Peak 31(12p13.1) cnv correlated to 'PRIMARY.SITE.OF.DISEASE', 'GENDER', and 'HISTOLOGICAL.TYPE'.

- Del Peak 32(12q23.1) cnv correlated to 'PRIMARY.SITE.OF.DISEASE', 'GENDER', 'HISTOLOGICAL.TYPE', 'PATHOLOGY.T', 'PATHOLOGICSPREAD(M)', and 'TUMOR.STAGE'.

- Del Peak 33(12q24.33) cnv correlated to 'PRIMARY.SITE.OF.DISEASE', 'GENDER', 'HISTOLOGICAL.TYPE', 'PATHOLOGY.T', and 'TUMOR.STAGE'.

- Del Peak 34(13q11) cnv correlated to 'PRIMARY.SITE.OF.DISEASE', 'HISTOLOGICAL.TYPE', 'PATHOLOGY.T', 'PATHOLOGICSPREAD(M)', 'TUMOR.STAGE', and 'TOBACCOSMOKINGHISTORYINDICATOR'.

- Del Peak 35(13q14.2) cnv correlated to 'Time to Death', 'PRIMARY.SITE.OF.DISEASE', 'HISTOLOGICAL.TYPE', 'PATHOLOGY.T', 'PATHOLOGICSPREAD(M)', and 'TUMOR.STAGE'.

- Del Peak 36(14q24.1) cnv correlated to 'PRIMARY.SITE.OF.DISEASE', 'HISTOLOGICAL.TYPE', 'PATHOLOGY.T', 'PATHOLOGY.N', and 'TUMOR.STAGE'.

- Del Peak 37(15q11.2) cnv correlated to 'PRIMARY.SITE.OF.DISEASE', 'GENDER', 'HISTOLOGICAL.TYPE', 'PATHOLOGY.T', 'PATHOLOGY.N', 'TUMOR.STAGE', and 'RADIATIONS.RADIATION.REGIMENINDICATION'.

- Del Peak 38(15q15.1) cnv correlated to 'PRIMARY.SITE.OF.DISEASE', 'GENDER', 'HISTOLOGICAL.TYPE', 'PATHOLOGY.T', 'PATHOLOGY.N', 'TUMOR.STAGE', and 'RADIATIONS.RADIATION.REGIMENINDICATION'.

- Del Peak 39(16p13.3) cnv correlated to 'Time to Death', 'PRIMARY.SITE.OF.DISEASE', 'HISTOLOGICAL.TYPE', 'TUMOR.STAGE', 'RADIATIONS.RADIATION.REGIMENINDICATION', and 'NEOPLASM.DISEASESTAGE'.

- Del Peak 40(16q23.1) cnv correlated to 'PRIMARY.SITE.OF.DISEASE', 'GENDER', 'HISTOLOGICAL.TYPE', 'PATHOLOGY.T', 'TUMOR.STAGE', and 'RADIATIONS.RADIATION.REGIMENINDICATION'.

- Del Peak 41(17p12) cnv correlated to 'PRIMARY.SITE.OF.DISEASE', 'GENDER', 'KARNOFSKY.PERFORMANCE.SCORE', 'HISTOLOGICAL.TYPE', 'PATHOLOGY.T', 'PATHOLOGY.N', 'TUMOR.STAGE', and 'RADIATIONS.RADIATION.REGIMENINDICATION'.

- Del Peak 42(17q11.2) cnv correlated to 'AGE', 'PRIMARY.SITE.OF.DISEASE', 'GENDER', 'HISTOLOGICAL.TYPE', 'TUMOR.STAGE', and 'RADIATIONS.RADIATION.REGIMENINDICATION'.

- Del Peak 43(18q21.2) cnv correlated to 'AGE', 'PRIMARY.SITE.OF.DISEASE', 'HISTOLOGICAL.TYPE', 'PATHOLOGY.T', 'PATHOLOGY.N', 'PATHOLOGICSPREAD(M)', 'TUMOR.STAGE', and 'RADIATIONS.RADIATION.REGIMENINDICATION'.

- Del Peak 44(18q23) cnv correlated to 'PRIMARY.SITE.OF.DISEASE', 'HISTOLOGICAL.TYPE', 'PATHOLOGY.T', 'PATHOLOGY.N', 'PATHOLOGICSPREAD(M)', 'TUMOR.STAGE', and 'RADIATIONS.RADIATION.REGIMENINDICATION'.

- Del Peak 45(19p13.3) cnv correlated to 'PRIMARY.SITE.OF.DISEASE', 'GENDER', 'HISTOLOGICAL.TYPE', 'PATHOLOGY.T', 'PATHOLOGY.N', 'TUMOR.STAGE', and 'RADIATIONS.RADIATION.REGIMENINDICATION'.

- Del Peak 46(19q13.32) cnv correlated to 'PRIMARY.SITE.OF.DISEASE', 'GENDER', 'HISTOLOGICAL.TYPE', 'PATHOLOGY.T', and 'TUMOR.STAGE'.

- Del Peak 47(19q13.43) cnv correlated to 'PRIMARY.SITE.OF.DISEASE', 'GENDER', 'HISTOLOGICAL.TYPE', 'PATHOLOGY.T', and 'TUMOR.STAGE'.

- Del Peak 48(20p12.1) cnv correlated to 'PRIMARY.SITE.OF.DISEASE', 'HISTOLOGICAL.TYPE', and 'RADIATIONS.RADIATION.REGIMENINDICATION'.

- Del Peak 49(21q11.2) cnv correlated to 'PRIMARY.SITE.OF.DISEASE', 'HISTOLOGICAL.TYPE', 'PATHOLOGY.T', 'PATHOLOGY.N', and 'RADIATIONS.RADIATION.REGIMENINDICATION'.

- Del Peak 50(22q13.32) cnv correlated to 'PRIMARY.SITE.OF.DISEASE', 'GENDER', 'HISTOLOGICAL.TYPE', 'PATHOLOGY.T', 'TUMOR.STAGE', and 'COMPLETENESS.OF.RESECTION'.

- Del Peak 51(Xp21.1) cnv correlated 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 significant copy number variation of 92 arm-level results and 20 clinical features. Shown in the table are P values (Q values). Thresholded by Q value < 0.25, 515 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 | TOBACCOSMOKINGHISTORYINDICATOR | YEAROFTOBACCOSMOKINGONSET | DISTANT METASTASIS | LYMPH NODE METASTASIS | COMPLETENESS OF RESECTION | NUMBER OF LYMPH NODES | TUMOR STAGECODE | NEOPLASM DISEASESTAGE
| nCNV (%) | nWild-Type | 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 | 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 30(13q34) | 0 (0%) | 3687 | 0.676 (1.00) | 5.94e-06 (0.00794) | 3.58e-172 (6.15e-169) | 0.115 (1.00) | 0.192 (1.00) | 3.68e-134 (6.26e-131) | 5.87e-27 (9.03e-24) | 5.81e-08 (8.09e-05) | 3.46e-05 (0.0444) | 9.81e-11 (1.42e-07) | 2.15e-15 (3.19e-12) | 0.257 (1.00) | 9.51e-08 (0.000132) | 0.167 (1.00) | 0.332 (1.00) | 0.00635 (1.00) | 0.00176 (1.00) | 0.607 (1.00) |  | 2.86e-06 (0.00384)
Del Peak 11(5q11 2) | 0 (0%) | 3247 | 0.705 (1.00) | 0.0591 (1.00) | 5.24e-169 (8.99e-166) | 0.643 (1.00) | 8.31e-05 (0.105) | 1.1e-150 (1.87e-147) | 3.14e-17 (4.71e-14) | 2.66e-05 (0.0344) | 0.00177 (1.00) | 4.37e-06 (0.00584) | 9.91e-14 (1.46e-10) | 6.24e-06 (0.00833) | 5.67e-05 (0.0722) | 0.36 (1.00) | 0.156 (1.00) | 0.0205 (1.00) | 0.21 (1.00) | 0.0757 (1.00) |  | 2.6e-05 (0.0337)
Amp Peak 39(20q11 21) | 0 (0%) | 2477 | 0.00019 (0.235) | 1.91e-15 (2.84e-12) | 4.96e-100 (8.23e-97) | 8.43e-05 (0.106) | 0.0832 (1.00) | 3.74e-112 (6.27e-109) | 1.33e-23 (2.03e-20) | 1.18e-05 (0.0156) | 0.0021 (1.00) | 7.69e-10 (1.1e-06) | 1.76e-05 (0.0231) | 0.00618 (1.00) | 0.0196 (1.00) | 0.107 (1.00) | 0.688 (1.00) | 0.666 (1.00) | 0.00129 (1.00) | 0.422 (1.00) |  | 0.00646 (1.00)
Del Peak 12(5q21 3) | 0 (0%) | 3230 | 0.705 (1.00) | 0.00789 (1.00) | 8.65e-176 (1.49e-172) | 0.869 (1.00) | 1.8e-05 (0.0235) | 8.17e-150 (1.39e-146) | 3.33e-16 (4.96e-13) | 1.5e-05 (0.0197) | 4.4e-05 (0.0561) | 0.000538 (0.642) | 1.72e-14 (2.55e-11) | 0.00048 (0.578) | 3.54e-05 (0.0454) | 0.0707 (1.00) | 0.2 (1.00) | 0.121 (1.00) | 0.642 (1.00) | 0.661 (1.00) |  | 9.36e-06 (0.0124)
Amp Peak 8(3q26 2) | 0 (0%) | 2786 | 0.0442 (1.00) | 0.0195 (1.00) | 2.48e-239 (4.29e-236) | 0.321 (1.00) | 3.29e-05 (0.0424) | 7.01e-241 (1.22e-237) | 2.63e-22 (4.01e-19) | 4.82e-10 (6.89e-07) | 0.00212 (1.00) | 1.14e-23 (1.75e-20) | 1.41e-13 (2.07e-10) | 2.49e-05 (0.0323) | 0.016 (1.00) | 0.419 (1.00) | 0.361 (1.00) | 0.427 (1.00) | 0.0158 (1.00) | 0.0142 (1.00) |  | 0.000305 (0.373)
Amp Peak 21(8q24 21) | 0 (0%) | 2221 | 0.00193 (1.00) | 0.656 (1.00) | 1.94e-213 (3.35e-210) | 2.5e-08 (3.5e-05) | 1.3e-05 (0.0171) | 2.05e-129 (3.48e-126) | 2.1e-26 (3.23e-23) | 4.03e-11 (5.84e-08) | 0.00837 (1.00) | 6.46e-19 (9.75e-16) | 4.46e-22 (6.79e-19) | 0.987 (1.00) | 0.0379 (1.00) | 0.285 (1.00) | 0.115 (1.00) | 0.00829 (1.00) | 0.0912 (1.00) | 0.0329 (1.00) |  | 0.0631 (1.00)
Del Peak 7(3p14 2) | 0 (0%) | 2885 | 0.137 (1.00) | 0.674 (1.00) | 2.82e-247 (4.9e-244) | 3.08e-34 (4.82e-31) | 2.12e-05 (0.0276) | 1.54e-199 (2.66e-196) | 8.81e-20 (1.33e-16) | 0.0712 (1.00) | 0.119 (1.00) | 3.07e-17 (4.6e-14) | 4.04e-20 (6.11e-17) | 0.000361 (0.437) | 2.41e-17 (3.62e-14) | 0.802 (1.00) | 0.427 (1.00) | 0.941 (1.00) | 0.0116 (1.00) | 0.0399 (1.00) |  | 0.657 (1.00)
Del Peak 41(17p12) | 0 (0%) | 2547 | 0.0465 (1.00) | 0.315 (1.00) | 1.07e-240 (1.85e-237) | 1.18e-26 (1.81e-23) | 2.8e-05 (0.0362) | 1e-188 (1.72e-185) | 1.09e-12 (1.6e-09) | 1.42e-07 (0.000197) | 0.00213 (1.00) | 9.6e-31 (1.49e-27) | 1.53e-27 (2.36e-24) | 0.209 (1.00) | 0.559 (1.00) | 0.734 (1.00) | 0.961 (1.00) | 0.0216 (1.00) | 0.255 (1.00) | 0.011 (1.00) |  | 0.11 (1.00)
Del Peak 43(18q21 2) | 0 (0%) | 2838 | 0.273 (1.00) | 1.98e-06 (0.00267) | 2.16e-160 (3.7e-157) | 0.0396 (1.00) | 0.00615 (1.00) | 3.7e-112 (6.21e-109) | 1.41e-23 (2.15e-20) | 2.41e-10 (3.46e-07) | 8.73e-07 (0.00119) | 3.65e-17 (5.47e-14) | 6.39e-27 (9.84e-24) | 0.11 (1.00) | 0.216 (1.00) | 0.0197 (1.00) | 0.182 (1.00) | 0.0699 (1.00) | 0.00168 (1.00) | 0.0054 (1.00) |  | 0.124 (1.00)
Amp Peak 3(1q21 3) | 0 (0%) | 2591 | 1.44e-06 (0.00195) | 0.00644 (1.00) | 5.02e-206 (8.67e-203) | 1.59e-35 (2.49e-32) | 0.0281 (1.00) | 5.21e-127 (8.83e-124) | 1.17e-14 (1.74e-11) | 0.00195 (1.00) | 4.31e-05 (0.0551) | 3.44e-07 (0.000473) | 0.019 (1.00) | 0.736 (1.00) | 0.00255 (1.00) | 0.797 (1.00) | 0.652 (1.00) | 0.469 (1.00) | 0.393 (1.00) | 0.025 (1.00) |  | 0.18 (1.00)
Amp Peak 11(5p15 33) | 0 (0%) | 2938 | 0.115 (1.00) | 1.62e-05 (0.0212) | 2.24e-160 (3.83e-157) | 0.063 (1.00) | 0.000192 (0.237) | 1.59e-116 (2.68e-113) | 1.28e-19 (1.93e-16) | 0.202 (1.00) | 0.00756 (1.00) | 5.66e-05 (0.072) | 9.11e-16 (1.36e-12) | 0.357 (1.00) | 0.000648 (0.771) | 0.883 (1.00) | 0.607 (1.00) | 0.0282 (1.00) | 0.812 (1.00) | 0.342 (1.00) |  | 0.0343 (1.00)
Amp Peak 12(5q35 3) | 0 (0%) | 3697 | 9.9e-06 (0.0131) | 0.515 (1.00) | 1.49e-155 (2.55e-152) | 0.624 (1.00) | 0.287 (1.00) | 5.88e-130 (9.97e-127) | 1.77e-17 (2.66e-14) | 6.66e-05 (0.0846) | 0.000659 (0.784) | 9.07e-07 (0.00123) | 8.09e-08 (0.000112) | 0.323 (1.00) | 0.749 (1.00) | 0.686 (1.00) | 0.0912 (1.00) | 0.471 (1.00) | 0.0622 (1.00) | 0.636 (1.00) |  | 0.0548 (1.00)
Amp Peak 16(7p11 2) | 0 (0%) | 2594 | 0 (0) | 0.000519 (0.623) | 4.82e-156 (8.23e-153) | 4.27e-32 (6.65e-29) | 0.334 (1.00) | 1.33e-52 (2.13e-49) | 2.1e-09 (2.99e-06) | 4.56e-07 (0.000623) | 0.00263 (1.00) | 0.0511 (1.00) | 7.18e-13 (1.05e-09) | 0.859 (1.00) | 0.223 (1.00) | 0.0699 (1.00) | 0.192 (1.00) | 0.635 (1.00) | 0.0415 (1.00) | 0.0694 (1.00) |  | 0.00244 (1.00)
Amp Peak 23(10p15 1) | 0 (0%) | 3713 | 0.0144 (1.00) | 0.401 (1.00) | 8.14e-107 (1.36e-103) | 1.03e-21 (1.56e-18) | 0.42 (1.00) | 2.93e-70 (4.76e-67) | 3.06e-06 (0.00411) | 0.428 (1.00) | 0.315 (1.00) | 5.14e-16 (7.65e-13) | 8.77e-07 (0.00119) | 0.454 (1.00) | 7.11e-07 (0.000971) | 0.139 (1.00) | 0.221 (1.00) | 0.775 (1.00) | 0.000869 (1.00) | 0.686 (1.00) |  | 0.0385 (1.00)
Amp Peak 25(11q13 3) | 0 (0%) | 3501 | 0.0311 (1.00) | 0.201 (1.00) | 2.29e-120 (3.88e-117) | 0.000162 (0.201) | 0.167 (1.00) | 1.72e-67 (2.79e-64) | 3.36e-09 (4.78e-06) | 3.55e-06 (0.00476) | 0.0522 (1.00) | 2.61e-07 (0.00036) | 1.38e-05 (0.0181) | 0.112 (1.00) | 0.0467 (1.00) | 0.054 (1.00) | 0.96 (1.00) | 0.278 (1.00) | 0.314 (1.00) | 0.041 (1.00) |  | 0.746 (1.00)
Amp Peak 40(20q13 2) | 0 (0%) | 2395 | 0.0817 (1.00) | 2.73e-08 (3.82e-05) | 3.02e-111 (5.05e-108) | 0.378 (1.00) | 0.674 (1.00) | 2.81e-119 (4.73e-116) | 1.02e-23 (1.55e-20) | 0.000324 (0.395) | 0.000166 (0.206) | 3.26e-13 (4.78e-10) | 6.37e-06 (0.00847) | 0.764 (1.00) | 0.00544 (1.00) | 0.849 (1.00) | 0.0773 (1.00) | 0.506 (1.00) | 0.00354 (1.00) | 0.988 (1.00) |  | 0.206 (1.00)
Del Peak 2(1p36 11) | 0 (0%) | 3276 | 0.0382 (1.00) | 0.00417 (1.00) | 2.35e-75 (3.84e-72) | 0.0197 (1.00) | 0.0171 (1.00) | 1.16e-45 (1.84e-42) | 0.00424 (1.00) | 0.00895 (1.00) | 0.0279 (1.00) | 1.02e-05 (0.0135) | 2.95e-10 (4.23e-07) | 0.00739 (1.00) | 0.000119 (0.148) | 0.567 (1.00) | 0.567 (1.00) | 0.00793 (1.00) | 0.00605 (1.00) | 4.02e-05 (0.0515) |  | 5.18e-05 (0.066)
Del Peak 6(3p25 3) | 0 (0%) | 3021 | 0.88 (1.00) | 0.0653 (1.00) | 0 (0) | 1.72e-36 (2.71e-33) | 0.000337 (0.41) | 5.86e-225 (1.01e-221) | 2.3e-21 (3.49e-18) | 0.208 (1.00) | 0.00147 (1.00) | 1.54e-14 (2.28e-11) | 2.46e-27 (3.79e-24) | 0.00196 (1.00) | 8.43e-18 (1.27e-14) | 0.262 (1.00) | 0.112 (1.00) | 0.943 (1.00) | 0.156 (1.00) | 0.0172 (1.00) |  | 0.392 (1.00)
Del Peak 18(8p23 2) | 0 (0%) | 2583 | 0.0305 (1.00) | 0.000318 (0.388) | 4.6e-129 (7.79e-126) | 0.0276 (1.00) | 7.36e-05 (0.0931) | 9.65e-91 (1.59e-87) | 3.31e-05 (0.0427) | 5.54e-09 (7.85e-06) | 0.567 (1.00) | 2.21e-08 (3.09e-05) | 3.83e-21 (5.81e-18) | 0.00323 (1.00) | 0.0876 (1.00) | 0.719 (1.00) | 0.668 (1.00) | 0.0501 (1.00) | 0.0585 (1.00) | 0.00246 (1.00) |  | 0.968 (1.00)
Del Peak 19(8p21 2) | 0 (0%) | 2565 | 0.027 (1.00) | 0.000822 (0.964) | 5.87e-133 (9.97e-130) | 8.03e-05 (0.101) | 1.51e-05 (0.0199) | 5.32e-94 (8.78e-91) | 0.00206 (1.00) | 6.31e-09 (8.92e-06) | 0.247 (1.00) | 2.83e-11 (4.1e-08) | 6.66e-22 (1.01e-18) | 0.104 (1.00) | 0.135 (1.00) | 0.915 (1.00) | 0.72 (1.00) | 0.111 (1.00) | 0.221 (1.00) | 0.00127 (1.00) |  | 0.67 (1.00)
Del Peak 37(15q11 2) | 0 (0%) | 3152 | 0.0866 (1.00) | 0.00102 (1.00) | 7.95e-75 (1.3e-71) | 3.56e-05 (0.0456) | 0.0563 (1.00) | 3.04e-80 (4.98e-77) | 7.04e-07 (0.000961) | 7.75e-07 (0.00106) | 0.00411 (1.00) | 3.67e-10 (5.26e-07) | 1.66e-06 (0.00224) | 0.893 (1.00) | 0.558 (1.00) | 0.128 (1.00) | 0.261 (1.00) | 0.599 (1.00) | 0.391 (1.00) | 0.0828 (1.00) |  | 0.14 (1.00)
Del Peak 38(15q15 1) | 0 (0%) | 3027 | 0.0244 (1.00) | 0.00282 (1.00) | 4.09e-92 (6.73e-89) | 1.95e-07 (0.00027) | 0.111 (1.00) | 2.29e-101 (3.81e-98) | 4.02e-07 (0.000551) | 9.24e-07 (0.00125) | 0.00487 (1.00) | 1.31e-16 (1.96e-13) | 2.13e-05 (0.0278) | 0.872 (1.00) | 0.355 (1.00) | 0.423 (1.00) | 0.864 (1.00) | 0.652 (1.00) | 0.777 (1.00) | 0.179 (1.00) |  | 0.607 (1.00)
Del Peak 44(18q23) | 0 (0%) | 2778 | 0.35 (1.00) | 0.000251 (0.308) | 4.93e-163 (8.44e-160) | 0.0674 (1.00) | 0.0104 (1.00) | 2.15e-116 (3.62e-113) | 1.9e-22 (2.9e-19) | 6.46e-10 (9.22e-07) | 6.05e-05 (0.0769) | 2.49e-19 (3.76e-16) | 1.11e-25 (1.7e-22) | 0.186 (1.00) | 0.0327 (1.00) | 0.00732 (1.00) | 0.126 (1.00) | 0.028 (1.00) | 0.00719 (1.00) | 0.00118 (1.00) |  | 0.218 (1.00)
Del Peak 45(19p13 3) | 0 (0%) | 3088 | 0.0975 (1.00) | 0.789 (1.00) | 6.56e-269 (1.14e-265) | 1.22e-22 (1.86e-19) | 0.0867 (1.00) | 2.22e-237 (3.84e-234) | 7.92e-17 (1.18e-13) | 4.24e-06 (0.00568) | 0.000366 (0.442) | 8.26e-44 (1.31e-40) | 7.2e-19 (1.08e-15) | 0.339 (1.00) | 0.253 (1.00) | 0.0439 (1.00) | 0.379 (1.00) | 0.432 (1.00) | 0.00272 (1.00) | 0.113 (1.00) |  | 0.52 (1.00)
Amp Peak 4(1q32 1) | 0 (0%) | 2602 | 1.78e-05 (0.0233) | 0.0877 (1.00) | 6.43e-187 (1.11e-183) | 4.15e-28 (6.41e-25) | 0.00457 (1.00) | 1.42e-104 (2.37e-101) | 1.12e-15 (1.67e-12) | 0.00216 (1.00) | 0.000735 (0.866) | 0.0143 (1.00) | 0.701 (1.00) | 0.257 (1.00) | 0.00427 (1.00) | 0.0477 (1.00) | 0.413 (1.00) | 0.0829 (1.00) | 0.375 (1.00) | 0.0199 (1.00) |  | 9.71e-06 (0.0129)
Amp Peak 5(1q44) | 0 (0%) | 2698 | 1.25e-06 (0.00169) | 0.189 (1.00) | 4.2e-184 (7.22e-181) | 4.53e-31 (7.04e-28) | 0.014 (1.00) | 3.46e-96 (5.73e-93) | 7.27e-14 (1.07e-10) | 4.85e-05 (0.0618) | 0.00045 (0.542) | 0.000332 (0.403) | 0.0274 (1.00) | 0.477 (1.00) | 0.00328 (1.00) | 0.337 (1.00) | 0.577 (1.00) | 0.0319 (1.00) | 0.712 (1.00) | 0.0534 (1.00) |  | 0.000607 (0.723)
Amp Peak 9(4p16 3) | 0 (0%) | 4112 | 0.0205 (1.00) | 0.841 (1.00) | 2.63e-44 (4.16e-41) | 6.16e-05 (0.0783) | 0.284 (1.00) | 9.73e-47 (1.55e-43) | 1.38e-07 (0.000191) | 0.896 (1.00) | 0.034 (1.00) | 1.93e-08 (2.71e-05) | 0.107 (1.00) | 0.535 (1.00) | 0.791 (1.00) | 0.177 (1.00) | 0.0562 (1.00) | 0.118 (1.00) | 0.00199 (1.00) | 0.656 (1.00) |  | 7.36e-05 (0.0931)
Amp Peak 13(6p22 3) | 0 (0%) | 3586 | 0.0243 (1.00) | 0.102 (1.00) | 1.74e-115 (2.92e-112) | 6.53e-11 (9.45e-08) | 0.437 (1.00) | 2.66e-91 (4.38e-88) | 0.000905 (1.00) | 0.0228 (1.00) | 0.00017 (0.21) | 3.21e-13 (4.72e-10) | 1.61e-10 (2.33e-07) | 0.585 (1.00) | 0.00274 (1.00) | 0.182 (1.00) | 0.204 (1.00) | 0.172 (1.00) | 0.0494 (1.00) | 0.0631 (1.00) |  | 0.0205 (1.00)
Amp Peak 18(7q36 3) | 0 (0%) | 2783 | 0 (0) | 0.96 (1.00) | 4.4e-158 (7.52e-155) | 2.93e-13 (4.31e-10) | 0.033 (1.00) | 3.21e-53 (5.16e-50) | 0.00161 (1.00) | 0.0162 (1.00) | 0.000717 (0.848) | 1.84e-06 (0.00249) | 4.66e-08 (6.49e-05) | 0.688 (1.00) | 0.00505 (1.00) | 0.509 (1.00) | 0.729 (1.00) | 0.993 (1.00) | 0.162 (1.00) | 0.829 (1.00) |  | 0.0291 (1.00)
Amp Peak 20(8p11 21) | 0 (0%) | 3246 | 0.000308 (0.376) | 7.12e-06 (0.00946) | 7.88e-77 (1.29e-73) | 0.0108 (1.00) | 0.0025 (1.00) | 1.1e-45 (1.74e-42) | 1.34e-11 (1.95e-08) | 0.277 (1.00) | 0.00459 (1.00) | 2.88e-05 (0.0373) | 2.27e-08 (3.18e-05) | 0.568 (1.00) | 0.076 (1.00) | 0.049 (1.00) | 0.7 (1.00) | 0.67 (1.00) | 0.0373 (1.00) | 0.536 (1.00) |  | 0.45 (1.00)
Del Peak 3(1p13 2) | 0 (0%) | 3673 | 0.0714 (1.00) | 2.26e-05 (0.0294) | 1.18e-68 (1.92e-65) | 0.101 (1.00) | 0.00293 (1.00) | 3.6e-38 (5.67e-35) | 0.114 (1.00) | 0.00211 (1.00) | 0.273 (1.00) | 0.551 (1.00) | 1.14e-11 (1.66e-08) | 0.0174 (1.00) | 8.76e-05 (0.11) | 0.976 (1.00) | 0.522 (1.00) | 0.00448 (1.00) | 0.0165 (1.00) | 0.000101 (0.127) |  | 0.00125 (1.00)
Del Peak 8(4p16 3) | 0 (0%) | 3291 | 0.144 (1.00) | 0.167 (1.00) | 3.49e-53 (5.59e-50) | 0.0274 (1.00) | 0.00067 (0.795) | 6.2e-60 (1e-56) | 9.16e-07 (0.00124) | 0.000126 (0.157) | 0.202 (1.00) | 0.000177 (0.219) | 0.000184 (0.227) | 0.0159 (1.00) | 0.0013 (1.00) | 0.644 (1.00) | 0.793 (1.00) | 0.704 (1.00) | 0.242 (1.00) | 0.00534 (1.00) |  | 0.314 (1.00)
Del Peak 21(9p21 3) | 0 (0%) | 2719 | 0 (0) | 0.0163 (1.00) | 5.76e-162 (9.86e-159) | 2.67e-22 (4.06e-19) | 0.0181 (1.00) | 3.34e-109 (5.58e-106) | 2.4e-16 (3.58e-13) | 0.0613 (1.00) | 0.141 (1.00) | 0.203 (1.00) | 8.2e-07 (0.00112) | 0.0218 (1.00) | 0.147 (1.00) | 0.000529 (0.634) | 0.161 (1.00) | 0.000571 (0.681) | 0.824 (1.00) | 0.0247 (1.00) |  | 0.000212 (0.261)
Del Peak 22(9q21 11) | 0 (0%) | 3305 | 0.198 (1.00) | 3.24e-07 (0.000446) | 4.8e-86 (7.88e-83) | 0.0811 (1.00) | 0.0317 (1.00) | 4.54e-71 (7.37e-68) | 1.48e-09 (2.11e-06) | 0.0144 (1.00) | 0.006 (1.00) | 2.63e-09 (3.75e-06) | 9.63e-14 (1.42e-10) | 0.0642 (1.00) | 0.192 (1.00) | 0.0593 (1.00) | 0.0678 (1.00) | 0.272 (1.00) | 0.232 (1.00) | 0.231 (1.00) |  | 0.0858 (1.00)
Del Peak 23(9q34 13) | 0 (0%) | 3277 | 0.577 (1.00) | 7.74e-05 (0.0977) | 7.47e-104 (1.24e-100) | 0.000957 (1.00) | 0.228 (1.00) | 1.92e-84 (3.16e-81) | 1.73e-08 (2.44e-05) | 0.0208 (1.00) | 0.013 (1.00) | 2.46e-13 (3.62e-10) | 1.9e-14 (2.81e-11) | 0.0181 (1.00) | 0.13 (1.00) | 0.00379 (1.00) | 0.887 (1.00) | 0.0384 (1.00) | 0.612 (1.00) | 0.714 (1.00) |  | 0.243 (1.00)
Del Peak 24(9q34 3) | 0 (0%) | 3275 | 0.639 (1.00) | 0.000148 (0.184) | 8.36e-98 (1.39e-94) | 0.000759 (0.893) | 0.142 (1.00) | 9.53e-81 (1.56e-77) | 9.21e-09 (1.3e-05) | 0.0013 (1.00) | 0.0156 (1.00) | 2.71e-12 (3.95e-09) | 7.05e-14 (1.04e-10) | 0.028 (1.00) | 0.253 (1.00) | 0.00443 (1.00) | 0.947 (1.00) | 0.0583 (1.00) | 0.358 (1.00) | 0.408 (1.00) |  | 0.266 (1.00)
Del Peak 25(10p15 3) | 0 (0%) | 3409 | 0 (0) | 0.999 (1.00) | 4.91e-243 (8.52e-240) | 1.84e-25 (2.82e-22) | 0.0806 (1.00) | 2.64e-48 (4.22e-45) | 4.26e-07 (0.000583) | 0.00118 (1.00) | 0.587 (1.00) | 0.129 (1.00) | 1.22e-34 (1.91e-31) | 0.119 (1.00) | 0.0077 (1.00) | 0.0481 (1.00) | 0.435 (1.00) | 0.776 (1.00) | 0.755 (1.00) | 0.0162 (1.00) |  | 0.599 (1.00)
Del Peak 26(10q23 31) | 0 (0%) | 3001 | 0 (0) | 0.488 (1.00) | 5.8e-192 (9.99e-189) | 2.92e-11 (4.23e-08) | 0.235 (1.00) | 2.27e-44 (3.59e-41) | 0.0549 (1.00) | 0.0961 (1.00) | 0.407 (1.00) | 0.00646 (1.00) | 2.29e-29 (3.55e-26) | 0.0626 (1.00) | 0.129 (1.00) | 7.23e-05 (0.0916) | 0.406 (1.00) | 0.13 (1.00) | 0.179 (1.00) | 0.46 (1.00) |  | 0.0204 (1.00)
Del Peak 30(11q25) | 0 (0%) | 3383 | 0.826 (1.00) | 0.122 (1.00) | 4.75e-90 (7.81e-87) | 0.000114 (0.143) | 0.0102 (1.00) | 1.71e-62 (2.76e-59) | 9.7e-11 (1.4e-07) | 3.1e-09 (4.4e-06) | 0.215 (1.00) | 2.59e-05 (0.0336) | 0.368 (1.00) | 0.168 (1.00) | 0.26 (1.00) | 0.33 (1.00) | 0.481 (1.00) | 0.354 (1.00) | 0.595 (1.00) | 0.00433 (1.00) |  | 0.0511 (1.00)
Del Peak 32(12q23 1) | 0 (0%) | 3943 | 0.953 (1.00) | 0.233 (1.00) | 4.66e-53 (7.48e-50) | 1.3e-08 (1.83e-05) | 0.619 (1.00) | 2.77e-55 (4.45e-52) | 3.72e-05 (0.0476) | 0.0668 (1.00) | 1.39e-05 (0.0183) | 1.58e-06 (0.00214) | 0.00116 (1.00) | 0.294 (1.00) | 0.845 (1.00) | 0.471 (1.00) | 0.962 (1.00) | 0.412 (1.00) | 0.486 (1.00) | 0.245 (1.00) |  | 0.151 (1.00)
Del Peak 34(13q11) | 0 (0%) | 3055 | 0.000303 (0.37) | 0.78 (1.00) | 9.08e-157 (1.55e-153) | 0.2 (1.00) | 0.000368 (0.444) | 2.19e-151 (3.74e-148) | 1.89e-28 (2.93e-25) | 0.00442 (1.00) | 7.09e-06 (0.00943) | 9.02e-08 (0.000125) | 0.198 (1.00) | 0.00324 (1.00) | 1.62e-06 (0.00218) | 0.468 (1.00) | 0.938 (1.00) | 0.918 (1.00) | 0.268 (1.00) | 0.243 (1.00) |  | 0.472 (1.00)
Del Peak 35(13q14 2) | 0 (0%) | 2877 | 5.46e-06 (0.00729) | 0.0302 (1.00) | 1.57e-163 (2.68e-160) | 0.0134 (1.00) | 0.00113 (1.00) | 7.05e-156 (1.2e-152) | 2.06e-27 (3.18e-24) | 0.00341 (1.00) | 2.6e-05 (0.0337) | 1.27e-08 (1.79e-05) | 0.969 (1.00) | 0.0136 (1.00) | 0.000718 (0.848) | 0.914 (1.00) | 0.903 (1.00) | 0.465 (1.00) | 0.27 (1.00) | 0.544 (1.00) |  | 0.853 (1.00)
Del Peak 39(16p13 3) | 0 (0%) | 3888 | 3.06e-05 (0.0394) | 0.00642 (1.00) | 3.17e-130 (5.37e-127) | 0.0121 (1.00) | 0.109 (1.00) | 1.02e-100 (1.7e-97) | 0.000741 (0.872) | 0.253 (1.00) | 0.161 (1.00) | 8.54e-13 (1.25e-09) | 3.38e-09 (4.8e-06) | 0.484 (1.00) | 0.00476 (1.00) | 0.312 (1.00) | 0.0011 (1.00) | 0.445 (1.00) | 0.379 (1.00) | 0.173 (1.00) |  | 7.08e-09 (1e-05)
Del Peak 40(16q23 1) | 0 (0%) | 2998 | 0.0046 (1.00) | 0.37 (1.00) | 2.05e-249 (3.56e-246) | 5.49e-72 (8.94e-69) | 0.216 (1.00) | 8.25e-194 (1.42e-190) | 4.44e-10 (6.35e-07) | 0.0426 (1.00) | 0.051 (1.00) | 3.97e-34 (6.2e-31) | 9.07e-05 (0.114) | 0.241 (1.00) | 0.0153 (1.00) | 0.259 (1.00) | 0.0515 (1.00) | 0.256 (1.00) | 0.000591 (0.705) | 0.764 (1.00) |  | 0.000216 (0.266)
Del Peak 42(17q11 2) | 0 (0%) | 3504 | 0.803 (1.00) | 1.14e-05 (0.015) | 1.98e-263 (3.45e-260) | 1.06e-51 (1.7e-48) | 0.237 (1.00) | 9.39e-235 (1.62e-231) | 0.00178 (1.00) | 0.696 (1.00) | 0.237 (1.00) | 6.83e-59 (1.1e-55) | 3.35e-09 (4.76e-06) | 0.0662 (1.00) | 0.059 (1.00) | 0.514 (1.00) | 0.113 (1.00) | 0.859 (1.00) | 0.00172 (1.00) | 0.285 (1.00) |  | 0.0168 (1.00)
Del Peak 50(22q13 32) | 0 (0%) | 2835 | 0.000205 (0.253) | 0.308 (1.00) | 1.85e-172 (3.17e-169) | 4.14e-26 (6.35e-23) | 0.128 (1.00) | 8.76e-187 (1.51e-183) | 7.66e-05 (0.0968) | 0.00384 (1.00) | 0.00223 (1.00) | 2.75e-45 (4.37e-42) | 0.0418 (1.00) | 0.0863 (1.00) | 0.0907 (1.00) | 0.0148 (1.00) | 0.834 (1.00) | 0.0978 (1.00) | 0.000108 (0.135) | 0.309 (1.00) |  | 0.587 (1.00)
Amp Peak 1(1p34 2) | 0 (0%) | 3821 | 0.0251 (1.00) | 0.677 (1.00) | 4.52e-119 (7.61e-116) | 5.11e-13 (7.48e-10) | 0.17 (1.00) | 1.04e-111 (1.74e-108) | 6.36e-06 (0.00847) | 0.805 (1.00) | 0.00193 (1.00) | 2.25e-17 (3.37e-14) | 0.0126 (1.00) | 0.759 (1.00) | 0.145 (1.00) | 0.566 (1.00) | 0.13 (1.00) | 0.257 (1.00) | 0.0158 (1.00) | 0.942 (1.00) |  | 0.000712 (0.843)
Amp Peak 2(1p22 3) | 0 (0%) | 3856 | 0.701 (1.00) | 0.677 (1.00) | 2.34e-45 (3.7e-42) | 4.85e-11 (7.02e-08) | 0.283 (1.00) | 6.93e-41 (1.09e-37) | 8.67e-05 (0.109) | 0.224 (1.00) | 0.0509 (1.00) | 3.46e-05 (0.0444) | 0.839 (1.00) | 0.575 (1.00) | 0.0109 (1.00) | 0.272 (1.00) | 0.426 (1.00) | 0.765 (1.00) | 0.0688 (1.00) | 0.647 (1.00) |  | 0.189 (1.00)
Amp Peak 6(2p15) | 0 (0%) | 3570 | 0.929 (1.00) | 1.25e-06 (0.00169) | 4.91e-75 (8.02e-72) | 0.886 (1.00) | 0.000219 (0.269) | 2.14e-49 (3.41e-46) | 0.000663 (0.786) | 0.0182 (1.00) | 0.0819 (1.00) | 4.26e-05 (0.0545) | 4.72e-13 (6.92e-10) | 0.594 (1.00) | 0.00722 (1.00) | 0.754 (1.00) | 0.193 (1.00) | 0.0667 (1.00) | 0.486 (1.00) | 0.0256 (1.00) |  | 0.00081 (0.951)
Amp Peak 7(2q31 2) | 0 (0%) | 3724 | 0.215 (1.00) | 3.58e-06 (0.0048) | 5.68e-77 (9.3e-74) | 0.253 (1.00) | 0.197 (1.00) | 6.05e-36 (9.48e-33) | 0.00656 (1.00) | 0.0537 (1.00) | 0.0986 (1.00) | 2.17e-05 (0.0283) | 3.68e-13 (5.39e-10) | 0.295 (1.00) | 0.000382 (0.461) | 0.407 (1.00) | 0.613 (1.00) | 0.805 (1.00) | 0.441 (1.00) | 0.0039 (1.00) |  | 0.853 (1.00)
Amp Peak 14(6p21 1) | 0 (0%) | 3657 | 0.0149 (1.00) | 0.00145 (1.00) | 8.63e-74 (1.41e-70) | 2.33e-05 (0.0303) | 0.0929 (1.00) | 1.64e-59 (2.64e-56) | 0.00212 (1.00) | 0.00612 (1.00) | 0.000879 (1.00) | 1.23e-07 (0.00017) | 2.11e-07 (0.000292) | 0.222 (1.00) | 0.393 (1.00) | 0.127 (1.00) | 1 (1.00) | 0.5 (1.00) | 0.385 (1.00) | 0.203 (1.00) |  | 0.407 (1.00)
Amp Peak 17(7q21 2) | 0 (0%) | 2728 | 0 (0) | 0.101 (1.00) | 3.72e-139 (6.32e-136) | 8.63e-28 (1.33e-24) | 0.925 (1.00) | 4.86e-38 (7.65e-35) | 0.00142 (1.00) | 0.000338 (0.411) | 0.00463 (1.00) | 0.104 (1.00) | 5.62e-12 (8.2e-09) | 0.0358 (1.00) | 0.00316 (1.00) | 0.765 (1.00) | 0.413 (1.00) | 0.903 (1.00) | 0.0677 (1.00) | 0.0297 (1.00) |  | 0.0251 (1.00)
Amp Peak 26(12p13 33) | 0 (0%) | 3292 | 0.134 (1.00) | 0.00342 (1.00) | 1.48e-73 (2.41e-70) | 0.815 (1.00) | 0.00123 (1.00) | 7.83e-52 (1.25e-48) | 9.81e-06 (0.013) | 0.56 (1.00) | 0.123 (1.00) | 1.28e-08 (1.8e-05) | 7.44e-13 (1.09e-09) | 0.283 (1.00) | 0.391 (1.00) | 0.773 (1.00) | 0.816 (1.00) | 0.138 (1.00) | 0.734 (1.00) | 0.334 (1.00) |  | 0.0513 (1.00)
Amp Peak 27(12p12 1) | 0 (0%) | 3329 | 0.0199 (1.00) | 0.000341 (0.414) | 7.8e-71 (1.27e-67) | 0.946 (1.00) | 0.0023 (1.00) | 2.71e-47 (4.32e-44) | 1.78e-05 (0.0233) | 0.887 (1.00) | 0.123 (1.00) | 5.86e-08 (8.15e-05) | 1.86e-10 (2.67e-07) | 0.194 (1.00) | 0.161 (1.00) | 0.92 (1.00) | 0.41 (1.00) | 0.31 (1.00) | 0.925 (1.00) | 0.238 (1.00) |  | 0.0175 (1.00)
Amp Peak 28(12q14 1) | 0 (0%) | 3554 | 7.95e-05 (0.1) | 0.00011 (0.138) | 5.75e-23 (8.78e-20) | 0.0991 (1.00) | 0.168 (1.00) | 1.56e-17 (2.35e-14) | 0.0513 (1.00) | 0.239 (1.00) | 0.514 (1.00) | 9.74e-05 (0.122) | 0.00692 (1.00) | 0.743 (1.00) | 0.147 (1.00) | 0.0463 (1.00) | 0.818 (1.00) | 0.102 (1.00) | 0.755 (1.00) | 0.822 (1.00) |  | 0.036 (1.00)
Amp Peak 31(14q13 3) | 0 (0%) | 3888 | 0.523 (1.00) | 0.478 (1.00) | 3.33e-93 (5.5e-90) | 0.774 (1.00) | 0.0149 (1.00) | 1.21e-71 (1.97e-68) | 1.82e-11 (2.65e-08) | 0.0104 (1.00) | 4.45e-08 (6.21e-05) | 0.798 (1.00) | 2.98e-07 (0.000409) | 0.335 (1.00) | 0.00427 (1.00) | 0.0453 (1.00) | 0.877 (1.00) | 0.42 (1.00) | 0.124 (1.00) | 0.038 (1.00) |  | 0.0061 (1.00)
Amp Peak 33(17q12) | 0 (0%) | 3648 | 0.612 (1.00) | 4.28e-05 (0.0547) | 1.47e-88 (2.42e-85) | 0.018 (1.00) | 0.0638 (1.00) | 3.07e-71 (4.99e-68) | 1.44e-06 (0.00195) | 0.000784 (0.922) | 2.21e-06 (0.00297) | 0.00293 (1.00) | 0.00097 (1.00) | 0.332 (1.00) | 0.166 (1.00) | 0.475 (1.00) | 0.73 (1.00) | 0.0764 (1.00) | 0.148 (1.00) | 0.0894 (1.00) |  | 0.209 (1.00)
Amp Peak 34(17q25 3) | 0 (0%) | 3319 | 0.633 (1.00) | 0.0557 (1.00) | 8.39e-95 (1.39e-91) | 0.00716 (1.00) | 0.016 (1.00) | 1.85e-74 (3.01e-71) | 1.94e-07 (0.000268) | 0.000322 (0.393) | 5.94e-09 (8.41e-06) | 0.0571 (1.00) | 3.76e-07 (0.000516) | 0.34 (1.00) | 0.046 (1.00) | 0.0201 (1.00) | 0.445 (1.00) | 0.502 (1.00) | 0.257 (1.00) | 0.806 (1.00) |  | 0.157 (1.00)
Amp Peak 36(19p13 2) | 0 (0%) | 3794 | 1.09e-09 (1.55e-06) | 0.123 (1.00) | 2.35e-71 (3.82e-68) | 0.00851 (1.00) | 0.998 (1.00) | 1.17e-30 (1.82e-27) | 0.000492 (0.591) | 0.00114 (1.00) | 0.393 (1.00) | 7.78e-09 (1.1e-05) | 3.08e-11 (4.47e-08) | 0.705 (1.00) | 0.194 (1.00) | 0.516 (1.00) | 0.574 (1.00) | 0.975 (1.00) | 0.538 (1.00) | 0.245 (1.00) |  | 0.771 (1.00)
Amp Peak 41(Xq28) | 0 (0%) | 3672 | 0.939 (1.00) | 0.864 (1.00) | 2.19e-57 (3.53e-54) | 0.0154 (1.00) | 0.0443 (1.00) | 4.22e-30 (6.55e-27) | 2.67e-08 (3.74e-05) | 8.82e-05 (0.111) | 0.0388 (1.00) | 2.91e-07 (4e-04) | 0.00103 (1.00) | 0.975 (1.00) | 0.401 (1.00) | 0.617 (1.00) | 0.111 (1.00) | 0.525 (1.00) | 0.187 (1.00) | 0.32 (1.00) |  | 0.0328 (1.00)
Del Peak 9(4q22 1) | 0 (0%) | 3174 | 0.397 (1.00) | 0.0174 (1.00) | 1.3e-123 (2.19e-120) | 0.00292 (1.00) | 0.00493 (1.00) | 3.96e-108 (6.62e-105) | 3.4e-08 (4.75e-05) | 0.0105 (1.00) | 0.16 (1.00) | 8.59e-22 (1.31e-18) | 1.72e-14 (2.55e-11) | 0.0226 (1.00) | 0.0098 (1.00) | 0.0671 (1.00) | 0.799 (1.00) | 0.148 (1.00) | 0.213 (1.00) | 0.00127 (1.00) |  | 0.321 (1.00)
Del Peak 10(4q34 3) | 0 (0%) | 2971 | 0.0166 (1.00) | 0.0343 (1.00) | 2.74e-125 (4.63e-122) | 0.0124 (1.00) | 0.00238 (1.00) | 1.47e-119 (2.48e-116) | 5.9e-09 (8.35e-06) | 0.0128 (1.00) | 0.445 (1.00) | 8.71e-16 (1.3e-12) | 7.92e-11 (1.14e-07) | 0.00226 (1.00) | 0.00843 (1.00) | 0.863 (1.00) | 0.586 (1.00) | 0.148 (1.00) | 0.558 (1.00) | 0.0155 (1.00) |  | 0.256 (1.00)
Del Peak 16(7p22 3) | 0 (0%) | 4131 | 0.431 (1.00) | 0.00177 (1.00) | 1.33e-144 (2.26e-141) | 4.91e-27 (7.57e-24) | 0.258 (1.00) | 8.12e-126 (1.37e-122) | 3.04e-07 (0.000418) | 0.512 (1.00) | 0.0718 (1.00) | 2.28e-28 (3.53e-25) | 0.00105 (1.00) | 0.092 (1.00) | 0.65 (1.00) | 0.659 (1.00) | 1 (1.00) | 0.737 (1.00) | 0.17 (1.00) | 0.159 (1.00) |  | 0.00798 (1.00)
Del Peak 20(9p23) | 0 (0%) | 2997 | 0 (0) | 0.0133 (1.00) | 3.56e-93 (5.87e-90) | 1.64e-10 (2.36e-07) | 0.0593 (1.00) | 2.59e-84 (4.25e-81) | 1.05e-09 (1.49e-06) | 0.0709 (1.00) | 0.14 (1.00) | 0.0111 (1.00) | 0.402 (1.00) | 0.0515 (1.00) | 0.208 (1.00) | 0.115 (1.00) | 0.572 (1.00) | 0.00579 (1.00) | 0.713 (1.00) | 0.00768 (1.00) |  | 0.00663 (1.00)
Del Peak 27(10q26 3) | 0 (0%) | 3082 | 0 (0) | 0.413 (1.00) | 6.56e-206 (1.13e-202) | 1.1e-12 (1.61e-09) | 0.515 (1.00) | 3.27e-38 (5.16e-35) | 0.101 (1.00) | 0.297 (1.00) | 0.802 (1.00) | 0.156 (1.00) | 1.05e-33 (1.64e-30) | 0.113 (1.00) | 0.0376 (1.00) | 0.0249 (1.00) | 0.371 (1.00) | 0.258 (1.00) | 0.519 (1.00) | 0.144 (1.00) |  | 0.0223 (1.00)
Del Peak 28(11p15 5) | 0 (0%) | 3347 | 0.00713 (1.00) | 0.69 (1.00) | 6.24e-116 (1.05e-112) | 0.000255 (0.313) | 0.00987 (1.00) | 2.96e-119 (4.98e-116) | 3.58e-10 (5.13e-07) | 0.000168 (0.209) | 0.0233 (1.00) | 1.79e-16 (2.68e-13) | 0.00289 (1.00) | 0.0396 (1.00) | 0.000346 (0.419) | 0.722 (1.00) | 0.353 (1.00) | 0.503 (1.00) | 0.292 (1.00) | 0.000365 (0.441) |  | 0.0892 (1.00)
Del Peak 29(11q22 3) | 0 (0%) | 3399 | 0.849 (1.00) | 0.653 (1.00) | 2.27e-95 (3.76e-92) | 0.000537 (0.641) | 0.0216 (1.00) | 6e-56 (9.66e-53) | 4.74e-09 (6.72e-06) | 3.12e-08 (4.36e-05) | 0.556 (1.00) | 2.74e-05 (0.0355) | 0.464 (1.00) | 0.262 (1.00) | 0.285 (1.00) | 0.232 (1.00) | 0.518 (1.00) | 0.502 (1.00) | 0.919 (1.00) | 0.0175 (1.00) |  | 0.271 (1.00)
Del Peak 33(12q24 33) | 0 (0%) | 3878 | 0.0715 (1.00) | 0.415 (1.00) | 2.68e-59 (4.32e-56) | 1.54e-08 (2.17e-05) | 0.15 (1.00) | 1.4e-61 (2.27e-58) | 9.64e-06 (0.0128) | 0.041 (1.00) | 0.0227 (1.00) | 2.17e-08 (3.05e-05) | 0.0158 (1.00) | 0.891 (1.00) | 0.656 (1.00) | 0.184 (1.00) | 0.649 (1.00) | 0.833 (1.00) | 0.193 (1.00) | 0.178 (1.00) |  | 0.684 (1.00)
Del Peak 36(14q24 1) | 0 (0%) | 3161 | 0.00121 (1.00) | 0.783 (1.00) | 1.3e-49 (2.08e-46) | 0.72 (1.00) | 0.962 (1.00) | 2.93e-51 (4.69e-48) | 2.02e-05 (0.0263) | 3.01e-05 (0.0388) | 0.00278 (1.00) | 2.81e-08 (3.92e-05) | 0.000364 (0.44) | 0.784 (1.00) | 0.061 (1.00) | 0.794 (1.00) | 0.564 (1.00) | 0.237 (1.00) | 0.422 (1.00) | 0.66 (1.00) |  | 0.458 (1.00)
Del Peak 46(19q13 32) | 0 (0%) | 3653 | 0.00461 (1.00) | 0.38 (1.00) | 5.86e-114 (9.84e-111) | 1.1e-07 (0.000152) | 0.755 (1.00) | 6.78e-107 (1.13e-103) | 6.59e-06 (0.00877) | 0.0486 (1.00) | 0.0131 (1.00) | 2.14e-20 (3.24e-17) | 0.0199 (1.00) | 0.676 (1.00) | 0.0939 (1.00) | 0.0476 (1.00) | 0.429 (1.00) | 0.38 (1.00) | 0.00539 (1.00) | 0.089 (1.00) |  | 0.132 (1.00)
Del Peak 47(19q13 43) | 0 (0%) | 3737 | 0.0061 (1.00) | 0.755 (1.00) | 7.62e-104 (1.27e-100) | 2e-06 (0.00269) | 0.956 (1.00) | 8.06e-97 (1.34e-93) | 3.89e-06 (0.00521) | 0.0158 (1.00) | 0.0212 (1.00) | 2.97e-17 (4.45e-14) | 0.027 (1.00) | 0.138 (1.00) | 0.0812 (1.00) | 0.0821 (1.00) | 0.535 (1.00) | 0.952 (1.00) | 0.00146 (1.00) | 0.0455 (1.00) |  | 0.292 (1.00)
Del Peak 49(21q11 2) | 0 (0%) | 3526 | 0.206 (1.00) | 0.00111 (1.00) | 1.48e-67 (2.4e-64) | 0.0105 (1.00) | 0.00551 (1.00) | 6.88e-46 (1.09e-42) | 8.93e-06 (0.0119) | 8.8e-05 (0.11) | 0.0389 (1.00) | 0.0602 (1.00) | 1.78e-11 (2.59e-08) | 0.038 (1.00) | 0.00204 (1.00) | 0.674 (1.00) | 0.724 (1.00) | 0.352 (1.00) | 0.405 (1.00) | 0.139 (1.00) |  | 0.0264 (1.00)
Amp Peak 10(4q12) | 0 (0%) | 4044 | 8.29e-05 (0.104) | 0.151 (1.00) | 5.03e-36 (7.9e-33) | 0.136 (1.00) | 0.429 (1.00) | 3.41e-33 (5.31e-30) | 3.79e-10 (5.43e-07) | 0.058 (1.00) | 0.2 (1.00) | 0.0774 (1.00) | 0.308 (1.00) | 0.874 (1.00) | 0.103 (1.00) | 0.0378 (1.00) | 0.267 (1.00) | 0.142 (1.00) | 0.403 (1.00) | 0.414 (1.00) |  | 0.00193 (1.00)
Amp Peak 19(8p11 23) | 0 (0%) | 3419 | 0.00942 (1.00) | 0.00246 (1.00) | 3.4e-66 (5.5e-63) | 0.491 (1.00) | 0.000484 (0.582) | 1.65e-37 (2.59e-34) | 7.37e-09 (1.04e-05) | 0.263 (1.00) | 0.000713 (0.843) | 0.00932 (1.00) | 0.000163 (0.202) | 0.206 (1.00) | 0.0215 (1.00) | 0.182 (1.00) | 0.414 (1.00) | 0.0963 (1.00) | 0.563 (1.00) | 0.0947 (1.00) |  | 0.241 (1.00)
Amp Peak 24(10q22 2) | 0 (0%) | 4026 | 0.00707 (1.00) | 0.839 (1.00) | 3e-77 (4.91e-74) | 3.16e-20 (4.78e-17) | 0.497 (1.00) | 4.23e-46 (6.73e-43) | 0.000835 (0.977) | 0.0842 (1.00) | 0.631 (1.00) | 2.76e-10 (3.97e-07) | 0.00296 (1.00) | 0.451 (1.00) | 0.173 (1.00) | 0.124 (1.00) | 0.611 (1.00) | 0.524 (1.00) | 0.0778 (1.00) | 0.0524 (1.00) |  | 0.315 (1.00)
Amp Peak 29(12q15) | 0 (0%) | 3539 | 0.0148 (1.00) | 3.48e-05 (0.0446) | 1.88e-32 (2.93e-29) | 0.134 (1.00) | 0.0513 (1.00) | 9.77e-22 (1.48e-18) | 0.00452 (1.00) | 0.189 (1.00) | 0.203 (1.00) | 0.00811 (1.00) | 9.9e-07 (0.00134) | 0.886 (1.00) | 0.251 (1.00) | 0.396 (1.00) | 0.497 (1.00) | 0.0983 (1.00) | 0.786 (1.00) | 0.479 (1.00) |  | 0.0727 (1.00)
Amp Peak 32(15q26 3) | 0 (0%) | 3957 | 0.45 (1.00) | 0.325 (1.00) | 1.14e-50 (1.82e-47) | 0.0497 (1.00) | 0.00465 (1.00) | 3.88e-47 (6.17e-44) | 1.68e-10 (2.42e-07) | 0.0147 (1.00) | 0.207 (1.00) | 0.00973 (1.00) | 2.33e-07 (0.000322) | 0.559 (1.00) | 0.00128 (1.00) | 0.665 (1.00) | 0.0573 (1.00) | 0.975 (1.00) | 0.04 (1.00) | 0.986 (1.00) |  | 0.929 (1.00)
Amp Peak 37(19p13 12) | 0 (0%) | 3580 | 0.00107 (1.00) | 0.679 (1.00) | 3.26e-105 (5.44e-102) | 0.000345 (0.418) | 0.422 (1.00) | 3.65e-107 (6.1e-104) | 0.000327 (0.398) | 0.00401 (1.00) | 0.329 (1.00) | 8.9e-29 (1.38e-25) | 9.43e-05 (0.118) | 0.326 (1.00) | 0.262 (1.00) | 0.936 (1.00) | 0.319 (1.00) | 0.656 (1.00) | 0.0327 (1.00) | 0.256 (1.00) |  | 0.874 (1.00)
Amp Peak 38(19q12) | 0 (0%) | 3327 | 0.000215 (0.265) | 0.00751 (1.00) | 7.8e-78 (1.28e-74) | 0.189 (1.00) | 0.194 (1.00) | 7.99e-96 (1.32e-92) | 3.69e-06 (0.00494) | 0.00731 (1.00) | 0.105 (1.00) | 7.63e-17 (1.14e-13) | 0.498 (1.00) | 0.0795 (1.00) | 0.000728 (0.858) | 0.267 (1.00) | 0.757 (1.00) | 0.279 (1.00) | 0.112 (1.00) | 0.473 (1.00) |  | 0.0105 (1.00)
Del Peak 4(2q22 1) | 0 (0%) | 3959 | 0.142 (1.00) | 0.812 (1.00) | 1.6e-44 (2.53e-41) | 0.000535 (0.64) | 0.0411 (1.00) | 1.03e-36 (1.62e-33) | 1.24e-05 (0.0163) | 0.00168 (1.00) | 0.307 (1.00) | 1.08e-05 (0.0142) | 0.024 (1.00) | 0.312 (1.00) | 0.0472 (1.00) | 0.143 (1.00) | 0.224 (1.00) | 0.475 (1.00) | 0.0973 (1.00) | 0.792 (1.00) |  | 0.282 (1.00)
Del Peak 15(6q26) | 0 (0%) | 3167 | 0.0462 (1.00) | 6.33e-06 (0.00844) | 2.31e-104 (3.85e-101) | 0.00267 (1.00) | 0.572 (1.00) | 3.37e-104 (5.61e-101) | 0.00127 (1.00) | 0.676 (1.00) | 0.172 (1.00) | 1.02e-13 (1.5e-10) | 0.00159 (1.00) | 0.0781 (1.00) | 0.0649 (1.00) | 0.128 (1.00) | 0.798 (1.00) | 0.404 (1.00) | 0.405 (1.00) | 0.258 (1.00) |  | 0.173 (1.00)
Del Peak 17(7q36 1) | 0 (0%) | 4112 | 0.599 (1.00) | 0.235 (1.00) | 9.82e-56 (1.58e-52) | 0.00322 (1.00) | 0.00142 (1.00) | 1.46e-49 (2.32e-46) | 7.27e-11 (1.05e-07) | 0.0471 (1.00) | 0.000181 (0.224) | 0.189 (1.00) | 0.21 (1.00) | 0.0945 (1.00) | 0.854 (1.00) | 0.386 (1.00) | 0.213 (1.00) | 0.798 (1.00) | 0.249 (1.00) | 0.443 (1.00) |  | 0.428 (1.00)
Del Peak 51(Xp21 1) | 0 (0%) | 3441 | 1.5e-05 (0.0197) | 0.205 (1.00) | 1.34e-113 (2.25e-110) | 0.0201 (1.00) | 0.152 (1.00) | 6.27e-103 (1.04e-99) | 0.0101 (1.00) | 0.00924 (1.00) | 0.353 (1.00) | 1.1e-18 (1.65e-15) | 0.00199 (1.00) | 0.342 (1.00) | 0.384 (1.00) | 0.59 (1.00) | 0.818 (1.00) | 0.459 (1.00) | 0.0515 (1.00) | 0.193 (1.00) |  | 0.119 (1.00)
Amp Peak 15(6q21) | 0 (0%) | 4068 | 0.204 (1.00) | 0.0576 (1.00) | 6.27e-28 (9.69e-25) | 4.19e-07 (0.000573) | 0.638 (1.00) | 1.03e-26 (1.58e-23) | 0.00022 (0.27) | 0.183 (1.00) | 0.158 (1.00) | 0.000271 (0.332) | 0.0569 (1.00) | 0.639 (1.00) | 0.967 (1.00) | 0.596 (1.00) | 0.685 (1.00) | 0.55 (1.00) | 0.0192 (1.00) | 0.823 (1.00) |  | 0.0664 (1.00)
Amp Peak 22(9p13 3) | 0 (0%) | 3868 | 0.759 (1.00) | 0.431 (1.00) | 2.06e-34 (3.22e-31) | 0.417 (1.00) | 0.274 (1.00) | 2.44e-31 (3.8e-28) | 4.21e-07 (0.000576) | 0.00328 (1.00) | 0.36 (1.00) | 0.000534 (0.639) | 0.54 (1.00) | 0.344 (1.00) | 0.701 (1.00) | 0.684 (1.00) | 0.674 (1.00) | 0.781 (1.00) | 0.0605 (1.00) | 0.0325 (1.00) |  | 0.02 (1.00)
Amp Peak 35(18q11 2) | 0 (0%) | 3945 | 0.984 (1.00) | 0.00669 (1.00) | 1.36e-38 (2.14e-35) | 0.175 (1.00) | 0.00219 (1.00) | 5.07e-47 (8.08e-44) | 6.41e-12 (9.33e-09) | 0.0434 (1.00) | 0.00107 (1.00) | 0.0244 (1.00) | 0.151 (1.00) | 0.0469 (1.00) | 0.392 (1.00) | 0.877 (1.00) | 1 (1.00) | 0.0987 (1.00) | 0.434 (1.00) | 0.62 (1.00) |  | 0.545 (1.00)
Del Peak 5(2q37 3) | 0 (0%) | 3727 | 0.454 (1.00) | 0.0985 (1.00) | 3.31e-67 (5.35e-64) | 0.00136 (1.00) | 0.279 (1.00) | 2.82e-45 (4.46e-42) | 0.00366 (1.00) | 0.0697 (1.00) | 0.00102 (1.00) | 0.000815 (0.956) | 0.00546 (1.00) | 0.0376 (1.00) | 2.28e-06 (0.00307) | 0.0507 (1.00) | 0.414 (1.00) | 0.187 (1.00) | 0.674 (1.00) | 0.754 (1.00) |  | 0.0152 (1.00)
Del Peak 13(6p25 3) | 0 (0%) | 3859 | 0.0267 (1.00) | 0.796 (1.00) | 3.78e-16 (5.63e-13) | 7.04e-05 (0.0893) | 0.0194 (1.00) | 1.05e-13 (1.55e-10) | 0.321 (1.00) | 0.655 (1.00) | 0.766 (1.00) | 0.219 (1.00) | 0.127 (1.00) | 0.632 (1.00) | 0.327 (1.00) | 0.131 (1.00) | 0.891 (1.00) | 0.32 (1.00) | 0.0546 (1.00) | 0.764 (1.00) |  | 0.603 (1.00)
Del Peak 14(6q22 31) | 0 (0%) | 3285 | 0.00334 (1.00) | 0.000533 (0.639) | 3.9e-93 (6.44e-90) | 0.0569 (1.00) | 0.171 (1.00) | 1.53e-94 (2.52e-91) | 0.00105 (1.00) | 0.804 (1.00) | 0.171 (1.00) | 3.81e-10 (5.45e-07) | 0.00124 (1.00) | 0.0397 (1.00) | 0.148 (1.00) | 0.0146 (1.00) | 0.252 (1.00) | 0.258 (1.00) | 0.159 (1.00) | 0.0783 (1.00) |  | 0.0522 (1.00)
Del Peak 31(12p13 1) | 0 (0%) | 4036 | 0.268 (1.00) | 0.236 (1.00) | 5.87e-21 (8.9e-18) | 2.28e-07 (0.000315) | 0.926 (1.00) | 2.52e-36 (3.96e-33) | 0.401 (1.00) | 0.263 (1.00) | 0.000269 (0.329) | 0.0428 (1.00) | 0.499 (1.00) | 0.0571 (1.00) | 0.443 (1.00) | 0.0227 (1.00) | 0.26 (1.00) | 0.651 (1.00) | 0.2 (1.00) | 0.55 (1.00) |  | 0.633 (1.00)
Del Peak 48(20p12 1) | 0 (0%) | 4125 | 0.333 (1.00) | 0.48 (1.00) | 5.06e-36 (7.93e-33) | 0.25 (1.00) | 0.833 (1.00) | 3.04e-28 (4.7e-25) | 0.000662 (0.786) | 0.000911 (1.00) | 0.0274 (1.00) | 0.00576 (1.00) | 2.98e-05 (0.0385) | 0.225 (1.00) | 0.616 (1.00) | 0.0215 (1.00) | 0.864 (1.00) | 0.947 (1.00) | 0.234 (1.00) | 0.581 (1.00) |  | 0.303 (1.00)
Del Peak 1(1p36 23) | 0 (0%) | 3302 | 0.812 (1.00) | 0.101 (1.00) | 8.82e-39 (1.39e-35) | 0.503 (1.00) | 0.231 (1.00) | 3.35e-32 (5.22e-29) | 0.0118 (1.00) | 0.0108 (1.00) | 0.0434 (1.00) | 0.00307 (1.00) | 0.207 (1.00) | 0.0354 (1.00) | 0.00703 (1.00) | 0.24 (1.00) | 0.689 (1.00) | 0.0369 (1.00) | 0.142 (1.00) | 0.000722 (0.851) |  | 0.000694 (0.822)

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

P value = 4.52e-119 (Chi-square test), Q value = 7.6e-116

Table S1. Gene #1: 'Amp Peak 1(1p34.2)' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'

nPatients | BLADDER | BRAIN | BREAST | COLON | ENDOMETRIAL | HEAD/NECK | KIDNEY | LUNG | OMENTUM | OVARY | PERITONEUM (OVARY) | RECTUM
--- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | ---
ALL | 131 | 544 | 857 | 412 | 454 | 321 | 493 | 714 | 2 | 548 | 2 | 159
AMP PEAK 1(1P34.2) CNV | 40 | 77 | 124 | 22 | 52 | 46 | 16 | 163 | 1 | 276 | 1 | 7
AMP PEAK 1(1P34.2) WILD-TYPE | 91 | 467 | 733 | 390 | 402 | 275 | 477 | 551 | 1 | 272 | 1 | 152

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

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

P value = 5.11e-13 (Fisher's exact test), Q value = 7.5e-10

Table S2. Gene #1: 'Amp Peak 1(1p34.2)' versus Clinical Feature #4: 'GENDER'

nPatients | FEMALE | MALE
--- | --- | ---
ALL | 2924 | 1717
AMP PEAK 1(1P34.2) CNV | 609 | 216
AMP PEAK 1(1P34.2) WILD-TYPE | 2315 | 1501

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

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

P value = 1.04e-111 (Chi-square test), Q value = 1.7e-108

Table S3. Gene #1: 'Amp Peak 1(1p34.2)' versus Clinical Feature #6: 'HISTOLOGICAL.TYPE'

nPatients | COLON ADENOCARCINOMA | COLON MUCINOUS ADENOCARCINOMA | ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA | HEAD & NECK SQUAMOUS CELL CARCINOMA | INFILTRATING DUCTAL CARCINOMA | INFILTRATING LOBULAR 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 HISTOLOGY (PLEASE SPECIFY) | MIXED SEROUS AND ENDOMETRIOID | MUCINOUS (COLLOID) ADENOCARCINOMA | MUCINOUS (COLLOID) CARCINOMA | MUSCLE INVASIVE UROTHELIAL CARCINOMA (PT2 OR ABOVE) | OTHER SPECIFY | RECTAL ADENOCARCINOMA | RECTAL MUCINOUS ADENOCARCINOMA | SEROUS CYSTADENOCARCINOMA | SEROUS ENDOMETRIAL ADENOCARCINOMA | TREATED PRIMARY GBM | UNTREATED PRIMARY (DE NOVO) GBM
--- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | ---
ALL | 356 | 54 | 351 | 321 | 104 | 12 | 493 | 11 | 79 | 243 | 7 | 4 | 17 | 2 | 3 | 2 | 18 | 1 | 1 | 1 | 3 | 315 | 5 | 18 | 4 | 3 | 49 | 10 | 143 | 13 | 552 | 85 | 1 | 20
AMP PEAK 1(1P34.2) CNV | 20 | 2 | 14 | 46 | 22 | 0 | 16 | 4 | 15 | 73 | 3 | 1 | 5 | 0 | 1 | 0 | 6 | 0 | 0 | 1 | 1 | 52 | 0 | 5 | 1 | 0 | 13 | 1 | 5 | 2 | 278 | 33 | 0 | 2
AMP PEAK 1(1P34.2) WILD-TYPE | 336 | 52 | 337 | 275 | 82 | 12 | 477 | 7 | 64 | 170 | 4 | 3 | 12 | 2 | 2 | 2 | 12 | 1 | 1 | 0 | 2 | 263 | 5 | 13 | 3 | 3 | 36 | 9 | 138 | 11 | 274 | 52 | 1 | 18

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

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

P value = 6.36e-06 (Fisher's exact test), Q value = 0.0085

Table S4. Gene #1: 'Amp Peak 1(1p34.2)' versus Clinical Feature #7: 'PATHOLOGY.T'

nPatients | T0+T1 | T2 | T3 | T4
--- | --- | --- | --- | ---
ALL | 448 | 611 | 688 | 208
AMP PEAK 1(1P34.2) CNV | 43 | 97 | 50 | 29
AMP PEAK 1(1P34.2) WILD-TYPE | 405 | 514 | 638 | 179

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

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

P value = 2.25e-17 (Fisher's exact test), Q value = 3.4e-14

Table S5. Gene #1: 'Amp Peak 1(1p34.2)' versus Clinical Feature #10: 'TUMOR.STAGE'

nPatients | I | II | III | IV
--- | --- | --- | --- | ---
ALL | 685 | 487 | 876 | 420
AMP PEAK 1(1P34.2) CNV | 94 | 60 | 256 | 81
AMP PEAK 1(1P34.2) WILD-TYPE | 591 | 427 | 620 | 339

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

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

P value = 2.34e-45 (Chi-square test), Q value = 3.7e-42

Table S6. Gene #2: 'Amp Peak 2(1p22.3)' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'

nPatients | BLADDER | BRAIN | BREAST | COLON | ENDOMETRIAL | HEAD/NECK | KIDNEY | LUNG | OMENTUM | OVARY | PERITONEUM (OVARY) | RECTUM
--- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | ---
ALL | 131 | 544 | 857 | 412 | 454 | 321 | 493 | 714 | 2 | 548 | 2 | 159
AMP PEAK 2(1P22.3) CNV | 39 | 74 | 188 | 19 | 76 | 38 | 18 | 163 | 1 | 163 | 0 | 11
AMP PEAK 2(1P22.3) WILD-TYPE | 92 | 470 | 669 | 393 | 378 | 283 | 475 | 551 | 1 | 385 | 2 | 148

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

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

P value = 4.85e-11 (Fisher's exact test), Q value = 7e-08

Table S7. Gene #2: 'Amp Peak 2(1p22.3)' versus Clinical Feature #4: 'GENDER'

nPatients | FEMALE | MALE
--- | --- | ---
ALL | 2924 | 1717
AMP PEAK 2(1P22.3) CNV | 578 | 212
AMP PEAK 2(1P22.3) WILD-TYPE | 2346 | 1505

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

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

P value = 6.93e-41 (Chi-square test), Q value = 1.1e-37

Table S8. Gene #2: 'Amp Peak 2(1p22.3)' versus Clinical Feature #6: 'HISTOLOGICAL.TYPE'

nPatients | COLON ADENOCARCINOMA | COLON MUCINOUS ADENOCARCINOMA | ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA | HEAD & NECK SQUAMOUS CELL CARCINOMA | INFILTRATING DUCTAL CARCINOMA | INFILTRATING LOBULAR 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 HISTOLOGY (PLEASE SPECIFY) | MIXED SEROUS AND ENDOMETRIOID | MUCINOUS (COLLOID) ADENOCARCINOMA | MUCINOUS (COLLOID) CARCINOMA | MUSCLE INVASIVE UROTHELIAL CARCINOMA (PT2 OR ABOVE) | OTHER SPECIFY | RECTAL ADENOCARCINOMA | RECTAL MUCINOUS ADENOCARCINOMA | SEROUS CYSTADENOCARCINOMA | SEROUS ENDOMETRIAL ADENOCARCINOMA | TREATED PRIMARY GBM | UNTREATED PRIMARY (DE NOVO) GBM
--- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | ---
ALL | 356 | 54 | 351 | 321 | 104 | 12 | 493 | 11 | 79 | 243 | 7 | 4 | 17 | 2 | 3 | 2 | 18 | 1 | 1 | 1 | 3 | 315 | 5 | 18 | 4 | 3 | 49 | 10 | 143 | 13 | 552 | 85 | 1 | 20
AMP PEAK 2(1P22.3) CNV | 17 | 2 | 47 | 38 | 30 | 2 | 18 | 4 | 19 | 65 | 2 | 0 | 8 | 0 | 2 | 0 | 3 | 1 | 0 | 0 | 2 | 56 | 3 | 4 | 1 | 0 | 11 | 1 | 9 | 2 | 164 | 25 | 0 | 2
AMP PEAK 2(1P22.3) WILD-TYPE | 339 | 52 | 304 | 283 | 74 | 10 | 475 | 7 | 60 | 178 | 5 | 4 | 9 | 2 | 1 | 2 | 15 | 0 | 1 | 1 | 1 | 259 | 2 | 14 | 3 | 3 | 38 | 9 | 134 | 11 | 388 | 60 | 1 | 18

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

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

P value = 8.67e-05 (Fisher's exact test), Q value = 0.11

Table S9. Gene #2: 'Amp Peak 2(1p22.3)' versus Clinical Feature #7: 'PATHOLOGY.T'

nPatients | T0+T1 | T2 | T3 | T4
--- | --- | --- | --- | ---
ALL | 448 | 611 | 688 | 208
AMP PEAK 2(1P22.3) CNV | 41 | 93 | 53 | 28
AMP PEAK 2(1P22.3) WILD-TYPE | 407 | 518 | 635 | 180

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

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

P value = 3.46e-05 (Fisher's exact test), Q value = 0.044

Table S10. Gene #2: 'Amp Peak 2(1p22.3)' versus Clinical Feature #10: 'TUMOR.STAGE'

nPatients | I | II | III | IV
--- | --- | --- | --- | ---
ALL | 685 | 487 | 876 | 420
AMP PEAK 2(1P22.3) CNV | 83 | 57 | 173 | 61
AMP PEAK 2(1P22.3) WILD-TYPE | 602 | 430 | 703 | 359

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

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

P value = 1.44e-06 (logrank test), Q value = 0.002

Table S11. Gene #3: 'Amp Peak 3(1q21.3)' versus Clinical Feature #1: 'Time to Death'

| nPatients | nDeath | Duration Range (Median), Month
--- | --- | --- | ---
ALL | 4370 | 1406 | 0.0 - 224.0 (14.4)
AMP PEAK 3(1Q21.3) CNV | 1950 | 562 | 0.0 - 224.0 (14.9)
AMP PEAK 3(1Q21.3) WILD-TYPE | 2420 | 844 | 0.0 - 210.9 (14.1)

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

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

P value = 5.02e-206 (Chi-square test), Q value = 8.7e-203

Table S12. Gene #3: 'Amp Peak 3(1q21.3)' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'

nPatients | BLADDER | BRAIN | BREAST | COLON | ENDOMETRIAL | HEAD/NECK | KIDNEY | LUNG | OMENTUM | OVARY | PERITONEUM (OVARY) | RECTUM
--- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | ---
ALL | 131 | 544 | 857 | 412 | 454 | 321 | 493 | 714 | 2 | 548 | 2 | 159
AMP PEAK 3(1Q21.3) CNV | 68 | 92 | 616 | 79 | 200 | 87 | 60 | 458 | 0 | 344 | 2 | 45
AMP PEAK 3(1Q21.3) WILD-TYPE | 63 | 452 | 241 | 333 | 254 | 234 | 433 | 256 | 2 | 204 | 0 | 114

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

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

P value = 1.59e-35 (Fisher's exact test), Q value = 2.5e-32

Table S13. Gene #3: 'Amp Peak 3(1q21.3)' versus Clinical Feature #4: 'GENDER'

nPatients | FEMALE | MALE
--- | --- | ---
ALL | 2924 | 1717
AMP PEAK 3(1Q21.3) CNV | 1496 | 558
AMP PEAK 3(1Q21.3) WILD-TYPE | 1428 | 1159

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

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

P value = 5.21e-127 (Chi-square test), Q value = 8.8e-124

Table S14. Gene #3: 'Amp Peak 3(1q21.3)' versus Clinical Feature #6: 'HISTOLOGICAL.TYPE'

nPatients | COLON ADENOCARCINOMA | COLON MUCINOUS ADENOCARCINOMA | ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA | HEAD & NECK SQUAMOUS CELL CARCINOMA | INFILTRATING DUCTAL CARCINOMA | INFILTRATING LOBULAR 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 HISTOLOGY (PLEASE SPECIFY) | MIXED SEROUS AND ENDOMETRIOID | MUCINOUS (COLLOID) ADENOCARCINOMA | MUCINOUS (COLLOID) CARCINOMA | MUSCLE INVASIVE UROTHELIAL CARCINOMA (PT2 OR ABOVE) | OTHER SPECIFY | RECTAL ADENOCARCINOMA | RECTAL MUCINOUS ADENOCARCINOMA | SEROUS CYSTADENOCARCINOMA | SEROUS ENDOMETRIAL ADENOCARCINOMA | TREATED PRIMARY GBM | UNTREATED PRIMARY (DE NOVO) GBM
--- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | ---
ALL | 356 | 54 | 351 | 321 | 104 | 12 | 493 | 11 | 79 | 243 | 7 | 4 | 17 | 2 | 3 | 2 | 18 | 1 | 1 | 1 | 3 | 315 | 5 | 18 | 4 | 3 | 49 | 10 | 143 | 13 | 552 | 85 | 1 | 20
AMP PEAK 3(1Q21.3) CNV | 72 | 7 | 137 | 87 | 82 | 11 | 60 | 10 | 61 | 174 | 6 | 0 | 14 | 2 | 2 | 1 | 13 | 1 | 0 | 1 | 2 | 168 | 4 | 8 | 3 | 0 | 22 | 8 | 41 | 3 | 346 | 55 | 0 | 2
AMP PEAK 3(1Q21.3) WILD-TYPE | 284 | 47 | 214 | 234 | 22 | 1 | 433 | 1 | 18 | 69 | 1 | 4 | 3 | 0 | 1 | 1 | 5 | 0 | 1 | 0 | 1 | 147 | 1 | 10 | 1 | 3 | 27 | 2 | 102 | 10 | 206 | 30 | 1 | 18

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

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

P value = 1.17e-14 (Fisher's exact test), Q value = 1.7e-11

Table S15. Gene #3: 'Amp Peak 3(1q21.3)' versus Clinical Feature #7: 'PATHOLOGY.T'

nPatients | T0+T1 | T2 | T3 | T4
--- | --- | --- | --- | ---
ALL | 448 | 611 | 688 | 208
AMP PEAK 3(1Q21.3) CNV | 124 | 276 | 170 | 74
AMP PEAK 3(1Q21.3) WILD-TYPE | 324 | 335 | 518 | 134

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

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

P value = 4.31e-05 (Chi-square test), Q value = 0.055

Table S16. Gene #3: 'Amp Peak 3(1q21.3)' versus Clinical Feature #9: 'PATHOLOGICSPREAD(M)'

nPatients | M0 | M1 | M1A | M1B | MX
--- | --- | --- | --- | --- | ---
ALL | 1398 | 167 | 9 | 1 | 148
AMP PEAK 3(1Q21.3) CNV | 447 | 47 | 3 | 0 | 76
AMP PEAK 3(1Q21.3) WILD-TYPE | 951 | 120 | 6 | 1 | 72

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

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

P value = 3.44e-07 (Fisher's exact test), Q value = 0.00047

Table S17. Gene #3: 'Amp Peak 3(1q21.3)' versus Clinical Feature #10: 'TUMOR.STAGE'

nPatients | I | II | III | IV
--- | --- | --- | --- | ---
ALL | 685 | 487 | 876 | 420
AMP PEAK 3(1Q21.3) CNV | 247 | 167 | 414 | 151
AMP PEAK 3(1Q21.3) WILD-TYPE | 438 | 320 | 462 | 269

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

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

P value = 1.78e-05 (logrank test), Q value = 0.023

Table S18. Gene #4: 'Amp Peak 4(1q32.1)' versus Clinical Feature #1: 'Time to Death'

| nPatients | nDeath | Duration Range (Median), Month
--- | --- | --- | ---
ALL | 4370 | 1406 | 0.0 - 224.0 (14.4)
AMP PEAK 4(1Q32.1) CNV | 1936 | 556 | 0.0 - 223.4 (14.6)
AMP PEAK 4(1Q32.1) WILD-TYPE | 2434 | 850 | 0.0 - 224.0 (14.3)

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

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

P value = 6.43e-187 (Chi-square test), Q value = 1.1e-183

Table S19. Gene #4: 'Amp Peak 4(1q32.1)' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'

nPatients | BLADDER | BRAIN | BREAST | COLON | ENDOMETRIAL | HEAD/NECK | KIDNEY | LUNG | OMENTUM | OVARY | PERITONEUM (OVARY) | RECTUM
--- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | ---
ALL | 131 | 544 | 857 | 412 | 454 | 321 | 493 | 714 | 2 | 548 | 2 | 159
AMP PEAK 4(1Q32.1) CNV | 45 | 148 | 659 | 86 | 190 | 87 | 58 | 448 | 0 | 270 | 2 | 47
AMP PEAK 4(1Q32.1) WILD-TYPE | 86 | 396 | 198 | 326 | 264 | 234 | 435 | 266 | 2 | 278 | 0 | 112

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

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

P value = 4.15e-28 (Fisher's exact test), Q value = 6.4e-25

Table S20. Gene #4: 'Amp Peak 4(1q32.1)' versus Clinical Feature #4: 'GENDER'

nPatients | FEMALE | MALE
--- | --- | ---
ALL | 2924 | 1717
AMP PEAK 4(1Q32.1) CNV | 1465 | 577
AMP PEAK 4(1Q32.1) WILD-TYPE | 1459 | 1140

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

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

P value = 1.42e-104 (Chi-square test), Q value = 2.4e-101

Table S21. Gene #4: 'Amp Peak 4(1q32.1)' versus Clinical Feature #6: 'HISTOLOGICAL.TYPE'

nPatients | COLON ADENOCARCINOMA | COLON MUCINOUS ADENOCARCINOMA | ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA | HEAD & NECK SQUAMOUS CELL CARCINOMA | INFILTRATING DUCTAL CARCINOMA | INFILTRATING LOBULAR 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 HISTOLOGY (PLEASE SPECIFY) | MIXED SEROUS AND ENDOMETRIOID | MUCINOUS (COLLOID) ADENOCARCINOMA | MUCINOUS (COLLOID) CARCINOMA | MUSCLE INVASIVE UROTHELIAL CARCINOMA (PT2 OR ABOVE) | OTHER SPECIFY | RECTAL ADENOCARCINOMA | RECTAL MUCINOUS ADENOCARCINOMA | SEROUS CYSTADENOCARCINOMA | SEROUS ENDOMETRIAL ADENOCARCINOMA | TREATED PRIMARY GBM | UNTREATED PRIMARY (DE NOVO) GBM
--- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | ---
ALL | 356 | 54 | 351 | 321 | 104 | 12 | 493 | 11 | 79 | 243 | 7 | 4 | 17 | 2 | 3 | 2 | 18 | 1 | 1 | 1 | 3 | 315 | 5 | 18 | 4 | 3 | 49 | 10 | 143 | 13 | 552 | 85 | 1 | 20
AMP PEAK 4(1Q32.1) CNV | 79 | 7 | 146 | 87 | 86 | 11 | 58 | 10 | 56 | 173 | 6 | 0 | 14 | 2 | 2 | 0 | 13 | 1 | 0 | 1 | 3 | 164 | 4 | 6 | 2 | 1 | 9 | 7 | 42 | 4 | 272 | 38 | 0 | 4
AMP PEAK 4(1Q32.1) WILD-TYPE | 277 | 47 | 205 | 234 | 18 | 1 | 435 | 1 | 23 | 70 | 1 | 4 | 3 | 0 | 1 | 2 | 5 | 0 | 1 | 0 | 0 | 151 | 1 | 12 | 2 | 2 | 40 | 3 | 101 | 9 | 280 | 47 | 1 | 16

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

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

P value = 1.12e-15 (Fisher's exact test), Q value = 1.7e-12

Table S22. Gene #4: 'Amp Peak 4(1q32.1)' versus Clinical Feature #7: 'PATHOLOGY.T'

nPatients | T0+T1 | T2 | T3 | T4
--- | --- | --- | --- | ---
ALL | 448 | 611 | 688 | 208
AMP PEAK 4(1Q32.1) CNV | 121 | 278 | 169 | 75
AMP PEAK 4(1Q32.1) WILD-TYPE | 327 | 333 | 519 | 133

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

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

P value = 9.71e-06 (Chi-square test), Q value = 0.013

Table S23. Gene #4: 'Amp Peak 4(1q32.1)' versus Clinical Feature #20: '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 X
--- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | ---
ALL | 71 | 45 | 2 | 34 | 246 | 165 | 29 | 107 | 22 | 36 | 35 | 12
AMP PEAK 4(1Q32.1) CNV | 45 | 28 | 2 | 15 | 191 | 129 | 14 | 82 | 18 | 30 | 20 | 10
AMP PEAK 4(1Q32.1) WILD-TYPE | 26 | 17 | 0 | 19 | 55 | 36 | 15 | 25 | 4 | 6 | 15 | 2

Figure S23. Get High-res Image Gene #4: 'Amp Peak 4(1q32.1)' versus Clinical Feature #20: 'NEOPLASM.DISEASESTAGE'

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

P value = 1.25e-06 (logrank test), Q value = 0.0017

Table S24. Gene #5: 'Amp Peak 5(1q44)' versus Clinical Feature #1: 'Time to Death'

| nPatients | nDeath | Duration Range (Median), Month
--- | --- | --- | ---
ALL | 4370 | 1406 | 0.0 - 224.0 (14.4)
AMP PEAK 5(1Q44) CNV | 1848 | 528 | 0.0 - 223.4 (15.1)
AMP PEAK 5(1Q44) WILD-TYPE | 2522 | 878 | 0.0 - 224.0 (14.0)

Figure S24. Get High-res Image Gene #5: 'Amp Peak 5(1q44)' versus Clinical Feature #1: 'Time to Death'

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

P value = 4.2e-184 (Chi-square test), Q value = 7.2e-181

Table S25. Gene #5: 'Amp Peak 5(1q44)' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'

nPatients | BLADDER | BRAIN | BREAST | COLON | ENDOMETRIAL | HEAD/NECK | KIDNEY | LUNG | OMENTUM | OVARY | PERITONEUM (OVARY) | RECTUM
--- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | ---
ALL | 131 | 544 | 857 | 412 | 454 | 321 | 493 | 714 | 2 | 548 | 2 | 159
AMP PEAK 5(1Q44) CNV | 50 | 93 | 620 | 85 | 184 | 94 | 55 | 431 | 2 | 283 | 2 | 46
AMP PEAK 5(1Q44) WILD-TYPE | 81 | 451 | 237 | 327 | 270 | 227 | 438 | 283 | 0 | 265 | 0 | 113

Figure S25. Get High-res Image Gene #5: 'Amp Peak 5(1q44)' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'

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

P value = 4.53e-31 (Fisher's exact test), Q value = 7e-28

Table S26. Gene #5: 'Amp Peak 5(1q44)' versus Clinical Feature #4: 'GENDER'

nPatients | FEMALE | MALE
--- | --- | ---
ALL | 2924 | 1717
AMP PEAK 5(1Q44) CNV | 1413 | 533
AMP PEAK 5(1Q44) WILD-TYPE | 1511 | 1184

Figure S26. Get High-res Image Gene #5: 'Amp Peak 5(1q44)' versus Clinical Feature #4: 'GENDER'

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

P value = 3.46e-96 (Chi-square test), Q value = 5.7e-93

Table S27. Gene #5: 'Amp Peak 5(1q44)' versus Clinical Feature #6: 'HISTOLOGICAL.TYPE'

nPatients | COLON ADENOCARCINOMA | COLON MUCINOUS ADENOCARCINOMA | ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA | HEAD & NECK SQUAMOUS CELL CARCINOMA | INFILTRATING DUCTAL CARCINOMA | INFILTRATING LOBULAR 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 HISTOLOGY (PLEASE SPECIFY) | MIXED SEROUS AND ENDOMETRIOID | MUCINOUS (COLLOID) ADENOCARCINOMA | MUCINOUS (COLLOID) CARCINOMA | MUSCLE INVASIVE UROTHELIAL CARCINOMA (PT2 OR ABOVE) | OTHER SPECIFY | RECTAL ADENOCARCINOMA | RECTAL MUCINOUS ADENOCARCINOMA | SEROUS CYSTADENOCARCINOMA | SEROUS ENDOMETRIAL ADENOCARCINOMA | TREATED PRIMARY GBM | UNTREATED PRIMARY (DE NOVO) GBM
--- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | ---
ALL | 356 | 54 | 351 | 321 | 104 | 12 | 493 | 11 | 79 | 243 | 7 | 4 | 17 | 2 | 3 | 2 | 18 | 1 | 1 | 1 | 3 | 315 | 5 | 18 | 4 | 3 | 49 | 10 | 143 | 13 | 552 | 85 | 1 | 20
AMP PEAK 5(1Q44) CNV | 76 | 9 | 141 | 94 | 84 | 11 | 55 | 10 | 51 | 164 | 6 | 1 | 13 | 2 | 2 | 0 | 12 | 1 | 0 | 1 | 3 | 162 | 4 | 5 | 2 | 1 | 13 | 6 | 41 | 4 | 287 | 38 | 0 | 3
AMP PEAK 5(1Q44) WILD-TYPE | 280 | 45 | 210 | 227 | 20 | 1 | 438 | 1 | 28 | 79 | 1 | 3 | 4 | 0 | 1 | 2 | 6 | 0 | 1 | 0 | 0 | 153 | 1 | 13 | 2 | 2 | 36 | 4 | 102 | 9 | 265 | 47 | 1 | 17

Figure S27. Get High-res Image Gene #5: 'Amp Peak 5(1q44)' versus Clinical Feature #6: 'HISTOLOGICAL.TYPE'

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

P value = 7.27e-14 (Fisher's exact test), Q value = 1.1e-10

Table S28. Gene #5: 'Amp Peak 5(1q44)' versus Clinical Feature #7: 'PATHOLOGY.T'

nPatients | T0+T1 | T2 | T3 | T4
--- | --- | --- | --- | ---
ALL | 448 | 611 | 688 | 208
AMP PEAK 5(1Q44) CNV | 117 | 263 | 167 | 81
AMP PEAK 5(1Q44) WILD-TYPE | 331 | 348 | 521 | 127

Figure S28. Get High-res Image Gene #5: 'Amp Peak 5(1q44)' versus Clinical Feature #7: 'PATHOLOGY.T'

'Amp Peak 5(1q44)' versus 'PATHOLOGY.N'

P value = 4.85e-05 (Fisher's exact test), Q value = 0.062

Table S29. Gene #5: 'Amp Peak 5(1q44)' versus Clinical Feature #8: 'PATHOLOGY.N'

nPatients | N0 | N1 | N2 | N3
--- | --- | --- | --- | ---
ALL | 1036 | 343 | 279 | 11
AMP PEAK 5(1Q44) CNV | 318 | 149 | 110 | 5
AMP PEAK 5(1Q44) WILD-TYPE | 718 | 194 | 169 | 6

Figure S29. Get High-res Image Gene #5: 'Amp Peak 5(1q44)' versus Clinical Feature #8: 'PATHOLOGY.N'

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

P value = 1.25e-06 (t-test), Q value = 0.0017

Table S30. Gene #6: 'Amp Peak 6(2p15)' versus Clinical Feature #2: 'AGE'

| nPatients | Mean (Std.Dev)
--- | --- | ---
ALL | 4585 | 61.9 (12.6)
AMP PEAK 6(2P15) CNV | 1058 | 63.5 (11.7)
AMP PEAK 6(2P15) WILD-TYPE | 3527 | 61.4 (12.8)

Figure S30. Get High-res Image Gene #6: 'Amp Peak 6(2p15)' versus Clinical Feature #2: 'AGE'

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

P value = 4.91e-75 (Chi-square test), Q value = 8e-72

Table S31. Gene #6: 'Amp Peak 6(2p15)' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'

nPatients | BLADDER | BRAIN | BREAST | COLON | ENDOMETRIAL | HEAD/NECK | KIDNEY | LUNG | OMENTUM | OVARY | PERITONEUM (OVARY) | RECTUM
--- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | ---
ALL | 131 | 544 | 857 | 412 | 454 | 321 | 493 | 714 | 2 | 548 | 2 | 159
AMP PEAK 6(2P15) CNV | 49 | 30 | 149 | 73 | 85 | 71 | 69 | 296 | 0 | 218 | 0 | 36
AMP PEAK 6(2P15) WILD-TYPE | 82 | 514 | 708 | 339 | 369 | 250 | 424 | 418 | 2 | 330 | 2 | 123

Figure S31. Get High-res Image Gene #6: 'Amp Peak 6(2p15)' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'

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

P value = 2.14e-49 (Chi-square test), Q value = 3.4e-46

Table S32. Gene #6: 'Amp Peak 6(2p15)' versus Clinical Feature #6: 'HISTOLOGICAL.TYPE'

nPatients | COLON ADENOCARCINOMA | COLON MUCINOUS ADENOCARCINOMA | ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA | HEAD & NECK SQUAMOUS CELL CARCINOMA | INFILTRATING DUCTAL CARCINOMA | INFILTRATING LOBULAR 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 HISTOLOGY (PLEASE SPECIFY) | MIXED SEROUS AND ENDOMETRIOID | MUCINOUS (COLLOID) ADENOCARCINOMA | MUCINOUS (COLLOID) CARCINOMA | MUSCLE INVASIVE UROTHELIAL CARCINOMA (PT2 OR ABOVE) | OTHER SPECIFY | RECTAL ADENOCARCINOMA | RECTAL MUCINOUS ADENOCARCINOMA | SEROUS CYSTADENOCARCINOMA | SEROUS ENDOMETRIAL ADENOCARCINOMA | TREATED PRIMARY GBM | UNTREATED PRIMARY (DE NOVO) GBM
--- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | ---
ALL | 356 | 54 | 351 | 321 | 104 | 12 | 493 | 11 | 79 | 243 | 7 | 4 | 17 | 2 | 3 | 2 | 18 | 1 | 1 | 1 | 3 | 315 | 5 | 18 | 4 | 3 | 49 | 10 | 143 | 13 | 552 | 85 | 1 | 20
AMP PEAK 6(2P15) CNV | 67 | 6 | 44 | 71 | 22 | 0 | 69 | 3 | 27 | 77 | 6 | 0 | 3 | 2 | 1 | 0 | 4 | 1 | 0 | 0 | 1 | 169 | 0 | 5 | 2 | 0 | 20 | 1 | 36 | 0 | 218 | 36 | 0 | 2
AMP PEAK 6(2P15) WILD-TYPE | 289 | 48 | 307 | 250 | 82 | 12 | 424 | 8 | 52 | 166 | 1 | 4 | 14 | 0 | 2 | 2 | 14 | 0 | 1 | 1 | 2 | 146 | 5 | 13 | 2 | 3 | 29 | 9 | 107 | 13 | 334 | 49 | 1 | 18

Figure S32. Get High-res Image Gene #6: 'Amp Peak 6(2p15)' versus Clinical Feature #6: 'HISTOLOGICAL.TYPE'

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

P value = 4.26e-05 (Fisher's exact test), Q value = 0.054

Table S33. Gene #6: 'Amp Peak 6(2p15)' versus Clinical Feature #10: 'TUMOR.STAGE'

nPatients | I | II | III | IV
--- | --- | --- | --- | ---
ALL | 685 | 487 | 876 | 420
AMP PEAK 6(2P15) CNV | 169 | 141 | 302 | 103
AMP PEAK 6(2P15) WILD-TYPE | 516 | 346 | 574 | 317

Figure S33. Get High-res Image Gene #6: 'Amp Peak 6(2p15)' versus Clinical Feature #10: 'TUMOR.STAGE'

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

P value = 4.72e-13 (Fisher's exact test), Q value = 6.9e-10

Table S34. Gene #6: 'Amp Peak 6(2p15)' versus Clinical Feature #11: 'RADIATIONS.RADIATION.REGIMENINDICATION'

nPatients | NO | YES
--- | --- | ---
ALL | 835 | 3816
AMP PEAK 6(2P15) CNV | 117 | 964
AMP PEAK 6(2P15) WILD-TYPE | 718 | 2852

Figure S34. Get High-res Image Gene #6: 'Amp Peak 6(2p15)' versus Clinical Feature #11: 'RADIATIONS.RADIATION.REGIMENINDICATION'

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

P value = 3.58e-06 (t-test), Q value = 0.0048

Table S35. Gene #7: 'Amp Peak 7(2q31.2)' versus Clinical Feature #2: 'AGE'

| nPatients | Mean (Std.Dev)
--- | --- | ---
ALL | 4585 | 61.9 (12.6)
AMP PEAK 7(2Q31.2) CNV | 906 | 63.5 (11.6)
AMP PEAK 7(2Q31.2) WILD-TYPE | 3679 | 61.5 (12.8)

Figure S35. Get High-res Image Gene #7: 'Amp Peak 7(2q31.2)' versus Clinical Feature #2: 'AGE'

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

P value = 5.68e-77 (Chi-square test), Q value = 9.3e-74

Table S36. Gene #7: 'Amp Peak 7(2q31.2)' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'

nPatients | BLADDER | BRAIN | BREAST | COLON | ENDOMETRIAL | HEAD/NECK | KIDNEY | LUNG | OMENTUM | OVARY | PERITONEUM (OVARY) | RECTUM
--- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | ---
ALL | 131 | 544 | 857 | 412 | 454 | 321 | 493 | 714 | 2 | 548 | 2 | 159
AMP PEAK 7(2Q31.2) CNV | 20 | 28 | 82 | 70 | 75 | 68 | 75 | 233 | 0 | 230 | 1 | 40
AMP PEAK 7(2Q31.2) WILD-TYPE | 111 | 516 | 775 | 342 | 379 | 253 | 418 | 481 | 2 | 318 | 1 | 119

Figure S36. Get High-res Image Gene #7: 'Amp Peak 7(2q31.2)' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'

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

P value = 6.05e-36 (Chi-square test), Q value = 9.5e-33

Table S37. Gene #7: 'Amp Peak 7(2q31.2)' versus Clinical Feature #6: 'HISTOLOGICAL.TYPE'

nPatients | COLON ADENOCARCINOMA | COLON MUCINOUS ADENOCARCINOMA | ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA | HEAD & NECK SQUAMOUS CELL CARCINOMA | INFILTRATING DUCTAL CARCINOMA | INFILTRATING LOBULAR 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 HISTOLOGY (PLEASE SPECIFY) | MIXED SEROUS AND ENDOMETRIOID | MUCINOUS (COLLOID) ADENOCARCINOMA | MUCINOUS (COLLOID) CARCINOMA | MUSCLE INVASIVE UROTHELIAL CARCINOMA (PT2 OR ABOVE) | OTHER SPECIFY | RECTAL ADENOCARCINOMA | RECTAL MUCINOUS ADENOCARCINOMA | SEROUS CYSTADENOCARCINOMA | SEROUS ENDOMETRIAL ADENOCARCINOMA | TREATED PRIMARY GBM | UNTREATED PRIMARY (DE NOVO) GBM
--- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | ---
ALL | 356 | 54 | 351 | 321 | 104 | 12 | 493 | 11 | 79 | 243 | 7 | 4 | 17 | 2 | 3 | 2 | 18 | 1 | 1 | 1 | 3 | 315 | 5 | 18 | 4 | 3 | 49 | 10 | 143 | 13 | 552 | 85 | 1 | 20
AMP PEAK 7(2Q31.2) CNV | 64 | 6 | 36 | 68 | 13 | 0 | 75 | 3 | 32 | 73 | 4 | 0 | 4 | 0 | 1 | 0 | 5 | 1 | 0 | 1 | 1 | 106 | 0 | 3 | 2 | 0 | 8 | 0 | 40 | 0 | 231 | 36 | 0 | 1
AMP PEAK 7(2Q31.2) WILD-TYPE | 292 | 48 | 315 | 253 | 91 | 12 | 418 | 8 | 47 | 170 | 3 | 4 | 13 | 2 | 2 | 2 | 13 | 0 | 1 | 0 | 2 | 209 | 5 | 15 | 2 | 3 | 41 | 10 | 103 | 13 | 321 | 49 | 1 | 19

Figure S37. Get High-res Image Gene #7: 'Amp Peak 7(2q31.2)' versus Clinical Feature #6: 'HISTOLOGICAL.TYPE'

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

P value = 2.17e-05 (Fisher's exact test), Q value = 0.028

Table S38. Gene #7: 'Amp Peak 7(2q31.2)' versus Clinical Feature #10: 'TUMOR.STAGE'

nPatients | I | II | III | IV
--- | --- | --- | --- | ---
ALL | 685 | 487 | 876 | 420
AMP PEAK 7(2Q31.2) CNV | 161 | 121 | 287 | 94
AMP PEAK 7(2Q31.2) WILD-TYPE | 524 | 366 | 589 | 326

Figure S38. Get High-res Image Gene #7: 'Amp Peak 7(2q31.2)' versus Clinical Feature #10: 'TUMOR.STAGE'

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

P value = 3.68e-13 (Fisher's exact test), Q value = 5.4e-10

Table S39. Gene #7: 'Amp Peak 7(2q31.2)' versus Clinical Feature #11: 'RADIATIONS.RADIATION.REGIMENINDICATION'

nPatients | NO | YES
--- | --- | ---
ALL | 835 | 3816
AMP PEAK 7(2Q31.2) CNV | 94 | 833
AMP PEAK 7(2Q31.2) WILD-TYPE | 741 | 2983

Figure S39. Get High-res Image Gene #7: 'Amp Peak 7(2q31.2)' versus Clinical Feature #11: 'RADIATIONS.RADIATION.REGIMENINDICATION'

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

P value = 2.48e-239 (Chi-square test), Q value = 4.3e-236

Table S40. Gene #8: 'Amp Peak 8(3q26.2)' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'

nPatients | BLADDER | BRAIN | BREAST | COLON | ENDOMETRIAL | HEAD/NECK | KIDNEY | LUNG | OMENTUM | OVARY | PERITONEUM (OVARY) | RECTUM
--- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | ---
ALL | 131 | 544 | 857 | 412 | 454 | 321 | 493 | 714 | 2 | 548 | 2 | 159
AMP PEAK 8(3Q26.2) CNV | 76 | 79 | 274 | 65 | 126 | 238 | 78 | 428 | 1 | 453 | 2 | 37
AMP PEAK 8(3Q26.2) WILD-TYPE | 55 | 465 | 583 | 347 | 328 | 83 | 415 | 286 | 1 | 95 | 0 | 122

Figure S40. Get High-res Image Gene #8: 'Amp Peak 8(3q26.2)' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'

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

P value = 3.29e-05 (t-test), Q value = 0.042

Table S41. Gene #8: 'Amp Peak 8(3q26.2)' versus Clinical Feature #5: 'KARNOFSKY.PERFORMANCE.SCORE'

| nPatients | Mean (Std.Dev)
--- | --- | ---
ALL | 641 | 73.6 (23.9)
AMP PEAK 8(3Q26.2) CNV | 214 | 67.2 (30.4)
AMP PEAK 8(3Q26.2) WILD-TYPE | 427 | 76.8 (19.2)

Figure S41. Get High-res Image Gene #8: 'Amp Peak 8(3q26.2)' versus Clinical Feature #5: 'KARNOFSKY.PERFORMANCE.SCORE'

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

P value = 7.01e-241 (Chi-square test), Q value = 1.2e-237

Table S42. Gene #8: 'Amp Peak 8(3q26.2)' versus Clinical Feature #6: 'HISTOLOGICAL.TYPE'

nPatients | COLON ADENOCARCINOMA | COLON MUCINOUS ADENOCARCINOMA | ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA | HEAD & NECK SQUAMOUS CELL CARCINOMA | INFILTRATING DUCTAL CARCINOMA | INFILTRATING LOBULAR 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 HISTOLOGY (PLEASE SPECIFY) | MIXED SEROUS AND ENDOMETRIOID | MUCINOUS (COLLOID) ADENOCARCINOMA | MUCINOUS (COLLOID) CARCINOMA | MUSCLE INVASIVE UROTHELIAL CARCINOMA (PT2 OR ABOVE) | OTHER SPECIFY | RECTAL ADENOCARCINOMA | RECTAL MUCINOUS ADENOCARCINOMA | SEROUS CYSTADENOCARCINOMA | SEROUS ENDOMETRIAL ADENOCARCINOMA | TREATED PRIMARY GBM | UNTREATED PRIMARY (DE NOVO) GBM
--- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | ---
ALL | 356 | 54 | 351 | 321 | 104 | 12 | 493 | 11 | 79 | 243 | 7 | 4 | 17 | 2 | 3 | 2 | 18 | 1 | 1 | 1 | 3 | 315 | 5 | 18 | 4 | 3 | 49 | 10 | 143 | 13 | 552 | 85 | 1 | 20
AMP PEAK 8(3Q26.2) CNV | 59 | 6 | 57 | 238 | 43 | 0 | 78 | 4 | 31 | 83 | 7 | 1 | 5 | 1 | 1 | 0 | 4 | 1 | 0 | 1 | 1 | 288 | 1 | 6 | 0 | 0 | 28 | 3 | 36 | 1 | 456 | 63 | 0 | 3
AMP PEAK 8(3Q26.2) WILD-TYPE | 297 | 48 | 294 | 83 | 61 | 12 | 415 | 7 | 48 | 160 | 0 | 3 | 12 | 1 | 2 | 2 | 14 | 0 | 1 | 0 | 2 | 27 | 4 | 12 | 4 | 3 | 21 | 7 | 107 | 12 | 96 | 22 | 1 | 17

Figure S42. Get High-res Image Gene #8: 'Amp Peak 8(3q26.2)' versus Clinical Feature #6: 'HISTOLOGICAL.TYPE'

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

P value = 2.63e-22 (Fisher's exact test), Q value = 4e-19

Table S43. Gene #8: 'Amp Peak 8(3q26.2)' versus Clinical Feature #7: 'PATHOLOGY.T'

nPatients | T0+T1 | T2 | T3 | T4
--- | --- | --- | --- | ---
ALL | 448 | 611 | 688 | 208
AMP PEAK 8(3Q26.2) CNV | 147 | 321 | 202 | 116
AMP PEAK 8(3Q26.2) WILD-TYPE | 301 | 290 | 486 | 92

Figure S43. Get High-res Image Gene #8: 'Amp Peak 8(3q26.2)' versus Clinical Feature #7: 'PATHOLOGY.T'

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

P value = 4.82e-10 (Fisher's exact test), Q value = 6.9e-07

Table S44. Gene #8: 'Amp Peak 8(3q26.2)' versus Clinical Feature #8: 'PATHOLOGY.N'

nPatients | N0 | N1 | N2 | N3
--- | --- | --- | --- | ---
ALL | 1036 | 343 | 279 | 11
AMP PEAK 8(3Q26.2) CNV | 399 | 179 | 146 | 11
AMP PEAK 8(3Q26.2) WILD-TYPE | 637 | 164 | 133 | 0

Figure S44. Get High-res Image Gene #8: 'Amp Peak 8(3q26.2)' versus Clinical Feature #8: 'PATHOLOGY.N'

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

P value = 1.14e-23 (Fisher's exact test), Q value = 1.8e-20

Table S45. Gene #8: 'Amp Peak 8(3q26.2)' versus Clinical Feature #10: 'TUMOR.STAGE'

nPatients | I | II | III | IV
--- | --- | --- | --- | ---
ALL | 685 | 487 | 876 | 420
AMP PEAK 8(3Q26.2) CNV | 256 | 197 | 527 | 245
AMP PEAK 8(3Q26.2) WILD-TYPE | 429 | 290 | 349 | 175

Figure S45. Get High-res Image Gene #8: 'Amp Peak 8(3q26.2)' versus Clinical Feature #10: 'TUMOR.STAGE'

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

P value = 1.41e-13 (Fisher's exact test), Q value = 2.1e-10

Table S46. Gene #8: 'Amp Peak 8(3q26.2)' versus Clinical Feature #11: 'RADIATIONS.RADIATION.REGIMENINDICATION'

nPatients | NO | YES
--- | --- | ---
ALL | 835 | 3816
AMP PEAK 8(3Q26.2) CNV | 241 | 1624
AMP PEAK 8(3Q26.2) WILD-TYPE | 594 | 2192

Figure S46. Get High-res Image Gene #8: 'Amp Peak 8(3q26.2)' versus Clinical Feature #11: 'RADIATIONS.RADIATION.REGIMENINDICATION'

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

P value = 2.49e-05 (t-test), Q value = 0.032

Table S47. Gene #8: 'Amp Peak 8(3q26.2)' versus Clinical Feature #12: 'NUMBERPACKYEARSSMOKED'

| nPatients | Mean (Std.Dev)
--- | --- | ---
ALL | 804 | 46.7 (32.6)
AMP PEAK 8(3Q26.2) CNV | 524 | 50.0 (34.8)
AMP PEAK 8(3Q26.2) WILD-TYPE | 280 | 40.5 (27.2)

Figure S47. Get High-res Image Gene #8: 'Amp Peak 8(3q26.2)' versus Clinical Feature #12: 'NUMBERPACKYEARSSMOKED'

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

P value = 2.63e-44 (Chi-square test), Q value = 4.2e-41

Table S48. Gene #9: 'Amp Peak 9(4p16.3)' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'

nPatients | BLADDER | BRAIN | BREAST | COLON | ENDOMETRIAL | HEAD/NECK | KIDNEY | LUNG | OMENTUM | OVARY | PERITONEUM (OVARY) | RECTUM
--- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | ---
ALL | 131 | 544 | 857 | 412 | 454 | 321 | 493 | 714 | 2 | 548 | 2 | 159
AMP PEAK 9(4P16.3) CNV | 27 | 45 | 93 | 12 | 42 | 38 | 13 | 104 | 0 | 150 | 1 | 10
AMP PEAK 9(4P16.3) WILD-TYPE | 104 | 499 | 764 | 400 | 412 | 283 | 480 | 610 | 2 | 398 | 1 | 149

Figure S48. Get High-res Image Gene #9: 'Amp Peak 9(4p16.3)' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'

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

P value = 6.16e-05 (Fisher's exact test), Q value = 0.078

Table S49. Gene #9: 'Amp Peak 9(4p16.3)' versus Clinical Feature #4: 'GENDER'

nPatients | FEMALE | MALE
--- | --- | ---
ALL | 2924 | 1717
AMP PEAK 9(4P16.3) CNV | 379 | 156
AMP PEAK 9(4P16.3) WILD-TYPE | 2545 | 1561

Figure S49. Get High-res Image Gene #9: 'Amp Peak 9(4p16.3)' versus Clinical Feature #4: 'GENDER'

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

P value = 9.73e-47 (Chi-square test), Q value = 1.5e-43

Table S50. Gene #9: 'Amp Peak 9(4p16.3)' versus Clinical Feature #6: 'HISTOLOGICAL.TYPE'

nPatients | COLON ADENOCARCINOMA | COLON MUCINOUS ADENOCARCINOMA | ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA | HEAD & NECK SQUAMOUS CELL CARCINOMA | INFILTRATING DUCTAL CARCINOMA | INFILTRATING LOBULAR 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 HISTOLOGY (PLEASE SPECIFY) | MIXED SEROUS AND ENDOMETRIOID | MUCINOUS (COLLOID) ADENOCARCINOMA | MUCINOUS (COLLOID) CARCINOMA | MUSCLE INVASIVE UROTHELIAL CARCINOMA (PT2 OR ABOVE) | OTHER SPECIFY | RECTAL ADENOCARCINOMA | RECTAL MUCINOUS ADENOCARCINOMA | SEROUS CYSTADENOCARCINOMA | SEROUS ENDOMETRIAL ADENOCARCINOMA | TREATED PRIMARY GBM | UNTREATED PRIMARY (DE NOVO) GBM
--- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | ---
ALL | 356 | 54 | 351 | 321 | 104 | 12 | 493 | 11 | 79 | 243 | 7 | 4 | 17 | 2 | 3 | 2 | 18 | 1 | 1 | 1 | 3 | 315 | 5 | 18 | 4 | 3 | 49 | 10 | 143 | 13 | 552 | 85 | 1 | 20
AMP PEAK 9(4P16.3) CNV | 12 | 0 | 12 | 38 | 13 | 0 | 13 | 2 | 10 | 52 | 3 | 0 | 3 | 0 | 1 | 0 | 2 | 0 | 0 | 0 | 0 | 30 | 0 | 1 | 1 | 0 | 13 | 1 | 10 | 0 | 151 | 29 | 0 | 3
AMP PEAK 9(4P16.3) WILD-TYPE | 344 | 54 | 339 | 283 | 91 | 12 | 480 | 9 | 69 | 191 | 4 | 4 | 14 | 2 | 2 | 2 | 16 | 1 | 1 | 1 | 3 | 285 | 5 | 17 | 3 | 3 | 36 | 9 | 133 | 13 | 401 | 56 | 1 | 17

Figure S50. Get High-res Image Gene #9: 'Amp Peak 9(4p16.3)' versus Clinical Feature #6: 'HISTOLOGICAL.TYPE'

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

P value = 1.38e-07 (Fisher's exact test), Q value = 0.00019

Table S51. Gene #9: 'Amp Peak 9(4p16.3)' versus Clinical Feature #7: 'PATHOLOGY.T'

nPatients | T0+T1 | T2 | T3 | T4
--- | --- | --- | --- | ---
ALL | 448 | 611 | 688 | 208
AMP PEAK 9(4P16.3) CNV | 18 | 76 | 36 | 21
AMP PEAK 9(4P16.3) WILD-TYPE | 430 | 535 | 652 | 187

Figure S51. Get High-res Image Gene #9: 'Amp Peak 9(4p16.3)' versus Clinical Feature #7: 'PATHOLOGY.T'

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

P value = 1.93e-08 (Fisher's exact test), Q value = 2.7e-05

Table S52. Gene #9: 'Amp Peak 9(4p16.3)' versus Clinical Feature #10: 'TUMOR.STAGE'

nPatients | I | II | III | IV
--- | --- | --- | --- | ---
ALL | 685 | 487 | 876 | 420
AMP PEAK 9(4P16.3) CNV | 56 | 40 | 152 | 51
AMP PEAK 9(4P16.3) WILD-TYPE | 629 | 447 | 724 | 369

Figure S52. Get High-res Image Gene #9: 'Amp Peak 9(4p16.3)' versus Clinical Feature #10: 'TUMOR.STAGE'

'Amp Peak 9(4p16.3)' versus 'NEOPLASM.DISEASESTAGE'

P value = 7.36e-05 (Chi-square test), Q value = 0.093

Table S53. Gene #9: 'Amp Peak 9(4p16.3)' versus Clinical Feature #20: '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 X
--- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | ---
ALL | 71 | 45 | 2 | 34 | 246 | 165 | 29 | 107 | 22 | 36 | 35 | 12
AMP PEAK 9(4P16.3) CNV | 6 | 2 | 1 | 10 | 25 | 15 | 4 | 9 | 8 | 8 | 4 | 0
AMP PEAK 9(4P16.3) WILD-TYPE | 65 | 43 | 1 | 24 | 221 | 150 | 25 | 98 | 14 | 28 | 31 | 12

Figure S53. Get High-res Image Gene #9: 'Amp Peak 9(4p16.3)' versus Clinical Feature #20: 'NEOPLASM.DISEASESTAGE'

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

P value = 8.29e-05 (logrank test), Q value = 0.1

Table S54. Gene #10: 'Amp Peak 10(4q12)' versus Clinical Feature #1: 'Time to Death'

| nPatients | nDeath | Duration Range (Median), Month
--- | --- | --- | ---
ALL | 4370 | 1406 | 0.0 - 224.0 (14.4)
AMP PEAK 10(4Q12) CNV | 576 | 220 | 0.1 - 224.0 (13.0)
AMP PEAK 10(4Q12) WILD-TYPE | 3794 | 1186 | 0.0 - 223.4 (14.8)

Figure S54. Get High-res Image Gene #10: 'Amp Peak 10(4q12)' versus Clinical Feature #1: 'Time to Death'

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

P value = 5.03e-36 (Chi-square test), Q value = 7.9e-33

Table S55. Gene #10: 'Amp Peak 10(4q12)' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'

nPatients | BLADDER | BRAIN | BREAST | COLON | ENDOMETRIAL | HEAD/NECK | KIDNEY | LUNG | OMENTUM | OVARY | PERITONEUM (OVARY) | RECTUM
--- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | ---
ALL | 131 | 544 | 857 | 412 | 454 | 321 | 493 | 714 | 2 | 548 | 2 | 159
AMP PEAK 10(4Q12) CNV | 15 | 101 | 117 | 18 | 19 | 52 | 12 | 149 | 1 | 108 | 1 | 11
AMP PEAK 10(4Q12) WILD-TYPE | 116 | 443 | 740 | 394 | 435 | 269 | 481 | 565 | 1 | 440 | 1 | 148

Figure S55. Get High-res Image Gene #10: 'Amp Peak 10(4q12)' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'

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

P value = 3.41e-33 (Chi-square test), Q value = 5.3e-30

Table S56. Gene #10: 'Amp Peak 10(4q12)' versus Clinical Feature #6: 'HISTOLOGICAL.TYPE'

nPatients | COLON ADENOCARCINOMA | COLON MUCINOUS ADENOCARCINOMA | ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA | HEAD & NECK SQUAMOUS CELL CARCINOMA | INFILTRATING DUCTAL CARCINOMA | INFILTRATING LOBULAR 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 HISTOLOGY (PLEASE SPECIFY) | MIXED SEROUS AND ENDOMETRIOID | MUCINOUS (COLLOID) ADENOCARCINOMA | MUCINOUS (COLLOID) CARCINOMA | MUSCLE INVASIVE UROTHELIAL CARCINOMA (PT2 OR ABOVE) | OTHER SPECIFY | RECTAL ADENOCARCINOMA | RECTAL MUCINOUS ADENOCARCINOMA | SEROUS CYSTADENOCARCINOMA | SEROUS ENDOMETRIAL ADENOCARCINOMA | TREATED PRIMARY GBM | UNTREATED PRIMARY (DE NOVO) GBM
--- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | ---
ALL | 356 | 54 | 351 | 321 | 104 | 12 | 493 | 11 | 79 | 243 | 7 | 4 | 17 | 2 | 3 | 2 | 18 | 1 | 1 | 1 | 3 | 315 | 5 | 18 | 4 | 3 | 49 | 10 | 143 | 13 | 552 | 85 | 1 | 20
AMP PEAK 10(4Q12) CNV | 17 | 1 | 6 | 52 | 21 | 0 | 12 | 4 | 11 | 50 | 3 | 0 | 4 | 1 | 1 | 0 | 1 | 0 | 0 | 0 | 1 | 73 | 0 | 1 | 0 | 0 | 6 | 1 | 11 | 0 | 110 | 12 | 0 | 8
AMP PEAK 10(4Q12) WILD-TYPE | 339 | 53 | 345 | 269 | 83 | 12 | 481 | 7 | 68 | 193 | 4 | 4 | 13 | 1 | 2 | 2 | 17 | 1 | 1 | 1 | 2 | 242 | 5 | 17 | 4 | 3 | 43 | 9 | 132 | 13 | 442 | 73 | 1 | 12

Figure S56. Get High-res Image Gene #10: 'Amp Peak 10(4q12)' versus Clinical Feature #6: 'HISTOLOGICAL.TYPE'

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

P value = 3.79e-10 (Fisher's exact test), Q value = 5.4e-07

Table S57. Gene #10: 'Amp Peak 10(4q12)' versus Clinical Feature #7: 'PATHOLOGY.T'

nPatients | T0+T1 | T2 | T3 | T4
--- | --- | --- | --- | ---
ALL | 448 | 611 | 688 | 208
AMP PEAK 10(4Q12) CNV | 30 | 104 | 48 | 33
AMP PEAK 10(4Q12) WILD-TYPE | 418 | 507 | 640 | 175

Figure S57. Get High-res Image Gene #10: 'Amp Peak 10(4q12)' versus Clinical Feature #7: 'PATHOLOGY.T'

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

P value = 1.62e-05 (t-test), Q value = 0.021

Table S58. Gene #11: 'Amp Peak 11(5p15.33)' versus Clinical Feature #2: 'AGE'

| nPatients | Mean (Std.Dev)
--- | --- | ---
ALL | 4585 | 61.9 (12.6)
AMP PEAK 11(5P15.33) CNV | 1676 | 62.9 (11.8)
AMP PEAK 11(5P15.33) WILD-TYPE | 2909 | 61.3 (13.0)

Figure S58. Get High-res Image Gene #11: 'Amp Peak 11(5p15.33)' versus Clinical Feature #2: 'AGE'

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

P value = 2.24e-160 (Chi-square test), Q value = 3.8e-157

Table S59. Gene #11: 'Amp Peak 11(5p15.33)' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'

nPatients | BLADDER | BRAIN | BREAST | COLON | ENDOMETRIAL | HEAD/NECK | KIDNEY | LUNG | OMENTUM | OVARY | PERITONEUM (OVARY) | RECTUM
--- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | ---
ALL | 131 | 544 | 857 | 412 | 454 | 321 | 493 | 714 | 2 | 548 | 2 | 159
AMP PEAK 11(5P15.33) CNV | 61 | 54 | 308 | 78 | 67 | 145 | 158 | 509 | 1 | 289 | 2 | 37
AMP PEAK 11(5P15.33) WILD-TYPE | 70 | 490 | 549 | 334 | 387 | 176 | 335 | 205 | 1 | 259 | 0 | 122

Figure S59. Get High-res Image Gene #11: 'Amp Peak 11(5p15.33)' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'

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

P value = 0.000192 (t-test), Q value = 0.24

Table S60. Gene #11: 'Amp Peak 11(5p15.33)' versus Clinical Feature #5: 'KARNOFSKY.PERFORMANCE.SCORE'

| nPatients | Mean (Std.Dev)
--- | --- | ---
ALL | 641 | 73.6 (23.9)
AMP PEAK 11(5P15.33) CNV | 173 | 66.1 (33.6)
AMP PEAK 11(5P15.33) WILD-TYPE | 468 | 76.3 (18.5)

Figure S60. Get High-res Image Gene #11: 'Amp Peak 11(5p15.33)' versus Clinical Feature #5: 'KARNOFSKY.PERFORMANCE.SCORE'

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

P value = 1.59e-116 (Chi-square test), Q value = 2.7e-113

Table S61. Gene #11: 'Amp Peak 11(5p15.33)' versus Clinical Feature #6: 'HISTOLOGICAL.TYPE'

nPatients | COLON ADENOCARCINOMA | COLON MUCINOUS ADENOCARCINOMA | ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA | HEAD & NECK SQUAMOUS CELL CARCINOMA | INFILTRATING DUCTAL CARCINOMA | INFILTRATING LOBULAR 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 HISTOLOGY (PLEASE SPECIFY) | MIXED SEROUS AND ENDOMETRIOID | MUCINOUS (COLLOID) ADENOCARCINOMA | MUCINOUS (COLLOID) CARCINOMA | MUSCLE INVASIVE UROTHELIAL CARCINOMA (PT2 OR ABOVE) | OTHER SPECIFY | RECTAL ADENOCARCINOMA | RECTAL MUCINOUS ADENOCARCINOMA | SEROUS CYSTADENOCARCINOMA | SEROUS ENDOMETRIAL ADENOCARCINOMA | TREATED PRIMARY GBM | UNTREATED PRIMARY (DE NOVO) GBM
--- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | ---
ALL | 356 | 54 | 351 | 321 | 104 | 12 | 493 | 11 | 79 | 243 | 7 | 4 | 17 | 2 | 3 | 2 | 18 | 1 | 1 | 1 | 3 | 315 | 5 | 18 | 4 | 3 | 49 | 10 | 143 | 13 | 552 | 85 | 1 | 20
AMP PEAK 11(5P15.33) CNV | 69 | 9 | 24 | 145 | 38 | 5 | 158 | 8 | 45 | 166 | 5 | 1 | 13 | 2 | 2 | 0 | 12 | 1 | 0 | 1 | 3 | 249 | 0 | 3 | 1 | 0 | 15 | 3 | 36 | 1 | 292 | 40 | 1 | 2
AMP PEAK 11(5P15.33) WILD-TYPE | 287 | 45 | 327 | 176 | 66 | 7 | 335 | 3 | 34 | 77 | 2 | 3 | 4 | 0 | 1 | 2 | 6 | 0 | 1 | 0 | 0 | 66 | 5 | 15 | 3 | 3 | 34 | 7 | 107 | 12 | 260 | 45 | 0 | 18

Figure S61. Get High-res Image Gene #11: 'Amp Peak 11(5p15.33)' versus Clinical Feature #6: 'HISTOLOGICAL.TYPE'

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

P value = 1.28e-19 (Fisher's exact test), Q value = 1.9e-16

Table S62. Gene #11: 'Amp Peak 11(5p15.33)' versus Clinical Feature #7: 'PATHOLOGY.T'

nPatients | T0+T1 | T2 | T3 | T4
--- | --- | --- | --- | ---
ALL | 448 | 611 | 688 | 208
AMP PEAK 11(5P15.33) CNV | 196 | 344 | 208 | 87
AMP PEAK 11(5P15.33) WILD-TYPE | 252 | 267 | 480 | 121

Figure S62. Get High-res Image Gene #11: 'Amp Peak 11(5p15.33)' versus Clinical Feature #7: 'PATHOLOGY.T'

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

P value = 5.66e-05 (Fisher's exact test), Q value = 0.072

Table S63. Gene #11: 'Amp Peak 11(5p15.33)' versus Clinical Feature #10: 'TUMOR.STAGE'

nPatients | I | II | III | IV
--- | --- | --- | --- | ---
ALL | 685 | 487 | 876 | 420
AMP PEAK 11(5P15.33) CNV | 328 | 185 | 429 | 167
AMP PEAK 11(5P15.33) WILD-TYPE | 357 | 302 | 447 | 253

Figure S63. Get High-res Image Gene #11: 'Amp Peak 11(5p15.33)' versus Clinical Feature #10: 'TUMOR.STAGE'

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

P value = 9.11e-16 (Fisher's exact test), Q value = 1.4e-12

Table S64. Gene #11: 'Amp Peak 11(5p15.33)' versus Clinical Feature #11: 'RADIATIONS.RADIATION.REGIMENINDICATION'

nPatients | NO | YES
--- | --- | ---
ALL | 835 | 3816
AMP PEAK 11(5P15.33) CNV | 208 | 1505
AMP PEAK 11(5P15.33) WILD-TYPE | 627 | 2311

Figure S64. Get High-res Image Gene #11: 'Amp Peak 11(5p15.33)' versus Clinical Feature #11: 'RADIATIONS.RADIATION.REGIMENINDICATION'

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

P value = 9.9e-06 (logrank test), Q value = 0.013

Table S65. Gene #12: 'Amp Peak 12(5q35.3)' versus Clinical Feature #1: 'Time to Death'

| nPatients | nDeath | Duration Range (Median), Month
--- | --- | --- | ---
ALL | 4370 | 1406 | 0.0 - 224.0 (14.4)
AMP PEAK 12(5Q35.3) CNV | 908 | 268 | 0.0 - 224.0 (19.6)
AMP PEAK 12(5Q35.3) WILD-TYPE | 3462 | 1138 | 0.0 - 223.4 (13.3)

Figure S65. Get High-res Image Gene #12: 'Amp Peak 12(5q35.3)' versus Clinical Feature #1: 'Time to Death'

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

P value = 1.49e-155 (Chi-square test), Q value = 2.5e-152

Table S66. Gene #12: 'Amp Peak 12(5q35.3)' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'

nPatients | BLADDER | BRAIN | BREAST | COLON | ENDOMETRIAL | HEAD/NECK | KIDNEY | LUNG | OMENTUM | OVARY | PERITONEUM (OVARY) | RECTUM
--- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | ---
ALL | 131 | 544 | 857 | 412 | 454 | 321 | 493 | 714 | 2 | 548 | 2 | 159
AMP PEAK 12(5Q35.3) CNV | 11 | 48 | 220 | 37 | 38 | 20 | 311 | 108 | 0 | 136 | 0 | 22
AMP PEAK 12(5Q35.3) WILD-TYPE | 120 | 496 | 637 | 375 | 416 | 301 | 182 | 606 | 2 | 412 | 2 | 137

Figure S66. Get High-res Image Gene #12: 'Amp Peak 12(5q35.3)' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'

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

P value = 5.88e-130 (Chi-square test), Q value = 1e-126

Table S67. Gene #12: 'Amp Peak 12(5q35.3)' versus Clinical Feature #6: 'HISTOLOGICAL.TYPE'

nPatients | COLON ADENOCARCINOMA | COLON MUCINOUS ADENOCARCINOMA | ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA | HEAD & NECK SQUAMOUS CELL CARCINOMA | INFILTRATING DUCTAL CARCINOMA | INFILTRATING LOBULAR 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 HISTOLOGY (PLEASE SPECIFY) | MIXED SEROUS AND ENDOMETRIOID | MUCINOUS (COLLOID) ADENOCARCINOMA | MUCINOUS (COLLOID) CARCINOMA | MUSCLE INVASIVE UROTHELIAL CARCINOMA (PT2 OR ABOVE) | OTHER SPECIFY | RECTAL ADENOCARCINOMA | RECTAL MUCINOUS ADENOCARCINOMA | SEROUS CYSTADENOCARCINOMA | SEROUS ENDOMETRIAL ADENOCARCINOMA | TREATED PRIMARY GBM | UNTREATED PRIMARY (DE NOVO) GBM
--- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | ---
ALL | 356 | 54 | 351 | 321 | 104 | 12 | 493 | 11 | 79 | 243 | 7 | 4 | 17 | 2 | 3 | 2 | 18 | 1 | 1 | 1 | 3 | 315 | 5 | 18 | 4 | 3 | 49 | 10 | 143 | 13 | 552 | 85 | 1 | 20
AMP PEAK 12(5Q35.3) CNV | 33 | 4 | 15 | 20 | 25 | 5 | 311 | 4 | 15 | 54 | 1 | 1 | 5 | 1 | 0 | 0 | 4 | 0 | 0 | 0 | 0 | 22 | 0 | 3 | 1 | 0 | 4 | 2 | 21 | 1 | 136 | 20 | 1 | 2
AMP PEAK 12(5Q35.3) WILD-TYPE | 323 | 50 | 336 | 301 | 79 | 7 | 182 | 7 | 64 | 189 | 6 | 3 | 12 | 1 | 3 | 2 | 14 | 1 | 1 | 1 | 3 | 293 | 5 | 15 | 3 | 3 | 45 | 8 | 122 | 12 | 416 | 65 | 0 | 18

Figure S67. Get High-res Image Gene #12: 'Amp Peak 12(5q35.3)' versus Clinical Feature #6: 'HISTOLOGICAL.TYPE'

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

P value = 1.77e-17 (Fisher's exact test), Q value = 2.7e-14

Table S68. Gene #12: 'Amp Peak 12(5q35.3)' versus Clinical Feature #7: 'PATHOLOGY.T'

nPatients | T0+T1 | T2 | T3 | T4
--- | --- | --- | --- | ---
ALL | 448 | 611 | 688 | 208
AMP PEAK 12(5Q35.3) CNV | 172 | 112 | 168 | 22
AMP PEAK 12(5Q35.3) WILD-TYPE | 276 | 499 | 520 | 186

Figure S68. Get High-res Image Gene #12: 'Amp Peak 12(5q35.3)' versus Clinical Feature #7: 'PATHOLOGY.T'

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

P value = 6.66e-05 (Fisher's exact test), Q value = 0.085

Table S69. Gene #12: 'Amp Peak 12(5q35.3)' versus Clinical Feature #8: 'PATHOLOGY.N'

nPatients | N0 | N1 | N2 | N3
--- | --- | --- | --- | ---
ALL | 1036 | 343 | 279 | 11
AMP PEAK 12(5Q35.3) CNV | 227 | 47 | 36 | 4
AMP PEAK 12(5Q35.3) WILD-TYPE | 809 | 296 | 243 | 7

Figure S69. Get High-res Image Gene #12: 'Amp Peak 12(5q35.3)' versus Clinical Feature #8: 'PATHOLOGY.N'

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

P value = 9.07e-07 (Fisher's exact test), Q value = 0.0012

Table S70. Gene #12: 'Amp Peak 12(5q35.3)' versus Clinical Feature #10: 'TUMOR.STAGE'

nPatients | I | II | III | IV
--- | --- | --- | --- | ---
ALL | 685 | 487 | 876 | 420
AMP PEAK 12(5Q35.3) CNV | 196 | 77 | 235 | 96
AMP PEAK 12(5Q35.3) WILD-TYPE | 489 | 410 | 641 | 324

Figure S70. Get High-res Image Gene #12: 'Amp Peak 12(5q35.3)' versus Clinical Feature #10: 'TUMOR.STAGE'

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

P value = 8.09e-08 (Fisher's exact test), Q value = 0.00011

Table S71. Gene #12: 'Amp Peak 12(5q35.3)' versus Clinical Feature #11: 'RADIATIONS.RADIATION.REGIMENINDICATION'

nPatients | NO | YES
--- | --- | ---
ALL | 835 | 3816
AMP PEAK 12(5Q35.3) CNV | 116 | 838
AMP PEAK 12(5Q35.3) WILD-TYPE | 719 | 2978

Figure S71. Get High-res Image Gene #12: 'Amp Peak 12(5q35.3)' versus Clinical Feature #11: 'RADIATIONS.RADIATION.REGIMENINDICATION'

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

P value = 1.74e-115 (Chi-square test), Q value = 2.9e-112

Table S72. Gene #13: 'Amp Peak 13(6p22.3)' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'

nPatients | BLADDER | BRAIN | BREAST | COLON | ENDOMETRIAL | HEAD/NECK | KIDNEY | LUNG | OMENTUM | OVARY | PERITONEUM (OVARY) | RECTUM
--- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | ---
ALL | 131 | 544 | 857 | 412 | 454 | 321 | 493 | 714 | 2 | 548 | 2 | 159
AMP PEAK 13(6P22.3) CNV | 54 | 28 | 217 | 74 | 72 | 50 | 8 | 237 | 1 | 280 | 1 | 38
AMP PEAK 13(6P22.3) WILD-TYPE | 77 | 516 | 640 | 338 | 382 | 271 | 485 | 477 | 1 | 268 | 1 | 121

Figure S72. Get High-res Image Gene #13: 'Amp Peak 13(6p22.3)' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'

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

P value = 6.53e-11 (Fisher's exact test), Q value = 9.4e-08

Table S73. Gene #13: 'Amp Peak 13(6p22.3)' versus Clinical Feature #4: 'GENDER'

nPatients | FEMALE | MALE
--- | --- | ---
ALL | 2924 | 1717
AMP PEAK 13(6P22.3) CNV | 758 | 303
AMP PEAK 13(6P22.3) WILD-TYPE | 2166 | 1414

Figure S73. Get High-res Image Gene #13: 'Amp Peak 13(6p22.3)' versus Clinical Feature #4: 'GENDER'

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

P value = 2.66e-91 (Chi-square test), Q value = 4.4e-88

Table S74. Gene #13: 'Amp Peak 13(6p22.3)' versus Clinical Feature #6: 'HISTOLOGICAL.TYPE'

nPatients | COLON ADENOCARCINOMA | COLON MUCINOUS ADENOCARCINOMA | ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA | HEAD & NECK SQUAMOUS CELL CARCINOMA | INFILTRATING DUCTAL CARCINOMA | INFILTRATING LOBULAR 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 HISTOLOGY (PLEASE SPECIFY) | MIXED SEROUS AND ENDOMETRIOID | MUCINOUS (COLLOID) ADENOCARCINOMA | MUCINOUS (COLLOID) CARCINOMA | MUSCLE INVASIVE UROTHELIAL CARCINOMA (PT2 OR ABOVE) | OTHER SPECIFY | RECTAL ADENOCARCINOMA | RECTAL MUCINOUS ADENOCARCINOMA | SEROUS CYSTADENOCARCINOMA | SEROUS ENDOMETRIAL ADENOCARCINOMA | TREATED PRIMARY GBM | UNTREATED PRIMARY (DE NOVO) GBM
--- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | ---
ALL | 356 | 54 | 351 | 321 | 104 | 12 | 493 | 11 | 79 | 243 | 7 | 4 | 17 | 2 | 3 | 2 | 18 | 1 | 1 | 1 | 3 | 315 | 5 | 18 | 4 | 3 | 49 | 10 | 143 | 13 | 552 | 85 | 1 | 20
AMP PEAK 13(6P22.3) CNV | 67 | 7 | 30 | 50 | 43 | 0 | 8 | 7 | 26 | 92 | 3 | 0 | 8 | 1 | 1 | 0 | 8 | 0 | 0 | 1 | 2 | 87 | 0 | 3 | 1 | 0 | 18 | 5 | 36 | 2 | 282 | 39 | 1 | 0
AMP PEAK 13(6P22.3) WILD-TYPE | 289 | 47 | 321 | 271 | 61 | 12 | 485 | 4 | 53 | 151 | 4 | 4 | 9 | 1 | 2 | 2 | 10 | 1 | 1 | 0 | 1 | 228 | 5 | 15 | 3 | 3 | 31 | 5 | 107 | 11 | 270 | 46 | 0 | 20

Figure S74. Get High-res Image Gene #13: 'Amp Peak 13(6p22.3)' versus Clinical Feature #6: 'HISTOLOGICAL.TYPE'

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

P value = 0.00017 (Chi-square test), Q value = 0.21

Table S75. Gene #13: 'Amp Peak 13(6p22.3)' versus Clinical Feature #9: 'PATHOLOGICSPREAD(M)'

nPatients | M0 | M1 | M1A | M1B | MX
--- | --- | --- | --- | --- | ---
ALL | 1398 | 167 | 9 | 1 | 148
AMP PEAK 13(6P22.3) CNV | 236 | 26 | 3 | 0 | 47
AMP PEAK 13(6P22.3) WILD-TYPE | 1162 | 141 | 6 | 1 | 101

Figure S75. Get High-res Image Gene #13: 'Amp Peak 13(6p22.3)' versus Clinical Feature #9: 'PATHOLOGICSPREAD(M)'

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

P value = 3.21e-13 (Fisher's exact test), Q value = 4.7e-10

Table S76. Gene #13: 'Amp Peak 13(6p22.3)' versus Clinical Feature #10: 'TUMOR.STAGE'

nPatients | I | II | III | IV
--- | --- | --- | --- | ---
ALL | 685 | 487 | 876 | 420
AMP PEAK 13(6P22.3) CNV | 132 | 97 | 303 | 93
AMP PEAK 13(6P22.3) WILD-TYPE | 553 | 390 | 573 | 327

Figure S76. Get High-res Image Gene #13: 'Amp Peak 13(6p22.3)' versus Clinical Feature #10: 'TUMOR.STAGE'

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

P value = 1.61e-10 (Fisher's exact test), Q value = 2.3e-07

Table S77. Gene #13: 'Amp Peak 13(6p22.3)' versus Clinical Feature #11: 'RADIATIONS.RADIATION.REGIMENINDICATION'

nPatients | NO | YES
--- | --- | ---
ALL | 835 | 3816
AMP PEAK 13(6P22.3) CNV | 123 | 942
AMP PEAK 13(6P22.3) WILD-TYPE | 712 | 2874

Figure S77. Get High-res Image Gene #13: 'Amp Peak 13(6p22.3)' versus Clinical Feature #11: 'RADIATIONS.RADIATION.REGIMENINDICATION'

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

P value = 8.63e-74 (Chi-square test), Q value = 1.4e-70

Table S78. Gene #14: 'Amp Peak 14(6p21.1)' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'

nPatients | BLADDER | BRAIN | BREAST | COLON | ENDOMETRIAL | HEAD/NECK | KIDNEY | LUNG | OMENTUM | OVARY | PERITONEUM (OVARY) | RECTUM
--- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | ---
ALL | 131 | 544 | 857 | 412 | 454 | 321 | 493 | 714 | 2 | 548 | 2 | 159
AMP PEAK 14(6P21.1) CNV | 27 | 32 | 199 | 91 | 73 | 53 | 10 | 240 | 0 | 213 | 1 | 49
AMP PEAK 14(6P21.1) WILD-TYPE | 104 | 512 | 658 | 321 | 381 | 268 | 483 | 474 | 2 | 335 | 1 | 110

Figure S78. Get High-res Image Gene #14: 'Amp Peak 14(6p21.1)' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'

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

P value = 2.33e-05 (Fisher's exact test), Q value = 0.03

Table S79. Gene #14: 'Amp Peak 14(6p21.1)' versus Clinical Feature #4: 'GENDER'

nPatients | FEMALE | MALE
--- | --- | ---
ALL | 2924 | 1717
AMP PEAK 14(6P21.1) CNV | 681 | 310
AMP PEAK 14(6P21.1) WILD-TYPE | 2243 | 1407

Figure S79. Get High-res Image Gene #14: 'Amp Peak 14(6p21.1)' versus Clinical Feature #4: 'GENDER'

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

P value = 1.64e-59 (Chi-square test), Q value = 2.6e-56

Table S80. Gene #14: 'Amp Peak 14(6p21.1)' versus Clinical Feature #6: 'HISTOLOGICAL.TYPE'

nPatients | COLON ADENOCARCINOMA | COLON MUCINOUS ADENOCARCINOMA | ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA | HEAD & NECK SQUAMOUS CELL CARCINOMA | INFILTRATING DUCTAL CARCINOMA | INFILTRATING LOBULAR 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 HISTOLOGY (PLEASE SPECIFY) | MIXED SEROUS AND ENDOMETRIOID | MUCINOUS (COLLOID) ADENOCARCINOMA | MUCINOUS (COLLOID) CARCINOMA | MUSCLE INVASIVE UROTHELIAL CARCINOMA (PT2 OR ABOVE) | OTHER SPECIFY | RECTAL ADENOCARCINOMA | RECTAL MUCINOUS ADENOCARCINOMA | SEROUS CYSTADENOCARCINOMA | SEROUS ENDOMETRIAL ADENOCARCINOMA | TREATED PRIMARY GBM | UNTREATED PRIMARY (DE NOVO) GBM
--- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | ---
ALL | 356 | 54 | 351 | 321 | 104 | 12 | 493 | 11 | 79 | 243 | 7 | 4 | 17 | 2 | 3 | 2 | 18 | 1 | 1 | 1 | 3 | 315 | 5 | 18 | 4 | 3 | 49 | 10 | 143 | 13 | 552 | 85 | 1 | 20
AMP PEAK 14(6P21.1) CNV | 85 | 6 | 35 | 53 | 36 | 0 | 10 | 6 | 27 | 92 | 2 | 0 | 9 | 0 | 1 | 0 | 8 | 1 | 0 | 1 | 1 | 91 | 0 | 0 | 1 | 0 | 6 | 4 | 48 | 1 | 214 | 38 | 0 | 0
AMP PEAK 14(6P21.1) WILD-TYPE | 271 | 48 | 316 | 268 | 68 | 12 | 483 | 5 | 52 | 151 | 5 | 4 | 8 | 2 | 2 | 2 | 10 | 0 | 1 | 0 | 2 | 224 | 5 | 18 | 3 | 3 | 43 | 6 | 95 | 12 | 338 | 47 | 1 | 20

Figure S80. Get High-res Image Gene #14: 'Amp Peak 14(6p21.1)' versus Clinical Feature #6: 'HISTOLOGICAL.TYPE'

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

P value = 1.23e-07 (Fisher's exact test), Q value = 0.00017

Table S81. Gene #14: 'Amp Peak 14(6p21.1)' versus Clinical Feature #10: 'TUMOR.STAGE'

nPatients | I | II | III | IV
--- | --- | --- | --- | ---
ALL | 685 | 487 | 876 | 420
AMP PEAK 14(6P21.1) CNV | 126 | 107 | 270 | 95
AMP PEAK 14(6P21.1) WILD-TYPE | 559 | 380 | 606 | 325

Figure S81. Get High-res Image Gene #14: 'Amp Peak 14(6p21.1)' versus Clinical Feature #10: 'TUMOR.STAGE'

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

P value = 2.11e-07 (Fisher's exact test), Q value = 0.00029

Table S82. Gene #14: 'Amp Peak 14(6p21.1)' versus Clinical Feature #11: 'RADIATIONS.RADIATION.REGIMENINDICATION'

nPatients | NO | YES
--- | --- | ---
ALL | 835 | 3816
AMP PEAK 14(6P21.1) CNV | 124 | 870
AMP PEAK 14(6P21.1) WILD-TYPE | 711 | 2946

Figure S82. Get High-res Image Gene #14: 'Amp Peak 14(6p21.1)' versus Clinical Feature #11: 'RADIATIONS.RADIATION.REGIMENINDICATION'

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

P value = 6.27e-28 (Chi-square test), Q value = 9.7e-25

Table S83. Gene #15: 'Amp Peak 15(6q21)' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'

nPatients | BLADDER | BRAIN | BREAST | COLON | ENDOMETRIAL | HEAD/NECK | KIDNEY | LUNG | OMENTUM | OVARY | PERITONEUM (OVARY) | RECTUM
--- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | ---
ALL | 131 | 544 | 857 | 412 | 454 | 321 | 493 | 714 | 2 | 548 | 2 | 159
AMP PEAK 15(6Q21) CNV | 14 | 24 | 159 | 59 | 59 | 27 | 9 | 89 | 0 | 106 | 1 | 34
AMP PEAK 15(6Q21) WILD-TYPE | 117 | 520 | 698 | 353 | 395 | 294 | 484 | 625 | 2 | 442 | 1 | 125

Figure S83. Get High-res Image Gene #15: 'Amp Peak 15(6q21)' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'

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

P value = 4.19e-07 (Fisher's exact test), Q value = 0.00057

Table S84. Gene #15: 'Amp Peak 15(6q21)' versus Clinical Feature #4: 'GENDER'

nPatients | FEMALE | MALE
--- | --- | ---
ALL | 2924 | 1717
AMP PEAK 15(6Q21) CNV | 421 | 161
AMP PEAK 15(6Q21) WILD-TYPE | 2503 | 1556

Figure S84. Get High-res Image Gene #15: 'Amp Peak 15(6q21)' versus Clinical Feature #4: 'GENDER'

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

P value = 1.03e-26 (Chi-square test), Q value = 1.6e-23

Table S85. Gene #15: 'Amp Peak 15(6q21)' versus Clinical Feature #6: 'HISTOLOGICAL.TYPE'

nPatients | COLON ADENOCARCINOMA | COLON MUCINOUS ADENOCARCINOMA | ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA | HEAD & NECK SQUAMOUS CELL CARCINOMA | INFILTRATING DUCTAL CARCINOMA | INFILTRATING LOBULAR 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 HISTOLOGY (PLEASE SPECIFY) | MIXED SEROUS AND ENDOMETRIOID | MUCINOUS (COLLOID) ADENOCARCINOMA | MUCINOUS (COLLOID) CARCINOMA | MUSCLE INVASIVE UROTHELIAL CARCINOMA (PT2 OR ABOVE) | OTHER SPECIFY | RECTAL ADENOCARCINOMA | RECTAL MUCINOUS ADENOCARCINOMA | SEROUS CYSTADENOCARCINOMA | SEROUS ENDOMETRIAL ADENOCARCINOMA | TREATED PRIMARY GBM | UNTREATED PRIMARY (DE NOVO) GBM
--- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | ---
ALL | 356 | 54 | 351 | 321 | 104 | 12 | 493 | 11 | 79 | 243 | 7 | 4 | 17 | 2 | 3 | 2 | 18 | 1 | 1 | 1 | 3 | 315 | 5 | 18 | 4 | 3 | 49 | 10 | 143 | 13 | 552 | 85 | 1 | 20
AMP PEAK 15(6Q21) CNV | 54 | 5 | 30 | 27 | 30 | 1 | 9 | 1 | 5 | 17 | 0 | 0 | 2 | 0 | 0 | 0 | 2 | 0 | 0 | 1 | 1 | 59 | 0 | 0 | 1 | 0 | 8 | 0 | 34 | 0 | 107 | 29 | 0 | 0
AMP PEAK 15(6Q21) WILD-TYPE | 302 | 49 | 321 | 294 | 74 | 11 | 484 | 10 | 74 | 226 | 7 | 4 | 15 | 2 | 3 | 2 | 16 | 1 | 1 | 0 | 2 | 256 | 5 | 18 | 3 | 3 | 41 | 10 | 109 | 13 | 445 | 56 | 1 | 20

Figure S85. Get High-res Image Gene #15: 'Amp Peak 15(6q21)' versus Clinical Feature #6: 'HISTOLOGICAL.TYPE'

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

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

Table S86. Gene #16: 'Amp Peak 16(7p11.2)' versus Clinical Feature #1: 'Time to Death'

| nPatients | nDeath | Duration Range (Median), Month
--- | --- | --- | ---
ALL | 4370 | 1406 | 0.0 - 224.0 (14.4)
AMP PEAK 16(7P11.2) CNV | 1927 | 780 | 0.0 - 224.0 (11.5)
AMP PEAK 16(7P11.2) WILD-TYPE | 2443 | 626 | 0.0 - 220.9 (18.1)

Figure S86. Get High-res Image Gene #16: 'Amp Peak 16(7p11.2)' versus Clinical Feature #1: 'Time to Death'

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

P value = 4.82e-156 (Chi-square test), Q value = 8.2e-153

Table S87. Gene #16: 'Amp Peak 16(7p11.2)' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'

nPatients | BLADDER | BRAIN | BREAST | COLON | ENDOMETRIAL | HEAD/NECK | KIDNEY | LUNG | OMENTUM | OVARY | PERITONEUM (OVARY) | RECTUM
--- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | ---
ALL | 131 | 544 | 857 | 412 | 454 | 321 | 493 | 714 | 2 | 548 | 2 | 159
AMP PEAK 16(7P11.2) CNV | 70 | 477 | 263 | 227 | 65 | 137 | 160 | 371 | 1 | 182 | 1 | 98
AMP PEAK 16(7P11.2) WILD-TYPE | 61 | 67 | 594 | 185 | 389 | 184 | 333 | 343 | 1 | 366 | 1 | 61

Figure S87. Get High-res Image Gene #16: 'Amp Peak 16(7p11.2)' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'

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

P value = 4.27e-32 (Fisher's exact test), Q value = 6.7e-29

Table S88. Gene #16: 'Amp Peak 16(7p11.2)' versus Clinical Feature #4: 'GENDER'

nPatients | FEMALE | MALE
--- | --- | ---
ALL | 2924 | 1717
AMP PEAK 16(7P11.2) CNV | 1101 | 953
AMP PEAK 16(7P11.2) WILD-TYPE | 1823 | 764

Figure S88. Get High-res Image Gene #16: 'Amp Peak 16(7p11.2)' versus Clinical Feature #4: 'GENDER'

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

P value = 1.33e-52 (Chi-square test), Q value = 2.1e-49

Table S89. Gene #16: 'Amp Peak 16(7p11.2)' versus Clinical Feature #6: 'HISTOLOGICAL.TYPE'

nPatients | COLON ADENOCARCINOMA | COLON MUCINOUS ADENOCARCINOMA | ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA | HEAD & NECK SQUAMOUS CELL CARCINOMA | INFILTRATING DUCTAL CARCINOMA | INFILTRATING LOBULAR 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 HISTOLOGY (PLEASE SPECIFY) | MIXED SEROUS AND ENDOMETRIOID | MUCINOUS (COLLOID) ADENOCARCINOMA | MUCINOUS (COLLOID) CARCINOMA | MUSCLE INVASIVE UROTHELIAL CARCINOMA (PT2 OR ABOVE) | OTHER SPECIFY | RECTAL ADENOCARCINOMA | RECTAL MUCINOUS ADENOCARCINOMA | SEROUS CYSTADENOCARCINOMA | SEROUS ENDOMETRIAL ADENOCARCINOMA | TREATED PRIMARY GBM | UNTREATED PRIMARY (DE NOVO) GBM
--- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | ---
ALL | 356 | 54 | 351 | 321 | 104 | 12 | 493 | 11 | 79 | 243 | 7 | 4 | 17 | 2 | 3 | 2 | 18 | 1 | 1 | 1 | 3 | 315 | 5 | 18 | 4 | 3 | 49 | 10 | 143 | 13 | 552 | 85 | 1 | 20
AMP PEAK 16(7P11.2) CNV | 206 | 21 | 38 | 137 | 31 | 1 | 160 | 5 | 37 | 141 | 5 | 3 | 8 | 0 | 2 | 0 | 9 | 1 | 0 | 0 | 2 | 156 | 0 | 4 | 2 | 0 | 25 | 4 | 94 | 3 | 184 | 23 | 1 | 17
AMP PEAK 16(7P11.2) WILD-TYPE | 150 | 33 | 313 | 184 | 73 | 11 | 333 | 6 | 42 | 102 | 2 | 1 | 9 | 2 | 1 | 2 | 9 | 0 | 1 | 1 | 1 | 159 | 5 | 14 | 2 | 3 | 24 | 6 | 49 | 10 | 368 | 62 | 0 | 3

Figure S89. Get High-res Image Gene #16: 'Amp Peak 16(7p11.2)' versus Clinical Feature #6: 'HISTOLOGICAL.TYPE'

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

P value = 2.1e-09 (Fisher's exact test), Q value = 3e-06

Table S90. Gene #16: 'Amp Peak 16(7p11.2)' versus Clinical Feature #7: 'PATHOLOGY.T'

nPatients | T0+T1 | T2 | T3 | T4
--- | --- | --- | --- | ---
ALL | 448 | 611 | 688 | 208
AMP PEAK 16(7P11.2) CNV | 151 | 308 | 360 | 101
AMP PEAK 16(7P11.2) WILD-TYPE | 297 | 303 | 328 | 107

Figure S90. Get High-res Image Gene #16: 'Amp Peak 16(7p11.2)' versus Clinical Feature #7: 'PATHOLOGY.T'

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

P value = 4.56e-07 (Fisher's exact test), Q value = 0.00062

Table S91. Gene #16: 'Amp Peak 16(7p11.2)' versus Clinical Feature #8: 'PATHOLOGY.N'

nPatients | N0 | N1 | N2 | N3
--- | --- | --- | --- | ---
ALL | 1036 | 343 | 279 | 11
AMP PEAK 16(7P11.2) CNV | 458 | 200 | 163 | 6
AMP PEAK 16(7P11.2) WILD-TYPE | 578 | 143 | 116 | 5

Figure S91. Get High-res Image Gene #16: 'Amp Peak 16(7p11.2)' versus Clinical Feature #8: 'PATHOLOGY.N'

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

P value = 7.18e-13 (Fisher's exact test), Q value = 1.1e-09

Table S92. Gene #16: 'Amp Peak 16(7p11.2)' versus Clinical Feature #11: 'RADIATIONS.RADIATION.REGIMENINDICATION'

nPatients | NO | YES
--- | --- | ---
ALL | 835 | 3816
AMP PEAK 16(7P11.2) CNV | 463 | 1594
AMP PEAK 16(7P11.2) WILD-TYPE | 372 | 2222

Figure S92. Get High-res Image Gene #16: 'Amp Peak 16(7p11.2)' versus Clinical Feature #11: 'RADIATIONS.RADIATION.REGIMENINDICATION'

'Amp Peak 17(7q21.2)' versus 'Time to Death'

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

Table S93. Gene #17: 'Amp Peak 17(7q21.2)' versus Clinical Feature #1: 'Time to Death'

| nPatients | nDeath | Duration Range (Median), Month
--- | --- | --- | ---
ALL | 4370 | 1406 | 0.0 - 224.0 (14.4)
AMP PEAK 17(7Q21.2) CNV | 1811 | 754 | 0.0 - 224.0 (12.0)
AMP PEAK 17(7Q21.2) WILD-TYPE | 2559 | 652 | 0.0 - 220.9 (17.0)

Figure S93. Get High-res Image Gene #17: 'Amp Peak 17(7q21.2)' versus Clinical Feature #1: 'Time to Death'

'Amp Peak 17(7q21.2)' versus 'PRIMARY.SITE.OF.DISEASE'

P value = 3.72e-139 (Chi-square test), Q value = 6.3e-136

Table S94. Gene #17: 'Amp Peak 17(7q21.2)' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'

nPatients | BLADDER | BRAIN | BREAST | COLON | ENDOMETRIAL | HEAD/NECK | KIDNEY | LUNG | OMENTUM | OVARY | PERITONEUM (OVARY) | RECTUM
--- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | ---
ALL | 131 | 544 | 857 | 412 | 454 | 321 | 493 | 714 | 2 | 548 | 2 | 159
AMP PEAK 17(7Q21.2) CNV | 52 | 453 | 222 | 203 | 59 | 109 | 165 | 345 | 1 | 223 | 1 | 83
AMP PEAK 17(7Q21.2) WILD-TYPE | 79 | 91 | 635 | 209 | 395 | 212 | 328 | 369 | 1 | 325 | 1 | 76

Figure S94. Get High-res Image Gene #17: 'Amp Peak 17(7q21.2)' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'

'Amp Peak 17(7q21.2)' versus 'GENDER'

P value = 8.63e-28 (Fisher's exact test), Q value = 1.3e-24

Table S95. Gene #17: 'Amp Peak 17(7q21.2)' versus Clinical Feature #4: 'GENDER'

nPatients | FEMALE | MALE
--- | --- | ---
ALL | 2924 | 1717
AMP PEAK 17(7Q21.2) CNV | 1031 | 887
AMP PEAK 17(7Q21.2) WILD-TYPE | 1893 | 830

Figure S95. Get High-res Image Gene #17: 'Amp Peak 17(7q21.2)' versus Clinical Feature #4: 'GENDER'

'Amp Peak 17(7q21.2)' versus 'HISTOLOGICAL.TYPE'

P value = 4.86e-38 (Chi-square test), Q value = 7.7e-35

Table S96. Gene #17: 'Amp Peak 17(7q21.2)' versus Clinical Feature #6: 'HISTOLOGICAL.TYPE'

nPatients | COLON ADENOCARCINOMA | COLON MUCINOUS ADENOCARCINOMA | ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA | HEAD & NECK SQUAMOUS CELL CARCINOMA | INFILTRATING DUCTAL CARCINOMA | INFILTRATING LOBULAR 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 HISTOLOGY (PLEASE SPECIFY) | MIXED SEROUS AND ENDOMETRIOID | MUCINOUS (COLLOID) ADENOCARCINOMA | MUCINOUS (COLLOID) CARCINOMA | MUSCLE INVASIVE UROTHELIAL CARCINOMA (PT2 OR ABOVE) | OTHER SPECIFY | RECTAL ADENOCARCINOMA | RECTAL MUCINOUS ADENOCARCINOMA | SEROUS CYSTADENOCARCINOMA | SEROUS ENDOMETRIAL ADENOCARCINOMA | TREATED PRIMARY GBM | UNTREATED PRIMARY (DE NOVO) GBM
--- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | ---
ALL | 356 | 54 | 351 | 321 | 104 | 12 | 493 | 11 | 79 | 243 | 7 | 4 | 17 | 2 | 3 | 2 | 18 | 1 | 1 | 1 | 3 | 315 | 5 | 18 | 4 | 3 | 49 | 10 | 143 | 13 | 552 | 85 | 1 | 20
AMP PEAK 17(7Q21.2) CNV | 185 | 18 | 40 | 109 | 26 | 1 | 165 | 3 | 30 | 114 | 4 | 2 | 8 | 0 | 2 | 0 | 8 | 1 | 0 | 0 | 1 | 172 | 1 | 4 | 0 | 0 | 18 | 1 | 79 | 3 | 225 | 15 | 1 | 14
AMP PEAK 17(7Q21.2) WILD-TYPE | 171 | 36 | 311 | 212 | 78 | 11 | 328 | 8 | 49 | 129 | 3 | 2 | 9 | 2 | 1 | 2 | 10 | 0 | 1 | 1 | 2 | 143 | 4 | 14 | 4 | 3 | 31 | 9 | 64 | 10 | 327 | 70 | 0 | 6

Figure S96. Get High-res Image Gene #17: 'Amp Peak 17(7q21.2)' versus Clinical Feature #6: 'HISTOLOGICAL.TYPE'

'Amp Peak 17(7q21.2)' versus 'RADIATIONS.RADIATION.REGIMENINDICATION'

P value = 5.62e-12 (Fisher's exact test), Q value = 8.2e-09

Table S97. Gene #17: 'Amp Peak 17(7q21.2)' versus Clinical Feature #11: 'RADIATIONS.RADIATION.REGIMENINDICATION'

nPatients | NO | YES
--- | --- | ---
ALL | 835 | 3816
AMP PEAK 17(7Q21.2) CNV | 435 | 1488
AMP PEAK 17(7Q21.2) WILD-TYPE | 400 | 2328

Figure S97. Get High-res Image Gene #17: 'Amp Peak 17(7q21.2)' versus Clinical Feature #11: 'RADIATIONS.RADIATION.REGIMENINDICATION'

'Amp Peak 18(7q36.3)' versus 'Time to Death'

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

Table S98. Gene #18: 'Amp Peak 18(7q36.3)' versus Clinical Feature #1: 'Time to Death'

| nPatients | nDeath | Duration Range (Median), Month
--- | --- | --- | ---
ALL | 4370 | 1406 | 0.0 - 224.0 (14.4)
AMP PEAK 18(7Q36.3) CNV | 1759 | 711 | 0.0 - 223.4 (12.0)
AMP PEAK 18(7Q36.3) WILD-TYPE | 2611 | 695 | 0.0 - 224.0 (16.3)

Figure S98. Get High-res Image Gene #18: 'Amp Peak 18(7q36.3)' versus Clinical Feature #1: 'Time to Death'

'Amp Peak 18(7q36.3)' versus 'PRIMARY.SITE.OF.DISEASE'

P value = 4.4e-158 (Chi-square test), Q value = 7.5e-155

Table S99. Gene #18: 'Amp Peak 18(7q36.3)' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'

nPatients | BLADDER | BRAIN | BREAST | COLON | ENDOMETRIAL | HEAD/NECK | KIDNEY | LUNG | OMENTUM | OVARY | PERITONEUM (OVARY) | RECTUM
--- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | ---
ALL | 131 | 544 | 857 | 412 | 454 | 321 | 493 | 714 | 2 | 548 | 2 | 159
AMP PEAK 18(7Q36.3) CNV | 40 | 447 | 209 | 201 | 58 | 60 | 164 | 306 | 1 | 293 | 1 | 82
AMP PEAK 18(7Q36.3) WILD-TYPE | 91 | 97 | 648 | 211 | 396 | 261 | 329 | 408 | 1 | 255 | 1 | 77

Figure S99. Get High-res Image Gene #18: 'Amp Peak 18(7q36.3)' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'

'Amp Peak 18(7q36.3)' versus 'GENDER'

P value = 2.93e-13 (Fisher's exact test), Q value = 4.3e-10

Table S100. Gene #18: 'Amp Peak 18(7q36.3)' versus Clinical Feature #4: 'GENDER'

nPatients | FEMALE | MALE
--- | --- | ---
ALL | 2924 | 1717
AMP PEAK 18(7Q36.3) CNV | 1056 | 808
AMP PEAK 18(7Q36.3) WILD-TYPE | 1868 | 909

Figure S100. Get High-res Image Gene #18: 'Amp Peak 18(7q36.3)' versus Clinical Feature #4: 'GENDER'

'Amp Peak 18(7q36.3)' versus 'HISTOLOGICAL.TYPE'

P value = 3.21e-53 (Chi-square test), Q value = 5.2e-50

Table S101. Gene #18: 'Amp Peak 18(7q36.3)' versus Clinical Feature #6: 'HISTOLOGICAL.TYPE'

nPatients | COLON ADENOCARCINOMA | COLON MUCINOUS ADENOCARCINOMA | ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA | HEAD & NECK SQUAMOUS CELL CARCINOMA | INFILTRATING DUCTAL CARCINOMA | INFILTRATING LOBULAR 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 HISTOLOGY (PLEASE SPECIFY) | MIXED SEROUS AND ENDOMETRIOID | MUCINOUS (COLLOID) ADENOCARCINOMA | MUCINOUS (COLLOID) CARCINOMA | MUSCLE INVASIVE UROTHELIAL CARCINOMA (PT2 OR ABOVE) | OTHER SPECIFY | RECTAL ADENOCARCINOMA | RECTAL MUCINOUS ADENOCARCINOMA | SEROUS CYSTADENOCARCINOMA | SEROUS ENDOMETRIAL ADENOCARCINOMA | TREATED PRIMARY GBM | UNTREATED PRIMARY (DE NOVO) GBM
--- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | ---
ALL | 356 | 54 | 351 | 321 | 104 | 12 | 493 | 11 | 79 | 243 | 7 | 4 | 17 | 2 | 3 | 2 | 18 | 1 | 1 | 1 | 3 | 315 | 5 | 18 | 4 | 3 | 49 | 10 | 143 | 13 | 552 | 85 | 1 | 20
AMP PEAK 18(7Q36.3) CNV | 181 | 19 | 38 | 60 | 25 | 0 | 164 | 4 | 29 | 115 | 2 | 2 | 9 | 0 | 1 | 0 | 7 | 1 | 0 | 1 | 2 | 132 | 1 | 3 | 1 | 0 | 9 | 3 | 79 | 2 | 295 | 17 | 1 | 14
AMP PEAK 18(7Q36.3) WILD-TYPE | 175 | 35 | 313 | 261 | 79 | 12 | 329 | 7 | 50 | 128 | 5 | 2 | 8 | 2 | 2 | 2 | 11 | 0 | 1 | 0 | 1 | 183 | 4 | 15 | 3 | 3 | 40 | 7 | 64 | 11 | 257 | 68 | 0 | 6

Figure S101. Get High-res Image Gene #18: 'Amp Peak 18(7q36.3)' versus Clinical Feature #6: 'HISTOLOGICAL.TYPE'

'Amp Peak 18(7q36.3)' versus 'TUMOR.STAGE'

P value = 1.84e-06 (Fisher's exact test), Q value = 0.0025

Table S102. Gene #18: 'Amp Peak 18(7q36.3)' versus Clinical Feature #10: 'TUMOR.STAGE'

nPatients | I | II | III | IV
--- | --- | --- | --- | ---
ALL | 685 | 487 | 876 | 420
AMP PEAK 18(7Q36.3) CNV | 247 | 191 | 429 | 169
AMP PEAK 18(7Q36.3) WILD-TYPE | 438 | 296 | 447 | 251

Figure S102. Get High-res Image Gene #18: 'Amp Peak 18(7q36.3)' versus Clinical Feature #10: 'TUMOR.STAGE'

'Amp Peak 18(7q36.3)' versus 'RADIATIONS.RADIATION.REGIMENINDICATION'

P value = 4.66e-08 (Fisher's exact test), Q value = 6.5e-05

Table S103. Gene #18: 'Amp Peak 18(7q36.3)' versus Clinical Feature #11: 'RADIATIONS.RADIATION.REGIMENINDICATION'

nPatients | NO | YES
--- | --- | ---
ALL | 835 | 3816
AMP PEAK 18(7Q36.3) CNV | 406 | 1462
AMP PEAK 18(7Q36.3) WILD-TYPE | 429 | 2354

Figure S103. Get High-res Image Gene #18: 'Amp Peak 18(7q36.3)' versus Clinical Feature #11: 'RADIATIONS.RADIATION.REGIMENINDICATION'

'Amp Peak 19(8p11.23)' versus 'PRIMARY.SITE.OF.DISEASE'

P value = 3.4e-66 (Chi-square test), Q value = 5.5e-63

Table S104. Gene #19: 'Amp Peak 19(8p11.23)' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'

nPatients | BLADDER | BRAIN | BREAST | COLON | ENDOMETRIAL | HEAD/NECK | KIDNEY | LUNG | OMENTUM | OVARY | PERITONEUM (OVARY) | RECTUM
--- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | ---
ALL | 131 | 544 | 857 | 412 | 454 | 321 | 493 | 714 | 2 | 548 | 2 | 159
AMP PEAK 19(8P11.23) CNV | 46 | 41 | 319 | 143 | 106 | 102 | 27 | 266 | 0 | 125 | 1 | 52
AMP PEAK 19(8P11.23) WILD-TYPE | 85 | 503 | 538 | 269 | 348 | 219 | 466 | 448 | 2 | 423 | 1 | 107

Figure S104. Get High-res Image Gene #19: 'Amp Peak 19(8p11.23)' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'

'Amp Peak 19(8p11.23)' versus 'HISTOLOGICAL.TYPE'

P value = 1.65e-37 (Chi-square test), Q value = 2.6e-34

Table S105. Gene #19: 'Amp Peak 19(8p11.23)' versus Clinical Feature #6: 'HISTOLOGICAL.TYPE'

nPatients | COLON ADENOCARCINOMA | COLON MUCINOUS ADENOCARCINOMA | ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA | HEAD & NECK SQUAMOUS CELL CARCINOMA | INFILTRATING DUCTAL CARCINOMA | INFILTRATING LOBULAR 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 HISTOLOGY (PLEASE SPECIFY) | MIXED SEROUS AND ENDOMETRIOID | MUCINOUS (COLLOID) ADENOCARCINOMA | MUCINOUS (COLLOID) CARCINOMA | MUSCLE INVASIVE UROTHELIAL CARCINOMA (PT2 OR ABOVE) | OTHER SPECIFY | RECTAL ADENOCARCINOMA | RECTAL MUCINOUS ADENOCARCINOMA | SEROUS CYSTADENOCARCINOMA | SEROUS ENDOMETRIAL ADENOCARCINOMA | TREATED PRIMARY GBM | UNTREATED PRIMARY (DE NOVO) GBM
--- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | ---
ALL | 356 | 54 | 351 | 321 | 104 | 12 | 493 | 11 | 79 | 243 | 7 | 4 | 17 | 2 | 3 | 2 | 18 | 1 | 1 | 1 | 3 | 315 | 5 | 18 | 4 | 3 | 49 | 10 | 143 | 13 | 552 | 85 | 1 | 20
AMP PEAK 19(8P11.23) CNV | 129 | 14 | 80 | 102 | 40 | 4 | 27 | 5 | 29 | 62 | 3 | 0 | 3 | 0 | 1 | 0 | 4 | 0 | 0 | 1 | 2 | 155 | 3 | 6 | 1 | 0 | 14 | 5 | 50 | 2 | 126 | 20 | 0 | 2
AMP PEAK 19(8P11.23) WILD-TYPE | 227 | 40 | 271 | 219 | 64 | 8 | 466 | 6 | 50 | 181 | 4 | 4 | 14 | 2 | 2 | 2 | 14 | 1 | 1 | 0 | 1 | 160 | 2 | 12 | 3 | 3 | 35 | 5 | 93 | 11 | 426 | 65 | 1 | 18

Figure S105. Get High-res Image Gene #19: 'Amp Peak 19(8p11.23)' versus Clinical Feature #6: 'HISTOLOGICAL.TYPE'

'Amp Peak 19(8p11.23)' versus 'PATHOLOGY.T'

P value = 7.37e-09 (Fisher's exact test), Q value = 1e-05

Table S106. Gene #19: 'Amp Peak 19(8p11.23)' versus Clinical Feature #7: 'PATHOLOGY.T'

nPatients | T0+T1 | T2 | T3 | T4
--- | --- | --- | --- | ---
ALL | 448 | 611 | 688 | 208
AMP PEAK 19(8P11.23) CNV | 82 | 213 | 183 | 71
AMP PEAK 19(8P11.23) WILD-TYPE | 366 | 398 | 505 | 137

Figure S106. Get High-res Image Gene #19: 'Amp Peak 19(8p11.23)' versus Clinical Feature #7: 'PATHOLOGY.T'

'Amp Peak 19(8p11.23)' versus 'RADIATIONS.RADIATION.REGIMENINDICATION'

P value = 0.000163 (Fisher's exact test), Q value = 0.2

Table S107. Gene #19: 'Amp Peak 19(8p11.23)' versus Clinical Feature #11: 'RADIATIONS.RADIATION.REGIMENINDICATION'

nPatients | NO | YES
--- | --- | ---
ALL | 835 | 3816
AMP PEAK 19(8P11.23) CNV | 178 | 1054
AMP PEAK 19(8P11.23) WILD-TYPE | 657 | 2762

Figure S107. Get High-res Image Gene #19: 'Amp Peak 19(8p11.23)' versus Clinical Feature #11: 'RADIATIONS.RADIATION.REGIMENINDICATION'

'Amp Peak 20(8p11.21)' versus 'AGE'

P value = 7.12e-06 (t-test), Q value = 0.0095

Table S108. Gene #20: 'Amp Peak 20(8p11.21)' versus Clinical Feature #2: 'AGE'

| nPatients | Mean (Std.Dev)
--- | --- | ---
ALL | 4585 | 61.9 (12.6)
AMP PEAK 20(8P11.21) CNV | 1380 | 63.1 (12.0)
AMP PEAK 20(8P11.21) WILD-TYPE | 3205 | 61.4 (12.8)

Figure S108. Get High-res Image Gene #20: 'Amp Peak 20(8p11.21)' versus Clinical Feature #2: 'AGE'

'Amp Peak 20(8p11.21)' versus 'PRIMARY.SITE.OF.DISEASE'

P value = 7.88e-77 (Chi-square test), Q value = 1.3e-73

Table S109. Gene #20: 'Amp Peak 20(8p11.21)' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'

nPatients | BLADDER | BRAIN | BREAST | COLON | ENDOMETRIAL | HEAD/NECK | KIDNEY | LUNG | OMENTUM | OVARY | PERITONEUM (OVARY) | RECTUM
--- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | ---
ALL | 131 | 544 | 857 | 412 | 454 | 321 | 493 | 714 | 2 | 548 | 2 | 159
AMP PEAK 20(8P11.21) CNV | 45 | 42 | 337 | 173 | 135 | 89 | 29 | 281 | 0 | 194 | 2 | 72
AMP PEAK 20(8P11.21) WILD-TYPE | 86 | 502 | 520 | 239 | 319 | 232 | 464 | 433 | 2 | 354 | 0 | 87

Figure S109. Get High-res Image Gene #20: 'Amp Peak 20(8p11.21)' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'

'Amp Peak 20(8p11.21)' versus 'HISTOLOGICAL.TYPE'

P value = 1.1e-45 (Chi-square test), Q value = 1.7e-42

Table S110. Gene #20: 'Amp Peak 20(8p11.21)' versus Clinical Feature #6: 'HISTOLOGICAL.TYPE'

nPatients | COLON ADENOCARCINOMA | COLON MUCINOUS ADENOCARCINOMA | ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA | HEAD & NECK SQUAMOUS CELL CARCINOMA | INFILTRATING DUCTAL CARCINOMA | INFILTRATING LOBULAR 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 HISTOLOGY (PLEASE SPECIFY) | MIXED SEROUS AND ENDOMETRIOID | MUCINOUS (COLLOID) ADENOCARCINOMA | MUCINOUS (COLLOID) CARCINOMA | MUSCLE INVASIVE UROTHELIAL CARCINOMA (PT2 OR ABOVE) | OTHER SPECIFY | RECTAL ADENOCARCINOMA | RECTAL MUCINOUS ADENOCARCINOMA | SEROUS CYSTADENOCARCINOMA | SEROUS ENDOMETRIAL ADENOCARCINOMA | TREATED PRIMARY GBM | UNTREATED PRIMARY (DE NOVO) GBM
--- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | ---
ALL | 356 | 54 | 351 | 321 | 104 | 12 | 493 | 11 | 79 | 243 | 7 | 4 | 17 | 2 | 3 | 2 | 18 | 1 | 1 | 1 | 3 | 315 | 5 | 18 | 4 | 3 | 49 | 10 | 143 | 13 | 552 | 85 | 1 | 20
AMP PEAK 20(8P11.21) CNV | 155 | 18 | 82 | 89 | 42 | 4 | 29 | 7 | 31 | 80 | 3 | 0 | 4 | 0 | 0 | 0 | 5 | 0 | 0 | 1 | 3 | 147 | 3 | 6 | 0 | 0 | 12 | 6 | 67 | 3 | 196 | 47 | 0 | 2
AMP PEAK 20(8P11.21) WILD-TYPE | 201 | 36 | 269 | 232 | 62 | 8 | 464 | 4 | 48 | 163 | 4 | 4 | 13 | 2 | 3 | 2 | 13 | 1 | 1 | 0 | 0 | 168 | 2 | 12 | 4 | 3 | 37 | 4 | 76 | 10 | 356 | 38 | 1 | 18

Figure S110. Get High-res Image Gene #20: 'Amp Peak 20(8p11.21)' versus Clinical Feature #6: 'HISTOLOGICAL.TYPE'

'Amp Peak 20(8p11.21)' versus 'PATHOLOGY.T'

P value = 1.34e-11 (Fisher's exact test), Q value = 2e-08

Table S111. Gene #20: 'Amp Peak 20(8p11.21)' versus Clinical Feature #7: 'PATHOLOGY.T'

nPatients | T0+T1 | T2 | T3 | T4
--- | --- | --- | --- | ---
ALL | 448 | 611 | 688 | 208
AMP PEAK 20(8P11.21) CNV | 78 | 227 | 222 | 67
AMP PEAK 20(8P11.21) WILD-TYPE | 370 | 384 | 466 | 141

Figure S111. Get High-res Image Gene #20: 'Amp Peak 20(8p11.21)' versus Clinical Feature #7: 'PATHOLOGY.T'

'Amp Peak 20(8p11.21)' versus 'TUMOR.STAGE'

P value = 2.88e-05 (Fisher's exact test), Q value = 0.037

Table S112. Gene #20: 'Amp Peak 20(8p11.21)' versus Clinical Feature #10: 'TUMOR.STAGE'

nPatients | I | II | III | IV
--- | --- | --- | --- | ---
ALL | 685 | 487 | 876 | 420
AMP PEAK 20(8P11.21) CNV | 181 | 186 | 292 | 113
AMP PEAK 20(8P11.21) WILD-TYPE | 504 | 301 | 584 | 307

Figure S112. Get High-res Image Gene #20: 'Amp Peak 20(8p11.21)' versus Clinical Feature #10: 'TUMOR.STAGE'

'Amp Peak 20(8p11.21)' versus 'RADIATIONS.RADIATION.REGIMENINDICATION'

P value = 2.27e-08 (Fisher's exact test), Q value = 3.2e-05

Table S113. Gene #20: 'Amp Peak 20(8p11.21)' versus Clinical Feature #11: 'RADIATIONS.RADIATION.REGIMENINDICATION'

nPatients | NO | YES
--- | --- | ---
ALL | 835 | 3816
AMP PEAK 20(8P11.21) CNV | 186 | 1219
AMP PEAK 20(8P11.21) WILD-TYPE | 649 | 2597

Figure S113. Get High-res Image Gene #20: 'Amp Peak 20(8p11.21)' versus Clinical Feature #11: 'RADIATIONS.RADIATION.REGIMENINDICATION'

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

P value = 1.94e-213 (Chi-square test), Q value = 3.4e-210

Table S114. Gene #21: 'Amp Peak 21(8q24.21)' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'

nPatients | BLADDER | BRAIN | BREAST | COLON | ENDOMETRIAL | HEAD/NECK | KIDNEY | LUNG | OMENTUM | OVARY | PERITONEUM (OVARY) | RECTUM
--- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | ---
ALL | 131 | 544 | 857 | 412 | 454 | 321 | 493 | 714 | 2 | 548 | 2 | 159
AMP PEAK 21(8Q24.21) CNV | 79 | 62 | 558 | 239 | 168 | 231 | 71 | 475 | 2 | 429 | 2 | 105
AMP PEAK 21(8Q24.21) WILD-TYPE | 52 | 482 | 299 | 173 | 286 | 90 | 422 | 239 | 0 | 119 | 0 | 54

Figure S114. Get High-res Image Gene #21: 'Amp Peak 21(8q24.21)' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'

'Amp Peak 21(8q24.21)' versus 'GENDER'

P value = 2.5e-08 (Fisher's exact test), Q value = 3.5e-05

Table S115. Gene #21: 'Amp Peak 21(8q24.21)' versus Clinical Feature #4: 'GENDER'

nPatients | FEMALE | MALE
--- | --- | ---
ALL | 2924 | 1717
AMP PEAK 21(8Q24.21) CNV | 1618 | 804
AMP PEAK 21(8Q24.21) WILD-TYPE | 1306 | 913

Figure S115. Get High-res Image Gene #21: 'Amp Peak 21(8q24.21)' versus Clinical Feature #4: 'GENDER'

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

P value = 1.3e-05 (t-test), Q value = 0.017

Table S116. Gene #21: 'Amp Peak 21(8q24.21)' versus Clinical Feature #5: 'KARNOFSKY.PERFORMANCE.SCORE'

| nPatients | Mean (Std.Dev)
--- | --- | ---
ALL | 641 | 73.6 (23.9)
AMP PEAK 21(8Q24.21) CNV | 194 | 66.2 (30.7)
AMP PEAK 21(8Q24.21) WILD-TYPE | 447 | 76.8 (19.5)

Figure S116. Get High-res Image Gene #21: 'Amp Peak 21(8q24.21)' versus Clinical Feature #5: 'KARNOFSKY.PERFORMANCE.SCORE'

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

P value = 2.05e-129 (Chi-square test), Q value = 3.5e-126

Table S117. Gene #21: 'Amp Peak 21(8q24.21)' versus Clinical Feature #6: 'HISTOLOGICAL.TYPE'

nPatients | COLON ADENOCARCINOMA | COLON MUCINOUS ADENOCARCINOMA | ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA | HEAD & NECK SQUAMOUS CELL CARCINOMA | INFILTRATING DUCTAL CARCINOMA | INFILTRATING LOBULAR 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 HISTOLOGY (PLEASE SPECIFY) | MIXED SEROUS AND ENDOMETRIOID | MUCINOUS (COLLOID) ADENOCARCINOMA | MUCINOUS (COLLOID) CARCINOMA | MUSCLE INVASIVE UROTHELIAL CARCINOMA (PT2 OR ABOVE) | OTHER SPECIFY | RECTAL ADENOCARCINOMA | RECTAL MUCINOUS ADENOCARCINOMA | SEROUS CYSTADENOCARCINOMA | SEROUS ENDOMETRIAL ADENOCARCINOMA | TREATED PRIMARY GBM | UNTREATED PRIMARY (DE NOVO) GBM
--- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | ---
ALL | 356 | 54 | 351 | 321 | 104 | 12 | 493 | 11 | 79 | 243 | 7 | 4 | 17 | 2 | 3 | 2 | 18 | 1 | 1 | 1 | 3 | 315 | 5 | 18 | 4 | 3 | 49 | 10 | 143 | 13 | 552 | 85 | 1 | 20
AMP PEAK 21(8Q24.21) CNV | 213 | 25 | 99 | 231 | 73 | 4 | 71 | 8 | 45 | 162 | 6 | 1 | 10 | 1 | 2 | 0 | 12 | 1 | 0 | 1 | 3 | 223 | 4 | 8 | 0 | 0 | 30 | 7 | 98 | 5 | 433 | 61 | 0 | 3
AMP PEAK 21(8Q24.21) WILD-TYPE | 143 | 29 | 252 | 90 | 31 | 8 | 422 | 3 | 34 | 81 | 1 | 3 | 7 | 1 | 1 | 2 | 6 | 0 | 1 | 0 | 0 | 92 | 1 | 10 | 4 | 3 | 19 | 3 | 45 | 8 | 119 | 24 | 1 | 17

Figure S117. Get High-res Image Gene #21: 'Amp Peak 21(8q24.21)' versus Clinical Feature #6: 'HISTOLOGICAL.TYPE'

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

P value = 2.1e-26 (Fisher's exact test), Q value = 3.2e-23

Table S118. Gene #21: 'Amp Peak 21(8q24.21)' versus Clinical Feature #7: 'PATHOLOGY.T'

nPatients | T0+T1 | T2 | T3 | T4
--- | --- | --- | --- | ---
ALL | 448 | 611 | 688 | 208
AMP PEAK 21(8Q24.21) CNV | 141 | 378 | 369 | 141
AMP PEAK 21(8Q24.21) WILD-TYPE | 307 | 233 | 319 | 67

Figure S118. Get High-res Image Gene #21: 'Amp Peak 21(8q24.21)' versus Clinical Feature #7: 'PATHOLOGY.T'

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

P value = 4.03e-11 (Fisher's exact test), Q value = 5.8e-08

Table S119. Gene #21: 'Amp Peak 21(8q24.21)' versus Clinical Feature #8: 'PATHOLOGY.N'

nPatients | N0 | N1 | N2 | N3
--- | --- | --- | --- | ---
ALL | 1036 | 343 | 279 | 11
AMP PEAK 21(8Q24.21) CNV | 532 | 218 | 202 | 9
AMP PEAK 21(8Q24.21) WILD-TYPE | 504 | 125 | 77 | 2

Figure S119. Get High-res Image Gene #21: 'Amp Peak 21(8q24.21)' versus Clinical Feature #8: 'PATHOLOGY.N'

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

P value = 6.46e-19 (Fisher's exact test), Q value = 9.7e-16

Table S120. Gene #21: 'Amp Peak 21(8q24.21)' versus Clinical Feature #10: 'TUMOR.STAGE'

nPatients | I | II | III | IV
--- | --- | --- | --- | ---
ALL | 685 | 487 | 876 | 420
AMP PEAK 21(8Q24.21) CNV | 296 | 294 | 570 | 272
AMP PEAK 21(8Q24.21) WILD-TYPE | 389 | 193 | 306 | 148

Figure S120. Get High-res Image Gene #21: 'Amp Peak 21(8q24.21)' versus Clinical Feature #10: 'TUMOR.STAGE'

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

P value = 4.46e-22 (Fisher's exact test), Q value = 6.8e-19

Table S121. Gene #21: 'Amp Peak 21(8q24.21)' versus Clinical Feature #11: 'RADIATIONS.RADIATION.REGIMENINDICATION'

nPatients | NO | YES
--- | --- | ---
ALL | 835 | 3816
AMP PEAK 21(8Q24.21) CNV | 310 | 2120
AMP PEAK 21(8Q24.21) WILD-TYPE | 525 | 1696

Figure S121. Get High-res Image Gene #21: 'Amp Peak 21(8q24.21)' versus Clinical Feature #11: 'RADIATIONS.RADIATION.REGIMENINDICATION'

'Amp Peak 22(9p13.3)' versus 'PRIMARY.SITE.OF.DISEASE'

P value = 2.06e-34 (Chi-square test), Q value = 3.2e-31

Table S122. Gene #22: 'Amp Peak 22(9p13.3)' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'

nPatients | BLADDER | BRAIN | BREAST | COLON | ENDOMETRIAL | HEAD/NECK | KIDNEY | LUNG | OMENTUM | OVARY | PERITONEUM (OVARY) | RECTUM
--- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | ---
ALL | 131 | 544 | 857 | 412 | 454 | 321 | 493 | 714 | 2 | 548 | 2 | 159
AMP PEAK 22(9P13.3) CNV | 30 | 66 | 152 | 70 | 34 | 90 | 12 | 151 | 0 | 132 | 0 | 45
AMP PEAK 22(9P13.3) WILD-TYPE | 101 | 478 | 705 | 342 | 420 | 231 | 481 | 563 | 2 | 416 | 2 | 114

Figure S122. Get High-res Image Gene #22: 'Amp Peak 22(9p13.3)' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'

'Amp Peak 22(9p13.3)' versus 'HISTOLOGICAL.TYPE'

P value = 2.44e-31 (Chi-square test), Q value = 3.8e-28

Table S123. Gene #22: 'Amp Peak 22(9p13.3)' versus Clinical Feature #6: 'HISTOLOGICAL.TYPE'

nPatients | COLON ADENOCARCINOMA | COLON MUCINOUS ADENOCARCINOMA | ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA | HEAD & NECK SQUAMOUS CELL CARCINOMA | INFILTRATING DUCTAL CARCINOMA | INFILTRATING LOBULAR 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 HISTOLOGY (PLEASE SPECIFY) | MIXED SEROUS AND ENDOMETRIOID | MUCINOUS (COLLOID) ADENOCARCINOMA | MUCINOUS (COLLOID) CARCINOMA | MUSCLE INVASIVE UROTHELIAL CARCINOMA (PT2 OR ABOVE) | OTHER SPECIFY | RECTAL ADENOCARCINOMA | RECTAL MUCINOUS ADENOCARCINOMA | SEROUS CYSTADENOCARCINOMA | SEROUS ENDOMETRIAL ADENOCARCINOMA | TREATED PRIMARY GBM | UNTREATED PRIMARY (DE NOVO) GBM
--- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | ---
ALL | 356 | 54 | 351 | 321 | 104 | 12 | 493 | 11 | 79 | 243 | 7 | 4 | 17 | 2 | 3 | 2 | 18 | 1 | 1 | 1 | 3 | 315 | 5 | 18 | 4 | 3 | 49 | 10 | 143 | 13 | 552 | 85 | 1 | 20
AMP PEAK 22(9P13.3) CNV | 56 | 14 | 16 | 90 | 25 | 1 | 12 | 3 | 16 | 36 | 4 | 0 | 3 | 0 | 1 | 0 | 4 | 0 | 0 | 1 | 0 | 83 | 0 | 2 | 0 | 0 | 14 | 3 | 39 | 5 | 132 | 16 | 1 | 1
AMP PEAK 22(9P13.3) WILD-TYPE | 300 | 40 | 335 | 231 | 79 | 11 | 481 | 8 | 63 | 207 | 3 | 4 | 14 | 2 | 2 | 2 | 14 | 1 | 1 | 0 | 3 | 232 | 5 | 16 | 4 | 3 | 35 | 7 | 104 | 8 | 420 | 69 | 0 | 19

Figure S123. Get High-res Image Gene #22: 'Amp Peak 22(9p13.3)' versus Clinical Feature #6: 'HISTOLOGICAL.TYPE'

'Amp Peak 22(9p13.3)' versus 'PATHOLOGY.T'

P value = 4.21e-07 (Fisher's exact test), Q value = 0.00058

Table S124. Gene #22: 'Amp Peak 22(9p13.3)' versus Clinical Feature #7: 'PATHOLOGY.T'

nPatients | T0+T1 | T2 | T3 | T4
--- | --- | --- | --- | ---
ALL | 448 | 611 | 688 | 208
AMP PEAK 22(9P13.3) CNV | 50 | 123 | 112 | 59
AMP PEAK 22(9P13.3) WILD-TYPE | 398 | 488 | 576 | 149

Figure S124. Get High-res Image Gene #22: 'Amp Peak 22(9p13.3)' versus Clinical Feature #7: 'PATHOLOGY.T'

'Amp Peak 23(10p15.1)' versus 'PRIMARY.SITE.OF.DISEASE'

P value = 8.14e-107 (Chi-square test), Q value = 1.4e-103

Table S125. Gene #23: 'Amp Peak 23(10p15.1)' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'

nPatients | BLADDER | BRAIN | BREAST | COLON | ENDOMETRIAL | HEAD/NECK | KIDNEY | LUNG | OMENTUM | OVARY | PERITONEUM (OVARY) | RECTUM
--- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | ---
ALL | 131 | 544 | 857 | 412 | 454 | 321 | 493 | 714 | 2 | 548 | 2 | 159
AMP PEAK 23(10P15.1) CNV | 54 | 17 | 242 | 38 | 112 | 29 | 16 | 170 | 0 | 239 | 2 | 15
AMP PEAK 23(10P15.1) WILD-TYPE | 77 | 527 | 615 | 374 | 342 | 292 | 477 | 544 | 2 | 309 | 0 | 144

Figure S125. Get High-res Image Gene #23: 'Amp Peak 23(10p15.1)' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'

'Amp Peak 23(10p15.1)' versus 'GENDER'

P value = 1.03e-21 (Fisher's exact test), Q value = 1.6e-18

Table S126. Gene #23: 'Amp Peak 23(10p15.1)' versus Clinical Feature #4: 'GENDER'

nPatients | FEMALE | MALE
--- | --- | ---
ALL | 2924 | 1717
AMP PEAK 23(10P15.1) CNV | 712 | 222
AMP PEAK 23(10P15.1) WILD-TYPE | 2212 | 1495

Figure S126. Get High-res Image Gene #23: 'Amp Peak 23(10p15.1)' versus Clinical Feature #4: 'GENDER'

'Amp Peak 23(10p15.1)' versus 'HISTOLOGICAL.TYPE'

P value = 2.93e-70 (Chi-square test), Q value = 4.8e-67

Table S127. Gene #23: 'Amp Peak 23(10p15.1)' versus Clinical Feature #6: 'HISTOLOGICAL.TYPE'

nPatients | COLON ADENOCARCINOMA | COLON MUCINOUS ADENOCARCINOMA | ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA | HEAD & NECK SQUAMOUS CELL CARCINOMA | INFILTRATING DUCTAL CARCINOMA | INFILTRATING LOBULAR 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 HISTOLOGY (PLEASE SPECIFY) | MIXED SEROUS AND ENDOMETRIOID | MUCINOUS (COLLOID) ADENOCARCINOMA | MUCINOUS (COLLOID) CARCINOMA | MUSCLE INVASIVE UROTHELIAL CARCINOMA (PT2 OR ABOVE) | OTHER SPECIFY | RECTAL ADENOCARCINOMA | RECTAL MUCINOUS ADENOCARCINOMA | SEROUS CYSTADENOCARCINOMA | SEROUS ENDOMETRIAL ADENOCARCINOMA | TREATED PRIMARY GBM | UNTREATED PRIMARY (DE NOVO) GBM
--- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | ---
ALL | 356 | 54 | 351 | 321 | 104 | 12 | 493 | 11 | 79 | 243 | 7 | 4 | 17 | 2 | 3 | 2 | 18 | 1 | 1 | 1 | 3 | 315 | 5 | 18 | 4 | 3 | 49 | 10 | 143 | 13 | 552 | 85 | 1 | 20
AMP PEAK 23(10P15.1) CNV | 34 | 3 | 84 | 29 | 45 | 0 | 16 | 4 | 27 | 62 | 2 | 0 | 4 | 0 | 2 | 0 | 7 | 0 | 0 | 0 | 2 | 59 | 2 | 4 | 1 | 0 | 20 | 2 | 14 | 1 | 241 | 24 | 0 | 0
AMP PEAK 23(10P15.1) WILD-TYPE | 322 | 51 | 267 | 292 | 59 | 12 | 477 | 7 | 52 | 181 | 5 | 4 | 13 | 2 | 1 | 2 | 11 | 1 | 1 | 1 | 1 | 256 | 3 | 14 | 3 | 3 | 29 | 8 | 129 | 12 | 311 | 61 | 1 | 20

Figure S127. Get High-res Image Gene #23: 'Amp Peak 23(10p15.1)' versus Clinical Feature #6: 'HISTOLOGICAL.TYPE'

'Amp Peak 23(10p15.1)' versus 'PATHOLOGY.T'

P value = 3.06e-06 (Fisher's exact test), Q value = 0.0041

Table S128. Gene #23: 'Amp Peak 23(10p15.1)' versus Clinical Feature #7: 'PATHOLOGY.T'

nPatients | T0+T1 | T2 | T3 | T4
--- | --- | --- | --- | ---
ALL | 448 | 611 | 688 | 208
AMP PEAK 23(10P15.1) CNV | 38 | 111 | 67 | 25
AMP PEAK 23(10P15.1) WILD-TYPE | 410 | 500 | 621 | 183

Figure S128. Get High-res Image Gene #23: 'Amp Peak 23(10p15.1)' versus Clinical Feature #7: 'PATHOLOGY.T'

'Amp Peak 23(10p15.1)' versus 'TUMOR.STAGE'

P value = 5.14e-16 (Fisher's exact test), Q value = 7.6e-13

Table S129. Gene #23: 'Amp Peak 23(10p15.1)' versus Clinical Feature #10: 'TUMOR.STAGE'

nPatients | I | II | III | IV
--- | --- | --- | --- | ---
ALL | 685 | 487 | 876 | 420
AMP PEAK 23(10P15.1) CNV | 88 | 76 | 250 | 61
AMP PEAK 23(10P15.1) WILD-TYPE | 597 | 411 | 626 | 359

Figure S129. Get High-res Image Gene #23: 'Amp Peak 23(10p15.1)' versus Clinical Feature #10: 'TUMOR.STAGE'

'Amp Peak 23(10p15.1)' versus 'RADIATIONS.RADIATION.REGIMENINDICATION'

P value = 8.77e-07 (Fisher's exact test), Q value = 0.0012

Table S130. Gene #23: 'Amp Peak 23(10p15.1)' versus Clinical Feature #11: 'RADIATIONS.RADIATION.REGIMENINDICATION'

nPatients | NO | YES
--- | --- | ---
ALL | 835 | 3816
AMP PEAK 23(10P15.1) CNV | 118 | 820
AMP PEAK 23(10P15.1) WILD-TYPE | 717 | 2996

Figure S130. Get High-res Image Gene #23: 'Amp Peak 23(10p15.1)' versus Clinical Feature #11: 'RADIATIONS.RADIATION.REGIMENINDICATION'

'Amp Peak 23(10p15.1)' versus 'TOBACCOSMOKINGHISTORYINDICATOR'

P value = 7.11e-07 (Chi-square test), Q value = 0.00097

Table S131. Gene #23: 'Amp Peak 23(10p15.1)' versus Clinical Feature #13: '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 | 15 | 16 | 22 | 25 | 2 | 342 | 208 | 237 | 116
AMP PEAK 23(10P15.1) CNV | 7 | 6 | 12 | 8 | 0 | 78 | 35 | 47 | 8
AMP PEAK 23(10P15.1) WILD-TYPE | 8 | 10 | 10 | 17 | 2 | 264 | 173 | 190 | 108

Figure S131. Get High-res Image Gene #23: 'Amp Peak 23(10p15.1)' versus Clinical Feature #13: 'TOBACCOSMOKINGHISTORYINDICATOR'

'Amp Peak 24(10q22.2)' versus 'PRIMARY.SITE.OF.DISEASE'

P value = 3e-77 (Chi-square test), Q value = 4.9e-74

Table S132. Gene #24: 'Amp Peak 24(10q22.2)' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'

nPatients | BLADDER | BRAIN | BREAST | COLON | ENDOMETRIAL | HEAD/NECK | KIDNEY | LUNG | OMENTUM | OVARY | PERITONEUM (OVARY) | RECTUM
--- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | ---
ALL | 131 | 544 | 857 | 412 | 454 | 321 | 493 | 714 | 2 | 548 | 2 | 159
AMP PEAK 24(10Q22.2) CNV | 18 | 2 | 135 | 23 | 123 | 29 | 10 | 102 | 1 | 169 | 1 | 11
AMP PEAK 24(10Q22.2) WILD-TYPE | 113 | 542 | 722 | 389 | 331 | 292 | 483 | 612 | 1 | 379 | 1 | 148

Figure S132. Get High-res Image Gene #24: 'Amp Peak 24(10q22.2)' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'

'Amp Peak 24(10q22.2)' versus 'GENDER'

P value = 3.16e-20 (Fisher's exact test), Q value = 4.8e-17

Table S133. Gene #24: 'Amp Peak 24(10q22.2)' versus Clinical Feature #4: 'GENDER'

nPatients | FEMALE | MALE
--- | --- | ---
ALL | 2924 | 1717
AMP PEAK 24(10Q22.2) CNV | 493 | 131
AMP PEAK 24(10Q22.2) WILD-TYPE | 2431 | 1586

Figure S133. Get High-res Image Gene #24: 'Amp Peak 24(10q22.2)' versus Clinical Feature #4: 'GENDER'

'Amp Peak 24(10q22.2)' versus 'HISTOLOGICAL.TYPE'

P value = 4.23e-46 (Chi-square test), Q value = 6.7e-43

Table S134. Gene #24: 'Amp Peak 24(10q22.2)' versus Clinical Feature #6: 'HISTOLOGICAL.TYPE'

nPatients | COLON ADENOCARCINOMA | COLON MUCINOUS ADENOCARCINOMA | ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA | HEAD & NECK SQUAMOUS CELL CARCINOMA | INFILTRATING DUCTAL CARCINOMA | INFILTRATING LOBULAR 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 HISTOLOGY (PLEASE SPECIFY) | MIXED SEROUS AND ENDOMETRIOID | MUCINOUS (COLLOID) ADENOCARCINOMA | MUCINOUS (COLLOID) CARCINOMA | MUSCLE INVASIVE UROTHELIAL CARCINOMA (PT2 OR ABOVE) | OTHER SPECIFY | RECTAL ADENOCARCINOMA | RECTAL MUCINOUS ADENOCARCINOMA | SEROUS CYSTADENOCARCINOMA | SEROUS ENDOMETRIAL ADENOCARCINOMA | TREATED PRIMARY GBM | UNTREATED PRIMARY (DE NOVO) GBM
--- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | ---
ALL | 356 | 54 | 351 | 321 | 104 | 12 | 493 | 11 | 79 | 243 | 7 | 4 | 17 | 2 | 3 | 2 | 18 | 1 | 1 | 1 | 3 | 315 | 5 | 18 | 4 | 3 | 49 | 10 | 143 | 13 | 552 | 85 | 1 | 20
AMP PEAK 24(10Q22.2) CNV | 20 | 3 | 88 | 29 | 21 | 2 | 10 | 2 | 19 | 38 | 0 | 0 | 1 | 0 | 1 | 0 | 4 | 0 | 0 | 0 | 0 | 37 | 1 | 3 | 0 | 0 | 4 | 1 | 9 | 1 | 171 | 32 | 0 | 0
AMP PEAK 24(10Q22.2) WILD-TYPE | 336 | 51 | 263 | 292 | 83 | 10 | 483 | 9 | 60 | 205 | 7 | 4 | 16 | 2 | 2 | 2 | 14 | 1 | 1 | 1 | 3 | 278 | 4 | 15 | 4 | 3 | 45 | 9 | 134 | 12 | 381 | 53 | 1 | 20

Figure S134. Get High-res Image Gene #24: 'Amp Peak 24(10q22.2)' versus Clinical Feature #6: 'HISTOLOGICAL.TYPE'

'Amp Peak 24(10q22.2)' versus 'TUMOR.STAGE'

P value = 2.76e-10 (Fisher's exact test), Q value = 4e-07

Table S135. Gene #24: 'Amp Peak 24(10q22.2)' versus Clinical Feature #10: 'TUMOR.STAGE'

nPatients | I | II | III | IV
--- | --- | --- | --- | ---
ALL | 685 | 487 | 876 | 420
AMP PEAK 24(10Q22.2) CNV | 58 | 45 | 169 | 54
AMP PEAK 24(10Q22.2) WILD-TYPE | 627 | 442 | 707 | 366

Figure S135. Get High-res Image Gene #24: 'Amp Peak 24(10q22.2)' versus Clinical Feature #10: 'TUMOR.STAGE'

'Amp Peak 25(11q13.3)' versus 'PRIMARY.SITE.OF.DISEASE'

P value = 2.29e-120 (Chi-square test), Q value = 3.9e-117

Table S136. Gene #25: 'Amp Peak 25(11q13.3)' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'

nPatients | BLADDER | BRAIN | BREAST | COLON | ENDOMETRIAL | HEAD/NECK | KIDNEY | LUNG | OMENTUM | OVARY | PERITONEUM (OVARY) | RECTUM
--- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | ---
ALL | 131 | 544 | 857 | 412 | 454 | 321 | 493 | 714 | 2 | 548 | 2 | 159
AMP PEAK 25(11Q13.3) CNV | 49 | 17 | 325 | 48 | 47 | 145 | 27 | 253 | 0 | 211 | 0 | 25
AMP PEAK 25(11Q13.3) WILD-TYPE | 82 | 527 | 532 | 364 | 407 | 176 | 466 | 461 | 2 | 337 | 2 | 134

Figure S136. Get High-res Image Gene #25: 'Amp Peak 25(11q13.3)' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'

'Amp Peak 25(11q13.3)' versus 'GENDER'

P value = 0.000162 (Fisher's exact test), Q value = 0.2

Table S137. Gene #25: 'Amp Peak 25(11q13.3)' versus Clinical Feature #4: 'GENDER'

nPatients | FEMALE | MALE
--- | --- | ---
ALL | 2924 | 1717
AMP PEAK 25(11Q13.3) CNV | 776 | 371
AMP PEAK 25(11Q13.3) WILD-TYPE | 2148 | 1346

Figure S137. Get High-res Image Gene #25: 'Amp Peak 25(11q13.3)' versus Clinical Feature #4: 'GENDER'

'Amp Peak 25(11q13.3)' versus 'HISTOLOGICAL.TYPE'

P value = 1.72e-67 (Chi-square test), Q value = 2.8e-64

Table S138. Gene #25: 'Amp Peak 25(11q13.3)' versus Clinical Feature #6: 'HISTOLOGICAL.TYPE'

nPatients | COLON ADENOCARCINOMA | COLON MUCINOUS ADENOCARCINOMA | ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA | HEAD & NECK SQUAMOUS CELL CARCINOMA | INFILTRATING DUCTAL CARCINOMA | INFILTRATING LOBULAR 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 HISTOLOGY (PLEASE SPECIFY) | MIXED SEROUS AND ENDOMETRIOID | MUCINOUS (COLLOID) ADENOCARCINOMA | MUCINOUS (COLLOID) CARCINOMA | MUSCLE INVASIVE UROTHELIAL CARCINOMA (PT2 OR ABOVE) | OTHER SPECIFY | RECTAL ADENOCARCINOMA | RECTAL MUCINOUS ADENOCARCINOMA | SEROUS CYSTADENOCARCINOMA | SEROUS ENDOMETRIAL ADENOCARCINOMA | TREATED PRIMARY GBM | UNTREATED PRIMARY (DE NOVO) GBM
--- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | ---
ALL | 356 | 54 | 351 | 321 | 104 | 12 | 493 | 11 | 79 | 243 | 7 | 4 | 17 | 2 | 3 | 2 | 18 | 1 | 1 | 1 | 3 | 315 | 5 | 18 | 4 | 3 | 49 | 10 | 143 | 13 | 552 | 85 | 1 | 20
AMP PEAK 25(11Q13.3) CNV | 47 | 1 | 28 | 145 | 40 | 3 | 27 | 4 | 26 | 92 | 2 | 1 | 5 | 1 | 2 | 0 | 2 | 1 | 0 | 0 | 1 | 116 | 3 | 1 | 0 | 0 | 18 | 3 | 24 | 1 | 211 | 18 | 0 | 0
AMP PEAK 25(11Q13.3) WILD-TYPE | 309 | 53 | 323 | 176 | 64 | 9 | 466 | 7 | 53 | 151 | 5 | 3 | 12 | 1 | 1 | 2 | 16 | 0 | 1 | 1 | 2 | 199 | 2 | 17 | 4 | 3 | 31 | 7 | 119 | 12 | 341 | 67 | 1 | 20

Figure S138. Get High-res Image Gene #25: 'Amp Peak 25(11q13.3)' versus Clinical Feature #6: 'HISTOLOGICAL.TYPE'

'Amp Peak 25(11q13.3)' versus 'PATHOLOGY.T'

P value = 3.36e-09 (Fisher's exact test), Q value = 4.8e-06

Table S139. Gene #25: 'Amp Peak 25(11q13.3)' versus Clinical Feature #7: 'PATHOLOGY.T'

nPatients | T0+T1 | T2 | T3 | T4
--- | --- | --- | --- | ---
ALL | 448 | 611 | 688 | 208
AMP PEAK 25(11Q13.3) CNV | 82 | 175 | 117 | 69
AMP PEAK 25(11Q13.3) WILD-TYPE | 366 | 436 | 571 | 139

Figure S139. Get High-res Image Gene #25: 'Amp Peak 25(11q13.3)' versus Clinical Feature #7: 'PATHOLOGY.T'

'Amp Peak 25(11q13.3)' versus 'PATHOLOGY.N'

P value = 3.55e-06 (Fisher's exact test), Q value = 0.0048

Table S140. Gene #25: 'Amp Peak 25(11q13.3)' versus Clinical Feature #8: 'PATHOLOGY.N'

nPatients | N0 | N1 | N2 | N3
--- | --- | --- | --- | ---
ALL | 1036 | 343 | 279 | 11
AMP PEAK 25(11Q13.3) CNV | 224 | 86 | 100 | 6
AMP PEAK 25(11Q13.3) WILD-TYPE | 812 | 257 | 179 | 5

Figure S140. Get High-res Image Gene #25: 'Amp Peak 25(11q13.3)' versus Clinical Feature #8: 'PATHOLOGY.N'

'Amp Peak 25(11q13.3)' versus 'TUMOR.STAGE'

P value = 2.61e-07 (Fisher's exact test), Q value = 0.00036

Table S141. Gene #25: 'Amp Peak 25(11q13.3)' versus Clinical Feature #10: 'TUMOR.STAGE'

nPatients | I | II | III | IV
--- | --- | --- | --- | ---
ALL | 685 | 487 | 876 | 420
AMP PEAK 25(11Q13.3) CNV | 133 | 121 | 249 | 144
AMP PEAK 25(11Q13.3) WILD-TYPE | 552 | 366 | 627 | 276

Figure S141. Get High-res Image Gene #25: 'Amp Peak 25(11q13.3)' versus Clinical Feature #10: 'TUMOR.STAGE'

'Amp Peak 25(11q13.3)' versus 'RADIATIONS.RADIATION.REGIMENINDICATION'

P value = 1.38e-05 (Fisher's exact test), Q value = 0.018

Table S142. Gene #25: 'Amp Peak 25(11q13.3)' versus Clinical Feature #11: 'RADIATIONS.RADIATION.REGIMENINDICATION'

nPatients | NO | YES
--- | --- | ---
ALL | 835 | 3816
AMP PEAK 25(11Q13.3) CNV | 158 | 992
AMP PEAK 25(11Q13.3) WILD-TYPE | 677 | 2824

Figure S142. Get High-res Image Gene #25: 'Amp Peak 25(11q13.3)' versus Clinical Feature #11: 'RADIATIONS.RADIATION.REGIMENINDICATION'

'Amp Peak 26(12p13.33)' versus 'PRIMARY.SITE.OF.DISEASE'

P value = 1.48e-73 (Chi-square test), Q value = 2.4e-70

Table S143. Gene #26: 'Amp Peak 26(12p13.33)' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'

nPatients | BLADDER | BRAIN | BREAST | COLON | ENDOMETRIAL | HEAD/NECK | KIDNEY | LUNG | OMENTUM | OVARY | PERITONEUM (OVARY) | RECTUM
--- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | ---
ALL | 131 | 544 | 857 | 412 | 454 | 321 | 493 | 714 | 2 | 548 | 2 | 159
AMP PEAK 26(12P13.33) CNV | 44 | 64 | 224 | 103 | 67 | 108 | 115 | 278 | 2 | 306 | 1 | 38
AMP PEAK 26(12P13.33) WILD-TYPE | 87 | 480 | 633 | 309 | 387 | 213 | 378 | 436 | 0 | 242 | 1 | 121

Figure S143. Get High-res Image Gene #26: 'Amp Peak 26(12p13.33)' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'

'Amp Peak 26(12p13.33)' versus 'HISTOLOGICAL.TYPE'

P value = 7.83e-52 (Chi-square test), Q value = 1.3e-48

Table S144. Gene #26: 'Amp Peak 26(12p13.33)' versus Clinical Feature #6: 'HISTOLOGICAL.TYPE'

nPatients | COLON ADENOCARCINOMA | COLON MUCINOUS ADENOCARCINOMA | ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA | HEAD & NECK SQUAMOUS CELL CARCINOMA | INFILTRATING DUCTAL CARCINOMA | INFILTRATING LOBULAR 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 HISTOLOGY (PLEASE SPECIFY) | MIXED SEROUS AND ENDOMETRIOID | MUCINOUS (COLLOID) ADENOCARCINOMA | MUCINOUS (COLLOID) CARCINOMA | MUSCLE INVASIVE UROTHELIAL CARCINOMA (PT2 OR ABOVE) | OTHER SPECIFY | RECTAL ADENOCARCINOMA | RECTAL MUCINOUS ADENOCARCINOMA | SEROUS CYSTADENOCARCINOMA | SEROUS ENDOMETRIAL ADENOCARCINOMA | TREATED PRIMARY GBM | UNTREATED PRIMARY (DE NOVO) GBM
--- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | ---
ALL | 356 | 54 | 351 | 321 | 104 | 12 | 493 | 11 | 79 | 243 | 7 | 4 | 17 | 2 | 3 | 2 | 18 | 1 | 1 | 1 | 3 | 315 | 5 | 18 | 4 | 3 | 49 | 10 | 143 | 13 | 552 | 85 | 1 | 20
AMP PEAK 26(12P13.33) CNV | 91 | 11 | 37 | 108 | 34 | 1 | 115 | 2 | 26 | 75 | 3 | 0 | 4 | 1 | 0 | 0 | 2 | 1 | 0 | 1 | 1 | 160 | 0 | 4 | 2 | 0 | 12 | 2 | 32 | 5 | 309 | 26 | 0 | 1
AMP PEAK 26(12P13.33) WILD-TYPE | 265 | 43 | 314 | 213 | 70 | 11 | 378 | 9 | 53 | 168 | 4 | 4 | 13 | 1 | 3 | 2 | 16 | 0 | 1 | 0 | 2 | 155 | 5 | 14 | 2 | 3 | 37 | 8 | 111 | 8 | 243 | 59 | 1 | 19

Figure S144. Get High-res Image Gene #26: 'Amp Peak 26(12p13.33)' versus Clinical Feature #6: 'HISTOLOGICAL.TYPE'

'Amp Peak 26(12p13.33)' versus 'PATHOLOGY.T'

P value = 9.81e-06 (Fisher's exact test), Q value = 0.013

Table S145. Gene #26: 'Amp Peak 26(12p13.33)' versus Clinical Feature #7: 'PATHOLOGY.T'

nPatients | T0+T1 | T2 | T3 | T4
--- | --- | --- | --- | ---
ALL | 448 | 611 | 688 | 208
AMP PEAK 26(12P13.33) CNV | 103 | 224 | 205 | 75
AMP PEAK 26(12P13.33) WILD-TYPE | 345 | 387 | 483 | 133

Figure S145. Get High-res Image Gene #26: 'Amp Peak 26(12p13.33)' versus Clinical Feature #7: 'PATHOLOGY.T'

'Amp Peak 26(12p13.33)' versus 'TUMOR.STAGE'

P value = 1.28e-08 (Fisher's exact test), Q value = 1.8e-05

Table S146. Gene #26: 'Amp Peak 26(12p13.33)' versus Clinical Feature #10: 'TUMOR.STAGE'

nPatients | I | II | III | IV
--- | --- | --- | --- | ---
ALL | 685 | 487 | 876 | 420
AMP PEAK 26(12P13.33) CNV | 190 | 183 | 377 | 153
AMP PEAK 26(12P13.33) WILD-TYPE | 495 | 304 | 499 | 267

Figure S146. Get High-res Image Gene #26: 'Amp Peak 26(12p13.33)' versus Clinical Feature #10: 'TUMOR.STAGE'

'Amp Peak 26(12p13.33)' versus 'RADIATIONS.RADIATION.REGIMENINDICATION'

P value = 7.44e-13 (Fisher's exact test), Q value = 1.1e-09

Table S147. Gene #26: 'Amp Peak 26(12p13.33)' versus Clinical Feature #11: 'RADIATIONS.RADIATION.REGIMENINDICATION'

nPatients | NO | YES
--- | --- | ---
ALL | 835 | 3816
AMP PEAK 26(12P13.33) CNV | 161 | 1198
AMP PEAK 26(12P13.33) WILD-TYPE | 674 | 2618

Figure S147. Get High-res Image Gene #26: 'Amp Peak 26(12p13.33)' versus Clinical Feature #11: 'RADIATIONS.RADIATION.REGIMENINDICATION'

'Amp Peak 27(12p12.1)' versus 'PRIMARY.SITE.OF.DISEASE'

P value = 7.8e-71 (Chi-square test), Q value = 1.3e-67

Table S148. Gene #27: 'Amp Peak 27(12p12.1)' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'

nPatients | BLADDER | BRAIN | BREAST | COLON | ENDOMETRIAL | HEAD/NECK | KIDNEY | LUNG | OMENTUM | OVARY | PERITONEUM (OVARY) | RECTUM
--- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | ---
ALL | 131 | 544 | 857 | 412 | 454 | 321 | 493 | 714 | 2 | 548 | 2 | 159
AMP PEAK 27(12P12.1) CNV | 42 | 62 | 217 | 90 | 70 | 96 | 113 | 293 | 2 | 288 | 2 | 38
AMP PEAK 27(12P12.1) WILD-TYPE | 89 | 482 | 640 | 322 | 384 | 225 | 380 | 421 | 0 | 260 | 0 | 121

Figure S148. Get High-res Image Gene #27: 'Amp Peak 27(12p12.1)' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'

'Amp Peak 27(12p12.1)' versus 'HISTOLOGICAL.TYPE'

P value = 2.71e-47 (Chi-square test), Q value = 4.3e-44

Table S149. Gene #27: 'Amp Peak 27(12p12.1)' versus Clinical Feature #6: 'HISTOLOGICAL.TYPE'

nPatients | COLON ADENOCARCINOMA | COLON MUCINOUS ADENOCARCINOMA | ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA | HEAD & NECK SQUAMOUS CELL CARCINOMA | INFILTRATING DUCTAL CARCINOMA | INFILTRATING LOBULAR 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 HISTOLOGY (PLEASE SPECIFY) | MIXED SEROUS AND ENDOMETRIOID | MUCINOUS (COLLOID) ADENOCARCINOMA | MUCINOUS (COLLOID) CARCINOMA | MUSCLE INVASIVE UROTHELIAL CARCINOMA (PT2 OR ABOVE) | OTHER SPECIFY | RECTAL ADENOCARCINOMA | RECTAL MUCINOUS ADENOCARCINOMA | SEROUS CYSTADENOCARCINOMA | SEROUS ENDOMETRIAL ADENOCARCINOMA | TREATED PRIMARY GBM | UNTREATED PRIMARY (DE NOVO) GBM
--- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | ---
ALL | 356 | 54 | 351 | 321 | 104 | 12 | 493 | 11 | 79 | 243 | 7 | 4 | 17 | 2 | 3 | 2 | 18 | 1 | 1 | 1 | 3 | 315 | 5 | 18 | 4 | 3 | 49 | 10 | 143 | 13 | 552 | 85 | 1 | 20
AMP PEAK 27(12P12.1) CNV | 76 | 13 | 36 | 96 | 31 | 1 | 113 | 3 | 22 | 93 | 3 | 0 | 7 | 1 | 1 | 0 | 3 | 1 | 0 | 0 | 1 | 156 | 0 | 2 | 2 | 0 | 13 | 2 | 32 | 5 | 292 | 32 | 0 | 2
AMP PEAK 27(12P12.1) WILD-TYPE | 280 | 41 | 315 | 225 | 73 | 11 | 380 | 8 | 57 | 150 | 4 | 4 | 10 | 1 | 2 | 2 | 15 | 0 | 1 | 1 | 2 | 159 | 5 | 16 | 2 | 3 | 36 | 8 | 111 | 8 | 260 | 53 | 1 | 18

Figure S149. Get High-res Image Gene #27: 'Amp Peak 27(12p12.1)' versus Clinical Feature #6: 'HISTOLOGICAL.TYPE'

'Amp Peak 27(12p12.1)' versus 'PATHOLOGY.T'

P value = 1.78e-05 (Fisher's exact test), Q value = 0.023

Table S150. Gene #27: 'Amp Peak 27(12p12.1)' versus Clinical Feature #7: 'PATHOLOGY.T'

nPatients | T0+T1 | T2 | T3 | T4
--- | --- | --- | --- | ---
ALL | 448 | 611 | 688 | 208
AMP PEAK 27(12P12.1) CNV | 104 | 226 | 196 | 64
AMP PEAK 27(12P12.1) WILD-TYPE | 344 | 385 | 492 | 144

Figure S150. Get High-res Image Gene #27: 'Amp Peak 27(12p12.1)' versus Clinical Feature #7: 'PATHOLOGY.T'

'Amp Peak 27(12p12.1)' versus 'TUMOR.STAGE'

P value = 5.86e-08 (Fisher's exact test), Q value = 8.2e-05

Table S151. Gene #27: 'Amp Peak 27(12p12.1)' versus Clinical Feature #10: 'TUMOR.STAGE'

nPatients | I | II | III | IV
--- | --- | --- | --- | ---
ALL | 685 | 487 | 876 | 420
AMP PEAK 27(12P12.1) CNV | 198 | 165 | 375 | 133
AMP PEAK 27(12P12.1) WILD-TYPE | 487 | 322 | 501 | 287

Figure S151. Get High-res Image Gene #27: 'Amp Peak 27(12p12.1)' versus Clinical Feature #10: 'TUMOR.STAGE'

'Amp Peak 27(12p12.1)' versus 'RADIATIONS.RADIATION.REGIMENINDICATION'

P value = 1.86e-10 (Fisher's exact test), Q value = 2.7e-07

Table S152. Gene #27: 'Amp Peak 27(12p12.1)' versus Clinical Feature #11: 'RADIATIONS.RADIATION.REGIMENINDICATION'

nPatients | NO | YES
--- | --- | ---
ALL | 835 | 3816
AMP PEAK 27(12P12.1) CNV | 164 | 1158
AMP PEAK 27(12P12.1) WILD-TYPE | 671 | 2658

Figure S152. Get High-res Image Gene #27: 'Amp Peak 27(12p12.1)' versus Clinical Feature #11: 'RADIATIONS.RADIATION.REGIMENINDICATION'

'Amp Peak 28(12q14.1)' versus 'Time to Death'

P value = 7.95e-05 (logrank test), Q value = 0.1

Table S153. Gene #28: 'Amp Peak 28(12q14.1)' versus Clinical Feature #1: 'Time to Death'

| nPatients | nDeath | Duration Range (Median), Month
--- | --- | --- | ---
ALL | 4370 | 1406 | 0.0 - 224.0 (14.4)
AMP PEAK 28(12Q14.1) CNV | 1032 | 375 | 0.1 - 180.2 (14.1)
AMP PEAK 28(12Q14.1) WILD-TYPE | 3338 | 1031 | 0.0 - 224.0 (14.5)

Figure S153. Get High-res Image Gene #28: 'Amp Peak 28(12q14.1)' versus Clinical Feature #1: 'Time to Death'

'Amp Peak 28(12q14.1)' versus 'AGE'

P value = 0.00011 (t-test), Q value = 0.14

Table S154. Gene #28: 'Amp Peak 28(12q14.1)' versus Clinical Feature #2: 'AGE'

| nPatients | Mean (Std.Dev)
--- | --- | ---
ALL | 4585 | 61.9 (12.6)
AMP PEAK 28(12Q14.1) CNV | 1072 | 63.2 (12.5)
AMP PEAK 28(12Q14.1) WILD-TYPE | 3513 | 61.5 (12.6)

Figure S154. Get High-res Image Gene #28: 'Amp Peak 28(12q14.1)' versus Clinical Feature #2: 'AGE'

'Amp Peak 28(12q14.1)' versus 'PRIMARY.SITE.OF.DISEASE'

P value = 5.75e-23 (Chi-square test), Q value = 8.8e-20

Table S155. Gene #28: 'Amp Peak 28(12q14.1)' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'

nPatients | BLADDER | BRAIN | BREAST | COLON | ENDOMETRIAL | HEAD/NECK | KIDNEY | LUNG | OMENTUM | OVARY | PERITONEUM (OVARY) | RECTUM
--- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | ---
ALL | 131 | 544 | 857 | 412 | 454 | 321 | 493 | 714 | 2 | 548 | 2 | 159
AMP PEAK 28(12Q14.1) CNV | 30 | 125 | 189 | 85 | 48 | 56 | 113 | 235 | 1 | 184 | 2 | 23
AMP PEAK 28(12Q14.1) WILD-TYPE | 101 | 419 | 668 | 327 | 406 | 265 | 380 | 479 | 1 | 364 | 0 | 136

Figure S155. Get High-res Image Gene #28: 'Amp Peak 28(12q14.1)' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'

'Amp Peak 28(12q14.1)' versus 'HISTOLOGICAL.TYPE'

P value = 1.56e-17 (Chi-square test), Q value = 2.4e-14

Table S156. Gene #28: 'Amp Peak 28(12q14.1)' versus Clinical Feature #6: 'HISTOLOGICAL.TYPE'

nPatients | COLON ADENOCARCINOMA | COLON MUCINOUS ADENOCARCINOMA | ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA | HEAD & NECK SQUAMOUS CELL CARCINOMA | INFILTRATING DUCTAL CARCINOMA | INFILTRATING LOBULAR 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 HISTOLOGY (PLEASE SPECIFY) | MIXED SEROUS AND ENDOMETRIOID | MUCINOUS (COLLOID) ADENOCARCINOMA | MUCINOUS (COLLOID) CARCINOMA | MUSCLE INVASIVE UROTHELIAL CARCINOMA (PT2 OR ABOVE) | OTHER SPECIFY | RECTAL ADENOCARCINOMA | RECTAL MUCINOUS ADENOCARCINOMA | SEROUS CYSTADENOCARCINOMA | SEROUS ENDOMETRIAL ADENOCARCINOMA | TREATED PRIMARY GBM | UNTREATED PRIMARY (DE NOVO) GBM
--- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | ---
ALL | 356 | 54 | 351 | 321 | 104 | 12 | 493 | 11 | 79 | 243 | 7 | 4 | 17 | 2 | 3 | 2 | 18 | 1 | 1 | 1 | 3 | 315 | 5 | 18 | 4 | 3 | 49 | 10 | 143 | 13 | 552 | 85 | 1 | 20
AMP PEAK 28(12Q14.1) CNV | 72 | 12 | 30 | 56 | 32 | 1 | 113 | 4 | 23 | 84 | 2 | 0 | 4 | 1 | 0 | 0 | 3 | 1 | 0 | 0 | 2 | 109 | 0 | 2 | 2 | 0 | 12 | 1 | 21 | 2 | 187 | 16 | 0 | 3
AMP PEAK 28(12Q14.1) WILD-TYPE | 284 | 42 | 321 | 265 | 72 | 11 | 380 | 7 | 56 | 159 | 5 | 4 | 13 | 1 | 3 | 2 | 15 | 0 | 1 | 1 | 1 | 206 | 5 | 16 | 2 | 3 | 37 | 9 | 122 | 11 | 365 | 69 | 1 | 17

Figure S156. Get High-res Image Gene #28: 'Amp Peak 28(12q14.1)' versus Clinical Feature #6: 'HISTOLOGICAL.TYPE'

'Amp Peak 28(12q14.1)' versus 'TUMOR.STAGE'

P value = 9.74e-05 (Fisher's exact test), Q value = 0.12

Table S157. Gene #28: 'Amp Peak 28(12q14.1)' versus Clinical Feature #10: 'TUMOR.STAGE'

nPatients | I | II | III | IV
--- | --- | --- | --- | ---
ALL | 685 | 487 | 876 | 420
AMP PEAK 28(12Q14.1) CNV | 150 | 133 | 275 | 96
AMP PEAK 28(12Q14.1) WILD-TYPE | 535 | 354 | 601 | 324

Figure S157. Get High-res Image Gene #28: 'Amp Peak 28(12q14.1)' versus Clinical Feature #10: 'TUMOR.STAGE'

'Amp Peak 29(12q15)' versus 'AGE'

P value = 3.48e-05 (t-test), Q value = 0.045

Table S158. Gene #29: 'Amp Peak 29(12q15)' versus Clinical Feature #2: 'AGE'

| nPatients | Mean (Std.Dev)
--- | --- | ---
ALL | 4585 | 61.9 (12.6)
AMP PEAK 29(12Q15) CNV | 1085 | 63.3 (12.3)
AMP PEAK 29(12Q15) WILD-TYPE | 3500 | 61.5 (12.7)

Figure S158. Get High-res Image Gene #29: 'Amp Peak 29(12q15)' versus Clinical Feature #2: 'AGE'

'Amp Peak 29(12q15)' versus 'PRIMARY.SITE.OF.DISEASE'

P value = 1.88e-32 (Chi-square test), Q value = 2.9e-29

Table S159. Gene #29: 'Amp Peak 29(12q15)' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'

nPatients | BLADDER | BRAIN | BREAST | COLON | ENDOMETRIAL | HEAD/NECK | KIDNEY | LUNG | OMENTUM | OVARY | PERITONEUM (OVARY) | RECTUM
--- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | ---
ALL | 131 | 544 | 857 | 412 | 454 | 321 | 493 | 714 | 2 | 548 | 2 | 159
AMP PEAK 29(12Q15) CNV | 42 | 87 | 219 | 81 | 46 | 62 | 114 | 247 | 2 | 184 | 2 | 19
AMP PEAK 29(12Q15) WILD-TYPE | 89 | 457 | 638 | 331 | 408 | 259 | 379 | 467 | 0 | 364 | 0 | 140

Figure S159. Get High-res Image Gene #29: 'Amp Peak 29(12q15)' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'

'Amp Peak 29(12q15)' versus 'HISTOLOGICAL.TYPE'

P value = 9.77e-22 (Chi-square test), Q value = 1.5e-18

Table S160. Gene #29: 'Amp Peak 29(12q15)' versus Clinical Feature #6: 'HISTOLOGICAL.TYPE'

nPatients | COLON ADENOCARCINOMA | COLON MUCINOUS ADENOCARCINOMA | ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA | HEAD & NECK SQUAMOUS CELL CARCINOMA | INFILTRATING DUCTAL CARCINOMA | INFILTRATING LOBULAR 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 HISTOLOGY (PLEASE SPECIFY) | MIXED SEROUS AND ENDOMETRIOID | MUCINOUS (COLLOID) ADENOCARCINOMA | MUCINOUS (COLLOID) CARCINOMA | MUSCLE INVASIVE UROTHELIAL CARCINOMA (PT2 OR ABOVE) | OTHER SPECIFY | RECTAL ADENOCARCINOMA | RECTAL MUCINOUS ADENOCARCINOMA | SEROUS CYSTADENOCARCINOMA | SEROUS ENDOMETRIAL ADENOCARCINOMA | TREATED PRIMARY GBM | UNTREATED PRIMARY (DE NOVO) GBM
--- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | ---
ALL | 356 | 54 | 351 | 321 | 104 | 12 | 493 | 11 | 79 | 243 | 7 | 4 | 17 | 2 | 3 | 2 | 18 | 1 | 1 | 1 | 3 | 315 | 5 | 18 | 4 | 3 | 49 | 10 | 143 | 13 | 552 | 85 | 1 | 20
AMP PEAK 29(12Q15) CNV | 68 | 12 | 31 | 62 | 35 | 1 | 114 | 4 | 26 | 84 | 2 | 0 | 3 | 1 | 0 | 0 | 4 | 1 | 0 | 0 | 2 | 118 | 0 | 2 | 2 | 0 | 20 | 1 | 17 | 2 | 188 | 13 | 0 | 4
AMP PEAK 29(12Q15) WILD-TYPE | 288 | 42 | 320 | 259 | 69 | 11 | 379 | 7 | 53 | 159 | 5 | 4 | 14 | 1 | 3 | 2 | 14 | 0 | 1 | 1 | 1 | 197 | 5 | 16 | 2 | 3 | 29 | 9 | 126 | 11 | 364 | 72 | 1 | 16

Figure S160. Get High-res Image Gene #29: 'Amp Peak 29(12q15)' versus Clinical Feature #6: 'HISTOLOGICAL.TYPE'

'Amp Peak 29(12q15)' versus 'RADIATIONS.RADIATION.REGIMENINDICATION'

P value = 9.9e-07 (Fisher's exact test), Q value = 0.0013

Table S161. Gene #29: 'Amp Peak 29(12q15)' versus Clinical Feature #11: 'RADIATIONS.RADIATION.REGIMENINDICATION'

nPatients | NO | YES
--- | --- | ---
ALL | 835 | 3816
AMP PEAK 29(12Q15) CNV | 146 | 966
AMP PEAK 29(12Q15) WILD-TYPE | 689 | 2850

Figure S161. Get High-res Image Gene #29: 'Amp Peak 29(12q15)' versus Clinical Feature #11: 'RADIATIONS.RADIATION.REGIMENINDICATION'

'Amp Peak 30(13q34)' versus 'AGE'

P value = 5.94e-06 (t-test), Q value = 0.0079

Table S162. Gene #30: 'Amp Peak 30(13q34)' versus Clinical Feature #2: 'AGE'

| nPatients | Mean (Std.Dev)
--- | --- | ---
ALL | 4585 | 61.9 (12.6)
AMP PEAK 30(13Q34) CNV | 954 | 63.5 (12.4)
AMP PEAK 30(13Q34) WILD-TYPE | 3631 | 61.5 (12.6)

Figure S162. Get High-res Image Gene #30: 'Amp Peak 30(13q34)' versus Clinical Feature #2: 'AGE'

'Amp Peak 30(13q34)' versus 'PRIMARY.SITE.OF.DISEASE'

P value = 3.58e-172 (Chi-square test), Q value = 6.1e-169

Table S163. Gene #30: 'Amp Peak 30(13q34)' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'

nPatients | BLADDER | BRAIN | BREAST | COLON | ENDOMETRIAL | HEAD/NECK | KIDNEY | LUNG | OMENTUM | OVARY | PERITONEUM (OVARY) | RECTUM
--- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | ---
ALL | 131 | 544 | 857 | 412 | 454 | 321 | 493 | 714 | 2 | 548 | 2 | 159
AMP PEAK 30(13Q34) CNV | 49 | 29 | 143 | 242 | 42 | 59 | 27 | 117 | 1 | 135 | 0 | 112
AMP PEAK 30(13Q34) WILD-TYPE | 82 | 515 | 714 | 170 | 412 | 262 | 466 | 597 | 1 | 413 | 2 | 47

Figure S163. Get High-res Image Gene #30: 'Amp Peak 30(13q34)' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'

'Amp Peak 30(13q34)' versus 'HISTOLOGICAL.TYPE'

P value = 3.68e-134 (Chi-square test), Q value = 6.3e-131

Table S164. Gene #30: 'Amp Peak 30(13q34)' versus Clinical Feature #6: 'HISTOLOGICAL.TYPE'

nPatients | COLON ADENOCARCINOMA | COLON MUCINOUS ADENOCARCINOMA | ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA | HEAD & NECK SQUAMOUS CELL CARCINOMA | INFILTRATING DUCTAL CARCINOMA | INFILTRATING LOBULAR 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 HISTOLOGY (PLEASE SPECIFY) | MIXED SEROUS AND ENDOMETRIOID | MUCINOUS (COLLOID) ADENOCARCINOMA | MUCINOUS (COLLOID) CARCINOMA | MUSCLE INVASIVE UROTHELIAL CARCINOMA (PT2 OR ABOVE) | OTHER SPECIFY | RECTAL ADENOCARCINOMA | RECTAL MUCINOUS ADENOCARCINOMA | SEROUS CYSTADENOCARCINOMA | SEROUS ENDOMETRIAL ADENOCARCINOMA | TREATED PRIMARY GBM | UNTREATED PRIMARY (DE NOVO) GBM
--- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | ---
ALL | 356 | 54 | 351 | 321 | 104 | 12 | 493 | 11 | 79 | 243 | 7 | 4 | 17 | 2 | 3 | 2 | 18 | 1 | 1 | 1 | 3 | 315 | 5 | 18 | 4 | 3 | 49 | 10 | 143 | 13 | 552 | 85 | 1 | 20
AMP PEAK 30(13Q34) CNV | 224 | 18 | 13 | 59 | 29 | 0 | 27 | 3 | 13 | 38 | 3 | 0 | 2 | 1 | 0 | 0 | 3 | 1 | 0 | 1 | 0 | 51 | 0 | 2 | 1 | 0 | 14 | 3 | 107 | 4 | 136 | 27 | 0 | 1
AMP PEAK 30(13Q34) WILD-TYPE | 132 | 36 | 338 | 262 | 75 | 12 | 466 | 8 | 66 | 205 | 4 | 4 | 15 | 1 | 3 | 2 | 15 | 0 | 1 | 0 | 3 | 264 | 5 | 16 | 3 | 3 | 35 | 7 | 36 | 9 | 416 | 58 | 1 | 19

Figure S164. Get High-res Image Gene #30: 'Amp Peak 30(13q34)' versus Clinical Feature #6: 'HISTOLOGICAL.TYPE'

'Amp Peak 30(13q34)' versus 'PATHOLOGY.T'

P value = 5.87e-27 (Fisher's exact test), Q value = 9e-24

Table S165. Gene #30: 'Amp Peak 30(13q34)' versus Clinical Feature #7: 'PATHOLOGY.T'

nPatients | T0+T1 | T2 | T3 | T4
--- | --- | --- | --- | ---
ALL | 448 | 611 | 688 | 208
AMP PEAK 30(13Q34) CNV | 53 | 144 | 280 | 57
AMP PEAK 30(13Q34) WILD-TYPE | 395 | 467 | 408 | 151

Figure S165. Get High-res Image Gene #30: 'Amp Peak 30(13q34)' versus Clinical Feature #7: 'PATHOLOGY.T'

'Amp Peak 30(13q34)' versus 'PATHOLOGY.N'

P value = 5.81e-08 (Fisher's exact test), Q value = 8.1e-05

Table S166. Gene #30: 'Amp Peak 30(13q34)' versus Clinical Feature #8: 'PATHOLOGY.N'

nPatients | N0 | N1 | N2 | N3
--- | --- | --- | --- | ---
ALL | 1036 | 343 | 279 | 11
AMP PEAK 30(13Q34) CNV | 261 | 134 | 107 | 1
AMP PEAK 30(13Q34) WILD-TYPE | 775 | 209 | 172 | 10

Figure S166. Get High-res Image Gene #30: 'Amp Peak 30(13q34)' versus Clinical Feature #8: 'PATHOLOGY.N'

'Amp Peak 30(13q34)' versus 'PATHOLOGICSPREAD(M)'

P value = 3.46e-05 (Chi-square test), Q value = 0.044

Table S167. Gene #30: 'Amp Peak 30(13q34)' versus Clinical Feature #9: 'PATHOLOGICSPREAD(M)'

nPatients | M0 | M1 | M1A | M1B | MX
--- | --- | --- | --- | --- | ---
ALL | 1398 | 167 | 9 | 1 | 148
AMP PEAK 30(13Q34) CNV | 371 | 62 | 8 | 0 | 46
AMP PEAK 30(13Q34) WILD-TYPE | 1027 | 105 | 1 | 1 | 102

Figure S167. Get High-res Image Gene #30: 'Amp Peak 30(13q34)' versus Clinical Feature #9: 'PATHOLOGICSPREAD(M)'

'Amp Peak 30(13q34)' versus 'TUMOR.STAGE'

P value = 9.81e-11 (Fisher's exact test), Q value = 1.4e-07

Table S168. Gene #30: 'Amp Peak 30(13q34)' versus Clinical Feature #10: 'TUMOR.STAGE'

nPatients | I | II | III | IV
--- | --- | --- | --- | ---
ALL | 685 | 487 | 876 | 420
AMP PEAK 30(13Q34) CNV | 118 | 159 | 268 | 107
AMP PEAK 30(13Q34) WILD-TYPE | 567 | 328 | 608 | 313

Figure S168. Get High-res Image Gene #30: 'Amp Peak 30(13q34)' versus Clinical Feature #10: 'TUMOR.STAGE'

'Amp Peak 30(13q34)' versus 'RADIATIONS.RADIATION.REGIMENINDICATION'

P value = 2.15e-15 (Fisher's exact test), Q value = 3.2e-12

Table S169. Gene #30: 'Amp Peak 30(13q34)' versus Clinical Feature #11: 'RADIATIONS.RADIATION.REGIMENINDICATION'

nPatients | NO | YES
--- | --- | ---
ALL | 835 | 3816
AMP PEAK 30(13Q34) CNV | 93 | 871
AMP PEAK 30(13Q34) WILD-TYPE | 742 | 2945

Figure S169. Get High-res Image Gene #30: 'Amp Peak 30(13q34)' versus Clinical Feature #11: 'RADIATIONS.RADIATION.REGIMENINDICATION'

'Amp Peak 30(13q34)' versus 'TOBACCOSMOKINGHISTORYINDICATOR'

P value = 9.51e-08 (Chi-square test), Q value = 0.00013

Table S170. Gene #30: 'Amp Peak 30(13q34)' versus Clinical Feature #13: '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 | 15 | 16 | 22 | 25 | 2 | 342 | 208 | 237 | 116
AMP PEAK 30(13Q34) CNV | 2 | 8 | 9 | 13 | 2 | 52 | 33 | 45 | 26
AMP PEAK 30(13Q34) WILD-TYPE | 13 | 8 | 13 | 12 | 0 | 290 | 175 | 192 | 90

Figure S170. Get High-res Image Gene #30: 'Amp Peak 30(13q34)' versus Clinical Feature #13: 'TOBACCOSMOKINGHISTORYINDICATOR'

'Amp Peak 30(13q34)' versus 'NEOPLASM.DISEASESTAGE'

P value = 2.86e-06 (Chi-square test), Q value = 0.0038

Table S171. Gene #30: 'Amp Peak 30(13q34)' versus Clinical Feature #20: '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 X
--- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | ---
ALL | 71 | 45 | 2 | 34 | 246 | 165 | 29 | 107 | 22 | 36 | 35 | 12
AMP PEAK 30(13Q34) CNV | 6 | 4 | 0 | 11 | 51 | 21 | 9 | 15 | 1 | 8 | 17 | 3
AMP PEAK 30(13Q34) WILD-TYPE | 65 | 41 | 2 | 23 | 195 | 144 | 20 | 92 | 21 | 28 | 18 | 9

Figure S171. Get High-res Image Gene #30: 'Amp Peak 30(13q34)' versus Clinical Feature #20: 'NEOPLASM.DISEASESTAGE'

'Amp Peak 31(14q13.3)' versus 'PRIMARY.SITE.OF.DISEASE'

P value = 3.33e-93 (Chi-square test), Q value = 5.5e-90

Table S172. Gene #31: 'Amp Peak 31(14q13.3)' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'

nPatients | BLADDER | BRAIN | BREAST | COLON | ENDOMETRIAL | HEAD/NECK | KIDNEY | LUNG | OMENTUM | OVARY | PERITONEUM (OVARY) | RECTUM
--- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | ---
ALL | 131 | 544 | 857 | 412 | 454 | 321 | 493 | 714 | 2 | 548 | 2 | 159
AMP PEAK 31(14Q13.3) CNV | 23 | 20 | 169 | 38 | 30 | 91 | 14 | 270 | 1 | 95 | 0 | 12
AMP PEAK 31(14Q13.3) WILD-TYPE | 108 | 524 | 688 | 374 | 424 | 230 | 479 | 444 | 1 | 453 | 2 | 147

Figure S172. Get High-res Image Gene #31: 'Amp Peak 31(14q13.3)' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'

'Amp Peak 31(14q13.3)' versus 'HISTOLOGICAL.TYPE'

P value = 1.21e-71 (Chi-square test), Q value = 2e-68

Table S173. Gene #31: 'Amp Peak 31(14q13.3)' versus Clinical Feature #6: 'HISTOLOGICAL.TYPE'

nPatients | COLON ADENOCARCINOMA | COLON MUCINOUS ADENOCARCINOMA | ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA | HEAD & NECK SQUAMOUS CELL CARCINOMA | INFILTRATING DUCTAL CARCINOMA | INFILTRATING LOBULAR 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 HISTOLOGY (PLEASE SPECIFY) | MIXED SEROUS AND ENDOMETRIOID | MUCINOUS (COLLOID) ADENOCARCINOMA | MUCINOUS (COLLOID) CARCINOMA | MUSCLE INVASIVE UROTHELIAL CARCINOMA (PT2 OR ABOVE) | OTHER SPECIFY | RECTAL ADENOCARCINOMA | RECTAL MUCINOUS ADENOCARCINOMA | SEROUS CYSTADENOCARCINOMA | SEROUS ENDOMETRIAL ADENOCARCINOMA | TREATED PRIMARY GBM | UNTREATED PRIMARY (DE NOVO) GBM
--- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | ---
ALL | 356 | 54 | 351 | 321 | 104 | 12 | 493 | 11 | 79 | 243 | 7 | 4 | 17 | 2 | 3 | 2 | 18 | 1 | 1 | 1 | 3 | 315 | 5 | 18 | 4 | 3 | 49 | 10 | 143 | 13 | 552 | 85 | 1 | 20
AMP PEAK 31(14Q13.3) CNV | 28 | 10 | 14 | 91 | 24 | 1 | 14 | 6 | 27 | 116 | 1 | 1 | 6 | 1 | 2 | 0 | 6 | 1 | 0 | 0 | 2 | 100 | 0 | 1 | 1 | 0 | 11 | 3 | 12 | 0 | 96 | 15 | 1 | 0
AMP PEAK 31(14Q13.3) WILD-TYPE | 328 | 44 | 337 | 230 | 80 | 11 | 479 | 5 | 52 | 127 | 6 | 3 | 11 | 1 | 1 | 2 | 12 | 0 | 1 | 1 | 1 | 215 | 5 | 17 | 3 | 3 | 38 | 7 | 131 | 13 | 456 | 70 | 0 | 20

Figure S173. Get High-res Image Gene #31: 'Amp Peak 31(14q13.3)' versus Clinical Feature #6: 'HISTOLOGICAL.TYPE'

'Amp Peak 31(14q13.3)' versus 'PATHOLOGY.T'

P value = 1.82e-11 (Fisher's exact test), Q value = 2.6e-08

Table S174. Gene #31: 'Amp Peak 31(14q13.3)' versus Clinical Feature #7: 'PATHOLOGY.T'

nPatients | T0+T1 | T2 | T3 | T4
--- | --- | --- | --- | ---
ALL | 448 | 611 | 688 | 208
AMP PEAK 31(14Q13.3) CNV | 75 | 163 | 83 | 54
AMP PEAK 31(14Q13.3) WILD-TYPE | 373 | 448 | 605 | 154

Figure S174. Get High-res Image Gene #31: 'Amp Peak 31(14q13.3)' versus Clinical Feature #7: 'PATHOLOGY.T'

'Amp Peak 31(14q13.3)' versus 'PATHOLOGICSPREAD(M)'

P value = 4.45e-08 (Chi-square test), Q value = 6.2e-05

Table S175. Gene #31: 'Amp Peak 31(14q13.3)' versus Clinical Feature #9: 'PATHOLOGICSPREAD(M)'

nPatients | M0 | M1 | M1A | M1B | MX
--- | --- | --- | --- | --- | ---
ALL | 1398 | 167 | 9 | 1 | 148
AMP PEAK 31(14Q13.3) CNV | 234 | 14 | 4 | 0 | 49
AMP PEAK 31(14Q13.3) WILD-TYPE | 1164 | 153 | 5 | 1 | 99

Figure S175. Get High-res Image Gene #31: 'Amp Peak 31(14q13.3)' versus Clinical Feature #9: 'PATHOLOGICSPREAD(M)'

'Amp Peak 31(14q13.3)' versus 'RADIATIONS.RADIATION.REGIMENINDICATION'

P value = 2.98e-07 (Fisher's exact test), Q value = 0.00041

Table S176. Gene #31: 'Amp Peak 31(14q13.3)' versus Clinical Feature #11: 'RADIATIONS.RADIATION.REGIMENINDICATION'

nPatients | NO | YES
--- | --- | ---
ALL | 835 | 3816
AMP PEAK 31(14Q13.3) CNV | 89 | 674
AMP PEAK 31(14Q13.3) WILD-TYPE | 746 | 3142

Figure S176. Get High-res Image Gene #31: 'Amp Peak 31(14q13.3)' versus Clinical Feature #11: 'RADIATIONS.RADIATION.REGIMENINDICATION'

'Amp Peak 32(15q26.3)' versus 'PRIMARY.SITE.OF.DISEASE'

P value = 1.14e-50 (Chi-square test), Q value = 1.8e-47

Table S177. Gene #32: 'Amp Peak 32(15q26.3)' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'

nPatients | BLADDER | BRAIN | BREAST | COLON | ENDOMETRIAL | HEAD/NECK | KIDNEY | LUNG | OMENTUM | OVARY | PERITONEUM (OVARY) | RECTUM
--- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | ---
ALL | 131 | 544 | 857 | 412 | 454 | 321 | 493 | 714 | 2 | 548 | 2 | 159
AMP PEAK 32(15Q26.3) CNV | 20 | 31 | 161 | 26 | 29 | 70 | 24 | 165 | 1 | 153 | 0 | 13
AMP PEAK 32(15Q26.3) WILD-TYPE | 111 | 513 | 696 | 386 | 425 | 251 | 469 | 549 | 1 | 395 | 2 | 146

Figure S177. Get High-res Image Gene #32: 'Amp Peak 32(15q26.3)' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'

'Amp Peak 32(15q26.3)' versus 'HISTOLOGICAL.TYPE'

P value = 3.88e-47 (Chi-square test), Q value = 6.2e-44

Table S178. Gene #32: 'Amp Peak 32(15q26.3)' versus Clinical Feature #6: 'HISTOLOGICAL.TYPE'

nPatients | COLON ADENOCARCINOMA | COLON MUCINOUS ADENOCARCINOMA | ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA | HEAD & NECK SQUAMOUS CELL CARCINOMA | INFILTRATING DUCTAL CARCINOMA | INFILTRATING LOBULAR 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 HISTOLOGY (PLEASE SPECIFY) | MIXED SEROUS AND ENDOMETRIOID | MUCINOUS (COLLOID) ADENOCARCINOMA | MUCINOUS (COLLOID) CARCINOMA | MUSCLE INVASIVE UROTHELIAL CARCINOMA (PT2 OR ABOVE) | OTHER SPECIFY | RECTAL ADENOCARCINOMA | RECTAL MUCINOUS ADENOCARCINOMA | SEROUS CYSTADENOCARCINOMA | SEROUS ENDOMETRIAL ADENOCARCINOMA | TREATED PRIMARY GBM | UNTREATED PRIMARY (DE NOVO) GBM
--- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | ---
ALL | 356 | 54 | 351 | 321 | 104 | 12 | 493 | 11 | 79 | 243 | 7 | 4 | 17 | 2 | 3 | 2 | 18 | 1 | 1 | 1 | 3 | 315 | 5 | 18 | 4 | 3 | 49 | 10 | 143 | 13 | 552 | 85 | 1 | 20
AMP PEAK 32(15Q26.3) CNV | 22 | 4 | 16 | 70 | 23 | 0 | 24 | 1 | 15 | 26 | 4 | 1 | 1 | 0 | 0 | 0 | 4 | 0 | 0 | 0 | 1 | 109 | 0 | 0 | 3 | 0 | 7 | 1 | 11 | 2 | 154 | 13 | 0 | 1
AMP PEAK 32(15Q26.3) WILD-TYPE | 334 | 50 | 335 | 251 | 81 | 12 | 469 | 10 | 64 | 217 | 3 | 3 | 16 | 2 | 3 | 2 | 14 | 1 | 1 | 1 | 2 | 206 | 5 | 18 | 1 | 3 | 42 | 9 | 132 | 11 | 398 | 72 | 1 | 19

Figure S178. Get High-res Image Gene #32: 'Amp Peak 32(15q26.3)' versus Clinical Feature #6: 'HISTOLOGICAL.TYPE'

'Amp Peak 32(15q26.3)' versus 'PATHOLOGY.T'

P value = 1.68e-10 (Fisher's exact test), Q value = 2.4e-07

Table S179. Gene #32: 'Amp Peak 32(15q26.3)' versus Clinical Feature #7: 'PATHOLOGY.T'

nPatients | T0+T1 | T2 | T3 | T4
--- | --- | --- | --- | ---
ALL | 448 | 611 | 688 | 208
AMP PEAK 32(15Q26.3) CNV | 49 | 126 | 60 | 43
AMP PEAK 32(15Q26.3) WILD-TYPE | 399 | 485 | 628 | 165

Figure S179. Get High-res Image Gene #32: 'Amp Peak 32(15q26.3)' versus Clinical Feature #7: 'PATHOLOGY.T'

'Amp Peak 32(15q26.3)' versus 'RADIATIONS.RADIATION.REGIMENINDICATION'

P value = 2.33e-07 (Fisher's exact test), Q value = 0.00032

Table S180. Gene #32: 'Amp Peak 32(15q26.3)' versus Clinical Feature #11: 'RADIATIONS.RADIATION.REGIMENINDICATION'

nPatients | NO | YES
--- | --- | ---
ALL | 835 | 3816
AMP PEAK 32(15Q26.3) CNV | 78 | 616
AMP PEAK 32(15Q26.3) WILD-TYPE | 757 | 3200

Figure S180. Get High-res Image Gene #32: 'Amp Peak 32(15q26.3)' versus Clinical Feature #11: 'RADIATIONS.RADIATION.REGIMENINDICATION'

'Amp Peak 33(17q12)' versus 'AGE'

P value = 4.28e-05 (t-test), Q value = 0.055

Table S181. Gene #33: 'Amp Peak 33(17q12)' versus Clinical Feature #2: 'AGE'

| nPatients | Mean (Std.Dev)
--- | --- | ---
ALL | 4585 | 61.9 (12.6)
AMP PEAK 33(17Q12) CNV | 988 | 63.3 (12.1)
AMP PEAK 33(17Q12) WILD-TYPE | 3597 | 61.5 (12.7)

Figure S181. Get High-res Image Gene #33: 'Amp Peak 33(17q12)' versus Clinical Feature #2: 'AGE'

'Amp Peak 33(17q12)' versus 'PRIMARY.SITE.OF.DISEASE'

P value = 1.47e-88 (Chi-square test), Q value = 2.4e-85

Table S182. Gene #33: 'Amp Peak 33(17q12)' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'

nPatients | BLADDER | BRAIN | BREAST | COLON | ENDOMETRIAL | HEAD/NECK | KIDNEY | LUNG | OMENTUM | OVARY | PERITONEUM (OVARY) | RECTUM
--- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | ---
ALL | 131 | 544 | 857 | 412 | 454 | 321 | 493 | 714 | 2 | 548 | 2 | 159
AMP PEAK 33(17Q12) CNV | 55 | 48 | 281 | 101 | 57 | 56 | 25 | 284 | 0 | 52 | 0 | 43
AMP PEAK 33(17Q12) WILD-TYPE | 76 | 496 | 576 | 311 | 397 | 265 | 468 | 430 | 2 | 496 | 2 | 116

Figure S182. Get High-res Image Gene #33: 'Amp Peak 33(17q12)' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'

'Amp Peak 33(17q12)' versus 'HISTOLOGICAL.TYPE'

P value = 3.07e-71 (Chi-square test), Q value = 5e-68

Table S183. Gene #33: 'Amp Peak 33(17q12)' versus Clinical Feature #6: 'HISTOLOGICAL.TYPE'

nPatients | COLON ADENOCARCINOMA | COLON MUCINOUS ADENOCARCINOMA | ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA | HEAD & NECK SQUAMOUS CELL CARCINOMA | INFILTRATING DUCTAL CARCINOMA | INFILTRATING LOBULAR 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 HISTOLOGY (PLEASE SPECIFY) | MIXED SEROUS AND ENDOMETRIOID | MUCINOUS (COLLOID) ADENOCARCINOMA | MUCINOUS (COLLOID) CARCINOMA | MUSCLE INVASIVE UROTHELIAL CARCINOMA (PT2 OR ABOVE) | OTHER SPECIFY | RECTAL ADENOCARCINOMA | RECTAL MUCINOUS ADENOCARCINOMA | SEROUS CYSTADENOCARCINOMA | SEROUS ENDOMETRIAL ADENOCARCINOMA | TREATED PRIMARY GBM | UNTREATED PRIMARY (DE NOVO) GBM
--- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | ---
ALL | 356 | 54 | 351 | 321 | 104 | 12 | 493 | 11 | 79 | 243 | 7 | 4 | 17 | 2 | 3 | 2 | 18 | 1 | 1 | 1 | 3 | 315 | 5 | 18 | 4 | 3 | 49 | 10 | 143 | 13 | 552 | 85 | 1 | 20
AMP PEAK 33(17Q12) CNV | 90 | 10 | 16 | 56 | 31 | 2 | 25 | 5 | 39 | 110 | 2 | 1 | 5 | 2 | 1 | 1 | 5 | 1 | 0 | 0 | 2 | 109 | 0 | 3 | 1 | 0 | 21 | 2 | 41 | 2 | 52 | 38 | 0 | 1
AMP PEAK 33(17Q12) WILD-TYPE | 266 | 44 | 335 | 265 | 73 | 10 | 468 | 6 | 40 | 133 | 5 | 3 | 12 | 0 | 2 | 1 | 13 | 0 | 1 | 1 | 1 | 206 | 5 | 15 | 3 | 3 | 28 | 8 | 102 | 11 | 500 | 47 | 1 | 19

Figure S183. Get High-res Image Gene #33: 'Amp Peak 33(17q12)' versus Clinical Feature #6: 'HISTOLOGICAL.TYPE'

'Amp Peak 33(17q12)' versus 'PATHOLOGY.T'

P value = 1.44e-06 (Fisher's exact test), Q value = 0.0019

Table S184. Gene #33: 'Amp Peak 33(17q12)' versus Clinical Feature #7: 'PATHOLOGY.T'

nPatients | T0+T1 | T2 | T3 | T4
--- | --- | --- | --- | ---
ALL | 448 | 611 | 688 | 208
AMP PEAK 33(17Q12) CNV | 79 | 189 | 142 | 48
AMP PEAK 33(17Q12) WILD-TYPE | 369 | 422 | 546 | 160

Figure S184. Get High-res Image Gene #33: 'Amp Peak 33(17q12)' versus Clinical Feature #7: 'PATHOLOGY.T'

'Amp Peak 33(17q12)' versus 'PATHOLOGICSPREAD(M)'

P value = 2.21e-06 (Chi-square test), Q value = 0.003

Table S185. Gene #33: 'Amp Peak 33(17q12)' versus Clinical Feature #9: 'PATHOLOGICSPREAD(M)'

nPatients | M0 | M1 | M1A | M1B | MX
--- | --- | --- | --- | --- | ---
ALL | 1398 | 167 | 9 | 1 | 148
AMP PEAK 33(17Q12) CNV | 311 | 38 | 4 | 1 | 61
AMP PEAK 33(17Q12) WILD-TYPE | 1087 | 129 | 5 | 0 | 87

Figure S185. Get High-res Image Gene #33: 'Amp Peak 33(17q12)' versus Clinical Feature #9: 'PATHOLOGICSPREAD(M)'

'Amp Peak 34(17q25.3)' versus 'PRIMARY.SITE.OF.DISEASE'

P value = 8.39e-95 (Chi-square test), Q value = 1.4e-91

Table S186. Gene #34: 'Amp Peak 34(17q25.3)' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'

nPatients | BLADDER | BRAIN | BREAST | COLON | ENDOMETRIAL | HEAD/NECK | KIDNEY | LUNG | OMENTUM | OVARY | PERITONEUM (OVARY) | RECTUM
--- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | ---
ALL | 131 | 544 | 857 | 412 | 454 | 321 | 493 | 714 | 2 | 548 | 2 | 159
AMP PEAK 34(17Q25.3) CNV | 70 | 67 | 338 | 95 | 72 | 68 | 38 | 346 | 1 | 200 | 1 | 34
AMP PEAK 34(17Q25.3) WILD-TYPE | 61 | 477 | 519 | 317 | 382 | 253 | 455 | 368 | 1 | 348 | 1 | 125

Figure S186. Get High-res Image Gene #34: 'Amp Peak 34(17q25.3)' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'

'Amp Peak 34(17q25.3)' versus 'HISTOLOGICAL.TYPE'

P value = 1.85e-74 (Chi-square test), Q value = 3e-71

Table S187. Gene #34: 'Amp Peak 34(17q25.3)' versus Clinical Feature #6: 'HISTOLOGICAL.TYPE'

nPatients | COLON ADENOCARCINOMA | COLON MUCINOUS ADENOCARCINOMA | ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA | HEAD & NECK SQUAMOUS CELL CARCINOMA | INFILTRATING DUCTAL CARCINOMA | INFILTRATING LOBULAR 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 HISTOLOGY (PLEASE SPECIFY) | MIXED SEROUS AND ENDOMETRIOID | MUCINOUS (COLLOID) ADENOCARCINOMA | MUCINOUS (COLLOID) CARCINOMA | MUSCLE INVASIVE UROTHELIAL CARCINOMA (PT2 OR ABOVE) | OTHER SPECIFY | RECTAL ADENOCARCINOMA | RECTAL MUCINOUS ADENOCARCINOMA | SEROUS CYSTADENOCARCINOMA | SEROUS ENDOMETRIAL ADENOCARCINOMA | TREATED PRIMARY GBM | UNTREATED PRIMARY (DE NOVO) GBM
--- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | ---
ALL | 356 | 54 | 351 | 321 | 104 | 12 | 493 | 11 | 79 | 243 | 7 | 4 | 17 | 2 | 3 | 2 | 18 | 1 | 1 | 1 | 3 | 315 | 5 | 18 | 4 | 3 | 49 | 10 | 143 | 13 | 552 | 85 | 1 | 20
AMP PEAK 34(17Q25.3) CNV | 88 | 6 | 27 | 68 | 46 | 1 | 38 | 4 | 41 | 134 | 3 | 1 | 5 | 2 | 2 | 1 | 7 | 1 | 0 | 0 | 3 | 141 | 1 | 5 | 1 | 0 | 28 | 2 | 33 | 0 | 202 | 40 | 1 | 2
AMP PEAK 34(17Q25.3) WILD-TYPE | 268 | 48 | 324 | 253 | 58 | 11 | 455 | 7 | 38 | 109 | 4 | 3 | 12 | 0 | 1 | 1 | 11 | 0 | 1 | 1 | 0 | 174 | 4 | 13 | 3 | 3 | 21 | 8 | 110 | 13 | 350 | 45 | 0 | 18

Figure S187. Get High-res Image Gene #34: 'Amp Peak 34(17q25.3)' versus Clinical Feature #6: 'HISTOLOGICAL.TYPE'

'Amp Peak 34(17q25.3)' versus 'PATHOLOGY.T'

P value = 1.94e-07 (Fisher's exact test), Q value = 0.00027

Table S188. Gene #34: 'Amp Peak 34(17q25.3)' versus Clinical Feature #7: 'PATHOLOGY.T'

nPatients | T0+T1 | T2 | T3 | T4
--- | --- | --- | --- | ---
ALL | 448 | 611 | 688 | 208
AMP PEAK 34(17Q25.3) CNV | 95 | 213 | 153 | 54
AMP PEAK 34(17Q25.3) WILD-TYPE | 353 | 398 | 535 | 154

Figure S188. Get High-res Image Gene #34: 'Amp Peak 34(17q25.3)' versus Clinical Feature #7: 'PATHOLOGY.T'

'Amp Peak 34(17q25.3)' versus 'PATHOLOGICSPREAD(M)'

P value = 5.94e-09 (Chi-square test), Q value = 8.4e-06

Table S189. Gene #34: 'Amp Peak 34(17q25.3)' versus Clinical Feature #9: 'PATHOLOGICSPREAD(M)'

nPatients | M0 | M1 | M1A | M1B | MX
--- | --- | --- | --- | --- | ---
ALL | 1398 | 167 | 9 | 1 | 148
AMP PEAK 34(17Q25.3) CNV | 352 | 36 | 4 | 1 | 72
AMP PEAK 34(17Q25.3) WILD-TYPE | 1046 | 131 | 5 | 0 | 76

Figure S189. Get High-res Image Gene #34: 'Amp Peak 34(17q25.3)' versus Clinical Feature #9: 'PATHOLOGICSPREAD(M)'

'Amp Peak 34(17q25.3)' versus 'RADIATIONS.RADIATION.REGIMENINDICATION'

P value = 3.76e-07 (Fisher's exact test), Q value = 0.00052

Table S190. Gene #34: 'Amp Peak 34(17q25.3)' versus Clinical Feature #11: 'RADIATIONS.RADIATION.REGIMENINDICATION'

nPatients | NO | YES
--- | --- | ---
ALL | 835 | 3816
AMP PEAK 34(17Q25.3) CNV | 180 | 1152
AMP PEAK 34(17Q25.3) WILD-TYPE | 655 | 2664

Figure S190. Get High-res Image Gene #34: 'Amp Peak 34(17q25.3)' versus Clinical Feature #11: 'RADIATIONS.RADIATION.REGIMENINDICATION'

'Amp Peak 35(18q11.2)' versus 'PRIMARY.SITE.OF.DISEASE'

P value = 1.36e-38 (Chi-square test), Q value = 2.1e-35

Table S191. Gene #35: 'Amp Peak 35(18q11.2)' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'

nPatients | BLADDER | BRAIN | BREAST | COLON | ENDOMETRIAL | HEAD/NECK | KIDNEY | LUNG | OMENTUM | OVARY | PERITONEUM (OVARY) | RECTUM
--- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | ---
ALL | 131 | 544 | 857 | 412 | 454 | 321 | 493 | 714 | 2 | 548 | 2 | 159
AMP PEAK 35(18Q11.2) CNV | 29 | 54 | 148 | 20 | 56 | 53 | 25 | 178 | 0 | 132 | 2 | 7
AMP PEAK 35(18Q11.2) WILD-TYPE | 102 | 490 | 709 | 392 | 398 | 268 | 468 | 536 | 2 | 416 | 0 | 152

Figure S191. Get High-res Image Gene #35: 'Amp Peak 35(18q11.2)' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'

'Amp Peak 35(18q11.2)' versus 'HISTOLOGICAL.TYPE'

P value = 5.07e-47 (Chi-square test), Q value = 8.1e-44

Table S192. Gene #35: 'Amp Peak 35(18q11.2)' versus Clinical Feature #6: 'HISTOLOGICAL.TYPE'

nPatients | COLON ADENOCARCINOMA | COLON MUCINOUS ADENOCARCINOMA | ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA | HEAD & NECK SQUAMOUS CELL CARCINOMA | INFILTRATING DUCTAL CARCINOMA | INFILTRATING LOBULAR 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 HISTOLOGY (PLEASE SPECIFY) | MIXED SEROUS AND ENDOMETRIOID | MUCINOUS (COLLOID) ADENOCARCINOMA | MUCINOUS (COLLOID) CARCINOMA | MUSCLE INVASIVE UROTHELIAL CARCINOMA (PT2 OR ABOVE) | OTHER SPECIFY | RECTAL ADENOCARCINOMA | RECTAL MUCINOUS ADENOCARCINOMA | SEROUS CYSTADENOCARCINOMA | SEROUS ENDOMETRIAL ADENOCARCINOMA | TREATED PRIMARY GBM | UNTREATED PRIMARY (DE NOVO) GBM
--- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | ---
ALL | 356 | 54 | 351 | 321 | 104 | 12 | 493 | 11 | 79 | 243 | 7 | 4 | 17 | 2 | 3 | 2 | 18 | 1 | 1 | 1 | 3 | 315 | 5 | 18 | 4 | 3 | 49 | 10 | 143 | 13 | 552 | 85 | 1 | 20
AMP PEAK 35(18Q11.2) CNV | 13 | 7 | 18 | 53 | 21 | 1 | 25 | 5 | 12 | 42 | 3 | 0 | 3 | 2 | 1 | 0 | 5 | 1 | 0 | 0 | 1 | 103 | 0 | 3 | 0 | 0 | 10 | 3 | 6 | 1 | 134 | 35 | 0 | 2
AMP PEAK 35(18Q11.2) WILD-TYPE | 343 | 47 | 333 | 268 | 83 | 11 | 468 | 6 | 67 | 201 | 4 | 4 | 14 | 0 | 2 | 2 | 13 | 0 | 1 | 1 | 2 | 212 | 5 | 15 | 4 | 3 | 39 | 7 | 137 | 12 | 418 | 50 | 1 | 18

Figure S192. Get High-res Image Gene #35: 'Amp Peak 35(18q11.2)' versus Clinical Feature #6: 'HISTOLOGICAL.TYPE'

'Amp Peak 35(18q11.2)' versus 'PATHOLOGY.T'

P value = 6.41e-12 (Fisher's exact test), Q value = 9.3e-09

Table S193. Gene #35: 'Amp Peak 35(18q11.2)' versus Clinical Feature #7: 'PATHOLOGY.T'

nPatients | T0+T1 | T2 | T3 | T4
--- | --- | --- | --- | ---
ALL | 448 | 611 | 688 | 208
AMP PEAK 35(18Q11.2) CNV | 59 | 119 | 42 | 29
AMP PEAK 35(18Q11.2) WILD-TYPE | 389 | 492 | 646 | 179

Figure S193. Get High-res Image Gene #35: 'Amp Peak 35(18q11.2)' versus Clinical Feature #7: 'PATHOLOGY.T'

'Amp Peak 36(19p13.2)' versus 'Time to Death'

P value = 1.09e-09 (logrank test), Q value = 1.5e-06

Table S194. Gene #36: 'Amp Peak 36(19p13.2)' versus Clinical Feature #1: 'Time to Death'

| nPatients | nDeath | Duration Range (Median), Month
--- | --- | --- | ---
ALL | 4370 | 1406 | 0.0 - 224.0 (14.4)
AMP PEAK 36(19P13.2) CNV | 818 | 338 | 0.1 - 224.0 (14.1)
AMP PEAK 36(19P13.2) WILD-TYPE | 3552 | 1068 | 0.0 - 223.4 (14.7)

Figure S194. Get High-res Image Gene #36: 'Amp Peak 36(19p13.2)' versus Clinical Feature #1: 'Time to Death'

'Amp Peak 36(19p13.2)' versus 'PRIMARY.SITE.OF.DISEASE'

P value = 2.35e-71 (Chi-square test), Q value = 3.8e-68

Table S195. Gene #36: 'Amp Peak 36(19p13.2)' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'

nPatients | BLADDER | BRAIN | BREAST | COLON | ENDOMETRIAL | HEAD/NECK | KIDNEY | LUNG | OMENTUM | OVARY | PERITONEUM (OVARY) | RECTUM
--- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | ---
ALL | 131 | 544 | 857 | 412 | 454 | 321 | 493 | 714 | 2 | 548 | 2 | 159
AMP PEAK 36(19P13.2) CNV | 20 | 231 | 144 | 65 | 24 | 37 | 43 | 95 | 0 | 160 | 1 | 32
AMP PEAK 36(19P13.2) WILD-TYPE | 111 | 313 | 713 | 347 | 430 | 284 | 450 | 619 | 2 | 388 | 1 | 127

Figure S195. Get High-res Image Gene #36: 'Amp Peak 36(19p13.2)' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'

'Amp Peak 36(19p13.2)' versus 'HISTOLOGICAL.TYPE'

P value = 1.17e-30 (Chi-square test), Q value = 1.8e-27

Table S196. Gene #36: 'Amp Peak 36(19p13.2)' versus Clinical Feature #6: 'HISTOLOGICAL.TYPE'

nPatients | COLON ADENOCARCINOMA | COLON MUCINOUS ADENOCARCINOMA | ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA | HEAD & NECK SQUAMOUS CELL CARCINOMA | INFILTRATING DUCTAL CARCINOMA | INFILTRATING LOBULAR 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 HISTOLOGY (PLEASE SPECIFY) | MIXED SEROUS AND ENDOMETRIOID | MUCINOUS (COLLOID) ADENOCARCINOMA | MUCINOUS (COLLOID) CARCINOMA | MUSCLE INVASIVE UROTHELIAL CARCINOMA (PT2 OR ABOVE) | OTHER SPECIFY | RECTAL ADENOCARCINOMA | RECTAL MUCINOUS ADENOCARCINOMA | SEROUS CYSTADENOCARCINOMA | SEROUS ENDOMETRIAL ADENOCARCINOMA | TREATED PRIMARY GBM | UNTREATED PRIMARY (DE NOVO) GBM
--- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | ---
ALL | 356 | 54 | 351 | 321 | 104 | 12 | 493 | 11 | 79 | 243 | 7 | 4 | 17 | 2 | 3 | 2 | 18 | 1 | 1 | 1 | 3 | 315 | 5 | 18 | 4 | 3 | 49 | 10 | 143 | 13 | 552 | 85 | 1 | 20
AMP PEAK 36(19P13.2) CNV | 60 | 5 | 11 | 37 | 19 | 1 | 43 | 0 | 7 | 15 | 3 | 0 | 1 | 0 | 1 | 0 | 1 | 1 | 0 | 0 | 0 | 66 | 0 | 3 | 0 | 0 | 8 | 2 | 32 | 0 | 161 | 10 | 1 | 10
AMP PEAK 36(19P13.2) WILD-TYPE | 296 | 49 | 340 | 284 | 85 | 11 | 450 | 11 | 72 | 228 | 4 | 4 | 16 | 2 | 2 | 2 | 17 | 0 | 1 | 1 | 3 | 249 | 5 | 15 | 4 | 3 | 41 | 8 | 111 | 13 | 391 | 75 | 0 | 10

Figure S196. Get High-res Image Gene #36: 'Amp Peak 36(19p13.2)' versus Clinical Feature #6: 'HISTOLOGICAL.TYPE'

'Amp Peak 36(19p13.2)' versus 'TUMOR.STAGE'

P value = 7.78e-09 (Fisher's exact test), Q value = 1.1e-05

Table S197. Gene #36: 'Amp Peak 36(19p13.2)' versus Clinical Feature #10: 'TUMOR.STAGE'

nPatients | I | II | III | IV
--- | --- | --- | --- | ---
ALL | 685 | 487 | 876 | 420
AMP PEAK 36(19P13.2) CNV | 70 | 79 | 194 | 68
AMP PEAK 36(19P13.2) WILD-TYPE | 615 | 408 | 682 | 352

Figure S197. Get High-res Image Gene #36: 'Amp Peak 36(19p13.2)' versus Clinical Feature #10: 'TUMOR.STAGE'

'Amp Peak 36(19p13.2)' versus 'RADIATIONS.RADIATION.REGIMENINDICATION'

P value = 3.08e-11 (Fisher's exact test), Q value = 4.5e-08

Table S198. Gene #36: 'Amp Peak 36(19p13.2)' versus Clinical Feature #11: 'RADIATIONS.RADIATION.REGIMENINDICATION'

nPatients | NO | YES
--- | --- | ---
ALL | 835 | 3816
AMP PEAK 36(19P13.2) CNV | 224 | 633
AMP PEAK 36(19P13.2) WILD-TYPE | 611 | 3183

Figure S198. Get High-res Image Gene #36: 'Amp Peak 36(19p13.2)' versus Clinical Feature #11: 'RADIATIONS.RADIATION.REGIMENINDICATION'

'Amp Peak 37(19p13.12)' versus 'PRIMARY.SITE.OF.DISEASE'

P value = 3.26e-105 (Chi-square test), Q value = 5.4e-102

Table S199. Gene #37: 'Amp Peak 37(19p13.12)' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'

nPatients | BLADDER | BRAIN | BREAST | COLON | ENDOMETRIAL | HEAD/NECK | KIDNEY | LUNG | OMENTUM | OVARY | PERITONEUM (OVARY) | RECTUM
--- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | ---
ALL | 131 | 544 | 857 | 412 | 454 | 321 | 493 | 714 | 2 | 548 | 2 | 159
AMP PEAK 37(19P13.12) CNV | 21 | 210 | 182 | 65 | 75 | 42 | 43 | 98 | 0 | 299 | 1 | 30
AMP PEAK 37(19P13.12) WILD-TYPE | 110 | 334 | 675 | 347 | 379 | 279 | 450 | 616 | 2 | 249 | 1 | 129

Figure S199. Get High-res Image Gene #37: 'Amp Peak 37(19p13.12)' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'

'Amp Peak 37(19p13.12)' versus 'HISTOLOGICAL.TYPE'

P value = 3.65e-107 (Chi-square test), Q value = 6.1e-104

Table S200. Gene #37: 'Amp Peak 37(19p13.12)' versus Clinical Feature #6: 'HISTOLOGICAL.TYPE'

nPatients | COLON ADENOCARCINOMA | COLON MUCINOUS ADENOCARCINOMA | ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA | HEAD & NECK SQUAMOUS CELL CARCINOMA | INFILTRATING DUCTAL CARCINOMA | INFILTRATING LOBULAR 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 HISTOLOGY (PLEASE SPECIFY) | MIXED SEROUS AND ENDOMETRIOID | MUCINOUS (COLLOID) ADENOCARCINOMA | MUCINOUS (COLLOID) CARCINOMA | MUSCLE INVASIVE UROTHELIAL CARCINOMA (PT2 OR ABOVE) | OTHER SPECIFY | RECTAL ADENOCARCINOMA | RECTAL MUCINOUS ADENOCARCINOMA | SEROUS CYSTADENOCARCINOMA | SEROUS ENDOMETRIAL ADENOCARCINOMA | TREATED PRIMARY GBM | UNTREATED PRIMARY (DE NOVO) GBM
--- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | ---
ALL | 356 | 54 | 351 | 321 | 104 | 12 | 493 | 11 | 79 | 243 | 7 | 4 | 17 | 2 | 3 | 2 | 18 | 1 | 1 | 1 | 3 | 315 | 5 | 18 | 4 | 3 | 49 | 10 | 143 | 13 | 552 | 85 | 1 | 20
AMP PEAK 37(19P13.12) CNV | 59 | 6 | 24 | 42 | 23 | 1 | 43 | 0 | 5 | 14 | 3 | 0 | 0 | 0 | 1 | 0 | 2 | 1 | 0 | 0 | 0 | 71 | 0 | 6 | 1 | 0 | 8 | 3 | 30 | 0 | 300 | 45 | 1 | 9
AMP PEAK 37(19P13.12) WILD-TYPE | 297 | 48 | 327 | 279 | 81 | 11 | 450 | 11 | 74 | 229 | 4 | 4 | 17 | 2 | 2 | 2 | 16 | 0 | 1 | 1 | 3 | 244 | 5 | 12 | 3 | 3 | 41 | 7 | 113 | 13 | 252 | 40 | 0 | 11

Figure S200. Get High-res Image Gene #37: 'Amp Peak 37(19p13.12)' versus Clinical Feature #6: 'HISTOLOGICAL.TYPE'

'Amp Peak 37(19p13.12)' versus 'TUMOR.STAGE'

P value = 8.9e-29 (Fisher's exact test), Q value = 1.4e-25

Table S201. Gene #37: 'Amp Peak 37(19p13.12)' versus Clinical Feature #10: 'TUMOR.STAGE'

nPatients | I | II | III | IV
--- | --- | --- | --- | ---
ALL | 685 | 487 | 876 | 420
AMP PEAK 37(19P13.12) CNV | 76 | 92 | 305 | 83
AMP PEAK 37(19P13.12) WILD-TYPE | 609 | 395 | 571 | 337

Figure S201. Get High-res Image Gene #37: 'Amp Peak 37(19p13.12)' versus Clinical Feature #10: 'TUMOR.STAGE'

'Amp Peak 37(19p13.12)' versus 'RADIATIONS.RADIATION.REGIMENINDICATION'

P value = 9.43e-05 (Fisher's exact test), Q value = 0.12

Table S202. Gene #37: 'Amp Peak 37(19p13.12)' versus Clinical Feature #11: 'RADIATIONS.RADIATION.REGIMENINDICATION'

nPatients | NO | YES
--- | --- | ---
ALL | 835 | 3816
AMP PEAK 37(19P13.12) CNV | 236 | 835
AMP PEAK 37(19P13.12) WILD-TYPE | 599 | 2981

Figure S202. Get High-res Image Gene #37: 'Amp Peak 37(19p13.12)' versus Clinical Feature #11: 'RADIATIONS.RADIATION.REGIMENINDICATION'

'Amp Peak 38(19q12)' versus 'PRIMARY.SITE.OF.DISEASE'

P value = 7.8e-78 (Chi-square test), Q value = 1.3e-74

Table S203. Gene #38: 'Amp Peak 38(19q12)' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'

nPatients | BLADDER | BRAIN | BREAST | COLON | ENDOMETRIAL | HEAD/NECK | KIDNEY | LUNG | OMENTUM | OVARY | PERITONEUM (OVARY) | RECTUM
--- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | ---
ALL | 131 | 544 | 857 | 412 | 454 | 321 | 493 | 714 | 2 | 548 | 2 | 159
AMP PEAK 38(19Q12) CNV | 56 | 195 | 218 | 83 | 84 | 44 | 51 | 245 | 0 | 303 | 2 | 38
AMP PEAK 38(19Q12) WILD-TYPE | 75 | 349 | 639 | 329 | 370 | 277 | 442 | 469 | 2 | 245 | 0 | 121

Figure S203. Get High-res Image Gene #38: 'Amp Peak 38(19q12)' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'

'Amp Peak 38(19q12)' versus 'HISTOLOGICAL.TYPE'

P value = 7.99e-96 (Chi-square test), Q value = 1.3e-92

Table S204. Gene #38: 'Amp Peak 38(19q12)' versus Clinical Feature #6: 'HISTOLOGICAL.TYPE'

nPatients | COLON ADENOCARCINOMA | COLON MUCINOUS ADENOCARCINOMA | ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA | HEAD & NECK SQUAMOUS CELL CARCINOMA | INFILTRATING DUCTAL CARCINOMA | INFILTRATING LOBULAR 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 HISTOLOGY (PLEASE SPECIFY) | MIXED SEROUS AND ENDOMETRIOID | MUCINOUS (COLLOID) ADENOCARCINOMA | MUCINOUS (COLLOID) CARCINOMA | MUSCLE INVASIVE UROTHELIAL CARCINOMA (PT2 OR ABOVE) | OTHER SPECIFY | RECTAL ADENOCARCINOMA | RECTAL MUCINOUS ADENOCARCINOMA | SEROUS CYSTADENOCARCINOMA | SEROUS ENDOMETRIAL ADENOCARCINOMA | TREATED PRIMARY GBM | UNTREATED PRIMARY (DE NOVO) GBM
--- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | ---
ALL | 356 | 54 | 351 | 321 | 104 | 12 | 493 | 11 | 79 | 243 | 7 | 4 | 17 | 2 | 3 | 2 | 18 | 1 | 1 | 1 | 3 | 315 | 5 | 18 | 4 | 3 | 49 | 10 | 143 | 13 | 552 | 85 | 1 | 20
AMP PEAK 38(19Q12) CNV | 76 | 7 | 18 | 44 | 33 | 2 | 51 | 5 | 24 | 62 | 5 | 0 | 6 | 1 | 1 | 0 | 8 | 1 | 0 | 0 | 1 | 129 | 0 | 9 | 2 | 0 | 22 | 3 | 38 | 0 | 305 | 57 | 1 | 8
AMP PEAK 38(19Q12) WILD-TYPE | 280 | 47 | 333 | 277 | 71 | 10 | 442 | 6 | 55 | 181 | 2 | 4 | 11 | 1 | 2 | 2 | 10 | 0 | 1 | 1 | 2 | 186 | 5 | 9 | 2 | 3 | 27 | 7 | 105 | 13 | 247 | 28 | 0 | 12

Figure S204. Get High-res Image Gene #38: 'Amp Peak 38(19q12)' versus Clinical Feature #6: 'HISTOLOGICAL.TYPE'

'Amp Peak 38(19q12)' versus 'PATHOLOGY.T'

P value = 3.69e-06 (Fisher's exact test), Q value = 0.0049

Table S205. Gene #38: 'Amp Peak 38(19q12)' versus Clinical Feature #7: 'PATHOLOGY.T'

nPatients | T0+T1 | T2 | T3 | T4
--- | --- | --- | --- | ---
ALL | 448 | 611 | 688 | 208
AMP PEAK 38(19Q12) CNV | 68 | 172 | 136 | 41
AMP PEAK 38(19Q12) WILD-TYPE | 380 | 439 | 552 | 167

Figure S205. Get High-res Image Gene #38: 'Amp Peak 38(19q12)' versus Clinical Feature #7: 'PATHOLOGY.T'

'Amp Peak 38(19q12)' versus 'TUMOR.STAGE'

P value = 7.63e-17 (Fisher's exact test), Q value = 1.1e-13

Table S206. Gene #38: 'Amp Peak 38(19q12)' versus Clinical Feature #10: 'TUMOR.STAGE'

nPatients | I | II | III | IV
--- | --- | --- | --- | ---
ALL | 685 | 487 | 876 | 420
AMP PEAK 38(19Q12) CNV | 142 | 125 | 347 | 99
AMP PEAK 38(19Q12) WILD-TYPE | 543 | 362 | 529 | 321

Figure S206. Get High-res Image Gene #38: 'Amp Peak 38(19q12)' versus Clinical Feature #10: 'TUMOR.STAGE'

'Amp Peak 39(20q11.21)' versus 'Time to Death'

P value = 0.00019 (logrank test), Q value = 0.23

Table S207. Gene #39: 'Amp Peak 39(20q11.21)' versus Clinical Feature #1: 'Time to Death'

| nPatients | nDeath | Duration Range (Median), Month
--- | --- | --- | ---
ALL | 4370 | 1406 | 0.0 - 224.0 (14.4)
AMP PEAK 39(20Q11.21) CNV | 2002 | 670 | 0.0 - 224.0 (13.0)
AMP PEAK 39(20Q11.21) WILD-TYPE | 2368 | 736 | 0.0 - 223.4 (15.5)

Figure S207. Get High-res Image Gene #39: 'Amp Peak 39(20q11.21)' versus Clinical Feature #1: 'Time to Death'

'Amp Peak 39(20q11.21)' versus 'AGE'

P value = 1.91e-15 (t-test), Q value = 2.8e-12

Table S208. Gene #39: 'Amp Peak 39(20q11.21)' versus Clinical Feature #2: 'AGE'

| nPatients | Mean (Std.Dev)
--- | --- | ---
ALL | 4585 | 61.9 (12.6)
AMP PEAK 39(20Q11.21) CNV | 2146 | 63.5 (12.1)
AMP PEAK 39(20Q11.21) WILD-TYPE | 2439 | 60.5 (12.9)

Figure S208. Get High-res Image Gene #39: 'Amp Peak 39(20q11.21)' versus Clinical Feature #2: 'AGE'

'Amp Peak 39(20q11.21)' versus 'PRIMARY.SITE.OF.DISEASE'

P value = 4.96e-100 (Chi-square test), Q value = 8.2e-97

Table S209. Gene #39: 'Amp Peak 39(20q11.21)' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'

nPatients | BLADDER | BRAIN | BREAST | COLON | ENDOMETRIAL | HEAD/NECK | KIDNEY | LUNG | OMENTUM | OVARY | PERITONEUM (OVARY) | RECTUM
--- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | ---
ALL | 131 | 544 | 857 | 412 | 454 | 321 | 493 | 714 | 2 | 548 | 2 | 159
AMP PEAK 39(20Q11.21) CNV | 92 | 211 | 369 | 295 | 116 | 147 | 109 | 363 | 1 | 320 | 1 | 141
AMP PEAK 39(20Q11.21) WILD-TYPE | 39 | 333 | 488 | 117 | 338 | 174 | 384 | 351 | 1 | 228 | 1 | 18

Figure S209. Get High-res Image Gene #39: 'Amp Peak 39(20q11.21)' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'

'Amp Peak 39(20q11.21)' versus 'GENDER'

P value = 8.43e-05 (Fisher's exact test), Q value = 0.11

Table S210. Gene #39: 'Amp Peak 39(20q11.21)' versus Clinical Feature #4: 'GENDER'

nPatients | FEMALE | MALE
--- | --- | ---
ALL | 2924 | 1717
AMP PEAK 39(20Q11.21) CNV | 1301 | 867
AMP PEAK 39(20Q11.21) WILD-TYPE | 1623 | 850

Figure S210. Get High-res Image Gene #39: 'Amp Peak 39(20q11.21)' versus Clinical Feature #4: 'GENDER'

'Amp Peak 39(20q11.21)' versus 'HISTOLOGICAL.TYPE'

P value = 3.74e-112 (Chi-square test), Q value = 6.3e-109

Table S211. Gene #39: 'Amp Peak 39(20q11.21)' versus Clinical Feature #6: 'HISTOLOGICAL.TYPE'

nPatients | COLON ADENOCARCINOMA | COLON MUCINOUS ADENOCARCINOMA | ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA | HEAD & NECK SQUAMOUS CELL CARCINOMA | INFILTRATING DUCTAL CARCINOMA | INFILTRATING LOBULAR 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 HISTOLOGY (PLEASE SPECIFY) | MIXED SEROUS AND ENDOMETRIOID | MUCINOUS (COLLOID) ADENOCARCINOMA | MUCINOUS (COLLOID) CARCINOMA | MUSCLE INVASIVE UROTHELIAL CARCINOMA (PT2 OR ABOVE) | OTHER SPECIFY | RECTAL ADENOCARCINOMA | RECTAL MUCINOUS ADENOCARCINOMA | SEROUS CYSTADENOCARCINOMA | SEROUS ENDOMETRIAL ADENOCARCINOMA | TREATED PRIMARY GBM | UNTREATED PRIMARY (DE NOVO) GBM
--- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | ---
ALL | 356 | 54 | 351 | 321 | 104 | 12 | 493 | 11 | 79 | 243 | 7 | 4 | 17 | 2 | 3 | 2 | 18 | 1 | 1 | 1 | 3 | 315 | 5 | 18 | 4 | 3 | 49 | 10 | 143 | 13 | 552 | 85 | 1 | 20
AMP PEAK 39(20Q11.21) CNV | 269 | 24 | 48 | 147 | 50 | 1 | 109 | 5 | 27 | 119 | 6 | 1 | 7 | 0 | 2 | 0 | 6 | 0 | 0 | 0 | 2 | 187 | 0 | 6 | 1 | 0 | 34 | 2 | 132 | 7 | 322 | 62 | 1 | 7
AMP PEAK 39(20Q11.21) WILD-TYPE | 87 | 30 | 303 | 174 | 54 | 11 | 384 | 6 | 52 | 124 | 1 | 3 | 10 | 2 | 1 | 2 | 12 | 1 | 1 | 1 | 1 | 128 | 5 | 12 | 3 | 3 | 15 | 8 | 11 | 6 | 230 | 23 | 0 | 13

Figure S211. Get High-res Image Gene #39: 'Amp Peak 39(20q11.21)' versus Clinical Feature #6: 'HISTOLOGICAL.TYPE'

'Amp Peak 39(20q11.21)' versus 'PATHOLOGY.T'

P value = 1.33e-23 (Fisher's exact test), Q value = 2e-20

Table S212. Gene #39: 'Amp Peak 39(20q11.21)' versus Clinical Feature #7: 'PATHOLOGY.T'

nPatients | T0+T1 | T2 | T3 | T4
--- | --- | --- | --- | ---
ALL | 448 | 611 | 688 | 208
AMP PEAK 39(20Q11.21) CNV | 133 | 329 | 415 | 110
AMP PEAK 39(20Q11.21) WILD-TYPE | 315 | 282 | 273 | 98

Figure S212. Get High-res Image Gene #39: 'Amp Peak 39(20q11.21)' versus Clinical Feature #7: 'PATHOLOGY.T'

'Amp Peak 39(20q11.21)' versus 'PATHOLOGY.N'

P value = 1.18e-05 (Fisher's exact test), Q value = 0.016

Table S213. Gene #39: 'Amp Peak 39(20q11.21)' versus Clinical Feature #8: 'PATHOLOGY.N'

nPatients | N0 | N1 | N2 | N3
--- | --- | --- | --- | ---
ALL | 1036 | 343 | 279 | 11
AMP PEAK 39(20Q11.21) CNV | 525 | 224 | 160 | 4
AMP PEAK 39(20Q11.21) WILD-TYPE | 511 | 119 | 119 | 7

Figure S213. Get High-res Image Gene #39: 'Amp Peak 39(20q11.21)' versus Clinical Feature #8: 'PATHOLOGY.N'

'Amp Peak 39(20q11.21)' versus 'TUMOR.STAGE'

P value = 7.69e-10 (Fisher's exact test), Q value = 1.1e-06

Table S214. Gene #39: 'Amp Peak 39(20q11.21)' versus Clinical Feature #10: 'TUMOR.STAGE'

nPatients | I | II | III | IV
--- | --- | --- | --- | ---
ALL | 685 | 487 | 876 | 420
AMP PEAK 39(20Q11.21) CNV | 285 | 272 | 508 | 214
AMP PEAK 39(20Q11.21) WILD-TYPE | 400 | 215 | 368 | 206

Figure S214. Get High-res Image Gene #39: 'Amp Peak 39(20q11.21)' versus Clinical Feature #10: 'TUMOR.STAGE'

'Amp Peak 39(20q11.21)' versus 'RADIATIONS.RADIATION.REGIMENINDICATION'

P value = 1.76e-05 (Fisher's exact test), Q value = 0.023

Table S215. Gene #39: 'Amp Peak 39(20q11.21)' versus Clinical Feature #11: 'RADIATIONS.RADIATION.REGIMENINDICATION'

nPatients | NO | YES
--- | --- | ---
ALL | 835 | 3816
AMP PEAK 39(20Q11.21) CNV | 334 | 1840
AMP PEAK 39(20Q11.21) WILD-TYPE | 501 | 1976

Figure S215. Get High-res Image Gene #39: 'Amp Peak 39(20q11.21)' versus Clinical Feature #11: 'RADIATIONS.RADIATION.REGIMENINDICATION'

'Amp Peak 40(20q13.2)' versus 'AGE'

P value = 2.73e-08 (t-test), Q value = 3.8e-05

Table S216. Gene #40: 'Amp Peak 40(20q13.2)' versus Clinical Feature #2: 'AGE'

| nPatients | Mean (Std.Dev)
--- | --- | ---
ALL | 4585 | 61.9 (12.6)
AMP PEAK 40(20Q13.2) CNV | 2228 | 63.0 (12.2)
AMP PEAK 40(20Q13.2) WILD-TYPE | 2357 | 60.9 (12.9)

Figure S216. Get High-res Image Gene #40: 'Amp Peak 40(20q13.2)' versus Clinical Feature #2: 'AGE'

'Amp Peak 40(20q13.2)' versus 'PRIMARY.SITE.OF.DISEASE'

P value = 3.02e-111 (Chi-square test), Q value = 5.1e-108

Table S217. Gene #40: 'Amp Peak 40(20q13.2)' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'

nPatients | BLADDER | BRAIN | BREAST | COLON | ENDOMETRIAL | HEAD/NECK | KIDNEY | LUNG | OMENTUM | OVARY | PERITONEUM (OVARY) | RECTUM
--- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | ---
ALL | 131 | 544 | 857 | 412 | 454 | 321 | 493 | 714 | 2 | 548 | 2 | 159
AMP PEAK 40(20Q13.2) CNV | 86 | 206 | 447 | 299 | 122 | 123 | 111 | 343 | 1 | 367 | 2 | 141
AMP PEAK 40(20Q13.2) WILD-TYPE | 45 | 338 | 410 | 113 | 332 | 198 | 382 | 371 | 1 | 181 | 0 | 18

Figure S217. Get High-res Image Gene #40: 'Amp Peak 40(20q13.2)' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'

'Amp Peak 40(20q13.2)' versus 'HISTOLOGICAL.TYPE'

P value = 2.81e-119 (Chi-square test), Q value = 4.7e-116

Table S218. Gene #40: 'Amp Peak 40(20q13.2)' versus Clinical Feature #6: 'HISTOLOGICAL.TYPE'

nPatients | COLON ADENOCARCINOMA | COLON MUCINOUS ADENOCARCINOMA | ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA | HEAD & NECK SQUAMOUS CELL CARCINOMA | INFILTRATING DUCTAL CARCINOMA | INFILTRATING LOBULAR 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 HISTOLOGY (PLEASE SPECIFY) | MIXED SEROUS AND ENDOMETRIOID | MUCINOUS (COLLOID) ADENOCARCINOMA | MUCINOUS (COLLOID) CARCINOMA | MUSCLE INVASIVE UROTHELIAL CARCINOMA (PT2 OR ABOVE) | OTHER SPECIFY | RECTAL ADENOCARCINOMA | RECTAL MUCINOUS ADENOCARCINOMA | SEROUS CYSTADENOCARCINOMA | SEROUS ENDOMETRIAL ADENOCARCINOMA | TREATED PRIMARY GBM | UNTREATED PRIMARY (DE NOVO) GBM
--- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | ---
ALL | 356 | 54 | 351 | 321 | 104 | 12 | 493 | 11 | 79 | 243 | 7 | 4 | 17 | 2 | 3 | 2 | 18 | 1 | 1 | 1 | 3 | 315 | 5 | 18 | 4 | 3 | 49 | 10 | 143 | 13 | 552 | 85 | 1 | 20
AMP PEAK 40(20Q13.2) CNV | 273 | 24 | 54 | 123 | 61 | 1 | 111 | 8 | 33 | 121 | 5 | 1 | 7 | 1 | 2 | 0 | 7 | 0 | 0 | 1 | 3 | 154 | 1 | 6 | 0 | 0 | 31 | 3 | 132 | 7 | 370 | 62 | 1 | 6
AMP PEAK 40(20Q13.2) WILD-TYPE | 83 | 30 | 297 | 198 | 43 | 11 | 382 | 3 | 46 | 122 | 2 | 3 | 10 | 1 | 1 | 2 | 11 | 1 | 1 | 0 | 0 | 161 | 4 | 12 | 4 | 3 | 18 | 7 | 11 | 6 | 182 | 23 | 0 | 14

Figure S218. Get High-res Image Gene #40: 'Amp Peak 40(20q13.2)' versus Clinical Feature #6: 'HISTOLOGICAL.TYPE'

'Amp Peak 40(20q13.2)' versus 'PATHOLOGY.T'

P value = 1.02e-23 (Fisher's exact test), Q value = 1.6e-20

Table S219. Gene #40: 'Amp Peak 40(20q13.2)' versus Clinical Feature #7: 'PATHOLOGY.T'

nPatients | T0+T1 | T2 | T3 | T4
--- | --- | --- | --- | ---
ALL | 448 | 611 | 688 | 208
AMP PEAK 40(20Q13.2) CNV | 130 | 303 | 415 | 108
AMP PEAK 40(20Q13.2) WILD-TYPE | 318 | 308 | 273 | 100

Figure S219. Get High-res Image Gene #40: 'Amp Peak 40(20q13.2)' versus Clinical Feature #7: 'PATHOLOGY.T'

'Amp Peak 40(20q13.2)' versus 'PATHOLOGICSPREAD(M)'

P value = 0.000166 (Chi-square test), Q value = 0.21

Table S220. Gene #40: 'Amp Peak 40(20q13.2)' versus Clinical Feature #9: 'PATHOLOGICSPREAD(M)'

nPatients | M0 | M1 | M1A | M1B | MX
--- | --- | --- | --- | --- | ---
ALL | 1398 | 167 | 9 | 1 | 148
AMP PEAK 40(20Q13.2) CNV | 668 | 97 | 9 | 0 | 88
AMP PEAK 40(20Q13.2) WILD-TYPE | 730 | 70 | 0 | 1 | 60

Figure S220. Get High-res Image Gene #40: 'Amp Peak 40(20q13.2)' versus Clinical Feature #9: 'PATHOLOGICSPREAD(M)'

'Amp Peak 40(20q13.2)' versus 'TUMOR.STAGE'

P value = 3.26e-13 (Fisher's exact test), Q value = 4.8e-10

Table S221. Gene #40: 'Amp Peak 40(20q13.2)' versus Clinical Feature #10: 'TUMOR.STAGE'

nPatients | I | II | III | IV
--- | --- | --- | --- | ---
ALL | 685 | 487 | 876 | 420
AMP PEAK 40(20Q13.2) CNV | 280 | 265 | 531 | 220
AMP PEAK 40(20Q13.2) WILD-TYPE | 405 | 222 | 345 | 200

Figure S221. Get High-res Image Gene #40: 'Amp Peak 40(20q13.2)' versus Clinical Feature #10: 'TUMOR.STAGE'

'Amp Peak 40(20q13.2)' versus 'RADIATIONS.RADIATION.REGIMENINDICATION'

P value = 6.37e-06 (Fisher's exact test), Q value = 0.0085

Table S222. Gene #40: 'Amp Peak 40(20q13.2)' versus Clinical Feature #11: 'RADIATIONS.RADIATION.REGIMENINDICATION'

nPatients | NO | YES
--- | --- | ---
ALL | 835 | 3816
AMP PEAK 40(20Q13.2) CNV | 346 | 1910
AMP PEAK 40(20Q13.2) WILD-TYPE | 489 | 1906

Figure S222. Get High-res Image Gene #40: 'Amp Peak 40(20q13.2)' versus Clinical Feature #11: 'RADIATIONS.RADIATION.REGIMENINDICATION'

'Amp Peak 41(Xq28)' versus 'PRIMARY.SITE.OF.DISEASE'

P value = 2.19e-57 (Chi-square test), Q value = 3.5e-54

Table S223. Gene #41: 'Amp Peak 41(Xq28)' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'

nPatients | BLADDER | BRAIN | BREAST | COLON | ENDOMETRIAL | HEAD/NECK | KIDNEY | LUNG | OMENTUM | OVARY | PERITONEUM (OVARY) | RECTUM
--- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | ---
ALL | 131 | 544 | 857 | 412 | 454 | 321 | 493 | 714 | 2 | 548 | 2 | 159
AMP PEAK 41(XQ28) CNV | 25 | 30 | 167 | 82 | 75 | 97 | 38 | 207 | 0 | 217 | 1 | 36
AMP PEAK 41(XQ28) WILD-TYPE | 106 | 514 | 690 | 330 | 379 | 224 | 455 | 507 | 2 | 331 | 1 | 123

Figure S223. Get High-res Image Gene #41: 'Amp Peak 41(Xq28)' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'

'Amp Peak 41(Xq28)' versus 'HISTOLOGICAL.TYPE'

P value = 4.22e-30 (Chi-square test), Q value = 6.5e-27

Table S224. Gene #41: 'Amp Peak 41(Xq28)' versus Clinical Feature #6: 'HISTOLOGICAL.TYPE'

nPatients | COLON ADENOCARCINOMA | COLON MUCINOUS ADENOCARCINOMA | ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA | HEAD & NECK SQUAMOUS CELL CARCINOMA | INFILTRATING DUCTAL CARCINOMA | INFILTRATING LOBULAR 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 HISTOLOGY (PLEASE SPECIFY) | MIXED SEROUS AND ENDOMETRIOID | MUCINOUS (COLLOID) ADENOCARCINOMA | MUCINOUS (COLLOID) CARCINOMA | MUSCLE INVASIVE UROTHELIAL CARCINOMA (PT2 OR ABOVE) | OTHER SPECIFY | RECTAL ADENOCARCINOMA | RECTAL MUCINOUS ADENOCARCINOMA | SEROUS CYSTADENOCARCINOMA | SEROUS ENDOMETRIAL ADENOCARCINOMA | TREATED PRIMARY GBM | UNTREATED PRIMARY (DE NOVO) GBM
--- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | ---
ALL | 356 | 54 | 351 | 321 | 104 | 12 | 493 | 11 | 79 | 243 | 7 | 4 | 17 | 2 | 3 | 2 | 18 | 1 | 1 | 1 | 3 | 315 | 5 | 18 | 4 | 3 | 49 | 10 | 143 | 13 | 552 | 85 | 1 | 20
AMP PEAK 41(XQ28) CNV | 77 | 5 | 46 | 97 | 25 | 1 | 38 | 4 | 24 | 85 | 2 | 1 | 3 | 1 | 1 | 0 | 5 | 1 | 0 | 0 | 0 | 80 | 1 | 2 | 0 | 0 | 11 | 1 | 34 | 1 | 218 | 27 | 0 | 1
AMP PEAK 41(XQ28) WILD-TYPE | 279 | 49 | 305 | 224 | 79 | 11 | 455 | 7 | 55 | 158 | 5 | 3 | 14 | 1 | 2 | 2 | 13 | 0 | 1 | 1 | 3 | 235 | 4 | 16 | 4 | 3 | 38 | 9 | 109 | 12 | 334 | 58 | 1 | 19

Figure S224. Get High-res Image Gene #41: 'Amp Peak 41(Xq28)' versus Clinical Feature #6: 'HISTOLOGICAL.TYPE'

'Amp Peak 41(Xq28)' versus 'PATHOLOGY.T'

P value = 2.67e-08 (Fisher's exact test), Q value = 3.7e-05

Table S225. Gene #41: 'Amp Peak 41(Xq28)' versus Clinical Feature #7: 'PATHOLOGY.T'

nPatients | T0+T1 | T2 | T3 | T4
--- | --- | --- | --- | ---
ALL | 448 | 611 | 688 | 208
AMP PEAK 41(XQ28) CNV | 57 | 167 | 144 | 56
AMP PEAK 41(XQ28) WILD-TYPE | 391 | 444 | 544 | 152

Figure S225. Get High-res Image Gene #41: 'Amp Peak 41(Xq28)' versus Clinical Feature #7: 'PATHOLOGY.T'

'Amp Peak 41(Xq28)' versus 'PATHOLOGY.N'

P value = 8.82e-05 (Fisher's exact test), Q value = 0.11

Table S226. Gene #41: 'Amp Peak 41(Xq28)' versus Clinical Feature #8: 'PATHOLOGY.N'

nPatients | N0 | N1 | N2 | N3
--- | --- | --- | --- | ---
ALL | 1036 | 343 | 279 | 11
AMP PEAK 41(XQ28) CNV | 212 | 93 | 92 | 2
AMP PEAK 41(XQ28) WILD-TYPE | 824 | 250 | 187 | 9

Figure S226. Get High-res Image Gene #41: 'Amp Peak 41(Xq28)' versus Clinical Feature #8: 'PATHOLOGY.N'

'Amp Peak 41(Xq28)' versus 'TUMOR.STAGE'

P value = 2.91e-07 (Fisher's exact test), Q value = 4e-04

Table S227. Gene #41: 'Amp Peak 41(Xq28)' versus Clinical Feature #10: 'TUMOR.STAGE'

nPatients | I | II | III | IV
--- | --- | --- | --- | ---
ALL | 685 | 487 | 876 | 420
AMP PEAK 41(XQ28) CNV | 125 | 120 | 255 | 131
AMP PEAK 41(XQ28) WILD-TYPE | 560 | 367 | 621 | 289

Figure S227. Get High-res Image Gene #41: 'Amp Peak 41(Xq28)' versus Clinical Feature #10: 'TUMOR.STAGE'

'Del Peak 1(1p36.23)' versus 'PRIMARY.SITE.OF.DISEASE'

P value = 8.82e-39 (Chi-square test), Q value = 1.4e-35

Table S228. Gene #42: 'Del Peak 1(1p36.23)' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'

nPatients | BLADDER | BRAIN | BREAST | COLON | ENDOMETRIAL | HEAD/NECK | KIDNEY | LUNG | OMENTUM | OVARY | PERITONEUM (OVARY) | RECTUM
--- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | ---
ALL | 131 | 544 | 857 | 412 | 454 | 321 | 493 | 714 | 2 | 548 | 2 | 159
DEL PEAK 1(1P36.23) CNV | 22 | 129 | 352 | 135 | 55 | 65 | 97 | 223 | 2 | 200 | 0 | 65
DEL PEAK 1(1P36.23) WILD-TYPE | 109 | 415 | 505 | 277 | 399 | 256 | 396 | 491 | 0 | 348 | 2 | 94

Figure S228. Get High-res Image Gene #42: 'Del Peak 1(1p36.23)' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'

'Del Peak 1(1p36.23)' versus 'HISTOLOGICAL.TYPE'

P value = 3.35e-32 (Chi-square test), Q value = 5.2e-29

Table S229. Gene #42: 'Del Peak 1(1p36.23)' versus Clinical Feature #6: 'HISTOLOGICAL.TYPE'

nPatients | COLON ADENOCARCINOMA | COLON MUCINOUS ADENOCARCINOMA | ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA | HEAD & NECK SQUAMOUS CELL CARCINOMA | INFILTRATING DUCTAL CARCINOMA | INFILTRATING LOBULAR 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 HISTOLOGY (PLEASE SPECIFY) | MIXED SEROUS AND ENDOMETRIOID | MUCINOUS (COLLOID) ADENOCARCINOMA | MUCINOUS (COLLOID) CARCINOMA | MUSCLE INVASIVE UROTHELIAL CARCINOMA (PT2 OR ABOVE) | OTHER SPECIFY | RECTAL ADENOCARCINOMA | RECTAL MUCINOUS ADENOCARCINOMA | SEROUS CYSTADENOCARCINOMA | SEROUS ENDOMETRIAL ADENOCARCINOMA | TREATED PRIMARY GBM | UNTREATED PRIMARY (DE NOVO) GBM
--- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | ---
ALL | 356 | 54 | 351 | 321 | 104 | 12 | 493 | 11 | 79 | 243 | 7 | 4 | 17 | 2 | 3 | 2 | 18 | 1 | 1 | 1 | 3 | 315 | 5 | 18 | 4 | 3 | 49 | 10 | 143 | 13 | 552 | 85 | 1 | 20
DEL PEAK 1(1P36.23) CNV | 125 | 10 | 23 | 65 | 45 | 5 | 97 | 3 | 21 | 53 | 4 | 0 | 3 | 1 | 0 | 0 | 1 | 1 | 0 | 1 | 0 | 134 | 1 | 4 | 1 | 0 | 7 | 5 | 57 | 7 | 202 | 28 | 0 | 6
DEL PEAK 1(1P36.23) WILD-TYPE | 231 | 44 | 328 | 256 | 59 | 7 | 396 | 8 | 58 | 190 | 3 | 4 | 14 | 1 | 3 | 2 | 17 | 0 | 1 | 0 | 3 | 181 | 4 | 14 | 3 | 3 | 42 | 5 | 86 | 6 | 350 | 57 | 1 | 14

Figure S229. Get High-res Image Gene #42: 'Del Peak 1(1p36.23)' versus Clinical Feature #6: 'HISTOLOGICAL.TYPE'

'Del Peak 2(1p36.11)' versus 'PRIMARY.SITE.OF.DISEASE'

P value = 2.35e-75 (Chi-square test), Q value = 3.8e-72

Table S230. Gene #43: 'Del Peak 2(1p36.11)' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'

nPatients | BLADDER | BRAIN | BREAST | COLON | ENDOMETRIAL | HEAD/NECK | KIDNEY | LUNG | OMENTUM | OVARY | PERITONEUM (OVARY) | RECTUM
--- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | ---
ALL | 131 | 544 | 857 | 412 | 454 | 321 | 493 | 714 | 2 | 548 | 2 | 159
DEL PEAK 2(1P36.11) CNV | 25 | 47 | 357 | 150 | 63 | 64 | 95 | 245 | 1 | 255 | 0 | 69
DEL PEAK 2(1P36.11) WILD-TYPE | 106 | 497 | 500 | 262 | 391 | 257 | 398 | 469 | 1 | 293 | 2 | 90

Figure S230. Get High-res Image Gene #43: 'Del Peak 2(1p36.11)' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'

'Del Peak 2(1p36.11)' versus 'HISTOLOGICAL.TYPE'

P value = 1.16e-45 (Chi-square test), Q value = 1.8e-42

Table S231. Gene #43: 'Del Peak 2(1p36.11)' versus Clinical Feature #6: 'HISTOLOGICAL.TYPE'

nPatients | COLON ADENOCARCINOMA | COLON MUCINOUS ADENOCARCINOMA | ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA | HEAD & NECK SQUAMOUS CELL CARCINOMA | INFILTRATING DUCTAL CARCINOMA | INFILTRATING LOBULAR 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 HISTOLOGY (PLEASE SPECIFY) | MIXED SEROUS AND ENDOMETRIOID | MUCINOUS (COLLOID) ADENOCARCINOMA | MUCINOUS (COLLOID) CARCINOMA | MUSCLE INVASIVE UROTHELIAL CARCINOMA (PT2 OR ABOVE) | OTHER SPECIFY | RECTAL ADENOCARCINOMA | RECTAL MUCINOUS ADENOCARCINOMA | SEROUS CYSTADENOCARCINOMA | SEROUS ENDOMETRIAL ADENOCARCINOMA | TREATED PRIMARY GBM | UNTREATED PRIMARY (DE NOVO) GBM
--- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | ---
ALL | 356 | 54 | 351 | 321 | 104 | 12 | 493 | 11 | 79 | 243 | 7 | 4 | 17 | 2 | 3 | 2 | 18 | 1 | 1 | 1 | 3 | 315 | 5 | 18 | 4 | 3 | 49 | 10 | 143 | 13 | 552 | 85 | 1 | 20
DEL PEAK 2(1P36.11) CNV | 139 | 10 | 24 | 64 | 46 | 5 | 95 | 5 | 22 | 63 | 3 | 0 | 3 | 1 | 0 | 0 | 2 | 1 | 0 | 1 | 1 | 142 | 1 | 4 | 1 | 0 | 11 | 4 | 61 | 7 | 256 | 35 | 0 | 3
DEL PEAK 2(1P36.11) WILD-TYPE | 217 | 44 | 327 | 257 | 58 | 7 | 398 | 6 | 57 | 180 | 4 | 4 | 14 | 1 | 3 | 2 | 16 | 0 | 1 | 0 | 2 | 173 | 4 | 14 | 3 | 3 | 38 | 6 | 82 | 6 | 296 | 50 | 1 | 17

Figure S231. Get High-res Image Gene #43: 'Del Peak 2(1p36.11)' versus Clinical Feature #6: 'HISTOLOGICAL.TYPE'

'Del Peak 2(1p36.11)' versus 'TUMOR.STAGE'

P value = 1.02e-05 (Fisher's exact test), Q value = 0.014

Table S232. Gene #43: 'Del Peak 2(1p36.11)' versus Clinical Feature #10: 'TUMOR.STAGE'

nPatients | I | II | III | IV
--- | --- | --- | --- | ---
ALL | 685 | 487 | 876 | 420
DEL PEAK 2(1P36.11) CNV | 193 | 149 | 348 | 147
DEL PEAK 2(1P36.11) WILD-TYPE | 492 | 338 | 528 | 273

Figure S232. Get High-res Image Gene #43: 'Del Peak 2(1p36.11)' versus Clinical Feature #10: 'TUMOR.STAGE'

'Del Peak 2(1p36.11)' versus 'RADIATIONS.RADIATION.REGIMENINDICATION'

P value = 2.95e-10 (Fisher's exact test), Q value = 4.2e-07

Table S233. Gene #43: 'Del Peak 2(1p36.11)' versus Clinical Feature #11: 'RADIATIONS.RADIATION.REGIMENINDICATION'

nPatients | NO | YES
--- | --- | ---
ALL | 835 | 3816
DEL PEAK 2(1P36.11) CNV | 173 | 1202
DEL PEAK 2(1P36.11) WILD-TYPE | 662 | 2614

Figure S233. Get High-res Image Gene #43: 'Del Peak 2(1p36.11)' versus Clinical Feature #11: 'RADIATIONS.RADIATION.REGIMENINDICATION'

'Del Peak 2(1p36.11)' versus 'TOBACCOSMOKINGHISTORYINDICATOR'

P value = 0.000119 (Chi-square test), Q value = 0.15

Table S234. Gene #43: 'Del Peak 2(1p36.11)' versus Clinical Feature #13: '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 | 15 | 16 | 22 | 25 | 2 | 342 | 208 | 237 | 116
DEL PEAK 2(1P36.11) CNV | 1 | 3 | 7 | 3 | 0 | 122 | 57 | 86 | 18
DEL PEAK 2(1P36.11) WILD-TYPE | 14 | 13 | 15 | 22 | 2 | 220 | 151 | 151 | 98

Figure S234. Get High-res Image Gene #43: 'Del Peak 2(1p36.11)' versus Clinical Feature #13: 'TOBACCOSMOKINGHISTORYINDICATOR'

'Del Peak 2(1p36.11)' versus 'NUMBER.OF.LYMPH.NODES'

P value = 4.02e-05 (t-test), Q value = 0.051

Table S235. Gene #43: 'Del Peak 2(1p36.11)' versus Clinical Feature #18: 'NUMBER.OF.LYMPH.NODES'

| nPatients | Mean (Std.Dev)
--- | --- | ---
ALL | 1592 | 2.3 (4.6)
DEL PEAK 2(1P36.11) CNV | 573 | 3.0 (5.8)
DEL PEAK 2(1P36.11) WILD-TYPE | 1019 | 1.9 (3.7)

Figure S235. Get High-res Image Gene #43: 'Del Peak 2(1p36.11)' versus Clinical Feature #18: 'NUMBER.OF.LYMPH.NODES'

'Del Peak 2(1p36.11)' versus 'NEOPLASM.DISEASESTAGE'

P value = 5.18e-05 (Chi-square test), Q value = 0.066

Table S236. Gene #43: 'Del Peak 2(1p36.11)' versus Clinical Feature #20: '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 X
--- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | ---
ALL | 71 | 45 | 2 | 34 | 246 | 165 | 29 | 107 | 22 | 36 | 35 | 12
DEL PEAK 2(1P36.11) CNV | 18 | 12 | 1 | 4 | 102 | 72 | 7 | 54 | 14 | 16 | 9 | 6
DEL PEAK 2(1P36.11) WILD-TYPE | 53 | 33 | 1 | 30 | 144 | 93 | 22 | 53 | 8 | 20 | 26 | 6

Figure S236. Get High-res Image Gene #43: 'Del Peak 2(1p36.11)' versus Clinical Feature #20: 'NEOPLASM.DISEASESTAGE'

'Del Peak 3(1p13.2)' versus 'AGE'

P value = 2.26e-05 (t-test), Q value = 0.029

Table S237. Gene #44: 'Del Peak 3(1p13.2)' versus Clinical Feature #2: 'AGE'

| nPatients | Mean (Std.Dev)
--- | --- | ---
ALL | 4585 | 61.9 (12.6)
DEL PEAK 3(1P13.2) CNV | 964 | 63.4 (12.1)
DEL PEAK 3(1P13.2) WILD-TYPE | 3621 | 61.5 (12.7)

Figure S237. Get High-res Image Gene #44: 'Del Peak 3(1p13.2)' versus Clinical Feature #2: 'AGE'

'Del Peak 3(1p13.2)' versus 'PRIMARY.SITE.OF.DISEASE'

P value = 1.18e-68 (Chi-square test), Q value = 1.9e-65

Table S238. Gene #44: 'Del Peak 3(1p13.2)' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'

nPatients | BLADDER | BRAIN | BREAST | COLON | ENDOMETRIAL | HEAD/NECK | KIDNEY | LUNG | OMENTUM | OVARY | PERITONEUM (OVARY) | RECTUM
--- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | ---
ALL | 131 | 544 | 857 | 412 | 454 | 321 | 493 | 714 | 2 | 548 | 2 | 159
DEL PEAK 3(1P13.2) CNV | 19 | 23 | 252 | 107 | 25 | 78 | 59 | 261 | 0 | 97 | 1 | 51
DEL PEAK 3(1P13.2) WILD-TYPE | 112 | 521 | 605 | 305 | 429 | 243 | 434 | 453 | 2 | 451 | 1 | 108

Figure S238. Get High-res Image Gene #44: 'Del Peak 3(1p13.2)' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'

'Del Peak 3(1p13.2)' versus 'HISTOLOGICAL.TYPE'

P value = 3.6e-38 (Chi-square test), Q value = 5.7e-35

Table S239. Gene #44: 'Del Peak 3(1p13.2)' versus Clinical Feature #6: 'HISTOLOGICAL.TYPE'

nPatients | COLON ADENOCARCINOMA | COLON MUCINOUS ADENOCARCINOMA | ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA | HEAD & NECK SQUAMOUS CELL CARCINOMA | INFILTRATING DUCTAL CARCINOMA | INFILTRATING LOBULAR 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 HISTOLOGY (PLEASE SPECIFY) | MIXED SEROUS AND ENDOMETRIOID | MUCINOUS (COLLOID) ADENOCARCINOMA | MUCINOUS (COLLOID) CARCINOMA | MUSCLE INVASIVE UROTHELIAL CARCINOMA (PT2 OR ABOVE) | OTHER SPECIFY | RECTAL ADENOCARCINOMA | RECTAL MUCINOUS ADENOCARCINOMA | SEROUS CYSTADENOCARCINOMA | SEROUS ENDOMETRIAL ADENOCARCINOMA | TREATED PRIMARY GBM | UNTREATED PRIMARY (DE NOVO) GBM
--- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | ---
ALL | 356 | 54 | 351 | 321 | 104 | 12 | 493 | 11 | 79 | 243 | 7 | 4 | 17 | 2 | 3 | 2 | 18 | 1 | 1 | 1 | 3 | 315 | 5 | 18 | 4 | 3 | 49 | 10 | 143 | 13 | 552 | 85 | 1 | 20
DEL PEAK 3(1P13.2) CNV | 98 | 9 | 11 | 78 | 34 | 3 | 59 | 5 | 26 | 68 | 3 | 1 | 6 | 1 | 0 | 0 | 6 | 1 | 0 | 0 | 1 | 141 | 1 | 3 | 1 | 1 | 9 | 2 | 48 | 2 | 98 | 11 | 0 | 0
DEL PEAK 3(1P13.2) WILD-TYPE | 258 | 45 | 340 | 243 | 70 | 9 | 434 | 6 | 53 | 175 | 4 | 3 | 11 | 1 | 3 | 2 | 12 | 0 | 1 | 1 | 2 | 174 | 4 | 15 | 3 | 2 | 40 | 8 | 95 | 11 | 454 | 74 | 1 | 20

Figure S239. Get High-res Image Gene #44: 'Del Peak 3(1p13.2)' versus Clinical Feature #6: 'HISTOLOGICAL.TYPE'

'Del Peak 3(1p13.2)' versus 'RADIATIONS.RADIATION.REGIMENINDICATION'

P value = 1.14e-11 (Fisher's exact test), Q value = 1.7e-08

Table S240. Gene #44: 'Del Peak 3(1p13.2)' versus Clinical Feature #11: 'RADIATIONS.RADIATION.REGIMENINDICATION'

nPatients | NO | YES
--- | --- | ---
ALL | 835 | 3816
DEL PEAK 3(1P13.2) CNV | 106 | 872
DEL PEAK 3(1P13.2) WILD-TYPE | 729 | 2944

Figure S240. Get High-res Image Gene #44: 'Del Peak 3(1p13.2)' versus Clinical Feature #11: 'RADIATIONS.RADIATION.REGIMENINDICATION'

'Del Peak 3(1p13.2)' versus 'TOBACCOSMOKINGHISTORYINDICATOR'

P value = 8.76e-05 (Chi-square test), Q value = 0.11

Table S241. Gene #44: 'Del Peak 3(1p13.2)' versus Clinical Feature #13: '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 | 15 | 16 | 22 | 25 | 2 | 342 | 208 | 237 | 116
DEL PEAK 3(1P13.2) CNV | 1 | 2 | 3 | 4 | 0 | 134 | 61 | 89 | 25
DEL PEAK 3(1P13.2) WILD-TYPE | 14 | 14 | 19 | 21 | 2 | 208 | 147 | 148 | 91

Figure S241. Get High-res Image Gene #44: 'Del Peak 3(1p13.2)' versus Clinical Feature #13: 'TOBACCOSMOKINGHISTORYINDICATOR'

'Del Peak 3(1p13.2)' versus 'NUMBER.OF.LYMPH.NODES'

P value = 0.000101 (t-test), Q value = 0.13

Table S242. Gene #44: 'Del Peak 3(1p13.2)' versus Clinical Feature #18: 'NUMBER.OF.LYMPH.NODES'

| nPatients | Mean (Std.Dev)
--- | --- | ---
ALL | 1592 | 2.3 (4.6)
DEL PEAK 3(1P13.2) CNV | 426 | 3.1 (5.5)
DEL PEAK 3(1P13.2) WILD-TYPE | 1166 | 1.9 (4.2)

Figure S242. Get High-res Image Gene #44: 'Del Peak 3(1p13.2)' versus Clinical Feature #18: 'NUMBER.OF.LYMPH.NODES'

'Del Peak 4(2q22.1)' versus 'PRIMARY.SITE.OF.DISEASE'

P value = 1.6e-44 (Chi-square test), Q value = 2.5e-41

Table S243. Gene #45: 'Del Peak 4(2q22.1)' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'

nPatients | BLADDER | BRAIN | BREAST | COLON | ENDOMETRIAL | HEAD/NECK | KIDNEY | LUNG | OMENTUM | OVARY | PERITONEUM (OVARY) | RECTUM
--- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | ---
ALL | 131 | 544 | 857 | 412 | 454 | 321 | 493 | 714 | 2 | 548 | 2 | 159
DEL PEAK 4(2Q22.1) CNV | 40 | 43 | 195 | 24 | 35 | 65 | 19 | 130 | 0 | 128 | 1 | 10
DEL PEAK 4(2Q22.1) WILD-TYPE | 91 | 501 | 662 | 388 | 419 | 256 | 474 | 584 | 2 | 420 | 1 | 149

Figure S243. Get High-res Image Gene #45: 'Del Peak 4(2q22.1)' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'

'Del Peak 4(2q22.1)' versus 'HISTOLOGICAL.TYPE'

P value = 1.03e-36 (Chi-square test), Q value = 1.6e-33

Table S244. Gene #45: 'Del Peak 4(2q22.1)' versus Clinical Feature #6: 'HISTOLOGICAL.TYPE'

nPatients | COLON ADENOCARCINOMA | COLON MUCINOUS ADENOCARCINOMA | ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA | HEAD & NECK SQUAMOUS CELL CARCINOMA | INFILTRATING DUCTAL CARCINOMA | INFILTRATING LOBULAR 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 HISTOLOGY (PLEASE SPECIFY) | MIXED SEROUS AND ENDOMETRIOID | MUCINOUS (COLLOID) ADENOCARCINOMA | MUCINOUS (COLLOID) CARCINOMA | MUSCLE INVASIVE UROTHELIAL CARCINOMA (PT2 OR ABOVE) | OTHER SPECIFY | RECTAL ADENOCARCINOMA | RECTAL MUCINOUS ADENOCARCINOMA | SEROUS CYSTADENOCARCINOMA | SEROUS ENDOMETRIAL ADENOCARCINOMA | TREATED PRIMARY GBM | UNTREATED PRIMARY (DE NOVO) GBM
--- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | ---
ALL | 356 | 54 | 351 | 321 | 104 | 12 | 493 | 11 | 79 | 243 | 7 | 4 | 17 | 2 | 3 | 2 | 18 | 1 | 1 | 1 | 3 | 315 | 5 | 18 | 4 | 3 | 49 | 10 | 143 | 13 | 552 | 85 | 1 | 20
DEL PEAK 4(2Q22.1) CNV | 22 | 2 | 15 | 65 | 25 | 2 | 19 | 4 | 7 | 24 | 0 | 0 | 3 | 0 | 0 | 0 | 4 | 1 | 0 | 1 | 0 | 85 | 0 | 1 | 1 | 0 | 16 | 2 | 9 | 0 | 129 | 19 | 0 | 1
DEL PEAK 4(2Q22.1) WILD-TYPE | 334 | 52 | 336 | 256 | 79 | 10 | 474 | 7 | 72 | 219 | 7 | 4 | 14 | 2 | 3 | 2 | 14 | 0 | 1 | 0 | 3 | 230 | 5 | 17 | 3 | 3 | 33 | 8 | 134 | 13 | 423 | 66 | 1 | 19

Figure S244. Get High-res Image Gene #45: 'Del Peak 4(2q22.1)' versus Clinical Feature #6: 'HISTOLOGICAL.TYPE'

'Del Peak 4(2q22.1)' versus 'PATHOLOGY.T'

P value = 1.24e-05 (Fisher's exact test), Q value = 0.016

Table S245. Gene #45: 'Del Peak 4(2q22.1)' versus Clinical Feature #7: 'PATHOLOGY.T'

nPatients | T0+T1 | T2 | T3 | T4
--- | --- | --- | --- | ---
ALL | 448 | 611 | 688 | 208
DEL PEAK 4(2Q22.1) CNV | 39 | 93 | 58 | 37
DEL PEAK 4(2Q22.1) WILD-TYPE | 409 | 518 | 630 | 171

Figure S245. Get High-res Image Gene #45: 'Del Peak 4(2q22.1)' versus Clinical Feature #7: 'PATHOLOGY.T'

'Del Peak 4(2q22.1)' versus 'TUMOR.STAGE'

P value = 1.08e-05 (Fisher's exact test), Q value = 0.014

Table S246. Gene #45: 'Del Peak 4(2q22.1)' versus Clinical Feature #10: 'TUMOR.STAGE'

nPatients | I | II | III | IV
--- | --- | --- | --- | ---
ALL | 685 | 487 | 876 | 420
DEL PEAK 4(2Q22.1) CNV | 62 | 72 | 155 | 66
DEL PEAK 4(2Q22.1) WILD-TYPE | 623 | 415 | 721 | 354

Figure S246. Get High-res Image Gene #45: 'Del Peak 4(2q22.1)' versus Clinical Feature #10: 'TUMOR.STAGE'

'Del Peak 5(2q37.3)' versus 'PRIMARY.SITE.OF.DISEASE'

P value = 3.31e-67 (Chi-square test), Q value = 5.4e-64

Table S247. Gene #46: 'Del Peak 5(2q37.3)' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'

nPatients | BLADDER | BRAIN | BREAST | COLON | ENDOMETRIAL | HEAD/NECK | KIDNEY | LUNG | OMENTUM | OVARY | PERITONEUM (OVARY) | RECTUM
--- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | ---
ALL | 131 | 544 | 857 | 412 | 454 | 321 | 493 | 714 | 2 | 548 | 2 | 159
DEL PEAK 5(2Q37.3) CNV | 63 | 58 | 255 | 21 | 43 | 92 | 47 | 160 | 1 | 169 | 1 | 12
DEL PEAK 5(2Q37.3) WILD-TYPE | 68 | 486 | 602 | 391 | 411 | 229 | 446 | 554 | 1 | 379 | 1 | 147

Figure S247. Get High-res Image Gene #46: 'Del Peak 5(2q37.3)' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'

'Del Peak 5(2q37.3)' versus 'HISTOLOGICAL.TYPE'

P value = 2.82e-45 (Chi-square test), Q value = 4.5e-42

Table S248. Gene #46: 'Del Peak 5(2q37.3)' versus Clinical Feature #6: 'HISTOLOGICAL.TYPE'

nPatients | COLON ADENOCARCINOMA | COLON MUCINOUS ADENOCARCINOMA | ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA | HEAD & NECK SQUAMOUS CELL CARCINOMA | INFILTRATING DUCTAL CARCINOMA | INFILTRATING LOBULAR 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 HISTOLOGY (PLEASE SPECIFY) | MIXED SEROUS AND ENDOMETRIOID | MUCINOUS (COLLOID) ADENOCARCINOMA | MUCINOUS (COLLOID) CARCINOMA | MUSCLE INVASIVE UROTHELIAL CARCINOMA (PT2 OR ABOVE) | OTHER SPECIFY | RECTAL ADENOCARCINOMA | RECTAL MUCINOUS ADENOCARCINOMA | SEROUS CYSTADENOCARCINOMA | SEROUS ENDOMETRIAL ADENOCARCINOMA | TREATED PRIMARY GBM | UNTREATED PRIMARY (DE NOVO) GBM
--- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | ---
ALL | 356 | 54 | 351 | 321 | 104 | 12 | 493 | 11 | 79 | 243 | 7 | 4 | 17 | 2 | 3 | 2 | 18 | 1 | 1 | 1 | 3 | 315 | 5 | 18 | 4 | 3 | 49 | 10 | 143 | 13 | 552 | 85 | 1 | 20
DEL PEAK 5(2Q37.3) CNV | 19 | 1 | 24 | 92 | 38 | 2 | 47 | 3 | 7 | 35 | 2 | 0 | 5 | 1 | 0 | 0 | 5 | 1 | 0 | 0 | 0 | 100 | 0 | 2 | 1 | 0 | 20 | 3 | 11 | 0 | 171 | 17 | 0 | 2
DEL PEAK 5(2Q37.3) WILD-TYPE | 337 | 53 | 327 | 229 | 66 | 10 | 446 | 8 | 72 | 208 | 5 | 4 | 12 | 1 | 3 | 2 | 13 | 0 | 1 | 1 | 3 | 215 | 5 | 16 | 3 | 3 | 29 | 7 | 132 | 13 | 381 | 68 | 1 | 18

Figure S248. Get High-res Image Gene #46: 'Del Peak 5(2q37.3)' versus Clinical Feature #6: 'HISTOLOGICAL.TYPE'

'Del Peak 5(2q37.3)' versus 'TOBACCOSMOKINGHISTORYINDICATOR'

P value = 2.28e-06 (Chi-square test), Q value = 0.0031

Table S249. Gene #46: 'Del Peak 5(2q37.3)' versus Clinical Feature #13: '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 | 15 | 16 | 22 | 25 | 2 | 342 | 208 | 237 | 116
DEL PEAK 5(2Q37.3) CNV | 9 | 6 | 11 | 14 | 2 | 86 | 40 | 77 | 29
DEL PEAK 5(2Q37.3) WILD-TYPE | 6 | 10 | 11 | 11 | 0 | 256 | 168 | 160 | 87

Figure S249. Get High-res Image Gene #46: 'Del Peak 5(2q37.3)' versus Clinical Feature #13: 'TOBACCOSMOKINGHISTORYINDICATOR'

'Del Peak 6(3p25.3)' versus 'PRIMARY.SITE.OF.DISEASE'

P value = 0 (Chi-square test), Q value = 0

Table S250. Gene #47: 'Del Peak 6(3p25.3)' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'

nPatients | BLADDER | BRAIN | BREAST | COLON | ENDOMETRIAL | HEAD/NECK | KIDNEY | LUNG | OMENTUM | OVARY | PERITONEUM (OVARY) | RECTUM
--- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | ---
ALL | 131 | 544 | 857 | 412 | 454 | 321 | 493 | 714 | 2 | 548 | 2 | 159
DEL PEAK 6(3P25.3) CNV | 25 | 42 | 138 | 60 | 48 | 227 | 432 | 435 | 2 | 196 | 0 | 19
DEL PEAK 6(3P25.3) WILD-TYPE | 106 | 502 | 719 | 352 | 406 | 94 | 61 | 279 | 0 | 352 | 2 | 140

Figure S250. Get High-res Image Gene #47: 'Del Peak 6(3p25.3)' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'

'Del Peak 6(3p25.3)' versus 'GENDER'

P value = 1.72e-36 (Fisher's exact test), Q value = 2.7e-33

Table S251. Gene #47: 'Del Peak 6(3p25.3)' versus Clinical Feature #4: 'GENDER'

nPatients | FEMALE | MALE
--- | --- | ---
ALL | 2924 | 1717
DEL PEAK 6(3P25.3) CNV | 825 | 801
DEL PEAK 6(3P25.3) WILD-TYPE | 2099 | 916

Figure S251. Get High-res Image Gene #47: 'Del Peak 6(3p25.3)' versus Clinical Feature #4: 'GENDER'

'Del Peak 6(3p25.3)' versus 'HISTOLOGICAL.TYPE'

P value = 5.86e-225 (Chi-square test), Q value = 1e-221

Table S252. Gene #47: 'Del Peak 6(3p25.3)' versus Clinical Feature #6: 'HISTOLOGICAL.TYPE'

nPatients | COLON ADENOCARCINOMA | COLON MUCINOUS ADENOCARCINOMA | ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA | HEAD & NECK SQUAMOUS CELL CARCINOMA | INFILTRATING DUCTAL CARCINOMA | INFILTRATING LOBULAR 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 HISTOLOGY (PLEASE SPECIFY) | MIXED SEROUS AND ENDOMETRIOID | MUCINOUS (COLLOID) ADENOCARCINOMA | MUCINOUS (COLLOID) CARCINOMA | MUSCLE INVASIVE UROTHELIAL CARCINOMA (PT2 OR ABOVE) | OTHER SPECIFY | RECTAL ADENOCARCINOMA | RECTAL MUCINOUS ADENOCARCINOMA | SEROUS CYSTADENOCARCINOMA | SEROUS ENDOMETRIAL ADENOCARCINOMA | TREATED PRIMARY GBM | UNTREATED PRIMARY (DE NOVO) GBM
--- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | ---
ALL | 356 | 54 | 351 | 321 | 104 | 12 | 493 | 11 | 79 | 243 | 7 | 4 | 17 | 2 | 3 | 2 | 18 | 1 | 1 | 1 | 3 | 315 | 5 | 18 | 4 | 3 | 49 | 10 | 143 | 13 | 552 | 85 | 1 | 20
DEL PEAK 6(3P25.3) CNV | 56 | 4 | 16 | 227 | 18 | 0 | 432 | 5 | 35 | 114 | 6 | 0 | 7 | 1 | 2 | 0 | 8 | 1 | 0 | 1 | 1 | 251 | 1 | 6 | 2 | 1 | 10 | 2 | 15 | 3 | 198 | 26 | 0 | 2
DEL PEAK 6(3P25.3) WILD-TYPE | 300 | 50 | 335 | 94 | 86 | 12 | 61 | 6 | 44 | 129 | 1 | 4 | 10 | 1 | 1 | 2 | 10 | 0 | 1 | 0 | 2 | 64 | 4 | 12 | 2 | 2 | 39 | 8 | 128 | 10 | 354 | 59 | 1 | 18

Figure S252. Get High-res Image Gene #47: 'Del Peak 6(3p25.3)' versus Clinical Feature #6: 'HISTOLOGICAL.TYPE'

'Del Peak 6(3p25.3)' versus 'PATHOLOGY.T'

P value = 2.3e-21 (Fisher's exact test), Q value = 3.5e-18

Table S253. Gene #47: 'Del Peak 6(3p25.3)' versus Clinical Feature #7: 'PATHOLOGY.T'

nPatients | T0+T1 | T2 | T3 | T4
--- | --- | --- | --- | ---
ALL | 448 | 611 | 688 | 208
DEL PEAK 6(3P25.3) CNV | 334 | 340 | 310 | 118
DEL PEAK 6(3P25.3) WILD-TYPE | 114 | 271 | 378 | 90

Figure S253. Get High-res Image Gene #47: 'Del Peak 6(3p25.3)' versus Clinical Feature #7: 'PATHOLOGY.T'

'Del Peak 6(3p25.3)' versus 'TUMOR.STAGE'

P value = 1.54e-14 (Fisher's exact test), Q value = 2.3e-11

Table S254. Gene #47: 'Del Peak 6(3p25.3)' versus Clinical Feature #10: 'TUMOR.STAGE'

nPatients | I | II | III | IV
--- | --- | --- | --- | ---
ALL | 685 | 487 | 876 | 420
DEL PEAK 6(3P25.3) CNV | 425 | 206 | 408 | 252
DEL PEAK 6(3P25.3) WILD-TYPE | 260 | 281 | 468 | 168

Figure S254. Get High-res Image Gene #47: 'Del Peak 6(3p25.3)' versus Clinical Feature #10: 'TUMOR.STAGE'

'Del Peak 6(3p25.3)' versus 'RADIATIONS.RADIATION.REGIMENINDICATION'

P value = 2.46e-27 (Fisher's exact test), Q value = 3.8e-24

Table S255. Gene #47: 'Del Peak 6(3p25.3)' versus Clinical Feature #11: 'RADIATIONS.RADIATION.REGIMENINDICATION'

nPatients | NO | YES
--- | --- | ---
ALL | 835 | 3816
DEL PEAK 6(3P25.3) CNV | 162 | 1468
DEL PEAK 6(3P25.3) WILD-TYPE | 673 | 2348

Figure S255. Get High-res Image Gene #47: 'Del Peak 6(3p25.3)' versus Clinical Feature #11: 'RADIATIONS.RADIATION.REGIMENINDICATION'

'Del Peak 6(3p25.3)' versus 'TOBACCOSMOKINGHISTORYINDICATOR'

P value = 8.43e-18 (Chi-square test), Q value = 1.3e-14

Table S256. Gene #47: 'Del Peak 6(3p25.3)' versus Clinical Feature #13: '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 | 15 | 16 | 22 | 25 | 2 | 342 | 208 | 237 | 116
DEL PEAK 6(3P25.3) CNV | 0 | 4 | 5 | 4 | 1 | 240 | 119 | 174 | 63
DEL PEAK 6(3P25.3) WILD-TYPE | 15 | 12 | 17 | 21 | 1 | 102 | 89 | 63 | 53

Figure S256. Get High-res Image Gene #47: 'Del Peak 6(3p25.3)' versus Clinical Feature #13: 'TOBACCOSMOKINGHISTORYINDICATOR'

'Del Peak 7(3p14.2)' versus 'PRIMARY.SITE.OF.DISEASE'

P value = 2.82e-247 (Chi-square test), Q value = 4.9e-244

Table S257. Gene #48: 'Del Peak 7(3p14.2)' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'

nPatients | BLADDER | BRAIN | BREAST | COLON | ENDOMETRIAL | HEAD/NECK | KIDNEY | LUNG | OMENTUM | OVARY | PERITONEUM (OVARY) | RECTUM
--- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | ---
ALL | 131 | 544 | 857 | 412 | 454 | 321 | 493 | 714 | 2 | 548 | 2 | 159
DEL PEAK 7(3P14.2) CNV | 43 | 51 | 260 | 75 | 59 | 242 | 387 | 456 | 1 | 162 | 0 | 27
DEL PEAK 7(3P14.2) WILD-TYPE | 88 | 493 | 597 | 337 | 395 | 79 | 106 | 258 | 1 | 386 | 2 | 132

Figure S257. Get High-res Image Gene #48: 'Del Peak 7(3p14.2)' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'

'Del Peak 7(3p14.2)' versus 'GENDER'

P value = 3.08e-34 (Fisher's exact test), Q value = 4.8e-31

Table S258. Gene #48: 'Del Peak 7(3p14.2)' versus Clinical Feature #4: 'GENDER'

nPatients | FEMALE | MALE
--- | --- | ---
ALL | 2924 | 1717
DEL PEAK 7(3P14.2) CNV | 916 | 849
DEL PEAK 7(3P14.2) WILD-TYPE | 2008 | 868

Figure S258. Get High-res Image Gene #48: 'Del Peak 7(3p14.2)' versus Clinical Feature #4: 'GENDER'

'Del Peak 7(3p14.2)' versus 'KARNOFSKY.PERFORMANCE.SCORE'

P value = 2.12e-05 (t-test), Q value = 0.028

Table S259. Gene #48: 'Del Peak 7(3p14.2)' versus Clinical Feature #5: 'KARNOFSKY.PERFORMANCE.SCORE'

| nPatients | Mean (Std.Dev)
--- | --- | ---
ALL | 641 | 73.6 (23.9)
DEL PEAK 7(3P14.2) CNV | 161 | 64.1 (35.4)
DEL PEAK 7(3P14.2) WILD-TYPE | 480 | 76.8 (17.5)

Figure S259. Get High-res Image Gene #48: 'Del Peak 7(3p14.2)' versus Clinical Feature #5: 'KARNOFSKY.PERFORMANCE.SCORE'

'Del Peak 7(3p14.2)' versus 'HISTOLOGICAL.TYPE'

P value = 1.54e-199 (Chi-square test), Q value = 2.7e-196

Table S260. Gene #48: 'Del Peak 7(3p14.2)' versus Clinical Feature #6: 'HISTOLOGICAL.TYPE'

nPatients | COLON ADENOCARCINOMA | COLON MUCINOUS ADENOCARCINOMA | ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA | HEAD & NECK SQUAMOUS CELL CARCINOMA | INFILTRATING DUCTAL CARCINOMA | INFILTRATING LOBULAR 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 HISTOLOGY (PLEASE SPECIFY) | MIXED SEROUS AND ENDOMETRIOID | MUCINOUS (COLLOID) ADENOCARCINOMA | MUCINOUS (COLLOID) CARCINOMA | MUSCLE INVASIVE UROTHELIAL CARCINOMA (PT2 OR ABOVE) | OTHER SPECIFY | RECTAL ADENOCARCINOMA | RECTAL MUCINOUS ADENOCARCINOMA | SEROUS CYSTADENOCARCINOMA | SEROUS ENDOMETRIAL ADENOCARCINOMA | TREATED PRIMARY GBM | UNTREATED PRIMARY (DE NOVO) GBM
--- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | ---
ALL | 356 | 54 | 351 | 321 | 104 | 12 | 493 | 11 | 79 | 243 | 7 | 4 | 17 | 2 | 3 | 2 | 18 | 1 | 1 | 1 | 3 | 315 | 5 | 18 | 4 | 3 | 49 | 10 | 143 | 13 | 552 | 85 | 1 | 20
DEL PEAK 7(3P14.2) CNV | 69 | 6 | 19 | 242 | 39 | 0 | 387 | 4 | 39 | 115 | 6 | 0 | 6 | 1 | 1 | 0 | 7 | 1 | 0 | 1 | 1 | 270 | 0 | 6 | 3 | 1 | 16 | 4 | 23 | 3 | 163 | 34 | 0 | 2
DEL PEAK 7(3P14.2) WILD-TYPE | 287 | 48 | 332 | 79 | 65 | 12 | 106 | 7 | 40 | 128 | 1 | 4 | 11 | 1 | 2 | 2 | 11 | 0 | 1 | 0 | 2 | 45 | 5 | 12 | 1 | 2 | 33 | 6 | 120 | 10 | 389 | 51 | 1 | 18

Figure S260. Get High-res Image Gene #48: 'Del Peak 7(3p14.2)' versus Clinical Feature #6: 'HISTOLOGICAL.TYPE'

'Del Peak 7(3p14.2)' versus 'PATHOLOGY.T'

P value = 8.81e-20 (Fisher's exact test), Q value = 1.3e-16

Table S261. Gene #48: 'Del Peak 7(3p14.2)' versus Clinical Feature #7: 'PATHOLOGY.T'

nPatients | T0+T1 | T2 | T3 | T4
--- | --- | --- | --- | ---
ALL | 448 | 611 | 688 | 208
DEL PEAK 7(3P14.2) CNV | 324 | 360 | 304 | 124
DEL PEAK 7(3P14.2) WILD-TYPE | 124 | 251 | 384 | 84

Figure S261. Get High-res Image Gene #48: 'Del Peak 7(3p14.2)' versus Clinical Feature #7: 'PATHOLOGY.T'

'Del Peak 7(3p14.2)' versus 'TUMOR.STAGE'

P value = 3.07e-17 (Fisher's exact test), Q value = 4.6e-14

Table S262. Gene #48: 'Del Peak 7(3p14.2)' versus Clinical Feature #10: 'TUMOR.STAGE'

nPatients | I | II | III | IV
--- | --- | --- | --- | ---
ALL | 685 | 487 | 876 | 420
DEL PEAK 7(3P14.2) CNV | 426 | 208 | 379 | 248
DEL PEAK 7(3P14.2) WILD-TYPE | 259 | 279 | 497 | 172

Figure S262. Get High-res Image Gene #48: 'Del Peak 7(3p14.2)' versus Clinical Feature #10: 'TUMOR.STAGE'

'Del Peak 7(3p14.2)' versus 'RADIATIONS.RADIATION.REGIMENINDICATION'

P value = 4.04e-20 (Fisher's exact test), Q value = 6.1e-17

Table S263. Gene #48: 'Del Peak 7(3p14.2)' versus Clinical Feature #11: 'RADIATIONS.RADIATION.REGIMENINDICATION'

nPatients | NO | YES
--- | --- | ---
ALL | 835 | 3816
DEL PEAK 7(3P14.2) CNV | 203 | 1563
DEL PEAK 7(3P14.2) WILD-TYPE | 632 | 2253

Figure S263. Get High-res Image Gene #48: 'Del Peak 7(3p14.2)' versus Clinical Feature #11: 'RADIATIONS.RADIATION.REGIMENINDICATION'

'Del Peak 7(3p14.2)' versus 'TOBACCOSMOKINGHISTORYINDICATOR'

P value = 2.41e-17 (Chi-square test), Q value = 3.6e-14

Table S264. Gene #48: 'Del Peak 7(3p14.2)' versus Clinical Feature #13: '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 | 15 | 16 | 22 | 25 | 2 | 342 | 208 | 237 | 116
DEL PEAK 7(3P14.2) CNV | 1 | 9 | 11 | 4 | 2 | 255 | 126 | 188 | 63
DEL PEAK 7(3P14.2) WILD-TYPE | 14 | 7 | 11 | 21 | 0 | 87 | 82 | 49 | 53

Figure S264. Get High-res Image Gene #48: 'Del Peak 7(3p14.2)' versus Clinical Feature #13: 'TOBACCOSMOKINGHISTORYINDICATOR'

'Del Peak 8(4p16.3)' versus 'PRIMARY.SITE.OF.DISEASE'

P value = 3.49e-53 (Chi-square test), Q value = 5.6e-50

Table S265. Gene #49: 'Del Peak 8(4p16.3)' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'

nPatients | BLADDER | BRAIN | BREAST | COLON | ENDOMETRIAL | HEAD/NECK | KIDNEY | LUNG | OMENTUM | OVARY | PERITONEUM (OVARY) | RECTUM
--- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | ---
ALL | 131 | 544 | 857 | 412 | 454 | 321 | 493 | 714 | 2 | 548 | 2 | 159
DEL PEAK 8(4P16.3) CNV | 46 | 78 | 269 | 117 | 69 | 137 | 67 | 286 | 2 | 223 | 0 | 59
DEL PEAK 8(4P16.3) WILD-TYPE | 85 | 466 | 588 | 295 | 385 | 184 | 426 | 428 | 0 | 325 | 2 | 100

Figure S265. Get High-res Image Gene #49: 'Del Peak 8(4p16.3)' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'

'Del Peak 8(4p16.3)' versus 'HISTOLOGICAL.TYPE'

P value = 6.2e-60 (Chi-square test), Q value = 1e-56

Table S266. Gene #49: 'Del Peak 8(4p16.3)' versus Clinical Feature #6: 'HISTOLOGICAL.TYPE'

nPatients | COLON ADENOCARCINOMA | COLON MUCINOUS ADENOCARCINOMA | ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA | HEAD & NECK SQUAMOUS CELL CARCINOMA | INFILTRATING DUCTAL CARCINOMA | INFILTRATING LOBULAR 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 HISTOLOGY (PLEASE SPECIFY) | MIXED SEROUS AND ENDOMETRIOID | MUCINOUS (COLLOID) ADENOCARCINOMA | MUCINOUS (COLLOID) CARCINOMA | MUSCLE INVASIVE UROTHELIAL CARCINOMA (PT2 OR ABOVE) | OTHER SPECIFY | RECTAL ADENOCARCINOMA | RECTAL MUCINOUS ADENOCARCINOMA | SEROUS CYSTADENOCARCINOMA | SEROUS ENDOMETRIAL ADENOCARCINOMA | TREATED PRIMARY GBM | UNTREATED PRIMARY (DE NOVO) GBM
--- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | ---
ALL | 356 | 54 | 351 | 321 | 104 | 12 | 493 | 11 | 79 | 243 | 7 | 4 | 17 | 2 | 3 | 2 | 18 | 1 | 1 | 1 | 3 | 315 | 5 | 18 | 4 | 3 | 49 | 10 | 143 | 13 | 552 | 85 | 1 | 20
DEL PEAK 8(4P16.3) CNV | 108 | 9 | 27 | 137 | 36 | 0 | 67 | 3 | 19 | 65 | 3 | 0 | 1 | 1 | 0 | 1 | 2 | 1 | 0 | 1 | 1 | 187 | 0 | 4 | 1 | 0 | 18 | 4 | 54 | 4 | 225 | 38 | 0 | 2
DEL PEAK 8(4P16.3) WILD-TYPE | 248 | 45 | 324 | 184 | 68 | 12 | 426 | 8 | 60 | 178 | 4 | 4 | 16 | 1 | 3 | 1 | 16 | 0 | 1 | 0 | 2 | 128 | 5 | 14 | 3 | 3 | 31 | 6 | 89 | 9 | 327 | 47 | 1 | 18

Figure S266. Get High-res Image Gene #49: 'Del Peak 8(4p16.3)' versus Clinical Feature #6: 'HISTOLOGICAL.TYPE'

'Del Peak 8(4p16.3)' versus 'PATHOLOGY.T'

P value = 9.16e-07 (Fisher's exact test), Q value = 0.0012

Table S267. Gene #49: 'Del Peak 8(4p16.3)' versus Clinical Feature #7: 'PATHOLOGY.T'

nPatients | T0+T1 | T2 | T3 | T4
--- | --- | --- | --- | ---
ALL | 448 | 611 | 688 | 208
DEL PEAK 8(4P16.3) CNV | 104 | 224 | 216 | 86
DEL PEAK 8(4P16.3) WILD-TYPE | 344 | 387 | 472 | 122

Figure S267. Get High-res Image Gene #49: 'Del Peak 8(4p16.3)' versus Clinical Feature #7: 'PATHOLOGY.T'

'Del Peak 8(4p16.3)' versus 'PATHOLOGY.N'

P value = 0.000126 (Fisher's exact test), Q value = 0.16

Table S268. Gene #49: 'Del Peak 8(4p16.3)' versus Clinical Feature #8: 'PATHOLOGY.N'

nPatients | N0 | N1 | N2 | N3
--- | --- | --- | --- | ---
ALL | 1036 | 343 | 279 | 11
DEL PEAK 8(4P16.3) CNV | 321 | 130 | 120 | 7
DEL PEAK 8(4P16.3) WILD-TYPE | 715 | 213 | 159 | 4

Figure S268. Get High-res Image Gene #49: 'Del Peak 8(4p16.3)' versus Clinical Feature #8: 'PATHOLOGY.N'

'Del Peak 8(4p16.3)' versus 'TUMOR.STAGE'

P value = 0.000177 (Fisher's exact test), Q value = 0.22

Table S269. Gene #49: 'Del Peak 8(4p16.3)' versus Clinical Feature #10: 'TUMOR.STAGE'

nPatients | I | II | III | IV
--- | --- | --- | --- | ---
ALL | 685 | 487 | 876 | 420
DEL PEAK 8(4P16.3) CNV | 202 | 146 | 324 | 168
DEL PEAK 8(4P16.3) WILD-TYPE | 483 | 341 | 552 | 252

Figure S269. Get High-res Image Gene #49: 'Del Peak 8(4p16.3)' versus Clinical Feature #10: 'TUMOR.STAGE'

'Del Peak 8(4p16.3)' versus 'RADIATIONS.RADIATION.REGIMENINDICATION'

P value = 0.000184 (Fisher's exact test), Q value = 0.23

Table S270. Gene #49: 'Del Peak 8(4p16.3)' versus Clinical Feature #11: 'RADIATIONS.RADIATION.REGIMENINDICATION'

nPatients | NO | YES
--- | --- | ---
ALL | 835 | 3816
DEL PEAK 8(4P16.3) CNV | 200 | 1160
DEL PEAK 8(4P16.3) WILD-TYPE | 635 | 2656

Figure S270. Get High-res Image Gene #49: 'Del Peak 8(4p16.3)' versus Clinical Feature #11: 'RADIATIONS.RADIATION.REGIMENINDICATION'

'Del Peak 9(4q22.1)' versus 'PRIMARY.SITE.OF.DISEASE'

P value = 1.3e-123 (Chi-square test), Q value = 2.2e-120

Table S271. Gene #50: 'Del Peak 9(4q22.1)' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'

nPatients | BLADDER | BRAIN | BREAST | COLON | ENDOMETRIAL | HEAD/NECK | KIDNEY | LUNG | OMENTUM | OVARY | PERITONEUM (OVARY) | RECTUM
--- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | ---
ALL | 131 | 544 | 857 | 412 | 454 | 321 | 493 | 714 | 2 | 548 | 2 | 159
DEL PEAK 9(4Q22.1) CNV | 52 | 58 | 237 | 125 | 79 | 102 | 67 | 304 | 2 | 367 | 1 | 69
DEL PEAK 9(4Q22.1) WILD-TYPE | 79 | 486 | 620 | 287 | 375 | 219 | 426 | 410 | 0 | 181 | 1 | 90

Figure S271. Get High-res Image Gene #50: 'Del Peak 9(4q22.1)' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'

'Del Peak 9(4q22.1)' versus 'HISTOLOGICAL.TYPE'

P value = 3.96e-108 (Chi-square test), Q value = 6.6e-105

Table S272. Gene #50: 'Del Peak 9(4q22.1)' versus Clinical Feature #6: 'HISTOLOGICAL.TYPE'

nPatients | COLON ADENOCARCINOMA | COLON MUCINOUS ADENOCARCINOMA | ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA | HEAD & NECK SQUAMOUS CELL CARCINOMA | INFILTRATING DUCTAL CARCINOMA | INFILTRATING LOBULAR 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 HISTOLOGY (PLEASE SPECIFY) | MIXED SEROUS AND ENDOMETRIOID | MUCINOUS (COLLOID) ADENOCARCINOMA | MUCINOUS (COLLOID) CARCINOMA | MUSCLE INVASIVE UROTHELIAL CARCINOMA (PT2 OR ABOVE) | OTHER SPECIFY | RECTAL ADENOCARCINOMA | RECTAL MUCINOUS ADENOCARCINOMA | SEROUS CYSTADENOCARCINOMA | SEROUS ENDOMETRIAL ADENOCARCINOMA | TREATED PRIMARY GBM | UNTREATED PRIMARY (DE NOVO) GBM
--- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | ---
ALL | 356 | 54 | 351 | 321 | 104 | 12 | 493 | 11 | 79 | 243 | 7 | 4 | 17 | 2 | 3 | 2 | 18 | 1 | 1 | 1 | 3 | 315 | 5 | 18 | 4 | 3 | 49 | 10 | 143 | 13 | 552 | 85 | 1 | 20
DEL PEAK 9(4Q22.1) CNV | 116 | 9 | 25 | 102 | 29 | 0 | 67 | 2 | 21 | 85 | 3 | 0 | 3 | 2 | 1 | 0 | 4 | 1 | 0 | 1 | 1 | 179 | 0 | 5 | 1 | 0 | 24 | 3 | 64 | 4 | 370 | 49 | 0 | 0
DEL PEAK 9(4Q22.1) WILD-TYPE | 240 | 45 | 326 | 219 | 75 | 12 | 426 | 9 | 58 | 158 | 4 | 4 | 14 | 0 | 2 | 2 | 14 | 0 | 1 | 0 | 2 | 136 | 5 | 13 | 3 | 3 | 25 | 7 | 79 | 9 | 182 | 36 | 1 | 20

Figure S272. Get High-res Image Gene #50: 'Del Peak 9(4q22.1)' versus Clinical Feature #6: 'HISTOLOGICAL.TYPE'

'Del Peak 9(4q22.1)' versus 'PATHOLOGY.T'

P value = 3.4e-08 (Fisher's exact test), Q value = 4.7e-05

Table S273. Gene #50: 'Del Peak 9(4q22.1)' versus Clinical Feature #7: 'PATHOLOGY.T'

nPatients | T0+T1 | T2 | T3 | T4
--- | --- | --- | --- | ---
ALL | 448 | 611 | 688 | 208
DEL PEAK 9(4Q22.1) CNV | 93 | 227 | 231 | 75
DEL PEAK 9(4Q22.1) WILD-TYPE | 355 | 384 | 457 | 133

Figure S273. Get High-res Image Gene #50: 'Del Peak 9(4q22.1)' versus Clinical Feature #7: 'PATHOLOGY.T'

'Del Peak 9(4q22.1)' versus 'TUMOR.STAGE'

P value = 8.59e-22 (Fisher's exact test), Q value = 1.3e-18

Table S274. Gene #50: 'Del Peak 9(4q22.1)' versus Clinical Feature #10: 'TUMOR.STAGE'

nPatients | I | II | III | IV
--- | --- | --- | --- | ---
ALL | 685 | 487 | 876 | 420
DEL PEAK 9(4Q22.1) CNV | 206 | 154 | 461 | 159
DEL PEAK 9(4Q22.1) WILD-TYPE | 479 | 333 | 415 | 261

Figure S274. Get High-res Image Gene #50: 'Del Peak 9(4q22.1)' versus Clinical Feature #10: 'TUMOR.STAGE'

'Del Peak 9(4q22.1)' versus 'RADIATIONS.RADIATION.REGIMENINDICATION'

P value = 1.72e-14 (Fisher's exact test), Q value = 2.5e-11

Table S275. Gene #50: 'Del Peak 9(4q22.1)' versus Clinical Feature #11: 'RADIATIONS.RADIATION.REGIMENINDICATION'

nPatients | NO | YES
--- | --- | ---
ALL | 835 | 3816
DEL PEAK 9(4Q22.1) CNV | 174 | 1303
DEL PEAK 9(4Q22.1) WILD-TYPE | 661 | 2513

Figure S275. Get High-res Image Gene #50: 'Del Peak 9(4q22.1)' versus Clinical Feature #11: 'RADIATIONS.RADIATION.REGIMENINDICATION'

'Del Peak 10(4q34.3)' versus 'PRIMARY.SITE.OF.DISEASE'

P value = 2.74e-125 (Chi-square test), Q value = 4.6e-122

Table S276. Gene #51: 'Del Peak 10(4q34.3)' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'

nPatients | BLADDER | BRAIN | BREAST | COLON | ENDOMETRIAL | HEAD/NECK | KIDNEY | LUNG | OMENTUM | OVARY | PERITONEUM (OVARY) | RECTUM
--- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | ---
ALL | 131 | 544 | 857 | 412 | 454 | 321 | 493 | 714 | 2 | 548 | 2 | 159
DEL PEAK 10(4Q34.3) CNV | 56 | 89 | 274 | 132 | 97 | 118 | 76 | 357 | 2 | 396 | 1 | 70
DEL PEAK 10(4Q34.3) WILD-TYPE | 75 | 455 | 583 | 280 | 357 | 203 | 417 | 357 | 0 | 152 | 1 | 89

Figure S276. Get High-res Image Gene #51: 'Del Peak 10(4q34.3)' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'

'Del Peak 10(4q34.3)' versus 'HISTOLOGICAL.TYPE'

P value = 1.47e-119 (Chi-square test), Q value = 2.5e-116

Table S277. Gene #51: 'Del Peak 10(4q34.3)' versus Clinical Feature #6: 'HISTOLOGICAL.TYPE'

nPatients | COLON ADENOCARCINOMA | COLON MUCINOUS ADENOCARCINOMA | ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA | HEAD & NECK SQUAMOUS CELL CARCINOMA | INFILTRATING DUCTAL CARCINOMA | INFILTRATING LOBULAR 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 HISTOLOGY (PLEASE SPECIFY) | MIXED SEROUS AND ENDOMETRIOID | MUCINOUS (COLLOID) ADENOCARCINOMA | MUCINOUS (COLLOID) CARCINOMA | MUSCLE INVASIVE UROTHELIAL CARCINOMA (PT2 OR ABOVE) | OTHER SPECIFY | RECTAL ADENOCARCINOMA | RECTAL MUCINOUS ADENOCARCINOMA | SEROUS CYSTADENOCARCINOMA | SEROUS ENDOMETRIAL ADENOCARCINOMA | TREATED PRIMARY GBM | UNTREATED PRIMARY (DE NOVO) GBM
--- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | ---
ALL | 356 | 54 | 351 | 321 | 104 | 12 | 493 | 11 | 79 | 243 | 7 | 4 | 17 | 2 | 3 | 2 | 18 | 1 | 1 | 1 | 3 | 315 | 5 | 18 | 4 | 3 | 49 | 10 | 143 | 13 | 552 | 85 | 1 | 20
DEL PEAK 10(4Q34.3) CNV | 121 | 11 | 35 | 118 | 39 | 0 | 76 | 3 | 32 | 94 | 3 | 0 | 4 | 2 | 1 | 0 | 4 | 1 | 0 | 1 | 2 | 209 | 0 | 6 | 1 | 0 | 23 | 3 | 66 | 3 | 399 | 56 | 0 | 3
DEL PEAK 10(4Q34.3) WILD-TYPE | 235 | 43 | 316 | 203 | 65 | 12 | 417 | 8 | 47 | 149 | 4 | 4 | 13 | 0 | 2 | 2 | 14 | 0 | 1 | 0 | 1 | 106 | 5 | 12 | 3 | 3 | 26 | 7 | 77 | 10 | 153 | 29 | 1 | 17

Figure S277. Get High-res Image Gene #51: 'Del Peak 10(4q34.3)' versus Clinical Feature #6: 'HISTOLOGICAL.TYPE'

'Del Peak 10(4q34.3)' versus 'PATHOLOGY.T'

P value = 5.9e-09 (Fisher's exact test), Q value = 8.3e-06

Table S278. Gene #51: 'Del Peak 10(4q34.3)' versus Clinical Feature #7: 'PATHOLOGY.T'

nPatients | T0+T1 | T2 | T3 | T4
--- | --- | --- | --- | ---
ALL | 448 | 611 | 688 | 208
DEL PEAK 10(4Q34.3) CNV | 112 | 267 | 245 | 82
DEL PEAK 10(4Q34.3) WILD-TYPE | 336 | 344 | 443 | 126

Figure S278. Get High-res Image Gene #51: 'Del Peak 10(4q34.3)' versus Clinical Feature #7: 'PATHOLOGY.T'

'Del Peak 10(4q34.3)' versus 'TUMOR.STAGE'

P value = 8.71e-16 (Fisher's exact test), Q value = 1.3e-12

Table S279. Gene #51: 'Del Peak 10(4q34.3)' versus Clinical Feature #10: 'TUMOR.STAGE'

nPatients | I | II | III | IV
--- | --- | --- | --- | ---
ALL | 685 | 487 | 876 | 420
DEL PEAK 10(4Q34.3) CNV | 241 | 183 | 482 | 180
DEL PEAK 10(4Q34.3) WILD-TYPE | 444 | 304 | 394 | 240

Figure S279. Get High-res Image Gene #51: 'Del Peak 10(4q34.3)' versus Clinical Feature #10: 'TUMOR.STAGE'

'Del Peak 10(4q34.3)' versus 'RADIATIONS.RADIATION.REGIMENINDICATION'

P value = 7.92e-11 (Fisher's exact test), Q value = 1.1e-07

Table S280. Gene #51: 'Del Peak 10(4q34.3)' versus Clinical Feature #11: 'RADIATIONS.RADIATION.REGIMENINDICATION'

nPatients | NO | YES
--- | --- | ---
ALL | 835 | 3816
DEL PEAK 10(4Q34.3) CNV | 221 | 1459
DEL PEAK 10(4Q34.3) WILD-TYPE | 614 | 2357

Figure S280. Get High-res Image Gene #51: 'Del Peak 10(4q34.3)' versus Clinical Feature #11: 'RADIATIONS.RADIATION.REGIMENINDICATION'

'Del Peak 11(5q11.2)' versus 'PRIMARY.SITE.OF.DISEASE'

P value = 5.24e-169 (Chi-square test), Q value = 9e-166

Table S281. Gene #52: 'Del Peak 11(5q11.2)' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'

nPatients | BLADDER | BRAIN | BREAST | COLON | ENDOMETRIAL | HEAD/NECK | KIDNEY | LUNG | OMENTUM | OVARY | PERITONEUM (OVARY) | RECTUM
--- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | ---
ALL | 131 | 544 | 857 | 412 | 454 | 321 | 493 | 714 | 2 | 548 | 2 | 159
DEL PEAK 11(5Q11.2) CNV | 68 | 43 | 216 | 91 | 81 | 134 | 10 | 377 | 2 | 326 | 1 | 49
DEL PEAK 11(5Q11.2) WILD-TYPE | 63 | 501 | 641 | 321 | 373 | 187 | 483 | 337 | 0 | 222 | 1 | 110

Figure S281. Get High-res Image Gene #52: 'Del Peak 11(5q11.2)' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'

'Del Peak 11(5q11.2)' versus 'KARNOFSKY.PERFORMANCE.SCORE'

P value = 8.31e-05 (t-test), Q value = 0.1

Table S282. Gene #52: 'Del Peak 11(5q11.2)' versus Clinical Feature #5: 'KARNOFSKY.PERFORMANCE.SCORE'

| nPatients | Mean (Std.Dev)
--- | --- | ---
ALL | 641 | 73.6 (23.9)
DEL PEAK 11(5Q11.2) CNV | 152 | 65.3 (31.2)
DEL PEAK 11(5Q11.2) WILD-TYPE | 489 | 76.2 (20.6)

Figure S282. Get High-res Image Gene #52: 'Del Peak 11(5q11.2)' versus Clinical Feature #5: 'KARNOFSKY.PERFORMANCE.SCORE'

'Del Peak 11(5q11.2)' versus 'HISTOLOGICAL.TYPE'

P value = 1.1e-150 (Chi-square test), Q value = 1.9e-147

Table S283. Gene #52: 'Del Peak 11(5q11.2)' versus Clinical Feature #6: 'HISTOLOGICAL.TYPE'

nPatients | COLON ADENOCARCINOMA | COLON MUCINOUS ADENOCARCINOMA | ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA | HEAD & NECK SQUAMOUS CELL CARCINOMA | INFILTRATING DUCTAL CARCINOMA | INFILTRATING LOBULAR 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 HISTOLOGY (PLEASE SPECIFY) | MIXED SEROUS AND ENDOMETRIOID | MUCINOUS (COLLOID) ADENOCARCINOMA | MUCINOUS (COLLOID) CARCINOMA | MUSCLE INVASIVE UROTHELIAL CARCINOMA (PT2 OR ABOVE) | OTHER SPECIFY | RECTAL ADENOCARCINOMA | RECTAL MUCINOUS ADENOCARCINOMA | SEROUS CYSTADENOCARCINOMA | SEROUS ENDOMETRIAL ADENOCARCINOMA | TREATED PRIMARY GBM | UNTREATED PRIMARY (DE NOVO) GBM
--- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | ---
ALL | 356 | 54 | 351 | 321 | 104 | 12 | 493 | 11 | 79 | 243 | 7 | 4 | 17 | 2 | 3 | 2 | 18 | 1 | 1 | 1 | 3 | 315 | 5 | 18 | 4 | 3 | 49 | 10 | 143 | 13 | 552 | 85 | 1 | 20
DEL PEAK 11(5Q11.2) CNV | 84 | 7 | 29 | 134 | 35 | 0 | 10 | 4 | 28 | 91 | 5 | 0 | 3 | 0 | 2 | 1 | 5 | 1 | 0 | 0 | 3 | 233 | 2 | 2 | 1 | 0 | 20 | 3 | 46 | 2 | 329 | 50 | 0 | 0
DEL PEAK 11(5Q11.2) WILD-TYPE | 272 | 47 | 322 | 187 | 69 | 12 | 483 | 7 | 51 | 152 | 2 | 4 | 14 | 2 | 1 | 1 | 13 | 0 | 1 | 1 | 0 | 82 | 3 | 16 | 3 | 3 | 29 | 7 | 97 | 11 | 223 | 35 | 1 | 20

Figure S283. Get High-res Image Gene #52: 'Del Peak 11(5q11.2)' versus Clinical Feature #6: 'HISTOLOGICAL.TYPE'

'Del Peak 11(5q11.2)' versus 'PATHOLOGY.T'

P value = 3.14e-17 (Fisher's exact test), Q value = 4.7e-14

Table S284. Gene #52: 'Del Peak 11(5q11.2)' versus Clinical Feature #7: 'PATHOLOGY.T'

nPatients | T0+T1 | T2 | T3 | T4
--- | --- | --- | --- | ---
ALL | 448 | 611 | 688 | 208
DEL PEAK 11(5Q11.2) CNV | 107 | 261 | 157 | 85
DEL PEAK 11(5Q11.2) WILD-TYPE | 341 | 350 | 531 | 123

Figure S284. Get High-res Image Gene #52: 'Del Peak 11(5q11.2)' versus Clinical Feature #7: 'PATHOLOGY.T'

'Del Peak 11(5q11.2)' versus 'PATHOLOGY.N'

P value = 2.66e-05 (Fisher's exact test), Q value = 0.034

Table S285. Gene #52: 'Del Peak 11(5q11.2)' versus Clinical Feature #8: 'PATHOLOGY.N'

nPatients | N0 | N1 | N2 | N3
--- | --- | --- | --- | ---
ALL | 1036 | 343 | 279 | 11
DEL PEAK 11(5Q11.2) CNV | 320 | 150 | 113 | 5
DEL PEAK 11(5Q11.2) WILD-TYPE | 716 | 193 | 166 | 6

Figure S285. Get High-res Image Gene #52: 'Del Peak 11(5q11.2)' versus Clinical Feature #8: 'PATHOLOGY.N'

'Del Peak 11(5q11.2)' versus 'TUMOR.STAGE'

P value = 4.37e-06 (Fisher's exact test), Q value = 0.0058

Table S286. Gene #52: 'Del Peak 11(5q11.2)' versus Clinical Feature #10: 'TUMOR.STAGE'

nPatients | I | II | III | IV
--- | --- | --- | --- | ---
ALL | 685 | 487 | 876 | 420
DEL PEAK 11(5Q11.2) CNV | 214 | 164 | 378 | 168
DEL PEAK 11(5Q11.2) WILD-TYPE | 471 | 323 | 498 | 252

Figure S286. Get High-res Image Gene #52: 'Del Peak 11(5q11.2)' versus Clinical Feature #10: 'TUMOR.STAGE'

'Del Peak 11(5q11.2)' versus 'RADIATIONS.RADIATION.REGIMENINDICATION'

P value = 9.91e-14 (Fisher's exact test), Q value = 1.5e-10

Table S287. Gene #52: 'Del Peak 11(5q11.2)' versus Clinical Feature #11: 'RADIATIONS.RADIATION.REGIMENINDICATION'

nPatients | NO | YES
--- | --- | ---
ALL | 835 | 3816
DEL PEAK 11(5Q11.2) CNV | 165 | 1239
DEL PEAK 11(5Q11.2) WILD-TYPE | 670 | 2577

Figure S287. Get High-res Image Gene #52: 'Del Peak 11(5q11.2)' versus Clinical Feature #11: 'RADIATIONS.RADIATION.REGIMENINDICATION'

'Del Peak 11(5q11.2)' versus 'NUMBERPACKYEARSSMOKED'

P value = 6.24e-06 (t-test), Q value = 0.0083

Table S288. Gene #52: 'Del Peak 11(5q11.2)' versus Clinical Feature #12: 'NUMBERPACKYEARSSMOKED'

| nPatients | Mean (Std.Dev)
--- | --- | ---
ALL | 804 | 46.7 (32.6)
DEL PEAK 11(5Q11.2) CNV | 415 | 51.7 (34.6)
DEL PEAK 11(5Q11.2) WILD-TYPE | 389 | 41.4 (29.6)

Figure S288. Get High-res Image Gene #52: 'Del Peak 11(5q11.2)' versus Clinical Feature #12: 'NUMBERPACKYEARSSMOKED'

'Del Peak 11(5q11.2)' versus 'TOBACCOSMOKINGHISTORYINDICATOR'

P value = 5.67e-05 (Chi-square test), Q value = 0.072

Table S289. Gene #52: 'Del Peak 11(5q11.2)' versus Clinical Feature #13: '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 | 15 | 16 | 22 | 25 | 2 | 342 | 208 | 237 | 116
DEL PEAK 11(5Q11.2) CNV | 9 | 6 | 15 | 16 | 0 | 200 | 95 | 130 | 39
DEL PEAK 11(5Q11.2) WILD-TYPE | 6 | 10 | 7 | 9 | 2 | 142 | 113 | 107 | 77

Figure S289. Get High-res Image Gene #52: 'Del Peak 11(5q11.2)' versus Clinical Feature #13: 'TOBACCOSMOKINGHISTORYINDICATOR'

'Del Peak 11(5q11.2)' versus 'NEOPLASM.DISEASESTAGE'

P value = 2.6e-05 (Chi-square test), Q value = 0.034

Table S290. Gene #52: 'Del Peak 11(5q11.2)' versus Clinical Feature #20: '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 X
--- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | ---
ALL | 71 | 45 | 2 | 34 | 246 | 165 | 29 | 107 | 22 | 36 | 35 | 12
DEL PEAK 11(5Q11.2) CNV | 18 | 7 | 1 | 17 | 67 | 42 | 10 | 25 | 4 | 5 | 22 | 3
DEL PEAK 11(5Q11.2) WILD-TYPE | 53 | 38 | 1 | 17 | 179 | 123 | 19 | 82 | 18 | 31 | 13 | 9

Figure S290. Get High-res Image Gene #52: 'Del Peak 11(5q11.2)' versus Clinical Feature #20: 'NEOPLASM.DISEASESTAGE'

'Del Peak 12(5q21.3)' versus 'PRIMARY.SITE.OF.DISEASE'

P value = 8.65e-176 (Chi-square test), Q value = 1.5e-172

Table S291. Gene #53: 'Del Peak 12(5q21.3)' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'

nPatients | BLADDER | BRAIN | BREAST | COLON | ENDOMETRIAL | HEAD/NECK | KIDNEY | LUNG | OMENTUM | OVARY | PERITONEUM (OVARY) | RECTUM
--- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | ---
ALL | 131 | 544 | 857 | 412 | 454 | 321 | 493 | 714 | 2 | 548 | 2 | 159
DEL PEAK 12(5Q21.3) CNV | 67 | 43 | 213 | 117 | 70 | 128 | 5 | 406 | 2 | 311 | 1 | 51
DEL PEAK 12(5Q21.3) WILD-TYPE | 64 | 501 | 644 | 295 | 384 | 193 | 488 | 308 | 0 | 237 | 1 | 108

Figure S291. Get High-res Image Gene #53: 'Del Peak 12(5q21.3)' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'

'Del Peak 12(5q21.3)' versus 'KARNOFSKY.PERFORMANCE.SCORE'

P value = 1.8e-05 (t-test), Q value = 0.023

Table S292. Gene #53: 'Del Peak 12(5q21.3)' versus Clinical Feature #5: 'KARNOFSKY.PERFORMANCE.SCORE'

| nPatients | Mean (Std.Dev)
--- | --- | ---
ALL | 641 | 73.6 (23.9)
DEL PEAK 12(5Q21.3) CNV | 149 | 64.2 (32.2)
DEL PEAK 12(5Q21.3) WILD-TYPE | 492 | 76.4 (20.0)

Figure S292. Get High-res Image Gene #53: 'Del Peak 12(5q21.3)' versus Clinical Feature #5: 'KARNOFSKY.PERFORMANCE.SCORE'

'Del Peak 12(5q21.3)' versus 'HISTOLOGICAL.TYPE'

P value = 8.17e-150 (Chi-square test), Q value = 1.4e-146

Table S293. Gene #53: 'Del Peak 12(5q21.3)' versus Clinical Feature #6: 'HISTOLOGICAL.TYPE'

nPatients | COLON ADENOCARCINOMA | COLON MUCINOUS ADENOCARCINOMA | ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA | HEAD & NECK SQUAMOUS CELL CARCINOMA | INFILTRATING DUCTAL CARCINOMA | INFILTRATING LOBULAR 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 HISTOLOGY (PLEASE SPECIFY) | MIXED SEROUS AND ENDOMETRIOID | MUCINOUS (COLLOID) ADENOCARCINOMA | MUCINOUS (COLLOID) CARCINOMA | MUSCLE INVASIVE UROTHELIAL CARCINOMA (PT2 OR ABOVE) | OTHER SPECIFY | RECTAL ADENOCARCINOMA | RECTAL MUCINOUS ADENOCARCINOMA | SEROUS CYSTADENOCARCINOMA | SEROUS ENDOMETRIAL ADENOCARCINOMA | TREATED PRIMARY GBM | UNTREATED PRIMARY (DE NOVO) GBM
--- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | ---
ALL | 356 | 54 | 351 | 321 | 104 | 12 | 493 | 11 | 79 | 243 | 7 | 4 | 17 | 2 | 3 | 2 | 18 | 1 | 1 | 1 | 3 | 315 | 5 | 18 | 4 | 3 | 49 | 10 | 143 | 13 | 552 | 85 | 1 | 20
DEL PEAK 12(5Q21.3) CNV | 107 | 10 | 23 | 128 | 34 | 0 | 5 | 5 | 34 | 99 | 5 | 0 | 4 | 1 | 2 | 1 | 6 | 1 | 0 | 1 | 3 | 243 | 2 | 3 | 1 | 0 | 17 | 3 | 48 | 2 | 314 | 44 | 0 | 0
DEL PEAK 12(5Q21.3) WILD-TYPE | 249 | 44 | 328 | 193 | 70 | 12 | 488 | 6 | 45 | 144 | 2 | 4 | 13 | 1 | 1 | 1 | 12 | 0 | 1 | 0 | 0 | 72 | 3 | 15 | 3 | 3 | 32 | 7 | 95 | 11 | 238 | 41 | 1 | 20

Figure S293. Get High-res Image Gene #53: 'Del Peak 12(5q21.3)' versus Clinical Feature #6: 'HISTOLOGICAL.TYPE'

'Del Peak 12(5q21.3)' versus 'PATHOLOGY.T'

P value = 3.33e-16 (Fisher's exact test), Q value = 5e-13

Table S294. Gene #53: 'Del Peak 12(5q21.3)' versus Clinical Feature #7: 'PATHOLOGY.T'

nPatients | T0+T1 | T2 | T3 | T4
--- | --- | --- | --- | ---
ALL | 448 | 611 | 688 | 208
DEL PEAK 12(5Q21.3) CNV | 113 | 276 | 177 | 86
DEL PEAK 12(5Q21.3) WILD-TYPE | 335 | 335 | 511 | 122

Figure S294. Get High-res Image Gene #53: 'Del Peak 12(5q21.3)' versus Clinical Feature #7: 'PATHOLOGY.T'

'Del Peak 12(5q21.3)' versus 'PATHOLOGY.N'

P value = 1.5e-05 (Fisher's exact test), Q value = 0.02

Table S295. Gene #53: 'Del Peak 12(5q21.3)' versus Clinical Feature #8: 'PATHOLOGY.N'

nPatients | N0 | N1 | N2 | N3
--- | --- | --- | --- | ---
ALL | 1036 | 343 | 279 | 11
DEL PEAK 12(5Q21.3) CNV | 346 | 162 | 116 | 6
DEL PEAK 12(5Q21.3) WILD-TYPE | 690 | 181 | 163 | 5

Figure S295. Get High-res Image Gene #53: 'Del Peak 12(5q21.3)' versus Clinical Feature #8: 'PATHOLOGY.N'

'Del Peak 12(5q21.3)' versus 'PATHOLOGICSPREAD(M)'

P value = 4.4e-05 (Chi-square test), Q value = 0.056

Table S296. Gene #53: 'Del Peak 12(5q21.3)' versus Clinical Feature #9: 'PATHOLOGICSPREAD(M)'

nPatients | M0 | M1 | M1A | M1B | MX
--- | --- | --- | --- | --- | ---
ALL | 1398 | 167 | 9 | 1 | 148
DEL PEAK 12(5Q21.3) CNV | 437 | 40 | 6 | 0 | 69
DEL PEAK 12(5Q21.3) WILD-TYPE | 961 | 127 | 3 | 1 | 79

Figure S296. Get High-res Image Gene #53: 'Del Peak 12(5q21.3)' versus Clinical Feature #9: 'PATHOLOGICSPREAD(M)'

'Del Peak 12(5q21.3)' versus 'RADIATIONS.RADIATION.REGIMENINDICATION'

P value = 1.72e-14 (Fisher's exact test), Q value = 2.5e-11

Table S297. Gene #53: 'Del Peak 12(5q21.3)' versus Clinical Feature #11: 'RADIATIONS.RADIATION.REGIMENINDICATION'

nPatients | NO | YES
--- | --- | ---
ALL | 835 | 3816
DEL PEAK 12(5Q21.3) CNV | 165 | 1256
DEL PEAK 12(5Q21.3) WILD-TYPE | 670 | 2560

Figure S297. Get High-res Image Gene #53: 'Del Peak 12(5q21.3)' versus Clinical Feature #11: 'RADIATIONS.RADIATION.REGIMENINDICATION'

'Del Peak 12(5q21.3)' versus 'TOBACCOSMOKINGHISTORYINDICATOR'

P value = 3.54e-05 (Chi-square test), Q value = 0.045

Table S298. Gene #53: 'Del Peak 12(5q21.3)' versus Clinical Feature #13: '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 | 15 | 16 | 22 | 25 | 2 | 342 | 208 | 237 | 116
DEL PEAK 12(5Q21.3) CNV | 10 | 8 | 15 | 14 | 1 | 206 | 100 | 139 | 38
DEL PEAK 12(5Q21.3) WILD-TYPE | 5 | 8 | 7 | 11 | 1 | 136 | 108 | 98 | 78

Figure S298. Get High-res Image Gene #53: 'Del Peak 12(5q21.3)' versus Clinical Feature #13: 'TOBACCOSMOKINGHISTORYINDICATOR'

'Del Peak 12(5q21.3)' versus 'NEOPLASM.DISEASESTAGE'

P value = 9.36e-06 (Chi-square test), Q value = 0.012

Table S299. Gene #53: 'Del Peak 12(5q21.3)' versus Clinical Feature #20: '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 X
--- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | ---
ALL | 71 | 45 | 2 | 34 | 246 | 165 | 29 | 107 | 22 | 36 | 35 | 12
DEL PEAK 12(5Q21.3) CNV | 17 | 6 | 1 | 16 | 72 | 39 | 11 | 22 | 3 | 7 | 22 | 4
DEL PEAK 12(5Q21.3) WILD-TYPE | 54 | 39 | 1 | 18 | 174 | 126 | 18 | 85 | 19 | 29 | 13 | 8

Figure S299. Get High-res Image Gene #53: 'Del Peak 12(5q21.3)' versus Clinical Feature #20: 'NEOPLASM.DISEASESTAGE'

'Del Peak 13(6p25.3)' versus 'PRIMARY.SITE.OF.DISEASE'

P value = 3.78e-16 (Chi-square test), Q value = 5.6e-13

Table S300. Gene #54: 'Del Peak 13(6p25.3)' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'

nPatients | BLADDER | BRAIN | BREAST | COLON | ENDOMETRIAL | HEAD/NECK | KIDNEY | LUNG | OMENTUM | OVARY | PERITONEUM (OVARY) | RECTUM
--- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | ---
ALL | 131 | 544 | 857 | 412 | 454 | 321 | 493 | 714 | 2 | 548 | 2 | 159
DEL PEAK 13(6P25.3) CNV | 34 | 84 | 160 | 54 | 14 | 64 | 93 | 134 | 0 | 126 | 0 | 21
DEL PEAK 13(6P25.3) WILD-TYPE | 97 | 460 | 697 | 358 | 440 | 257 | 400 | 580 | 2 | 422 | 2 | 138

Figure S300. Get High-res Image Gene #54: 'Del Peak 13(6p25.3)' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'

'Del Peak 13(6p25.3)' versus 'GENDER'

P value = 7.04e-05 (Fisher's exact test), Q value = 0.089

Table S301. Gene #54: 'Del Peak 13(6p25.3)' versus Clinical Feature #4: 'GENDER'

nPatients | FEMALE | MALE
--- | --- | ---
ALL | 2924 | 1717
DEL PEAK 13(6P25.3) CNV | 446 | 341
DEL PEAK 13(6P25.3) WILD-TYPE | 2478 | 1376

Figure S301. Get High-res Image Gene #54: 'Del Peak 13(6p25.3)' versus Clinical Feature #4: 'GENDER'

'Del Peak 13(6p25.3)' versus 'HISTOLOGICAL.TYPE'

P value = 1.05e-13 (Chi-square test), Q value = 1.5e-10

Table S302. Gene #54: 'Del Peak 13(6p25.3)' versus Clinical Feature #6: 'HISTOLOGICAL.TYPE'

nPatients | COLON ADENOCARCINOMA | COLON MUCINOUS ADENOCARCINOMA | ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA | HEAD & NECK SQUAMOUS CELL CARCINOMA | INFILTRATING DUCTAL CARCINOMA | INFILTRATING LOBULAR 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 HISTOLOGY (PLEASE SPECIFY) | MIXED SEROUS AND ENDOMETRIOID | MUCINOUS (COLLOID) ADENOCARCINOMA | MUCINOUS (COLLOID) CARCINOMA | MUSCLE INVASIVE UROTHELIAL CARCINOMA (PT2 OR ABOVE) | OTHER SPECIFY | RECTAL ADENOCARCINOMA | RECTAL MUCINOUS ADENOCARCINOMA | SEROUS CYSTADENOCARCINOMA | SEROUS ENDOMETRIAL ADENOCARCINOMA | TREATED PRIMARY GBM | UNTREATED PRIMARY (DE NOVO) GBM
--- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | ---
ALL | 356 | 54 | 351 | 321 | 104 | 12 | 493 | 11 | 79 | 243 | 7 | 4 | 17 | 2 | 3 | 2 | 18 | 1 | 1 | 1 | 3 | 315 | 5 | 18 | 4 | 3 | 49 | 10 | 143 | 13 | 552 | 85 | 1 | 20
DEL PEAK 13(6P25.3) CNV | 49 | 5 | 6 | 64 | 15 | 2 | 93 | 1 | 9 | 33 | 2 | 0 | 2 | 0 | 0 | 0 | 3 | 1 | 0 | 0 | 0 | 82 | 0 | 1 | 1 | 0 | 12 | 4 | 18 | 3 | 126 | 7 | 0 | 5
DEL PEAK 13(6P25.3) WILD-TYPE | 307 | 49 | 345 | 257 | 89 | 10 | 400 | 10 | 70 | 210 | 5 | 4 | 15 | 2 | 3 | 2 | 15 | 0 | 1 | 1 | 3 | 233 | 5 | 17 | 3 | 3 | 37 | 6 | 125 | 10 | 426 | 78 | 1 | 15

Figure S302. Get High-res Image Gene #54: 'Del Peak 13(6p25.3)' versus Clinical Feature #6: 'HISTOLOGICAL.TYPE'

'Del Peak 14(6q22.31)' versus 'PRIMARY.SITE.OF.DISEASE'

P value = 3.9e-93 (Chi-square test), Q value = 6.4e-90

Table S303. Gene #55: 'Del Peak 14(6q22.31)' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'

nPatients | BLADDER | BRAIN | BREAST | COLON | ENDOMETRIAL | HEAD/NECK | KIDNEY | LUNG | OMENTUM | OVARY | PERITONEUM (OVARY) | RECTUM
--- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | ---
ALL | 131 | 544 | 857 | 412 | 454 | 321 | 493 | 714 | 2 | 548 | 2 | 159
DEL PEAK 14(6Q22.31) CNV | 52 | 152 | 260 | 57 | 25 | 54 | 138 | 274 | 2 | 315 | 2 | 25
DEL PEAK 14(6Q22.31) WILD-TYPE | 79 | 392 | 597 | 355 | 429 | 267 | 355 | 440 | 0 | 233 | 0 | 134

Figure S303. Get High-res Image Gene #55: 'Del Peak 14(6q22.31)' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'

'Del Peak 14(6q22.31)' versus 'HISTOLOGICAL.TYPE'

P value = 1.53e-94 (Chi-square test), Q value = 2.5e-91

Table S304. Gene #55: 'Del Peak 14(6q22.31)' versus Clinical Feature #6: 'HISTOLOGICAL.TYPE'

nPatients | COLON ADENOCARCINOMA | COLON MUCINOUS ADENOCARCINOMA | ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA | HEAD & NECK SQUAMOUS CELL CARCINOMA | INFILTRATING DUCTAL CARCINOMA | INFILTRATING LOBULAR 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 HISTOLOGY (PLEASE SPECIFY) | MIXED SEROUS AND ENDOMETRIOID | MUCINOUS (COLLOID) ADENOCARCINOMA | MUCINOUS (COLLOID) CARCINOMA | MUSCLE INVASIVE UROTHELIAL CARCINOMA (PT2 OR ABOVE) | OTHER SPECIFY | RECTAL ADENOCARCINOMA | RECTAL MUCINOUS ADENOCARCINOMA | SEROUS CYSTADENOCARCINOMA | SEROUS ENDOMETRIAL ADENOCARCINOMA | TREATED PRIMARY GBM | UNTREATED PRIMARY (DE NOVO) GBM
--- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | ---
ALL | 356 | 54 | 351 | 321 | 104 | 12 | 493 | 11 | 79 | 243 | 7 | 4 | 17 | 2 | 3 | 2 | 18 | 1 | 1 | 1 | 3 | 315 | 5 | 18 | 4 | 3 | 49 | 10 | 143 | 13 | 552 | 85 | 1 | 20
DEL PEAK 14(6Q22.31) CNV | 49 | 8 | 5 | 54 | 28 | 3 | 138 | 5 | 44 | 120 | 2 | 2 | 9 | 1 | 1 | 0 | 9 | 1 | 0 | 0 | 1 | 77 | 2 | 2 | 1 | 1 | 17 | 5 | 19 | 6 | 319 | 18 | 1 | 8
DEL PEAK 14(6Q22.31) WILD-TYPE | 307 | 46 | 346 | 267 | 76 | 9 | 355 | 6 | 35 | 123 | 5 | 2 | 8 | 1 | 2 | 2 | 9 | 0 | 1 | 1 | 2 | 238 | 3 | 16 | 3 | 2 | 32 | 5 | 124 | 7 | 233 | 67 | 0 | 12

Figure S304. Get High-res Image Gene #55: 'Del Peak 14(6q22.31)' versus Clinical Feature #6: 'HISTOLOGICAL.TYPE'

'Del Peak 14(6q22.31)' versus 'TUMOR.STAGE'

P value = 3.81e-10 (Fisher's exact test), Q value = 5.4e-07

Table S305. Gene #55: 'Del Peak 14(6q22.31)' versus Clinical Feature #10: 'TUMOR.STAGE'

nPatients | I | II | III | IV
--- | --- | --- | --- | ---
ALL | 685 | 487 | 876 | 420
DEL PEAK 14(6Q22.31) CNV | 202 | 118 | 356 | 121
DEL PEAK 14(6Q22.31) WILD-TYPE | 483 | 369 | 520 | 299

Figure S305. Get High-res Image Gene #55: 'Del Peak 14(6q22.31)' versus Clinical Feature #10: 'TUMOR.STAGE'

'Del Peak 15(6q26)' versus 'AGE'

P value = 6.33e-06 (t-test), Q value = 0.0084

Table S306. Gene #56: 'Del Peak 15(6q26)' versus Clinical Feature #2: 'AGE'

| nPatients | Mean (Std.Dev)
--- | --- | ---
ALL | 4585 | 61.9 (12.6)
DEL PEAK 15(6Q26) CNV | 1451 | 60.7 (12.4)
DEL PEAK 15(6Q26) WILD-TYPE | 3134 | 62.5 (12.7)

Figure S306. Get High-res Image Gene #56: 'Del Peak 15(6q26)' versus Clinical Feature #2: 'AGE'

'Del Peak 15(6q26)' versus 'PRIMARY.SITE.OF.DISEASE'

P value = 2.31e-104 (Chi-square test), Q value = 3.8e-101

Table S307. Gene #56: 'Del Peak 15(6q26)' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'

nPatients | BLADDER | BRAIN | BREAST | COLON | ENDOMETRIAL | HEAD/NECK | KIDNEY | LUNG | OMENTUM | OVARY | PERITONEUM (OVARY) | RECTUM
--- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | ---
ALL | 131 | 544 | 857 | 412 | 454 | 321 | 493 | 714 | 2 | 548 | 2 | 159
DEL PEAK 15(6Q26) CNV | 57 | 162 | 295 | 60 | 37 | 55 | 142 | 285 | 1 | 351 | 1 | 28
DEL PEAK 15(6Q26) WILD-TYPE | 74 | 382 | 562 | 352 | 417 | 266 | 351 | 429 | 1 | 197 | 1 | 131

Figure S307. Get High-res Image Gene #56: 'Del Peak 15(6q26)' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'

'Del Peak 15(6q26)' versus 'HISTOLOGICAL.TYPE'

P value = 3.37e-104 (Chi-square test), Q value = 5.6e-101

Table S308. Gene #56: 'Del Peak 15(6q26)' versus Clinical Feature #6: 'HISTOLOGICAL.TYPE'

nPatients | COLON ADENOCARCINOMA | COLON MUCINOUS ADENOCARCINOMA | ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA | HEAD & NECK SQUAMOUS CELL CARCINOMA | INFILTRATING DUCTAL CARCINOMA | INFILTRATING LOBULAR 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 HISTOLOGY (PLEASE SPECIFY) | MIXED SEROUS AND ENDOMETRIOID | MUCINOUS (COLLOID) ADENOCARCINOMA | MUCINOUS (COLLOID) CARCINOMA | MUSCLE INVASIVE UROTHELIAL CARCINOMA (PT2 OR ABOVE) | OTHER SPECIFY | RECTAL ADENOCARCINOMA | RECTAL MUCINOUS ADENOCARCINOMA | SEROUS CYSTADENOCARCINOMA | SEROUS ENDOMETRIAL ADENOCARCINOMA | TREATED PRIMARY GBM | UNTREATED PRIMARY (DE NOVO) GBM
--- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | ---
ALL | 356 | 54 | 351 | 321 | 104 | 12 | 493 | 11 | 79 | 243 | 7 | 4 | 17 | 2 | 3 | 2 | 18 | 1 | 1 | 1 | 3 | 315 | 5 | 18 | 4 | 3 | 49 | 10 | 143 | 13 | 552 | 85 | 1 | 20
DEL PEAK 15(6Q26) CNV | 52 | 8 | 12 | 55 | 37 | 3 | 142 | 5 | 43 | 123 | 2 | 2 | 7 | 1 | 1 | 0 | 11 | 1 | 0 | 0 | 1 | 86 | 2 | 3 | 1 | 1 | 19 | 5 | 22 | 6 | 353 | 22 | 1 | 11
DEL PEAK 15(6Q26) WILD-TYPE | 304 | 46 | 339 | 266 | 67 | 9 | 351 | 6 | 36 | 120 | 5 | 2 | 10 | 1 | 2 | 2 | 7 | 0 | 1 | 1 | 2 | 229 | 3 | 15 | 3 | 2 | 30 | 5 | 121 | 7 | 199 | 63 | 0 | 9

Figure S308. Get High-res Image Gene #56: 'Del Peak 15(6q26)' versus Clinical Feature #6: 'HISTOLOGICAL.TYPE'

'Del Peak 15(6q26)' versus 'TUMOR.STAGE'

P value = 1.02e-13 (Fisher's exact test), Q value = 1.5e-10

Table S309. Gene #56: 'Del Peak 15(6q26)' versus Clinical Feature #10: 'TUMOR.STAGE'

nPatients | I | II | III | IV
--- | --- | --- | --- | ---
ALL | 685 | 487 | 876 | 420
DEL PEAK 15(6Q26) CNV | 209 | 120 | 388 | 136
DEL PEAK 15(6Q26) WILD-TYPE | 476 | 367 | 488 | 284

Figure S309. Get High-res Image Gene #56: 'Del Peak 15(6q26)' versus Clinical Feature #10: 'TUMOR.STAGE'

'Del Peak 16(7p22.3)' versus 'PRIMARY.SITE.OF.DISEASE'

P value = 1.33e-144 (Chi-square test), Q value = 2.3e-141

Table S310. Gene #57: 'Del Peak 16(7p22.3)' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'

nPatients | BLADDER | BRAIN | BREAST | COLON | ENDOMETRIAL | HEAD/NECK | KIDNEY | LUNG | OMENTUM | OVARY | PERITONEUM (OVARY) | RECTUM
--- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | ---
ALL | 131 | 544 | 857 | 412 | 454 | 321 | 493 | 714 | 2 | 548 | 2 | 159
DEL PEAK 16(7P22.3) CNV | 8 | 13 | 115 | 2 | 57 | 17 | 2 | 70 | 0 | 229 | 1 | 2
DEL PEAK 16(7P22.3) WILD-TYPE | 123 | 531 | 742 | 410 | 397 | 304 | 491 | 644 | 2 | 319 | 1 | 157

Figure S310. Get High-res Image Gene #57: 'Del Peak 16(7p22.3)' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'

'Del Peak 16(7p22.3)' versus 'GENDER'

P value = 4.91e-27 (Fisher's exact test), Q value = 7.6e-24

Table S311. Gene #57: 'Del Peak 16(7p22.3)' versus Clinical Feature #4: 'GENDER'

nPatients | FEMALE | MALE
--- | --- | ---
ALL | 2924 | 1717
DEL PEAK 16(7P22.3) CNV | 431 | 85
DEL PEAK 16(7P22.3) WILD-TYPE | 2493 | 1632

Figure S311. Get High-res Image Gene #57: 'Del Peak 16(7p22.3)' versus Clinical Feature #4: 'GENDER'

'Del Peak 16(7p22.3)' versus 'HISTOLOGICAL.TYPE'

P value = 8.12e-126 (Chi-square test), Q value = 1.4e-122

Table S312. Gene #57: 'Del Peak 16(7p22.3)' versus Clinical Feature #6: 'HISTOLOGICAL.TYPE'

nPatients | COLON ADENOCARCINOMA | COLON MUCINOUS ADENOCARCINOMA | ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA | HEAD & NECK SQUAMOUS CELL CARCINOMA | INFILTRATING DUCTAL CARCINOMA | INFILTRATING LOBULAR 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 HISTOLOGY (PLEASE SPECIFY) | MIXED SEROUS AND ENDOMETRIOID | MUCINOUS (COLLOID) ADENOCARCINOMA | MUCINOUS (COLLOID) CARCINOMA | MUSCLE INVASIVE UROTHELIAL CARCINOMA (PT2 OR ABOVE) | OTHER SPECIFY | RECTAL ADENOCARCINOMA | RECTAL MUCINOUS ADENOCARCINOMA | SEROUS CYSTADENOCARCINOMA | SEROUS ENDOMETRIAL ADENOCARCINOMA | TREATED PRIMARY GBM | UNTREATED PRIMARY (DE NOVO) GBM
--- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | ---
ALL | 356 | 54 | 351 | 321 | 104 | 12 | 493 | 11 | 79 | 243 | 7 | 4 | 17 | 2 | 3 | 2 | 18 | 1 | 1 | 1 | 3 | 315 | 5 | 18 | 4 | 3 | 49 | 10 | 143 | 13 | 552 | 85 | 1 | 20
DEL PEAK 16(7P22.3) CNV | 2 | 0 | 21 | 17 | 22 | 0 | 2 | 0 | 4 | 17 | 1 | 0 | 0 | 0 | 0 | 0 | 2 | 1 | 0 | 0 | 0 | 45 | 0 | 4 | 0 | 0 | 2 | 2 | 1 | 1 | 230 | 32 | 0 | 0
DEL PEAK 16(7P22.3) WILD-TYPE | 354 | 54 | 330 | 304 | 82 | 12 | 491 | 11 | 75 | 226 | 6 | 4 | 17 | 2 | 3 | 2 | 16 | 0 | 1 | 1 | 3 | 270 | 5 | 14 | 4 | 3 | 47 | 8 | 142 | 12 | 322 | 53 | 1 | 20

Figure S312. Get High-res Image Gene #57: 'Del Peak 16(7p22.3)' versus Clinical Feature #6: 'HISTOLOGICAL.TYPE'

'Del Peak 16(7p22.3)' versus 'PATHOLOGY.T'

P value = 3.04e-07 (Fisher's exact test), Q value = 0.00042

Table S313. Gene #57: 'Del Peak 16(7p22.3)' versus Clinical Feature #7: 'PATHOLOGY.T'

nPatients | T0+T1 | T2 | T3 | T4
--- | --- | --- | --- | ---
ALL | 448 | 611 | 688 | 208
DEL PEAK 16(7P22.3) CNV | 15 | 48 | 11 | 12
DEL PEAK 16(7P22.3) WILD-TYPE | 433 | 563 | 677 | 196

Figure S313. Get High-res Image Gene #57: 'Del Peak 16(7p22.3)' versus Clinical Feature #7: 'PATHOLOGY.T'

'Del Peak 16(7p22.3)' versus 'TUMOR.STAGE'

P value = 2.28e-28 (Fisher's exact test), Q value = 3.5e-25

Table S314. Gene #57: 'Del Peak 16(7p22.3)' versus Clinical Feature #10: 'TUMOR.STAGE'

nPatients | I | II | III | IV
--- | --- | --- | --- | ---
ALL | 685 | 487 | 876 | 420
DEL PEAK 16(7P22.3) CNV | 38 | 29 | 200 | 45
DEL PEAK 16(7P22.3) WILD-TYPE | 647 | 458 | 676 | 375

Figure S314. Get High-res Image Gene #57: 'Del Peak 16(7p22.3)' versus Clinical Feature #10: 'TUMOR.STAGE'

'Del Peak 17(7q36.1)' versus 'PRIMARY.SITE.OF.DISEASE'

P value = 9.82e-56 (Chi-square test), Q value = 1.6e-52

Table S315. Gene #58: 'Del Peak 17(7q36.1)' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'

nPatients | BLADDER | BRAIN | BREAST | COLON | ENDOMETRIAL | HEAD/NECK | KIDNEY | LUNG | OMENTUM | OVARY | PERITONEUM (OVARY) | RECTUM
--- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | ---
ALL | 131 | 544 | 857 | 412 | 454 | 321 | 493 | 714 | 2 | 548 | 2 | 159
DEL PEAK 17(7Q36.1) CNV | 15 | 8 | 172 | 8 | 51 | 80 | 6 | 122 | 0 | 67 | 1 | 8
DEL PEAK 17(7Q36.1) WILD-TYPE | 116 | 536 | 685 | 404 | 403 | 241 | 487 | 592 | 2 | 481 | 1 | 151

Figure S315. Get High-res Image Gene #58: 'Del Peak 17(7q36.1)' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'

'Del Peak 17(7q36.1)' versus 'HISTOLOGICAL.TYPE'

P value = 1.46e-49 (Chi-square test), Q value = 2.3e-46

Table S316. Gene #58: 'Del Peak 17(7q36.1)' versus Clinical Feature #6: 'HISTOLOGICAL.TYPE'

nPatients | COLON ADENOCARCINOMA | COLON MUCINOUS ADENOCARCINOMA | ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA | HEAD & NECK SQUAMOUS CELL CARCINOMA | INFILTRATING DUCTAL CARCINOMA | INFILTRATING LOBULAR 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 HISTOLOGY (PLEASE SPECIFY) | MIXED SEROUS AND ENDOMETRIOID | MUCINOUS (COLLOID) ADENOCARCINOMA | MUCINOUS (COLLOID) CARCINOMA | MUSCLE INVASIVE UROTHELIAL CARCINOMA (PT2 OR ABOVE) | OTHER SPECIFY | RECTAL ADENOCARCINOMA | RECTAL MUCINOUS ADENOCARCINOMA | SEROUS CYSTADENOCARCINOMA | SEROUS ENDOMETRIAL ADENOCARCINOMA | TREATED PRIMARY GBM | UNTREATED PRIMARY (DE NOVO) GBM
--- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | ---
ALL | 356 | 54 | 351 | 321 | 104 | 12 | 493 | 11 | 79 | 243 | 7 | 4 | 17 | 2 | 3 | 2 | 18 | 1 | 1 | 1 | 3 | 315 | 5 | 18 | 4 | 3 | 49 | 10 | 143 | 13 | 552 | 85 | 1 | 20
DEL PEAK 17(7Q36.1) CNV | 7 | 1 | 12 | 80 | 22 | 1 | 6 | 0 | 6 | 36 | 2 | 1 | 2 | 1 | 1 | 0 | 3 | 0 | 0 | 0 | 0 | 67 | 0 | 4 | 2 | 1 | 4 | 2 | 5 | 3 | 68 | 35 | 0 | 0
DEL PEAK 17(7Q36.1) WILD-TYPE | 349 | 53 | 339 | 241 | 82 | 11 | 487 | 11 | 73 | 207 | 5 | 3 | 15 | 1 | 2 | 2 | 15 | 1 | 1 | 1 | 3 | 248 | 5 | 14 | 2 | 2 | 45 | 8 | 138 | 10 | 484 | 50 | 1 | 20

Figure S316. Get High-res Image Gene #58: 'Del Peak 17(7q36.1)' versus Clinical Feature #6: 'HISTOLOGICAL.TYPE'

'Del Peak 17(7q36.1)' versus 'PATHOLOGY.T'

P value = 7.27e-11 (Fisher's exact test), Q value = 1.1e-07

Table S317. Gene #58: 'Del Peak 17(7q36.1)' versus Clinical Feature #7: 'PATHOLOGY.T'

nPatients | T0+T1 | T2 | T3 | T4
--- | --- | --- | --- | ---
ALL | 448 | 611 | 688 | 208
DEL PEAK 17(7Q36.1) CNV | 33 | 95 | 38 | 36
DEL PEAK 17(7Q36.1) WILD-TYPE | 415 | 516 | 650 | 172

Figure S317. Get High-res Image Gene #58: 'Del Peak 17(7q36.1)' versus Clinical Feature #7: 'PATHOLOGY.T'

'Del Peak 17(7q36.1)' versus 'PATHOLOGICSPREAD(M)'

P value = 0.000181 (Chi-square test), Q value = 0.22

Table S318. Gene #58: 'Del Peak 17(7q36.1)' versus Clinical Feature #9: 'PATHOLOGICSPREAD(M)'

nPatients | M0 | M1 | M1A | M1B | MX
--- | --- | --- | --- | --- | ---
ALL | 1398 | 167 | 9 | 1 | 148
DEL PEAK 17(7Q36.1) CNV | 126 | 3 | 0 | 1 | 12
DEL PEAK 17(7Q36.1) WILD-TYPE | 1272 | 164 | 9 | 0 | 136

Figure S318. Get High-res Image Gene #58: 'Del Peak 17(7q36.1)' versus Clinical Feature #9: 'PATHOLOGICSPREAD(M)'

'Del Peak 18(8p23.2)' versus 'PRIMARY.SITE.OF.DISEASE'

P value = 4.6e-129 (Chi-square test), Q value = 7.8e-126

Table S319. Gene #59: 'Del Peak 18(8p23.2)' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'

nPatients | BLADDER | BRAIN | BREAST | COLON | ENDOMETRIAL | HEAD/NECK | KIDNEY | LUNG | OMENTUM | OVARY | PERITONEUM (OVARY) | RECTUM
--- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | ---
ALL | 131 | 544 | 857 | 412 | 454 | 321 | 493 | 714 | 2 | 548 | 2 | 159
DEL PEAK 18(8P23.2) CNV | 71 | 65 | 456 | 172 | 87 | 184 | 146 | 411 | 2 | 367 | 2 | 98
DEL PEAK 18(8P23.2) WILD-TYPE | 60 | 479 | 401 | 240 | 367 | 137 | 347 | 303 | 0 | 181 | 0 | 61

Figure S319. Get High-res Image Gene #59: 'Del Peak 18(8p23.2)' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'

'Del Peak 18(8p23.2)' versus 'KARNOFSKY.PERFORMANCE.SCORE'

P value = 7.36e-05 (t-test), Q value = 0.093

Table S320. Gene #59: 'Del Peak 18(8p23.2)' versus Clinical Feature #5: 'KARNOFSKY.PERFORMANCE.SCORE'

| nPatients | Mean (Std.Dev)
--- | --- | ---
ALL | 641 | 73.6 (23.9)
DEL PEAK 18(8P23.2) CNV | 183 | 66.2 (32.4)
DEL PEAK 18(8P23.2) WILD-TYPE | 458 | 76.5 (18.8)

Figure S320. Get High-res Image Gene #59: 'Del Peak 18(8p23.2)' versus Clinical Feature #5: 'KARNOFSKY.PERFORMANCE.SCORE'

'Del Peak 18(8p23.2)' versus 'HISTOLOGICAL.TYPE'

P value = 9.65e-91 (Chi-square test), Q value = 1.6e-87

Table S321. Gene #59: 'Del Peak 18(8p23.2)' versus Clinical Feature #6: 'HISTOLOGICAL.TYPE'

nPatients | COLON ADENOCARCINOMA | COLON MUCINOUS ADENOCARCINOMA | ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA | HEAD & NECK SQUAMOUS CELL CARCINOMA | INFILTRATING DUCTAL CARCINOMA | INFILTRATING LOBULAR 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 HISTOLOGY (PLEASE SPECIFY) | MIXED SEROUS AND ENDOMETRIOID | MUCINOUS (COLLOID) ADENOCARCINOMA | MUCINOUS (COLLOID) CARCINOMA | MUSCLE INVASIVE UROTHELIAL CARCINOMA (PT2 OR ABOVE) | OTHER SPECIFY | RECTAL ADENOCARCINOMA | RECTAL MUCINOUS ADENOCARCINOMA | SEROUS CYSTADENOCARCINOMA | SEROUS ENDOMETRIAL ADENOCARCINOMA | TREATED PRIMARY GBM | UNTREATED PRIMARY (DE NOVO) GBM
--- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | ---
ALL | 356 | 54 | 351 | 321 | 104 | 12 | 493 | 11 | 79 | 243 | 7 | 4 | 17 | 2 | 3 | 2 | 18 | 1 | 1 | 1 | 3 | 315 | 5 | 18 | 4 | 3 | 49 | 10 | 143 | 13 | 552 | 85 | 1 | 20
DEL PEAK 18(8P23.2) CNV | 156 | 15 | 28 | 184 | 60 | 2 | 146 | 4 | 31 | 126 | 4 | 1 | 9 | 2 | 3 | 0 | 7 | 1 | 0 | 0 | 3 | 220 | 2 | 4 | 0 | 0 | 22 | 8 | 89 | 7 | 371 | 55 | 0 | 4
DEL PEAK 18(8P23.2) WILD-TYPE | 200 | 39 | 323 | 137 | 44 | 10 | 347 | 7 | 48 | 117 | 3 | 3 | 8 | 0 | 0 | 2 | 11 | 0 | 1 | 1 | 0 | 95 | 3 | 14 | 4 | 3 | 27 | 2 | 54 | 6 | 181 | 30 | 1 | 16

Figure S321. Get High-res Image Gene #59: 'Del Peak 18(8p23.2)' versus Clinical Feature #6: 'HISTOLOGICAL.TYPE'

'Del Peak 18(8p23.2)' versus 'PATHOLOGY.T'

P value = 3.31e-05 (Fisher's exact test), Q value = 0.043

Table S322. Gene #59: 'Del Peak 18(8p23.2)' versus Clinical Feature #7: 'PATHOLOGY.T'

nPatients | T0+T1 | T2 | T3 | T4
--- | --- | --- | --- | ---
ALL | 448 | 611 | 688 | 208
DEL PEAK 18(8P23.2) CNV | 181 | 327 | 325 | 117
DEL PEAK 18(8P23.2) WILD-TYPE | 267 | 284 | 363 | 91

Figure S322. Get High-res Image Gene #59: 'Del Peak 18(8p23.2)' versus Clinical Feature #7: 'PATHOLOGY.T'

'Del Peak 18(8p23.2)' versus 'PATHOLOGY.N'

P value = 5.54e-09 (Fisher's exact test), Q value = 7.8e-06

Table S323. Gene #59: 'Del Peak 18(8p23.2)' versus Clinical Feature #8: 'PATHOLOGY.N'

nPatients | N0 | N1 | N2 | N3
--- | --- | --- | --- | ---
ALL | 1036 | 343 | 279 | 11
DEL PEAK 18(8P23.2) CNV | 462 | 199 | 174 | 8
DEL PEAK 18(8P23.2) WILD-TYPE | 574 | 144 | 105 | 3

Figure S323. Get High-res Image Gene #59: 'Del Peak 18(8p23.2)' versus Clinical Feature #8: 'PATHOLOGY.N'

'Del Peak 18(8p23.2)' versus 'TUMOR.STAGE'

P value = 2.21e-08 (Fisher's exact test), Q value = 3.1e-05

Table S324. Gene #59: 'Del Peak 18(8p23.2)' versus Clinical Feature #10: 'TUMOR.STAGE'

nPatients | I | II | III | IV
--- | --- | --- | --- | ---
ALL | 685 | 487 | 876 | 420
DEL PEAK 18(8P23.2) CNV | 306 | 238 | 514 | 245
DEL PEAK 18(8P23.2) WILD-TYPE | 379 | 249 | 362 | 175

Figure S324. Get High-res Image Gene #59: 'Del Peak 18(8p23.2)' versus Clinical Feature #10: 'TUMOR.STAGE'

'Del Peak 18(8p23.2)' versus 'RADIATIONS.RADIATION.REGIMENINDICATION'

P value = 3.83e-21 (Fisher's exact test), Q value = 5.8e-18

Table S325. Gene #59: 'Del Peak 18(8p23.2)' versus Clinical Feature #11: 'RADIATIONS.RADIATION.REGIMENINDICATION'

nPatients | NO | YES
--- | --- | ---
ALL | 835 | 3816
DEL PEAK 18(8P23.2) CNV | 250 | 1818
DEL PEAK 18(8P23.2) WILD-TYPE | 585 | 1998

Figure S325. Get High-res Image Gene #59: 'Del Peak 18(8p23.2)' versus Clinical Feature #11: 'RADIATIONS.RADIATION.REGIMENINDICATION'

'Del Peak 19(8p21.2)' versus 'PRIMARY.SITE.OF.DISEASE'

P value = 5.87e-133 (Chi-square test), Q value = 1e-129

Table S326. Gene #60: 'Del Peak 19(8p21.2)' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'

nPatients | BLADDER | BRAIN | BREAST | COLON | ENDOMETRIAL | HEAD/NECK | KIDNEY | LUNG | OMENTUM | OVARY | PERITONEUM (OVARY) | RECTUM
--- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | ---
ALL | 131 | 544 | 857 | 412 | 454 | 321 | 493 | 714 | 2 | 548 | 2 | 159
DEL PEAK 19(8P21.2) CNV | 73 | 66 | 470 | 179 | 86 | 161 | 148 | 415 | 2 | 382 | 2 | 94
DEL PEAK 19(8P21.2) WILD-TYPE | 58 | 478 | 387 | 233 | 368 | 160 | 345 | 299 | 0 | 166 | 0 | 65

Figure S326. Get High-res Image Gene #60: 'Del Peak 19(8p21.2)' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'

'Del Peak 19(8p21.2)' versus 'GENDER'

P value = 8.03e-05 (Fisher's exact test), Q value = 0.1

Table S327. Gene #60: 'Del Peak 19(8p21.2)' versus Clinical Feature #4: 'GENDER'

nPatients | FEMALE | MALE
--- | --- | ---
ALL | 2924 | 1717
DEL PEAK 19(8P21.2) CNV | 1375 | 705
DEL PEAK 19(8P21.2) WILD-TYPE | 1549 | 1012

Figure S327. Get High-res Image Gene #60: 'Del Peak 19(8p21.2)' versus Clinical Feature #4: 'GENDER'

'Del Peak 19(8p21.2)' versus 'KARNOFSKY.PERFORMANCE.SCORE'

P value = 1.51e-05 (t-test), Q value = 0.02

Table S328. Gene #60: 'Del Peak 19(8p21.2)' versus Clinical Feature #5: 'KARNOFSKY.PERFORMANCE.SCORE'

| nPatients | Mean (Std.Dev)
--- | --- | ---
ALL | 641 | 73.6 (23.9)
DEL PEAK 19(8P21.2) CNV | 188 | 65.7 (32.3)
DEL PEAK 19(8P21.2) WILD-TYPE | 453 | 76.8 (18.5)

Figure S328. Get High-res Image Gene #60: 'Del Peak 19(8p21.2)' versus Clinical Feature #5: 'KARNOFSKY.PERFORMANCE.SCORE'

'Del Peak 19(8p21.2)' versus 'HISTOLOGICAL.TYPE'

P value = 5.32e-94 (Chi-square test), Q value = 8.8e-91

Table S329. Gene #60: 'Del Peak 19(8p21.2)' versus Clinical Feature #6: 'HISTOLOGICAL.TYPE'

nPatients | COLON ADENOCARCINOMA | COLON MUCINOUS ADENOCARCINOMA | ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA | HEAD & NECK SQUAMOUS CELL CARCINOMA | INFILTRATING DUCTAL CARCINOMA | INFILTRATING LOBULAR 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 HISTOLOGY (PLEASE SPECIFY) | MIXED SEROUS AND ENDOMETRIOID | MUCINOUS (COLLOID) ADENOCARCINOMA | MUCINOUS (COLLOID) CARCINOMA | MUSCLE INVASIVE UROTHELIAL CARCINOMA (PT2 OR ABOVE) | OTHER SPECIFY | RECTAL ADENOCARCINOMA | RECTAL MUCINOUS ADENOCARCINOMA | SEROUS CYSTADENOCARCINOMA | SEROUS ENDOMETRIAL ADENOCARCINOMA | TREATED PRIMARY GBM | UNTREATED PRIMARY (DE NOVO) GBM
--- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | ---
ALL | 356 | 54 | 351 | 321 | 104 | 12 | 493 | 11 | 79 | 243 | 7 | 4 | 17 | 2 | 3 | 2 | 18 | 1 | 1 | 1 | 3 | 315 | 5 | 18 | 4 | 3 | 49 | 10 | 143 | 13 | 552 | 85 | 1 | 20
DEL PEAK 19(8P21.2) CNV | 163 | 15 | 22 | 161 | 63 | 1 | 148 | 4 | 36 | 133 | 4 | 1 | 9 | 2 | 3 | 0 | 10 | 1 | 0 | 0 | 3 | 209 | 2 | 5 | 0 | 0 | 21 | 8 | 85 | 7 | 386 | 59 | 0 | 5
DEL PEAK 19(8P21.2) WILD-TYPE | 193 | 39 | 329 | 160 | 41 | 11 | 345 | 7 | 43 | 110 | 3 | 3 | 8 | 0 | 0 | 2 | 8 | 0 | 1 | 1 | 0 | 106 | 3 | 13 | 4 | 3 | 28 | 2 | 58 | 6 | 166 | 26 | 1 | 15

Figure S329. Get High-res Image Gene #60: 'Del Peak 19(8p21.2)' versus Clinical Feature #6: 'HISTOLOGICAL.TYPE'

'Del Peak 19(8p21.2)' versus 'PATHOLOGY.N'

P value = 6.31e-09 (Fisher's exact test), Q value = 8.9e-06

Table S330. Gene #60: 'Del Peak 19(8p21.2)' versus Clinical Feature #8: 'PATHOLOGY.N'

nPatients | N0 | N1 | N2 | N3
--- | --- | --- | --- | ---
ALL | 1036 | 343 | 279 | 11
DEL PEAK 19(8P21.2) CNV | 452 | 197 | 170 | 8
DEL PEAK 19(8P21.2) WILD-TYPE | 584 | 146 | 109 | 3

Figure S330. Get High-res Image Gene #60: 'Del Peak 19(8p21.2)' versus Clinical Feature #8: 'PATHOLOGY.N'

'Del Peak 19(8p21.2)' versus 'TUMOR.STAGE'

P value = 2.83e-11 (Fisher's exact test), Q value = 4.1e-08

Table S331. Gene #60: 'Del Peak 19(8p21.2)' versus Clinical Feature #10: 'TUMOR.STAGE'

nPatients | I | II | III | IV
--- | --- | --- | --- | ---
ALL | 685 | 487 | 876 | 420
DEL PEAK 19(8P21.2) CNV | 302 | 227 | 530 | 239
DEL PEAK 19(8P21.2) WILD-TYPE | 383 | 260 | 346 | 181

Figure S331. Get High-res Image Gene #60: 'Del Peak 19(8p21.2)' versus Clinical Feature #10: 'TUMOR.STAGE'

'Del Peak 19(8p21.2)' versus 'RADIATIONS.RADIATION.REGIMENINDICATION'

P value = 6.66e-22 (Fisher's exact test), Q value = 1e-18

Table S332. Gene #60: 'Del Peak 19(8p21.2)' versus Clinical Feature #11: 'RADIATIONS.RADIATION.REGIMENINDICATION'

nPatients | NO | YES
--- | --- | ---
ALL | 835 | 3816
DEL PEAK 19(8P21.2) CNV | 251 | 1835
DEL PEAK 19(8P21.2) WILD-TYPE | 584 | 1981

Figure S332. Get High-res Image Gene #60: 'Del Peak 19(8p21.2)' versus Clinical Feature #11: 'RADIATIONS.RADIATION.REGIMENINDICATION'

'Del Peak 20(9p23)' versus 'Time to Death'

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

Table S333. Gene #61: 'Del Peak 20(9p23)' versus Clinical Feature #1: 'Time to Death'

| nPatients | nDeath | Duration Range (Median), Month
--- | --- | --- | ---
ALL | 4370 | 1406 | 0.0 - 224.0 (14.4)
DEL PEAK 20(9P23) CNV | 1564 | 625 | 0.0 - 163.1 (14.0)
DEL PEAK 20(9P23) WILD-TYPE | 2806 | 781 | 0.0 - 224.0 (14.9)

Figure S333. Get High-res Image Gene #61: 'Del Peak 20(9p23)' versus Clinical Feature #1: 'Time to Death'

'Del Peak 20(9p23)' versus 'PRIMARY.SITE.OF.DISEASE'

P value = 3.56e-93 (Chi-square test), Q value = 5.9e-90

Table S334. Gene #61: 'Del Peak 20(9p23)' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'

nPatients | BLADDER | BRAIN | BREAST | COLON | ENDOMETRIAL | HEAD/NECK | KIDNEY | LUNG | OMENTUM | OVARY | PERITONEUM (OVARY) | RECTUM
--- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | ---
ALL | 131 | 544 | 857 | 412 | 454 | 321 | 493 | 714 | 2 | 548 | 2 | 159
DEL PEAK 20(9P23) CNV | 58 | 232 | 266 | 53 | 53 | 151 | 144 | 415 | 1 | 245 | 2 | 25
DEL PEAK 20(9P23) WILD-TYPE | 73 | 312 | 591 | 359 | 401 | 170 | 349 | 299 | 1 | 303 | 0 | 134

Figure S334. Get High-res Image Gene #61: 'Del Peak 20(9p23)' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'

'Del Peak 20(9p23)' versus 'GENDER'

P value = 1.64e-10 (Fisher's exact test), Q value = 2.4e-07

Table S335. Gene #61: 'Del Peak 20(9p23)' versus Clinical Feature #4: 'GENDER'

nPatients | FEMALE | MALE
--- | --- | ---
ALL | 2924 | 1717
DEL PEAK 20(9P23) CNV | 936 | 710
DEL PEAK 20(9P23) WILD-TYPE | 1988 | 1007

Figure S335. Get High-res Image Gene #61: 'Del Peak 20(9p23)' versus Clinical Feature #4: 'GENDER'

'Del Peak 20(9p23)' versus 'HISTOLOGICAL.TYPE'

P value = 2.59e-84 (Chi-square test), Q value = 4.2e-81

Table S336. Gene #61: 'Del Peak 20(9p23)' versus Clinical Feature #6: 'HISTOLOGICAL.TYPE'

nPatients | COLON ADENOCARCINOMA | COLON MUCINOUS ADENOCARCINOMA | ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA | HEAD & NECK SQUAMOUS CELL CARCINOMA | INFILTRATING DUCTAL CARCINOMA | INFILTRATING LOBULAR 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 HISTOLOGY (PLEASE SPECIFY) | MIXED SEROUS AND ENDOMETRIOID | MUCINOUS (COLLOID) ADENOCARCINOMA | MUCINOUS (COLLOID) CARCINOMA | MUSCLE INVASIVE UROTHELIAL CARCINOMA (PT2 OR ABOVE) | OTHER SPECIFY | RECTAL ADENOCARCINOMA | RECTAL MUCINOUS ADENOCARCINOMA | SEROUS CYSTADENOCARCINOMA | SEROUS ENDOMETRIAL ADENOCARCINOMA | TREATED PRIMARY GBM | UNTREATED PRIMARY (DE NOVO) GBM
--- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | ---
ALL | 356 | 54 | 351 | 321 | 104 | 12 | 493 | 11 | 79 | 243 | 7 | 4 | 17 | 2 | 3 | 2 | 18 | 1 | 1 | 1 | 3 | 315 | 5 | 18 | 4 | 3 | 49 | 10 | 143 | 13 | 552 | 85 | 1 | 20
DEL PEAK 20(9P23) CNV | 49 | 4 | 20 | 151 | 37 | 2 | 144 | 6 | 44 | 129 | 3 | 2 | 11 | 1 | 3 | 1 | 7 | 1 | 0 | 0 | 2 | 203 | 1 | 3 | 2 | 0 | 21 | 2 | 24 | 1 | 248 | 30 | 0 | 10
DEL PEAK 20(9P23) WILD-TYPE | 307 | 50 | 331 | 170 | 67 | 10 | 349 | 5 | 35 | 114 | 4 | 2 | 6 | 1 | 0 | 1 | 11 | 0 | 1 | 1 | 1 | 112 | 4 | 15 | 2 | 3 | 28 | 8 | 119 | 12 | 304 | 55 | 1 | 10

Figure S336. Get High-res Image Gene #61: 'Del Peak 20(9p23)' versus Clinical Feature #6: 'HISTOLOGICAL.TYPE'

'Del Peak 20(9p23)' versus 'PATHOLOGY.T'

P value = 1.05e-09 (Fisher's exact test), Q value = 1.5e-06

Table S337. Gene #61: 'Del Peak 20(9p23)' versus Clinical Feature #7: 'PATHOLOGY.T'

nPatients | T0+T1 | T2 | T3 | T4
--- | --- | --- | --- | ---
ALL | 448 | 611 | 688 | 208
DEL PEAK 20(9P23) CNV | 163 | 280 | 194 | 84
DEL PEAK 20(9P23) WILD-TYPE | 285 | 331 | 494 | 124

Figure S337. Get High-res Image Gene #61: 'Del Peak 20(9p23)' versus Clinical Feature #7: 'PATHOLOGY.T'

'Del Peak 21(9p21.3)' versus 'Time to Death'

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

Table S338. Gene #62: 'Del Peak 21(9p21.3)' versus Clinical Feature #1: 'Time to Death'

| nPatients | nDeath | Duration Range (Median), Month
--- | --- | --- | ---
ALL | 4370 | 1406 | 0.0 - 224.0 (14.4)
DEL PEAK 21(9P21.3) CNV | 1831 | 792 | 0.0 - 177.0 (13.1)
DEL PEAK 21(9P21.3) WILD-TYPE | 2539 | 614 | 0.0 - 224.0 (15.6)

Figure S338. Get High-res Image Gene #62: 'Del Peak 21(9p21.3)' versus Clinical Feature #1: 'Time to Death'

'Del Peak 21(9p21.3)' versus 'PRIMARY.SITE.OF.DISEASE'

P value = 5.76e-162 (Chi-square test), Q value = 9.9e-159

Table S339. Gene #62: 'Del Peak 21(9p21.3)' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'

nPatients | BLADDER | BRAIN | BREAST | COLON | ENDOMETRIAL | HEAD/NECK | KIDNEY | LUNG | OMENTUM | OVARY | PERITONEUM (OVARY) | RECTUM
--- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | ---
ALL | 131 | 544 | 857 | 412 | 454 | 321 | 493 | 714 | 2 | 548 | 2 | 159
DEL PEAK 21(9P21.3) CNV | 73 | 405 | 294 | 56 | 59 | 162 | 148 | 454 | 1 | 245 | 2 | 24
DEL PEAK 21(9P21.3) WILD-TYPE | 58 | 139 | 563 | 356 | 395 | 159 | 345 | 260 | 1 | 303 | 0 | 135

Figure S339. Get High-res Image Gene #62: 'Del Peak 21(9p21.3)' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'

'Del Peak 21(9p21.3)' versus 'GENDER'

P value = 2.67e-22 (Fisher's exact test), Q value = 4.1e-19

Table S340. Gene #62: 'Del Peak 21(9p21.3)' versus Clinical Feature #4: 'GENDER'

nPatients | FEMALE | MALE
--- | --- | ---
ALL | 2924 | 1717
DEL PEAK 21(9P21.3) CNV | 1054 | 870
DEL PEAK 21(9P21.3) WILD-TYPE | 1870 | 847

Figure S340. Get High-res Image Gene #62: 'Del Peak 21(9p21.3)' versus Clinical Feature #4: 'GENDER'

'Del Peak 21(9p21.3)' versus 'HISTOLOGICAL.TYPE'

P value = 3.34e-109 (Chi-square test), Q value = 5.6e-106

Table S341. Gene #62: 'Del Peak 21(9p21.3)' versus Clinical Feature #6: 'HISTOLOGICAL.TYPE'

nPatients | COLON ADENOCARCINOMA | COLON MUCINOUS ADENOCARCINOMA | ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA | HEAD & NECK SQUAMOUS CELL CARCINOMA | INFILTRATING DUCTAL CARCINOMA | INFILTRATING LOBULAR 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 HISTOLOGY (PLEASE SPECIFY) | MIXED SEROUS AND ENDOMETRIOID | MUCINOUS (COLLOID) ADENOCARCINOMA | MUCINOUS (COLLOID) CARCINOMA | MUSCLE INVASIVE UROTHELIAL CARCINOMA (PT2 OR ABOVE) | OTHER SPECIFY | RECTAL ADENOCARCINOMA | RECTAL MUCINOUS ADENOCARCINOMA | SEROUS CYSTADENOCARCINOMA | SEROUS ENDOMETRIAL ADENOCARCINOMA | TREATED PRIMARY GBM | UNTREATED PRIMARY (DE NOVO) GBM
--- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | ---
ALL | 356 | 54 | 351 | 321 | 104 | 12 | 493 | 11 | 79 | 243 | 7 | 4 | 17 | 2 | 3 | 2 | 18 | 1 | 1 | 1 | 3 | 315 | 5 | 18 | 4 | 3 | 49 | 10 | 143 | 13 | 552 | 85 | 1 | 20
DEL PEAK 21(9P21.3) CNV | 52 | 4 | 21 | 162 | 43 | 2 | 148 | 5 | 43 | 133 | 3 | 4 | 10 | 1 | 3 | 1 | 8 | 1 | 0 | 0 | 3 | 237 | 1 | 3 | 2 | 0 | 27 | 2 | 23 | 1 | 248 | 35 | 1 | 16
DEL PEAK 21(9P21.3) WILD-TYPE | 304 | 50 | 330 | 159 | 61 | 10 | 345 | 6 | 36 | 110 | 4 | 0 | 7 | 1 | 0 | 1 | 10 | 0 | 1 | 1 | 0 | 78 | 4 | 15 | 2 | 3 | 22 | 8 | 120 | 12 | 304 | 50 | 0 | 4

Figure S341. Get High-res Image Gene #62: 'Del Peak 21(9p21.3)' versus Clinical Feature #6: 'HISTOLOGICAL.TYPE'

'Del Peak 21(9p21.3)' versus 'PATHOLOGY.T'

P value = 2.4e-16 (Fisher's exact test), Q value = 3.6e-13

Table S342. Gene #62: 'Del Peak 21(9p21.3)' versus Clinical Feature #7: 'PATHOLOGY.T'

nPatients | T0+T1 | T2 | T3 | T4
--- | --- | --- | --- | ---
ALL | 448 | 611 | 688 | 208
DEL PEAK 21(9P21.3) CNV | 176 | 321 | 199 | 85
DEL PEAK 21(9P21.3) WILD-TYPE | 272 | 290 | 489 | 123

Figure S342. Get High-res Image Gene #62: 'Del Peak 21(9p21.3)' versus Clinical Feature #7: 'PATHOLOGY.T'

'Del Peak 21(9p21.3)' versus 'RADIATIONS.RADIATION.REGIMENINDICATION'

P value = 8.2e-07 (Fisher's exact test), Q value = 0.0011

Table S343. Gene #62: 'Del Peak 21(9p21.3)' versus Clinical Feature #11: 'RADIATIONS.RADIATION.REGIMENINDICATION'

nPatients | NO | YES
--- | --- | ---
ALL | 835 | 3816
DEL PEAK 21(9P21.3) CNV | 411 | 1521
DEL PEAK 21(9P21.3) WILD-TYPE | 424 | 2295

Figure S343. Get High-res Image Gene #62: 'Del Peak 21(9p21.3)' versus Clinical Feature #11: 'RADIATIONS.RADIATION.REGIMENINDICATION'

'Del Peak 22(9q21.11)' versus 'AGE'

P value = 3.24e-07 (t-test), Q value = 0.00045

Table S344. Gene #63: 'Del Peak 22(9q21.11)' versus Clinical Feature #2: 'AGE'

| nPatients | Mean (Std.Dev)
--- | --- | ---
ALL | 4585 | 61.9 (12.6)
DEL PEAK 22(9Q21.11) CNV | 1310 | 63.3 (11.9)
DEL PEAK 22(9Q21.11) WILD-TYPE | 3275 | 61.3 (12.8)

Figure S344. Get High-res Image Gene #63: 'Del Peak 22(9q21.11)' versus Clinical Feature #2: 'AGE'

'Del Peak 22(9q21.11)' versus 'PRIMARY.SITE.OF.DISEASE'

P value = 4.8e-86 (Chi-square test), Q value = 7.9e-83

Table S345. Gene #63: 'Del Peak 22(9q21.11)' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'

nPatients | BLADDER | BRAIN | BREAST | COLON | ENDOMETRIAL | HEAD/NECK | KIDNEY | LUNG | OMENTUM | OVARY | PERITONEUM (OVARY) | RECTUM
--- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | ---
ALL | 131 | 544 | 857 | 412 | 454 | 321 | 493 | 714 | 2 | 548 | 2 | 159
DEL PEAK 22(9Q21.11) CNV | 56 | 72 | 237 | 49 | 94 | 50 | 143 | 346 | 2 | 262 | 2 | 23
DEL PEAK 22(9Q21.11) WILD-TYPE | 75 | 472 | 620 | 363 | 360 | 271 | 350 | 368 | 0 | 286 | 0 | 136

Figure S345. Get High-res Image Gene #63: 'Del Peak 22(9q21.11)' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'

'Del Peak 22(9q21.11)' versus 'HISTOLOGICAL.TYPE'

P value = 4.54e-71 (Chi-square test), Q value = 7.4e-68

Table S346. Gene #63: 'Del Peak 22(9q21.11)' versus Clinical Feature #6: 'HISTOLOGICAL.TYPE'

nPatients | COLON ADENOCARCINOMA | COLON MUCINOUS ADENOCARCINOMA | ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA | HEAD & NECK SQUAMOUS CELL CARCINOMA | INFILTRATING DUCTAL CARCINOMA | INFILTRATING LOBULAR 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 HISTOLOGY (PLEASE SPECIFY) | MIXED SEROUS AND ENDOMETRIOID | MUCINOUS (COLLOID) ADENOCARCINOMA | MUCINOUS (COLLOID) CARCINOMA | MUSCLE INVASIVE UROTHELIAL CARCINOMA (PT2 OR ABOVE) | OTHER SPECIFY | RECTAL ADENOCARCINOMA | RECTAL MUCINOUS ADENOCARCINOMA | SEROUS CYSTADENOCARCINOMA | SEROUS ENDOMETRIAL ADENOCARCINOMA | TREATED PRIMARY GBM | UNTREATED PRIMARY (DE NOVO) GBM
--- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | ---
ALL | 356 | 54 | 351 | 321 | 104 | 12 | 493 | 11 | 79 | 243 | 7 | 4 | 17 | 2 | 3 | 2 | 18 | 1 | 1 | 1 | 3 | 315 | 5 | 18 | 4 | 3 | 49 | 10 | 143 | 13 | 552 | 85 | 1 | 20
DEL PEAK 22(9Q21.11) CNV | 47 | 2 | 38 | 50 | 37 | 3 | 143 | 5 | 29 | 131 | 3 | 1 | 9 | 1 | 3 | 0 | 6 | 0 | 0 | 1 | 3 | 152 | 1 | 7 | 2 | 0 | 21 | 3 | 21 | 1 | 266 | 49 | 0 | 5
DEL PEAK 22(9Q21.11) WILD-TYPE | 309 | 52 | 313 | 271 | 67 | 9 | 350 | 6 | 50 | 112 | 4 | 3 | 8 | 1 | 0 | 2 | 12 | 1 | 1 | 0 | 0 | 163 | 4 | 11 | 2 | 3 | 28 | 7 | 122 | 12 | 286 | 36 | 1 | 15

Figure S346. Get High-res Image Gene #63: 'Del Peak 22(9q21.11)' versus Clinical Feature #6: 'HISTOLOGICAL.TYPE'

'Del Peak 22(9q21.11)' versus 'PATHOLOGY.T'

P value = 1.48e-09 (Fisher's exact test), Q value = 2.1e-06

Table S347. Gene #63: 'Del Peak 22(9q21.11)' versus Clinical Feature #7: 'PATHOLOGY.T'

nPatients | T0+T1 | T2 | T3 | T4
--- | --- | --- | --- | ---
ALL | 448 | 611 | 688 | 208
DEL PEAK 22(9Q21.11) CNV | 142 | 223 | 151 | 41
DEL PEAK 22(9Q21.11) WILD-TYPE | 306 | 388 | 537 | 167

Figure S347. Get High-res Image Gene #63: 'Del Peak 22(9q21.11)' versus Clinical Feature #7: 'PATHOLOGY.T'

'Del Peak 22(9q21.11)' versus 'TUMOR.STAGE'

P value = 2.63e-09 (Fisher's exact test), Q value = 3.7e-06

Table S348. Gene #63: 'Del Peak 22(9q21.11)' versus Clinical Feature #10: 'TUMOR.STAGE'

nPatients | I | II | III | IV
--- | --- | --- | --- | ---
ALL | 685 | 487 | 876 | 420
DEL PEAK 22(9Q21.11) CNV | 227 | 129 | 352 | 104
DEL PEAK 22(9Q21.11) WILD-TYPE | 458 | 358 | 524 | 316

Figure S348. Get High-res Image Gene #63: 'Del Peak 22(9q21.11)' versus Clinical Feature #10: 'TUMOR.STAGE'

'Del Peak 22(9q21.11)' versus 'RADIATIONS.RADIATION.REGIMENINDICATION'

P value = 9.63e-14 (Fisher's exact test), Q value = 1.4e-10

Table S349. Gene #63: 'Del Peak 22(9q21.11)' versus Clinical Feature #11: 'RADIATIONS.RADIATION.REGIMENINDICATION'

nPatients | NO | YES
--- | --- | ---
ALL | 835 | 3816
DEL PEAK 22(9Q21.11) CNV | 156 | 1190
DEL PEAK 22(9Q21.11) WILD-TYPE | 679 | 2626

Figure S349. Get High-res Image Gene #63: 'Del Peak 22(9q21.11)' versus Clinical Feature #11: 'RADIATIONS.RADIATION.REGIMENINDICATION'

'Del Peak 23(9q34.13)' versus 'AGE'

P value = 7.74e-05 (t-test), Q value = 0.098

Table S350. Gene #64: 'Del Peak 23(9q34.13)' versus Clinical Feature #2: 'AGE'

| nPatients | Mean (Std.Dev)
--- | --- | ---
ALL | 4585 | 61.9 (12.6)
DEL PEAK 23(9Q34.13) CNV | 1337 | 63.0 (11.9)
DEL PEAK 23(9Q34.13) WILD-TYPE | 3248 | 61.4 (12.8)

Figure S350. Get High-res Image Gene #64: 'Del Peak 23(9q34.13)' versus Clinical Feature #2: 'AGE'

'Del Peak 23(9q34.13)' versus 'PRIMARY.SITE.OF.DISEASE'

P value = 7.47e-104 (Chi-square test), Q value = 1.2e-100

Table S351. Gene #64: 'Del Peak 23(9q34.13)' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'

nPatients | BLADDER | BRAIN | BREAST | COLON | ENDOMETRIAL | HEAD/NECK | KIDNEY | LUNG | OMENTUM | OVARY | PERITONEUM (OVARY) | RECTUM
--- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | ---
ALL | 131 | 544 | 857 | 412 | 454 | 321 | 493 | 714 | 2 | 548 | 2 | 159
DEL PEAK 23(9Q34.13) CNV | 46 | 70 | 227 | 51 | 103 | 43 | 149 | 315 | 1 | 328 | 2 | 30
DEL PEAK 23(9Q34.13) WILD-TYPE | 85 | 474 | 630 | 361 | 351 | 278 | 344 | 399 | 1 | 220 | 0 | 129

Figure S351. Get High-res Image Gene #64: 'Del Peak 23(9q34.13)' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'

'Del Peak 23(9q34.13)' versus 'HISTOLOGICAL.TYPE'

P value = 1.92e-84 (Chi-square test), Q value = 3.2e-81

Table S352. Gene #64: 'Del Peak 23(9q34.13)' versus Clinical Feature #6: 'HISTOLOGICAL.TYPE'

nPatients | COLON ADENOCARCINOMA | COLON MUCINOUS ADENOCARCINOMA | ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA | HEAD & NECK SQUAMOUS CELL CARCINOMA | INFILTRATING DUCTAL CARCINOMA | INFILTRATING LOBULAR 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 HISTOLOGY (PLEASE SPECIFY) | MIXED SEROUS AND ENDOMETRIOID | MUCINOUS (COLLOID) ADENOCARCINOMA | MUCINOUS (COLLOID) CARCINOMA | MUSCLE INVASIVE UROTHELIAL CARCINOMA (PT2 OR ABOVE) | OTHER SPECIFY | RECTAL ADENOCARCINOMA | RECTAL MUCINOUS ADENOCARCINOMA | SEROUS CYSTADENOCARCINOMA | SEROUS ENDOMETRIAL ADENOCARCINOMA | TREATED PRIMARY GBM | UNTREATED PRIMARY (DE NOVO) GBM
--- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | ---
ALL | 356 | 54 | 351 | 321 | 104 | 12 | 493 | 11 | 79 | 243 | 7 | 4 | 17 | 2 | 3 | 2 | 18 | 1 | 1 | 1 | 3 | 315 | 5 | 18 | 4 | 3 | 49 | 10 | 143 | 13 | 552 | 85 | 1 | 20
DEL PEAK 23(9Q34.13) CNV | 49 | 2 | 45 | 43 | 31 | 2 | 149 | 4 | 26 | 111 | 3 | 1 | 9 | 1 | 3 | 0 | 5 | 0 | 0 | 0 | 3 | 147 | 1 | 8 | 2 | 0 | 20 | 1 | 29 | 1 | 331 | 50 | 0 | 6
DEL PEAK 23(9Q34.13) WILD-TYPE | 307 | 52 | 306 | 278 | 73 | 10 | 344 | 7 | 53 | 132 | 4 | 3 | 8 | 1 | 0 | 2 | 13 | 1 | 1 | 1 | 0 | 168 | 4 | 10 | 2 | 3 | 29 | 9 | 114 | 12 | 221 | 35 | 1 | 14

Figure S352. Get High-res Image Gene #64: 'Del Peak 23(9q34.13)' versus Clinical Feature #6: 'HISTOLOGICAL.TYPE'

'Del Peak 23(9q34.13)' versus 'PATHOLOGY.T'

P value = 1.73e-08 (Fisher's exact test), Q value = 2.4e-05

Table S353. Gene #64: 'Del Peak 23(9q34.13)' versus Clinical Feature #7: 'PATHOLOGY.T'

nPatients | T0+T1 | T2 | T3 | T4
--- | --- | --- | --- | ---
ALL | 448 | 611 | 688 | 208
DEL PEAK 23(9Q34.13) CNV | 138 | 212 | 158 | 34
DEL PEAK 23(9Q34.13) WILD-TYPE | 310 | 399 | 530 | 174

Figure S353. Get High-res Image Gene #64: 'Del Peak 23(9q34.13)' versus Clinical Feature #7: 'PATHOLOGY.T'

'Del Peak 23(9q34.13)' versus 'TUMOR.STAGE'

P value = 2.46e-13 (Fisher's exact test), Q value = 3.6e-10

Table S354. Gene #64: 'Del Peak 23(9q34.13)' versus Clinical Feature #10: 'TUMOR.STAGE'

nPatients | I | II | III | IV
--- | --- | --- | --- | ---
ALL | 685 | 487 | 876 | 420
DEL PEAK 23(9Q34.13) CNV | 217 | 129 | 393 | 123
DEL PEAK 23(9Q34.13) WILD-TYPE | 468 | 358 | 483 | 297

Figure S354. Get High-res Image Gene #64: 'Del Peak 23(9q34.13)' versus Clinical Feature #10: 'TUMOR.STAGE'

'Del Peak 23(9q34.13)' versus 'RADIATIONS.RADIATION.REGIMENINDICATION'

P value = 1.9e-14 (Fisher's exact test), Q value = 2.8e-11

Table S355. Gene #64: 'Del Peak 23(9q34.13)' versus Clinical Feature #11: 'RADIATIONS.RADIATION.REGIMENINDICATION'

nPatients | NO | YES
--- | --- | ---
ALL | 835 | 3816
DEL PEAK 23(9Q34.13) CNV | 158 | 1216
DEL PEAK 23(9Q34.13) WILD-TYPE | 677 | 2600

Figure S355. Get High-res Image Gene #64: 'Del Peak 23(9q34.13)' versus Clinical Feature #11: 'RADIATIONS.RADIATION.REGIMENINDICATION'

'Del Peak 24(9q34.3)' versus 'AGE'

P value = 0.000148 (t-test), Q value = 0.18

Table S356. Gene #65: 'Del Peak 24(9q34.3)' versus Clinical Feature #2: 'AGE'

| nPatients | Mean (Std.Dev)
--- | --- | ---
ALL | 4585 | 61.9 (12.6)
DEL PEAK 24(9Q34.3) CNV | 1341 | 63.0 (12.0)
DEL PEAK 24(9Q34.3) WILD-TYPE | 3244 | 61.5 (12.8)

Figure S356. Get High-res Image Gene #65: 'Del Peak 24(9q34.3)' versus Clinical Feature #2: 'AGE'

'Del Peak 24(9q34.3)' versus 'PRIMARY.SITE.OF.DISEASE'

P value = 8.36e-98 (Chi-square test), Q value = 1.4e-94

Table S357. Gene #65: 'Del Peak 24(9q34.3)' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'

nPatients | BLADDER | BRAIN | BREAST | COLON | ENDOMETRIAL | HEAD/NECK | KIDNEY | LUNG | OMENTUM | OVARY | PERITONEUM (OVARY) | RECTUM
--- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | ---
ALL | 131 | 544 | 857 | 412 | 454 | 321 | 493 | 714 | 2 | 548 | 2 | 159
DEL PEAK 24(9Q34.3) CNV | 47 | 73 | 235 | 49 | 102 | 45 | 149 | 313 | 1 | 321 | 2 | 30
DEL PEAK 24(9Q34.3) WILD-TYPE | 84 | 471 | 622 | 363 | 352 | 276 | 344 | 401 | 1 | 227 | 0 | 129

Figure S357. Get High-res Image Gene #65: 'Del Peak 24(9q34.3)' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'

'Del Peak 24(9q34.3)' versus 'HISTOLOGICAL.TYPE'

P value = 9.53e-81 (Chi-square test), Q value = 1.6e-77

Table S358. Gene #65: 'Del Peak 24(9q34.3)' versus Clinical Feature #6: 'HISTOLOGICAL.TYPE'

nPatients | COLON ADENOCARCINOMA | COLON MUCINOUS ADENOCARCINOMA | ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA | HEAD & NECK SQUAMOUS CELL CARCINOMA | INFILTRATING DUCTAL CARCINOMA | INFILTRATING LOBULAR 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 HISTOLOGY (PLEASE SPECIFY) | MIXED SEROUS AND ENDOMETRIOID | MUCINOUS (COLLOID) ADENOCARCINOMA | MUCINOUS (COLLOID) CARCINOMA | MUSCLE INVASIVE UROTHELIAL CARCINOMA (PT2 OR ABOVE) | OTHER SPECIFY | RECTAL ADENOCARCINOMA | RECTAL MUCINOUS ADENOCARCINOMA | SEROUS CYSTADENOCARCINOMA | SEROUS ENDOMETRIAL ADENOCARCINOMA | TREATED PRIMARY GBM | UNTREATED PRIMARY (DE NOVO) GBM
--- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | ---
ALL | 356 | 54 | 351 | 321 | 104 | 12 | 493 | 11 | 79 | 243 | 7 | 4 | 17 | 2 | 3 | 2 | 18 | 1 | 1 | 1 | 3 | 315 | 5 | 18 | 4 | 3 | 49 | 10 | 143 | 13 | 552 | 85 | 1 | 20
DEL PEAK 24(9Q34.3) CNV | 47 | 2 | 45 | 45 | 33 | 2 | 149 | 4 | 25 | 107 | 3 | 1 | 9 | 1 | 3 | 0 | 5 | 0 | 0 | 0 | 3 | 150 | 1 | 8 | 2 | 0 | 20 | 1 | 29 | 1 | 324 | 49 | 0 | 6
DEL PEAK 24(9Q34.3) WILD-TYPE | 309 | 52 | 306 | 276 | 71 | 10 | 344 | 7 | 54 | 136 | 4 | 3 | 8 | 1 | 0 | 2 | 13 | 1 | 1 | 1 | 0 | 165 | 4 | 10 | 2 | 3 | 29 | 9 | 114 | 12 | 228 | 36 | 1 | 14

Figure S358. Get High-res Image Gene #65: 'Del Peak 24(9q34.3)' versus Clinical Feature #6: 'HISTOLOGICAL.TYPE'

'Del Peak 24(9q34.3)' versus 'PATHOLOGY.T'

P value = 9.21e-09 (Fisher's exact test), Q value = 1.3e-05

Table S359. Gene #65: 'Del Peak 24(9q34.3)' versus Clinical Feature #7: 'PATHOLOGY.T'

nPatients | T0+T1 | T2 | T3 | T4
--- | --- | --- | --- | ---
ALL | 448 | 611 | 688 | 208
DEL PEAK 24(9Q34.3) CNV | 132 | 216 | 158 | 34
DEL PEAK 24(9Q34.3) WILD-TYPE | 316 | 395 | 530 | 174

Figure S359. Get High-res Image Gene #65: 'Del Peak 24(9q34.3)' versus Clinical Feature #7: 'PATHOLOGY.T'

'Del Peak 24(9q34.3)' versus 'TUMOR.STAGE'

P value = 2.71e-12 (Fisher's exact test), Q value = 4e-09

Table S360. Gene #65: 'Del Peak 24(9q34.3)' versus Clinical Feature #10: 'TUMOR.STAGE'

nPatients | I | II | III | IV
--- | --- | --- | --- | ---
ALL | 685 | 487 | 876 | 420
DEL PEAK 24(9Q34.3) CNV | 212 | 131 | 387 | 123
DEL PEAK 24(9Q34.3) WILD-TYPE | 473 | 356 | 489 | 297

Figure S360. Get High-res Image Gene #65: 'Del Peak 24(9q34.3)' versus Clinical Feature #10: 'TUMOR.STAGE'

'Del Peak 24(9q34.3)' versus 'RADIATIONS.RADIATION.REGIMENINDICATION'

P value = 7.05e-14 (Fisher's exact test), Q value = 1e-10

Table S361. Gene #65: 'Del Peak 24(9q34.3)' versus Clinical Feature #11: 'RADIATIONS.RADIATION.REGIMENINDICATION'

nPatients | NO | YES
--- | --- | ---
ALL | 835 | 3816
DEL PEAK 24(9Q34.3) CNV | 160 | 1216
DEL PEAK 24(9Q34.3) WILD-TYPE | 675 | 2600

Figure S361. Get High-res Image Gene #65: 'Del Peak 24(9q34.3)' versus Clinical Feature #11: 'RADIATIONS.RADIATION.REGIMENINDICATION'

'Del Peak 25(10p15.3)' versus 'Time to Death'

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

Table S362. Gene #66: 'Del Peak 25(10p15.3)' versus Clinical Feature #1: 'Time to Death'

| nPatients | nDeath | Duration Range (Median), Month
--- | --- | --- | ---
ALL | 4370 | 1406 | 0.0 - 224.0 (14.4)
DEL PEAK 25(10P15.3) CNV | 1197 | 570 | 0.0 - 177.4 (11.5)
DEL PEAK 25(10P15.3) WILD-TYPE | 3173 | 836 | 0.0 - 224.0 (16.1)

Figure S362. Get High-res Image Gene #66: 'Del Peak 25(10p15.3)' versus Clinical Feature #1: 'Time to Death'

'Del Peak 25(10p15.3)' versus 'PRIMARY.SITE.OF.DISEASE'

P value = 4.91e-243 (Chi-square test), Q value = 8.5e-240

Table S363. Gene #66: 'Del Peak 25(10p15.3)' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'

nPatients | BLADDER | BRAIN | BREAST | COLON | ENDOMETRIAL | HEAD/NECK | KIDNEY | LUNG | OMENTUM | OVARY | PERITONEUM (OVARY) | RECTUM
--- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | ---
ALL | 131 | 544 | 857 | 412 | 454 | 321 | 493 | 714 | 2 | 548 | 2 | 159
DEL PEAK 25(10P15.3) CNV | 22 | 449 | 109 | 68 | 30 | 108 | 62 | 242 | 1 | 114 | 0 | 33
DEL PEAK 25(10P15.3) WILD-TYPE | 109 | 95 | 748 | 344 | 424 | 213 | 431 | 472 | 1 | 434 | 2 | 126

Figure S363. Get High-res Image Gene #66: 'Del Peak 25(10p15.3)' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'

'Del Peak 25(10p15.3)' versus 'GENDER'

P value = 1.84e-25 (Fisher's exact test), Q value = 2.8e-22

Table S364. Gene #66: 'Del Peak 25(10p15.3)' versus Clinical Feature #4: 'GENDER'

nPatients | FEMALE | MALE
--- | --- | ---
ALL | 2924 | 1717
DEL PEAK 25(10P15.3) CNV | 627 | 612
DEL PEAK 25(10P15.3) WILD-TYPE | 2297 | 1105

Figure S364. Get High-res Image Gene #66: 'Del Peak 25(10p15.3)' versus Clinical Feature #4: 'GENDER'

'Del Peak 25(10p15.3)' versus 'HISTOLOGICAL.TYPE'

P value = 2.64e-48 (Chi-square test), Q value = 4.2e-45

Table S365. Gene #66: 'Del Peak 25(10p15.3)' versus Clinical Feature #6: 'HISTOLOGICAL.TYPE'

nPatients | COLON ADENOCARCINOMA | COLON MUCINOUS ADENOCARCINOMA | ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA | HEAD & NECK SQUAMOUS CELL CARCINOMA | INFILTRATING DUCTAL CARCINOMA | INFILTRATING LOBULAR 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 HISTOLOGY (PLEASE SPECIFY) | MIXED SEROUS AND ENDOMETRIOID | MUCINOUS (COLLOID) ADENOCARCINOMA | MUCINOUS (COLLOID) CARCINOMA | MUSCLE INVASIVE UROTHELIAL CARCINOMA (PT2 OR ABOVE) | OTHER SPECIFY | RECTAL ADENOCARCINOMA | RECTAL MUCINOUS ADENOCARCINOMA | SEROUS CYSTADENOCARCINOMA | SEROUS ENDOMETRIAL ADENOCARCINOMA | TREATED PRIMARY GBM | UNTREATED PRIMARY (DE NOVO) GBM
--- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | ---
ALL | 356 | 54 | 351 | 321 | 104 | 12 | 493 | 11 | 79 | 243 | 7 | 4 | 17 | 2 | 3 | 2 | 18 | 1 | 1 | 1 | 3 | 315 | 5 | 18 | 4 | 3 | 49 | 10 | 143 | 13 | 552 | 85 | 1 | 20
DEL PEAK 25(10P15.3) CNV | 61 | 7 | 11 | 108 | 11 | 1 | 62 | 3 | 12 | 68 | 5 | 1 | 4 | 0 | 1 | 0 | 3 | 1 | 0 | 0 | 0 | 142 | 0 | 1 | 1 | 1 | 11 | 2 | 29 | 4 | 115 | 18 | 1 | 16
DEL PEAK 25(10P15.3) WILD-TYPE | 295 | 47 | 340 | 213 | 93 | 11 | 431 | 8 | 67 | 175 | 2 | 3 | 13 | 2 | 2 | 2 | 15 | 0 | 1 | 1 | 3 | 173 | 5 | 17 | 3 | 2 | 38 | 8 | 114 | 9 | 437 | 67 | 0 | 4

Figure S365. Get High-res Image Gene #66: 'Del Peak 25(10p15.3)' versus Clinical Feature #6: 'HISTOLOGICAL.TYPE'

'Del Peak 25(10p15.3)' versus 'PATHOLOGY.T'

P value = 4.26e-07 (Fisher's exact test), Q value = 0.00058

Table S366. Gene #66: 'Del Peak 25(10p15.3)' versus Clinical Feature #7: 'PATHOLOGY.T'

nPatients | T0+T1 | T2 | T3 | T4
--- | --- | --- | --- | ---
ALL | 448 | 611 | 688 | 208
DEL PEAK 25(10P15.3) CNV | 94 | 186 | 132 | 68
DEL PEAK 25(10P15.3) WILD-TYPE | 354 | 425 | 556 | 140

Figure S366. Get High-res Image Gene #66: 'Del Peak 25(10p15.3)' versus Clinical Feature #7: 'PATHOLOGY.T'

'Del Peak 25(10p15.3)' versus 'RADIATIONS.RADIATION.REGIMENINDICATION'

P value = 1.22e-34 (Fisher's exact test), Q value = 1.9e-31

Table S367. Gene #66: 'Del Peak 25(10p15.3)' versus Clinical Feature #11: 'RADIATIONS.RADIATION.REGIMENINDICATION'

nPatients | NO | YES
--- | --- | ---
ALL | 835 | 3816
DEL PEAK 25(10P15.3) CNV | 371 | 871
DEL PEAK 25(10P15.3) WILD-TYPE | 464 | 2945

Figure S367. Get High-res Image Gene #66: 'Del Peak 25(10p15.3)' versus Clinical Feature #11: 'RADIATIONS.RADIATION.REGIMENINDICATION'

'Del Peak 26(10q23.31)' versus 'Time to Death'

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

Table S368. Gene #67: 'Del Peak 26(10q23.31)' versus Clinical Feature #1: 'Time to Death'

| nPatients | nDeath | Duration Range (Median), Month
--- | --- | --- | ---
ALL | 4370 | 1406 | 0.0 - 224.0 (14.4)
DEL PEAK 26(10Q23.31) CNV | 1570 | 690 | 0.0 - 211.5 (12.0)
DEL PEAK 26(10Q23.31) WILD-TYPE | 2800 | 716 | 0.0 - 224.0 (16.3)

Figure S368. Get High-res Image Gene #67: 'Del Peak 26(10q23.31)' versus Clinical Feature #1: 'Time to Death'

'Del Peak 26(10q23.31)' versus 'PRIMARY.SITE.OF.DISEASE'

P value = 5.8e-192 (Chi-square test), Q value = 1e-188

Table S369. Gene #67: 'Del Peak 26(10q23.31)' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'

nPatients | BLADDER | BRAIN | BREAST | COLON | ENDOMETRIAL | HEAD/NECK | KIDNEY | LUNG | OMENTUM | OVARY | PERITONEUM (OVARY) | RECTUM
--- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | ---
ALL | 131 | 544 | 857 | 412 | 454 | 321 | 493 | 714 | 2 | 548 | 2 | 159
DEL PEAK 26(10Q23.31) CNV | 57 | 486 | 247 | 94 | 56 | 82 | 90 | 268 | 1 | 212 | 1 | 50
DEL PEAK 26(10Q23.31) WILD-TYPE | 74 | 58 | 610 | 318 | 398 | 239 | 403 | 446 | 1 | 336 | 1 | 109

Figure S369. Get High-res Image Gene #67: 'Del Peak 26(10q23.31)' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'

'Del Peak 26(10q23.31)' versus 'GENDER'

P value = 2.92e-11 (Fisher's exact test), Q value = 4.2e-08

Table S370. Gene #67: 'Del Peak 26(10q23.31)' versus Clinical Feature #4: 'GENDER'

nPatients | FEMALE | MALE
--- | --- | ---
ALL | 2924 | 1717
DEL PEAK 26(10Q23.31) CNV | 931 | 714
DEL PEAK 26(10Q23.31) WILD-TYPE | 1993 | 1003

Figure S370. Get High-res Image Gene #67: 'Del Peak 26(10q23.31)' versus Clinical Feature #4: 'GENDER'

'Del Peak 26(10q23.31)' versus 'HISTOLOGICAL.TYPE'

P value = 2.27e-44 (Chi-square test), Q value = 3.6e-41

Table S371. Gene #67: 'Del Peak 26(10q23.31)' versus Clinical Feature #6: 'HISTOLOGICAL.TYPE'

nPatients | COLON ADENOCARCINOMA | COLON MUCINOUS ADENOCARCINOMA | ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA | HEAD & NECK SQUAMOUS CELL CARCINOMA | INFILTRATING DUCTAL CARCINOMA | INFILTRATING LOBULAR 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 HISTOLOGY (PLEASE SPECIFY) | MIXED SEROUS AND ENDOMETRIOID | MUCINOUS (COLLOID) ADENOCARCINOMA | MUCINOUS (COLLOID) CARCINOMA | MUSCLE INVASIVE UROTHELIAL CARCINOMA (PT2 OR ABOVE) | OTHER SPECIFY | RECTAL ADENOCARCINOMA | RECTAL MUCINOUS ADENOCARCINOMA | SEROUS CYSTADENOCARCINOMA | SEROUS ENDOMETRIAL ADENOCARCINOMA | TREATED PRIMARY GBM | UNTREATED PRIMARY (DE NOVO) GBM
--- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | ---
ALL | 356 | 54 | 351 | 321 | 104 | 12 | 493 | 11 | 79 | 243 | 7 | 4 | 17 | 2 | 3 | 2 | 18 | 1 | 1 | 1 | 3 | 315 | 5 | 18 | 4 | 3 | 49 | 10 | 143 | 13 | 552 | 85 | 1 | 20
DEL PEAK 26(10Q23.31) CNV | 85 | 8 | 28 | 82 | 33 | 3 | 90 | 3 | 13 | 72 | 4 | 1 | 4 | 0 | 3 | 0 | 3 | 1 | 0 | 1 | 2 | 159 | 0 | 3 | 1 | 1 | 18 | 1 | 41 | 7 | 214 | 25 | 1 | 19
DEL PEAK 26(10Q23.31) WILD-TYPE | 271 | 46 | 323 | 239 | 71 | 9 | 403 | 8 | 66 | 171 | 3 | 3 | 13 | 2 | 0 | 2 | 15 | 0 | 1 | 0 | 1 | 156 | 5 | 15 | 3 | 2 | 31 | 9 | 102 | 6 | 338 | 60 | 0 | 1

Figure S371. Get High-res Image Gene #67: 'Del Peak 26(10q23.31)' versus Clinical Feature #6: 'HISTOLOGICAL.TYPE'

'Del Peak 26(10q23.31)' versus 'RADIATIONS.RADIATION.REGIMENINDICATION'

P value = 2.29e-29 (Fisher's exact test), Q value = 3.5e-26

Table S372. Gene #67: 'Del Peak 26(10q23.31)' versus Clinical Feature #11: 'RADIATIONS.RADIATION.REGIMENINDICATION'

nPatients | NO | YES
--- | --- | ---
ALL | 835 | 3816
DEL PEAK 26(10Q23.31) CNV | 440 | 1210
DEL PEAK 26(10Q23.31) WILD-TYPE | 395 | 2606

Figure S372. Get High-res Image Gene #67: 'Del Peak 26(10q23.31)' versus Clinical Feature #11: 'RADIATIONS.RADIATION.REGIMENINDICATION'

'Del Peak 26(10q23.31)' versus 'YEAROFTOBACCOSMOKINGONSET'

P value = 7.23e-05 (t-test), Q value = 0.092

Table S373. Gene #67: 'Del Peak 26(10q23.31)' versus Clinical Feature #14: 'YEAROFTOBACCOSMOKINGONSET'

| nPatients | Mean (Std.Dev)
--- | --- | ---
ALL | 605 | 1962.9 (12.6)
DEL PEAK 26(10Q23.31) CNV | 202 | 1960.2 (10.9)
DEL PEAK 26(10Q23.31) WILD-TYPE | 403 | 1964.2 (13.1)

Figure S373. Get High-res Image Gene #67: 'Del Peak 26(10q23.31)' versus Clinical Feature #14: 'YEAROFTOBACCOSMOKINGONSET'

'Del Peak 27(10q26.3)' versus 'Time to Death'

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

Table S374. Gene #68: 'Del Peak 27(10q26.3)' versus Clinical Feature #1: 'Time to Death'

| nPatients | nDeath | Duration Range (Median), Month
--- | --- | --- | ---
ALL | 4370 | 1406 | 0.0 - 224.0 (14.4)
DEL PEAK 27(10Q26.3) CNV | 1493 | 677 | 0.0 - 211.5 (11.8)
DEL PEAK 27(10Q26.3) WILD-TYPE | 2877 | 729 | 0.0 - 224.0 (16.4)

Figure S374. Get High-res Image Gene #68: 'Del Peak 27(10q26.3)' versus Clinical Feature #1: 'Time to Death'

'Del Peak 27(10q26.3)' versus 'PRIMARY.SITE.OF.DISEASE'

P value = 6.56e-206 (Chi-square test), Q value = 1.1e-202

Table S375. Gene #68: 'Del Peak 27(10q26.3)' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'

nPatients | BLADDER | BRAIN | BREAST | COLON | ENDOMETRIAL | HEAD/NECK | KIDNEY | LUNG | OMENTUM | OVARY | PERITONEUM (OVARY) | RECTUM
--- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | ---
ALL | 131 | 544 | 857 | 412 | 454 | 321 | 493 | 714 | 2 | 548 | 2 | 159
DEL PEAK 27(10Q26.3) CNV | 47 | 487 | 251 | 89 | 37 | 74 | 94 | 254 | 0 | 185 | 1 | 46
DEL PEAK 27(10Q26.3) WILD-TYPE | 84 | 57 | 606 | 323 | 417 | 247 | 399 | 460 | 2 | 363 | 1 | 113

Figure S375. Get High-res Image Gene #68: 'Del Peak 27(10q26.3)' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'

'Del Peak 27(10q26.3)' versus 'GENDER'

P value = 1.1e-12 (Fisher's exact test), Q value = 1.6e-09

Table S376. Gene #68: 'Del Peak 27(10q26.3)' versus Clinical Feature #4: 'GENDER'

nPatients | FEMALE | MALE
--- | --- | ---
ALL | 2924 | 1717
DEL PEAK 27(10Q26.3) CNV | 875 | 691
DEL PEAK 27(10Q26.3) WILD-TYPE | 2049 | 1026

Figure S376. Get High-res Image Gene #68: 'Del Peak 27(10q26.3)' versus Clinical Feature #4: 'GENDER'

'Del Peak 27(10q26.3)' versus 'HISTOLOGICAL.TYPE'

P value = 3.27e-38 (Chi-square test), Q value = 5.2e-35

Table S377. Gene #68: 'Del Peak 27(10q26.3)' versus Clinical Feature #6: 'HISTOLOGICAL.TYPE'

nPatients | COLON ADENOCARCINOMA | COLON MUCINOUS ADENOCARCINOMA | ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA | HEAD & NECK SQUAMOUS CELL CARCINOMA | INFILTRATING DUCTAL CARCINOMA | INFILTRATING LOBULAR 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 HISTOLOGY (PLEASE SPECIFY) | MIXED SEROUS AND ENDOMETRIOID | MUCINOUS (COLLOID) ADENOCARCINOMA | MUCINOUS (COLLOID) CARCINOMA | MUSCLE INVASIVE UROTHELIAL CARCINOMA (PT2 OR ABOVE) | OTHER SPECIFY | RECTAL ADENOCARCINOMA | RECTAL MUCINOUS ADENOCARCINOMA | SEROUS CYSTADENOCARCINOMA | SEROUS ENDOMETRIAL ADENOCARCINOMA | TREATED PRIMARY GBM | UNTREATED PRIMARY (DE NOVO) GBM
--- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | ---
ALL | 356 | 54 | 351 | 321 | 104 | 12 | 493 | 11 | 79 | 243 | 7 | 4 | 17 | 2 | 3 | 2 | 18 | 1 | 1 | 1 | 3 | 315 | 5 | 18 | 4 | 3 | 49 | 10 | 143 | 13 | 552 | 85 | 1 | 20
DEL PEAK 27(10Q26.3) CNV | 81 | 8 | 20 | 74 | 28 | 1 | 94 | 3 | 16 | 71 | 3 | 1 | 5 | 0 | 2 | 0 | 3 | 0 | 0 | 1 | 1 | 146 | 0 | 2 | 1 | 1 | 13 | 2 | 38 | 6 | 186 | 15 | 1 | 20
DEL PEAK 27(10Q26.3) WILD-TYPE | 275 | 46 | 331 | 247 | 76 | 11 | 399 | 8 | 63 | 172 | 4 | 3 | 12 | 2 | 1 | 2 | 15 | 1 | 1 | 0 | 2 | 169 | 5 | 16 | 3 | 2 | 36 | 8 | 105 | 7 | 366 | 70 | 0 | 0

Figure S377. Get High-res Image Gene #68: 'Del Peak 27(10q26.3)' versus Clinical Feature #6: 'HISTOLOGICAL.TYPE'

'Del Peak 27(10q26.3)' versus 'RADIATIONS.RADIATION.REGIMENINDICATION'

P value = 1.05e-33 (Fisher's exact test), Q value = 1.6e-30

Table S378. Gene #68: 'Del Peak 27(10q26.3)' versus Clinical Feature #11: 'RADIATIONS.RADIATION.REGIMENINDICATION'

nPatients | NO | YES
--- | --- | ---
ALL | 835 | 3816
DEL PEAK 27(10Q26.3) CNV | 435 | 1134
DEL PEAK 27(10Q26.3) WILD-TYPE | 400 | 2682

Figure S378. Get High-res Image Gene #68: 'Del Peak 27(10q26.3)' versus Clinical Feature #11: 'RADIATIONS.RADIATION.REGIMENINDICATION'

'Del Peak 28(11p15.5)' versus 'PRIMARY.SITE.OF.DISEASE'

P value = 6.24e-116 (Chi-square test), Q value = 1e-112

Table S379. Gene #69: 'Del Peak 28(11p15.5)' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'

nPatients | BLADDER | BRAIN | BREAST | COLON | ENDOMETRIAL | HEAD/NECK | KIDNEY | LUNG | OMENTUM | OVARY | PERITONEUM (OVARY) | RECTUM
--- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | ---
ALL | 131 | 544 | 857 | 412 | 454 | 321 | 493 | 714 | 2 | 548 | 2 | 159
DEL PEAK 28(11P15.5) CNV | 66 | 125 | 249 | 54 | 78 | 101 | 17 | 259 | 0 | 327 | 0 | 23
DEL PEAK 28(11P15.5) WILD-TYPE | 65 | 419 | 608 | 358 | 376 | 220 | 476 | 455 | 2 | 221 | 2 | 136

Figure S379. Get High-res Image Gene #69: 'Del Peak 28(11p15.5)' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'

'Del Peak 28(11p15.5)' versus 'HISTOLOGICAL.TYPE'

P value = 2.96e-119 (Chi-square test), Q value = 5e-116

Table S380. Gene #69: 'Del Peak 28(11p15.5)' versus Clinical Feature #6: 'HISTOLOGICAL.TYPE'

nPatients | COLON ADENOCARCINOMA | COLON MUCINOUS ADENOCARCINOMA | ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA | HEAD & NECK SQUAMOUS CELL CARCINOMA | INFILTRATING DUCTAL CARCINOMA | INFILTRATING LOBULAR 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 HISTOLOGY (PLEASE SPECIFY) | MIXED SEROUS AND ENDOMETRIOID | MUCINOUS (COLLOID) ADENOCARCINOMA | MUCINOUS (COLLOID) CARCINOMA | MUSCLE INVASIVE UROTHELIAL CARCINOMA (PT2 OR ABOVE) | OTHER SPECIFY | RECTAL ADENOCARCINOMA | RECTAL MUCINOUS ADENOCARCINOMA | SEROUS CYSTADENOCARCINOMA | SEROUS ENDOMETRIAL ADENOCARCINOMA | TREATED PRIMARY GBM | UNTREATED PRIMARY (DE NOVO) GBM
--- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | ---
ALL | 356 | 54 | 351 | 321 | 104 | 12 | 493 | 11 | 79 | 243 | 7 | 4 | 17 | 2 | 3 | 2 | 18 | 1 | 1 | 1 | 3 | 315 | 5 | 18 | 4 | 3 | 49 | 10 | 143 | 13 | 552 | 85 | 1 | 20
DEL PEAK 28(11P15.5) CNV | 47 | 7 | 28 | 101 | 38 | 3 | 17 | 1 | 21 | 71 | 4 | 0 | 5 | 2 | 0 | 0 | 3 | 1 | 0 | 1 | 0 | 149 | 1 | 5 | 1 | 0 | 25 | 2 | 19 | 3 | 327 | 45 | 0 | 6
DEL PEAK 28(11P15.5) WILD-TYPE | 309 | 47 | 323 | 220 | 66 | 9 | 476 | 10 | 58 | 172 | 3 | 4 | 12 | 0 | 3 | 2 | 15 | 0 | 1 | 0 | 3 | 166 | 4 | 13 | 3 | 3 | 24 | 8 | 124 | 10 | 225 | 40 | 1 | 14

Figure S380. Get High-res Image Gene #69: 'Del Peak 28(11p15.5)' versus Clinical Feature #6: 'HISTOLOGICAL.TYPE'

'Del Peak 28(11p15.5)' versus 'PATHOLOGY.T'

P value = 3.58e-10 (Fisher's exact test), Q value = 5.1e-07

Table S381. Gene #69: 'Del Peak 28(11p15.5)' versus Clinical Feature #7: 'PATHOLOGY.T'

nPatients | T0+T1 | T2 | T3 | T4
--- | --- | --- | --- | ---
ALL | 448 | 611 | 688 | 208
DEL PEAK 28(11P15.5) CNV | 70 | 173 | 106 | 59
DEL PEAK 28(11P15.5) WILD-TYPE | 378 | 438 | 582 | 149

Figure S381. Get High-res Image Gene #69: 'Del Peak 28(11p15.5)' versus Clinical Feature #7: 'PATHOLOGY.T'

'Del Peak 28(11p15.5)' versus 'PATHOLOGY.N'

P value = 0.000168 (Fisher's exact test), Q value = 0.21

Table S382. Gene #69: 'Del Peak 28(11p15.5)' versus Clinical Feature #8: 'PATHOLOGY.N'

nPatients | N0 | N1 | N2 | N3
--- | --- | --- | --- | ---
ALL | 1036 | 343 | 279 | 11
DEL PEAK 28(11P15.5) CNV | 207 | 98 | 76 | 6
DEL PEAK 28(11P15.5) WILD-TYPE | 829 | 245 | 203 | 5

Figure S382. Get High-res Image Gene #69: 'Del Peak 28(11p15.5)' versus Clinical Feature #8: 'PATHOLOGY.N'

'Del Peak 28(11p15.5)' versus 'TUMOR.STAGE'

P value = 1.79e-16 (Fisher's exact test), Q value = 2.7e-13

Table S383. Gene #69: 'Del Peak 28(11p15.5)' versus Clinical Feature #10: 'TUMOR.STAGE'

nPatients | I | II | III | IV
--- | --- | --- | --- | ---
ALL | 685 | 487 | 876 | 420
DEL PEAK 28(11P15.5) CNV | 149 | 105 | 346 | 127
DEL PEAK 28(11P15.5) WILD-TYPE | 536 | 382 | 530 | 293

Figure S383. Get High-res Image Gene #69: 'Del Peak 28(11p15.5)' versus Clinical Feature #10: 'TUMOR.STAGE'

'Del Peak 29(11q22.3)' versus 'PRIMARY.SITE.OF.DISEASE'

P value = 2.27e-95 (Chi-square test), Q value = 3.8e-92

Table S384. Gene #70: 'Del Peak 29(11q22.3)' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'

nPatients | BLADDER | BRAIN | BREAST | COLON | ENDOMETRIAL | HEAD/NECK | KIDNEY | LUNG | OMENTUM | OVARY | PERITONEUM (OVARY) | RECTUM
--- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | ---
ALL | 131 | 544 | 857 | 412 | 454 | 321 | 493 | 714 | 2 | 548 | 2 | 159
DEL PEAK 29(11Q22.3) CNV | 48 | 90 | 408 | 63 | 68 | 149 | 27 | 189 | 2 | 165 | 2 | 35
DEL PEAK 29(11Q22.3) WILD-TYPE | 83 | 454 | 449 | 349 | 386 | 172 | 466 | 525 | 0 | 383 | 0 | 124

Figure S384. Get High-res Image Gene #70: 'Del Peak 29(11q22.3)' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'

'Del Peak 29(11q22.3)' versus 'HISTOLOGICAL.TYPE'

P value = 6e-56 (Chi-square test), Q value = 9.7e-53

Table S385. Gene #70: 'Del Peak 29(11q22.3)' versus Clinical Feature #6: 'HISTOLOGICAL.TYPE'

nPatients | COLON ADENOCARCINOMA | COLON MUCINOUS ADENOCARCINOMA | ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA | HEAD & NECK SQUAMOUS CELL CARCINOMA | INFILTRATING DUCTAL CARCINOMA | INFILTRATING LOBULAR 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 HISTOLOGY (PLEASE SPECIFY) | MIXED SEROUS AND ENDOMETRIOID | MUCINOUS (COLLOID) ADENOCARCINOMA | MUCINOUS (COLLOID) CARCINOMA | MUSCLE INVASIVE UROTHELIAL CARCINOMA (PT2 OR ABOVE) | OTHER SPECIFY | RECTAL ADENOCARCINOMA | RECTAL MUCINOUS ADENOCARCINOMA | SEROUS CYSTADENOCARCINOMA | SEROUS ENDOMETRIAL ADENOCARCINOMA | TREATED PRIMARY GBM | UNTREATED PRIMARY (DE NOVO) GBM
--- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | ---
ALL | 356 | 54 | 351 | 321 | 104 | 12 | 493 | 11 | 79 | 243 | 7 | 4 | 17 | 2 | 3 | 2 | 18 | 1 | 1 | 1 | 3 | 315 | 5 | 18 | 4 | 3 | 49 | 10 | 143 | 13 | 552 | 85 | 1 | 20
DEL PEAK 29(11Q22.3) CNV | 56 | 7 | 27 | 149 | 50 | 6 | 27 | 2 | 19 | 55 | 4 | 0 | 4 | 1 | 0 | 0 | 4 | 0 | 0 | 0 | 0 | 98 | 2 | 5 | 2 | 0 | 18 | 6 | 28 | 6 | 169 | 36 | 0 | 5
DEL PEAK 29(11Q22.3) WILD-TYPE | 300 | 47 | 324 | 172 | 54 | 6 | 466 | 9 | 60 | 188 | 3 | 4 | 13 | 1 | 3 | 2 | 14 | 1 | 1 | 1 | 3 | 217 | 3 | 13 | 2 | 3 | 31 | 4 | 115 | 7 | 383 | 49 | 1 | 15

Figure S385. Get High-res Image Gene #70: 'Del Peak 29(11q22.3)' versus Clinical Feature #6: 'HISTOLOGICAL.TYPE'

'Del Peak 29(11q22.3)' versus 'PATHOLOGY.T'

P value = 4.74e-09 (Fisher's exact test), Q value = 6.7e-06

Table S386. Gene #70: 'Del Peak 29(11q22.3)' versus Clinical Feature #7: 'PATHOLOGY.T'

nPatients | T0+T1 | T2 | T3 | T4
--- | --- | --- | --- | ---
ALL | 448 | 611 | 688 | 208
DEL PEAK 29(11Q22.3) CNV | 66 | 154 | 125 | 72
DEL PEAK 29(11Q22.3) WILD-TYPE | 382 | 457 | 563 | 136

Figure S386. Get High-res Image Gene #70: 'Del Peak 29(11q22.3)' versus Clinical Feature #7: 'PATHOLOGY.T'

'Del Peak 29(11q22.3)' versus 'PATHOLOGY.N'

P value = 3.12e-08 (Fisher's exact test), Q value = 4.4e-05

Table S387. Gene #70: 'Del Peak 29(11q22.3)' versus Clinical Feature #8: 'PATHOLOGY.N'

nPatients | N0 | N1 | N2 | N3
--- | --- | --- | --- | ---
ALL | 1036 | 343 | 279 | 11
DEL PEAK 29(11Q22.3) CNV | 193 | 95 | 97 | 4
DEL PEAK 29(11Q22.3) WILD-TYPE | 843 | 248 | 182 | 7

Figure S387. Get High-res Image Gene #70: 'Del Peak 29(11q22.3)' versus Clinical Feature #8: 'PATHOLOGY.N'

'Del Peak 29(11q22.3)' versus 'TUMOR.STAGE'

P value = 2.74e-05 (Fisher's exact test), Q value = 0.035

Table S388. Gene #70: 'Del Peak 29(11q22.3)' versus Clinical Feature #10: 'TUMOR.STAGE'

nPatients | I | II | III | IV
--- | --- | --- | --- | ---
ALL | 685 | 487 | 876 | 420
DEL PEAK 29(11Q22.3) CNV | 124 | 102 | 219 | 126
DEL PEAK 29(11Q22.3) WILD-TYPE | 561 | 385 | 657 | 294

Figure S388. Get High-res Image Gene #70: 'Del Peak 29(11q22.3)' versus Clinical Feature #10: 'TUMOR.STAGE'

'Del Peak 30(11q25)' versus 'PRIMARY.SITE.OF.DISEASE'

P value = 4.75e-90 (Chi-square test), Q value = 7.8e-87

Table S389. Gene #71: 'Del Peak 30(11q25)' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'

nPatients | BLADDER | BRAIN | BREAST | COLON | ENDOMETRIAL | HEAD/NECK | KIDNEY | LUNG | OMENTUM | OVARY | PERITONEUM (OVARY) | RECTUM
--- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | ---
ALL | 131 | 544 | 857 | 412 | 454 | 321 | 493 | 714 | 2 | 548 | 2 | 159
DEL PEAK 30(11Q25) CNV | 42 | 91 | 401 | 59 | 72 | 141 | 26 | 206 | 1 | 189 | 2 | 32
DEL PEAK 30(11Q25) WILD-TYPE | 89 | 453 | 456 | 353 | 382 | 180 | 467 | 508 | 1 | 359 | 0 | 127

Figure S389. Get High-res Image Gene #71: 'Del Peak 30(11q25)' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'

'Del Peak 30(11q25)' versus 'GENDER'

P value = 0.000114 (Fisher's exact test), Q value = 0.14

Table S390. Gene #71: 'Del Peak 30(11q25)' versus Clinical Feature #4: 'GENDER'

nPatients | FEMALE | MALE
--- | --- | ---
ALL | 2924 | 1717
DEL PEAK 30(11Q25) CNV | 854 | 412
DEL PEAK 30(11Q25) WILD-TYPE | 2070 | 1305

Figure S390. Get High-res Image Gene #71: 'Del Peak 30(11q25)' versus Clinical Feature #4: 'GENDER'

'Del Peak 30(11q25)' versus 'HISTOLOGICAL.TYPE'

P value = 1.71e-62 (Chi-square test), Q value = 2.8e-59

Table S391. Gene #71: 'Del Peak 30(11q25)' versus Clinical Feature #6: 'HISTOLOGICAL.TYPE'

nPatients | COLON ADENOCARCINOMA | COLON MUCINOUS ADENOCARCINOMA | ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA | HEAD & NECK SQUAMOUS CELL CARCINOMA | INFILTRATING DUCTAL CARCINOMA | INFILTRATING LOBULAR 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 HISTOLOGY (PLEASE SPECIFY) | MIXED SEROUS AND ENDOMETRIOID | MUCINOUS (COLLOID) ADENOCARCINOMA | MUCINOUS (COLLOID) CARCINOMA | MUSCLE INVASIVE UROTHELIAL CARCINOMA (PT2 OR ABOVE) | OTHER SPECIFY | RECTAL ADENOCARCINOMA | RECTAL MUCINOUS ADENOCARCINOMA | SEROUS CYSTADENOCARCINOMA | SEROUS ENDOMETRIAL ADENOCARCINOMA | TREATED PRIMARY GBM | UNTREATED PRIMARY (DE NOVO) GBM
--- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | ---
ALL | 356 | 54 | 351 | 321 | 104 | 12 | 493 | 11 | 79 | 243 | 7 | 4 | 17 | 2 | 3 | 2 | 18 | 1 | 1 | 1 | 3 | 315 | 5 | 18 | 4 | 3 | 49 | 10 | 143 | 13 | 552 | 85 | 1 | 20
DEL PEAK 30(11Q25) CNV | 53 | 6 | 27 | 141 | 51 | 6 | 26 | 2 | 20 | 50 | 4 | 0 | 3 | 1 | 0 | 0 | 4 | 0 | 0 | 1 | 1 | 118 | 2 | 5 | 2 | 0 | 12 | 4 | 25 | 6 | 192 | 40 | 0 | 4
DEL PEAK 30(11Q25) WILD-TYPE | 303 | 48 | 324 | 180 | 53 | 6 | 467 | 9 | 59 | 193 | 3 | 4 | 14 | 1 | 3 | 2 | 14 | 1 | 1 | 0 | 2 | 197 | 3 | 13 | 2 | 3 | 37 | 6 | 118 | 7 | 360 | 45 | 1 | 16

Figure S391. Get High-res Image Gene #71: 'Del Peak 30(11q25)' versus Clinical Feature #6: 'HISTOLOGICAL.TYPE'

'Del Peak 30(11q25)' versus 'PATHOLOGY.T'

P value = 9.7e-11 (Fisher's exact test), Q value = 1.4e-07

Table S392. Gene #71: 'Del Peak 30(11q25)' versus Clinical Feature #7: 'PATHOLOGY.T'

nPatients | T0+T1 | T2 | T3 | T4
--- | --- | --- | --- | ---
ALL | 448 | 611 | 688 | 208
DEL PEAK 30(11Q25) CNV | 70 | 170 | 117 | 71
DEL PEAK 30(11Q25) WILD-TYPE | 378 | 441 | 571 | 137

Figure S392. Get High-res Image Gene #71: 'Del Peak 30(11q25)' versus Clinical Feature #7: 'PATHOLOGY.T'

'Del Peak 30(11q25)' versus 'PATHOLOGY.N'

P value = 3.1e-09 (Fisher's exact test), Q value = 4.4e-06

Table S393. Gene #71: 'Del Peak 30(11q25)' versus Clinical Feature #8: 'PATHOLOGY.N'

nPatients | N0 | N1 | N2 | N3
--- | --- | --- | --- | ---
ALL | 1036 | 343 | 279 | 11
DEL PEAK 30(11Q25) CNV | 195 | 105 | 98 | 3
DEL PEAK 30(11Q25) WILD-TYPE | 841 | 238 | 181 | 8

Figure S393. Get High-res Image Gene #71: 'Del Peak 30(11q25)' versus Clinical Feature #8: 'PATHOLOGY.N'

'Del Peak 30(11q25)' versus 'TUMOR.STAGE'

P value = 2.59e-05 (Fisher's exact test), Q value = 0.034

Table S394. Gene #71: 'Del Peak 30(11q25)' versus Clinical Feature #10: 'TUMOR.STAGE'

nPatients | I | II | III | IV
--- | --- | --- | --- | ---
ALL | 685 | 487 | 876 | 420
DEL PEAK 30(11Q25) CNV | 136 | 102 | 235 | 131
DEL PEAK 30(11Q25) WILD-TYPE | 549 | 385 | 641 | 289

Figure S394. Get High-res Image Gene #71: 'Del Peak 30(11q25)' versus Clinical Feature #10: 'TUMOR.STAGE'

'Del Peak 31(12p13.1)' versus 'PRIMARY.SITE.OF.DISEASE'

P value = 5.87e-21 (Chi-square test), Q value = 8.9e-18

Table S395. Gene #72: 'Del Peak 31(12p13.1)' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'

nPatients | BLADDER | BRAIN | BREAST | COLON | ENDOMETRIAL | HEAD/NECK | KIDNEY | LUNG | OMENTUM | OVARY | PERITONEUM (OVARY) | RECTUM
--- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | ---
ALL | 131 | 544 | 857 | 412 | 454 | 321 | 493 | 714 | 2 | 548 | 2 | 159
DEL PEAK 31(12P13.1) CNV | 17 | 72 | 150 | 45 | 37 | 30 | 6 | 134 | 0 | 90 | 1 | 29
DEL PEAK 31(12P13.1) WILD-TYPE | 114 | 472 | 707 | 367 | 417 | 291 | 487 | 580 | 2 | 458 | 1 | 130

Figure S395. Get High-res Image Gene #72: 'Del Peak 31(12p13.1)' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'

'Del Peak 31(12p13.1)' versus 'GENDER'

P value = 2.28e-07 (Fisher's exact test), Q value = 0.00031

Table S396. Gene #72: 'Del Peak 31(12p13.1)' versus Clinical Feature #4: 'GENDER'

nPatients | FEMALE | MALE
--- | --- | ---
ALL | 2924 | 1717
DEL PEAK 31(12P13.1) CNV | 444 | 170
DEL PEAK 31(12P13.1) WILD-TYPE | 2480 | 1547

Figure S396. Get High-res Image Gene #72: 'Del Peak 31(12p13.1)' versus Clinical Feature #4: 'GENDER'

'Del Peak 31(12p13.1)' versus 'HISTOLOGICAL.TYPE'

P value = 2.52e-36 (Chi-square test), Q value = 4e-33

Table S397. Gene #72: 'Del Peak 31(12p13.1)' versus Clinical Feature #6: 'HISTOLOGICAL.TYPE'

nPatients | COLON ADENOCARCINOMA | COLON MUCINOUS ADENOCARCINOMA | ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA | HEAD & NECK SQUAMOUS CELL CARCINOMA | INFILTRATING DUCTAL CARCINOMA | INFILTRATING LOBULAR 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 HISTOLOGY (PLEASE SPECIFY) | MIXED SEROUS AND ENDOMETRIOID | MUCINOUS (COLLOID) ADENOCARCINOMA | MUCINOUS (COLLOID) CARCINOMA | MUSCLE INVASIVE UROTHELIAL CARCINOMA (PT2 OR ABOVE) | OTHER SPECIFY | RECTAL ADENOCARCINOMA | RECTAL MUCINOUS ADENOCARCINOMA | SEROUS CYSTADENOCARCINOMA | SEROUS ENDOMETRIAL ADENOCARCINOMA | TREATED PRIMARY GBM | UNTREATED PRIMARY (DE NOVO) GBM
--- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | ---
ALL | 356 | 54 | 351 | 321 | 104 | 12 | 493 | 11 | 79 | 243 | 7 | 4 | 17 | 2 | 3 | 2 | 18 | 1 | 1 | 1 | 3 | 315 | 5 | 18 | 4 | 3 | 49 | 10 | 143 | 13 | 552 | 85 | 1 | 20
DEL PEAK 31(12P13.1) CNV | 45 | 0 | 13 | 30 | 24 | 1 | 6 | 1 | 25 | 69 | 1 | 0 | 7 | 1 | 1 | 0 | 5 | 0 | 0 | 0 | 1 | 21 | 2 | 2 | 1 | 1 | 5 | 1 | 28 | 1 | 91 | 22 | 0 | 3
DEL PEAK 31(12P13.1) WILD-TYPE | 311 | 54 | 338 | 291 | 80 | 11 | 487 | 10 | 54 | 174 | 6 | 4 | 10 | 1 | 2 | 2 | 13 | 1 | 1 | 1 | 2 | 294 | 3 | 16 | 3 | 2 | 44 | 9 | 115 | 12 | 461 | 63 | 1 | 17

Figure S397. Get High-res Image Gene #72: 'Del Peak 31(12p13.1)' versus Clinical Feature #6: 'HISTOLOGICAL.TYPE'

'Del Peak 32(12q23.1)' versus 'PRIMARY.SITE.OF.DISEASE'

P value = 4.66e-53 (Chi-square test), Q value = 7.5e-50

Table S398. Gene #73: 'Del Peak 32(12q23.1)' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'

nPatients | BLADDER | BRAIN | BREAST | COLON | ENDOMETRIAL | HEAD/NECK | KIDNEY | LUNG | OMENTUM | OVARY | PERITONEUM (OVARY) | RECTUM
--- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | ---
ALL | 131 | 544 | 857 | 412 | 454 | 321 | 493 | 714 | 2 | 548 | 2 | 159
DEL PEAK 32(12Q23.1) CNV | 21 | 61 | 149 | 48 | 34 | 36 | 6 | 138 | 1 | 187 | 0 | 24
DEL PEAK 32(12Q23.1) WILD-TYPE | 110 | 483 | 708 | 364 | 420 | 285 | 487 | 576 | 1 | 361 | 2 | 135

Figure S398. Get High-res Image Gene #73: 'Del Peak 32(12q23.1)' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'

'Del Peak 32(12q23.1)' versus 'GENDER'

P value = 1.3e-08 (Fisher's exact test), Q value = 1.8e-05

Table S399. Gene #73: 'Del Peak 32(12q23.1)' versus Clinical Feature #4: 'GENDER'

nPatients | FEMALE | MALE
--- | --- | ---
ALL | 2924 | 1717
DEL PEAK 32(12Q23.1) CNV | 511 | 195
DEL PEAK 32(12Q23.1) WILD-TYPE | 2413 | 1522

Figure S399. Get High-res Image Gene #73: 'Del Peak 32(12q23.1)' versus Clinical Feature #4: 'GENDER'

'Del Peak 32(12q23.1)' versus 'HISTOLOGICAL.TYPE'

P value = 2.77e-55 (Chi-square test), Q value = 4.5e-52

Table S400. Gene #73: 'Del Peak 32(12q23.1)' versus Clinical Feature #6: 'HISTOLOGICAL.TYPE'

nPatients | COLON ADENOCARCINOMA | COLON MUCINOUS ADENOCARCINOMA | ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA | HEAD & NECK SQUAMOUS CELL CARCINOMA | INFILTRATING DUCTAL CARCINOMA | INFILTRATING LOBULAR 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 HISTOLOGY (PLEASE SPECIFY) | MIXED SEROUS AND ENDOMETRIOID | MUCINOUS (COLLOID) ADENOCARCINOMA | MUCINOUS (COLLOID) CARCINOMA | MUSCLE INVASIVE UROTHELIAL CARCINOMA (PT2 OR ABOVE) | OTHER SPECIFY | RECTAL ADENOCARCINOMA | RECTAL MUCINOUS ADENOCARCINOMA | SEROUS CYSTADENOCARCINOMA | SEROUS ENDOMETRIAL ADENOCARCINOMA | TREATED PRIMARY GBM | UNTREATED PRIMARY (DE NOVO) GBM
--- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | ---
ALL | 356 | 54 | 351 | 321 | 104 | 12 | 493 | 11 | 79 | 243 | 7 | 4 | 17 | 2 | 3 | 2 | 18 | 1 | 1 | 1 | 3 | 315 | 5 | 18 | 4 | 3 | 49 | 10 | 143 | 13 | 552 | 85 | 1 | 20
DEL PEAK 32(12Q23.1) CNV | 44 | 3 | 10 | 36 | 18 | 0 | 6 | 0 | 17 | 54 | 2 | 0 | 9 | 1 | 0 | 0 | 8 | 0 | 0 | 0 | 1 | 44 | 1 | 1 | 0 | 2 | 4 | 1 | 23 | 1 | 188 | 23 | 0 | 3
DEL PEAK 32(12Q23.1) WILD-TYPE | 312 | 51 | 341 | 285 | 86 | 12 | 487 | 11 | 62 | 189 | 5 | 4 | 8 | 1 | 3 | 2 | 10 | 1 | 1 | 1 | 2 | 271 | 4 | 17 | 4 | 1 | 45 | 9 | 120 | 12 | 364 | 62 | 1 | 17

Figure S400. Get High-res Image Gene #73: 'Del Peak 32(12q23.1)' versus Clinical Feature #6: 'HISTOLOGICAL.TYPE'

'Del Peak 32(12q23.1)' versus 'PATHOLOGY.T'

P value = 3.72e-05 (Fisher's exact test), Q value = 0.048

Table S401. Gene #73: 'Del Peak 32(12q23.1)' versus Clinical Feature #7: 'PATHOLOGY.T'

nPatients | T0+T1 | T2 | T3 | T4
--- | --- | --- | --- | ---
ALL | 448 | 611 | 688 | 208
DEL PEAK 32(12Q23.1) CNV | 29 | 96 | 82 | 20
DEL PEAK 32(12Q23.1) WILD-TYPE | 419 | 515 | 606 | 188

Figure S401. Get High-res Image Gene #73: 'Del Peak 32(12q23.1)' versus Clinical Feature #7: 'PATHOLOGY.T'

'Del Peak 32(12q23.1)' versus 'PATHOLOGICSPREAD(M)'

P value = 1.39e-05 (Chi-square test), Q value = 0.018

Table S402. Gene #73: 'Del Peak 32(12q23.1)' versus Clinical Feature #9: 'PATHOLOGICSPREAD(M)'

nPatients | M0 | M1 | M1A | M1B | MX
--- | --- | --- | --- | --- | ---
ALL | 1398 | 167 | 9 | 1 | 148
DEL PEAK 32(12Q23.1) CNV | 145 | 15 | 1 | 1 | 33
DEL PEAK 32(12Q23.1) WILD-TYPE | 1253 | 152 | 8 | 0 | 115

Figure S402. Get High-res Image Gene #73: 'Del Peak 32(12q23.1)' versus Clinical Feature #9: 'PATHOLOGICSPREAD(M)'

'Del Peak 32(12q23.1)' versus 'TUMOR.STAGE'

P value = 1.58e-06 (Fisher's exact test), Q value = 0.0021

Table S403. Gene #73: 'Del Peak 32(12q23.1)' versus Clinical Feature #10: 'TUMOR.STAGE'

nPatients | I | II | III | IV
--- | --- | --- | --- | ---
ALL | 685 | 487 | 876 | 420
DEL PEAK 32(12Q23.1) CNV | 85 | 62 | 189 | 74
DEL PEAK 32(12Q23.1) WILD-TYPE | 600 | 425 | 687 | 346

Figure S403. Get High-res Image Gene #73: 'Del Peak 32(12q23.1)' versus Clinical Feature #10: 'TUMOR.STAGE'

'Del Peak 33(12q24.33)' versus 'PRIMARY.SITE.OF.DISEASE'

P value = 2.68e-59 (Chi-square test), Q value = 4.3e-56

Table S404. Gene #74: 'Del Peak 33(12q24.33)' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'

nPatients | BLADDER | BRAIN | BREAST | COLON | ENDOMETRIAL | HEAD/NECK | KIDNEY | LUNG | OMENTUM | OVARY | PERITONEUM (OVARY) | RECTUM
--- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | ---
ALL | 131 | 544 | 857 | 412 | 454 | 321 | 493 | 714 | 2 | 548 | 2 | 159
DEL PEAK 33(12Q24.33) CNV | 24 | 68 | 150 | 45 | 46 | 42 | 8 | 152 | 2 | 205 | 0 | 26
DEL PEAK 33(12Q24.33) WILD-TYPE | 107 | 476 | 707 | 367 | 408 | 279 | 485 | 562 | 0 | 343 | 2 | 133

Figure S404. Get High-res Image Gene #74: 'Del Peak 33(12q24.33)' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'

'Del Peak 33(12q24.33)' versus 'GENDER'

P value = 1.54e-08 (Fisher's exact test), Q value = 2.2e-05

Table S405. Gene #74: 'Del Peak 33(12q24.33)' versus Clinical Feature #4: 'GENDER'

nPatients | FEMALE | MALE
--- | --- | ---
ALL | 2924 | 1717
DEL PEAK 33(12Q24.33) CNV | 553 | 216
DEL PEAK 33(12Q24.33) WILD-TYPE | 2371 | 1501

Figure S405. Get High-res Image Gene #74: 'Del Peak 33(12q24.33)' versus Clinical Feature #4: 'GENDER'

'Del Peak 33(12q24.33)' versus 'HISTOLOGICAL.TYPE'

P value = 1.4e-61 (Chi-square test), Q value = 2.3e-58

Table S406. Gene #74: 'Del Peak 33(12q24.33)' versus Clinical Feature #6: 'HISTOLOGICAL.TYPE'

nPatients | COLON ADENOCARCINOMA | COLON MUCINOUS ADENOCARCINOMA | ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA | HEAD & NECK SQUAMOUS CELL CARCINOMA | INFILTRATING DUCTAL CARCINOMA | INFILTRATING LOBULAR 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 HISTOLOGY (PLEASE SPECIFY) | MIXED SEROUS AND ENDOMETRIOID | MUCINOUS (COLLOID) ADENOCARCINOMA | MUCINOUS (COLLOID) CARCINOMA | MUSCLE INVASIVE UROTHELIAL CARCINOMA (PT2 OR ABOVE) | OTHER SPECIFY | RECTAL ADENOCARCINOMA | RECTAL MUCINOUS ADENOCARCINOMA | SEROUS CYSTADENOCARCINOMA | SEROUS ENDOMETRIAL ADENOCARCINOMA | TREATED PRIMARY GBM | UNTREATED PRIMARY (DE NOVO) GBM
--- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | ---
ALL | 356 | 54 | 351 | 321 | 104 | 12 | 493 | 11 | 79 | 243 | 7 | 4 | 17 | 2 | 3 | 2 | 18 | 1 | 1 | 1 | 3 | 315 | 5 | 18 | 4 | 3 | 49 | 10 | 143 | 13 | 552 | 85 | 1 | 20
DEL PEAK 33(12Q24.33) CNV | 42 | 2 | 14 | 42 | 21 | 0 | 8 | 2 | 17 | 60 | 4 | 0 | 7 | 0 | 1 | 0 | 7 | 0 | 0 | 0 | 1 | 51 | 3 | 1 | 0 | 2 | 7 | 1 | 25 | 1 | 207 | 31 | 0 | 3
DEL PEAK 33(12Q24.33) WILD-TYPE | 314 | 52 | 337 | 279 | 83 | 12 | 485 | 9 | 62 | 183 | 3 | 4 | 10 | 2 | 2 | 2 | 11 | 1 | 1 | 1 | 2 | 264 | 2 | 17 | 4 | 1 | 42 | 9 | 118 | 12 | 345 | 54 | 1 | 17

Figure S406. Get High-res Image Gene #74: 'Del Peak 33(12q24.33)' versus Clinical Feature #6: 'HISTOLOGICAL.TYPE'

'Del Peak 33(12q24.33)' versus 'PATHOLOGY.T'

P value = 9.64e-06 (Fisher's exact test), Q value = 0.013

Table S407. Gene #74: 'Del Peak 33(12q24.33)' versus Clinical Feature #7: 'PATHOLOGY.T'

nPatients | T0+T1 | T2 | T3 | T4
--- | --- | --- | --- | ---
ALL | 448 | 611 | 688 | 208
DEL PEAK 33(12Q24.33) CNV | 33 | 106 | 77 | 30
DEL PEAK 33(12Q24.33) WILD-TYPE | 415 | 505 | 611 | 178

Figure S407. Get High-res Image Gene #74: 'Del Peak 33(12q24.33)' versus Clinical Feature #7: 'PATHOLOGY.T'

'Del Peak 33(12q24.33)' versus 'TUMOR.STAGE'

P value = 2.17e-08 (Fisher's exact test), Q value = 3e-05

Table S408. Gene #74: 'Del Peak 33(12q24.33)' versus Clinical Feature #10: 'TUMOR.STAGE'

nPatients | I | II | III | IV
--- | --- | --- | --- | ---
ALL | 685 | 487 | 876 | 420
DEL PEAK 33(12Q24.33) CNV | 94 | 61 | 208 | 82
DEL PEAK 33(12Q24.33) WILD-TYPE | 591 | 426 | 668 | 338

Figure S408. Get High-res Image Gene #74: 'Del Peak 33(12q24.33)' versus Clinical Feature #10: 'TUMOR.STAGE'

'Del Peak 34(13q11)' versus 'PRIMARY.SITE.OF.DISEASE'

P value = 9.08e-157 (Chi-square test), Q value = 1.6e-153

Table S409. Gene #75: 'Del Peak 34(13q11)' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'

nPatients | BLADDER | BRAIN | BREAST | COLON | ENDOMETRIAL | HEAD/NECK | KIDNEY | LUNG | OMENTUM | OVARY | PERITONEUM (OVARY) | RECTUM
--- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | ---
ALL | 131 | 544 | 857 | 412 | 454 | 321 | 493 | 714 | 2 | 548 | 2 | 159
DEL PEAK 34(13Q11) CNV | 31 | 177 | 345 | 10 | 69 | 132 | 73 | 431 | 1 | 308 | 2 | 9
DEL PEAK 34(13Q11) WILD-TYPE | 100 | 367 | 512 | 402 | 385 | 189 | 420 | 283 | 1 | 240 | 0 | 150

Figure S409. Get High-res Image Gene #75: 'Del Peak 34(13q11)' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'

'Del Peak 34(13q11)' versus 'HISTOLOGICAL.TYPE'

P value = 2.19e-151 (Chi-square test), Q value = 3.7e-148

Table S410. Gene #75: 'Del Peak 34(13q11)' versus Clinical Feature #6: 'HISTOLOGICAL.TYPE'

nPatients | COLON ADENOCARCINOMA | COLON MUCINOUS ADENOCARCINOMA | ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA | HEAD & NECK SQUAMOUS CELL CARCINOMA | INFILTRATING DUCTAL CARCINOMA | INFILTRATING LOBULAR 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 HISTOLOGY (PLEASE SPECIFY) | MIXED SEROUS AND ENDOMETRIOID | MUCINOUS (COLLOID) ADENOCARCINOMA | MUCINOUS (COLLOID) CARCINOMA | MUSCLE INVASIVE UROTHELIAL CARCINOMA (PT2 OR ABOVE) | OTHER SPECIFY | RECTAL ADENOCARCINOMA | RECTAL MUCINOUS ADENOCARCINOMA | SEROUS CYSTADENOCARCINOMA | SEROUS ENDOMETRIAL ADENOCARCINOMA | TREATED PRIMARY GBM | UNTREATED PRIMARY (DE NOVO) GBM
--- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | ---
ALL | 356 | 54 | 351 | 321 | 104 | 12 | 493 | 11 | 79 | 243 | 7 | 4 | 17 | 2 | 3 | 2 | 18 | 1 | 1 | 1 | 3 | 315 | 5 | 18 | 4 | 3 | 49 | 10 | 143 | 13 | 552 | 85 | 1 | 20
DEL PEAK 34(13Q11) CNV | 8 | 2 | 32 | 132 | 35 | 2 | 73 | 6 | 42 | 140 | 4 | 1 | 13 | 2 | 0 | 0 | 8 | 1 | 0 | 1 | 2 | 210 | 3 | 3 | 1 | 0 | 13 | 3 | 5 | 4 | 311 | 34 | 0 | 9
DEL PEAK 34(13Q11) WILD-TYPE | 348 | 52 | 319 | 189 | 69 | 10 | 420 | 5 | 37 | 103 | 3 | 3 | 4 | 0 | 3 | 2 | 10 | 0 | 1 | 0 | 1 | 105 | 2 | 15 | 3 | 3 | 36 | 7 | 138 | 9 | 241 | 51 | 1 | 11

Figure S410. Get High-res Image Gene #75: 'Del Peak 34(13q11)' versus Clinical Feature #6: 'HISTOLOGICAL.TYPE'

'Del Peak 34(13q11)' versus 'PATHOLOGY.T'

P value = 1.89e-28 (Fisher's exact test), Q value = 2.9e-25

Table S411. Gene #75: 'Del Peak 34(13q11)' versus Clinical Feature #7: 'PATHOLOGY.T'

nPatients | T0+T1 | T2 | T3 | T4
--- | --- | --- | --- | ---
ALL | 448 | 611 | 688 | 208
DEL PEAK 34(13Q11) CNV | 122 | 266 | 109 | 80
DEL PEAK 34(13Q11) WILD-TYPE | 326 | 345 | 579 | 128

Figure S411. Get High-res Image Gene #75: 'Del Peak 34(13q11)' versus Clinical Feature #7: 'PATHOLOGY.T'

'Del Peak 34(13q11)' versus 'PATHOLOGICSPREAD(M)'

P value = 7.09e-06 (Chi-square test), Q value = 0.0094

Table S412. Gene #75: 'Del Peak 34(13q11)' versus Clinical Feature #9: 'PATHOLOGICSPREAD(M)'

nPatients | M0 | M1 | M1A | M1B | MX
--- | --- | --- | --- | --- | ---
ALL | 1398 | 167 | 9 | 1 | 148
DEL PEAK 34(13Q11) CNV | 384 | 32 | 0 | 0 | 65
DEL PEAK 34(13Q11) WILD-TYPE | 1014 | 135 | 9 | 1 | 83

Figure S412. Get High-res Image Gene #75: 'Del Peak 34(13q11)' versus Clinical Feature #9: 'PATHOLOGICSPREAD(M)'

'Del Peak 34(13q11)' versus 'TUMOR.STAGE'

P value = 9.02e-08 (Fisher's exact test), Q value = 0.00013

Table S413. Gene #75: 'Del Peak 34(13q11)' versus Clinical Feature #10: 'TUMOR.STAGE'

nPatients | I | II | III | IV
--- | --- | --- | --- | ---
ALL | 685 | 487 | 876 | 420
DEL PEAK 34(13Q11) CNV | 234 | 126 | 364 | 158
DEL PEAK 34(13Q11) WILD-TYPE | 451 | 361 | 512 | 262

Figure S413. Get High-res Image Gene #75: 'Del Peak 34(13q11)' versus Clinical Feature #10: 'TUMOR.STAGE'

'Del Peak 34(13q11)' versus 'TOBACCOSMOKINGHISTORYINDICATOR'

P value = 1.62e-06 (Chi-square test), Q value = 0.0022

Table S414. Gene #75: 'Del Peak 34(13q11)' versus Clinical Feature #13: '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 | 15 | 16 | 22 | 25 | 2 | 342 | 208 | 237 | 116
DEL PEAK 34(13Q11) CNV | 3 | 4 | 6 | 4 | 1 | 205 | 101 | 129 | 52
DEL PEAK 34(13Q11) WILD-TYPE | 12 | 12 | 16 | 21 | 1 | 137 | 107 | 108 | 64

Figure S414. Get High-res Image Gene #75: 'Del Peak 34(13q11)' versus Clinical Feature #13: 'TOBACCOSMOKINGHISTORYINDICATOR'

'Del Peak 35(13q14.2)' versus 'Time to Death'

P value = 5.46e-06 (logrank test), Q value = 0.0073

Table S415. Gene #76: 'Del Peak 35(13q14.2)' versus Clinical Feature #1: 'Time to Death'

| nPatients | nDeath | Duration Range (Median), Month
--- | --- | --- | ---
ALL | 4370 | 1406 | 0.0 - 224.0 (14.4)
DEL PEAK 35(13Q14.2) CNV | 1689 | 634 | 0.0 - 211.5 (15.1)
DEL PEAK 35(13Q14.2) WILD-TYPE | 2681 | 772 | 0.0 - 224.0 (14.1)

Figure S415. Get High-res Image Gene #76: 'Del Peak 35(13q14.2)' versus Clinical Feature #1: 'Time to Death'

'Del Peak 35(13q14.2)' versus 'PRIMARY.SITE.OF.DISEASE'

P value = 1.57e-163 (Chi-square test), Q value = 2.7e-160

Table S416. Gene #76: 'Del Peak 35(13q14.2)' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'

nPatients | BLADDER | BRAIN | BREAST | COLON | ENDOMETRIAL | HEAD/NECK | KIDNEY | LUNG | OMENTUM | OVARY | PERITONEUM (OVARY) | RECTUM
--- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | ---
ALL | 131 | 544 | 857 | 412 | 454 | 321 | 493 | 714 | 2 | 548 | 2 | 159
DEL PEAK 35(13Q14.2) CNV | 51 | 230 | 396 | 15 | 74 | 136 | 77 | 434 | 1 | 340 | 2 | 10
DEL PEAK 35(13Q14.2) WILD-TYPE | 80 | 314 | 461 | 397 | 380 | 185 | 416 | 280 | 1 | 208 | 0 | 149

Figure S416. Get High-res Image Gene #76: 'Del Peak 35(13q14.2)' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'

'Del Peak 35(13q14.2)' versus 'HISTOLOGICAL.TYPE'

P value = 7.05e-156 (Chi-square test), Q value = 1.2e-152

Table S417. Gene #76: 'Del Peak 35(13q14.2)' versus Clinical Feature #6: 'HISTOLOGICAL.TYPE'

nPatients | COLON ADENOCARCINOMA | COLON MUCINOUS ADENOCARCINOMA | ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA | HEAD & NECK SQUAMOUS CELL CARCINOMA | INFILTRATING DUCTAL CARCINOMA | INFILTRATING LOBULAR 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 HISTOLOGY (PLEASE SPECIFY) | MIXED SEROUS AND ENDOMETRIOID | MUCINOUS (COLLOID) ADENOCARCINOMA | MUCINOUS (COLLOID) CARCINOMA | MUSCLE INVASIVE UROTHELIAL CARCINOMA (PT2 OR ABOVE) | OTHER SPECIFY | RECTAL ADENOCARCINOMA | RECTAL MUCINOUS ADENOCARCINOMA | SEROUS CYSTADENOCARCINOMA | SEROUS ENDOMETRIAL ADENOCARCINOMA | TREATED PRIMARY GBM | UNTREATED PRIMARY (DE NOVO) GBM
--- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | ---
ALL | 356 | 54 | 351 | 321 | 104 | 12 | 493 | 11 | 79 | 243 | 7 | 4 | 17 | 2 | 3 | 2 | 18 | 1 | 1 | 1 | 3 | 315 | 5 | 18 | 4 | 3 | 49 | 10 | 143 | 13 | 552 | 85 | 1 | 20
DEL PEAK 35(13Q14.2) CNV | 12 | 2 | 42 | 136 | 44 | 3 | 77 | 7 | 40 | 136 | 3 | 1 | 11 | 2 | 1 | 0 | 7 | 1 | 0 | 1 | 2 | 221 | 3 | 4 | 1 | 0 | 20 | 4 | 6 | 4 | 343 | 28 | 0 | 11
DEL PEAK 35(13Q14.2) WILD-TYPE | 344 | 52 | 309 | 185 | 60 | 9 | 416 | 4 | 39 | 107 | 4 | 3 | 6 | 0 | 2 | 2 | 11 | 0 | 1 | 0 | 1 | 94 | 2 | 14 | 3 | 3 | 29 | 6 | 137 | 9 | 209 | 57 | 1 | 9

Figure S417. Get High-res Image Gene #76: 'Del Peak 35(13q14.2)' versus Clinical Feature #6: 'HISTOLOGICAL.TYPE'

'Del Peak 35(13q14.2)' versus 'PATHOLOGY.T'

P value = 2.06e-27 (Fisher's exact test), Q value = 3.2e-24

Table S418. Gene #76: 'Del Peak 35(13q14.2)' versus Clinical Feature #7: 'PATHOLOGY.T'

nPatients | T0+T1 | T2 | T3 | T4
--- | --- | --- | --- | ---
ALL | 448 | 611 | 688 | 208
DEL PEAK 35(13Q14.2) CNV | 141 | 266 | 109 | 74
DEL PEAK 35(13Q14.2) WILD-TYPE | 307 | 345 | 579 | 134

Figure S418. Get High-res Image Gene #76: 'Del Peak 35(13q14.2)' versus Clinical Feature #7: 'PATHOLOGY.T'

'Del Peak 35(13q14.2)' versus 'PATHOLOGICSPREAD(M)'

P value = 2.6e-05 (Chi-square test), Q value = 0.034

Table S419. Gene #76: 'Del Peak 35(13q14.2)' versus Clinical Feature #9: 'PATHOLOGICSPREAD(M)'

nPatients | M0 | M1 | M1A | M1B | MX
--- | --- | --- | --- | --- | ---
ALL | 1398 | 167 | 9 | 1 | 148
DEL PEAK 35(13Q14.2) CNV | 400 | 32 | 1 | 1 | 64
DEL PEAK 35(13Q14.2) WILD-TYPE | 998 | 135 | 8 | 0 | 84

Figure S419. Get High-res Image Gene #76: 'Del Peak 35(13q14.2)' versus Clinical Feature #9: 'PATHOLOGICSPREAD(M)'

'Del Peak 35(13q14.2)' versus 'TUMOR.STAGE'

P value = 1.27e-08 (Fisher's exact test), Q value = 1.8e-05

Table S420. Gene #76: 'Del Peak 35(13q14.2)' versus Clinical Feature #10: 'TUMOR.STAGE'

nPatients | I | II | III | IV
--- | --- | --- | --- | ---
ALL | 685 | 487 | 876 | 420
DEL PEAK 35(13Q14.2) CNV | 247 | 134 | 389 | 156
DEL PEAK 35(13Q14.2) WILD-TYPE | 438 | 353 | 487 | 264

Figure S420. Get High-res Image Gene #76: 'Del Peak 35(13q14.2)' versus Clinical Feature #10: 'TUMOR.STAGE'

'Del Peak 36(14q24.1)' versus 'PRIMARY.SITE.OF.DISEASE'

P value = 1.3e-49 (Chi-square test), Q value = 2.1e-46

Table S421. Gene #77: 'Del Peak 36(14q24.1)' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'

nPatients | BLADDER | BRAIN | BREAST | COLON | ENDOMETRIAL | HEAD/NECK | KIDNEY | LUNG | OMENTUM | OVARY | PERITONEUM (OVARY) | RECTUM
--- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | ---
ALL | 131 | 544 | 857 | 412 | 454 | 321 | 493 | 714 | 2 | 548 | 2 | 159
DEL PEAK 36(14Q24.1) CNV | 40 | 168 | 267 | 125 | 55 | 40 | 218 | 229 | 1 | 273 | 1 | 66
DEL PEAK 36(14Q24.1) WILD-TYPE | 91 | 376 | 590 | 287 | 399 | 281 | 275 | 485 | 1 | 275 | 1 | 93

Figure S421. Get High-res Image Gene #77: 'Del Peak 36(14q24.1)' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'

'Del Peak 36(14q24.1)' versus 'HISTOLOGICAL.TYPE'

P value = 2.93e-51 (Chi-square test), Q value = 4.7e-48

Table S422. Gene #77: 'Del Peak 36(14q24.1)' versus Clinical Feature #6: 'HISTOLOGICAL.TYPE'

nPatients | COLON ADENOCARCINOMA | COLON MUCINOUS ADENOCARCINOMA | ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA | HEAD & NECK SQUAMOUS CELL CARCINOMA | INFILTRATING DUCTAL CARCINOMA | INFILTRATING LOBULAR 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 HISTOLOGY (PLEASE SPECIFY) | MIXED SEROUS AND ENDOMETRIOID | MUCINOUS (COLLOID) ADENOCARCINOMA | MUCINOUS (COLLOID) CARCINOMA | MUSCLE INVASIVE UROTHELIAL CARCINOMA (PT2 OR ABOVE) | OTHER SPECIFY | RECTAL ADENOCARCINOMA | RECTAL MUCINOUS ADENOCARCINOMA | SEROUS CYSTADENOCARCINOMA | SEROUS ENDOMETRIAL ADENOCARCINOMA | TREATED PRIMARY GBM | UNTREATED PRIMARY (DE NOVO) GBM
--- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | ---
ALL | 356 | 54 | 351 | 321 | 104 | 12 | 493 | 11 | 79 | 243 | 7 | 4 | 17 | 2 | 3 | 2 | 18 | 1 | 1 | 1 | 3 | 315 | 5 | 18 | 4 | 3 | 49 | 10 | 143 | 13 | 552 | 85 | 1 | 20
DEL PEAK 36(14Q24.1) CNV | 119 | 5 | 21 | 40 | 36 | 1 | 218 | 5 | 21 | 70 | 3 | 0 | 4 | 1 | 0 | 1 | 3 | 0 | 0 | 1 | 0 | 117 | 0 | 4 | 2 | 1 | 16 | 2 | 64 | 1 | 275 | 30 | 0 | 5
DEL PEAK 36(14Q24.1) WILD-TYPE | 237 | 49 | 330 | 281 | 68 | 11 | 275 | 6 | 58 | 173 | 4 | 4 | 13 | 1 | 3 | 1 | 15 | 1 | 1 | 0 | 3 | 198 | 5 | 14 | 2 | 2 | 33 | 8 | 79 | 12 | 277 | 55 | 1 | 15

Figure S422. Get High-res Image Gene #77: 'Del Peak 36(14q24.1)' versus Clinical Feature #6: 'HISTOLOGICAL.TYPE'

'Del Peak 36(14q24.1)' versus 'PATHOLOGY.T'

P value = 2.02e-05 (Fisher's exact test), Q value = 0.026

Table S423. Gene #77: 'Del Peak 36(14q24.1)' versus Clinical Feature #7: 'PATHOLOGY.T'

nPatients | T0+T1 | T2 | T3 | T4
--- | --- | --- | --- | ---
ALL | 448 | 611 | 688 | 208
DEL PEAK 36(14Q24.1) CNV | 149 | 191 | 257 | 41
DEL PEAK 36(14Q24.1) WILD-TYPE | 299 | 420 | 431 | 167

Figure S423. Get High-res Image Gene #77: 'Del Peak 36(14q24.1)' versus Clinical Feature #7: 'PATHOLOGY.T'

'Del Peak 36(14q24.1)' versus 'PATHOLOGY.N'

P value = 3.01e-05 (Fisher's exact test), Q value = 0.039

Table S424. Gene #77: 'Del Peak 36(14q24.1)' versus Clinical Feature #8: 'PATHOLOGY.N'

nPatients | N0 | N1 | N2 | N3
--- | --- | --- | --- | ---
ALL | 1036 | 343 | 279 | 11
DEL PEAK 36(14Q24.1) CNV | 327 | 133 | 59 | 4
DEL PEAK 36(14Q24.1) WILD-TYPE | 709 | 210 | 220 | 7

Figure S424. Get High-res Image Gene #77: 'Del Peak 36(14q24.1)' versus Clinical Feature #8: 'PATHOLOGY.N'

'Del Peak 36(14q24.1)' versus 'TUMOR.STAGE'

P value = 2.81e-08 (Fisher's exact test), Q value = 3.9e-05

Table S425. Gene #77: 'Del Peak 36(14q24.1)' versus Clinical Feature #10: 'TUMOR.STAGE'

nPatients | I | II | III | IV
--- | --- | --- | --- | ---
ALL | 685 | 487 | 876 | 420
DEL PEAK 36(14Q24.1) CNV | 227 | 152 | 389 | 130
DEL PEAK 36(14Q24.1) WILD-TYPE | 458 | 335 | 487 | 290

Figure S425. Get High-res Image Gene #77: 'Del Peak 36(14q24.1)' versus Clinical Feature #10: 'TUMOR.STAGE'

'Del Peak 37(15q11.2)' versus 'PRIMARY.SITE.OF.DISEASE'

P value = 7.95e-75 (Chi-square test), Q value = 1.3e-71

Table S426. Gene #78: 'Del Peak 37(15q11.2)' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'

nPatients | BLADDER | BRAIN | BREAST | COLON | ENDOMETRIAL | HEAD/NECK | KIDNEY | LUNG | OMENTUM | OVARY | PERITONEUM (OVARY) | RECTUM
--- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | ---
ALL | 131 | 544 | 857 | 412 | 454 | 321 | 493 | 714 | 2 | 548 | 2 | 159
DEL PEAK 37(15Q11.2) CNV | 49 | 116 | 295 | 159 | 93 | 68 | 39 | 314 | 2 | 283 | 2 | 71
DEL PEAK 37(15Q11.2) WILD-TYPE | 82 | 428 | 562 | 253 | 361 | 253 | 454 | 400 | 0 | 265 | 0 | 88

Figure S426. Get High-res Image Gene #78: 'Del Peak 37(15q11.2)' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'

'Del Peak 37(15q11.2)' versus 'GENDER'

P value = 3.56e-05 (Fisher's exact test), Q value = 0.046

Table S427. Gene #78: 'Del Peak 37(15q11.2)' versus Clinical Feature #4: 'GENDER'

nPatients | FEMALE | MALE
--- | --- | ---
ALL | 2924 | 1717
DEL PEAK 37(15Q11.2) CNV | 1005 | 489
DEL PEAK 37(15Q11.2) WILD-TYPE | 1919 | 1228

Figure S427. Get High-res Image Gene #78: 'Del Peak 37(15q11.2)' versus Clinical Feature #4: 'GENDER'

'Del Peak 37(15q11.2)' versus 'HISTOLOGICAL.TYPE'

P value = 3.04e-80 (Chi-square test), Q value = 5e-77

Table S428. Gene #78: 'Del Peak 37(15q11.2)' versus Clinical Feature #6: 'HISTOLOGICAL.TYPE'

nPatients | COLON ADENOCARCINOMA | COLON MUCINOUS ADENOCARCINOMA | ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA | HEAD & NECK SQUAMOUS CELL CARCINOMA | INFILTRATING DUCTAL CARCINOMA | INFILTRATING LOBULAR 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 HISTOLOGY (PLEASE SPECIFY) | MIXED SEROUS AND ENDOMETRIOID | MUCINOUS (COLLOID) ADENOCARCINOMA | MUCINOUS (COLLOID) CARCINOMA | MUSCLE INVASIVE UROTHELIAL CARCINOMA (PT2 OR ABOVE) | OTHER SPECIFY | RECTAL ADENOCARCINOMA | RECTAL MUCINOUS ADENOCARCINOMA | SEROUS CYSTADENOCARCINOMA | SEROUS ENDOMETRIAL ADENOCARCINOMA | TREATED PRIMARY GBM | UNTREATED PRIMARY (DE NOVO) GBM
--- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | ---
ALL | 356 | 54 | 351 | 321 | 104 | 12 | 493 | 11 | 79 | 243 | 7 | 4 | 17 | 2 | 3 | 2 | 18 | 1 | 1 | 1 | 3 | 315 | 5 | 18 | 4 | 3 | 49 | 10 | 143 | 13 | 552 | 85 | 1 | 20
DEL PEAK 37(15Q11.2) CNV | 145 | 13 | 38 | 68 | 40 | 4 | 39 | 4 | 33 | 143 | 2 | 0 | 9 | 1 | 3 | 0 | 11 | 0 | 0 | 1 | 2 | 104 | 1 | 5 | 1 | 0 | 16 | 3 | 64 | 6 | 287 | 50 | 0 | 6
DEL PEAK 37(15Q11.2) WILD-TYPE | 211 | 41 | 313 | 253 | 64 | 8 | 454 | 7 | 46 | 100 | 5 | 4 | 8 | 1 | 0 | 2 | 7 | 1 | 1 | 0 | 1 | 211 | 4 | 13 | 3 | 3 | 33 | 7 | 79 | 7 | 265 | 35 | 1 | 14

Figure S428. Get High-res Image Gene #78: 'Del Peak 37(15q11.2)' versus Clinical Feature #6: 'HISTOLOGICAL.TYPE'

'Del Peak 37(15q11.2)' versus 'PATHOLOGY.T'

P value = 7.04e-07 (Fisher's exact test), Q value = 0.00096

Table S429. Gene #78: 'Del Peak 37(15q11.2)' versus Clinical Feature #7: 'PATHOLOGY.T'

nPatients | T0+T1 | T2 | T3 | T4
--- | --- | --- | --- | ---
ALL | 448 | 611 | 688 | 208
DEL PEAK 37(15Q11.2) CNV | 92 | 215 | 229 | 60
DEL PEAK 37(15Q11.2) WILD-TYPE | 356 | 396 | 459 | 148

Figure S429. Get High-res Image Gene #78: 'Del Peak 37(15q11.2)' versus Clinical Feature #7: 'PATHOLOGY.T'

'Del Peak 37(15q11.2)' versus 'PATHOLOGY.N'

P value = 7.75e-07 (Fisher's exact test), Q value = 0.0011

Table S430. Gene #78: 'Del Peak 37(15q11.2)' versus Clinical Feature #8: 'PATHOLOGY.N'

nPatients | N0 | N1 | N2 | N3
--- | --- | --- | --- | ---
ALL | 1036 | 343 | 279 | 11
DEL PEAK 37(15Q11.2) CNV | 299 | 144 | 117 | 5
DEL PEAK 37(15Q11.2) WILD-TYPE | 737 | 199 | 162 | 6

Figure S430. Get High-res Image Gene #78: 'Del Peak 37(15q11.2)' versus Clinical Feature #8: 'PATHOLOGY.N'

'Del Peak 37(15q11.2)' versus 'TUMOR.STAGE'

P value = 3.67e-10 (Fisher's exact test), Q value = 5.3e-07

Table S431. Gene #78: 'Del Peak 37(15q11.2)' versus Clinical Feature #10: 'TUMOR.STAGE'

nPatients | I | II | III | IV
--- | --- | --- | --- | ---
ALL | 685 | 487 | 876 | 420
DEL PEAK 37(15Q11.2) CNV | 182 | 170 | 377 | 140
DEL PEAK 37(15Q11.2) WILD-TYPE | 503 | 317 | 499 | 280

Figure S431. Get High-res Image Gene #78: 'Del Peak 37(15q11.2)' versus Clinical Feature #10: 'TUMOR.STAGE'

'Del Peak 37(15q11.2)' versus 'RADIATIONS.RADIATION.REGIMENINDICATION'

P value = 1.66e-06 (Fisher's exact test), Q value = 0.0022

Table S432. Gene #78: 'Del Peak 37(15q11.2)' versus Clinical Feature #11: 'RADIATIONS.RADIATION.REGIMENINDICATION'

nPatients | NO | YES
--- | --- | ---
ALL | 835 | 3816
DEL PEAK 37(15Q11.2) CNV | 211 | 1288
DEL PEAK 37(15Q11.2) WILD-TYPE | 624 | 2528

Figure S432. Get High-res Image Gene #78: 'Del Peak 37(15q11.2)' versus Clinical Feature #11: 'RADIATIONS.RADIATION.REGIMENINDICATION'

'Del Peak 38(15q15.1)' versus 'PRIMARY.SITE.OF.DISEASE'

P value = 4.09e-92 (Chi-square test), Q value = 6.7e-89

Table S433. Gene #79: 'Del Peak 38(15q15.1)' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'

nPatients | BLADDER | BRAIN | BREAST | COLON | ENDOMETRIAL | HEAD/NECK | KIDNEY | LUNG | OMENTUM | OVARY | PERITONEUM (OVARY) | RECTUM
--- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | ---
ALL | 131 | 544 | 857 | 412 | 454 | 321 | 493 | 714 | 2 | 548 | 2 | 159
DEL PEAK 38(15Q15.1) CNV | 50 | 140 | 313 | 149 | 108 | 74 | 38 | 322 | 2 | 343 | 2 | 74
DEL PEAK 38(15Q15.1) WILD-TYPE | 81 | 404 | 544 | 263 | 346 | 247 | 455 | 392 | 0 | 205 | 0 | 85

Figure S433. Get High-res Image Gene #79: 'Del Peak 38(15q15.1)' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'

'Del Peak 38(15q15.1)' versus 'GENDER'

P value = 1.95e-07 (Fisher's exact test), Q value = 0.00027

Table S434. Gene #79: 'Del Peak 38(15q15.1)' versus Clinical Feature #4: 'GENDER'

nPatients | FEMALE | MALE
--- | --- | ---
ALL | 2924 | 1717
DEL PEAK 38(15Q15.1) CNV | 1101 | 517
DEL PEAK 38(15Q15.1) WILD-TYPE | 1823 | 1200

Figure S434. Get High-res Image Gene #79: 'Del Peak 38(15q15.1)' versus Clinical Feature #4: 'GENDER'

'Del Peak 38(15q15.1)' versus 'HISTOLOGICAL.TYPE'

P value = 2.29e-101 (Chi-square test), Q value = 3.8e-98

Table S435. Gene #79: 'Del Peak 38(15q15.1)' versus Clinical Feature #6: 'HISTOLOGICAL.TYPE'

nPatients | COLON ADENOCARCINOMA | COLON MUCINOUS ADENOCARCINOMA | ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA | HEAD & NECK SQUAMOUS CELL CARCINOMA | INFILTRATING DUCTAL CARCINOMA | INFILTRATING LOBULAR 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 HISTOLOGY (PLEASE SPECIFY) | MIXED SEROUS AND ENDOMETRIOID | MUCINOUS (COLLOID) ADENOCARCINOMA | MUCINOUS (COLLOID) CARCINOMA | MUSCLE INVASIVE UROTHELIAL CARCINOMA (PT2 OR ABOVE) | OTHER SPECIFY | RECTAL ADENOCARCINOMA | RECTAL MUCINOUS ADENOCARCINOMA | SEROUS CYSTADENOCARCINOMA | SEROUS ENDOMETRIAL ADENOCARCINOMA | TREATED PRIMARY GBM | UNTREATED PRIMARY (DE NOVO) GBM
--- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | ---
ALL | 356 | 54 | 351 | 321 | 104 | 12 | 493 | 11 | 79 | 243 | 7 | 4 | 17 | 2 | 3 | 2 | 18 | 1 | 1 | 1 | 3 | 315 | 5 | 18 | 4 | 3 | 49 | 10 | 143 | 13 | 552 | 85 | 1 | 20
DEL PEAK 38(15Q15.1) CNV | 136 | 12 | 46 | 74 | 43 | 4 | 38 | 4 | 34 | 147 | 2 | 0 | 9 | 1 | 3 | 0 | 11 | 0 | 0 | 1 | 1 | 108 | 1 | 7 | 1 | 0 | 18 | 3 | 67 | 6 | 347 | 55 | 0 | 6
DEL PEAK 38(15Q15.1) WILD-TYPE | 220 | 42 | 305 | 247 | 61 | 8 | 455 | 7 | 45 | 96 | 5 | 4 | 8 | 1 | 0 | 2 | 7 | 1 | 1 | 0 | 2 | 207 | 4 | 11 | 3 | 3 | 31 | 7 | 76 | 7 | 205 | 30 | 1 | 14

Figure S435. Get High-res Image Gene #79: 'Del Peak 38(15q15.1)' versus Clinical Feature #6: 'HISTOLOGICAL.TYPE'

'Del Peak 38(15q15.1)' versus 'PATHOLOGY.T'

P value = 4.02e-07 (Fisher's exact test), Q value = 0.00055

Table S436. Gene #79: 'Del Peak 38(15q15.1)' versus Clinical Feature #7: 'PATHOLOGY.T'

nPatients | T0+T1 | T2 | T3 | T4
--- | --- | --- | --- | ---
ALL | 448 | 611 | 688 | 208
DEL PEAK 38(15Q15.1) CNV | 92 | 220 | 225 | 62
DEL PEAK 38(15Q15.1) WILD-TYPE | 356 | 391 | 463 | 146

Figure S436. Get High-res Image Gene #79: 'Del Peak 38(15q15.1)' versus Clinical Feature #7: 'PATHOLOGY.T'

'Del Peak 38(15q15.1)' versus 'PATHOLOGY.N'

P value = 9.24e-07 (Fisher's exact test), Q value = 0.0013

Table S437. Gene #79: 'Del Peak 38(15q15.1)' versus Clinical Feature #8: 'PATHOLOGY.N'

nPatients | N0 | N1 | N2 | N3
--- | --- | --- | --- | ---
ALL | 1036 | 343 | 279 | 11
DEL PEAK 38(15Q15.1) CNV | 300 | 146 | 115 | 5
DEL PEAK 38(15Q15.1) WILD-TYPE | 736 | 197 | 164 | 6

Figure S437. Get High-res Image Gene #79: 'Del Peak 38(15q15.1)' versus Clinical Feature #8: 'PATHOLOGY.N'

'Del Peak 38(15q15.1)' versus 'TUMOR.STAGE'

P value = 1.31e-16 (Fisher's exact test), Q value = 2e-13

Table S438. Gene #79: 'Del Peak 38(15q15.1)' versus Clinical Feature #10: 'TUMOR.STAGE'

nPatients | I | II | III | IV
--- | --- | --- | --- | ---
ALL | 685 | 487 | 876 | 420
DEL PEAK 38(15Q15.1) CNV | 187 | 174 | 424 | 145
DEL PEAK 38(15Q15.1) WILD-TYPE | 498 | 313 | 452 | 275

Figure S438. Get High-res Image Gene #79: 'Del Peak 38(15q15.1)' versus Clinical Feature #10: 'TUMOR.STAGE'

'Del Peak 38(15q15.1)' versus 'RADIATIONS.RADIATION.REGIMENINDICATION'

P value = 2.13e-05 (Fisher's exact test), Q value = 0.028

Table S439. Gene #79: 'Del Peak 38(15q15.1)' versus Clinical Feature #11: 'RADIATIONS.RADIATION.REGIMENINDICATION'

nPatients | NO | YES
--- | --- | ---
ALL | 835 | 3816
DEL PEAK 38(15Q15.1) CNV | 239 | 1385
DEL PEAK 38(15Q15.1) WILD-TYPE | 596 | 2431

Figure S439. Get High-res Image Gene #79: 'Del Peak 38(15q15.1)' versus Clinical Feature #11: 'RADIATIONS.RADIATION.REGIMENINDICATION'

'Del Peak 39(16p13.3)' versus 'Time to Death'

P value = 3.06e-05 (logrank test), Q value = 0.039

Table S440. Gene #80: 'Del Peak 39(16p13.3)' versus Clinical Feature #1: 'Time to Death'

| nPatients | nDeath | Duration Range (Median), Month
--- | --- | --- | ---
ALL | 4370 | 1406 | 0.0 - 224.0 (14.4)
DEL PEAK 39(16P13.3) CNV | 722 | 291 | 0.0 - 211.5 (15.3)
DEL PEAK 39(16P13.3) WILD-TYPE | 3648 | 1115 | 0.0 - 224.0 (14.3)

Figure S440. Get High-res Image Gene #80: 'Del Peak 39(16p13.3)' versus Clinical Feature #1: 'Time to Death'

'Del Peak 39(16p13.3)' versus 'PRIMARY.SITE.OF.DISEASE'

P value = 3.17e-130 (Chi-square test), Q value = 5.4e-127

Table S441. Gene #80: 'Del Peak 39(16p13.3)' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'

nPatients | BLADDER | BRAIN | BREAST | COLON | ENDOMETRIAL | HEAD/NECK | KIDNEY | LUNG | OMENTUM | OVARY | PERITONEUM (OVARY) | RECTUM
--- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | ---
ALL | 131 | 544 | 857 | 412 | 454 | 321 | 493 | 714 | 2 | 548 | 2 | 159
DEL PEAK 39(16P13.3) CNV | 39 | 66 | 49 | 45 | 58 | 37 | 12 | 172 | 2 | 264 | 1 | 13
DEL PEAK 39(16P13.3) WILD-TYPE | 92 | 478 | 808 | 367 | 396 | 284 | 481 | 542 | 0 | 284 | 1 | 146

Figure S441. Get High-res Image Gene #80: 'Del Peak 39(16p13.3)' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'

'Del Peak 39(16p13.3)' versus 'HISTOLOGICAL.TYPE'

P value = 1.02e-100 (Chi-square test), Q value = 1.7e-97

Table S442. Gene #80: 'Del Peak 39(16p13.3)' versus Clinical Feature #6: 'HISTOLOGICAL.TYPE'

nPatients | COLON ADENOCARCINOMA | COLON MUCINOUS ADENOCARCINOMA | ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA | HEAD & NECK SQUAMOUS CELL CARCINOMA | INFILTRATING DUCTAL CARCINOMA | INFILTRATING LOBULAR 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 HISTOLOGY (PLEASE SPECIFY) | MIXED SEROUS AND ENDOMETRIOID | MUCINOUS (COLLOID) ADENOCARCINOMA | MUCINOUS (COLLOID) CARCINOMA | MUSCLE INVASIVE UROTHELIAL CARCINOMA (PT2 OR ABOVE) | OTHER SPECIFY | RECTAL ADENOCARCINOMA | RECTAL MUCINOUS ADENOCARCINOMA | SEROUS CYSTADENOCARCINOMA | SEROUS ENDOMETRIAL ADENOCARCINOMA | TREATED PRIMARY GBM | UNTREATED PRIMARY (DE NOVO) GBM
--- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | ---
ALL | 356 | 54 | 351 | 321 | 104 | 12 | 493 | 11 | 79 | 243 | 7 | 4 | 17 | 2 | 3 | 2 | 18 | 1 | 1 | 1 | 3 | 315 | 5 | 18 | 4 | 3 | 49 | 10 | 143 | 13 | 552 | 85 | 1 | 20
DEL PEAK 39(16P13.3) CNV | 39 | 6 | 20 | 37 | 4 | 0 | 12 | 2 | 15 | 44 | 4 | 0 | 3 | 0 | 0 | 0 | 2 | 1 | 0 | 0 | 1 | 99 | 0 | 4 | 1 | 0 | 15 | 1 | 10 | 2 | 267 | 34 | 0 | 3
DEL PEAK 39(16P13.3) WILD-TYPE | 317 | 48 | 331 | 284 | 100 | 12 | 481 | 9 | 64 | 199 | 3 | 4 | 14 | 2 | 3 | 2 | 16 | 0 | 1 | 1 | 2 | 216 | 5 | 14 | 3 | 3 | 34 | 9 | 133 | 11 | 285 | 51 | 1 | 17

Figure S442. Get High-res Image Gene #80: 'Del Peak 39(16p13.3)' versus Clinical Feature #6: 'HISTOLOGICAL.TYPE'

'Del Peak 39(16p13.3)' versus 'TUMOR.STAGE'

P value = 8.54e-13 (Fisher's exact test), Q value = 1.2e-09

Table S443. Gene #80: 'Del Peak 39(16p13.3)' versus Clinical Feature #10: 'TUMOR.STAGE'

nPatients | I | II | III | IV
--- | --- | --- | --- | ---
ALL | 685 | 487 | 876 | 420
DEL PEAK 39(16P13.3) CNV | 103 | 81 | 260 | 79
DEL PEAK 39(16P13.3) WILD-TYPE | 582 | 406 | 616 | 341

Figure S443. Get High-res Image Gene #80: 'Del Peak 39(16p13.3)' versus Clinical Feature #10: 'TUMOR.STAGE'

'Del Peak 39(16p13.3)' versus 'RADIATIONS.RADIATION.REGIMENINDICATION'

P value = 3.38e-09 (Fisher's exact test), Q value = 4.8e-06

Table S444. Gene #80: 'Del Peak 39(16p13.3)' versus Clinical Feature #11: 'RADIATIONS.RADIATION.REGIMENINDICATION'

nPatients | NO | YES
--- | --- | ---
ALL | 835 | 3816
DEL PEAK 39(16P13.3) CNV | 82 | 681
DEL PEAK 39(16P13.3) WILD-TYPE | 753 | 3135

Figure S444. Get High-res Image Gene #80: 'Del Peak 39(16p13.3)' versus Clinical Feature #11: 'RADIATIONS.RADIATION.REGIMENINDICATION'

'Del Peak 39(16p13.3)' versus 'NEOPLASM.DISEASESTAGE'

P value = 7.08e-09 (Chi-square test), Q value = 1e-05

Table S445. Gene #80: 'Del Peak 39(16p13.3)' versus Clinical Feature #20: '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 X
--- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | ---
ALL | 71 | 45 | 2 | 34 | 246 | 165 | 29 | 107 | 22 | 36 | 35 | 12
DEL PEAK 39(16P13.3) CNV | 5 | 0 | 0 | 4 | 18 | 11 | 12 | 4 | 1 | 3 | 8 | 2
DEL PEAK 39(16P13.3) WILD-TYPE | 66 | 45 | 2 | 30 | 228 | 154 | 17 | 103 | 21 | 33 | 27 | 10

Figure S445. Get High-res Image Gene #80: 'Del Peak 39(16p13.3)' versus Clinical Feature #20: 'NEOPLASM.DISEASESTAGE'

'Del Peak 40(16q23.1)' versus 'PRIMARY.SITE.OF.DISEASE'

P value = 2.05e-249 (Chi-square test), Q value = 3.6e-246

Table S446. Gene #81: 'Del Peak 40(16q23.1)' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'

nPatients | BLADDER | BRAIN | BREAST | COLON | ENDOMETRIAL | HEAD/NECK | KIDNEY | LUNG | OMENTUM | OVARY | PERITONEUM (OVARY) | RECTUM
--- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | ---
ALL | 131 | 544 | 857 | 412 | 454 | 321 | 493 | 714 | 2 | 548 | 2 | 159
DEL PEAK 40(16Q23.1) CNV | 37 | 96 | 543 | 49 | 132 | 60 | 19 | 257 | 1 | 426 | 2 | 23
DEL PEAK 40(16Q23.1) WILD-TYPE | 94 | 448 | 314 | 363 | 322 | 261 | 474 | 457 | 1 | 122 | 0 | 136

Figure S446. Get High-res Image Gene #81: 'Del Peak 40(16q23.1)' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'

'Del Peak 40(16q23.1)' versus 'GENDER'

P value = 5.49e-72 (Fisher's exact test), Q value = 8.9e-69

Table S447. Gene #81: 'Del Peak 40(16q23.1)' versus Clinical Feature #4: 'GENDER'

nPatients | FEMALE | MALE
--- | --- | ---
ALL | 2924 | 1717
DEL PEAK 40(16Q23.1) CNV | 1312 | 333
DEL PEAK 40(16Q23.1) WILD-TYPE | 1612 | 1384

Figure S447. Get High-res Image Gene #81: 'Del Peak 40(16q23.1)' versus Clinical Feature #4: 'GENDER'

'Del Peak 40(16q23.1)' versus 'HISTOLOGICAL.TYPE'

P value = 8.25e-194 (Chi-square test), Q value = 1.4e-190

Table S448. Gene #81: 'Del Peak 40(16q23.1)' versus Clinical Feature #6: 'HISTOLOGICAL.TYPE'

nPatients | COLON ADENOCARCINOMA | COLON MUCINOUS ADENOCARCINOMA | ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA | HEAD & NECK SQUAMOUS CELL CARCINOMA | INFILTRATING DUCTAL CARCINOMA | INFILTRATING LOBULAR 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 HISTOLOGY (PLEASE SPECIFY) | MIXED SEROUS AND ENDOMETRIOID | MUCINOUS (COLLOID) ADENOCARCINOMA | MUCINOUS (COLLOID) CARCINOMA | MUSCLE INVASIVE UROTHELIAL CARCINOMA (PT2 OR ABOVE) | OTHER SPECIFY | RECTAL ADENOCARCINOMA | RECTAL MUCINOUS ADENOCARCINOMA | SEROUS CYSTADENOCARCINOMA | SEROUS ENDOMETRIAL ADENOCARCINOMA | TREATED PRIMARY GBM | UNTREATED PRIMARY (DE NOVO) GBM
--- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | ---
ALL | 356 | 54 | 351 | 321 | 104 | 12 | 493 | 11 | 79 | 243 | 7 | 4 | 17 | 2 | 3 | 2 | 18 | 1 | 1 | 1 | 3 | 315 | 5 | 18 | 4 | 3 | 49 | 10 | 143 | 13 | 552 | 85 | 1 | 20
DEL PEAK 40(16Q23.1) CNV | 40 | 9 | 59 | 60 | 49 | 12 | 19 | 5 | 26 | 79 | 3 | 1 | 7 | 2 | 1 | 0 | 6 | 0 | 0 | 0 | 1 | 123 | 4 | 6 | 2 | 1 | 10 | 6 | 20 | 2 | 429 | 67 | 0 | 6
DEL PEAK 40(16Q23.1) WILD-TYPE | 316 | 45 | 292 | 261 | 55 | 0 | 474 | 6 | 53 | 164 | 4 | 3 | 10 | 0 | 2 | 2 | 12 | 1 | 1 | 1 | 2 | 192 | 1 | 12 | 2 | 2 | 39 | 4 | 123 | 11 | 123 | 18 | 1 | 14

Figure S448. Get High-res Image Gene #81: 'Del Peak 40(16q23.1)' versus Clinical Feature #6: 'HISTOLOGICAL.TYPE'

'Del Peak 40(16q23.1)' versus 'PATHOLOGY.T'

P value = 4.44e-10 (Fisher's exact test), Q value = 6.4e-07

Table S449. Gene #81: 'Del Peak 40(16q23.1)' versus Clinical Feature #7: 'PATHOLOGY.T'

nPatients | T0+T1 | T2 | T3 | T4
--- | --- | --- | --- | ---
ALL | 448 | 611 | 688 | 208
DEL PEAK 40(16Q23.1) CNV | 63 | 161 | 88 | 45
DEL PEAK 40(16Q23.1) WILD-TYPE | 385 | 450 | 600 | 163

Figure S449. Get High-res Image Gene #81: 'Del Peak 40(16q23.1)' versus Clinical Feature #7: 'PATHOLOGY.T'

'Del Peak 40(16q23.1)' versus 'TUMOR.STAGE'

P value = 3.97e-34 (Fisher's exact test), Q value = 6.2e-31

Table S450. Gene #81: 'Del Peak 40(16q23.1)' versus Clinical Feature #10: 'TUMOR.STAGE'

nPatients | I | II | III | IV
--- | --- | --- | --- | ---
ALL | 685 | 487 | 876 | 420
DEL PEAK 40(16Q23.1) CNV | 139 | 108 | 412 | 116
DEL PEAK 40(16Q23.1) WILD-TYPE | 546 | 379 | 464 | 304

Figure S450. Get High-res Image Gene #81: 'Del Peak 40(16q23.1)' versus Clinical Feature #10: 'TUMOR.STAGE'

'Del Peak 40(16q23.1)' versus 'RADIATIONS.RADIATION.REGIMENINDICATION'

P value = 9.07e-05 (Fisher's exact test), Q value = 0.11

Table S451. Gene #81: 'Del Peak 40(16q23.1)' versus Clinical Feature #11: 'RADIATIONS.RADIATION.REGIMENINDICATION'

nPatients | NO | YES
--- | --- | ---
ALL | 835 | 3816
DEL PEAK 40(16Q23.1) CNV | 248 | 1405
DEL PEAK 40(16Q23.1) WILD-TYPE | 587 | 2411

Figure S451. Get High-res Image Gene #81: 'Del Peak 40(16q23.1)' versus Clinical Feature #11: 'RADIATIONS.RADIATION.REGIMENINDICATION'

'Del Peak 41(17p12)' versus 'PRIMARY.SITE.OF.DISEASE'

P value = 1.07e-240 (Chi-square test), Q value = 1.8e-237

Table S452. Gene #82: 'Del Peak 41(17p12)' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'

nPatients | BLADDER | BRAIN | BREAST | COLON | ENDOMETRIAL | HEAD/NECK | KIDNEY | LUNG | OMENTUM | OVARY | PERITONEUM (OVARY) | RECTUM
--- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | ---
ALL | 131 | 544 | 857 | 412 | 454 | 321 | 493 | 714 | 2 | 548 | 2 | 159
DEL PEAK 41(17P12) CNV | 67 | 68 | 519 | 228 | 102 | 76 | 50 | 405 | 2 | 463 | 1 | 110
DEL PEAK 41(17P12) WILD-TYPE | 64 | 476 | 338 | 184 | 352 | 245 | 443 | 309 | 0 | 85 | 1 | 49

Figure S452. Get High-res Image Gene #82: 'Del Peak 41(17p12)' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'

'Del Peak 41(17p12)' versus 'GENDER'

P value = 1.18e-26 (Fisher's exact test), Q value = 1.8e-23

Table S453. Gene #82: 'Del Peak 41(17p12)' versus Clinical Feature #4: 'GENDER'

nPatients | FEMALE | MALE
--- | --- | ---
ALL | 2924 | 1717
DEL PEAK 41(17P12) CNV | 1494 | 601
DEL PEAK 41(17P12) WILD-TYPE | 1430 | 1116

Figure S453. Get High-res Image Gene #82: 'Del Peak 41(17p12)' versus Clinical Feature #4: 'GENDER'

'Del Peak 41(17p12)' versus 'KARNOFSKY.PERFORMANCE.SCORE'

P value = 2.8e-05 (t-test), Q value = 0.036

Table S454. Gene #82: 'Del Peak 41(17p12)' versus Clinical Feature #5: 'KARNOFSKY.PERFORMANCE.SCORE'

| nPatients | Mean (Std.Dev)
--- | --- | ---
ALL | 641 | 73.6 (23.9)
DEL PEAK 41(17P12) CNV | 199 | 66.7 (30.4)
DEL PEAK 41(17P12) WILD-TYPE | 442 | 76.7 (19.6)

Figure S454. Get High-res Image Gene #82: 'Del Peak 41(17p12)' versus Clinical Feature #5: 'KARNOFSKY.PERFORMANCE.SCORE'

'Del Peak 41(17p12)' versus 'HISTOLOGICAL.TYPE'

P value = 1e-188 (Chi-square test), Q value = 1.7e-185

Table S455. Gene #82: 'Del Peak 41(17p12)' versus Clinical Feature #6: 'HISTOLOGICAL.TYPE'

nPatients | COLON ADENOCARCINOMA | COLON MUCINOUS ADENOCARCINOMA | ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA | HEAD & NECK SQUAMOUS CELL CARCINOMA | INFILTRATING DUCTAL CARCINOMA | INFILTRATING LOBULAR 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 HISTOLOGY (PLEASE SPECIFY) | MIXED SEROUS AND ENDOMETRIOID | MUCINOUS (COLLOID) ADENOCARCINOMA | MUCINOUS (COLLOID) CARCINOMA | MUSCLE INVASIVE UROTHELIAL CARCINOMA (PT2 OR ABOVE) | OTHER SPECIFY | RECTAL ADENOCARCINOMA | RECTAL MUCINOUS ADENOCARCINOMA | SEROUS CYSTADENOCARCINOMA | SEROUS ENDOMETRIAL ADENOCARCINOMA | TREATED PRIMARY GBM | UNTREATED PRIMARY (DE NOVO) GBM
--- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | ---
ALL | 356 | 54 | 351 | 321 | 104 | 12 | 493 | 11 | 79 | 243 | 7 | 4 | 17 | 2 | 3 | 2 | 18 | 1 | 1 | 1 | 3 | 315 | 5 | 18 | 4 | 3 | 49 | 10 | 143 | 13 | 552 | 85 | 1 | 20
DEL PEAK 41(17P12) CNV | 213 | 14 | 36 | 76 | 65 | 7 | 50 | 6 | 35 | 139 | 5 | 2 | 10 | 2 | 3 | 0 | 5 | 0 | 0 | 1 | 2 | 193 | 3 | 9 | 1 | 1 | 28 | 6 | 102 | 6 | 466 | 57 | 0 | 2
DEL PEAK 41(17P12) WILD-TYPE | 143 | 40 | 315 | 245 | 39 | 5 | 443 | 5 | 44 | 104 | 2 | 2 | 7 | 0 | 0 | 2 | 13 | 1 | 1 | 0 | 1 | 122 | 2 | 9 | 3 | 2 | 21 | 4 | 41 | 7 | 86 | 28 | 1 | 18

Figure S455. Get High-res Image Gene #82: 'Del Peak 41(17p12)' versus Clinical Feature #6: 'HISTOLOGICAL.TYPE'

'Del Peak 41(17p12)' versus 'PATHOLOGY.T'

P value = 1.09e-12 (Fisher's exact test), Q value = 1.6e-09

Table S456. Gene #82: 'Del Peak 41(17p12)' versus Clinical Feature #7: 'PATHOLOGY.T'

nPatients | T0+T1 | T2 | T3 | T4
--- | --- | --- | --- | ---
ALL | 448 | 611 | 688 | 208
DEL PEAK 41(17P12) CNV | 126 | 300 | 317 | 72
DEL PEAK 41(17P12) WILD-TYPE | 322 | 311 | 371 | 136

Figure S456. Get High-res Image Gene #82: 'Del Peak 41(17p12)' versus Clinical Feature #7: 'PATHOLOGY.T'

'Del Peak 41(17p12)' versus 'PATHOLOGY.N'

P value = 1.42e-07 (Fisher's exact test), Q value = 2e-04

Table S457. Gene #82: 'Del Peak 41(17p12)' versus Clinical Feature #8: 'PATHOLOGY.N'

nPatients | N0 | N1 | N2 | N3
--- | --- | --- | --- | ---
ALL | 1036 | 343 | 279 | 11
DEL PEAK 41(17P12) CNV | 421 | 196 | 146 | 5
DEL PEAK 41(17P12) WILD-TYPE | 615 | 147 | 133 | 6

Figure S457. Get High-res Image Gene #82: 'Del Peak 41(17p12)' versus Clinical Feature #8: 'PATHOLOGY.N'

'Del Peak 41(17p12)' versus 'TUMOR.STAGE'

P value = 9.6e-31 (Fisher's exact test), Q value = 1.5e-27

Table S458. Gene #82: 'Del Peak 41(17p12)' versus Clinical Feature #10: 'TUMOR.STAGE'

nPatients | I | II | III | IV
--- | --- | --- | --- | ---
ALL | 685 | 487 | 876 | 420
DEL PEAK 41(17P12) CNV | 256 | 235 | 581 | 189
DEL PEAK 41(17P12) WILD-TYPE | 429 | 252 | 295 | 231

Figure S458. Get High-res Image Gene #82: 'Del Peak 41(17p12)' versus Clinical Feature #10: 'TUMOR.STAGE'

'Del Peak 41(17p12)' versus 'RADIATIONS.RADIATION.REGIMENINDICATION'

P value = 1.53e-27 (Fisher's exact test), Q value = 2.4e-24

Table S459. Gene #82: 'Del Peak 41(17p12)' versus Clinical Feature #11: 'RADIATIONS.RADIATION.REGIMENINDICATION'

nPatients | NO | YES
--- | --- | ---
ALL | 835 | 3816
DEL PEAK 41(17P12) CNV | 238 | 1866
DEL PEAK 41(17P12) WILD-TYPE | 597 | 1950

Figure S459. Get High-res Image Gene #82: 'Del Peak 41(17p12)' versus Clinical Feature #11: 'RADIATIONS.RADIATION.REGIMENINDICATION'

'Del Peak 42(17q11.2)' versus 'AGE'

P value = 1.14e-05 (t-test), Q value = 0.015

Table S460. Gene #83: 'Del Peak 42(17q11.2)' versus Clinical Feature #2: 'AGE'

| nPatients | Mean (Std.Dev)
--- | --- | ---
ALL | 4585 | 61.9 (12.6)
DEL PEAK 42(17Q11.2) CNV | 1123 | 60.5 (12.2)
DEL PEAK 42(17Q11.2) WILD-TYPE | 3462 | 62.3 (12.7)

Figure S460. Get High-res Image Gene #83: 'Del Peak 42(17q11.2)' versus Clinical Feature #2: 'AGE'

'Del Peak 42(17q11.2)' versus 'PRIMARY.SITE.OF.DISEASE'

P value = 1.98e-263 (Chi-square test), Q value = 3.4e-260

Table S461. Gene #83: 'Del Peak 42(17q11.2)' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'

nPatients | BLADDER | BRAIN | BREAST | COLON | ENDOMETRIAL | HEAD/NECK | KIDNEY | LUNG | OMENTUM | OVARY | PERITONEUM (OVARY) | RECTUM
--- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | ---
ALL | 131 | 544 | 857 | 412 | 454 | 321 | 493 | 714 | 2 | 548 | 2 | 159
DEL PEAK 42(17Q11.2) CNV | 12 | 67 | 265 | 47 | 81 | 30 | 33 | 128 | 2 | 448 | 0 | 21
DEL PEAK 42(17Q11.2) WILD-TYPE | 119 | 477 | 592 | 365 | 373 | 291 | 460 | 586 | 0 | 100 | 2 | 138

Figure S461. Get High-res Image Gene #83: 'Del Peak 42(17q11.2)' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'

'Del Peak 42(17q11.2)' versus 'GENDER'

P value = 1.06e-51 (Fisher's exact test), Q value = 1.7e-48

Table S462. Gene #83: 'Del Peak 42(17q11.2)' versus Clinical Feature #4: 'GENDER'

nPatients | FEMALE | MALE
--- | --- | ---
ALL | 2924 | 1717
DEL PEAK 42(17Q11.2) CNV | 923 | 214
DEL PEAK 42(17Q11.2) WILD-TYPE | 2001 | 1503

Figure S462. Get High-res Image Gene #83: 'Del Peak 42(17q11.2)' versus Clinical Feature #4: 'GENDER'

'Del Peak 42(17q11.2)' versus 'HISTOLOGICAL.TYPE'

P value = 9.39e-235 (Chi-square test), Q value = 1.6e-231

Table S463. Gene #83: 'Del Peak 42(17q11.2)' versus Clinical Feature #6: 'HISTOLOGICAL.TYPE'

nPatients | COLON ADENOCARCINOMA | COLON MUCINOUS ADENOCARCINOMA | ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA | HEAD & NECK SQUAMOUS CELL CARCINOMA | INFILTRATING DUCTAL CARCINOMA | INFILTRATING LOBULAR 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 HISTOLOGY (PLEASE SPECIFY) | MIXED SEROUS AND ENDOMETRIOID | MUCINOUS (COLLOID) ADENOCARCINOMA | MUCINOUS (COLLOID) CARCINOMA | MUSCLE INVASIVE UROTHELIAL CARCINOMA (PT2 OR ABOVE) | OTHER SPECIFY | RECTAL ADENOCARCINOMA | RECTAL MUCINOUS ADENOCARCINOMA | SEROUS CYSTADENOCARCINOMA | SEROUS ENDOMETRIAL ADENOCARCINOMA | TREATED PRIMARY GBM | UNTREATED PRIMARY (DE NOVO) GBM
--- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | ---
ALL | 356 | 54 | 351 | 321 | 104 | 12 | 493 | 11 | 79 | 243 | 7 | 4 | 17 | 2 | 3 | 2 | 18 | 1 | 1 | 1 | 3 | 315 | 5 | 18 | 4 | 3 | 49 | 10 | 143 | 13 | 552 | 85 | 1 | 20
DEL PEAK 42(17Q11.2) CNV | 41 | 6 | 38 | 30 | 36 | 2 | 33 | 0 | 9 | 35 | 1 | 0 | 2 | 0 | 1 | 0 | 1 | 0 | 0 | 1 | 0 | 77 | 1 | 5 | 1 | 0 | 5 | 4 | 20 | 1 | 450 | 38 | 0 | 2
DEL PEAK 42(17Q11.2) WILD-TYPE | 315 | 48 | 313 | 291 | 68 | 10 | 460 | 11 | 70 | 208 | 6 | 4 | 15 | 2 | 2 | 2 | 17 | 1 | 1 | 0 | 3 | 238 | 4 | 13 | 3 | 3 | 44 | 6 | 123 | 12 | 102 | 47 | 1 | 18

Figure S463. Get High-res Image Gene #83: 'Del Peak 42(17q11.2)' versus Clinical Feature #6: 'HISTOLOGICAL.TYPE'

'Del Peak 42(17q11.2)' versus 'TUMOR.STAGE'

P value = 6.83e-59 (Fisher's exact test), Q value = 1.1e-55

Table S464. Gene #83: 'Del Peak 42(17q11.2)' versus Clinical Feature #10: 'TUMOR.STAGE'

nPatients | I | II | III | IV
--- | --- | --- | --- | ---
ALL | 685 | 487 | 876 | 420
DEL PEAK 42(17Q11.2) CNV | 100 | 72 | 418 | 100
DEL PEAK 42(17Q11.2) WILD-TYPE | 585 | 415 | 458 | 320

Figure S464. Get High-res Image Gene #83: 'Del Peak 42(17q11.2)' versus Clinical Feature #10: 'TUMOR.STAGE'

'Del Peak 42(17q11.2)' versus 'RADIATIONS.RADIATION.REGIMENINDICATION'

P value = 3.35e-09 (Fisher's exact test), Q value = 4.8e-06

Table S465. Gene #83: 'Del Peak 42(17q11.2)' versus Clinical Feature #11: 'RADIATIONS.RADIATION.REGIMENINDICATION'

nPatients | NO | YES
--- | --- | ---
ALL | 835 | 3816
DEL PEAK 42(17Q11.2) CNV | 141 | 1006
DEL PEAK 42(17Q11.2) WILD-TYPE | 694 | 2810

Figure S465. Get High-res Image Gene #83: 'Del Peak 42(17q11.2)' versus Clinical Feature #11: 'RADIATIONS.RADIATION.REGIMENINDICATION'

'Del Peak 43(18q21.2)' versus 'AGE'

P value = 1.98e-06 (t-test), Q value = 0.0027

Table S466. Gene #84: 'Del Peak 43(18q21.2)' versus Clinical Feature #2: 'AGE'

| nPatients | Mean (Std.Dev)
--- | --- | ---
ALL | 4585 | 61.9 (12.6)
DEL PEAK 43(18Q21.2) CNV | 1777 | 63.0 (12.0)
DEL PEAK 43(18Q21.2) WILD-TYPE | 2808 | 61.2 (12.9)

Figure S466. Get High-res Image Gene #84: 'Del Peak 43(18q21.2)' versus Clinical Feature #2: 'AGE'

'Del Peak 43(18q21.2)' versus 'PRIMARY.SITE.OF.DISEASE'

P value = 2.16e-160 (Chi-square test), Q value = 3.7e-157

Table S467. Gene #84: 'Del Peak 43(18q21.2)' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'

nPatients | BLADDER | BRAIN | BREAST | COLON | ENDOMETRIAL | HEAD/NECK | KIDNEY | LUNG | OMENTUM | OVARY | PERITONEUM (OVARY) | RECTUM
--- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | ---
ALL | 131 | 544 | 857 | 412 | 454 | 321 | 493 | 714 | 2 | 548 | 2 | 159
DEL PEAK 43(18Q21.2) CNV | 61 | 67 | 279 | 260 | 67 | 170 | 97 | 329 | 1 | 331 | 0 | 140
DEL PEAK 43(18Q21.2) WILD-TYPE | 70 | 477 | 578 | 152 | 387 | 151 | 396 | 385 | 1 | 217 | 2 | 19

Figure S467. Get High-res Image Gene #84: 'Del Peak 43(18q21.2)' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'

'Del Peak 43(18q21.2)' versus 'HISTOLOGICAL.TYPE'

P value = 3.7e-112 (Chi-square test), Q value = 6.2e-109

Table S468. Gene #84: 'Del Peak 43(18q21.2)' versus Clinical Feature #6: 'HISTOLOGICAL.TYPE'

nPatients | COLON ADENOCARCINOMA | COLON MUCINOUS ADENOCARCINOMA | ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA | HEAD & NECK SQUAMOUS CELL CARCINOMA | INFILTRATING DUCTAL CARCINOMA | INFILTRATING LOBULAR 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 HISTOLOGY (PLEASE SPECIFY) | MIXED SEROUS AND ENDOMETRIOID | MUCINOUS (COLLOID) ADENOCARCINOMA | MUCINOUS (COLLOID) CARCINOMA | MUSCLE INVASIVE UROTHELIAL CARCINOMA (PT2 OR ABOVE) | OTHER SPECIFY | RECTAL ADENOCARCINOMA | RECTAL MUCINOUS ADENOCARCINOMA | SEROUS CYSTADENOCARCINOMA | SEROUS ENDOMETRIAL ADENOCARCINOMA | TREATED PRIMARY GBM | UNTREATED PRIMARY (DE NOVO) GBM
--- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | ---
ALL | 356 | 54 | 351 | 321 | 104 | 12 | 493 | 11 | 79 | 243 | 7 | 4 | 17 | 2 | 3 | 2 | 18 | 1 | 1 | 1 | 3 | 315 | 5 | 18 | 4 | 3 | 49 | 10 | 143 | 13 | 552 | 85 | 1 | 20
DEL PEAK 43(18Q21.2) CNV | 245 | 14 | 29 | 170 | 34 | 3 | 97 | 5 | 39 | 130 | 1 | 1 | 7 | 2 | 2 | 1 | 4 | 1 | 0 | 0 | 2 | 130 | 1 | 5 | 3 | 1 | 24 | 2 | 126 | 12 | 332 | 33 | 0 | 5
DEL PEAK 43(18Q21.2) WILD-TYPE | 111 | 40 | 322 | 151 | 70 | 9 | 396 | 6 | 40 | 113 | 6 | 3 | 10 | 0 | 1 | 1 | 14 | 0 | 1 | 1 | 1 | 185 | 4 | 13 | 1 | 2 | 25 | 8 | 17 | 1 | 220 | 52 | 1 | 15

Figure S468. Get High-res Image Gene #84: 'Del Peak 43(18q21.2)' versus Clinical Feature #6: 'HISTOLOGICAL.TYPE'

'Del Peak 43(18q21.2)' versus 'PATHOLOGY.T'

P value = 1.41e-23 (Fisher's exact test), Q value = 2.1e-20

Table S469. Gene #84: 'Del Peak 43(18q21.2)' versus Clinical Feature #7: 'PATHOLOGY.T'

nPatients | T0+T1 | T2 | T3 | T4
--- | --- | --- | --- | ---
ALL | 448 | 611 | 688 | 208
DEL PEAK 43(18Q21.2) CNV | 124 | 296 | 393 | 122
DEL PEAK 43(18Q21.2) WILD-TYPE | 324 | 315 | 295 | 86

Figure S469. Get High-res Image Gene #84: 'Del Peak 43(18q21.2)' versus Clinical Feature #7: 'PATHOLOGY.T'

'Del Peak 43(18q21.2)' versus 'PATHOLOGY.N'

P value = 2.41e-10 (Fisher's exact test), Q value = 3.5e-07

Table S470. Gene #84: 'Del Peak 43(18q21.2)' versus Clinical Feature #8: 'PATHOLOGY.N'

nPatients | N0 | N1 | N2 | N3
--- | --- | --- | --- | ---
ALL | 1036 | 343 | 279 | 11
DEL PEAK 43(18Q21.2) CNV | 473 | 210 | 180 | 5
DEL PEAK 43(18Q21.2) WILD-TYPE | 563 | 133 | 99 | 6

Figure S470. Get High-res Image Gene #84: 'Del Peak 43(18q21.2)' versus Clinical Feature #8: 'PATHOLOGY.N'

'Del Peak 43(18q21.2)' versus 'PATHOLOGICSPREAD(M)'

P value = 8.73e-07 (Chi-square test), Q value = 0.0012

Table S471. Gene #84: 'Del Peak 43(18q21.2)' versus Clinical Feature #9: 'PATHOLOGICSPREAD(M)'

nPatients | M0 | M1 | M1A | M1B | MX
--- | --- | --- | --- | --- | ---
ALL | 1398 | 167 | 9 | 1 | 148
DEL PEAK 43(18Q21.2) CNV | 608 | 99 | 8 | 1 | 88
DEL PEAK 43(18Q21.2) WILD-TYPE | 790 | 68 | 1 | 0 | 60

Figure S471. Get High-res Image Gene #84: 'Del Peak 43(18q21.2)' versus Clinical Feature #9: 'PATHOLOGICSPREAD(M)'

'Del Peak 43(18q21.2)' versus 'TUMOR.STAGE'

P value = 3.65e-17 (Fisher's exact test), Q value = 5.5e-14

Table S472. Gene #84: 'Del Peak 43(18q21.2)' versus Clinical Feature #10: 'TUMOR.STAGE'

nPatients | I | II | III | IV
--- | --- | --- | --- | ---
ALL | 685 | 487 | 876 | 420
DEL PEAK 43(18Q21.2) CNV | 249 | 260 | 478 | 254
DEL PEAK 43(18Q21.2) WILD-TYPE | 436 | 227 | 398 | 166

Figure S472. Get High-res Image Gene #84: 'Del Peak 43(18q21.2)' versus Clinical Feature #10: 'TUMOR.STAGE'

'Del Peak 43(18q21.2)' versus 'RADIATIONS.RADIATION.REGIMENINDICATION'

P value = 6.39e-27 (Fisher's exact test), Q value = 9.8e-24

Table S473. Gene #84: 'Del Peak 43(18q21.2)' versus Clinical Feature #11: 'RADIATIONS.RADIATION.REGIMENINDICATION'

nPatients | NO | YES
--- | --- | ---
ALL | 835 | 3816
DEL PEAK 43(18Q21.2) CNV | 192 | 1621
DEL PEAK 43(18Q21.2) WILD-TYPE | 643 | 2195

Figure S473. Get High-res Image Gene #84: 'Del Peak 43(18q21.2)' versus Clinical Feature #11: 'RADIATIONS.RADIATION.REGIMENINDICATION'

'Del Peak 44(18q23)' versus 'PRIMARY.SITE.OF.DISEASE'

P value = 4.93e-163 (Chi-square test), Q value = 8.4e-160

Table S474. Gene #85: 'Del Peak 44(18q23)' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'

nPatients | BLADDER | BRAIN | BREAST | COLON | ENDOMETRIAL | HEAD/NECK | KIDNEY | LUNG | OMENTUM | OVARY | PERITONEUM (OVARY) | RECTUM
--- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | ---
ALL | 131 | 544 | 857 | 412 | 454 | 321 | 493 | 714 | 2 | 548 | 2 | 159
DEL PEAK 44(18Q23) CNV | 58 | 73 | 279 | 258 | 75 | 181 | 101 | 341 | 1 | 360 | 0 | 136
DEL PEAK 44(18Q23) WILD-TYPE | 73 | 471 | 578 | 154 | 379 | 140 | 392 | 373 | 1 | 188 | 2 | 23

Figure S474. Get High-res Image Gene #85: 'Del Peak 44(18q23)' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'

'Del Peak 44(18q23)' versus 'HISTOLOGICAL.TYPE'

P value = 2.15e-116 (Chi-square test), Q value = 3.6e-113

Table S475. Gene #85: 'Del Peak 44(18q23)' versus Clinical Feature #6: 'HISTOLOGICAL.TYPE'

nPatients | COLON ADENOCARCINOMA | COLON MUCINOUS ADENOCARCINOMA | ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA | HEAD & NECK SQUAMOUS CELL CARCINOMA | INFILTRATING DUCTAL CARCINOMA | INFILTRATING LOBULAR 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 HISTOLOGY (PLEASE SPECIFY) | MIXED SEROUS AND ENDOMETRIOID | MUCINOUS (COLLOID) ADENOCARCINOMA | MUCINOUS (COLLOID) CARCINOMA | MUSCLE INVASIVE UROTHELIAL CARCINOMA (PT2 OR ABOVE) | OTHER SPECIFY | RECTAL ADENOCARCINOMA | RECTAL MUCINOUS ADENOCARCINOMA | SEROUS CYSTADENOCARCINOMA | SEROUS ENDOMETRIAL ADENOCARCINOMA | TREATED PRIMARY GBM | UNTREATED PRIMARY (DE NOVO) GBM
--- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | ---
ALL | 356 | 54 | 351 | 321 | 104 | 12 | 493 | 11 | 79 | 243 | 7 | 4 | 17 | 2 | 3 | 2 | 18 | 1 | 1 | 1 | 3 | 315 | 5 | 18 | 4 | 3 | 49 | 10 | 143 | 13 | 552 | 85 | 1 | 20
DEL PEAK 44(18Q23) CNV | 244 | 13 | 30 | 181 | 34 | 4 | 101 | 6 | 39 | 124 | 1 | 1 | 8 | 2 | 2 | 1 | 3 | 1 | 0 | 0 | 1 | 148 | 1 | 5 | 3 | 1 | 22 | 1 | 124 | 11 | 361 | 40 | 0 | 5
DEL PEAK 44(18Q23) WILD-TYPE | 112 | 41 | 321 | 140 | 70 | 8 | 392 | 5 | 40 | 119 | 6 | 3 | 9 | 0 | 1 | 1 | 15 | 0 | 1 | 1 | 2 | 167 | 4 | 13 | 1 | 2 | 27 | 9 | 19 | 2 | 191 | 45 | 1 | 15

Figure S475. Get High-res Image Gene #85: 'Del Peak 44(18q23)' versus Clinical Feature #6: 'HISTOLOGICAL.TYPE'

'Del Peak 44(18q23)' versus 'PATHOLOGY.T'

P value = 1.9e-22 (Fisher's exact test), Q value = 2.9e-19

Table S476. Gene #85: 'Del Peak 44(18q23)' versus Clinical Feature #7: 'PATHOLOGY.T'

nPatients | T0+T1 | T2 | T3 | T4
--- | --- | --- | --- | ---
ALL | 448 | 611 | 688 | 208
DEL PEAK 44(18Q23) CNV | 131 | 297 | 397 | 126
DEL PEAK 44(18Q23) WILD-TYPE | 317 | 314 | 291 | 82

Figure S476. Get High-res Image Gene #85: 'Del Peak 44(18q23)' versus Clinical Feature #7: 'PATHOLOGY.T'

'Del Peak 44(18q23)' versus 'PATHOLOGY.N'

P value = 6.46e-10 (Fisher's exact test), Q value = 9.2e-07

Table S477. Gene #85: 'Del Peak 44(18q23)' versus Clinical Feature #8: 'PATHOLOGY.N'

nPatients | N0 | N1 | N2 | N3
--- | --- | --- | --- | ---
ALL | 1036 | 343 | 279 | 11
DEL PEAK 44(18Q23) CNV | 482 | 206 | 185 | 6
DEL PEAK 44(18Q23) WILD-TYPE | 554 | 137 | 94 | 5

Figure S477. Get High-res Image Gene #85: 'Del Peak 44(18q23)' versus Clinical Feature #8: 'PATHOLOGY.N'

'Del Peak 44(18q23)' versus 'PATHOLOGICSPREAD(M)'

P value = 6.05e-05 (Chi-square test), Q value = 0.077

Table S478. Gene #85: 'Del Peak 44(18q23)' versus Clinical Feature #9: 'PATHOLOGICSPREAD(M)'

nPatients | M0 | M1 | M1A | M1B | MX
--- | --- | --- | --- | --- | ---
ALL | 1398 | 167 | 9 | 1 | 148
DEL PEAK 44(18Q23) CNV | 623 | 96 | 8 | 1 | 85
DEL PEAK 44(18Q23) WILD-TYPE | 775 | 71 | 1 | 0 | 63

Figure S478. Get High-res Image Gene #85: 'Del Peak 44(18q23)' versus Clinical Feature #9: 'PATHOLOGICSPREAD(M)'

'Del Peak 44(18q23)' versus 'TUMOR.STAGE'

P value = 2.49e-19 (Fisher's exact test), Q value = 3.8e-16

Table S479. Gene #85: 'Del Peak 44(18q23)' versus Clinical Feature #10: 'TUMOR.STAGE'

nPatients | I | II | III | IV
--- | --- | --- | --- | ---
ALL | 685 | 487 | 876 | 420
DEL PEAK 44(18Q23) CNV | 255 | 261 | 512 | 257
DEL PEAK 44(18Q23) WILD-TYPE | 430 | 226 | 364 | 163

Figure S479. Get High-res Image Gene #85: 'Del Peak 44(18q23)' versus Clinical Feature #10: 'TUMOR.STAGE'

'Del Peak 44(18q23)' versus 'RADIATIONS.RADIATION.REGIMENINDICATION'

P value = 1.11e-25 (Fisher's exact test), Q value = 1.7e-22

Table S480. Gene #85: 'Del Peak 44(18q23)' versus Clinical Feature #11: 'RADIATIONS.RADIATION.REGIMENINDICATION'

nPatients | NO | YES
--- | --- | ---
ALL | 835 | 3816
DEL PEAK 44(18Q23) CNV | 205 | 1668
DEL PEAK 44(18Q23) WILD-TYPE | 630 | 2148

Figure S480. Get High-res Image Gene #85: 'Del Peak 44(18q23)' versus Clinical Feature #11: 'RADIATIONS.RADIATION.REGIMENINDICATION'

'Del Peak 45(19p13.3)' versus 'PRIMARY.SITE.OF.DISEASE'

P value = 6.56e-269 (Chi-square test), Q value = 1.1e-265

Table S481. Gene #86: 'Del Peak 45(19p13.3)' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'

nPatients | BLADDER | BRAIN | BREAST | COLON | ENDOMETRIAL | HEAD/NECK | KIDNEY | LUNG | OMENTUM | OVARY | PERITONEUM (OVARY) | RECTUM
--- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | ---
ALL | 131 | 544 | 857 | 412 | 454 | 321 | 493 | 714 | 2 | 548 | 2 | 159
DEL PEAK 45(19P13.3) CNV | 50 | 36 | 296 | 56 | 112 | 108 | 18 | 360 | 2 | 478 | 2 | 34
DEL PEAK 45(19P13.3) WILD-TYPE | 81 | 508 | 561 | 356 | 342 | 213 | 475 | 354 | 0 | 70 | 0 | 125

Figure S481. Get High-res Image Gene #86: 'Del Peak 45(19p13.3)' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'

'Del Peak 45(19p13.3)' versus 'GENDER'

P value = 1.22e-22 (Fisher's exact test), Q value = 1.9e-19

Table S482. Gene #86: 'Del Peak 45(19p13.3)' versus Clinical Feature #4: 'GENDER'

nPatients | FEMALE | MALE
--- | --- | ---
ALL | 2924 | 1717
DEL PEAK 45(19P13.3) CNV | 1129 | 424
DEL PEAK 45(19P13.3) WILD-TYPE | 1795 | 1293

Figure S482. Get High-res Image Gene #86: 'Del Peak 45(19p13.3)' versus Clinical Feature #4: 'GENDER'

'Del Peak 45(19p13.3)' versus 'HISTOLOGICAL.TYPE'

P value = 2.22e-237 (Chi-square test), Q value = 3.8e-234

Table S483. Gene #86: 'Del Peak 45(19p13.3)' versus Clinical Feature #6: 'HISTOLOGICAL.TYPE'

nPatients | COLON ADENOCARCINOMA | COLON MUCINOUS ADENOCARCINOMA | ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA | HEAD & NECK SQUAMOUS CELL CARCINOMA | INFILTRATING DUCTAL CARCINOMA | INFILTRATING LOBULAR 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 HISTOLOGY (PLEASE SPECIFY) | MIXED SEROUS AND ENDOMETRIOID | MUCINOUS (COLLOID) ADENOCARCINOMA | MUCINOUS (COLLOID) CARCINOMA | MUSCLE INVASIVE UROTHELIAL CARCINOMA (PT2 OR ABOVE) | OTHER SPECIFY | RECTAL ADENOCARCINOMA | RECTAL MUCINOUS ADENOCARCINOMA | SEROUS CYSTADENOCARCINOMA | SEROUS ENDOMETRIAL ADENOCARCINOMA | TREATED PRIMARY GBM | UNTREATED PRIMARY (DE NOVO) GBM
--- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | ---
ALL | 356 | 54 | 351 | 321 | 104 | 12 | 493 | 11 | 79 | 243 | 7 | 4 | 17 | 2 | 3 | 2 | 18 | 1 | 1 | 1 | 3 | 315 | 5 | 18 | 4 | 3 | 49 | 10 | 143 | 13 | 552 | 85 | 1 | 20
DEL PEAK 45(19P13.3) CNV | 51 | 4 | 35 | 108 | 47 | 0 | 18 | 5 | 45 | 132 | 3 | 0 | 9 | 1 | 3 | 1 | 12 | 1 | 0 | 1 | 2 | 143 | 0 | 7 | 2 | 0 | 19 | 4 | 31 | 2 | 482 | 70 | 0 | 1
DEL PEAK 45(19P13.3) WILD-TYPE | 305 | 50 | 316 | 213 | 57 | 12 | 475 | 6 | 34 | 111 | 4 | 4 | 8 | 1 | 0 | 1 | 6 | 0 | 1 | 0 | 1 | 172 | 5 | 11 | 2 | 3 | 30 | 6 | 112 | 11 | 70 | 15 | 1 | 19

Figure S483. Get High-res Image Gene #86: 'Del Peak 45(19p13.3)' versus Clinical Feature #6: 'HISTOLOGICAL.TYPE'

'Del Peak 45(19p13.3)' versus 'PATHOLOGY.T'

P value = 7.92e-17 (Fisher's exact test), Q value = 1.2e-13

Table S484. Gene #86: 'Del Peak 45(19p13.3)' versus Clinical Feature #7: 'PATHOLOGY.T'

nPatients | T0+T1 | T2 | T3 | T4
--- | --- | --- | --- | ---
ALL | 448 | 611 | 688 | 208
DEL PEAK 45(19P13.3) CNV | 84 | 230 | 130 | 70
DEL PEAK 45(19P13.3) WILD-TYPE | 364 | 381 | 558 | 138

Figure S484. Get High-res Image Gene #86: 'Del Peak 45(19p13.3)' versus Clinical Feature #7: 'PATHOLOGY.T'

'Del Peak 45(19p13.3)' versus 'PATHOLOGY.N'

P value = 4.24e-06 (Fisher's exact test), Q value = 0.0057

Table S485. Gene #86: 'Del Peak 45(19p13.3)' versus Clinical Feature #8: 'PATHOLOGY.N'

nPatients | N0 | N1 | N2 | N3
--- | --- | --- | --- | ---
ALL | 1036 | 343 | 279 | 11
DEL PEAK 45(19P13.3) CNV | 261 | 112 | 112 | 5
DEL PEAK 45(19P13.3) WILD-TYPE | 775 | 231 | 167 | 6

Figure S485. Get High-res Image Gene #86: 'Del Peak 45(19p13.3)' versus Clinical Feature #8: 'PATHOLOGY.N'

'Del Peak 45(19p13.3)' versus 'TUMOR.STAGE'

P value = 8.26e-44 (Fisher's exact test), Q value = 1.3e-40

Table S486. Gene #86: 'Del Peak 45(19p13.3)' versus Clinical Feature #10: 'TUMOR.STAGE'

nPatients | I | II | III | IV
--- | --- | --- | --- | ---
ALL | 685 | 487 | 876 | 420
DEL PEAK 45(19P13.3) CNV | 180 | 134 | 507 | 165
DEL PEAK 45(19P13.3) WILD-TYPE | 505 | 353 | 369 | 255

Figure S486. Get High-res Image Gene #86: 'Del Peak 45(19p13.3)' versus Clinical Feature #10: 'TUMOR.STAGE'

'Del Peak 45(19p13.3)' versus 'RADIATIONS.RADIATION.REGIMENINDICATION'

P value = 7.2e-19 (Fisher's exact test), Q value = 1.1e-15

Table S487. Gene #86: 'Del Peak 45(19p13.3)' versus Clinical Feature #11: 'RADIATIONS.RADIATION.REGIMENINDICATION'

nPatients | NO | YES
--- | --- | ---
ALL | 835 | 3816
DEL PEAK 45(19P13.3) CNV | 174 | 1389
DEL PEAK 45(19P13.3) WILD-TYPE | 661 | 2427

Figure S487. Get High-res Image Gene #86: 'Del Peak 45(19p13.3)' versus Clinical Feature #11: 'RADIATIONS.RADIATION.REGIMENINDICATION'

'Del Peak 46(19q13.32)' versus 'PRIMARY.SITE.OF.DISEASE'

P value = 5.86e-114 (Chi-square test), Q value = 9.8e-111

Table S488. Gene #87: 'Del Peak 46(19q13.32)' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'

nPatients | BLADDER | BRAIN | BREAST | COLON | ENDOMETRIAL | HEAD/NECK | KIDNEY | LUNG | OMENTUM | OVARY | PERITONEUM (OVARY) | RECTUM
--- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | ---
ALL | 131 | 544 | 857 | 412 | 454 | 321 | 493 | 714 | 2 | 548 | 2 | 159
DEL PEAK 46(19Q13.32) CNV | 14 | 96 | 177 | 43 | 48 | 62 | 7 | 234 | 1 | 286 | 1 | 22
DEL PEAK 46(19Q13.32) WILD-TYPE | 117 | 448 | 680 | 369 | 406 | 259 | 486 | 480 | 1 | 262 | 1 | 137

Figure S488. Get High-res Image Gene #87: 'Del Peak 46(19q13.32)' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'

'Del Peak 46(19q13.32)' versus 'GENDER'

P value = 1.1e-07 (Fisher's exact test), Q value = 0.00015

Table S489. Gene #87: 'Del Peak 46(19q13.32)' versus Clinical Feature #4: 'GENDER'

nPatients | FEMALE | MALE
--- | --- | ---
ALL | 2924 | 1717
DEL PEAK 46(19Q13.32) CNV | 696 | 296
DEL PEAK 46(19Q13.32) WILD-TYPE | 2228 | 1421

Figure S489. Get High-res Image Gene #87: 'Del Peak 46(19q13.32)' versus Clinical Feature #4: 'GENDER'

'Del Peak 46(19q13.32)' versus 'HISTOLOGICAL.TYPE'

P value = 6.78e-107 (Chi-square test), Q value = 1.1e-103

Table S490. Gene #87: 'Del Peak 46(19q13.32)' versus Clinical Feature #6: 'HISTOLOGICAL.TYPE'

nPatients | COLON ADENOCARCINOMA | COLON MUCINOUS ADENOCARCINOMA | ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA | HEAD & NECK SQUAMOUS CELL CARCINOMA | INFILTRATING DUCTAL CARCINOMA | INFILTRATING LOBULAR 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 HISTOLOGY (PLEASE SPECIFY) | MIXED SEROUS AND ENDOMETRIOID | MUCINOUS (COLLOID) ADENOCARCINOMA | MUCINOUS (COLLOID) CARCINOMA | MUSCLE INVASIVE UROTHELIAL CARCINOMA (PT2 OR ABOVE) | OTHER SPECIFY | RECTAL ADENOCARCINOMA | RECTAL MUCINOUS ADENOCARCINOMA | SEROUS CYSTADENOCARCINOMA | SEROUS ENDOMETRIAL ADENOCARCINOMA | TREATED PRIMARY GBM | UNTREATED PRIMARY (DE NOVO) GBM
--- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | ---
ALL | 356 | 54 | 351 | 321 | 104 | 12 | 493 | 11 | 79 | 243 | 7 | 4 | 17 | 2 | 3 | 2 | 18 | 1 | 1 | 1 | 3 | 315 | 5 | 18 | 4 | 3 | 49 | 10 | 143 | 13 | 552 | 85 | 1 | 20
DEL PEAK 46(19Q13.32) CNV | 37 | 5 | 15 | 62 | 20 | 0 | 7 | 4 | 32 | 86 | 4 | 0 | 5 | 1 | 1 | 0 | 10 | 1 | 0 | 0 | 2 | 87 | 1 | 5 | 1 | 0 | 5 | 1 | 20 | 1 | 288 | 28 | 0 | 5
DEL PEAK 46(19Q13.32) WILD-TYPE | 319 | 49 | 336 | 259 | 84 | 12 | 486 | 7 | 47 | 157 | 3 | 4 | 12 | 1 | 2 | 2 | 8 | 0 | 1 | 1 | 1 | 228 | 4 | 13 | 3 | 3 | 44 | 9 | 123 | 12 | 264 | 57 | 1 | 15

Figure S490. Get High-res Image Gene #87: 'Del Peak 46(19q13.32)' versus Clinical Feature #6: 'HISTOLOGICAL.TYPE'

'Del Peak 46(19q13.32)' versus 'PATHOLOGY.T'

P value = 6.59e-06 (Fisher's exact test), Q value = 0.0088

Table S491. Gene #87: 'Del Peak 46(19q13.32)' versus Clinical Feature #7: 'PATHOLOGY.T'

nPatients | T0+T1 | T2 | T3 | T4
--- | --- | --- | --- | ---
ALL | 448 | 611 | 688 | 208
DEL PEAK 46(19Q13.32) CNV | 56 | 140 | 94 | 38
DEL PEAK 46(19Q13.32) WILD-TYPE | 392 | 471 | 594 | 170

Figure S491. Get High-res Image Gene #87: 'Del Peak 46(19q13.32)' versus Clinical Feature #7: 'PATHOLOGY.T'

'Del Peak 46(19q13.32)' versus 'TUMOR.STAGE'

P value = 2.14e-20 (Fisher's exact test), Q value = 3.2e-17

Table S492. Gene #87: 'Del Peak 46(19q13.32)' versus Clinical Feature #10: 'TUMOR.STAGE'

nPatients | I | II | III | IV
--- | --- | --- | --- | ---
ALL | 685 | 487 | 876 | 420
DEL PEAK 46(19Q13.32) CNV | 119 | 86 | 316 | 87
DEL PEAK 46(19Q13.32) WILD-TYPE | 566 | 401 | 560 | 333

Figure S492. Get High-res Image Gene #87: 'Del Peak 46(19q13.32)' versus Clinical Feature #10: 'TUMOR.STAGE'

'Del Peak 47(19q13.43)' versus 'PRIMARY.SITE.OF.DISEASE'

P value = 7.62e-104 (Chi-square test), Q value = 1.3e-100

Table S493. Gene #88: 'Del Peak 47(19q13.43)' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'

nPatients | BLADDER | BRAIN | BREAST | COLON | ENDOMETRIAL | HEAD/NECK | KIDNEY | LUNG | OMENTUM | OVARY | PERITONEUM (OVARY) | RECTUM
--- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | ---
ALL | 131 | 544 | 857 | 412 | 454 | 321 | 493 | 714 | 2 | 548 | 2 | 159
DEL PEAK 47(19Q13.43) CNV | 14 | 82 | 146 | 42 | 49 | 64 | 5 | 213 | 1 | 267 | 1 | 25
DEL PEAK 47(19Q13.43) WILD-TYPE | 117 | 462 | 711 | 370 | 405 | 257 | 488 | 501 | 1 | 281 | 1 | 134

Figure S493. Get High-res Image Gene #88: 'Del Peak 47(19q13.43)' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'

'Del Peak 47(19q13.43)' versus 'GENDER'

P value = 2e-06 (Fisher's exact test), Q value = 0.0027

Table S494. Gene #88: 'Del Peak 47(19q13.43)' versus Clinical Feature #4: 'GENDER'

nPatients | FEMALE | MALE
--- | --- | ---
ALL | 2924 | 1717
DEL PEAK 47(19Q13.43) CNV | 635 | 275
DEL PEAK 47(19Q13.43) WILD-TYPE | 2289 | 1442

Figure S494. Get High-res Image Gene #88: 'Del Peak 47(19q13.43)' versus Clinical Feature #4: 'GENDER'

'Del Peak 47(19q13.43)' versus 'HISTOLOGICAL.TYPE'

P value = 8.06e-97 (Chi-square test), Q value = 1.3e-93

Table S495. Gene #88: 'Del Peak 47(19q13.43)' versus Clinical Feature #6: 'HISTOLOGICAL.TYPE'

nPatients | COLON ADENOCARCINOMA | COLON MUCINOUS ADENOCARCINOMA | ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA | HEAD & NECK SQUAMOUS CELL CARCINOMA | INFILTRATING DUCTAL CARCINOMA | INFILTRATING LOBULAR 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 HISTOLOGY (PLEASE SPECIFY) | MIXED SEROUS AND ENDOMETRIOID | MUCINOUS (COLLOID) ADENOCARCINOMA | MUCINOUS (COLLOID) CARCINOMA | MUSCLE INVASIVE UROTHELIAL CARCINOMA (PT2 OR ABOVE) | OTHER SPECIFY | RECTAL ADENOCARCINOMA | RECTAL MUCINOUS ADENOCARCINOMA | SEROUS CYSTADENOCARCINOMA | SEROUS ENDOMETRIAL ADENOCARCINOMA | TREATED PRIMARY GBM | UNTREATED PRIMARY (DE NOVO) GBM
--- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | ---
ALL | 356 | 54 | 351 | 321 | 104 | 12 | 493 | 11 | 79 | 243 | 7 | 4 | 17 | 2 | 3 | 2 | 18 | 1 | 1 | 1 | 3 | 315 | 5 | 18 | 4 | 3 | 49 | 10 | 143 | 13 | 552 | 85 | 1 | 20
DEL PEAK 47(19Q13.43) CNV | 36 | 5 | 13 | 64 | 18 | 0 | 5 | 4 | 29 | 77 | 4 | 0 | 6 | 0 | 2 | 0 | 9 | 1 | 0 | 0 | 1 | 79 | 0 | 4 | 1 | 0 | 4 | 1 | 23 | 1 | 269 | 32 | 0 | 6
DEL PEAK 47(19Q13.43) WILD-TYPE | 320 | 49 | 338 | 257 | 86 | 12 | 488 | 7 | 50 | 166 | 3 | 4 | 11 | 2 | 1 | 2 | 9 | 0 | 1 | 1 | 2 | 236 | 5 | 14 | 3 | 3 | 45 | 9 | 120 | 12 | 283 | 53 | 1 | 14

Figure S495. Get High-res Image Gene #88: 'Del Peak 47(19q13.43)' versus Clinical Feature #6: 'HISTOLOGICAL.TYPE'

'Del Peak 47(19q13.43)' versus 'PATHOLOGY.T'

P value = 3.89e-06 (Fisher's exact test), Q value = 0.0052

Table S496. Gene #88: 'Del Peak 47(19q13.43)' versus Clinical Feature #7: 'PATHOLOGY.T'

nPatients | T0+T1 | T2 | T3 | T4
--- | --- | --- | --- | ---
ALL | 448 | 611 | 688 | 208
DEL PEAK 47(19Q13.43) CNV | 47 | 130 | 94 | 41
DEL PEAK 47(19Q13.43) WILD-TYPE | 401 | 481 | 594 | 167

Figure S496. Get High-res Image Gene #88: 'Del Peak 47(19q13.43)' versus Clinical Feature #7: 'PATHOLOGY.T'

'Del Peak 47(19q13.43)' versus 'TUMOR.STAGE'

P value = 2.97e-17 (Fisher's exact test), Q value = 4.5e-14

Table S497. Gene #88: 'Del Peak 47(19q13.43)' versus Clinical Feature #10: 'TUMOR.STAGE'

nPatients | I | II | III | IV
--- | --- | --- | --- | ---
ALL | 685 | 487 | 876 | 420
DEL PEAK 47(19Q13.43) CNV | 105 | 88 | 291 | 88
DEL PEAK 47(19Q13.43) WILD-TYPE | 580 | 399 | 585 | 332

Figure S497. Get High-res Image Gene #88: 'Del Peak 47(19q13.43)' versus Clinical Feature #10: 'TUMOR.STAGE'

'Del Peak 48(20p12.1)' versus 'PRIMARY.SITE.OF.DISEASE'

P value = 5.06e-36 (Chi-square test), Q value = 7.9e-33

Table S498. Gene #89: 'Del Peak 48(20p12.1)' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'

nPatients | BLADDER | BRAIN | BREAST | COLON | ENDOMETRIAL | HEAD/NECK | KIDNEY | LUNG | OMENTUM | OVARY | PERITONEUM (OVARY) | RECTUM
--- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | ---
ALL | 131 | 544 | 857 | 412 | 454 | 321 | 493 | 714 | 2 | 548 | 2 | 159
DEL PEAK 48(20P12.1) CNV | 9 | 18 | 104 | 79 | 26 | 45 | 9 | 120 | 0 | 68 | 0 | 46
DEL PEAK 48(20P12.1) WILD-TYPE | 122 | 526 | 753 | 333 | 428 | 276 | 484 | 594 | 2 | 480 | 2 | 113

Figure S498. Get High-res Image Gene #89: 'Del Peak 48(20p12.1)' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'

'Del Peak 48(20p12.1)' versus 'HISTOLOGICAL.TYPE'

P value = 3.04e-28 (Chi-square test), Q value = 4.7e-25

Table S499. Gene #89: 'Del Peak 48(20p12.1)' versus Clinical Feature #6: 'HISTOLOGICAL.TYPE'

nPatients | COLON ADENOCARCINOMA | COLON MUCINOUS ADENOCARCINOMA | ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA | HEAD & NECK SQUAMOUS CELL CARCINOMA | INFILTRATING DUCTAL CARCINOMA | INFILTRATING LOBULAR 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 HISTOLOGY (PLEASE SPECIFY) | MIXED SEROUS AND ENDOMETRIOID | MUCINOUS (COLLOID) ADENOCARCINOMA | MUCINOUS (COLLOID) CARCINOMA | MUSCLE INVASIVE UROTHELIAL CARCINOMA (PT2 OR ABOVE) | OTHER SPECIFY | RECTAL ADENOCARCINOMA | RECTAL MUCINOUS ADENOCARCINOMA | SEROUS CYSTADENOCARCINOMA | SEROUS ENDOMETRIAL ADENOCARCINOMA | TREATED PRIMARY GBM | UNTREATED PRIMARY (DE NOVO) GBM
--- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | ---
ALL | 356 | 54 | 351 | 321 | 104 | 12 | 493 | 11 | 79 | 243 | 7 | 4 | 17 | 2 | 3 | 2 | 18 | 1 | 1 | 1 | 3 | 315 | 5 | 18 | 4 | 3 | 49 | 10 | 143 | 13 | 552 | 85 | 1 | 20
DEL PEAK 48(20P12.1) CNV | 73 | 6 | 12 | 45 | 18 | 2 | 9 | 2 | 20 | 56 | 0 | 0 | 5 | 2 | 1 | 0 | 2 | 0 | 0 | 0 | 1 | 29 | 0 | 2 | 1 | 1 | 4 | 0 | 41 | 5 | 68 | 12 | 0 | 0
DEL PEAK 48(20P12.1) WILD-TYPE | 283 | 48 | 339 | 276 | 86 | 10 | 484 | 9 | 59 | 187 | 7 | 4 | 12 | 0 | 2 | 2 | 16 | 1 | 1 | 1 | 2 | 286 | 5 | 16 | 3 | 2 | 45 | 10 | 102 | 8 | 484 | 73 | 1 | 20

Figure S499. Get High-res Image Gene #89: 'Del Peak 48(20p12.1)' versus Clinical Feature #6: 'HISTOLOGICAL.TYPE'

'Del Peak 48(20p12.1)' versus 'RADIATIONS.RADIATION.REGIMENINDICATION'

P value = 2.98e-05 (Fisher's exact test), Q value = 0.038

Table S500. Gene #89: 'Del Peak 48(20p12.1)' versus Clinical Feature #11: 'RADIATIONS.RADIATION.REGIMENINDICATION'

nPatients | NO | YES
--- | --- | ---
ALL | 835 | 3816
DEL PEAK 48(20P12.1) CNV | 61 | 465
DEL PEAK 48(20P12.1) WILD-TYPE | 774 | 3351

Figure S500. Get High-res Image Gene #89: 'Del Peak 48(20p12.1)' versus Clinical Feature #11: 'RADIATIONS.RADIATION.REGIMENINDICATION'

'Del Peak 49(21q11.2)' versus 'PRIMARY.SITE.OF.DISEASE'

P value = 1.48e-67 (Chi-square test), Q value = 2.4e-64

Table S501. Gene #90: 'Del Peak 49(21q11.2)' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'

nPatients | BLADDER | BRAIN | BREAST | COLON | ENDOMETRIAL | HEAD/NECK | KIDNEY | LUNG | OMENTUM | OVARY | PERITONEUM (OVARY) | RECTUM
--- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | ---
ALL | 131 | 544 | 857 | 412 | 454 | 321 | 493 | 714 | 2 | 548 | 2 | 159
DEL PEAK 49(21Q11.2) CNV | 21 | 53 | 173 | 124 | 50 | 105 | 54 | 288 | 2 | 180 | 0 | 68
DEL PEAK 49(21Q11.2) WILD-TYPE | 110 | 491 | 684 | 288 | 404 | 216 | 439 | 426 | 0 | 368 | 2 | 91

Figure S501. Get High-res Image Gene #90: 'Del Peak 49(21q11.2)' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'

'Del Peak 49(21q11.2)' versus 'HISTOLOGICAL.TYPE'

P value = 6.88e-46 (Chi-square test), Q value = 1.1e-42

Table S502. Gene #90: 'Del Peak 49(21q11.2)' versus Clinical Feature #6: 'HISTOLOGICAL.TYPE'

nPatients | COLON ADENOCARCINOMA | COLON MUCINOUS ADENOCARCINOMA | ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA | HEAD & NECK SQUAMOUS CELL CARCINOMA | INFILTRATING DUCTAL CARCINOMA | INFILTRATING LOBULAR 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 HISTOLOGY (PLEASE SPECIFY) | MIXED SEROUS AND ENDOMETRIOID | MUCINOUS (COLLOID) ADENOCARCINOMA | MUCINOUS (COLLOID) CARCINOMA | MUSCLE INVASIVE UROTHELIAL CARCINOMA (PT2 OR ABOVE) | OTHER SPECIFY | RECTAL ADENOCARCINOMA | RECTAL MUCINOUS ADENOCARCINOMA | SEROUS CYSTADENOCARCINOMA | SEROUS ENDOMETRIAL ADENOCARCINOMA | TREATED PRIMARY GBM | UNTREATED PRIMARY (DE NOVO) GBM
--- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | ---
ALL | 356 | 54 | 351 | 321 | 104 | 12 | 493 | 11 | 79 | 243 | 7 | 4 | 17 | 2 | 3 | 2 | 18 | 1 | 1 | 1 | 3 | 315 | 5 | 18 | 4 | 3 | 49 | 10 | 143 | 13 | 552 | 85 | 1 | 20
DEL PEAK 49(21Q11.2) CNV | 115 | 8 | 17 | 105 | 22 | 1 | 54 | 7 | 23 | 85 | 3 | 0 | 5 | 0 | 1 | 0 | 6 | 1 | 0 | 1 | 1 | 152 | 2 | 5 | 2 | 1 | 8 | 2 | 63 | 3 | 182 | 28 | 0 | 2
DEL PEAK 49(21Q11.2) WILD-TYPE | 241 | 46 | 334 | 216 | 82 | 11 | 439 | 4 | 56 | 158 | 4 | 4 | 12 | 2 | 2 | 2 | 12 | 0 | 1 | 0 | 2 | 163 | 3 | 13 | 2 | 2 | 41 | 8 | 80 | 10 | 370 | 57 | 1 | 18

Figure S502. Get High-res Image Gene #90: 'Del Peak 49(21q11.2)' versus Clinical Feature #6: 'HISTOLOGICAL.TYPE'

'Del Peak 49(21q11.2)' versus 'PATHOLOGY.T'

P value = 8.93e-06 (Fisher's exact test), Q value = 0.012

Table S503. Gene #90: 'Del Peak 49(21q11.2)' versus Clinical Feature #7: 'PATHOLOGY.T'

nPatients | T0+T1 | T2 | T3 | T4
--- | --- | --- | --- | ---
ALL | 448 | 611 | 688 | 208
DEL PEAK 49(21Q11.2) CNV | 102 | 222 | 202 | 75
DEL PEAK 49(21Q11.2) WILD-TYPE | 346 | 389 | 486 | 133

Figure S503. Get High-res Image Gene #90: 'Del Peak 49(21q11.2)' versus Clinical Feature #7: 'PATHOLOGY.T'

'Del Peak 49(21q11.2)' versus 'PATHOLOGY.N'

P value = 8.8e-05 (Fisher's exact test), Q value = 0.11

Table S504. Gene #90: 'Del Peak 49(21q11.2)' versus Clinical Feature #8: 'PATHOLOGY.N'

nPatients | N0 | N1 | N2 | N3
--- | --- | --- | --- | ---
ALL | 1036 | 343 | 279 | 11
DEL PEAK 49(21Q11.2) CNV | 302 | 142 | 104 | 5
DEL PEAK 49(21Q11.2) WILD-TYPE | 734 | 201 | 175 | 6

Figure S504. Get High-res Image Gene #90: 'Del Peak 49(21q11.2)' versus Clinical Feature #8: 'PATHOLOGY.N'

'Del Peak 49(21q11.2)' versus 'RADIATIONS.RADIATION.REGIMENINDICATION'

P value = 1.78e-11 (Fisher's exact test), Q value = 2.6e-08

Table S505. Gene #90: 'Del Peak 49(21q11.2)' versus Clinical Feature #11: 'RADIATIONS.RADIATION.REGIMENINDICATION'

nPatients | NO | YES
--- | --- | ---
ALL | 835 | 3816
DEL PEAK 49(21Q11.2) CNV | 129 | 996
DEL PEAK 49(21Q11.2) WILD-TYPE | 706 | 2820

Figure S505. Get High-res Image Gene #90: 'Del Peak 49(21q11.2)' versus Clinical Feature #11: 'RADIATIONS.RADIATION.REGIMENINDICATION'

'Del Peak 50(22q13.32)' versus 'PRIMARY.SITE.OF.DISEASE'

P value = 1.85e-172 (Chi-square test), Q value = 3.2e-169

Table S506. Gene #91: 'Del Peak 50(22q13.32)' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'

nPatients | BLADDER | BRAIN | BREAST | COLON | ENDOMETRIAL | HEAD/NECK | KIDNEY | LUNG | OMENTUM | OVARY | PERITONEUM (OVARY) | RECTUM
--- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | ---
ALL | 131 | 544 | 857 | 412 | 454 | 321 | 493 | 714 | 2 | 548 | 2 | 159
DEL PEAK 50(22Q13.32) CNV | 54 | 206 | 384 | 143 | 110 | 64 | 37 | 264 | 2 | 474 | 1 | 63
DEL PEAK 50(22Q13.32) WILD-TYPE | 77 | 338 | 473 | 269 | 344 | 257 | 456 | 450 | 0 | 74 | 1 | 96

Figure S506. Get High-res Image Gene #91: 'Del Peak 50(22q13.32)' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'

'Del Peak 50(22q13.32)' versus 'GENDER'

P value = 4.14e-26 (Fisher's exact test), Q value = 6.4e-23

Table S507. Gene #91: 'Del Peak 50(22q13.32)' versus Clinical Feature #4: 'GENDER'

nPatients | FEMALE | MALE
--- | --- | ---
ALL | 2924 | 1717
DEL PEAK 50(22Q13.32) CNV | 1306 | 500
DEL PEAK 50(22Q13.32) WILD-TYPE | 1618 | 1217

Figure S507. Get High-res Image Gene #91: 'Del Peak 50(22q13.32)' versus Clinical Feature #4: 'GENDER'

'Del Peak 50(22q13.32)' versus 'HISTOLOGICAL.TYPE'

P value = 8.76e-187 (Chi-square test), Q value = 1.5e-183

Table S508. Gene #91: 'Del Peak 50(22q13.32)' versus Clinical Feature #6: 'HISTOLOGICAL.TYPE'

nPatients | COLON ADENOCARCINOMA | COLON MUCINOUS ADENOCARCINOMA | ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA | HEAD & NECK SQUAMOUS CELL CARCINOMA | INFILTRATING DUCTAL CARCINOMA | INFILTRATING LOBULAR 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 HISTOLOGY (PLEASE SPECIFY) | MIXED SEROUS AND ENDOMETRIOID | MUCINOUS (COLLOID) ADENOCARCINOMA | MUCINOUS (COLLOID) CARCINOMA | MUSCLE INVASIVE UROTHELIAL CARCINOMA (PT2 OR ABOVE) | OTHER SPECIFY | RECTAL ADENOCARCINOMA | RECTAL MUCINOUS ADENOCARCINOMA | SEROUS CYSTADENOCARCINOMA | SEROUS ENDOMETRIAL ADENOCARCINOMA | TREATED PRIMARY GBM | UNTREATED PRIMARY (DE NOVO) GBM
--- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | ---
ALL | 356 | 54 | 351 | 321 | 104 | 12 | 493 | 11 | 79 | 243 | 7 | 4 | 17 | 2 | 3 | 2 | 18 | 1 | 1 | 1 | 3 | 315 | 5 | 18 | 4 | 3 | 49 | 10 | 143 | 13 | 552 | 85 | 1 | 20
DEL PEAK 50(22Q13.32) CNV | 133 | 10 | 48 | 64 | 47 | 7 | 37 | 5 | 34 | 124 | 4 | 1 | 10 | 0 | 2 | 0 | 8 | 1 | 0 | 1 | 3 | 70 | 1 | 8 | 1 | 0 | 17 | 4 | 59 | 4 | 477 | 54 | 0 | 9
DEL PEAK 50(22Q13.32) WILD-TYPE | 223 | 44 | 303 | 257 | 57 | 5 | 456 | 6 | 45 | 119 | 3 | 3 | 7 | 2 | 1 | 2 | 10 | 0 | 1 | 0 | 0 | 245 | 4 | 10 | 3 | 3 | 32 | 6 | 84 | 9 | 75 | 31 | 1 | 11

Figure S508. Get High-res Image Gene #91: 'Del Peak 50(22q13.32)' versus Clinical Feature #6: 'HISTOLOGICAL.TYPE'

'Del Peak 50(22q13.32)' versus 'PATHOLOGY.T'

P value = 7.66e-05 (Fisher's exact test), Q value = 0.097

Table S509. Gene #91: 'Del Peak 50(22q13.32)' versus Clinical Feature #7: 'PATHOLOGY.T'

nPatients | T0+T1 | T2 | T3 | T4
--- | --- | --- | --- | ---
ALL | 448 | 611 | 688 | 208
DEL PEAK 50(22Q13.32) CNV | 83 | 184 | 198 | 52
DEL PEAK 50(22Q13.32) WILD-TYPE | 365 | 427 | 490 | 156

Figure S509. Get High-res Image Gene #91: 'Del Peak 50(22q13.32)' versus Clinical Feature #7: 'PATHOLOGY.T'

'Del Peak 50(22q13.32)' versus 'TUMOR.STAGE'

P value = 2.75e-45 (Fisher's exact test), Q value = 4.4e-42

Table S510. Gene #91: 'Del Peak 50(22q13.32)' versus Clinical Feature #10: 'TUMOR.STAGE'

nPatients | I | II | III | IV
--- | --- | --- | --- | ---
ALL | 685 | 487 | 876 | 420
DEL PEAK 50(22Q13.32) CNV | 165 | 147 | 506 | 158
DEL PEAK 50(22Q13.32) WILD-TYPE | 520 | 340 | 370 | 262

Figure S510. Get High-res Image Gene #91: 'Del Peak 50(22q13.32)' versus Clinical Feature #10: 'TUMOR.STAGE'

'Del Peak 50(22q13.32)' versus 'COMPLETENESS.OF.RESECTION'

P value = 0.000108 (Fisher's exact test), Q value = 0.14

Table S511. Gene #91: 'Del Peak 50(22q13.32)' versus Clinical Feature #17: 'COMPLETENESS.OF.RESECTION'

nPatients | R0 | R1 | R2 | RX
--- | --- | --- | --- | ---
ALL | 1221 | 69 | 59 | 80
DEL PEAK 50(22Q13.32) CNV | 399 | 41 | 23 | 31
DEL PEAK 50(22Q13.32) WILD-TYPE | 822 | 28 | 36 | 49

Figure S511. Get High-res Image Gene #91: 'Del Peak 50(22q13.32)' versus Clinical Feature #17: 'COMPLETENESS.OF.RESECTION'

'Del Peak 51(Xp21.1)' versus 'Time to Death'

P value = 1.5e-05 (logrank test), Q value = 0.02

Table S512. Gene #92: 'Del Peak 51(Xp21.1)' versus Clinical Feature #1: 'Time to Death'

| nPatients | nDeath | Duration Range (Median), Month
--- | --- | --- | ---
ALL | 4370 | 1406 | 0.0 - 224.0 (14.4)
DEL PEAK 51(XP21.1) CNV | 1133 | 440 | 0.0 - 173.8 (16.6)
DEL PEAK 51(XP21.1) WILD-TYPE | 3237 | 966 | 0.0 - 224.0 (13.9)

Figure S512. Get High-res Image Gene #92: 'Del Peak 51(Xp21.1)' versus Clinical Feature #1: 'Time to Death'

'Del Peak 51(Xp21.1)' versus 'PRIMARY.SITE.OF.DISEASE'

P value = 1.34e-113 (Chi-square test), Q value = 2.3e-110

Table S513. Gene #92: 'Del Peak 51(Xp21.1)' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'

nPatients | BLADDER | BRAIN | BREAST | COLON | ENDOMETRIAL | HEAD/NECK | KIDNEY | LUNG | OMENTUM | OVARY | PERITONEUM (OVARY) | RECTUM
--- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | ---
ALL | 131 | 544 | 857 | 412 | 454 | 321 | 493 | 714 | 2 | 548 | 2 | 159
DEL PEAK 51(XP21.1) CNV | 33 | 121 | 176 | 63 | 66 | 104 | 51 | 206 | 1 | 350 | 1 | 28
DEL PEAK 51(XP21.1) WILD-TYPE | 98 | 423 | 681 | 349 | 388 | 217 | 442 | 508 | 1 | 198 | 1 | 131

Figure S513. Get High-res Image Gene #92: 'Del Peak 51(Xp21.1)' versus Clinical Feature #3: 'PRIMARY.SITE.OF.DISEASE'

'Del Peak 51(Xp21.1)' versus 'HISTOLOGICAL.TYPE'

P value = 6.27e-103 (Chi-square test), Q value = 1e-99

Table S514. Gene #92: 'Del Peak 51(Xp21.1)' versus Clinical Feature #6: 'HISTOLOGICAL.TYPE'

nPatients | COLON ADENOCARCINOMA | COLON MUCINOUS ADENOCARCINOMA | ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA | HEAD & NECK SQUAMOUS CELL CARCINOMA | INFILTRATING DUCTAL CARCINOMA | INFILTRATING LOBULAR 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 HISTOLOGY (PLEASE SPECIFY) | MIXED SEROUS AND ENDOMETRIOID | MUCINOUS (COLLOID) ADENOCARCINOMA | MUCINOUS (COLLOID) CARCINOMA | MUSCLE INVASIVE UROTHELIAL CARCINOMA (PT2 OR ABOVE) | OTHER SPECIFY | RECTAL ADENOCARCINOMA | RECTAL MUCINOUS ADENOCARCINOMA | SEROUS CYSTADENOCARCINOMA | SEROUS ENDOMETRIAL ADENOCARCINOMA | TREATED PRIMARY GBM | UNTREATED PRIMARY (DE NOVO) GBM
--- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | ---
ALL | 356 | 54 | 351 | 321 | 104 | 12 | 493 | 11 | 79 | 243 | 7 | 4 | 17 | 2 | 3 | 2 | 18 | 1 | 1 | 1 | 3 | 315 | 5 | 18 | 4 | 3 | 49 | 10 | 143 | 13 | 552 | 85 | 1 | 20
DEL PEAK 51(XP21.1) CNV | 59 | 4 | 26 | 104 | 21 | 1 | 51 | 3 | 20 | 70 | 1 | 1 | 2 | 0 | 2 | 1 | 3 | 1 | 0 | 0 | 0 | 100 | 1 | 2 | 1 | 1 | 11 | 3 | 23 | 4 | 352 | 38 | 0 | 7
DEL PEAK 51(XP21.1) WILD-TYPE | 297 | 50 | 325 | 217 | 83 | 11 | 442 | 8 | 59 | 173 | 6 | 3 | 15 | 2 | 1 | 1 | 15 | 0 | 1 | 1 | 3 | 215 | 4 | 16 | 3 | 2 | 38 | 7 | 120 | 9 | 200 | 47 | 1 | 13

Figure S514. Get High-res Image Gene #92: 'Del Peak 51(Xp21.1)' versus Clinical Feature #6: 'HISTOLOGICAL.TYPE'

'Del Peak 51(Xp21.1)' versus 'TUMOR.STAGE'

P value = 1.1e-18 (Fisher's exact test), Q value = 1.7e-15

Table S515. Gene #92: 'Del Peak 51(Xp21.1)' versus Clinical Feature #10: 'TUMOR.STAGE'

nPatients | I | II | III | IV
--- | --- | --- | --- | ---
ALL | 685 | 487 | 876 | 420
DEL PEAK 51(XP21.1) CNV | 142 | 115 | 357 | 138
DEL PEAK 51(XP21.1) WILD-TYPE | 543 | 372 | 519 | 282

Figure S515. Get High-res Image Gene #92: 'Del Peak 51(Xp21.1)' versus Clinical Feature #10: 'TUMOR.STAGE'

Methods & Data
Input

- Mutation data file = all_lesions.conf_99.cnv.cluster.txt

- Clinical data file = PANCAN12-TP.clin.merged.picked.txt

- Number of patients = 4651

- Number of significantly arm-level cnvs = 92

- Number of selected clinical features = 20

- Exclude genes that fewer than K tumors have mutations, 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 tumors with and without gene mutations 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 or multi-class clinical features (nominal or ordinal), two-tailed Fisher's exact tests (Fisher 1922) were used to estimate the P values using the 'fisher.test' function in R

Q value calculation

For multiple hypothesis correction, Q value is the False Discovery Rate (FDR) analogue of the P value (Benjamini and Hochberg 1995), defined as the minimum FDR at which the test may be called significant. We used the 'Benjamini and Hochberg' method of 'p.adjust' function in R to convert P values into Q values.

Download Results

This is an experimental feature. The full results of the analysis summarized in this report can be downloaded from the TCGA Data Coordination Center.

- Analysis Results (MD5 checksum)

- Auxiliary Data (MD5 checksum)

- MAGE-TAB File (MD5 checksum)

References
[1] Bland and Altman, Statistics notes: The logrank test, BMJ 328(7447):1073 (2004)
[2] Lehmann and Romano, Testing Statistical Hypotheses (3E ed.), New York: Springer. ISBN 0387988645 (2005)
[3] Greenwood and Nikulin, A guide to chi-squared testing, Wiley, New York. ISBN 047155779X (1996)
[4] Fisher, R.A., On the interpretation of chi-square from contingency tables, and the calculation of P, Journal of the Royal Statistical Society 85(1):87-94 (1922)
[5] Benjamini and Hochberg, Controlling the false discovery rate: a practical and powerful approach to multiple testing, Journal of the Royal Statistical Society Series B 59:289-300 (1995)
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