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.

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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