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

Overview

Introduction

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

Summary

Testing the association between copy number variation 32 focal events and 14 clinical features across 882 patients, 211 significant findings detected with Q value < 0.25.

amp_1q32.1 cnv correlated to 'Time to Death', 'YEARS_TO_BIRTH', 'PATHOLOGIC_STAGE', 'PATHOLOGY_T_STAGE', 'PATHOLOGY_N_STAGE', 'KARNOFSKY_PERFORMANCE_SCORE', 'HISTOLOGICAL_TYPE', and 'YEAR_OF_TOBACCO_SMOKING_ONSET'.
amp_2q32.1 cnv correlated to 'PATHOLOGY_N_STAGE' and 'HISTOLOGICAL_TYPE'.
amp_3q26.32 cnv correlated to 'PATHOLOGY_N_STAGE', 'PATHOLOGY_M_STAGE', 'HISTOLOGICAL_TYPE', and 'RACE'.
amp_5q35.1 cnv correlated to 'PATHOLOGIC_STAGE', 'PATHOLOGY_T_STAGE', 'PATHOLOGY_N_STAGE', 'PATHOLOGY_M_STAGE', 'HISTOLOGICAL_TYPE', and 'RACE'.
amp_7q31.2 cnv correlated to 'PATHOLOGIC_STAGE', 'PATHOLOGY_N_STAGE', 'PATHOLOGY_M_STAGE', 'GENDER', 'RADIATION_THERAPY', 'HISTOLOGICAL_TYPE', and 'YEAR_OF_TOBACCO_SMOKING_ONSET'.
amp_8q24.22 cnv correlated to 'Time to Death', 'YEARS_TO_BIRTH', 'PATHOLOGIC_STAGE', 'PATHOLOGY_T_STAGE', 'PATHOLOGY_N_STAGE', 'PATHOLOGY_M_STAGE', 'HISTOLOGICAL_TYPE', and 'RACE'.
amp_10p14 cnv correlated to 'PATHOLOGIC_STAGE', 'PATHOLOGY_T_STAGE', and 'PATHOLOGY_N_STAGE'.
amp_17q24.3 cnv correlated to 'YEARS_TO_BIRTH', 'PATHOLOGIC_STAGE', 'PATHOLOGY_T_STAGE', 'PATHOLOGY_N_STAGE', 'GENDER', 'HISTOLOGICAL_TYPE', 'YEAR_OF_TOBACCO_SMOKING_ONSET', and 'RACE'.
amp_xq11.2 cnv correlated to 'Time to Death', 'PATHOLOGIC_STAGE', 'PATHOLOGY_T_STAGE', 'GENDER', 'HISTOLOGICAL_TYPE', and 'YEAR_OF_TOBACCO_SMOKING_ONSET'.
del_1p36.31 cnv correlated to 'Time to Death', 'YEARS_TO_BIRTH', 'PATHOLOGIC_STAGE', 'PATHOLOGY_T_STAGE', 'PATHOLOGY_N_STAGE', 'KARNOFSKY_PERFORMANCE_SCORE', and 'HISTOLOGICAL_TYPE'.
del_1p31.1 cnv correlated to 'YEARS_TO_BIRTH', 'PATHOLOGIC_STAGE', 'PATHOLOGY_T_STAGE', 'PATHOLOGY_N_STAGE', 'HISTOLOGICAL_TYPE', and 'ETHNICITY'.
del_1q44 cnv correlated to 'Time to Death', 'YEARS_TO_BIRTH', 'PATHOLOGIC_STAGE', 'PATHOLOGY_T_STAGE', and 'HISTOLOGICAL_TYPE'.
del_2q22.1 cnv correlated to 'Time to Death', 'YEARS_TO_BIRTH', 'PATHOLOGIC_STAGE', 'PATHOLOGY_T_STAGE', 'KARNOFSKY_PERFORMANCE_SCORE', and 'HISTOLOGICAL_TYPE'.
del_2q37.3 cnv correlated to 'Time to Death', 'YEARS_TO_BIRTH', 'PATHOLOGIC_STAGE', 'PATHOLOGY_T_STAGE', 'PATHOLOGY_M_STAGE', 'KARNOFSKY_PERFORMANCE_SCORE', and 'HISTOLOGICAL_TYPE'.
del_3p26.3 cnv correlated to 'Time to Death', 'PATHOLOGIC_STAGE', 'PATHOLOGY_T_STAGE', 'PATHOLOGY_N_STAGE', 'PATHOLOGY_M_STAGE', 'GENDER', 'KARNOFSKY_PERFORMANCE_SCORE', 'HISTOLOGICAL_TYPE', 'YEAR_OF_TOBACCO_SMOKING_ONSET', and 'RACE'.
del_3p21.2 cnv correlated to 'Time to Death', 'PATHOLOGIC_STAGE', 'PATHOLOGY_T_STAGE', 'PATHOLOGY_M_STAGE', 'GENDER', 'KARNOFSKY_PERFORMANCE_SCORE', 'HISTOLOGICAL_TYPE', 'YEAR_OF_TOBACCO_SMOKING_ONSET', and 'RACE'.
del_3p14.1 cnv correlated to 'Time to Death', 'PATHOLOGIC_STAGE', 'PATHOLOGY_T_STAGE', 'HISTOLOGICAL_TYPE', 'YEAR_OF_TOBACCO_SMOKING_ONSET', and 'RACE'.
del_3p12.2 cnv correlated to 'Time to Death', 'PATHOLOGIC_STAGE', 'PATHOLOGY_T_STAGE', 'HISTOLOGICAL_TYPE', 'YEAR_OF_TOBACCO_SMOKING_ONSET', and 'RACE'.
del_4q34.3 cnv correlated to 'Time to Death', 'PATHOLOGIC_STAGE', 'PATHOLOGY_T_STAGE', 'PATHOLOGY_N_STAGE', 'PATHOLOGY_M_STAGE', 'HISTOLOGICAL_TYPE', and 'RACE'.
del_5p15.33 cnv correlated to 'YEARS_TO_BIRTH', 'PATHOLOGIC_STAGE', 'PATHOLOGY_T_STAGE', 'PATHOLOGY_N_STAGE', 'KARNOFSKY_PERFORMANCE_SCORE', and 'HISTOLOGICAL_TYPE'.
del_6q26 cnv correlated to 'PATHOLOGIC_STAGE', 'PATHOLOGY_T_STAGE', 'PATHOLOGY_N_STAGE', 'HISTOLOGICAL_TYPE', 'NUMBER_PACK_YEARS_SMOKED', and 'RACE'.
del_6q26 cnv correlated to 'PATHOLOGIC_STAGE', 'PATHOLOGY_T_STAGE', 'PATHOLOGY_N_STAGE', 'HISTOLOGICAL_TYPE', 'NUMBER_PACK_YEARS_SMOKED', and 'RACE'.
del_8p23.2 cnv correlated to 'Time to Death', 'PATHOLOGIC_STAGE', 'PATHOLOGY_T_STAGE', 'PATHOLOGY_M_STAGE', 'HISTOLOGICAL_TYPE', and 'RACE'.
del_9p23 cnv correlated to 'Time to Death', 'YEARS_TO_BIRTH', 'PATHOLOGIC_STAGE', 'PATHOLOGY_T_STAGE', 'PATHOLOGY_N_STAGE', 'PATHOLOGY_M_STAGE', 'KARNOFSKY_PERFORMANCE_SCORE', 'HISTOLOGICAL_TYPE', and 'RACE'.
del_9p21.3 cnv correlated to 'Time to Death', 'YEARS_TO_BIRTH', 'PATHOLOGIC_STAGE', 'PATHOLOGY_T_STAGE', 'PATHOLOGY_N_STAGE', 'PATHOLOGY_M_STAGE', 'KARNOFSKY_PERFORMANCE_SCORE', 'HISTOLOGICAL_TYPE', and 'RACE'.
del_10q23.31 cnv correlated to 'YEARS_TO_BIRTH', 'PATHOLOGIC_STAGE', 'PATHOLOGY_T_STAGE', 'HISTOLOGICAL_TYPE', 'NUMBER_PACK_YEARS_SMOKED', and 'RACE'.
del_11q23.1 cnv correlated to 'Time to Death', 'YEARS_TO_BIRTH', 'PATHOLOGIC_STAGE', 'PATHOLOGY_T_STAGE', 'PATHOLOGY_N_STAGE', 'PATHOLOGY_M_STAGE', 'KARNOFSKY_PERFORMANCE_SCORE', and 'HISTOLOGICAL_TYPE'.
del_13q13.2 cnv correlated to 'Time to Death', 'YEARS_TO_BIRTH', 'PATHOLOGIC_STAGE', 'PATHOLOGY_T_STAGE', 'PATHOLOGY_N_STAGE', 'GENDER', 'HISTOLOGICAL_TYPE', and 'RACE'.
del_14q31.1 cnv correlated to 'Time to Death', 'PATHOLOGIC_STAGE', 'PATHOLOGY_T_STAGE', 'PATHOLOGY_N_STAGE', 'PATHOLOGY_M_STAGE', 'RADIATION_THERAPY', 'KARNOFSKY_PERFORMANCE_SCORE', 'HISTOLOGICAL_TYPE', 'YEAR_OF_TOBACCO_SMOKING_ONSET', and 'RACE'.
del_16q23.3 cnv correlated to 'Time to Death', 'PATHOLOGIC_STAGE', 'PATHOLOGY_T_STAGE', and 'PATHOLOGY_N_STAGE'.
del_19p13.3 cnv correlated to 'Time to Death', 'PATHOLOGIC_STAGE', 'PATHOLOGY_T_STAGE', 'PATHOLOGY_N_STAGE', 'PATHOLOGY_M_STAGE', 'KARNOFSKY_PERFORMANCE_SCORE', and 'HISTOLOGICAL_TYPE'.
del_xp22.2 cnv correlated to 'YEARS_TO_BIRTH', 'PATHOLOGIC_STAGE', 'PATHOLOGY_T_STAGE', 'PATHOLOGY_N_STAGE', and 'HISTOLOGICAL_TYPE'.

Results

Overview of the results

Table 1. Get Full Table Overview of the association between significant copy number variation of 32 focal events and 14 clinical features. Shown in the table are P values (Q values). Thresholded by Q value < 0.25, 211 significant findings detected.


		Clinical Features	Time to Death	YEARS TO BIRTH	PATHOLOGIC STAGE	PATHOLOGY T STAGE	PATHOLOGY N STAGE	PATHOLOGY M STAGE	GENDER	RADIATION THERAPY	KARNOFSKY PERFORMANCE SCORE	HISTOLOGICAL TYPE	NUMBER PACK YEARS SMOKED	YEAR OF TOBACCO SMOKING ONSET	RACE	ETHNICITY
	nCNV (%)	nWild-Type	logrank test	Wilcoxon-test	Fisher's exact test	Fisher's exact test	Fisher's exact test	Fisher's exact test	Fisher's exact test	Fisher's exact test	Wilcoxon-test	Fisher's exact test	Wilcoxon-test	Wilcoxon-test	Fisher's exact test	Fisher's exact test
del 3p26 3	489 (55%)	393	0.000258 (0.0013)	0.65 (0.794)	1e-05 (7.23e-05)	1e-05 (7.23e-05)	0.0274 (0.0762)	0.105 (0.229)	0.0441 (0.113)	0.275 (0.46)	0.102 (0.226)	1e-05 (7.23e-05)	0.419 (0.602)	0.0787 (0.185)	1e-05 (7.23e-05)	0.204 (0.374)
del 14q31 1	279 (32%)	603	5.96e-10 (5.34e-08)	0.134 (0.275)	1e-05 (7.23e-05)	1e-05 (7.23e-05)	0.00404 (0.0143)	4.66e-05 (0.000275)	0.591 (0.743)	0.115 (0.244)	0.000159 (0.000839)	1e-05 (7.23e-05)	0.359 (0.555)	0.00978 (0.032)	0.0174 (0.0509)	1 (1.00)
del 3p21 2	503 (57%)	379	5.54e-07 (4.13e-05)	0.547 (0.724)	1e-05 (7.23e-05)	1e-05 (7.23e-05)	0.221 (0.394)	0.00347 (0.0126)	0.112 (0.238)	0.295 (0.484)	0.0359 (0.0941)	1e-05 (7.23e-05)	0.274 (0.46)	0.042 (0.108)	1e-05 (7.23e-05)	0.75 (0.867)
del 9p23	198 (22%)	684	4.95e-13 (1.11e-10)	0.0296 (0.0813)	1e-05 (7.23e-05)	1e-05 (7.23e-05)	0.00204 (0.00802)	0.000211 (0.00109)	0.391 (0.573)	0.389 (0.572)	0.000567 (0.00259)	1e-05 (7.23e-05)	0.649 (0.794)	0.893 (0.985)	0.0201 (0.0575)	0.847 (0.958)
del 9p21 3	209 (24%)	673	5.55e-16 (2.49e-13)	0.0319 (0.0861)	1e-05 (7.23e-05)	1e-05 (7.23e-05)	2e-05 (0.000134)	9.3e-06 (7.23e-05)	0.24 (0.419)	0.404 (0.584)	0.00135 (0.00549)	1e-05 (7.23e-05)	0.88 (0.979)	0.923 (1.00)	0.00591 (0.0198)	0.853 (0.96)
amp 1q32 1	82 (9%)	800	6.46e-05 (0.000362)	0.0354 (0.0938)	3e-05 (0.000184)	0.0001 (0.00054)	0.0187 (0.0545)	0.137 (0.278)	0.538 (0.72)	1 (1.00)	0.049 (0.123)	0.00249 (0.00945)	0.282 (0.466)	0.103 (0.226)	0.121 (0.254)	0.254 (0.436)
amp 8q24 22	125 (14%)	757	0.00102 (0.00432)	0.0356 (0.0939)	1e-05 (7.23e-05)	1e-05 (7.23e-05)	0.015 (0.0453)	0.0101 (0.0322)	0.539 (0.72)	1 (1.00)	0.214 (0.387)	0.00113 (0.00473)	0.152 (0.297)	0.374 (0.56)	0.025 (0.07)	1 (1.00)
amp 17q24 3	243 (28%)	639	0.831 (0.945)	0.0305 (0.0828)	0.00058 (0.00262)	0.00207 (0.00806)	0.00049 (0.00229)	0.214 (0.387)	0.00102 (0.00432)	1 (1.00)	0.588 (0.742)	1e-05 (7.23e-05)	0.562 (0.733)	0.108 (0.234)	0.0145 (0.0443)	0.119 (0.251)
del 11q23 1	71 (8%)	811	0.000445 (0.0021)	0.00352 (0.0127)	2e-05 (0.000134)	1e-05 (7.23e-05)	3e-05 (0.000184)	0.111 (0.238)	0.599 (0.75)	0.247 (0.429)	0.0934 (0.211)	0.00456 (0.0158)	0.635 (0.786)	0.646 (0.794)	0.289 (0.476)	0.241 (0.42)
del 13q13 2	149 (17%)	733	0.0145 (0.0443)	5.17e-05 (0.000297)	1e-05 (7.23e-05)	1e-05 (7.23e-05)	0.00122 (0.00501)	0.172 (0.329)	0.00404 (0.0143)	1 (1.00)	0.596 (0.748)	1e-05 (7.23e-05)	0.839 (0.951)	0.542 (0.722)	0.0963 (0.217)	0.378 (0.564)
amp 7q31 2	377 (43%)	505	0.985 (1.00)	0.275 (0.46)	0.0146 (0.0443)	0.829 (0.945)	0.0286 (0.0791)	0.002 (0.00792)	9.7e-06 (7.23e-05)	0.101 (0.225)	0.864 (0.968)	1e-05 (7.23e-05)	0.379 (0.564)	0.00994 (0.0322)	0.21 (0.383)	0.199 (0.368)
del 1p36 31	209 (24%)	673	0.11 (0.236)	0.0822 (0.192)	1e-05 (7.23e-05)	1e-05 (7.23e-05)	0.00964 (0.0318)	0.422 (0.603)	0.355 (0.55)	0.565 (0.733)	0.093 (0.211)	1e-05 (7.23e-05)	0.402 (0.583)	0.278 (0.462)	0.666 (0.806)	0.336 (0.536)
del 2q37 3	111 (13%)	771	0.0298 (0.0814)	0.00311 (0.0114)	1e-05 (7.23e-05)	1e-05 (7.23e-05)	0.374 (0.56)	0.0849 (0.196)	0.518 (0.707)	1 (1.00)	0.0163 (0.048)	1e-05 (7.23e-05)	0.49 (0.68)	0.915 (1.00)	0.511 (0.699)	1 (1.00)
del 4q34 3	113 (13%)	769	4.07e-10 (4.56e-08)	0.717 (0.852)	1e-05 (7.23e-05)	1e-05 (7.23e-05)	0.00167 (0.00674)	0.0139 (0.0435)	0.749 (0.867)	1 (1.00)	0.249 (0.43)	0.0333 (0.0887)	0.348 (0.543)	0.703 (0.841)	0.0585 (0.143)	0.478 (0.665)
del 19p13 3	43 (5%)	839	5.05e-12 (7.55e-10)	0.418 (0.602)	2e-05 (0.000134)	1e-05 (7.23e-05)	6e-05 (0.00034)	0.0688 (0.165)	0.619 (0.772)	1 (1.00)	0.00517 (0.0177)	0.0108 (0.034)	0.15 (0.295)		0.326 (0.523)	0.72 (0.854)
amp 5q35 1	376 (43%)	506	0.128 (0.265)	0.185 (0.349)	3e-05 (0.000184)	0.0031 (0.0114)	0.052 (0.129)	0.0158 (0.0473)	0.385 (0.57)	0.199 (0.368)	0.149 (0.295)	1e-05 (7.23e-05)	0.77 (0.884)	0.277 (0.462)	3e-05 (0.000184)	1 (1.00)
amp xq11 2	136 (15%)	746	0.0518 (0.129)	0.373 (0.56)	0.0201 (0.0575)	0.0161 (0.0476)	0.813 (0.929)	0.568 (0.733)	0.000107 (0.00057)	1 (1.00)	0.393 (0.573)	1e-05 (7.23e-05)	0.743 (0.867)	0.0331 (0.0887)	0.183 (0.346)	0.522 (0.711)
del 1p31 1	166 (19%)	716	0.585 (0.742)	0.0402 (0.105)	8e-05 (0.000442)	2e-05 (0.000134)	0.0616 (0.15)	0.885 (0.981)	0.855 (0.96)	1 (1.00)	0.982 (1.00)	1e-05 (7.23e-05)	0.701 (0.841)	0.537 (0.72)	0.476 (0.665)	0.0884 (0.203)
del 2q22 1	75 (9%)	807	0.0459 (0.117)	0.000439 (0.00209)	1e-05 (7.23e-05)	1e-05 (7.23e-05)	0.259 (0.442)	0.527 (0.714)	0.124 (0.259)	1 (1.00)	0.0768 (0.182)	1e-05 (7.23e-05)	0.339 (0.536)	0.747 (0.867)	0.502 (0.694)	0.753 (0.867)
del 3p14 1	408 (46%)	474	0.0006 (0.00266)	0.953 (1.00)	0.00032 (0.00158)	2e-05 (0.000134)	0.173 (0.329)	0.564 (0.733)	0.252 (0.434)	0.221 (0.394)	0.344 (0.538)	1e-05 (7.23e-05)	0.355 (0.55)	0.0554 (0.136)	0.00024 (0.00122)	0.632 (0.785)
del 3p12 2	336 (38%)	546	0.000163 (0.000851)	0.751 (0.867)	0.0108 (0.034)	0.00275 (0.0103)	0.297 (0.485)	0.648 (0.794)	0.141 (0.283)	0.145 (0.288)	0.874 (0.974)	1e-05 (7.23e-05)	0.296 (0.484)	0.0829 (0.192)	0.00576 (0.0195)	0.743 (0.867)
del 5p15 33	31 (4%)	851	0.931 (1.00)	0.00425 (0.0149)	0.00028 (0.00139)	0.00056 (0.00259)	0.00582 (0.0196)	0.74 (0.867)	0.174 (0.329)	1 (1.00)	0.0994 (0.223)	1e-05 (7.23e-05)	0.537 (0.72)	0.438 (0.624)	0.586 (0.742)	0.141 (0.283)
del 6q26	233 (26%)	649	0.447 (0.632)	0.257 (0.44)	1e-05 (7.23e-05)	1e-05 (7.23e-05)	0.0145 (0.0443)	1 (1.00)	0.57 (0.733)	0.575 (0.733)	0.161 (0.311)	1e-05 (7.23e-05)	0.103 (0.226)	0.371 (0.56)	0.00084 (0.00365)	0.137 (0.278)
del 6q26	234 (27%)	648	0.442 (0.629)	0.264 (0.448)	3e-05 (0.000184)	3e-05 (0.000184)	0.0146 (0.0443)	1 (1.00)	0.686 (0.826)	0.573 (0.733)	0.161 (0.311)	1e-05 (7.23e-05)	0.103 (0.226)	0.371 (0.56)	0.00217 (0.00838)	0.14 (0.282)
del 8p23 2	184 (21%)	698	0.00033 (0.00161)	0.65 (0.794)	0.00177 (0.00708)	0.00095 (0.00409)	0.561 (0.733)	0.0189 (0.0546)	0.725 (0.855)	1 (1.00)	0.389 (0.572)	1e-05 (7.23e-05)	0.952 (1.00)	0.725 (0.855)	0.00365 (0.0131)	0.154 (0.3)
del 10q23 31	164 (19%)	718	0.628 (0.782)	0.0732 (0.174)	1e-05 (7.23e-05)	1e-05 (7.23e-05)	0.325 (0.523)	0.888 (0.982)	0.714 (0.85)	1 (1.00)	0.664 (0.806)	1e-05 (7.23e-05)	0.068 (0.164)	0.271 (0.458)	0.0772 (0.182)	0.381 (0.566)
del 1q44	116 (13%)	766	0.092 (0.21)	0.01 (0.0322)	0.0004 (0.00193)	0.00116 (0.00481)	0.341 (0.536)	0.305 (0.496)	0.17 (0.326)	1 (1.00)	0.466 (0.654)	1e-05 (7.23e-05)	0.807 (0.925)	0.567 (0.733)	0.226 (0.401)	0.22 (0.394)
del xp22 2	125 (14%)	757	0.576 (0.733)	0.00226 (0.00867)	9e-05 (0.000492)	4e-05 (0.000242)	0.0419 (0.108)	1 (1.00)	0.473 (0.663)	1 (1.00)	0.93 (1.00)	1e-05 (7.23e-05)	0.996 (1.00)	0.447 (0.632)	0.528 (0.714)	0.462 (0.65)
amp 3q26 32	193 (22%)	689	0.238 (0.419)	0.12 (0.252)	0.144 (0.287)	0.191 (0.357)	0.0482 (0.121)	0.00716 (0.0238)	0.194 (0.363)	1 (1.00)	0.51 (0.699)	1e-05 (7.23e-05)	0.571 (0.733)	0.341 (0.536)	0.0476 (0.121)	0.704 (0.841)
del 16q23 3	37 (4%)	845	4.66e-05 (0.000275)	0.543 (0.722)	0.00505 (0.0174)	5e-05 (0.000291)	0.00059 (0.00264)	0.363 (0.556)	1 (1.00)	1 (1.00)	0.332 (0.531)	0.13 (0.269)	0.556 (0.732)	0.867 (0.969)	0.51 (0.699)	1 (1.00)
amp 10p14	34 (4%)	848	0.371 (0.56)	0.338 (0.536)	0.0681 (0.164)	0.00067 (0.00294)	0.0235 (0.0667)	0.575 (0.733)	0.853 (0.96)	1 (1.00)	0.136 (0.278)	0.548 (0.724)	0.753 (0.867)		0.199 (0.368)	1 (1.00)
amp 2q32 1	136 (15%)	746	0.916 (1.00)	0.21 (0.383)	0.365 (0.558)	0.309 (0.5)	0.0238 (0.067)	1 (1.00)	0.236 (0.417)	0.362 (0.556)	0.233 (0.412)	0.00273 (0.0103)	0.974 (1.00)	0.394 (0.573)	0.681 (0.822)	0.654 (0.796)

'amp_1q32.1' versus 'Time to Death'

P value = 6.46e-05 (logrank test), Q value = 0.00036

Table S1. Gene #1: 'amp_1q32.1' versus Clinical Feature #1: 'Time to Death'

	nPatients	nDeath	Duration Range (Median), Month
ALL	876	228	0.1 - 194.8 (35.9)
AMP PEAK 1(1Q32.1) MUTATED	82	36	0.4 - 129.4 (27.6)
AMP PEAK 1(1Q32.1) WILD-TYPE	794	192	0.1 - 194.8 (36.5)

Figure S1. Get High-res Image Gene #1: 'amp_1q32.1' versus Clinical Feature #1: 'Time to Death'

'amp_1q32.1' versus 'YEARS_TO_BIRTH'

P value = 0.0354 (Wilcoxon-test), Q value = 0.094

Table S2. Gene #1: 'amp_1q32.1' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

	nPatients	Mean (Std.Dev)
ALL	876	60.1 (12.5)
AMP PEAK 1(1Q32.1) MUTATED	80	62.4 (12.2)
AMP PEAK 1(1Q32.1) WILD-TYPE	796	59.9 (12.5)

Figure S2. Get High-res Image Gene #1: 'amp_1q32.1' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'amp_1q32.1' versus 'PATHOLOGIC_STAGE'

P value = 3e-05 (Fisher's exact test), Q value = 0.00018

Table S3. Gene #1: 'amp_1q32.1' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

nPatients	STAGE I	STAGE II	STAGE III	STAGE IV
ALL	454	103	190	104
AMP PEAK 1(1Q32.1) MUTATED	24	10	31	16
AMP PEAK 1(1Q32.1) WILD-TYPE	430	93	159	88

Figure S3. Get High-res Image Gene #1: 'amp_1q32.1' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

'amp_1q32.1' versus 'PATHOLOGY_T_STAGE'

P value = 1e-04 (Fisher's exact test), Q value = 0.00054

Table S4. Gene #1: 'amp_1q32.1' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

nPatients	T1	T2	T3	T4
ALL	480	127	258	15
AMP PEAK 1(1Q32.1) MUTATED	27	12	42	1
AMP PEAK 1(1Q32.1) WILD-TYPE	453	115	216	14

Figure S4. Get High-res Image Gene #1: 'amp_1q32.1' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

'amp_1q32.1' versus 'PATHOLOGY_N_STAGE'

P value = 0.0187 (Fisher's exact test), Q value = 0.055

Table S5. Gene #1: 'amp_1q32.1' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

nPatients	N0	N1	N2
ALL	323	44	6
AMP PEAK 1(1Q32.1) MUTATED	35	10	2
AMP PEAK 1(1Q32.1) WILD-TYPE	288	34	4

Figure S5. Get High-res Image Gene #1: 'amp_1q32.1' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

'amp_1q32.1' versus 'KARNOFSKY_PERFORMANCE_SCORE'

P value = 0.049 (Wilcoxon-test), Q value = 0.12

Table S6. Gene #1: 'amp_1q32.1' versus Clinical Feature #9: 'KARNOFSKY_PERFORMANCE_SCORE'

	nPatients	Mean (Std.Dev)
ALL	143	87.7 (22.8)
AMP PEAK 1(1Q32.1) MUTATED	11	60.0 (47.7)
AMP PEAK 1(1Q32.1) WILD-TYPE	132	90.0 (17.8)

Figure S6. Get High-res Image Gene #1: 'amp_1q32.1' versus Clinical Feature #9: 'KARNOFSKY_PERFORMANCE_SCORE'

'amp_1q32.1' versus 'HISTOLOGICAL_TYPE'

P value = 0.00249 (Fisher's exact test), Q value = 0.0095

Table S7. Gene #1: 'amp_1q32.1' versus Clinical Feature #10: 'HISTOLOGICAL_TYPE'

nPatients	KIDNEY CHROMOPHOBE	KIDNEY CLEAR CELL RENAL CARCINOMA	KIDNEY PAPILLARY RENAL CELL CARCINOMA
ALL	66	528	288
AMP PEAK 1(1Q32.1) MUTATED	1	62	19
AMP PEAK 1(1Q32.1) WILD-TYPE	65	466	269

Figure S7. Get High-res Image Gene #1: 'amp_1q32.1' versus Clinical Feature #10: 'HISTOLOGICAL_TYPE'

'amp_1q32.1' versus 'YEAR_OF_TOBACCO_SMOKING_ONSET'

P value = 0.103 (Wilcoxon-test), Q value = 0.23

Table S8. Gene #1: 'amp_1q32.1' versus Clinical Feature #12: 'YEAR_OF_TOBACCO_SMOKING_ONSET'

	nPatients	Mean (Std.Dev)
ALL	74	1973.7 (16.0)
AMP PEAK 1(1Q32.1) MUTATED	3	1989.0 (19.2)
AMP PEAK 1(1Q32.1) WILD-TYPE	71	1973.1 (15.7)

Figure S8. Get High-res Image Gene #1: 'amp_1q32.1' versus Clinical Feature #12: 'YEAR_OF_TOBACCO_SMOKING_ONSET'

'amp_2q32.1' versus 'PATHOLOGY_N_STAGE'

P value = 0.0238 (Fisher's exact test), Q value = 0.067

Table S9. Gene #2: 'amp_2q32.1' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

nPatients	N0	N1	N2
ALL	323	44	6
AMP PEAK 2(2Q32.1) MUTATED	48	11	3
AMP PEAK 2(2Q32.1) WILD-TYPE	275	33	3

Figure S9. Get High-res Image Gene #2: 'amp_2q32.1' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

'amp_2q32.1' versus 'HISTOLOGICAL_TYPE'

P value = 0.00273 (Fisher's exact test), Q value = 0.01

Table S10. Gene #2: 'amp_2q32.1' versus Clinical Feature #10: 'HISTOLOGICAL_TYPE'

nPatients	KIDNEY CHROMOPHOBE	KIDNEY CLEAR CELL RENAL CARCINOMA	KIDNEY PAPILLARY RENAL CELL CARCINOMA
ALL	66	528	288
AMP PEAK 2(2Q32.1) MUTATED	2	81	53
AMP PEAK 2(2Q32.1) WILD-TYPE	64	447	235

Figure S10. Get High-res Image Gene #2: 'amp_2q32.1' versus Clinical Feature #10: 'HISTOLOGICAL_TYPE'

'amp_3q26.32' versus 'PATHOLOGY_N_STAGE'

P value = 0.0482 (Fisher's exact test), Q value = 0.12

Table S11. Gene #3: 'amp_3q26.32' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

nPatients	N0	N1	N2
ALL	323	44	6
AMP PEAK 3(3Q26.32) MUTATED	59	15	1
AMP PEAK 3(3Q26.32) WILD-TYPE	264	29	5

Figure S11. Get High-res Image Gene #3: 'amp_3q26.32' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

'amp_3q26.32' versus 'PATHOLOGY_M_STAGE'

P value = 0.00716 (Fisher's exact test), Q value = 0.024

Table S12. Gene #3: 'amp_3q26.32' versus Clinical Feature #6: 'PATHOLOGY_M_STAGE'

nPatients	0	1
ALL	546	89
AMP PEAK 3(3Q26.32) MUTATED	90	26
AMP PEAK 3(3Q26.32) WILD-TYPE	456	63

Figure S12. Get High-res Image Gene #3: 'amp_3q26.32' versus Clinical Feature #6: 'PATHOLOGY_M_STAGE'

'amp_3q26.32' versus 'HISTOLOGICAL_TYPE'

P value = 1e-05 (Fisher's exact test), Q value = 7.2e-05

Table S13. Gene #3: 'amp_3q26.32' versus Clinical Feature #10: 'HISTOLOGICAL_TYPE'

nPatients	KIDNEY CHROMOPHOBE	KIDNEY CLEAR CELL RENAL CARCINOMA	KIDNEY PAPILLARY RENAL CELL CARCINOMA
ALL	66	528	288
AMP PEAK 3(3Q26.32) MUTATED	6	87	100
AMP PEAK 3(3Q26.32) WILD-TYPE	60	441	188

Figure S13. Get High-res Image Gene #3: 'amp_3q26.32' versus Clinical Feature #10: 'HISTOLOGICAL_TYPE'

'amp_3q26.32' versus 'RACE'

P value = 0.0476 (Fisher's exact test), Q value = 0.12

Table S14. Gene #3: 'amp_3q26.32' versus Clinical Feature #13: 'RACE'

nPatients	AMERICAN INDIAN OR ALASKA NATIVE	ASIAN	BLACK OR AFRICAN AMERICAN	WHITE
ALL	2	16	121	719
AMP PEAK 3(3Q26.32) MUTATED	2	1	26	155
AMP PEAK 3(3Q26.32) WILD-TYPE	0	15	95	564

Figure S14. Get High-res Image Gene #3: 'amp_3q26.32' versus Clinical Feature #13: 'RACE'

'amp_5q35.1' versus 'PATHOLOGIC_STAGE'

P value = 3e-05 (Fisher's exact test), Q value = 0.00018

Table S15. Gene #4: 'amp_5q35.1' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

nPatients	STAGE I	STAGE II	STAGE III	STAGE IV
ALL	454	103	190	104
AMP PEAK 4(5Q35.1) MUTATED	173	42	91	66
AMP PEAK 4(5Q35.1) WILD-TYPE	281	61	99	38

Figure S15. Get High-res Image Gene #4: 'amp_5q35.1' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

'amp_5q35.1' versus 'PATHOLOGY_T_STAGE'

P value = 0.0031 (Fisher's exact test), Q value = 0.011

Table S16. Gene #4: 'amp_5q35.1' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

nPatients	T1	T2	T3	T4
ALL	480	127	258	15
AMP PEAK 4(5Q35.1) MUTATED	180	56	133	7
AMP PEAK 4(5Q35.1) WILD-TYPE	300	71	125	8

Figure S16. Get High-res Image Gene #4: 'amp_5q35.1' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

'amp_5q35.1' versus 'PATHOLOGY_N_STAGE'

P value = 0.052 (Fisher's exact test), Q value = 0.13

Table S17. Gene #4: 'amp_5q35.1' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

nPatients	N0	N1	N2
ALL	323	44	6
AMP PEAK 4(5Q35.1) MUTATED	163	14	2
AMP PEAK 4(5Q35.1) WILD-TYPE	160	30	4

Figure S17. Get High-res Image Gene #4: 'amp_5q35.1' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

'amp_5q35.1' versus 'PATHOLOGY_M_STAGE'

P value = 0.0158 (Fisher's exact test), Q value = 0.047

Table S18. Gene #4: 'amp_5q35.1' versus Clinical Feature #6: 'PATHOLOGY_M_STAGE'

nPatients	0	1
ALL	546	89
AMP PEAK 4(5Q35.1) MUTATED	278	58
AMP PEAK 4(5Q35.1) WILD-TYPE	268	31

Figure S18. Get High-res Image Gene #4: 'amp_5q35.1' versus Clinical Feature #6: 'PATHOLOGY_M_STAGE'

'amp_5q35.1' versus 'HISTOLOGICAL_TYPE'

P value = 1e-05 (Fisher's exact test), Q value = 7.2e-05

Table S19. Gene #4: 'amp_5q35.1' versus Clinical Feature #10: 'HISTOLOGICAL_TYPE'

nPatients	KIDNEY CHROMOPHOBE	KIDNEY CLEAR CELL RENAL CARCINOMA	KIDNEY PAPILLARY RENAL CELL CARCINOMA
ALL	66	528	288
AMP PEAK 4(5Q35.1) MUTATED	8	332	36
AMP PEAK 4(5Q35.1) WILD-TYPE	58	196	252

Figure S19. Get High-res Image Gene #4: 'amp_5q35.1' versus Clinical Feature #10: 'HISTOLOGICAL_TYPE'

'amp_5q35.1' versus 'RACE'

P value = 3e-05 (Fisher's exact test), Q value = 0.00018

Table S20. Gene #4: 'amp_5q35.1' versus Clinical Feature #13: 'RACE'

nPatients	AMERICAN INDIAN OR ALASKA NATIVE	ASIAN	BLACK OR AFRICAN AMERICAN	WHITE
ALL	2	16	121	719
AMP PEAK 4(5Q35.1) MUTATED	0	5	31	333
AMP PEAK 4(5Q35.1) WILD-TYPE	2	11	90	386

Figure S20. Get High-res Image Gene #4: 'amp_5q35.1' versus Clinical Feature #13: 'RACE'

'amp_7q31.2' versus 'PATHOLOGIC_STAGE'

P value = 0.0146 (Fisher's exact test), Q value = 0.044

Table S21. Gene #5: 'amp_7q31.2' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

nPatients	STAGE I	STAGE II	STAGE III	STAGE IV
ALL	454	103	190	104
AMP PEAK 5(7Q31.2) MUTATED	193	38	69	57
AMP PEAK 5(7Q31.2) WILD-TYPE	261	65	121	47

Figure S21. Get High-res Image Gene #5: 'amp_7q31.2' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

'amp_7q31.2' versus 'PATHOLOGY_N_STAGE'

P value = 0.0286 (Fisher's exact test), Q value = 0.079

Table S22. Gene #5: 'amp_7q31.2' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

nPatients	N0	N1	N2
ALL	323	44	6
AMP PEAK 5(7Q31.2) MUTATED	121	21	5
AMP PEAK 5(7Q31.2) WILD-TYPE	202	23	1

Figure S22. Get High-res Image Gene #5: 'amp_7q31.2' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

'amp_7q31.2' versus 'PATHOLOGY_M_STAGE'

P value = 0.002 (Fisher's exact test), Q value = 0.0079

Table S23. Gene #5: 'amp_7q31.2' versus Clinical Feature #6: 'PATHOLOGY_M_STAGE'

nPatients	0	1
ALL	546	89
AMP PEAK 5(7Q31.2) MUTATED	191	47
AMP PEAK 5(7Q31.2) WILD-TYPE	355	42

Figure S23. Get High-res Image Gene #5: 'amp_7q31.2' versus Clinical Feature #6: 'PATHOLOGY_M_STAGE'

'amp_7q31.2' versus 'GENDER'

P value = 9.7e-06 (Fisher's exact test), Q value = 7.2e-05

Table S24. Gene #5: 'amp_7q31.2' versus Clinical Feature #7: 'GENDER'

nPatients	FEMALE	MALE
ALL	292	590
AMP PEAK 5(7Q31.2) MUTATED	94	283
AMP PEAK 5(7Q31.2) WILD-TYPE	198	307

Figure S24. Get High-res Image Gene #5: 'amp_7q31.2' versus Clinical Feature #7: 'GENDER'

'amp_7q31.2' versus 'RADIATION_THERAPY'

P value = 0.101 (Fisher's exact test), Q value = 0.23

Table S25. Gene #5: 'amp_7q31.2' versus Clinical Feature #8: 'RADIATION_THERAPY'

nPatients	NO	YES
ALL	408	3
AMP PEAK 5(7Q31.2) MUTATED	189	3
AMP PEAK 5(7Q31.2) WILD-TYPE	219	0

Figure S25. Get High-res Image Gene #5: 'amp_7q31.2' versus Clinical Feature #8: 'RADIATION_THERAPY'

'amp_7q31.2' versus 'HISTOLOGICAL_TYPE'

P value = 1e-05 (Fisher's exact test), Q value = 7.2e-05

Table S26. Gene #5: 'amp_7q31.2' versus Clinical Feature #10: 'HISTOLOGICAL_TYPE'

nPatients	KIDNEY CHROMOPHOBE	KIDNEY CLEAR CELL RENAL CARCINOMA	KIDNEY PAPILLARY RENAL CELL CARCINOMA
ALL	66	528	288
AMP PEAK 5(7Q31.2) MUTATED	25	175	177
AMP PEAK 5(7Q31.2) WILD-TYPE	41	353	111

Figure S26. Get High-res Image Gene #5: 'amp_7q31.2' versus Clinical Feature #10: 'HISTOLOGICAL_TYPE'

'amp_7q31.2' versus 'YEAR_OF_TOBACCO_SMOKING_ONSET'

P value = 0.00994 (Wilcoxon-test), Q value = 0.032

Table S27. Gene #5: 'amp_7q31.2' versus Clinical Feature #12: 'YEAR_OF_TOBACCO_SMOKING_ONSET'

	nPatients	Mean (Std.Dev)
ALL	74	1973.7 (16.0)
AMP PEAK 5(7Q31.2) MUTATED	40	1969.4 (15.3)
AMP PEAK 5(7Q31.2) WILD-TYPE	34	1978.8 (15.5)

Figure S27. Get High-res Image Gene #5: 'amp_7q31.2' versus Clinical Feature #12: 'YEAR_OF_TOBACCO_SMOKING_ONSET'

'amp_8q24.22' versus 'Time to Death'

P value = 0.00102 (logrank test), Q value = 0.0043

Table S28. Gene #6: 'amp_8q24.22' versus Clinical Feature #1: 'Time to Death'

	nPatients	nDeath	Duration Range (Median), Month
ALL	876	228	0.1 - 194.8 (35.9)
AMP PEAK 6(8Q24.22) MUTATED	124	45	0.2 - 153.7 (27.6)
AMP PEAK 6(8Q24.22) WILD-TYPE	752	183	0.1 - 194.8 (36.8)

Figure S28. Get High-res Image Gene #6: 'amp_8q24.22' versus Clinical Feature #1: 'Time to Death'

'amp_8q24.22' versus 'YEARS_TO_BIRTH'

P value = 0.0356 (Wilcoxon-test), Q value = 0.094

Table S29. Gene #6: 'amp_8q24.22' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

	nPatients	Mean (Std.Dev)
ALL	876	60.1 (12.5)
AMP PEAK 6(8Q24.22) MUTATED	125	62.2 (12.6)
AMP PEAK 6(8Q24.22) WILD-TYPE	751	59.8 (12.5)

Figure S29. Get High-res Image Gene #6: 'amp_8q24.22' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'amp_8q24.22' versus 'PATHOLOGIC_STAGE'

P value = 1e-05 (Fisher's exact test), Q value = 7.2e-05

Table S30. Gene #6: 'amp_8q24.22' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

nPatients	STAGE I	STAGE II	STAGE III	STAGE IV
ALL	454	103	190	104
AMP PEAK 6(8Q24.22) MUTATED	35	23	38	27
AMP PEAK 6(8Q24.22) WILD-TYPE	419	80	152	77

Figure S30. Get High-res Image Gene #6: 'amp_8q24.22' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

'amp_8q24.22' versus 'PATHOLOGY_T_STAGE'

P value = 1e-05 (Fisher's exact test), Q value = 7.2e-05

Table S31. Gene #6: 'amp_8q24.22' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

nPatients	T1	T2	T3	T4
ALL	480	127	258	15
AMP PEAK 6(8Q24.22) MUTATED	36	24	61	4
AMP PEAK 6(8Q24.22) WILD-TYPE	444	103	197	11

Figure S31. Get High-res Image Gene #6: 'amp_8q24.22' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

'amp_8q24.22' versus 'PATHOLOGY_N_STAGE'

P value = 0.015 (Fisher's exact test), Q value = 0.045

Table S32. Gene #6: 'amp_8q24.22' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

nPatients	N0	N1	N2
ALL	323	44	6
AMP PEAK 6(8Q24.22) MUTATED	53	13	3
AMP PEAK 6(8Q24.22) WILD-TYPE	270	31	3

Figure S32. Get High-res Image Gene #6: 'amp_8q24.22' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

'amp_8q24.22' versus 'PATHOLOGY_M_STAGE'

P value = 0.0101 (Fisher's exact test), Q value = 0.032

Table S33. Gene #6: 'amp_8q24.22' versus Clinical Feature #6: 'PATHOLOGY_M_STAGE'

nPatients	0	1
ALL	546	89
AMP PEAK 6(8Q24.22) MUTATED	74	22
AMP PEAK 6(8Q24.22) WILD-TYPE	472	67

Figure S33. Get High-res Image Gene #6: 'amp_8q24.22' versus Clinical Feature #6: 'PATHOLOGY_M_STAGE'

'amp_8q24.22' versus 'HISTOLOGICAL_TYPE'

P value = 0.00113 (Fisher's exact test), Q value = 0.0047

Table S34. Gene #6: 'amp_8q24.22' versus Clinical Feature #10: 'HISTOLOGICAL_TYPE'

nPatients	KIDNEY CHROMOPHOBE	KIDNEY CLEAR CELL RENAL CARCINOMA	KIDNEY PAPILLARY RENAL CELL CARCINOMA
ALL	66	528	288
AMP PEAK 6(8Q24.22) MUTATED	18	79	28
AMP PEAK 6(8Q24.22) WILD-TYPE	48	449	260

Figure S34. Get High-res Image Gene #6: 'amp_8q24.22' versus Clinical Feature #10: 'HISTOLOGICAL_TYPE'

'amp_8q24.22' versus 'RACE'

P value = 0.025 (Fisher's exact test), Q value = 0.07

Table S35. Gene #6: 'amp_8q24.22' versus Clinical Feature #13: 'RACE'

nPatients	AMERICAN INDIAN OR ALASKA NATIVE	ASIAN	BLACK OR AFRICAN AMERICAN	WHITE
ALL	2	16	121	719
AMP PEAK 6(8Q24.22) MUTATED	0	4	8	110
AMP PEAK 6(8Q24.22) WILD-TYPE	2	12	113	609

Figure S35. Get High-res Image Gene #6: 'amp_8q24.22' versus Clinical Feature #13: 'RACE'

'amp_10p14' versus 'PATHOLOGIC_STAGE'

P value = 0.0681 (Fisher's exact test), Q value = 0.16

Table S36. Gene #7: 'amp_10p14' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

nPatients	STAGE I	STAGE II	STAGE III	STAGE IV
ALL	454	103	190	104
AMP PEAK 7(10P14) MUTATED	12	7	6	7
AMP PEAK 7(10P14) WILD-TYPE	442	96	184	97

Figure S36. Get High-res Image Gene #7: 'amp_10p14' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

'amp_10p14' versus 'PATHOLOGY_T_STAGE'

P value = 0.00067 (Fisher's exact test), Q value = 0.0029

Table S37. Gene #7: 'amp_10p14' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

nPatients	T1	T2	T3	T4
ALL	480	127	258	15
AMP PEAK 7(10P14) MUTATED	13	9	8	4
AMP PEAK 7(10P14) WILD-TYPE	467	118	250	11

Figure S37. Get High-res Image Gene #7: 'amp_10p14' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

'amp_10p14' versus 'PATHOLOGY_N_STAGE'

P value = 0.0235 (Fisher's exact test), Q value = 0.067

Table S38. Gene #7: 'amp_10p14' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

nPatients	N0	N1	N2
ALL	323	44	6
AMP PEAK 7(10P14) MUTATED	12	5	1
AMP PEAK 7(10P14) WILD-TYPE	311	39	5

Figure S38. Get High-res Image Gene #7: 'amp_10p14' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

'amp_17q24.3' versus 'YEARS_TO_BIRTH'

P value = 0.0305 (Wilcoxon-test), Q value = 0.083

Table S39. Gene #8: 'amp_17q24.3' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

	nPatients	Mean (Std.Dev)
ALL	876	60.1 (12.5)
AMP PEAK 8(17Q24.3) MUTATED	240	61.6 (12.2)
AMP PEAK 8(17Q24.3) WILD-TYPE	636	59.6 (12.6)

Figure S39. Get High-res Image Gene #8: 'amp_17q24.3' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'amp_17q24.3' versus 'PATHOLOGIC_STAGE'

P value = 0.00058 (Fisher's exact test), Q value = 0.0026

Table S40. Gene #8: 'amp_17q24.3' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

nPatients	STAGE I	STAGE II	STAGE III	STAGE IV
ALL	454	103	190	104
AMP PEAK 8(17Q24.3) MUTATED	145	22	41	16
AMP PEAK 8(17Q24.3) WILD-TYPE	309	81	149	88

Figure S40. Get High-res Image Gene #8: 'amp_17q24.3' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

'amp_17q24.3' versus 'PATHOLOGY_T_STAGE'

P value = 0.00207 (Fisher's exact test), Q value = 0.0081

Table S41. Gene #8: 'amp_17q24.3' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

nPatients	T1	T2	T3	T4
ALL	480	127	258	15
AMP PEAK 8(17Q24.3) MUTATED	156	31	51	4
AMP PEAK 8(17Q24.3) WILD-TYPE	324	96	207	11

Figure S41. Get High-res Image Gene #8: 'amp_17q24.3' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

'amp_17q24.3' versus 'PATHOLOGY_N_STAGE'

P value = 0.00049 (Fisher's exact test), Q value = 0.0023

Table S42. Gene #8: 'amp_17q24.3' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

nPatients	N0	N1	N2
ALL	323	44	6
AMP PEAK 8(17Q24.3) MUTATED	48	16	3
AMP PEAK 8(17Q24.3) WILD-TYPE	275	28	3

Figure S42. Get High-res Image Gene #8: 'amp_17q24.3' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

'amp_17q24.3' versus 'GENDER'

P value = 0.00102 (Fisher's exact test), Q value = 0.0043

Table S43. Gene #8: 'amp_17q24.3' versus Clinical Feature #7: 'GENDER'

nPatients	FEMALE	MALE
ALL	292	590
AMP PEAK 8(17Q24.3) MUTATED	60	183
AMP PEAK 8(17Q24.3) WILD-TYPE	232	407

Figure S43. Get High-res Image Gene #8: 'amp_17q24.3' versus Clinical Feature #7: 'GENDER'

'amp_17q24.3' versus 'HISTOLOGICAL_TYPE'

P value = 1e-05 (Fisher's exact test), Q value = 7.2e-05

Table S44. Gene #8: 'amp_17q24.3' versus Clinical Feature #10: 'HISTOLOGICAL_TYPE'

nPatients	KIDNEY CHROMOPHOBE	KIDNEY CLEAR CELL RENAL CARCINOMA	KIDNEY PAPILLARY RENAL CELL CARCINOMA
ALL	66	528	288
AMP PEAK 8(17Q24.3) MUTATED	1	42	200
AMP PEAK 8(17Q24.3) WILD-TYPE	65	486	88

Figure S44. Get High-res Image Gene #8: 'amp_17q24.3' versus Clinical Feature #10: 'HISTOLOGICAL_TYPE'

'amp_17q24.3' versus 'YEAR_OF_TOBACCO_SMOKING_ONSET'

P value = 0.108 (Wilcoxon-test), Q value = 0.23

Table S45. Gene #8: 'amp_17q24.3' versus Clinical Feature #12: 'YEAR_OF_TOBACCO_SMOKING_ONSET'

	nPatients	Mean (Std.Dev)
ALL	74	1973.7 (16.0)
AMP PEAK 8(17Q24.3) MUTATED	37	1971.2 (15.7)
AMP PEAK 8(17Q24.3) WILD-TYPE	37	1976.3 (16.1)

Figure S45. Get High-res Image Gene #8: 'amp_17q24.3' versus Clinical Feature #12: 'YEAR_OF_TOBACCO_SMOKING_ONSET'

'amp_17q24.3' versus 'RACE'

P value = 0.0145 (Fisher's exact test), Q value = 0.044

Table S46. Gene #8: 'amp_17q24.3' versus Clinical Feature #13: 'RACE'

nPatients	AMERICAN INDIAN OR ALASKA NATIVE	ASIAN	BLACK OR AFRICAN AMERICAN	WHITE
ALL	2	16	121	719
AMP PEAK 8(17Q24.3) MUTATED	2	7	40	184
AMP PEAK 8(17Q24.3) WILD-TYPE	0	9	81	535

Figure S46. Get High-res Image Gene #8: 'amp_17q24.3' versus Clinical Feature #13: 'RACE'

'amp_xq11.2' versus 'Time to Death'

P value = 0.0518 (logrank test), Q value = 0.13

Table S47. Gene #9: 'amp_xq11.2' versus Clinical Feature #1: 'Time to Death'

	nPatients	nDeath	Duration Range (Median), Month
ALL	876	228	0.1 - 194.8 (35.9)
AMP PEAK 9(XQ11.2) MUTATED	134	23	0.1 - 194.8 (29.8)
AMP PEAK 9(XQ11.2) WILD-TYPE	742	205	0.1 - 153.7 (36.5)

Figure S47. Get High-res Image Gene #9: 'amp_xq11.2' versus Clinical Feature #1: 'Time to Death'

'amp_xq11.2' versus 'PATHOLOGIC_STAGE'

P value = 0.0201 (Fisher's exact test), Q value = 0.057

Table S48. Gene #9: 'amp_xq11.2' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

nPatients	STAGE I	STAGE II	STAGE III	STAGE IV
ALL	454	103	190	104
AMP PEAK 9(XQ11.2) MUTATED	79	17	16	13
AMP PEAK 9(XQ11.2) WILD-TYPE	375	86	174	91

Figure S48. Get High-res Image Gene #9: 'amp_xq11.2' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

'amp_xq11.2' versus 'PATHOLOGY_T_STAGE'

P value = 0.0161 (Fisher's exact test), Q value = 0.048

Table S49. Gene #9: 'amp_xq11.2' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

nPatients	T1	T2	T3	T4
ALL	480	127	258	15
AMP PEAK 9(XQ11.2) MUTATED	86	23	25	2
AMP PEAK 9(XQ11.2) WILD-TYPE	394	104	233	13

Figure S49. Get High-res Image Gene #9: 'amp_xq11.2' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

'amp_xq11.2' versus 'GENDER'

P value = 0.000107 (Fisher's exact test), Q value = 0.00057

Table S50. Gene #9: 'amp_xq11.2' versus Clinical Feature #7: 'GENDER'

nPatients	FEMALE	MALE
ALL	292	590
AMP PEAK 9(XQ11.2) MUTATED	26	110
AMP PEAK 9(XQ11.2) WILD-TYPE	266	480

Figure S50. Get High-res Image Gene #9: 'amp_xq11.2' versus Clinical Feature #7: 'GENDER'

'amp_xq11.2' versus 'HISTOLOGICAL_TYPE'

P value = 1e-05 (Fisher's exact test), Q value = 7.2e-05

Table S51. Gene #9: 'amp_xq11.2' versus Clinical Feature #10: 'HISTOLOGICAL_TYPE'

nPatients	KIDNEY CHROMOPHOBE	KIDNEY CLEAR CELL RENAL CARCINOMA	KIDNEY PAPILLARY RENAL CELL CARCINOMA
ALL	66	528	288
AMP PEAK 9(XQ11.2) MUTATED	8	29	99
AMP PEAK 9(XQ11.2) WILD-TYPE	58	499	189

Figure S51. Get High-res Image Gene #9: 'amp_xq11.2' versus Clinical Feature #10: 'HISTOLOGICAL_TYPE'

'amp_xq11.2' versus 'YEAR_OF_TOBACCO_SMOKING_ONSET'

P value = 0.0331 (Wilcoxon-test), Q value = 0.089

Table S52. Gene #9: 'amp_xq11.2' versus Clinical Feature #12: 'YEAR_OF_TOBACCO_SMOKING_ONSET'

	nPatients	Mean (Std.Dev)
ALL	74	1973.7 (16.0)
AMP PEAK 9(XQ11.2) MUTATED	18	1966.9 (15.0)
AMP PEAK 9(XQ11.2) WILD-TYPE	56	1975.9 (15.8)

Figure S52. Get High-res Image Gene #9: 'amp_xq11.2' versus Clinical Feature #12: 'YEAR_OF_TOBACCO_SMOKING_ONSET'

'del_1p36.31' versus 'Time to Death'

P value = 0.11 (logrank test), Q value = 0.24

Table S53. Gene #10: 'del_1p36.31' versus Clinical Feature #1: 'Time to Death'

	nPatients	nDeath	Duration Range (Median), Month
ALL	876	228	0.1 - 194.8 (35.9)
DEL PEAK 1(1P36.31) MUTATED	208	70	0.1 - 153.7 (40.2)
DEL PEAK 1(1P36.31) WILD-TYPE	668	158	0.1 - 194.8 (34.3)

Figure S53. Get High-res Image Gene #10: 'del_1p36.31' versus Clinical Feature #1: 'Time to Death'

'del_1p36.31' versus 'YEARS_TO_BIRTH'

P value = 0.0822 (Wilcoxon-test), Q value = 0.19

Table S54. Gene #10: 'del_1p36.31' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

	nPatients	Mean (Std.Dev)
ALL	876	60.1 (12.5)
DEL PEAK 1(1P36.31) MUTATED	208	58.5 (13.6)
DEL PEAK 1(1P36.31) WILD-TYPE	668	60.7 (12.1)

Figure S54. Get High-res Image Gene #10: 'del_1p36.31' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'del_1p36.31' versus 'PATHOLOGIC_STAGE'

P value = 1e-05 (Fisher's exact test), Q value = 7.2e-05

Table S55. Gene #10: 'del_1p36.31' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

nPatients	STAGE I	STAGE II	STAGE III	STAGE IV
ALL	454	103	190	104
DEL PEAK 1(1P36.31) MUTATED	73	38	59	31
DEL PEAK 1(1P36.31) WILD-TYPE	381	65	131	73

Figure S55. Get High-res Image Gene #10: 'del_1p36.31' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

'del_1p36.31' versus 'PATHOLOGY_T_STAGE'

P value = 1e-05 (Fisher's exact test), Q value = 7.2e-05

Table S56. Gene #10: 'del_1p36.31' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

nPatients	T1	T2	T3	T4
ALL	480	127	258	15
DEL PEAK 1(1P36.31) MUTATED	80	47	76	6
DEL PEAK 1(1P36.31) WILD-TYPE	400	80	182	9

Figure S56. Get High-res Image Gene #10: 'del_1p36.31' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

'del_1p36.31' versus 'PATHOLOGY_N_STAGE'

P value = 0.00964 (Fisher's exact test), Q value = 0.032

Table S57. Gene #10: 'del_1p36.31' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

nPatients	N0	N1	N2
ALL	323	44	6
DEL PEAK 1(1P36.31) MUTATED	92	20	4
DEL PEAK 1(1P36.31) WILD-TYPE	231	24	2

Figure S57. Get High-res Image Gene #10: 'del_1p36.31' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

'del_1p36.31' versus 'KARNOFSKY_PERFORMANCE_SCORE'

P value = 0.093 (Wilcoxon-test), Q value = 0.21

Table S58. Gene #10: 'del_1p36.31' versus Clinical Feature #9: 'KARNOFSKY_PERFORMANCE_SCORE'

	nPatients	Mean (Std.Dev)
ALL	143	87.7 (22.8)
DEL PEAK 1(1P36.31) MUTATED	33	80.9 (30.2)
DEL PEAK 1(1P36.31) WILD-TYPE	110	89.7 (19.7)

Figure S58. Get High-res Image Gene #10: 'del_1p36.31' versus Clinical Feature #9: 'KARNOFSKY_PERFORMANCE_SCORE'

'del_1p36.31' versus 'HISTOLOGICAL_TYPE'

P value = 1e-05 (Fisher's exact test), Q value = 7.2e-05

Table S59. Gene #10: 'del_1p36.31' versus Clinical Feature #10: 'HISTOLOGICAL_TYPE'

nPatients	KIDNEY CHROMOPHOBE	KIDNEY CLEAR CELL RENAL CARCINOMA	KIDNEY PAPILLARY RENAL CELL CARCINOMA
ALL	66	528	288
DEL PEAK 1(1P36.31) MUTATED	53	102	54
DEL PEAK 1(1P36.31) WILD-TYPE	13	426	234

Figure S59. Get High-res Image Gene #10: 'del_1p36.31' versus Clinical Feature #10: 'HISTOLOGICAL_TYPE'

'del_1p31.1' versus 'YEARS_TO_BIRTH'

P value = 0.0402 (Wilcoxon-test), Q value = 0.1

Table S60. Gene #11: 'del_1p31.1' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

	nPatients	Mean (Std.Dev)
ALL	876	60.1 (12.5)
DEL PEAK 2(1P31.1) MUTATED	166	58.0 (13.9)
DEL PEAK 2(1P31.1) WILD-TYPE	710	60.7 (12.1)

Figure S60. Get High-res Image Gene #11: 'del_1p31.1' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'del_1p31.1' versus 'PATHOLOGIC_STAGE'

P value = 8e-05 (Fisher's exact test), Q value = 0.00044

Table S61. Gene #11: 'del_1p31.1' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

nPatients	STAGE I	STAGE II	STAGE III	STAGE IV
ALL	454	103	190	104
DEL PEAK 2(1P31.1) MUTATED	60	34	42	24
DEL PEAK 2(1P31.1) WILD-TYPE	394	69	148	80

Figure S61. Get High-res Image Gene #11: 'del_1p31.1' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

'del_1p31.1' versus 'PATHOLOGY_T_STAGE'

P value = 2e-05 (Fisher's exact test), Q value = 0.00013

Table S62. Gene #11: 'del_1p31.1' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

nPatients	T1	T2	T3	T4
ALL	480	127	258	15
DEL PEAK 2(1P31.1) MUTATED	66	40	54	6
DEL PEAK 2(1P31.1) WILD-TYPE	414	87	204	9

Figure S62. Get High-res Image Gene #11: 'del_1p31.1' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

'del_1p31.1' versus 'PATHOLOGY_N_STAGE'

P value = 0.0616 (Fisher's exact test), Q value = 0.15

Table S63. Gene #11: 'del_1p31.1' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

nPatients	N0	N1	N2
ALL	323	44	6
DEL PEAK 2(1P31.1) MUTATED	72	15	3
DEL PEAK 2(1P31.1) WILD-TYPE	251	29	3

Figure S63. Get High-res Image Gene #11: 'del_1p31.1' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

'del_1p31.1' versus 'HISTOLOGICAL_TYPE'

P value = 1e-05 (Fisher's exact test), Q value = 7.2e-05

Table S64. Gene #11: 'del_1p31.1' versus Clinical Feature #10: 'HISTOLOGICAL_TYPE'

nPatients	KIDNEY CHROMOPHOBE	KIDNEY CLEAR CELL RENAL CARCINOMA	KIDNEY PAPILLARY RENAL CELL CARCINOMA
ALL	66	528	288
DEL PEAK 2(1P31.1) MUTATED	53	77	36
DEL PEAK 2(1P31.1) WILD-TYPE	13	451	252

Figure S64. Get High-res Image Gene #11: 'del_1p31.1' versus Clinical Feature #10: 'HISTOLOGICAL_TYPE'

'del_1p31.1' versus 'ETHNICITY'

P value = 0.0884 (Fisher's exact test), Q value = 0.2

Table S65. Gene #11: 'del_1p31.1' versus Clinical Feature #14: 'ETHNICITY'

nPatients	HISPANIC OR LATINO	NOT HISPANIC OR LATINO
ALL	42	622
DEL PEAK 2(1P31.1) MUTATED	11	99
DEL PEAK 2(1P31.1) WILD-TYPE	31	523

Figure S65. Get High-res Image Gene #11: 'del_1p31.1' versus Clinical Feature #14: 'ETHNICITY'

'del_1q44' versus 'Time to Death'

P value = 0.092 (logrank test), Q value = 0.21

Table S66. Gene #12: 'del_1q44' versus Clinical Feature #1: 'Time to Death'

	nPatients	nDeath	Duration Range (Median), Month
ALL	876	228	0.1 - 194.8 (35.9)
DEL PEAK 3(1Q44) MUTATED	115	29	0.1 - 153.7 (50.0)
DEL PEAK 3(1Q44) WILD-TYPE	761	199	0.1 - 194.8 (33.5)

Figure S66. Get High-res Image Gene #12: 'del_1q44' versus Clinical Feature #1: 'Time to Death'

'del_1q44' versus 'YEARS_TO_BIRTH'

P value = 0.01 (Wilcoxon-test), Q value = 0.032

Table S67. Gene #12: 'del_1q44' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

	nPatients	Mean (Std.Dev)
ALL	876	60.1 (12.5)
DEL PEAK 3(1Q44) MUTATED	116	56.9 (14.4)
DEL PEAK 3(1Q44) WILD-TYPE	760	60.6 (12.1)

Figure S67. Get High-res Image Gene #12: 'del_1q44' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'del_1q44' versus 'PATHOLOGIC_STAGE'

P value = 4e-04 (Fisher's exact test), Q value = 0.0019

Table S68. Gene #12: 'del_1q44' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

nPatients	STAGE I	STAGE II	STAGE III	STAGE IV
ALL	454	103	190	104
DEL PEAK 3(1Q44) MUTATED	47	28	23	14
DEL PEAK 3(1Q44) WILD-TYPE	407	75	167	90

Figure S68. Get High-res Image Gene #12: 'del_1q44' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

'del_1q44' versus 'PATHOLOGY_T_STAGE'

P value = 0.00116 (Fisher's exact test), Q value = 0.0048

Table S69. Gene #12: 'del_1q44' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

nPatients	T1	T2	T3	T4
ALL	480	127	258	15
DEL PEAK 3(1Q44) MUTATED	49	29	34	4
DEL PEAK 3(1Q44) WILD-TYPE	431	98	224	11

Figure S69. Get High-res Image Gene #12: 'del_1q44' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

'del_1q44' versus 'HISTOLOGICAL_TYPE'

P value = 1e-05 (Fisher's exact test), Q value = 7.2e-05

Table S70. Gene #12: 'del_1q44' versus Clinical Feature #10: 'HISTOLOGICAL_TYPE'

nPatients	KIDNEY CHROMOPHOBE	KIDNEY CLEAR CELL RENAL CARCINOMA	KIDNEY PAPILLARY RENAL CELL CARCINOMA
ALL	66	528	288
DEL PEAK 3(1Q44) MUTATED	51	44	21
DEL PEAK 3(1Q44) WILD-TYPE	15	484	267

Figure S70. Get High-res Image Gene #12: 'del_1q44' versus Clinical Feature #10: 'HISTOLOGICAL_TYPE'

'del_2q22.1' versus 'Time to Death'

P value = 0.0459 (logrank test), Q value = 0.12

Table S71. Gene #13: 'del_2q22.1' versus Clinical Feature #1: 'Time to Death'

	nPatients	nDeath	Duration Range (Median), Month
ALL	876	228	0.1 - 194.8 (35.9)
DEL PEAK 4(2Q22.1) MUTATED	74	17	2.5 - 153.7 (52.6)
DEL PEAK 4(2Q22.1) WILD-TYPE	802	211	0.1 - 194.8 (33.5)

Figure S71. Get High-res Image Gene #13: 'del_2q22.1' versus Clinical Feature #1: 'Time to Death'

'del_2q22.1' versus 'YEARS_TO_BIRTH'

P value = 0.000439 (Wilcoxon-test), Q value = 0.0021

Table S72. Gene #13: 'del_2q22.1' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

	nPatients	Mean (Std.Dev)
ALL	876	60.1 (12.5)
DEL PEAK 4(2Q22.1) MUTATED	74	54.6 (14.6)
DEL PEAK 4(2Q22.1) WILD-TYPE	802	60.7 (12.2)

Figure S72. Get High-res Image Gene #13: 'del_2q22.1' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'del_2q22.1' versus 'PATHOLOGIC_STAGE'

P value = 1e-05 (Fisher's exact test), Q value = 7.2e-05

Table S73. Gene #13: 'del_2q22.1' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

nPatients	STAGE I	STAGE II	STAGE III	STAGE IV
ALL	454	103	190	104
DEL PEAK 4(2Q22.1) MUTATED	21	26	18	9
DEL PEAK 4(2Q22.1) WILD-TYPE	433	77	172	95

Figure S73. Get High-res Image Gene #13: 'del_2q22.1' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

'del_2q22.1' versus 'PATHOLOGY_T_STAGE'

P value = 1e-05 (Fisher's exact test), Q value = 7.2e-05

Table S74. Gene #13: 'del_2q22.1' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

nPatients	T1	T2	T3	T4
ALL	480	127	258	15
DEL PEAK 4(2Q22.1) MUTATED	23	26	24	2
DEL PEAK 4(2Q22.1) WILD-TYPE	457	101	234	13

Figure S74. Get High-res Image Gene #13: 'del_2q22.1' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

'del_2q22.1' versus 'KARNOFSKY_PERFORMANCE_SCORE'

P value = 0.0768 (Wilcoxon-test), Q value = 0.18

Table S75. Gene #13: 'del_2q22.1' versus Clinical Feature #9: 'KARNOFSKY_PERFORMANCE_SCORE'

	nPatients	Mean (Std.Dev)
ALL	143	87.7 (22.8)
DEL PEAK 4(2Q22.1) MUTATED	12	90.0 (28.6)
DEL PEAK 4(2Q22.1) WILD-TYPE	131	87.5 (22.3)

Figure S75. Get High-res Image Gene #13: 'del_2q22.1' versus Clinical Feature #9: 'KARNOFSKY_PERFORMANCE_SCORE'

'del_2q22.1' versus 'HISTOLOGICAL_TYPE'

P value = 1e-05 (Fisher's exact test), Q value = 7.2e-05

Table S76. Gene #13: 'del_2q22.1' versus Clinical Feature #10: 'HISTOLOGICAL_TYPE'

nPatients	KIDNEY CHROMOPHOBE	KIDNEY CLEAR CELL RENAL CARCINOMA	KIDNEY PAPILLARY RENAL CELL CARCINOMA
ALL	66	528	288
DEL PEAK 4(2Q22.1) MUTATED	46	19	10
DEL PEAK 4(2Q22.1) WILD-TYPE	20	509	278

Figure S76. Get High-res Image Gene #13: 'del_2q22.1' versus Clinical Feature #10: 'HISTOLOGICAL_TYPE'

'del_2q37.3' versus 'Time to Death'

P value = 0.0298 (logrank test), Q value = 0.081

Table S77. Gene #14: 'del_2q37.3' versus Clinical Feature #1: 'Time to Death'

	nPatients	nDeath	Duration Range (Median), Month
ALL	876	228	0.1 - 194.8 (35.9)
DEL PEAK 5(2Q37.3) MUTATED	110	23	0.4 - 153.7 (44.7)
DEL PEAK 5(2Q37.3) WILD-TYPE	766	205	0.1 - 194.8 (33.3)

Figure S77. Get High-res Image Gene #14: 'del_2q37.3' versus Clinical Feature #1: 'Time to Death'

'del_2q37.3' versus 'YEARS_TO_BIRTH'

P value = 0.00311 (Wilcoxon-test), Q value = 0.011

Table S78. Gene #14: 'del_2q37.3' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

	nPatients	Mean (Std.Dev)
ALL	876	60.1 (12.5)
DEL PEAK 5(2Q37.3) MUTATED	110	56.6 (14.1)
DEL PEAK 5(2Q37.3) WILD-TYPE	766	60.7 (12.2)

Figure S78. Get High-res Image Gene #14: 'del_2q37.3' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'del_2q37.3' versus 'PATHOLOGIC_STAGE'

P value = 1e-05 (Fisher's exact test), Q value = 7.2e-05

Table S79. Gene #14: 'del_2q37.3' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

nPatients	STAGE I	STAGE II	STAGE III	STAGE IV
ALL	454	103	190	104
DEL PEAK 5(2Q37.3) MUTATED	38	32	28	11
DEL PEAK 5(2Q37.3) WILD-TYPE	416	71	162	93

Figure S79. Get High-res Image Gene #14: 'del_2q37.3' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

'del_2q37.3' versus 'PATHOLOGY_T_STAGE'

P value = 1e-05 (Fisher's exact test), Q value = 7.2e-05

Table S80. Gene #14: 'del_2q37.3' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

nPatients	T1	T2	T3	T4
ALL	480	127	258	15
DEL PEAK 5(2Q37.3) MUTATED	39	34	35	3
DEL PEAK 5(2Q37.3) WILD-TYPE	441	93	223	12

Figure S80. Get High-res Image Gene #14: 'del_2q37.3' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

'del_2q37.3' versus 'PATHOLOGY_M_STAGE'

P value = 0.0849 (Fisher's exact test), Q value = 0.2

Table S81. Gene #14: 'del_2q37.3' versus Clinical Feature #6: 'PATHOLOGY_M_STAGE'

nPatients	0	1
ALL	546	89
DEL PEAK 5(2Q37.3) MUTATED	75	6
DEL PEAK 5(2Q37.3) WILD-TYPE	471	83

Figure S81. Get High-res Image Gene #14: 'del_2q37.3' versus Clinical Feature #6: 'PATHOLOGY_M_STAGE'

'del_2q37.3' versus 'KARNOFSKY_PERFORMANCE_SCORE'

P value = 0.0163 (Wilcoxon-test), Q value = 0.048

Table S82. Gene #14: 'del_2q37.3' versus Clinical Feature #9: 'KARNOFSKY_PERFORMANCE_SCORE'

	nPatients	Mean (Std.Dev)
ALL	143	87.7 (22.8)
DEL PEAK 5(2Q37.3) MUTATED	11	98.2 (4.0)
DEL PEAK 5(2Q37.3) WILD-TYPE	132	86.8 (23.5)

Figure S82. Get High-res Image Gene #14: 'del_2q37.3' versus Clinical Feature #9: 'KARNOFSKY_PERFORMANCE_SCORE'

'del_2q37.3' versus 'HISTOLOGICAL_TYPE'

P value = 1e-05 (Fisher's exact test), Q value = 7.2e-05

Table S83. Gene #14: 'del_2q37.3' versus Clinical Feature #10: 'HISTOLOGICAL_TYPE'

nPatients	KIDNEY CHROMOPHOBE	KIDNEY CLEAR CELL RENAL CARCINOMA	KIDNEY PAPILLARY RENAL CELL CARCINOMA
ALL	66	528	288
DEL PEAK 5(2Q37.3) MUTATED	49	50	12
DEL PEAK 5(2Q37.3) WILD-TYPE	17	478	276

Figure S83. Get High-res Image Gene #14: 'del_2q37.3' versus Clinical Feature #10: 'HISTOLOGICAL_TYPE'

'del_3p26.3' versus 'Time to Death'

P value = 0.000258 (logrank test), Q value = 0.0013

Table S84. Gene #15: 'del_3p26.3' versus Clinical Feature #1: 'Time to Death'

	nPatients	nDeath	Duration Range (Median), Month
ALL	876	228	0.1 - 194.8 (35.9)
DEL PEAK 6(3P26.3) MUTATED	488	159	0.1 - 153.7 (38.7)
DEL PEAK 6(3P26.3) WILD-TYPE	388	69	0.1 - 194.8 (29.2)

Figure S84. Get High-res Image Gene #15: 'del_3p26.3' versus Clinical Feature #1: 'Time to Death'

'del_3p26.3' versus 'PATHOLOGIC_STAGE'

P value = 1e-05 (Fisher's exact test), Q value = 7.2e-05

Table S85. Gene #15: 'del_3p26.3' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

nPatients	STAGE I	STAGE II	STAGE III	STAGE IV
ALL	454	103	190	104
DEL PEAK 6(3P26.3) MUTATED	227	57	128	74
DEL PEAK 6(3P26.3) WILD-TYPE	227	46	62	30

Figure S85. Get High-res Image Gene #15: 'del_3p26.3' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

'del_3p26.3' versus 'PATHOLOGY_T_STAGE'

P value = 1e-05 (Fisher's exact test), Q value = 7.2e-05

Table S86. Gene #15: 'del_3p26.3' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

nPatients	T1	T2	T3	T4
ALL	480	127	258	15
DEL PEAK 6(3P26.3) MUTATED	234	71	177	7
DEL PEAK 6(3P26.3) WILD-TYPE	246	56	81	8

Figure S86. Get High-res Image Gene #15: 'del_3p26.3' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

'del_3p26.3' versus 'PATHOLOGY_N_STAGE'

P value = 0.0274 (Fisher's exact test), Q value = 0.076

Table S87. Gene #15: 'del_3p26.3' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

nPatients	N0	N1	N2
ALL	323	44	6
DEL PEAK 6(3P26.3) MUTATED	214	22	2
DEL PEAK 6(3P26.3) WILD-TYPE	109	22	4

Figure S87. Get High-res Image Gene #15: 'del_3p26.3' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

'del_3p26.3' versus 'PATHOLOGY_M_STAGE'

P value = 0.105 (Fisher's exact test), Q value = 0.23

Table S88. Gene #15: 'del_3p26.3' versus Clinical Feature #6: 'PATHOLOGY_M_STAGE'

nPatients	0	1
ALL	546	89
DEL PEAK 6(3P26.3) MUTATED	374	69
DEL PEAK 6(3P26.3) WILD-TYPE	172	20

Figure S88. Get High-res Image Gene #15: 'del_3p26.3' versus Clinical Feature #6: 'PATHOLOGY_M_STAGE'

'del_3p26.3' versus 'GENDER'

P value = 0.0441 (Fisher's exact test), Q value = 0.11

Table S89. Gene #15: 'del_3p26.3' versus Clinical Feature #7: 'GENDER'

nPatients	FEMALE	MALE
ALL	292	590
DEL PEAK 6(3P26.3) MUTATED	176	313
DEL PEAK 6(3P26.3) WILD-TYPE	116	277

Figure S89. Get High-res Image Gene #15: 'del_3p26.3' versus Clinical Feature #7: 'GENDER'

'del_3p26.3' versus 'KARNOFSKY_PERFORMANCE_SCORE'

P value = 0.102 (Wilcoxon-test), Q value = 0.23

Table S90. Gene #15: 'del_3p26.3' versus Clinical Feature #9: 'KARNOFSKY_PERFORMANCE_SCORE'

	nPatients	Mean (Std.Dev)
ALL	143	87.7 (22.8)
DEL PEAK 6(3P26.3) MUTATED	54	82.4 (29.6)
DEL PEAK 6(3P26.3) WILD-TYPE	89	90.9 (16.8)

Figure S90. Get High-res Image Gene #15: 'del_3p26.3' versus Clinical Feature #9: 'KARNOFSKY_PERFORMANCE_SCORE'

'del_3p26.3' versus 'HISTOLOGICAL_TYPE'

P value = 1e-05 (Fisher's exact test), Q value = 7.2e-05

Table S91. Gene #15: 'del_3p26.3' versus Clinical Feature #10: 'HISTOLOGICAL_TYPE'

nPatients	KIDNEY CHROMOPHOBE	KIDNEY CLEAR CELL RENAL CARCINOMA	KIDNEY PAPILLARY RENAL CELL CARCINOMA
ALL	66	528	288
DEL PEAK 6(3P26.3) MUTATED	10	455	24
DEL PEAK 6(3P26.3) WILD-TYPE	56	73	264

Figure S91. Get High-res Image Gene #15: 'del_3p26.3' versus Clinical Feature #10: 'HISTOLOGICAL_TYPE'

'del_3p26.3' versus 'YEAR_OF_TOBACCO_SMOKING_ONSET'

P value = 0.0787 (Wilcoxon-test), Q value = 0.18

Table S92. Gene #15: 'del_3p26.3' versus Clinical Feature #12: 'YEAR_OF_TOBACCO_SMOKING_ONSET'

	nPatients	Mean (Std.Dev)
ALL	74	1973.7 (16.0)
DEL PEAK 6(3P26.3) MUTATED	19	1979.3 (18.0)
DEL PEAK 6(3P26.3) WILD-TYPE	55	1971.8 (14.9)

Figure S92. Get High-res Image Gene #15: 'del_3p26.3' versus Clinical Feature #12: 'YEAR_OF_TOBACCO_SMOKING_ONSET'

'del_3p26.3' versus 'RACE'

P value = 1e-05 (Fisher's exact test), Q value = 7.2e-05

Table S93. Gene #15: 'del_3p26.3' versus Clinical Feature #13: 'RACE'

nPatients	AMERICAN INDIAN OR ALASKA NATIVE	ASIAN	BLACK OR AFRICAN AMERICAN	WHITE
ALL	2	16	121	719
DEL PEAK 6(3P26.3) MUTATED	0	7	43	430
DEL PEAK 6(3P26.3) WILD-TYPE	2	9	78	289

Figure S93. Get High-res Image Gene #15: 'del_3p26.3' versus Clinical Feature #13: 'RACE'

'del_3p21.2' versus 'Time to Death'

P value = 5.54e-07 (logrank test), Q value = 4.1e-05

Table S94. Gene #16: 'del_3p21.2' versus Clinical Feature #1: 'Time to Death'

	nPatients	nDeath	Duration Range (Median), Month
ALL	876	228	0.1 - 194.8 (35.9)
DEL PEAK 7(3P21.2) MUTATED	502	171	0.1 - 153.7 (38.4)
DEL PEAK 7(3P21.2) WILD-TYPE	374	57	0.1 - 194.8 (30.1)

Figure S94. Get High-res Image Gene #16: 'del_3p21.2' versus Clinical Feature #1: 'Time to Death'

'del_3p21.2' versus 'PATHOLOGIC_STAGE'

P value = 1e-05 (Fisher's exact test), Q value = 7.2e-05

Table S95. Gene #16: 'del_3p21.2' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

nPatients	STAGE I	STAGE II	STAGE III	STAGE IV
ALL	454	103	190	104
DEL PEAK 7(3P21.2) MUTATED	227	57	134	81
DEL PEAK 7(3P21.2) WILD-TYPE	227	46	56	23

Figure S95. Get High-res Image Gene #16: 'del_3p21.2' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

'del_3p21.2' versus 'PATHOLOGY_T_STAGE'

P value = 1e-05 (Fisher's exact test), Q value = 7.2e-05

Table S96. Gene #16: 'del_3p21.2' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

nPatients	T1	T2	T3	T4
ALL	480	127	258	15
DEL PEAK 7(3P21.2) MUTATED	234	72	190	7
DEL PEAK 7(3P21.2) WILD-TYPE	246	55	68	8

Figure S96. Get High-res Image Gene #16: 'del_3p21.2' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

'del_3p21.2' versus 'PATHOLOGY_M_STAGE'

P value = 0.00347 (Fisher's exact test), Q value = 0.013

Table S97. Gene #16: 'del_3p21.2' versus Clinical Feature #6: 'PATHOLOGY_M_STAGE'

nPatients	0	1
ALL	546	89
DEL PEAK 7(3P21.2) MUTATED	379	75
DEL PEAK 7(3P21.2) WILD-TYPE	167	14

Figure S97. Get High-res Image Gene #16: 'del_3p21.2' versus Clinical Feature #6: 'PATHOLOGY_M_STAGE'

'del_3p21.2' versus 'GENDER'

P value = 0.112 (Fisher's exact test), Q value = 0.24

Table S98. Gene #16: 'del_3p21.2' versus Clinical Feature #7: 'GENDER'

nPatients	FEMALE	MALE
ALL	292	590
DEL PEAK 7(3P21.2) MUTATED	178	325
DEL PEAK 7(3P21.2) WILD-TYPE	114	265

Figure S98. Get High-res Image Gene #16: 'del_3p21.2' versus Clinical Feature #7: 'GENDER'

'del_3p21.2' versus 'KARNOFSKY_PERFORMANCE_SCORE'

P value = 0.0359 (Wilcoxon-test), Q value = 0.094

Table S99. Gene #16: 'del_3p21.2' versus Clinical Feature #9: 'KARNOFSKY_PERFORMANCE_SCORE'

	nPatients	Mean (Std.Dev)
ALL	143	87.7 (22.8)
DEL PEAK 7(3P21.2) MUTATED	57	81.2 (30.8)
DEL PEAK 7(3P21.2) WILD-TYPE	86	92.0 (13.9)

Figure S99. Get High-res Image Gene #16: 'del_3p21.2' versus Clinical Feature #9: 'KARNOFSKY_PERFORMANCE_SCORE'

'del_3p21.2' versus 'HISTOLOGICAL_TYPE'

P value = 1e-05 (Fisher's exact test), Q value = 7.2e-05

Table S100. Gene #16: 'del_3p21.2' versus Clinical Feature #10: 'HISTOLOGICAL_TYPE'

nPatients	KIDNEY CHROMOPHOBE	KIDNEY CLEAR CELL RENAL CARCINOMA	KIDNEY PAPILLARY RENAL CELL CARCINOMA
ALL	66	528	288
DEL PEAK 7(3P21.2) MUTATED	11	465	27
DEL PEAK 7(3P21.2) WILD-TYPE	55	63	261

Figure S100. Get High-res Image Gene #16: 'del_3p21.2' versus Clinical Feature #10: 'HISTOLOGICAL_TYPE'

'del_3p21.2' versus 'YEAR_OF_TOBACCO_SMOKING_ONSET'

P value = 0.042 (Wilcoxon-test), Q value = 0.11

Table S101. Gene #16: 'del_3p21.2' versus Clinical Feature #12: 'YEAR_OF_TOBACCO_SMOKING_ONSET'

	nPatients	Mean (Std.Dev)
ALL	74	1973.7 (16.0)
DEL PEAK 7(3P21.2) MUTATED	21	1979.4 (17.0)
DEL PEAK 7(3P21.2) WILD-TYPE	53	1971.5 (15.1)

Figure S101. Get High-res Image Gene #16: 'del_3p21.2' versus Clinical Feature #12: 'YEAR_OF_TOBACCO_SMOKING_ONSET'

'del_3p21.2' versus 'RACE'

P value = 1e-05 (Fisher's exact test), Q value = 7.2e-05

Table S102. Gene #16: 'del_3p21.2' versus Clinical Feature #13: 'RACE'

nPatients	AMERICAN INDIAN OR ALASKA NATIVE	ASIAN	BLACK OR AFRICAN AMERICAN	WHITE
ALL	2	16	121	719
DEL PEAK 7(3P21.2) MUTATED	0	8	43	444
DEL PEAK 7(3P21.2) WILD-TYPE	2	8	78	275

Figure S102. Get High-res Image Gene #16: 'del_3p21.2' versus Clinical Feature #13: 'RACE'

'del_3p14.1' versus 'Time to Death'

P value = 6e-04 (logrank test), Q value = 0.0027

Table S103. Gene #17: 'del_3p14.1' versus Clinical Feature #1: 'Time to Death'

	nPatients	nDeath	Duration Range (Median), Month
ALL	876	228	0.1 - 194.8 (35.9)
DEL PEAK 8(3P14.1) MUTATED	408	136	0.1 - 153.7 (39.0)
DEL PEAK 8(3P14.1) WILD-TYPE	468	92	0.1 - 194.8 (30.7)

Figure S103. Get High-res Image Gene #17: 'del_3p14.1' versus Clinical Feature #1: 'Time to Death'

'del_3p14.1' versus 'PATHOLOGIC_STAGE'

P value = 0.00032 (Fisher's exact test), Q value = 0.0016

Table S104. Gene #17: 'del_3p14.1' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

nPatients	STAGE I	STAGE II	STAGE III	STAGE IV
ALL	454	103	190	104
DEL PEAK 8(3P14.1) MUTATED	187	49	110	59
DEL PEAK 8(3P14.1) WILD-TYPE	267	54	80	45

Figure S104. Get High-res Image Gene #17: 'del_3p14.1' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

'del_3p14.1' versus 'PATHOLOGY_T_STAGE'

P value = 2e-05 (Fisher's exact test), Q value = 0.00013

Table S105. Gene #17: 'del_3p14.1' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

nPatients	T1	T2	T3	T4
ALL	480	127	258	15
DEL PEAK 8(3P14.1) MUTATED	192	60	151	5
DEL PEAK 8(3P14.1) WILD-TYPE	288	67	107	10

Figure S105. Get High-res Image Gene #17: 'del_3p14.1' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

'del_3p14.1' versus 'HISTOLOGICAL_TYPE'

P value = 1e-05 (Fisher's exact test), Q value = 7.2e-05

Table S106. Gene #17: 'del_3p14.1' versus Clinical Feature #10: 'HISTOLOGICAL_TYPE'

nPatients	KIDNEY CHROMOPHOBE	KIDNEY CLEAR CELL RENAL CARCINOMA	KIDNEY PAPILLARY RENAL CELL CARCINOMA
ALL	66	528	288
DEL PEAK 8(3P14.1) MUTATED	11	373	24
DEL PEAK 8(3P14.1) WILD-TYPE	55	155	264

Figure S106. Get High-res Image Gene #17: 'del_3p14.1' versus Clinical Feature #10: 'HISTOLOGICAL_TYPE'

'del_3p14.1' versus 'YEAR_OF_TOBACCO_SMOKING_ONSET'

P value = 0.0554 (Wilcoxon-test), Q value = 0.14

Table S107. Gene #17: 'del_3p14.1' versus Clinical Feature #12: 'YEAR_OF_TOBACCO_SMOKING_ONSET'

	nPatients	Mean (Std.Dev)
ALL	74	1973.7 (16.0)
DEL PEAK 8(3P14.1) MUTATED	17	1979.9 (18.1)
DEL PEAK 8(3P14.1) WILD-TYPE	57	1971.9 (15.0)

Figure S107. Get High-res Image Gene #17: 'del_3p14.1' versus Clinical Feature #12: 'YEAR_OF_TOBACCO_SMOKING_ONSET'

'del_3p14.1' versus 'RACE'

P value = 0.00024 (Fisher's exact test), Q value = 0.0012

Table S108. Gene #17: 'del_3p14.1' versus Clinical Feature #13: 'RACE'

nPatients	AMERICAN INDIAN OR ALASKA NATIVE	ASIAN	BLACK OR AFRICAN AMERICAN	WHITE
ALL	2	16	121	719
DEL PEAK 8(3P14.1) MUTATED	0	7	37	357
DEL PEAK 8(3P14.1) WILD-TYPE	2	9	84	362

Figure S108. Get High-res Image Gene #17: 'del_3p14.1' versus Clinical Feature #13: 'RACE'

'del_3p12.2' versus 'Time to Death'

P value = 0.000163 (logrank test), Q value = 0.00085

Table S109. Gene #18: 'del_3p12.2' versus Clinical Feature #1: 'Time to Death'

	nPatients	nDeath	Duration Range (Median), Month
ALL	876	228	0.1 - 194.8 (35.9)
DEL PEAK 9(3P12.2) MUTATED	336	117	0.1 - 153.7 (39.0)
DEL PEAK 9(3P12.2) WILD-TYPE	540	111	0.1 - 194.8 (31.3)

Figure S109. Get High-res Image Gene #18: 'del_3p12.2' versus Clinical Feature #1: 'Time to Death'

'del_3p12.2' versus 'PATHOLOGIC_STAGE'

P value = 0.0108 (Fisher's exact test), Q value = 0.034

Table S110. Gene #18: 'del_3p12.2' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

nPatients	STAGE I	STAGE II	STAGE III	STAGE IV
ALL	454	103	190	104
DEL PEAK 9(3P12.2) MUTATED	155	42	87	49
DEL PEAK 9(3P12.2) WILD-TYPE	299	61	103	55

Figure S110. Get High-res Image Gene #18: 'del_3p12.2' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

'del_3p12.2' versus 'PATHOLOGY_T_STAGE'

P value = 0.00275 (Fisher's exact test), Q value = 0.01

Table S111. Gene #18: 'del_3p12.2' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

nPatients	T1	T2	T3	T4
ALL	480	127	258	15
DEL PEAK 9(3P12.2) MUTATED	160	51	121	4
DEL PEAK 9(3P12.2) WILD-TYPE	320	76	137	11

Figure S111. Get High-res Image Gene #18: 'del_3p12.2' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

'del_3p12.2' versus 'HISTOLOGICAL_TYPE'

P value = 1e-05 (Fisher's exact test), Q value = 7.2e-05

Table S112. Gene #18: 'del_3p12.2' versus Clinical Feature #10: 'HISTOLOGICAL_TYPE'

nPatients	KIDNEY CHROMOPHOBE	KIDNEY CLEAR CELL RENAL CARCINOMA	KIDNEY PAPILLARY RENAL CELL CARCINOMA
ALL	66	528	288
DEL PEAK 9(3P12.2) MUTATED	11	305	20
DEL PEAK 9(3P12.2) WILD-TYPE	55	223	268

Figure S112. Get High-res Image Gene #18: 'del_3p12.2' versus Clinical Feature #10: 'HISTOLOGICAL_TYPE'

'del_3p12.2' versus 'YEAR_OF_TOBACCO_SMOKING_ONSET'

P value = 0.0829 (Wilcoxon-test), Q value = 0.19

Table S113. Gene #18: 'del_3p12.2' versus Clinical Feature #12: 'YEAR_OF_TOBACCO_SMOKING_ONSET'

	nPatients	Mean (Std.Dev)
ALL	74	1973.7 (16.0)
DEL PEAK 9(3P12.2) MUTATED	13	1980.2 (17.0)
DEL PEAK 9(3P12.2) WILD-TYPE	61	1972.3 (15.6)

Figure S113. Get High-res Image Gene #18: 'del_3p12.2' versus Clinical Feature #12: 'YEAR_OF_TOBACCO_SMOKING_ONSET'

'del_3p12.2' versus 'RACE'

P value = 0.00576 (Fisher's exact test), Q value = 0.02

Table S114. Gene #18: 'del_3p12.2' versus Clinical Feature #13: 'RACE'

nPatients	AMERICAN INDIAN OR ALASKA NATIVE	ASIAN	BLACK OR AFRICAN AMERICAN	WHITE
ALL	2	16	121	719
DEL PEAK 9(3P12.2) MUTATED	0	6	31	293
DEL PEAK 9(3P12.2) WILD-TYPE	2	10	90	426

Figure S114. Get High-res Image Gene #18: 'del_3p12.2' versus Clinical Feature #13: 'RACE'

'del_4q34.3' versus 'Time to Death'

P value = 4.07e-10 (logrank test), Q value = 4.6e-08

Table S115. Gene #19: 'del_4q34.3' versus Clinical Feature #1: 'Time to Death'

	nPatients	nDeath	Duration Range (Median), Month
ALL	876	228	0.1 - 194.8 (35.9)
DEL PEAK 10(4Q34.3) MUTATED	113	55	0.4 - 133.7 (31.3)
DEL PEAK 10(4Q34.3) WILD-TYPE	763	173	0.1 - 194.8 (36.4)

Figure S115. Get High-res Image Gene #19: 'del_4q34.3' versus Clinical Feature #1: 'Time to Death'

'del_4q34.3' versus 'PATHOLOGIC_STAGE'

P value = 1e-05 (Fisher's exact test), Q value = 7.2e-05

Table S116. Gene #19: 'del_4q34.3' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

nPatients	STAGE I	STAGE II	STAGE III	STAGE IV
ALL	454	103	190	104
DEL PEAK 10(4Q34.3) MUTATED	26	10	48	26
DEL PEAK 10(4Q34.3) WILD-TYPE	428	93	142	78

Figure S116. Get High-res Image Gene #19: 'del_4q34.3' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

'del_4q34.3' versus 'PATHOLOGY_T_STAGE'

P value = 1e-05 (Fisher's exact test), Q value = 7.2e-05

Table S117. Gene #19: 'del_4q34.3' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

nPatients	T1	T2	T3	T4
ALL	480	127	258	15
DEL PEAK 10(4Q34.3) MUTATED	29	15	62	7
DEL PEAK 10(4Q34.3) WILD-TYPE	451	112	196	8

Figure S117. Get High-res Image Gene #19: 'del_4q34.3' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

'del_4q34.3' versus 'PATHOLOGY_N_STAGE'

P value = 0.00167 (Fisher's exact test), Q value = 0.0067

Table S118. Gene #19: 'del_4q34.3' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

nPatients	N0	N1	N2
ALL	323	44	6
DEL PEAK 10(4Q34.3) MUTATED	40	15	1
DEL PEAK 10(4Q34.3) WILD-TYPE	283	29	5

Figure S118. Get High-res Image Gene #19: 'del_4q34.3' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

'del_4q34.3' versus 'PATHOLOGY_M_STAGE'

P value = 0.0139 (Fisher's exact test), Q value = 0.043

Table S119. Gene #19: 'del_4q34.3' versus Clinical Feature #6: 'PATHOLOGY_M_STAGE'

nPatients	0	1
ALL	546	89
DEL PEAK 10(4Q34.3) MUTATED	71	21
DEL PEAK 10(4Q34.3) WILD-TYPE	475	68

Figure S119. Get High-res Image Gene #19: 'del_4q34.3' versus Clinical Feature #6: 'PATHOLOGY_M_STAGE'

'del_4q34.3' versus 'HISTOLOGICAL_TYPE'

P value = 0.0333 (Fisher's exact test), Q value = 0.089

Table S120. Gene #19: 'del_4q34.3' versus Clinical Feature #10: 'HISTOLOGICAL_TYPE'

nPatients	KIDNEY CHROMOPHOBE	KIDNEY CLEAR CELL RENAL CARCINOMA	KIDNEY PAPILLARY RENAL CELL CARCINOMA
ALL	66	528	288
DEL PEAK 10(4Q34.3) MUTATED	3	78	32
DEL PEAK 10(4Q34.3) WILD-TYPE	63	450	256

Figure S120. Get High-res Image Gene #19: 'del_4q34.3' versus Clinical Feature #10: 'HISTOLOGICAL_TYPE'

'del_4q34.3' versus 'RACE'

P value = 0.0585 (Fisher's exact test), Q value = 0.14

Table S121. Gene #19: 'del_4q34.3' versus Clinical Feature #13: 'RACE'

nPatients	AMERICAN INDIAN OR ALASKA NATIVE	ASIAN	BLACK OR AFRICAN AMERICAN	WHITE
ALL	2	16	121	719
DEL PEAK 10(4Q34.3) MUTATED	0	4	8	95
DEL PEAK 10(4Q34.3) WILD-TYPE	2	12	113	624

Figure S121. Get High-res Image Gene #19: 'del_4q34.3' versus Clinical Feature #13: 'RACE'

'del_5p15.33' versus 'YEARS_TO_BIRTH'

P value = 0.00425 (Wilcoxon-test), Q value = 0.015

Table S122. Gene #20: 'del_5p15.33' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

	nPatients	Mean (Std.Dev)
ALL	876	60.1 (12.5)
DEL PEAK 11(5P15.33) MUTATED	30	52.4 (14.6)
DEL PEAK 11(5P15.33) WILD-TYPE	846	60.4 (12.4)

Figure S122. Get High-res Image Gene #20: 'del_5p15.33' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'del_5p15.33' versus 'PATHOLOGIC_STAGE'

P value = 0.00028 (Fisher's exact test), Q value = 0.0014

Table S123. Gene #20: 'del_5p15.33' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

nPatients	STAGE I	STAGE II	STAGE III	STAGE IV
ALL	454	103	190	104
DEL PEAK 11(5P15.33) MUTATED	6	10	9	5
DEL PEAK 11(5P15.33) WILD-TYPE	448	93	181	99

Figure S123. Get High-res Image Gene #20: 'del_5p15.33' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

'del_5p15.33' versus 'PATHOLOGY_T_STAGE'

P value = 0.00056 (Fisher's exact test), Q value = 0.0026

Table S124. Gene #20: 'del_5p15.33' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

nPatients	T1	T2	T3	T4
ALL	480	127	258	15
DEL PEAK 11(5P15.33) MUTATED	7	11	13	0
DEL PEAK 11(5P15.33) WILD-TYPE	473	116	245	15

Figure S124. Get High-res Image Gene #20: 'del_5p15.33' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

'del_5p15.33' versus 'PATHOLOGY_N_STAGE'

P value = 0.00582 (Fisher's exact test), Q value = 0.02

Table S125. Gene #20: 'del_5p15.33' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

nPatients	N0	N1	N2
ALL	323	44	6
DEL PEAK 11(5P15.33) MUTATED	13	5	2
DEL PEAK 11(5P15.33) WILD-TYPE	310	39	4

Figure S125. Get High-res Image Gene #20: 'del_5p15.33' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

'del_5p15.33' versus 'KARNOFSKY_PERFORMANCE_SCORE'

P value = 0.0994 (Wilcoxon-test), Q value = 0.22

Table S126. Gene #20: 'del_5p15.33' versus Clinical Feature #9: 'KARNOFSKY_PERFORMANCE_SCORE'

	nPatients	Mean (Std.Dev)
ALL	143	87.7 (22.8)
DEL PEAK 11(5P15.33) MUTATED	6	70.0 (38.5)
DEL PEAK 11(5P15.33) WILD-TYPE	137	88.5 (21.7)

Figure S126. Get High-res Image Gene #20: 'del_5p15.33' versus Clinical Feature #9: 'KARNOFSKY_PERFORMANCE_SCORE'

'del_5p15.33' versus 'HISTOLOGICAL_TYPE'

P value = 1e-05 (Fisher's exact test), Q value = 7.2e-05

Table S127. Gene #20: 'del_5p15.33' versus Clinical Feature #10: 'HISTOLOGICAL_TYPE'

nPatients	KIDNEY CHROMOPHOBE	KIDNEY CLEAR CELL RENAL CARCINOMA	KIDNEY PAPILLARY RENAL CELL CARCINOMA
ALL	66	528	288
DEL PEAK 11(5P15.33) MUTATED	10	8	13
DEL PEAK 11(5P15.33) WILD-TYPE	56	520	275

Figure S127. Get High-res Image Gene #20: 'del_5p15.33' versus Clinical Feature #10: 'HISTOLOGICAL_TYPE'

'del_6q26' versus 'PATHOLOGIC_STAGE'

P value = 1e-05 (Fisher's exact test), Q value = 7.2e-05

Table S128. Gene #21: 'del_6q26' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

nPatients	STAGE I	STAGE II	STAGE III	STAGE IV
ALL	454	103	190	104
DEL PEAK 12(6Q26) MUTATED	93	43	58	35
DEL PEAK 12(6Q26) WILD-TYPE	361	60	132	69

Figure S128. Get High-res Image Gene #21: 'del_6q26' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

'del_6q26' versus 'PATHOLOGY_T_STAGE'

P value = 1e-05 (Fisher's exact test), Q value = 7.2e-05

Table S129. Gene #21: 'del_6q26' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

nPatients	T1	T2	T3	T4
ALL	480	127	258	15
DEL PEAK 12(6Q26) MUTATED	96	46	85	6
DEL PEAK 12(6Q26) WILD-TYPE	384	81	173	9

Figure S129. Get High-res Image Gene #21: 'del_6q26' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

'del_6q26' versus 'PATHOLOGY_N_STAGE'

P value = 0.0145 (Fisher's exact test), Q value = 0.044

Table S130. Gene #21: 'del_6q26' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

nPatients	N0	N1	N2
ALL	323	44	6
DEL PEAK 12(6Q26) MUTATED	94	16	5
DEL PEAK 12(6Q26) WILD-TYPE	229	28	1

Figure S130. Get High-res Image Gene #21: 'del_6q26' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

'del_6q26' versus 'HISTOLOGICAL_TYPE'

P value = 1e-05 (Fisher's exact test), Q value = 7.2e-05

Table S131. Gene #21: 'del_6q26' versus Clinical Feature #10: 'HISTOLOGICAL_TYPE'

nPatients	KIDNEY CHROMOPHOBE	KIDNEY CLEAR CELL RENAL CARCINOMA	KIDNEY PAPILLARY RENAL CELL CARCINOMA
ALL	66	528	288
DEL PEAK 12(6Q26) MUTATED	51	151	31
DEL PEAK 12(6Q26) WILD-TYPE	15	377	257

Figure S131. Get High-res Image Gene #21: 'del_6q26' versus Clinical Feature #10: 'HISTOLOGICAL_TYPE'

'del_6q26' versus 'NUMBER_PACK_YEARS_SMOKED'

P value = 0.103 (Wilcoxon-test), Q value = 0.23

Table S132. Gene #21: 'del_6q26' versus Clinical Feature #11: 'NUMBER_PACK_YEARS_SMOKED'

	nPatients	Mean (Std.Dev)
ALL	106	30.8 (24.9)
DEL PEAK 12(6Q26) MUTATED	23	25.0 (20.0)
DEL PEAK 12(6Q26) WILD-TYPE	83	32.4 (25.9)

Figure S132. Get High-res Image Gene #21: 'del_6q26' versus Clinical Feature #11: 'NUMBER_PACK_YEARS_SMOKED'

'del_6q26' versus 'RACE'

P value = 0.00084 (Fisher's exact test), Q value = 0.0037

Table S133. Gene #21: 'del_6q26' versus Clinical Feature #13: 'RACE'

nPatients	AMERICAN INDIAN OR ALASKA NATIVE	ASIAN	BLACK OR AFRICAN AMERICAN	WHITE
ALL	2	16	121	719
DEL PEAK 12(6Q26) MUTATED	0	6	16	203
DEL PEAK 12(6Q26) WILD-TYPE	2	10	105	516

Figure S133. Get High-res Image Gene #21: 'del_6q26' versus Clinical Feature #13: 'RACE'

'del_6q26' versus 'PATHOLOGIC_STAGE'

P value = 3e-05 (Fisher's exact test), Q value = 0.00018

Table S134. Gene #22: 'del_6q26' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

nPatients	STAGE I	STAGE II	STAGE III	STAGE IV
ALL	454	103	190	104
DEL PEAK 13(6Q26) MUTATED	94	43	58	35
DEL PEAK 13(6Q26) WILD-TYPE	360	60	132	69

Figure S134. Get High-res Image Gene #22: 'del_6q26' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

'del_6q26' versus 'PATHOLOGY_T_STAGE'

P value = 3e-05 (Fisher's exact test), Q value = 0.00018

Table S135. Gene #22: 'del_6q26' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

nPatients	T1	T2	T3	T4
ALL	480	127	258	15
DEL PEAK 13(6Q26) MUTATED	97	46	85	6
DEL PEAK 13(6Q26) WILD-TYPE	383	81	173	9

Figure S135. Get High-res Image Gene #22: 'del_6q26' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

'del_6q26' versus 'PATHOLOGY_N_STAGE'

P value = 0.0146 (Fisher's exact test), Q value = 0.044

Table S136. Gene #22: 'del_6q26' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

nPatients	N0	N1	N2
ALL	323	44	6
DEL PEAK 13(6Q26) MUTATED	94	16	5
DEL PEAK 13(6Q26) WILD-TYPE	229	28	1

Figure S136. Get High-res Image Gene #22: 'del_6q26' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

'del_6q26' versus 'HISTOLOGICAL_TYPE'

P value = 1e-05 (Fisher's exact test), Q value = 7.2e-05

Table S137. Gene #22: 'del_6q26' versus Clinical Feature #10: 'HISTOLOGICAL_TYPE'

nPatients	KIDNEY CHROMOPHOBE	KIDNEY CLEAR CELL RENAL CARCINOMA	KIDNEY PAPILLARY RENAL CELL CARCINOMA
ALL	66	528	288
DEL PEAK 13(6Q26) MUTATED	51	151	32
DEL PEAK 13(6Q26) WILD-TYPE	15	377	256

Figure S137. Get High-res Image Gene #22: 'del_6q26' versus Clinical Feature #10: 'HISTOLOGICAL_TYPE'

'del_6q26' versus 'NUMBER_PACK_YEARS_SMOKED'

P value = 0.103 (Wilcoxon-test), Q value = 0.23

Table S138. Gene #22: 'del_6q26' versus Clinical Feature #11: 'NUMBER_PACK_YEARS_SMOKED'

	nPatients	Mean (Std.Dev)
ALL	106	30.8 (24.9)
DEL PEAK 13(6Q26) MUTATED	23	25.0 (20.0)
DEL PEAK 13(6Q26) WILD-TYPE	83	32.4 (25.9)

Figure S138. Get High-res Image Gene #22: 'del_6q26' versus Clinical Feature #11: 'NUMBER_PACK_YEARS_SMOKED'

'del_6q26' versus 'RACE'

P value = 0.00217 (Fisher's exact test), Q value = 0.0084

Table S139. Gene #22: 'del_6q26' versus Clinical Feature #13: 'RACE'

nPatients	AMERICAN INDIAN OR ALASKA NATIVE	ASIAN	BLACK OR AFRICAN AMERICAN	WHITE
ALL	2	16	121	719
DEL PEAK 13(6Q26) MUTATED	0	6	17	203
DEL PEAK 13(6Q26) WILD-TYPE	2	10	104	516

Figure S139. Get High-res Image Gene #22: 'del_6q26' versus Clinical Feature #13: 'RACE'

'del_8p23.2' versus 'Time to Death'

P value = 0.00033 (logrank test), Q value = 0.0016

Table S140. Gene #23: 'del_8p23.2' versus Clinical Feature #1: 'Time to Death'

	nPatients	nDeath	Duration Range (Median), Month
ALL	876	228	0.1 - 194.8 (35.9)
DEL PEAK 14(8P23.2) MUTATED	184	69	0.1 - 137.1 (37.2)
DEL PEAK 14(8P23.2) WILD-TYPE	692	159	0.1 - 194.8 (34.7)

Figure S140. Get High-res Image Gene #23: 'del_8p23.2' versus Clinical Feature #1: 'Time to Death'

'del_8p23.2' versus 'PATHOLOGIC_STAGE'

P value = 0.00177 (Fisher's exact test), Q value = 0.0071

Table S141. Gene #23: 'del_8p23.2' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

nPatients	STAGE I	STAGE II	STAGE III	STAGE IV
ALL	454	103	190	104
DEL PEAK 14(8P23.2) MUTATED	74	25	46	33
DEL PEAK 14(8P23.2) WILD-TYPE	380	78	144	71

Figure S141. Get High-res Image Gene #23: 'del_8p23.2' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

'del_8p23.2' versus 'PATHOLOGY_T_STAGE'

P value = 0.00095 (Fisher's exact test), Q value = 0.0041

Table S142. Gene #23: 'del_8p23.2' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

nPatients	T1	T2	T3	T4
ALL	480	127	258	15
DEL PEAK 14(8P23.2) MUTATED	78	31	69	6
DEL PEAK 14(8P23.2) WILD-TYPE	402	96	189	9

Figure S142. Get High-res Image Gene #23: 'del_8p23.2' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

'del_8p23.2' versus 'PATHOLOGY_M_STAGE'

P value = 0.0189 (Fisher's exact test), Q value = 0.055

Table S143. Gene #23: 'del_8p23.2' versus Clinical Feature #6: 'PATHOLOGY_M_STAGE'

nPatients	0	1
ALL	546	89
DEL PEAK 14(8P23.2) MUTATED	131	32
DEL PEAK 14(8P23.2) WILD-TYPE	415	57

Figure S143. Get High-res Image Gene #23: 'del_8p23.2' versus Clinical Feature #6: 'PATHOLOGY_M_STAGE'

'del_8p23.2' versus 'HISTOLOGICAL_TYPE'

P value = 1e-05 (Fisher's exact test), Q value = 7.2e-05

Table S144. Gene #23: 'del_8p23.2' versus Clinical Feature #10: 'HISTOLOGICAL_TYPE'

nPatients	KIDNEY CHROMOPHOBE	KIDNEY CLEAR CELL RENAL CARCINOMA	KIDNEY PAPILLARY RENAL CELL CARCINOMA
ALL	66	528	288
DEL PEAK 14(8P23.2) MUTATED	12	154	18
DEL PEAK 14(8P23.2) WILD-TYPE	54	374	270

Figure S144. Get High-res Image Gene #23: 'del_8p23.2' versus Clinical Feature #10: 'HISTOLOGICAL_TYPE'

'del_8p23.2' versus 'RACE'

P value = 0.00365 (Fisher's exact test), Q value = 0.013

Table S145. Gene #23: 'del_8p23.2' versus Clinical Feature #13: 'RACE'

nPatients	AMERICAN INDIAN OR ALASKA NATIVE	ASIAN	BLACK OR AFRICAN AMERICAN	WHITE
ALL	2	16	121	719
DEL PEAK 14(8P23.2) MUTATED	0	7	14	160
DEL PEAK 14(8P23.2) WILD-TYPE	2	9	107	559

Figure S145. Get High-res Image Gene #23: 'del_8p23.2' versus Clinical Feature #13: 'RACE'

'del_9p23' versus 'Time to Death'

P value = 4.95e-13 (logrank test), Q value = 1.1e-10

Table S146. Gene #24: 'del_9p23' versus Clinical Feature #1: 'Time to Death'

	nPatients	nDeath	Duration Range (Median), Month
ALL	876	228	0.1 - 194.8 (35.9)
DEL PEAK 15(9P23) MUTATED	196	92	0.5 - 153.7 (36.1)
DEL PEAK 15(9P23) WILD-TYPE	680	136	0.1 - 194.8 (35.9)

Figure S146. Get High-res Image Gene #24: 'del_9p23' versus Clinical Feature #1: 'Time to Death'

'del_9p23' versus 'YEARS_TO_BIRTH'

P value = 0.0296 (Wilcoxon-test), Q value = 0.081

Table S147. Gene #24: 'del_9p23' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

	nPatients	Mean (Std.Dev)
ALL	876	60.1 (12.5)
DEL PEAK 15(9P23) MUTATED	196	61.8 (12.0)
DEL PEAK 15(9P23) WILD-TYPE	680	59.7 (12.6)

Figure S147. Get High-res Image Gene #24: 'del_9p23' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'del_9p23' versus 'PATHOLOGIC_STAGE'

P value = 1e-05 (Fisher's exact test), Q value = 7.2e-05

Table S148. Gene #24: 'del_9p23' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

nPatients	STAGE I	STAGE II	STAGE III	STAGE IV
ALL	454	103	190	104
DEL PEAK 15(9P23) MUTATED	63	16	68	46
DEL PEAK 15(9P23) WILD-TYPE	391	87	122	58

Figure S148. Get High-res Image Gene #24: 'del_9p23' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

'del_9p23' versus 'PATHOLOGY_T_STAGE'

P value = 1e-05 (Fisher's exact test), Q value = 7.2e-05

Table S149. Gene #24: 'del_9p23' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

nPatients	T1	T2	T3	T4
ALL	480	127	258	15
DEL PEAK 15(9P23) MUTATED	68	23	100	7
DEL PEAK 15(9P23) WILD-TYPE	412	104	158	8

Figure S149. Get High-res Image Gene #24: 'del_9p23' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

'del_9p23' versus 'PATHOLOGY_N_STAGE'

P value = 0.00204 (Fisher's exact test), Q value = 0.008

Table S150. Gene #24: 'del_9p23' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

nPatients	N0	N1	N2
ALL	323	44	6
DEL PEAK 15(9P23) MUTATED	73	20	3
DEL PEAK 15(9P23) WILD-TYPE	250	24	3

Figure S150. Get High-res Image Gene #24: 'del_9p23' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

'del_9p23' versus 'PATHOLOGY_M_STAGE'

P value = 0.000211 (Fisher's exact test), Q value = 0.0011

Table S151. Gene #24: 'del_9p23' versus Clinical Feature #6: 'PATHOLOGY_M_STAGE'

nPatients	0	1
ALL	546	89
DEL PEAK 15(9P23) MUTATED	126	38
DEL PEAK 15(9P23) WILD-TYPE	420	51

Figure S151. Get High-res Image Gene #24: 'del_9p23' versus Clinical Feature #6: 'PATHOLOGY_M_STAGE'

'del_9p23' versus 'KARNOFSKY_PERFORMANCE_SCORE'

P value = 0.000567 (Wilcoxon-test), Q value = 0.0026

Table S152. Gene #24: 'del_9p23' versus Clinical Feature #9: 'KARNOFSKY_PERFORMANCE_SCORE'

	nPatients	Mean (Std.Dev)
ALL	143	87.7 (22.8)
DEL PEAK 15(9P23) MUTATED	29	74.1 (34.3)
DEL PEAK 15(9P23) WILD-TYPE	114	91.1 (17.3)

Figure S152. Get High-res Image Gene #24: 'del_9p23' versus Clinical Feature #9: 'KARNOFSKY_PERFORMANCE_SCORE'

'del_9p23' versus 'HISTOLOGICAL_TYPE'

P value = 1e-05 (Fisher's exact test), Q value = 7.2e-05

Table S153. Gene #24: 'del_9p23' versus Clinical Feature #10: 'HISTOLOGICAL_TYPE'

nPatients	KIDNEY CHROMOPHOBE	KIDNEY CLEAR CELL RENAL CARCINOMA	KIDNEY PAPILLARY RENAL CELL CARCINOMA
ALL	66	528	288
DEL PEAK 15(9P23) MUTATED	10	152	36
DEL PEAK 15(9P23) WILD-TYPE	56	376	252

Figure S153. Get High-res Image Gene #24: 'del_9p23' versus Clinical Feature #10: 'HISTOLOGICAL_TYPE'

'del_9p23' versus 'RACE'

P value = 0.0201 (Fisher's exact test), Q value = 0.057

Table S154. Gene #24: 'del_9p23' versus Clinical Feature #13: 'RACE'

nPatients	AMERICAN INDIAN OR ALASKA NATIVE	ASIAN	BLACK OR AFRICAN AMERICAN	WHITE
ALL	2	16	121	719
DEL PEAK 15(9P23) MUTATED	0	4	15	173
DEL PEAK 15(9P23) WILD-TYPE	2	12	106	546

Figure S154. Get High-res Image Gene #24: 'del_9p23' versus Clinical Feature #13: 'RACE'

'del_9p21.3' versus 'Time to Death'

P value = 5.55e-16 (logrank test), Q value = 2.5e-13

Table S155. Gene #25: 'del_9p21.3' versus Clinical Feature #1: 'Time to Death'

	nPatients	nDeath	Duration Range (Median), Month
ALL	876	228	0.1 - 194.8 (35.9)
DEL PEAK 16(9P21.3) MUTATED	206	99	0.5 - 153.7 (31.8)
DEL PEAK 16(9P21.3) WILD-TYPE	670	129	0.1 - 194.8 (36.5)

Figure S155. Get High-res Image Gene #25: 'del_9p21.3' versus Clinical Feature #1: 'Time to Death'

'del_9p21.3' versus 'YEARS_TO_BIRTH'

P value = 0.0319 (Wilcoxon-test), Q value = 0.086

Table S156. Gene #25: 'del_9p21.3' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

	nPatients	Mean (Std.Dev)
ALL	876	60.1 (12.5)
DEL PEAK 16(9P21.3) MUTATED	207	61.6 (12.2)
DEL PEAK 16(9P21.3) WILD-TYPE	669	59.7 (12.6)

Figure S156. Get High-res Image Gene #25: 'del_9p21.3' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'del_9p21.3' versus 'PATHOLOGIC_STAGE'

P value = 1e-05 (Fisher's exact test), Q value = 7.2e-05

Table S157. Gene #25: 'del_9p21.3' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

nPatients	STAGE I	STAGE II	STAGE III	STAGE IV
ALL	454	103	190	104
DEL PEAK 16(9P21.3) MUTATED	66	15	73	50
DEL PEAK 16(9P21.3) WILD-TYPE	388	88	117	54

Figure S157. Get High-res Image Gene #25: 'del_9p21.3' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

'del_9p21.3' versus 'PATHOLOGY_T_STAGE'

P value = 1e-05 (Fisher's exact test), Q value = 7.2e-05

Table S158. Gene #25: 'del_9p21.3' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

nPatients	T1	T2	T3	T4
ALL	480	127	258	15
DEL PEAK 16(9P21.3) MUTATED	71	22	108	8
DEL PEAK 16(9P21.3) WILD-TYPE	409	105	150	7

Figure S158. Get High-res Image Gene #25: 'del_9p21.3' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

'del_9p21.3' versus 'PATHOLOGY_N_STAGE'

P value = 2e-05 (Fisher's exact test), Q value = 0.00013

Table S159. Gene #25: 'del_9p21.3' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

nPatients	N0	N1	N2
ALL	323	44	6
DEL PEAK 16(9P21.3) MUTATED	79	25	3
DEL PEAK 16(9P21.3) WILD-TYPE	244	19	3

Figure S159. Get High-res Image Gene #25: 'del_9p21.3' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

'del_9p21.3' versus 'PATHOLOGY_M_STAGE'

P value = 9.3e-06 (Fisher's exact test), Q value = 7.2e-05

Table S160. Gene #25: 'del_9p21.3' versus Clinical Feature #6: 'PATHOLOGY_M_STAGE'

nPatients	0	1
ALL	546	89
DEL PEAK 16(9P21.3) MUTATED	132	43
DEL PEAK 16(9P21.3) WILD-TYPE	414	46

Figure S160. Get High-res Image Gene #25: 'del_9p21.3' versus Clinical Feature #6: 'PATHOLOGY_M_STAGE'

'del_9p21.3' versus 'KARNOFSKY_PERFORMANCE_SCORE'

P value = 0.00135 (Wilcoxon-test), Q value = 0.0055

Table S161. Gene #25: 'del_9p21.3' versus Clinical Feature #9: 'KARNOFSKY_PERFORMANCE_SCORE'

	nPatients	Mean (Std.Dev)
ALL	143	87.7 (22.8)
DEL PEAK 16(9P21.3) MUTATED	30	75.0 (34.0)
DEL PEAK 16(9P21.3) WILD-TYPE	113	91.1 (17.4)

Figure S161. Get High-res Image Gene #25: 'del_9p21.3' versus Clinical Feature #9: 'KARNOFSKY_PERFORMANCE_SCORE'

'del_9p21.3' versus 'HISTOLOGICAL_TYPE'

P value = 1e-05 (Fisher's exact test), Q value = 7.2e-05

Table S162. Gene #25: 'del_9p21.3' versus Clinical Feature #10: 'HISTOLOGICAL_TYPE'

nPatients	KIDNEY CHROMOPHOBE	KIDNEY CLEAR CELL RENAL CARCINOMA	KIDNEY PAPILLARY RENAL CELL CARCINOMA
ALL	66	528	288
DEL PEAK 16(9P21.3) MUTATED	10	159	40
DEL PEAK 16(9P21.3) WILD-TYPE	56	369	248

Figure S162. Get High-res Image Gene #25: 'del_9p21.3' versus Clinical Feature #10: 'HISTOLOGICAL_TYPE'

'del_9p21.3' versus 'RACE'

P value = 0.00591 (Fisher's exact test), Q value = 0.02

Table S163. Gene #25: 'del_9p21.3' versus Clinical Feature #13: 'RACE'

nPatients	AMERICAN INDIAN OR ALASKA NATIVE	ASIAN	BLACK OR AFRICAN AMERICAN	WHITE
ALL	2	16	121	719
DEL PEAK 16(9P21.3) MUTATED	0	4	15	185
DEL PEAK 16(9P21.3) WILD-TYPE	2	12	106	534

Figure S163. Get High-res Image Gene #25: 'del_9p21.3' versus Clinical Feature #13: 'RACE'

'del_10q23.31' versus 'YEARS_TO_BIRTH'

P value = 0.0732 (Wilcoxon-test), Q value = 0.17

Table S164. Gene #26: 'del_10q23.31' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

	nPatients	Mean (Std.Dev)
ALL	876	60.1 (12.5)
DEL PEAK 17(10Q23.31) MUTATED	162	58.3 (14.1)
DEL PEAK 17(10Q23.31) WILD-TYPE	714	60.6 (12.1)

Figure S164. Get High-res Image Gene #26: 'del_10q23.31' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'del_10q23.31' versus 'PATHOLOGIC_STAGE'

P value = 1e-05 (Fisher's exact test), Q value = 7.2e-05

Table S165. Gene #26: 'del_10q23.31' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

nPatients	STAGE I	STAGE II	STAGE III	STAGE IV
ALL	454	103	190	104
DEL PEAK 17(10Q23.31) MUTATED	52	32	53	26
DEL PEAK 17(10Q23.31) WILD-TYPE	402	71	137	78

Figure S165. Get High-res Image Gene #26: 'del_10q23.31' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

'del_10q23.31' versus 'PATHOLOGY_T_STAGE'

P value = 1e-05 (Fisher's exact test), Q value = 7.2e-05

Table S166. Gene #26: 'del_10q23.31' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

nPatients	T1	T2	T3	T4
ALL	480	127	258	15
DEL PEAK 17(10Q23.31) MUTATED	54	33	70	7
DEL PEAK 17(10Q23.31) WILD-TYPE	426	94	188	8

Figure S166. Get High-res Image Gene #26: 'del_10q23.31' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

'del_10q23.31' versus 'HISTOLOGICAL_TYPE'

P value = 1e-05 (Fisher's exact test), Q value = 7.2e-05

Table S167. Gene #26: 'del_10q23.31' versus Clinical Feature #10: 'HISTOLOGICAL_TYPE'

nPatients	KIDNEY CHROMOPHOBE	KIDNEY CLEAR CELL RENAL CARCINOMA	KIDNEY PAPILLARY RENAL CELL CARCINOMA
ALL	66	528	288
DEL PEAK 17(10Q23.31) MUTATED	49	96	19
DEL PEAK 17(10Q23.31) WILD-TYPE	17	432	269

Figure S167. Get High-res Image Gene #26: 'del_10q23.31' versus Clinical Feature #10: 'HISTOLOGICAL_TYPE'

'del_10q23.31' versus 'NUMBER_PACK_YEARS_SMOKED'

P value = 0.068 (Wilcoxon-test), Q value = 0.16

Table S168. Gene #26: 'del_10q23.31' versus Clinical Feature #11: 'NUMBER_PACK_YEARS_SMOKED'

	nPatients	Mean (Std.Dev)
ALL	106	30.8 (24.9)
DEL PEAK 17(10Q23.31) MUTATED	17	23.5 (20.3)
DEL PEAK 17(10Q23.31) WILD-TYPE	89	32.2 (25.5)

Figure S168. Get High-res Image Gene #26: 'del_10q23.31' versus Clinical Feature #11: 'NUMBER_PACK_YEARS_SMOKED'

'del_10q23.31' versus 'RACE'

P value = 0.0772 (Fisher's exact test), Q value = 0.18

Table S169. Gene #26: 'del_10q23.31' versus Clinical Feature #13: 'RACE'

nPatients	AMERICAN INDIAN OR ALASKA NATIVE	ASIAN	BLACK OR AFRICAN AMERICAN	WHITE
ALL	2	16	121	719
DEL PEAK 17(10Q23.31) MUTATED	0	4	13	141
DEL PEAK 17(10Q23.31) WILD-TYPE	2	12	108	578

Figure S169. Get High-res Image Gene #26: 'del_10q23.31' versus Clinical Feature #13: 'RACE'

'del_11q23.1' versus 'Time to Death'

P value = 0.000445 (logrank test), Q value = 0.0021

Table S170. Gene #27: 'del_11q23.1' versus Clinical Feature #1: 'Time to Death'

	nPatients	nDeath	Duration Range (Median), Month
ALL	876	228	0.1 - 194.8 (35.9)
DEL PEAK 18(11Q23.1) MUTATED	70	28	0.4 - 123.6 (21.6)
DEL PEAK 18(11Q23.1) WILD-TYPE	806	200	0.1 - 194.8 (36.8)

Figure S170. Get High-res Image Gene #27: 'del_11q23.1' versus Clinical Feature #1: 'Time to Death'

'del_11q23.1' versus 'YEARS_TO_BIRTH'

P value = 0.00352 (Wilcoxon-test), Q value = 0.013

Table S171. Gene #27: 'del_11q23.1' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

	nPatients	Mean (Std.Dev)
ALL	876	60.1 (12.5)
DEL PEAK 18(11Q23.1) MUTATED	70	64.0 (10.9)
DEL PEAK 18(11Q23.1) WILD-TYPE	806	59.8 (12.6)

Figure S171. Get High-res Image Gene #27: 'del_11q23.1' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'del_11q23.1' versus 'PATHOLOGIC_STAGE'

P value = 2e-05 (Fisher's exact test), Q value = 0.00013

Table S172. Gene #27: 'del_11q23.1' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

nPatients	STAGE I	STAGE II	STAGE III	STAGE IV
ALL	454	103	190	104
DEL PEAK 18(11Q23.1) MUTATED	18	13	23	16
DEL PEAK 18(11Q23.1) WILD-TYPE	436	90	167	88

Figure S172. Get High-res Image Gene #27: 'del_11q23.1' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

'del_11q23.1' versus 'PATHOLOGY_T_STAGE'

P value = 1e-05 (Fisher's exact test), Q value = 7.2e-05

Table S173. Gene #27: 'del_11q23.1' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

nPatients	T1	T2	T3	T4
ALL	480	127	258	15
DEL PEAK 18(11Q23.1) MUTATED	19	15	34	3
DEL PEAK 18(11Q23.1) WILD-TYPE	461	112	224	12

Figure S173. Get High-res Image Gene #27: 'del_11q23.1' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

'del_11q23.1' versus 'PATHOLOGY_N_STAGE'

P value = 3e-05 (Fisher's exact test), Q value = 0.00018

Table S174. Gene #27: 'del_11q23.1' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

nPatients	N0	N1	N2
ALL	323	44	6
DEL PEAK 18(11Q23.1) MUTATED	24	12	3
DEL PEAK 18(11Q23.1) WILD-TYPE	299	32	3

Figure S174. Get High-res Image Gene #27: 'del_11q23.1' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

'del_11q23.1' versus 'PATHOLOGY_M_STAGE'

P value = 0.111 (Fisher's exact test), Q value = 0.24

Table S175. Gene #27: 'del_11q23.1' versus Clinical Feature #6: 'PATHOLOGY_M_STAGE'

nPatients	0	1
ALL	546	89
DEL PEAK 18(11Q23.1) MUTATED	34	10
DEL PEAK 18(11Q23.1) WILD-TYPE	512	79

Figure S175. Get High-res Image Gene #27: 'del_11q23.1' versus Clinical Feature #6: 'PATHOLOGY_M_STAGE'

'del_11q23.1' versus 'KARNOFSKY_PERFORMANCE_SCORE'

P value = 0.0934 (Wilcoxon-test), Q value = 0.21

Table S176. Gene #27: 'del_11q23.1' versus Clinical Feature #9: 'KARNOFSKY_PERFORMANCE_SCORE'

	nPatients	Mean (Std.Dev)
ALL	143	87.7 (22.8)
DEL PEAK 18(11Q23.1) MUTATED	16	82.5 (25.4)
DEL PEAK 18(11Q23.1) WILD-TYPE	127	88.3 (22.4)

Figure S176. Get High-res Image Gene #27: 'del_11q23.1' versus Clinical Feature #9: 'KARNOFSKY_PERFORMANCE_SCORE'

'del_11q23.1' versus 'HISTOLOGICAL_TYPE'

P value = 0.00456 (Fisher's exact test), Q value = 0.016

Table S177. Gene #27: 'del_11q23.1' versus Clinical Feature #10: 'HISTOLOGICAL_TYPE'

nPatients	KIDNEY CHROMOPHOBE	KIDNEY CLEAR CELL RENAL CARCINOMA	KIDNEY PAPILLARY RENAL CELL CARCINOMA
ALL	66	528	288
DEL PEAK 18(11Q23.1) MUTATED	9	30	32
DEL PEAK 18(11Q23.1) WILD-TYPE	57	498	256

Figure S177. Get High-res Image Gene #27: 'del_11q23.1' versus Clinical Feature #10: 'HISTOLOGICAL_TYPE'

'del_13q13.2' versus 'Time to Death'

P value = 0.0145 (logrank test), Q value = 0.044

Table S178. Gene #28: 'del_13q13.2' versus Clinical Feature #1: 'Time to Death'

	nPatients	nDeath	Duration Range (Median), Month
ALL	876	228	0.1 - 194.8 (35.9)
DEL PEAK 19(13Q13.2) MUTATED	147	55	0.2 - 153.7 (37.1)
DEL PEAK 19(13Q13.2) WILD-TYPE	729	173	0.1 - 194.8 (35.2)

Figure S178. Get High-res Image Gene #28: 'del_13q13.2' versus Clinical Feature #1: 'Time to Death'

'del_13q13.2' versus 'YEARS_TO_BIRTH'

P value = 5.17e-05 (Wilcoxon-test), Q value = 3e-04

Table S179. Gene #28: 'del_13q13.2' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

	nPatients	Mean (Std.Dev)
ALL	876	60.1 (12.5)
DEL PEAK 19(13Q13.2) MUTATED	149	55.7 (14.9)
DEL PEAK 19(13Q13.2) WILD-TYPE	727	61.1 (11.8)

Figure S179. Get High-res Image Gene #28: 'del_13q13.2' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'del_13q13.2' versus 'PATHOLOGIC_STAGE'

P value = 1e-05 (Fisher's exact test), Q value = 7.2e-05

Table S180. Gene #28: 'del_13q13.2' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

nPatients	STAGE I	STAGE II	STAGE III	STAGE IV
ALL	454	103	190	104
DEL PEAK 19(13Q13.2) MUTATED	46	23	49	29
DEL PEAK 19(13Q13.2) WILD-TYPE	408	80	141	75

Figure S180. Get High-res Image Gene #28: 'del_13q13.2' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

'del_13q13.2' versus 'PATHOLOGY_T_STAGE'

P value = 1e-05 (Fisher's exact test), Q value = 7.2e-05

Table S181. Gene #28: 'del_13q13.2' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

nPatients	T1	T2	T3	T4
ALL	480	127	258	15
DEL PEAK 19(13Q13.2) MUTATED	48	25	68	8
DEL PEAK 19(13Q13.2) WILD-TYPE	432	102	190	7

Figure S181. Get High-res Image Gene #28: 'del_13q13.2' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

'del_13q13.2' versus 'PATHOLOGY_N_STAGE'

P value = 0.00122 (Fisher's exact test), Q value = 0.005

Table S182. Gene #28: 'del_13q13.2' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

nPatients	N0	N1	N2
ALL	323	44	6
DEL PEAK 19(13Q13.2) MUTATED	68	14	5
DEL PEAK 19(13Q13.2) WILD-TYPE	255	30	1

Figure S182. Get High-res Image Gene #28: 'del_13q13.2' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

'del_13q13.2' versus 'GENDER'

P value = 0.00404 (Fisher's exact test), Q value = 0.014

Table S183. Gene #28: 'del_13q13.2' versus Clinical Feature #7: 'GENDER'

nPatients	FEMALE	MALE
ALL	292	590
DEL PEAK 19(13Q13.2) MUTATED	65	84
DEL PEAK 19(13Q13.2) WILD-TYPE	227	506

Figure S183. Get High-res Image Gene #28: 'del_13q13.2' versus Clinical Feature #7: 'GENDER'

'del_13q13.2' versus 'HISTOLOGICAL_TYPE'

P value = 1e-05 (Fisher's exact test), Q value = 7.2e-05

Table S184. Gene #28: 'del_13q13.2' versus Clinical Feature #10: 'HISTOLOGICAL_TYPE'

nPatients	KIDNEY CHROMOPHOBE	KIDNEY CLEAR CELL RENAL CARCINOMA	KIDNEY PAPILLARY RENAL CELL CARCINOMA
ALL	66	528	288
DEL PEAK 19(13Q13.2) MUTATED	44	80	25
DEL PEAK 19(13Q13.2) WILD-TYPE	22	448	263

Figure S184. Get High-res Image Gene #28: 'del_13q13.2' versus Clinical Feature #10: 'HISTOLOGICAL_TYPE'

'del_13q13.2' versus 'RACE'

P value = 0.0963 (Fisher's exact test), Q value = 0.22

Table S185. Gene #28: 'del_13q13.2' versus Clinical Feature #13: 'RACE'

nPatients	AMERICAN INDIAN OR ALASKA NATIVE	ASIAN	BLACK OR AFRICAN AMERICAN	WHITE
ALL	2	16	121	719
DEL PEAK 19(13Q13.2) MUTATED	0	4	12	128
DEL PEAK 19(13Q13.2) WILD-TYPE	2	12	109	591

Figure S185. Get High-res Image Gene #28: 'del_13q13.2' versus Clinical Feature #13: 'RACE'

'del_14q31.1' versus 'Time to Death'

P value = 5.96e-10 (logrank test), Q value = 5.3e-08

Table S186. Gene #29: 'del_14q31.1' versus Clinical Feature #1: 'Time to Death'

	nPatients	nDeath	Duration Range (Median), Month
ALL	876	228	0.1 - 194.8 (35.9)
DEL PEAK 20(14Q31.1) MUTATED	278	112	0.1 - 133.7 (33.1)
DEL PEAK 20(14Q31.1) WILD-TYPE	598	116	0.1 - 194.8 (37.1)

Figure S186. Get High-res Image Gene #29: 'del_14q31.1' versus Clinical Feature #1: 'Time to Death'

'del_14q31.1' versus 'PATHOLOGIC_STAGE'

P value = 1e-05 (Fisher's exact test), Q value = 7.2e-05

Table S187. Gene #29: 'del_14q31.1' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

nPatients	STAGE I	STAGE II	STAGE III	STAGE IV
ALL	454	103	190	104
DEL PEAK 20(14Q31.1) MUTATED	103	31	81	56
DEL PEAK 20(14Q31.1) WILD-TYPE	351	72	109	48

Figure S187. Get High-res Image Gene #29: 'del_14q31.1' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

'del_14q31.1' versus 'PATHOLOGY_T_STAGE'

P value = 1e-05 (Fisher's exact test), Q value = 7.2e-05

Table S188. Gene #29: 'del_14q31.1' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

nPatients	T1	T2	T3	T4
ALL	480	127	258	15
DEL PEAK 20(14Q31.1) MUTATED	111	41	122	5
DEL PEAK 20(14Q31.1) WILD-TYPE	369	86	136	10

Figure S188. Get High-res Image Gene #29: 'del_14q31.1' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

'del_14q31.1' versus 'PATHOLOGY_N_STAGE'

P value = 0.00404 (Fisher's exact test), Q value = 0.014

Table S189. Gene #29: 'del_14q31.1' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

nPatients	N0	N1	N2
ALL	323	44	6
DEL PEAK 20(14Q31.1) MUTATED	110	25	4
DEL PEAK 20(14Q31.1) WILD-TYPE	213	19	2

Figure S189. Get High-res Image Gene #29: 'del_14q31.1' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

'del_14q31.1' versus 'PATHOLOGY_M_STAGE'

P value = 4.66e-05 (Fisher's exact test), Q value = 0.00027

Table S190. Gene #29: 'del_14q31.1' versus Clinical Feature #6: 'PATHOLOGY_M_STAGE'

nPatients	0	1
ALL	546	89
DEL PEAK 20(14Q31.1) MUTATED	185	51
DEL PEAK 20(14Q31.1) WILD-TYPE	361	38

Figure S190. Get High-res Image Gene #29: 'del_14q31.1' versus Clinical Feature #6: 'PATHOLOGY_M_STAGE'

'del_14q31.1' versus 'RADIATION_THERAPY'

P value = 0.115 (Fisher's exact test), Q value = 0.24

Table S191. Gene #29: 'del_14q31.1' versus Clinical Feature #8: 'RADIATION_THERAPY'

nPatients	NO	YES
ALL	408	3
DEL PEAK 20(14Q31.1) MUTATED	85	2
DEL PEAK 20(14Q31.1) WILD-TYPE	323	1

Figure S191. Get High-res Image Gene #29: 'del_14q31.1' versus Clinical Feature #8: 'RADIATION_THERAPY'

'del_14q31.1' versus 'KARNOFSKY_PERFORMANCE_SCORE'

P value = 0.000159 (Wilcoxon-test), Q value = 0.00084

Table S192. Gene #29: 'del_14q31.1' versus Clinical Feature #9: 'KARNOFSKY_PERFORMANCE_SCORE'

	nPatients	Mean (Std.Dev)
ALL	143	87.7 (22.8)
DEL PEAK 20(14Q31.1) MUTATED	36	71.9 (36.3)
DEL PEAK 20(14Q31.1) WILD-TYPE	107	93.0 (12.1)

Figure S192. Get High-res Image Gene #29: 'del_14q31.1' versus Clinical Feature #9: 'KARNOFSKY_PERFORMANCE_SCORE'

'del_14q31.1' versus 'HISTOLOGICAL_TYPE'

P value = 1e-05 (Fisher's exact test), Q value = 7.2e-05

Table S193. Gene #29: 'del_14q31.1' versus Clinical Feature #10: 'HISTOLOGICAL_TYPE'

nPatients	KIDNEY CHROMOPHOBE	KIDNEY CLEAR CELL RENAL CARCINOMA	KIDNEY PAPILLARY RENAL CELL CARCINOMA
ALL	66	528	288
DEL PEAK 20(14Q31.1) MUTATED	3	228	48
DEL PEAK 20(14Q31.1) WILD-TYPE	63	300	240

Figure S193. Get High-res Image Gene #29: 'del_14q31.1' versus Clinical Feature #10: 'HISTOLOGICAL_TYPE'

'del_14q31.1' versus 'YEAR_OF_TOBACCO_SMOKING_ONSET'

P value = 0.00978 (Wilcoxon-test), Q value = 0.032

Table S194. Gene #29: 'del_14q31.1' versus Clinical Feature #12: 'YEAR_OF_TOBACCO_SMOKING_ONSET'

	nPatients	Mean (Std.Dev)
ALL	74	1973.7 (16.0)
DEL PEAK 20(14Q31.1) MUTATED	15	1983.5 (14.8)
DEL PEAK 20(14Q31.1) WILD-TYPE	59	1971.2 (15.4)

Figure S194. Get High-res Image Gene #29: 'del_14q31.1' versus Clinical Feature #12: 'YEAR_OF_TOBACCO_SMOKING_ONSET'

'del_14q31.1' versus 'RACE'

P value = 0.0174 (Fisher's exact test), Q value = 0.051

Table S195. Gene #29: 'del_14q31.1' versus Clinical Feature #13: 'RACE'

nPatients	AMERICAN INDIAN OR ALASKA NATIVE	ASIAN	BLACK OR AFRICAN AMERICAN	WHITE
ALL	2	16	121	719
DEL PEAK 20(14Q31.1) MUTATED	0	3	26	243
DEL PEAK 20(14Q31.1) WILD-TYPE	2	13	95	476

Figure S195. Get High-res Image Gene #29: 'del_14q31.1' versus Clinical Feature #13: 'RACE'

'del_16q23.3' versus 'Time to Death'

P value = 4.66e-05 (logrank test), Q value = 0.00027

Table S196. Gene #30: 'del_16q23.3' versus Clinical Feature #1: 'Time to Death'

	nPatients	nDeath	Duration Range (Median), Month
ALL	876	228	0.1 - 194.8 (35.9)
DEL PEAK 21(16Q23.3) MUTATED	37	18	0.1 - 90.5 (30.2)
DEL PEAK 21(16Q23.3) WILD-TYPE	839	210	0.1 - 194.8 (36.4)

Figure S196. Get High-res Image Gene #30: 'del_16q23.3' versus Clinical Feature #1: 'Time to Death'

'del_16q23.3' versus 'PATHOLOGIC_STAGE'

P value = 0.00505 (Fisher's exact test), Q value = 0.017

Table S197. Gene #30: 'del_16q23.3' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

nPatients	STAGE I	STAGE II	STAGE III	STAGE IV
ALL	454	103	190	104
DEL PEAK 21(16Q23.3) MUTATED	11	4	12	10
DEL PEAK 21(16Q23.3) WILD-TYPE	443	99	178	94

Figure S197. Get High-res Image Gene #30: 'del_16q23.3' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

'del_16q23.3' versus 'PATHOLOGY_T_STAGE'

P value = 5e-05 (Fisher's exact test), Q value = 0.00029

Table S198. Gene #30: 'del_16q23.3' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

nPatients	T1	T2	T3	T4
ALL	480	127	258	15
DEL PEAK 21(16Q23.3) MUTATED	12	4	16	5
DEL PEAK 21(16Q23.3) WILD-TYPE	468	123	242	10

Figure S198. Get High-res Image Gene #30: 'del_16q23.3' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

'del_16q23.3' versus 'PATHOLOGY_N_STAGE'

P value = 0.00059 (Fisher's exact test), Q value = 0.0026

Table S199. Gene #30: 'del_16q23.3' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

nPatients	N0	N1	N2
ALL	323	44	6
DEL PEAK 21(16Q23.3) MUTATED	13	7	2
DEL PEAK 21(16Q23.3) WILD-TYPE	310	37	4

Figure S199. Get High-res Image Gene #30: 'del_16q23.3' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

'del_19p13.3' versus 'Time to Death'

P value = 5.05e-12 (logrank test), Q value = 7.5e-10

Table S200. Gene #31: 'del_19p13.3' versus Clinical Feature #1: 'Time to Death'

	nPatients	nDeath	Duration Range (Median), Month
ALL	876	228	0.1 - 194.8 (35.9)
DEL PEAK 22(19P13.3) MUTATED	43	24	0.9 - 109.9 (18.2)
DEL PEAK 22(19P13.3) WILD-TYPE	833	204	0.1 - 194.8 (37.0)

Figure S200. Get High-res Image Gene #31: 'del_19p13.3' versus Clinical Feature #1: 'Time to Death'

'del_19p13.3' versus 'PATHOLOGIC_STAGE'

P value = 2e-05 (Fisher's exact test), Q value = 0.00013

Table S201. Gene #31: 'del_19p13.3' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

nPatients	STAGE I	STAGE II	STAGE III	STAGE IV
ALL	454	103	190	104
DEL PEAK 22(19P13.3) MUTATED	10	1	18	11
DEL PEAK 22(19P13.3) WILD-TYPE	444	102	172	93

Figure S201. Get High-res Image Gene #31: 'del_19p13.3' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

'del_19p13.3' versus 'PATHOLOGY_T_STAGE'

P value = 1e-05 (Fisher's exact test), Q value = 7.2e-05

Table S202. Gene #31: 'del_19p13.3' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

nPatients	T1	T2	T3	T4
ALL	480	127	258	15
DEL PEAK 22(19P13.3) MUTATED	12	2	25	4
DEL PEAK 22(19P13.3) WILD-TYPE	468	125	233	11

Figure S202. Get High-res Image Gene #31: 'del_19p13.3' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

'del_19p13.3' versus 'PATHOLOGY_N_STAGE'

P value = 6e-05 (Fisher's exact test), Q value = 0.00034

Table S203. Gene #31: 'del_19p13.3' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

nPatients	N0	N1	N2
ALL	323	44	6
DEL PEAK 22(19P13.3) MUTATED	11	7	3
DEL PEAK 22(19P13.3) WILD-TYPE	312	37	3

Figure S203. Get High-res Image Gene #31: 'del_19p13.3' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

'del_19p13.3' versus 'PATHOLOGY_M_STAGE'

P value = 0.0688 (Fisher's exact test), Q value = 0.16

Table S204. Gene #31: 'del_19p13.3' versus Clinical Feature #6: 'PATHOLOGY_M_STAGE'

nPatients	0	1
ALL	546	89
DEL PEAK 22(19P13.3) MUTATED	18	7
DEL PEAK 22(19P13.3) WILD-TYPE	528	82

Figure S204. Get High-res Image Gene #31: 'del_19p13.3' versus Clinical Feature #6: 'PATHOLOGY_M_STAGE'

'del_19p13.3' versus 'KARNOFSKY_PERFORMANCE_SCORE'

P value = 0.00517 (Wilcoxon-test), Q value = 0.018

Table S205. Gene #31: 'del_19p13.3' versus Clinical Feature #9: 'KARNOFSKY_PERFORMANCE_SCORE'

	nPatients	Mean (Std.Dev)
ALL	143	87.7 (22.8)
DEL PEAK 22(19P13.3) MUTATED	12	67.5 (39.3)
DEL PEAK 22(19P13.3) WILD-TYPE	131	89.5 (19.8)

Figure S205. Get High-res Image Gene #31: 'del_19p13.3' versus Clinical Feature #9: 'KARNOFSKY_PERFORMANCE_SCORE'

'del_19p13.3' versus 'HISTOLOGICAL_TYPE'

P value = 0.0108 (Fisher's exact test), Q value = 0.034

Table S206. Gene #31: 'del_19p13.3' versus Clinical Feature #10: 'HISTOLOGICAL_TYPE'

nPatients	KIDNEY CHROMOPHOBE	KIDNEY CLEAR CELL RENAL CARCINOMA	KIDNEY PAPILLARY RENAL CELL CARCINOMA
ALL	66	528	288
DEL PEAK 22(19P13.3) MUTATED	3	17	23
DEL PEAK 22(19P13.3) WILD-TYPE	63	511	265

Figure S206. Get High-res Image Gene #31: 'del_19p13.3' versus Clinical Feature #10: 'HISTOLOGICAL_TYPE'

'del_xp22.2' versus 'YEARS_TO_BIRTH'

P value = 0.00226 (Wilcoxon-test), Q value = 0.0087

Table S207. Gene #32: 'del_xp22.2' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

	nPatients	Mean (Std.Dev)
ALL	876	60.1 (12.5)
DEL PEAK 23(XP22.2) MUTATED	125	56.4 (13.9)
DEL PEAK 23(XP22.2) WILD-TYPE	751	60.8 (12.2)

Figure S207. Get High-res Image Gene #32: 'del_xp22.2' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'del_xp22.2' versus 'PATHOLOGIC_STAGE'

P value = 9e-05 (Fisher's exact test), Q value = 0.00049

Table S208. Gene #32: 'del_xp22.2' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

nPatients	STAGE I	STAGE II	STAGE III	STAGE IV
ALL	454	103	190	104
DEL PEAK 23(XP22.2) MUTATED	41	23	39	15
DEL PEAK 23(XP22.2) WILD-TYPE	413	80	151	89

Figure S208. Get High-res Image Gene #32: 'del_xp22.2' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

'del_xp22.2' versus 'PATHOLOGY_T_STAGE'

P value = 4e-05 (Fisher's exact test), Q value = 0.00024

Table S209. Gene #32: 'del_xp22.2' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

nPatients	T1	T2	T3	T4
ALL	480	127	258	15
DEL PEAK 23(XP22.2) MUTATED	45	26	51	3
DEL PEAK 23(XP22.2) WILD-TYPE	435	101	207	12

Figure S209. Get High-res Image Gene #32: 'del_xp22.2' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

'del_xp22.2' versus 'PATHOLOGY_N_STAGE'

P value = 0.0419 (Fisher's exact test), Q value = 0.11

Table S210. Gene #32: 'del_xp22.2' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

nPatients	N0	N1	N2
ALL	323	44	6
DEL PEAK 23(XP22.2) MUTATED	47	12	2
DEL PEAK 23(XP22.2) WILD-TYPE	276	32	4

Figure S210. Get High-res Image Gene #32: 'del_xp22.2' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

'del_xp22.2' versus 'HISTOLOGICAL_TYPE'

P value = 1e-05 (Fisher's exact test), Q value = 7.2e-05

Table S211. Gene #32: 'del_xp22.2' versus Clinical Feature #10: 'HISTOLOGICAL_TYPE'

nPatients	KIDNEY CHROMOPHOBE	KIDNEY CLEAR CELL RENAL CARCINOMA	KIDNEY PAPILLARY RENAL CELL CARCINOMA
ALL	66	528	288
DEL PEAK 23(XP22.2) MUTATED	39	53	33
DEL PEAK 23(XP22.2) WILD-TYPE	27	475	255

Figure S211. Get High-res Image Gene #32: 'del_xp22.2' versus Clinical Feature #10: 'HISTOLOGICAL_TYPE'

Methods & Data

Input

Copy number data file = all_lesions.txt from GISTIC pipeline
Processed Copy number data file = /xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_Correlate_Genomic_Events_Preprocess/KIPAN-TP/22533781/transformed.cor.cli.txt
Clinical data file = /xchip/cga/gdac-prod/tcga-gdac/jobResults/Append_Data/KIPAN-TP/22506733/KIPAN-TP.merged_data.txt
Number of patients = 882
Number of significantly focal cnvs = 32
Number of selected clinical features = 14
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

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.

References

[1] Bland and Altman, Statistics notes: The logrank test, BMJ 328(7447):1073 (2004)

[2] 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)

[3] 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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