Correlation between copy number variations of arm-level result and selected clinical features

Pan-kidney cohort (KICH+KIRC+KIRP) (Primary solid tumor)

21 August 2015 | analyses__2015_08_21

Maintainer Information

Citation Information

Maintained by TCGA GDAC Team (Broad Institute/MD Anderson Cancer Center/Harvard Medical School)

Cite as Broad Institute TCGA Genome Data Analysis Center (2015): Correlation between copy number variations of arm-level result and selected clinical features. Broad Institute of MIT and Harvard. doi:10.7908/C1R210KK

Overview

Introduction

This pipeline computes the correlation between significant arm-level copy number variations (cnvs) and selected clinical features.

Summary

Testing the association between copy number variation 82 arm-level events and 14 clinical features across 881 patients, 413 significant findings detected with Q value < 0.25.

1p gain cnv correlated to 'Time to Death', 'PATHOLOGIC_STAGE', 'PATHOLOGY_T_STAGE', 'PATHOLOGY_N_STAGE', and 'KARNOFSKY_PERFORMANCE_SCORE'.
1q gain cnv correlated to 'Time to Death', 'YEARS_TO_BIRTH', 'PATHOLOGIC_STAGE', 'PATHOLOGY_T_STAGE', 'PATHOLOGY_N_STAGE', 'KARNOFSKY_PERFORMANCE_SCORE', and 'HISTOLOGICAL_TYPE'.
2p gain cnv correlated to 'PATHOLOGY_N_STAGE' and 'HISTOLOGICAL_TYPE'.
2q gain cnv correlated to 'PATHOLOGY_N_STAGE' and 'HISTOLOGICAL_TYPE'.
3p gain cnv correlated to 'PATHOLOGIC_STAGE', 'PATHOLOGY_T_STAGE', 'PATHOLOGY_N_STAGE', and 'HISTOLOGICAL_TYPE'.
3q gain cnv correlated to 'PATHOLOGY_N_STAGE', 'GENDER', 'HISTOLOGICAL_TYPE', and 'RACE'.
4p gain cnv correlated to 'YEARS_TO_BIRTH', 'PATHOLOGIC_STAGE', 'PATHOLOGY_T_STAGE', and 'HISTOLOGICAL_TYPE'.
4q gain cnv correlated to 'YEARS_TO_BIRTH', 'PATHOLOGIC_STAGE', 'PATHOLOGY_T_STAGE', and 'HISTOLOGICAL_TYPE'.
5p gain cnv correlated to 'YEARS_TO_BIRTH', 'PATHOLOGIC_STAGE', 'PATHOLOGY_T_STAGE', 'GENDER', 'HISTOLOGICAL_TYPE', and 'RACE'.
5q gain cnv correlated to 'YEARS_TO_BIRTH', 'PATHOLOGIC_STAGE', 'PATHOLOGY_T_STAGE', 'GENDER', 'HISTOLOGICAL_TYPE', and 'RACE'.
6p gain cnv correlated to 'PATHOLOGIC_STAGE', 'PATHOLOGY_T_STAGE', and 'PATHOLOGY_N_STAGE'.
6q gain cnv correlated to 'Time to Death', 'PATHOLOGIC_STAGE', 'PATHOLOGY_T_STAGE', and 'PATHOLOGY_N_STAGE'.
7p gain cnv correlated to 'PATHOLOGY_M_STAGE', 'GENDER', 'HISTOLOGICAL_TYPE', and 'YEAR_OF_TOBACCO_SMOKING_ONSET'.
7q gain cnv correlated to 'PATHOLOGIC_STAGE', 'PATHOLOGY_M_STAGE', 'GENDER', 'HISTOLOGICAL_TYPE', and 'YEAR_OF_TOBACCO_SMOKING_ONSET'.
8p gain cnv correlated to 'PATHOLOGIC_STAGE', 'PATHOLOGY_T_STAGE', 'PATHOLOGY_N_STAGE', and 'HISTOLOGICAL_TYPE'.
8q gain cnv correlated to 'Time to Death', 'PATHOLOGIC_STAGE', 'PATHOLOGY_T_STAGE', 'PATHOLOGY_N_STAGE', 'PATHOLOGY_M_STAGE', and 'HISTOLOGICAL_TYPE'.
9p gain cnv correlated to 'PATHOLOGIC_STAGE', 'PATHOLOGY_T_STAGE', 'PATHOLOGY_N_STAGE', 'GENDER', and 'HISTOLOGICAL_TYPE'.
9q gain cnv correlated to 'PATHOLOGIC_STAGE', 'PATHOLOGY_T_STAGE', 'PATHOLOGY_N_STAGE', 'GENDER', and 'HISTOLOGICAL_TYPE'.
10p gain cnv correlated to 'PATHOLOGY_T_STAGE' and 'PATHOLOGY_N_STAGE'.
10q gain cnv correlated to 'PATHOLOGY_T_STAGE' and 'PATHOLOGY_N_STAGE'.
11p gain cnv correlated to 'PATHOLOGIC_STAGE', 'PATHOLOGY_T_STAGE', 'PATHOLOGY_M_STAGE', 'HISTOLOGICAL_TYPE', and 'NUMBER_PACK_YEARS_SMOKED'.
11q gain cnv correlated to 'YEARS_TO_BIRTH', 'PATHOLOGIC_STAGE', 'PATHOLOGY_T_STAGE', 'HISTOLOGICAL_TYPE', 'NUMBER_PACK_YEARS_SMOKED', and 'YEAR_OF_TOBACCO_SMOKING_ONSET'.
12p gain cnv correlated to 'PATHOLOGIC_STAGE', 'PATHOLOGY_N_STAGE', 'PATHOLOGY_M_STAGE', 'GENDER', 'KARNOFSKY_PERFORMANCE_SCORE', 'HISTOLOGICAL_TYPE', and 'ETHNICITY'.
12q gain cnv correlated to 'Time to Death', 'PATHOLOGIC_STAGE', 'PATHOLOGY_T_STAGE', 'PATHOLOGY_N_STAGE', 'PATHOLOGY_M_STAGE', 'GENDER', 'KARNOFSKY_PERFORMANCE_SCORE', 'HISTOLOGICAL_TYPE', and 'ETHNICITY'.
13q gain cnv correlated to 'RADIATION_THERAPY' and 'HISTOLOGICAL_TYPE'.
14q gain cnv correlated to 'YEARS_TO_BIRTH', 'PATHOLOGIC_STAGE', 'PATHOLOGY_T_STAGE', 'HISTOLOGICAL_TYPE', and 'YEAR_OF_TOBACCO_SMOKING_ONSET'.
15q gain cnv correlated to 'PATHOLOGIC_STAGE', 'PATHOLOGY_T_STAGE', 'HISTOLOGICAL_TYPE', and 'YEAR_OF_TOBACCO_SMOKING_ONSET'.
16p gain cnv correlated to 'Time to Death', 'YEARS_TO_BIRTH', 'GENDER', 'HISTOLOGICAL_TYPE', and 'RACE'.
16q gain cnv correlated to 'Time to Death', 'YEARS_TO_BIRTH', 'GENDER', and 'HISTOLOGICAL_TYPE'.
17p gain cnv correlated to 'Time to Death', 'PATHOLOGIC_STAGE', 'PATHOLOGY_T_STAGE', 'PATHOLOGY_N_STAGE', 'PATHOLOGY_M_STAGE', 'GENDER', 'HISTOLOGICAL_TYPE', 'RACE', and 'ETHNICITY'.
17q gain cnv correlated to 'PATHOLOGIC_STAGE', 'PATHOLOGY_T_STAGE', 'PATHOLOGY_N_STAGE', 'PATHOLOGY_M_STAGE', 'GENDER', 'HISTOLOGICAL_TYPE', 'RACE', and 'ETHNICITY'.
18p gain cnv correlated to 'Time to Death', 'HISTOLOGICAL_TYPE', and 'RACE'.
18q gain cnv correlated to 'Time to Death', 'KARNOFSKY_PERFORMANCE_SCORE', and 'HISTOLOGICAL_TYPE'.
19p gain cnv correlated to 'PATHOLOGIC_STAGE', 'PATHOLOGY_T_STAGE', 'PATHOLOGY_M_STAGE', 'HISTOLOGICAL_TYPE', and 'RACE'.
19q gain cnv correlated to 'PATHOLOGIC_STAGE', 'PATHOLOGY_T_STAGE', 'PATHOLOGY_M_STAGE', 'HISTOLOGICAL_TYPE', and 'RACE'.
20p gain cnv correlated to 'PATHOLOGIC_STAGE', 'PATHOLOGY_T_STAGE', 'PATHOLOGY_N_STAGE', 'PATHOLOGY_M_STAGE', 'GENDER', and 'HISTOLOGICAL_TYPE'.
20q gain cnv correlated to 'PATHOLOGIC_STAGE', 'PATHOLOGY_T_STAGE', 'PATHOLOGY_N_STAGE', 'PATHOLOGY_M_STAGE', 'GENDER', and 'HISTOLOGICAL_TYPE'.
21q gain cnv correlated to 'KARNOFSKY_PERFORMANCE_SCORE' and 'RACE'.
22q gain cnv correlated to 'PATHOLOGIC_STAGE', 'PATHOLOGY_T_STAGE', and 'HISTOLOGICAL_TYPE'.
xp gain cnv correlated to 'PATHOLOGIC_STAGE', 'PATHOLOGY_T_STAGE', 'GENDER', 'HISTOLOGICAL_TYPE', 'YEAR_OF_TOBACCO_SMOKING_ONSET', and 'RACE'.
xq gain cnv correlated to 'PATHOLOGIC_STAGE', 'PATHOLOGY_T_STAGE', 'GENDER', 'HISTOLOGICAL_TYPE', and 'RACE'.
1p loss cnv correlated to 'YEARS_TO_BIRTH', 'PATHOLOGIC_STAGE', 'PATHOLOGY_T_STAGE', and 'HISTOLOGICAL_TYPE'.
1q loss cnv correlated to 'Time to Death', 'YEARS_TO_BIRTH', 'PATHOLOGIC_STAGE', 'PATHOLOGY_T_STAGE', and 'HISTOLOGICAL_TYPE'.
2p loss cnv correlated to 'Time to Death', 'YEARS_TO_BIRTH', 'PATHOLOGIC_STAGE', 'PATHOLOGY_T_STAGE', 'PATHOLOGY_M_STAGE', 'KARNOFSKY_PERFORMANCE_SCORE', and 'HISTOLOGICAL_TYPE'.
2q loss cnv correlated to 'Time to Death', 'YEARS_TO_BIRTH', 'PATHOLOGIC_STAGE', 'PATHOLOGY_T_STAGE', 'PATHOLOGY_M_STAGE', 'KARNOFSKY_PERFORMANCE_SCORE', and 'HISTOLOGICAL_TYPE'.
3p loss cnv correlated to 'Time to Death', 'PATHOLOGIC_STAGE', 'PATHOLOGY_T_STAGE', 'PATHOLOGY_N_STAGE', 'HISTOLOGICAL_TYPE', 'YEAR_OF_TOBACCO_SMOKING_ONSET', and 'RACE'.
3q loss cnv correlated to 'YEARS_TO_BIRTH', 'GENDER', 'RADIATION_THERAPY', 'HISTOLOGICAL_TYPE', and 'RACE'.
4p loss cnv correlated to 'Time to Death', 'PATHOLOGIC_STAGE', 'PATHOLOGY_T_STAGE', 'PATHOLOGY_N_STAGE', 'PATHOLOGY_M_STAGE', 'GENDER', and 'HISTOLOGICAL_TYPE'.
4q loss cnv correlated to 'Time to Death', 'PATHOLOGIC_STAGE', 'PATHOLOGY_T_STAGE', 'PATHOLOGY_N_STAGE', 'PATHOLOGY_M_STAGE', 'HISTOLOGICAL_TYPE', and 'RACE'.
5p loss cnv correlated to 'Time to Death', 'YEARS_TO_BIRTH', 'PATHOLOGIC_STAGE', 'PATHOLOGY_T_STAGE', 'PATHOLOGY_N_STAGE', 'GENDER', 'HISTOLOGICAL_TYPE', 'NUMBER_PACK_YEARS_SMOKED', and 'ETHNICITY'.
5q loss cnv correlated to 'YEARS_TO_BIRTH', 'PATHOLOGIC_STAGE', 'PATHOLOGY_T_STAGE', 'PATHOLOGY_N_STAGE', 'HISTOLOGICAL_TYPE', 'NUMBER_PACK_YEARS_SMOKED', and 'ETHNICITY'.
6p loss cnv correlated to 'YEARS_TO_BIRTH', 'PATHOLOGIC_STAGE', 'PATHOLOGY_T_STAGE', 'HISTOLOGICAL_TYPE', and 'RACE'.
6q loss cnv correlated to 'YEARS_TO_BIRTH', 'PATHOLOGIC_STAGE', 'PATHOLOGY_T_STAGE', 'HISTOLOGICAL_TYPE', and 'RACE'.
7p loss cnv correlated to 'Time to Death' and 'PATHOLOGY_N_STAGE'.
7q loss cnv correlated to 'Time to Death' and 'PATHOLOGY_N_STAGE'.
8p loss cnv correlated to 'Time to Death', 'PATHOLOGIC_STAGE', 'PATHOLOGY_T_STAGE', 'PATHOLOGY_M_STAGE', 'HISTOLOGICAL_TYPE', and 'RACE'.
8q loss cnv correlated to 'HISTOLOGICAL_TYPE'.
9p loss 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'.
9q loss 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'.
10p loss cnv correlated to 'YEARS_TO_BIRTH', 'PATHOLOGIC_STAGE', 'PATHOLOGY_T_STAGE', and 'HISTOLOGICAL_TYPE'.
10q loss cnv correlated to 'YEARS_TO_BIRTH', 'PATHOLOGIC_STAGE', 'PATHOLOGY_T_STAGE', and 'HISTOLOGICAL_TYPE'.
11p loss cnv correlated to 'Time to Death', 'YEARS_TO_BIRTH', 'PATHOLOGIC_STAGE', 'PATHOLOGY_T_STAGE', 'PATHOLOGY_N_STAGE', and 'HISTOLOGICAL_TYPE'.
11q loss cnv correlated to 'Time to Death', 'YEARS_TO_BIRTH', 'PATHOLOGIC_STAGE', 'PATHOLOGY_T_STAGE', 'PATHOLOGY_N_STAGE', 'KARNOFSKY_PERFORMANCE_SCORE', and 'HISTOLOGICAL_TYPE'.
12p loss cnv correlated to 'PATHOLOGY_N_STAGE'.
12q loss cnv correlated to 'PATHOLOGY_T_STAGE'.
13q loss cnv correlated to 'Time to Death', 'YEARS_TO_BIRTH', 'PATHOLOGIC_STAGE', 'PATHOLOGY_T_STAGE', 'PATHOLOGY_N_STAGE', 'GENDER', and 'HISTOLOGICAL_TYPE'.
14q loss cnv correlated to 'Time to Death', 'PATHOLOGIC_STAGE', 'PATHOLOGY_T_STAGE', 'PATHOLOGY_N_STAGE', 'PATHOLOGY_M_STAGE', 'KARNOFSKY_PERFORMANCE_SCORE', 'HISTOLOGICAL_TYPE', 'YEAR_OF_TOBACCO_SMOKING_ONSET', and 'RACE'.
15q loss cnv correlated to 'Time to Death', 'PATHOLOGIC_STAGE', 'PATHOLOGY_T_STAGE', 'PATHOLOGY_N_STAGE', 'PATHOLOGY_M_STAGE', 'KARNOFSKY_PERFORMANCE_SCORE', and 'HISTOLOGICAL_TYPE'.
16p loss cnv correlated to 'Time to Death', 'PATHOLOGIC_STAGE', 'PATHOLOGY_T_STAGE', 'PATHOLOGY_N_STAGE', and 'HISTOLOGICAL_TYPE'.
16q loss cnv correlated to 'Time to Death', 'PATHOLOGIC_STAGE', 'PATHOLOGY_T_STAGE', and 'PATHOLOGY_N_STAGE'.
17p loss cnv correlated to 'YEARS_TO_BIRTH', 'PATHOLOGIC_STAGE', 'PATHOLOGY_T_STAGE', 'PATHOLOGY_N_STAGE', and 'HISTOLOGICAL_TYPE'.
17q loss cnv correlated to 'Time to Death', 'YEARS_TO_BIRTH', 'PATHOLOGIC_STAGE', 'PATHOLOGY_T_STAGE', 'KARNOFSKY_PERFORMANCE_SCORE', and 'HISTOLOGICAL_TYPE'.
18p loss cnv correlated to 'Time to Death', 'PATHOLOGIC_STAGE', 'PATHOLOGY_T_STAGE', 'PATHOLOGY_N_STAGE', 'PATHOLOGY_M_STAGE', 'YEAR_OF_TOBACCO_SMOKING_ONSET', and 'RACE'.
18q loss cnv correlated to 'Time to Death', 'PATHOLOGIC_STAGE', 'PATHOLOGY_T_STAGE', 'PATHOLOGY_N_STAGE', 'PATHOLOGY_M_STAGE', and 'RACE'.
19p loss cnv correlated to 'Time to Death', 'PATHOLOGIC_STAGE', 'PATHOLOGY_T_STAGE', 'PATHOLOGY_N_STAGE', and 'HISTOLOGICAL_TYPE'.
19q loss cnv correlated to 'Time to Death', 'PATHOLOGIC_STAGE', 'PATHOLOGY_T_STAGE', 'PATHOLOGY_N_STAGE', and 'HISTOLOGICAL_TYPE'.
20p loss cnv correlated to 'HISTOLOGICAL_TYPE'.
20q loss cnv correlated to 'HISTOLOGICAL_TYPE' and 'ETHNICITY'.
21q loss cnv correlated to 'YEARS_TO_BIRTH', 'PATHOLOGIC_STAGE', 'PATHOLOGY_T_STAGE', 'PATHOLOGY_N_STAGE', 'HISTOLOGICAL_TYPE', and 'YEAR_OF_TOBACCO_SMOKING_ONSET'.
22q loss cnv correlated to 'Time to Death', 'PATHOLOGIC_STAGE', 'PATHOLOGY_T_STAGE', 'PATHOLOGY_N_STAGE', 'PATHOLOGY_M_STAGE', 'GENDER', 'KARNOFSKY_PERFORMANCE_SCORE', 'HISTOLOGICAL_TYPE', and 'ETHNICITY'.
xp loss cnv correlated to 'YEARS_TO_BIRTH', 'PATHOLOGIC_STAGE', 'PATHOLOGY_T_STAGE', 'PATHOLOGY_N_STAGE', and 'HISTOLOGICAL_TYPE'.
xq loss 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 82 arm-level events and 14 clinical features. Shown in the table are P values (Q values). Thresholded by Q value < 0.25, 413 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
12q gain	256 (29%)	625	0.0636 (0.19)	0.238 (0.474)	0.035 (0.124)	0.0691 (0.203)	0.00551 (0.0271)	0.0131 (0.0555)	0.00573 (0.0279)	1 (1.00)	0.0646 (0.191)	3e-05 (0.000292)	0.992 (1.00)	0.309 (0.55)	0.84 (1.00)	0.0556 (0.172)
17p gain	197 (22%)	684	0.0234 (0.0902)	0.629 (0.855)	1e-05 (0.000109)	1e-05 (0.000109)	0.0156 (0.0636)	0.0101 (0.0442)	0.000422 (0.00316)	1 (1.00)	0.788 (0.987)	1e-05 (0.000109)	0.781 (0.981)	0.0967 (0.262)	0.00721 (0.0334)	0.0103 (0.0447)
5p loss	24 (3%)	857	0.052 (0.163)	0.00256 (0.0143)	1e-05 (0.000109)	1e-05 (0.000109)	0.0248 (0.0943)	0.146 (0.346)	0.045 (0.146)	1 (1.00)	0.103 (0.276)	1e-05 (0.000109)	0.0793 (0.224)	0.333 (0.573)	0.354 (0.593)	0.0863 (0.242)
9p loss	192 (22%)	689	2.75e-12 (1.58e-09)	0.079 (0.224)	1e-05 (0.000109)	1e-05 (0.000109)	0.00502 (0.0254)	0.000356 (0.00274)	0.261 (0.504)	0.373 (0.605)	0.00208 (0.012)	1e-05 (0.000109)	0.796 (0.992)	0.893 (1.00)	0.0134 (0.0564)	0.561 (0.795)
9q loss	194 (22%)	687	3.54e-10 (1.02e-07)	0.0734 (0.211)	1e-05 (0.000109)	1e-05 (0.000109)	0.0146 (0.0601)	0.00107 (0.0069)	0.227 (0.456)	0.368 (0.602)	0.00132 (0.00817)	1e-05 (0.000109)	0.974 (1.00)	0.719 (0.927)	0.0113 (0.0484)	1 (1.00)
14q loss	265 (30%)	616	1.38e-09 (3.17e-07)	0.278 (0.522)	1e-05 (0.000109)	1e-05 (0.000109)	0.00926 (0.0414)	4.21e-05 (0.000396)	0.815 (1.00)	0.0972 (0.263)	0.000225 (0.00182)	1e-05 (0.000109)	0.264 (0.508)	0.00516 (0.0259)	0.0227 (0.0879)	0.864 (1.00)
22q loss	107 (12%)	774	0.000828 (0.00559)	0.641 (0.862)	1e-05 (0.000109)	0.00021 (0.00172)	2e-05 (0.000207)	0.0271 (0.1)	0.028 (0.103)	1 (1.00)	0.00515 (0.0259)	1e-05 (0.000109)	0.899 (1.00)	0.325 (0.57)	0.556 (0.79)	0.0283 (0.104)
17q gain	222 (25%)	659	0.171 (0.38)	0.326 (0.571)	2e-05 (0.000207)	5e-05 (0.000452)	0.00153 (0.00924)	0.045 (0.146)	0.0106 (0.0457)	1 (1.00)	0.562 (0.795)	1e-05 (0.000109)	0.697 (0.909)	0.128 (0.319)	0.0097 (0.0428)	0.034 (0.122)
1q gain	68 (8%)	813	2.09e-05 (0.000214)	0.0431 (0.143)	0.00023 (0.00185)	0.00058 (0.00416)	0.0561 (0.173)	0.232 (0.465)	0.505 (0.739)	1 (1.00)	0.0515 (0.162)	0.00326 (0.0175)	0.282 (0.527)	0.103 (0.275)	0.36 (0.6)	1 (1.00)
12p gain	252 (29%)	629	0.0919 (0.253)	0.128 (0.319)	0.0612 (0.185)	0.139 (0.336)	0.0122 (0.0517)	0.00883 (0.0396)	0.00558 (0.0274)	1 (1.00)	0.0646 (0.191)	2e-05 (0.000207)	0.797 (0.992)	0.153 (0.355)	0.961 (1.00)	0.0568 (0.173)
2p loss	65 (7%)	816	0.00434 (0.0226)	4.59e-05 (0.000428)	1e-05 (0.000109)	2e-05 (0.000207)	0.186 (0.397)	0.0701 (0.205)	0.17 (0.379)	1 (1.00)	0.0463 (0.149)	1e-05 (0.000109)	0.611 (0.844)	0.96 (1.00)	0.178 (0.388)	0.492 (0.723)
2q loss	63 (7%)	818	0.00302 (0.0167)	2.61e-05 (0.000265)	1e-05 (0.000109)	1e-05 (0.000109)	0.184 (0.395)	0.07 (0.205)	0.166 (0.373)	1 (1.00)	0.0463 (0.149)	1e-05 (0.000109)	0.331 (0.573)	0.96 (1.00)	0.125 (0.315)	0.492 (0.723)
3p loss	412 (47%)	469	0.00243 (0.0138)	0.898 (1.00)	0.00045 (0.00329)	4e-05 (0.00038)	0.0506 (0.16)	0.817 (1.00)	0.72 (0.927)	0.222 (0.449)	0.175 (0.384)	1e-05 (0.000109)	0.333 (0.573)	0.0264 (0.098)	0.00068 (0.00482)	0.522 (0.757)
4p loss	98 (11%)	783	5.05e-12 (1.93e-09)	0.381 (0.615)	1e-05 (0.000109)	1e-05 (0.000109)	0.00195 (0.0114)	0.0146 (0.0601)	0.068 (0.201)	1 (1.00)	0.165 (0.373)	0.00185 (0.0108)	0.976 (1.00)	0.223 (0.451)	0.113 (0.294)	0.447 (0.68)
4q loss	92 (10%)	789	9.44e-14 (1.08e-10)	0.478 (0.712)	1e-05 (0.000109)	1e-05 (0.000109)	0.00138 (0.00843)	0.000616 (0.00439)	0.415 (0.65)	1 (1.00)	0.144 (0.343)	0.00847 (0.0383)	0.886 (1.00)	0.162 (0.369)	0.0785 (0.223)	0.602 (0.836)
5q loss	22 (2%)	859	0.361 (0.6)	0.000184 (0.00155)	3e-05 (0.000292)	3e-05 (0.000292)	0.0495 (0.159)	0.702 (0.91)	0.108 (0.285)	1 (1.00)	0.795 (0.992)	1e-05 (0.000109)	0.037 (0.13)	0.128 (0.319)	0.439 (0.675)	0.0631 (0.19)
11q loss	52 (6%)	829	0.000416 (0.00316)	0.0146 (0.0601)	9e-05 (0.000783)	4e-05 (0.00038)	5e-05 (0.000452)	0.314 (0.556)	0.547 (0.784)	1 (1.00)	0.0459 (0.149)	0.0316 (0.115)	0.536 (0.773)	0.242 (0.48)	0.347 (0.586)	0.503 (0.737)
13q loss	137 (16%)	744	0.0366 (0.129)	0.000117 (0.001)	1e-05 (0.000109)	1e-05 (0.000109)	0.0164 (0.0658)	0.116 (0.298)	0.0175 (0.07)	1 (1.00)	0.664 (0.88)	1e-05 (0.000109)	0.933 (1.00)	0.6 (0.835)	0.135 (0.33)	0.641 (0.862)
15q loss	69 (8%)	812	2.86e-05 (0.000288)	0.372 (0.604)	1e-05 (0.000109)	1e-05 (0.000109)	0.00097 (0.00636)	0.0139 (0.0579)	0.506 (0.739)	1 (1.00)	0.0791 (0.224)	0.046 (0.149)	0.354 (0.593)		0.291 (0.538)	0.354 (0.593)
18p loss	142 (16%)	739	3.28e-07 (5.03e-05)	0.676 (0.888)	1e-05 (0.000109)	1e-05 (0.000109)	0.00689 (0.0323)	0.0256 (0.0963)	0.698 (0.909)	1 (1.00)	0.29 (0.538)	0.342 (0.582)	0.176 (0.386)	0.073 (0.211)	0.0867 (0.242)	0.181 (0.39)
5p gain	237 (27%)	644	0.418 (0.652)	0.000456 (0.00331)	0.00045 (0.00329)	0.00071 (0.00494)	0.874 (1.00)	0.18 (0.389)	0.044 (0.145)	0.467 (0.7)	0.183 (0.393)	1e-05 (0.000109)	0.932 (1.00)	0.644 (0.864)	0.00021 (0.00172)	0.857 (1.00)
5q gain	248 (28%)	633	0.48 (0.714)	0.000929 (0.00613)	0.00155 (0.00927)	0.00955 (0.0423)	0.746 (0.951)	0.151 (0.353)	0.0802 (0.226)	0.5 (0.734)	0.143 (0.343)	1e-05 (0.000109)	0.985 (1.00)	0.747 (0.951)	0.00043 (0.00321)	1 (1.00)
8q gain	99 (11%)	782	0.0295 (0.108)	0.19 (0.402)	1e-05 (0.000109)	1e-05 (0.000109)	0.0037 (0.0196)	0.0439 (0.145)	0.91 (1.00)	1 (1.00)	0.322 (0.567)	0.00147 (0.00893)	0.359 (0.599)	0.253 (0.495)	0.288 (0.535)	1 (1.00)
11q gain	55 (6%)	826	0.247 (0.488)	0.0536 (0.167)	0.0357 (0.126)	0.0093 (0.0414)	0.604 (0.836)	0.159 (0.363)	0.3 (0.546)	0.22 (0.448)	0.144 (0.343)	1e-05 (0.000109)	0.0422 (0.142)	0.0498 (0.159)	0.336 (0.576)	0.31 (0.55)
20p gain	232 (26%)	649	0.372 (0.604)	0.473 (0.706)	0.00664 (0.0315)	0.00326 (0.0175)	0.072 (0.209)	0.0344 (0.123)	0.00115 (0.00736)	0.2 (0.419)	0.805 (0.998)	0.0003 (0.00234)	0.206 (0.428)	0.67 (0.885)	0.288 (0.535)	0.364 (0.601)
20q gain	236 (27%)	645	0.237 (0.472)	0.28 (0.523)	0.0052 (0.0259)	0.00595 (0.0288)	0.026 (0.0971)	0.0645 (0.191)	0.00357 (0.019)	0.2 (0.419)	0.805 (0.998)	0.0002 (0.00168)	0.269 (0.513)	0.764 (0.967)	0.177 (0.386)	0.285 (0.53)
xp gain	124 (14%)	757	0.11 (0.287)	0.165 (0.373)	0.0194 (0.0766)	0.0377 (0.13)	1 (1.00)	0.323 (0.567)	0.0073 (0.0337)	1 (1.00)	0.202 (0.421)	1e-05 (0.000109)	0.487 (0.72)	0.0502 (0.16)	0.0295 (0.108)	0.661 (0.877)
8p loss	164 (19%)	717	0.0151 (0.0619)	0.822 (1.00)	0.0236 (0.0904)	0.0158 (0.064)	0.577 (0.814)	0.0572 (0.174)	0.582 (0.818)	1 (1.00)	0.79 (0.988)	1e-05 (0.000109)	0.957 (1.00)	0.666 (0.882)	0.00498 (0.0254)	0.143 (0.343)
11p loss	43 (5%)	838	0.00492 (0.0253)	0.0337 (0.121)	0.00129 (0.00805)	0.00078 (0.00533)	0.00107 (0.0069)	0.393 (0.627)	0.868 (1.00)	1 (1.00)	0.385 (0.618)	0.0161 (0.0649)	0.642 (0.862)	0.125 (0.315)	0.841 (1.00)	0.249 (0.489)
17q loss	81 (9%)	800	0.00754 (0.0346)	0.000261 (0.00207)	1e-05 (0.000109)	1e-05 (0.000109)	0.179 (0.389)	0.554 (0.788)	0.458 (0.691)	1 (1.00)	0.00699 (0.0325)	1e-05 (0.000109)	0.331 (0.573)	0.96 (1.00)	0.128 (0.319)	0.514 (0.748)
18q loss	149 (17%)	732	5.88e-07 (6.32e-05)	0.601 (0.835)	1e-05 (0.000109)	1e-05 (0.000109)	0.00155 (0.00927)	0.0388 (0.133)	0.924 (1.00)	1 (1.00)	0.362 (0.6)	0.636 (0.861)	0.304 (0.55)	0.152 (0.353)	0.0422 (0.142)	0.129 (0.319)
21q loss	133 (15%)	748	0.908 (1.00)	0.0566 (0.173)	0.0008 (0.00543)	1e-05 (0.000109)	0.00319 (0.0174)	1 (1.00)	0.426 (0.66)	1 (1.00)	0.195 (0.413)	1e-05 (0.000109)	0.447 (0.68)	0.0566 (0.173)	0.104 (0.277)	0.495 (0.728)
1p gain	30 (3%)	851	5.98e-08 (1.14e-05)	0.216 (0.442)	0.00299 (0.0166)	0.00377 (0.0197)	0.0298 (0.108)	0.118 (0.302)	0.24 (0.476)	1 (1.00)	0.0252 (0.0952)	0.366 (0.601)			0.367 (0.601)	0.389 (0.623)
7q gain	370 (42%)	511	0.978 (1.00)	0.208 (0.43)	0.0562 (0.173)	0.95 (1.00)	0.306 (0.55)	0.00312 (0.0172)	1.1e-06 (0.000105)	0.0959 (0.261)	0.507 (0.739)	1e-05 (0.000109)	0.408 (0.644)	0.00638 (0.0305)	0.122 (0.311)	0.421 (0.655)
9p gain	26 (3%)	855	0.159 (0.363)	0.672 (0.886)	0.00375 (0.0197)	0.00521 (0.0259)	0.0426 (0.142)	0.344 (0.583)	0.0102 (0.0446)	1 (1.00)	0.0907 (0.251)	5e-05 (0.000452)	0.298 (0.546)		0.38 (0.615)	0.389 (0.623)
9q gain	24 (3%)	857	0.47 (0.704)	0.675 (0.888)	0.00131 (0.00813)	9e-05 (0.000783)	0.0425 (0.142)	1 (1.00)	0.045 (0.146)	1 (1.00)	0.0907 (0.251)	2e-05 (0.000207)	0.298 (0.546)		0.218 (0.444)	0.366 (0.601)
11p gain	57 (6%)	824	0.728 (0.936)	0.125 (0.315)	0.00652 (0.0311)	0.00255 (0.0143)	0.299 (0.546)	0.0373 (0.13)	0.562 (0.795)	0.208 (0.43)	0.35 (0.589)	1e-05 (0.000109)	0.0636 (0.19)	0.152 (0.353)	0.25 (0.491)	0.33 (0.573)
14q gain	39 (4%)	842	0.819 (1.00)	0.0435 (0.144)	0.00178 (0.0105)	0.00045 (0.00329)	0.463 (0.696)	0.585 (0.82)	0.489 (0.721)	1 (1.00)	0.223 (0.451)	1e-05 (0.000109)	0.1 (0.27)	0.084 (0.236)	0.267 (0.511)	0.668 (0.884)
16p gain	281 (32%)	600	0.0206 (0.081)	0.0117 (0.05)	0.816 (1.00)	0.876 (1.00)	0.216 (0.442)	0.896 (1.00)	0.00211 (0.0122)	0.562 (0.795)	0.866 (1.00)	1e-05 (0.000109)	0.979 (1.00)	0.309 (0.55)	0.0368 (0.129)	0.613 (0.846)
19p gain	75 (9%)	806	0.651 (0.869)	0.735 (0.941)	1e-05 (0.000109)	2e-05 (0.000207)	0.153 (0.355)	0.00372 (0.0196)	0.522 (0.757)	0.214 (0.439)	0.991 (1.00)	1e-05 (0.000109)	0.407 (0.644)	0.126 (0.315)	0.00103 (0.00672)	1 (1.00)
19q gain	78 (9%)	803	0.514 (0.748)	0.817 (1.00)	1e-05 (0.000109)	6e-05 (0.00053)	0.625 (0.852)	0.00117 (0.00745)	0.53 (0.765)	0.201 (0.421)	0.991 (1.00)	1e-05 (0.000109)	0.731 (0.939)	0.202 (0.421)	0.00086 (0.00577)	1 (1.00)
xq gain	125 (14%)	756	0.136 (0.331)	0.218 (0.444)	0.0203 (0.0799)	0.0744 (0.213)	0.907 (1.00)	0.162 (0.369)	0.0104 (0.0449)	1 (1.00)	0.143 (0.343)	1e-05 (0.000109)	0.6 (0.835)	0.152 (0.353)	0.0352 (0.125)	0.661 (0.877)
1q loss	110 (12%)	771	0.0388 (0.133)	0.000693 (0.00488)	1e-05 (0.000109)	5e-05 (0.000452)	0.199 (0.419)	0.114 (0.295)	0.331 (0.573)	1 (1.00)	0.3 (0.546)	1e-05 (0.000109)	0.445 (0.68)	0.96 (1.00)	0.0923 (0.254)	0.309 (0.55)
3q loss	124 (14%)	757	0.173 (0.382)	0.0446 (0.146)	0.146 (0.346)	0.221 (0.449)	0.277 (0.521)	0.451 (0.684)	0.0397 (0.135)	0.0164 (0.0658)	0.367 (0.601)	1e-05 (0.000109)			0.0395 (0.134)	0.632 (0.858)
6p loss	172 (20%)	709	0.78 (0.981)	0.0737 (0.211)	1e-05 (0.000109)	1e-05 (0.000109)	0.129 (0.319)	0.89 (1.00)	0.527 (0.764)	1 (1.00)	0.186 (0.397)	1e-05 (0.000109)	0.367 (0.601)	0.701 (0.91)	0.00025 (0.00199)	0.672 (0.886)
6q loss	206 (23%)	675	0.123 (0.313)	0.0738 (0.211)	6e-05 (0.00053)	3e-05 (0.000292)	0.133 (0.325)	0.896 (1.00)	0.554 (0.788)	1 (1.00)	0.298 (0.546)	1e-05 (0.000109)	0.142 (0.342)	0.639 (0.862)	0.00022 (0.00179)	0.329 (0.573)
16p loss	18 (2%)	863	6.06e-07 (6.32e-05)	0.974 (1.00)	0.00851 (0.0383)	0.00042 (0.00316)	0.00127 (0.00801)	0.702 (0.91)	0.618 (0.847)	1 (1.00)		0.0689 (0.203)			1 (1.00)	1 (1.00)
17p loss	109 (12%)	772	0.548 (0.786)	0.00319 (0.0174)	1e-05 (0.000109)	1e-05 (0.000109)	0.00128 (0.00803)	0.165 (0.373)	0.328 (0.572)	1 (1.00)	0.206 (0.428)	1e-05 (0.000109)	0.86 (1.00)	0.837 (1.00)	0.485 (0.719)	1 (1.00)
19p loss	27 (3%)	854	0.00074 (0.00511)	0.148 (0.348)	0.00482 (0.0249)	0.00164 (0.00975)	0.0377 (0.13)	0.408 (0.644)	1 (1.00)	1 (1.00)	0.256 (0.497)	0.0135 (0.0565)	0.581 (0.818)		0.875 (1.00)	1 (1.00)
19q loss	22 (2%)	859	0.00121 (0.0077)	0.332 (0.573)	0.0007 (0.0049)	4e-05 (0.00038)	0.00011 (0.000949)	0.256 (0.497)	0.819 (1.00)	1 (1.00)	0.256 (0.497)	0.00021 (0.00172)	0.392 (0.626)	0.18 (0.389)	0.313 (0.556)	1 (1.00)
xp loss	118 (13%)	763	0.291 (0.538)	0.000927 (0.00613)	0.00051 (0.00368)	0.00015 (0.00128)	0.00611 (0.0295)	1 (1.00)	0.248 (0.488)	1 (1.00)	0.714 (0.923)	1e-05 (0.000109)	0.812 (1.00)	0.452 (0.684)	0.249 (0.49)	0.212 (0.437)
xq loss	116 (13%)	765	0.3 (0.546)	0.00135 (0.00829)	0.00076 (0.00522)	0.00033 (0.00256)	0.00566 (0.0276)	0.603 (0.836)	0.342 (0.582)	1 (1.00)	0.382 (0.615)	1e-05 (0.000109)	0.97 (1.00)	0.841 (1.00)	0.114 (0.295)	0.303 (0.549)
3p gain	102 (12%)	779	0.888 (1.00)	0.159 (0.363)	0.0328 (0.118)	0.0213 (0.0832)	0.0258 (0.0966)	1 (1.00)	0.146 (0.346)	1 (1.00)	0.156 (0.36)	1e-05 (0.000109)	0.882 (1.00)	0.472 (0.706)	0.338 (0.578)	0.808 (1.00)
3q gain	158 (18%)	723	0.342 (0.582)	0.138 (0.334)	0.637 (0.861)	0.416 (0.651)	0.0639 (0.19)	0.247 (0.488)	0.0249 (0.0944)	1 (1.00)	0.657 (0.876)	1e-05 (0.000109)	0.861 (1.00)	0.446 (0.68)	0.0782 (0.223)	0.84 (1.00)
4p gain	46 (5%)	835	0.583 (0.82)	0.0388 (0.133)	0.0034 (0.0182)	0.00669 (0.0315)	0.152 (0.353)	0.585 (0.82)	0.75 (0.953)	1 (1.00)	0.735 (0.941)	1e-05 (0.000109)	0.15 (0.353)	0.323 (0.567)	0.302 (0.549)	0.447 (0.68)
4q gain	46 (5%)	835	0.255 (0.497)	0.0425 (0.142)	0.0114 (0.049)	0.0211 (0.0827)	0.133 (0.326)	0.784 (0.984)	0.872 (1.00)	1 (1.00)	0.778 (0.981)	1e-05 (0.000109)	0.305 (0.55)	0.236 (0.471)	0.306 (0.55)	0.438 (0.673)
6q gain	16 (2%)	865	0.0127 (0.054)	0.677 (0.888)	0.0235 (0.0903)	0.0516 (0.162)	0.00842 (0.0382)	0.154 (0.355)	0.599 (0.835)	1 (1.00)	0.779 (0.981)	0.318 (0.563)	0.352 (0.592)	0.622 (0.849)	0.47 (0.704)	1 (1.00)
7p gain	368 (42%)	513	0.66 (0.877)	0.171 (0.379)	0.199 (0.418)	0.96 (1.00)	0.34 (0.58)	0.0241 (0.0918)	3.51e-07 (5.03e-05)	0.594 (0.832)	0.356 (0.595)	1e-05 (0.000109)	0.369 (0.602)	0.00638 (0.0305)	0.133 (0.326)	0.422 (0.655)
8p gain	67 (8%)	814	0.376 (0.609)	0.552 (0.788)	1e-05 (0.000109)	1e-05 (0.000109)	0.073 (0.211)	0.176 (0.385)	0.789 (0.987)	1 (1.00)	0.81 (1.00)	1e-05 (0.000109)	0.964 (1.00)	0.321 (0.567)	0.309 (0.55)	1 (1.00)
15q gain	52 (6%)	829	0.262 (0.505)	0.342 (0.582)	0.00091 (0.00607)	0.00321 (0.0174)	0.497 (0.73)	0.474 (0.707)	0.649 (0.867)	1 (1.00)	0.911 (1.00)	1e-05 (0.000109)	0.418 (0.652)	0.0588 (0.178)	0.373 (0.605)	0.269 (0.513)
16q gain	268 (30%)	613	0.00224 (0.0129)	0.0294 (0.108)	0.39 (0.623)	0.676 (0.888)	1 (1.00)	0.423 (0.656)	0.0102 (0.0446)	1 (1.00)	0.693 (0.907)	1e-05 (0.000109)	0.616 (0.846)	0.309 (0.55)	0.0908 (0.251)	0.735 (0.941)
1p loss	145 (16%)	736	0.165 (0.373)	0.0183 (0.073)	6e-05 (0.00053)	1e-05 (0.000109)	0.268 (0.512)	0.119 (0.305)	0.564 (0.797)	1 (1.00)	0.416 (0.651)	1e-05 (0.000109)	0.367 (0.601)	0.253 (0.495)	0.641 (0.862)	0.108 (0.285)
10p loss	131 (15%)	750	0.703 (0.91)	0.0621 (0.188)	1e-05 (0.000109)	1e-05 (0.000109)	0.167 (0.376)	1 (1.00)	0.616 (0.846)	1 (1.00)	0.537 (0.773)	1e-05 (0.000109)	0.173 (0.382)	0.448 (0.68)	0.382 (0.615)	0.22 (0.448)
10q loss	156 (18%)	725	0.987 (1.00)	0.035 (0.124)	1e-05 (0.000109)	1e-05 (0.000109)	0.382 (0.615)	1 (1.00)	1 (1.00)	1 (1.00)	0.809 (1.00)	1e-05 (0.000109)	0.173 (0.382)	0.448 (0.68)	0.14 (0.338)	0.263 (0.505)
16q loss	28 (3%)	853	4.99e-07 (6.32e-05)	0.401 (0.638)	0.00502 (0.0254)	0.00027 (0.00212)	0.00042 (0.00316)	0.72 (0.927)	1 (1.00)	1 (1.00)	0.168 (0.377)	0.113 (0.294)	0.179 (0.389)	0.867 (1.00)	0.87 (1.00)	0.621 (0.849)
6p gain	21 (2%)	860	0.131 (0.321)	0.553 (0.788)	0.00262 (0.0146)	0.00493 (0.0253)	0.00245 (0.0139)	0.0954 (0.26)	0.483 (0.717)	1 (1.00)	0.779 (0.981)	0.196 (0.413)	0.958 (1.00)	0.792 (0.99)	0.691 (0.905)	0.616 (0.846)
18p gain	54 (6%)	827	0.0223 (0.0864)	0.781 (0.981)	0.44 (0.675)	0.529 (0.765)	1 (1.00)	0.636 (0.861)	0.552 (0.788)	1 (1.00)	0.126 (0.315)	1e-05 (0.000109)	0.265 (0.508)	0.43 (0.663)	0.0715 (0.208)	0.3 (0.546)
18q gain	50 (6%)	831	0.00698 (0.0325)	0.798 (0.992)	0.404 (0.642)	0.429 (0.663)	0.453 (0.685)	0.461 (0.694)	0.284 (0.529)	1 (1.00)	0.0262 (0.0978)	1e-05 (0.000109)	0.886 (1.00)	0.43 (0.663)	0.104 (0.277)	0.276 (0.52)
22q gain	64 (7%)	817	0.536 (0.773)	0.364 (0.601)	0.0153 (0.0625)	0.00173 (0.0102)	0.196 (0.413)	0.834 (1.00)	0.411 (0.646)	0.214 (0.439)	1 (1.00)	1e-05 (0.000109)	0.716 (0.925)	0.413 (0.648)	0.0951 (0.26)	0.3 (0.546)
2p gain	119 (14%)	762	0.619 (0.848)	0.271 (0.514)	0.453 (0.685)	0.144 (0.343)	0.0436 (0.144)	0.869 (1.00)	1 (1.00)	0.323 (0.567)	0.158 (0.362)	0.0192 (0.0762)	0.185 (0.395)	0.849 (1.00)	0.699 (0.909)	0.813 (1.00)
2q gain	127 (14%)	754	0.679 (0.89)	0.233 (0.467)	0.52 (0.756)	0.272 (0.514)	0.022 (0.0855)	0.748 (0.951)	0.543 (0.78)	0.351 (0.591)	0.25 (0.49)	0.00829 (0.0378)	0.336 (0.576)	0.831 (1.00)	0.703 (0.91)	0.649 (0.867)
10p gain	30 (3%)	851	0.401 (0.638)	0.635 (0.861)	0.107 (0.284)	0.00533 (0.0264)	0.0403 (0.137)	1 (1.00)	0.695 (0.908)	1 (1.00)	0.636 (0.861)	0.419 (0.653)	0.753 (0.955)		0.139 (0.336)	0.625 (0.852)
10q gain	23 (3%)	858	0.212 (0.437)	0.26 (0.503)	0.434 (0.668)	0.0714 (0.208)	0.0374 (0.13)	0.752 (0.955)	0.369 (0.602)	1 (1.00)	1 (1.00)	0.839 (1.00)			0.111 (0.29)	0.616 (0.846)
13q gain	53 (6%)	828	0.17 (0.379)	0.277 (0.521)	0.755 (0.956)	0.832 (1.00)	0.409 (0.645)	0.798 (0.992)	0.0997 (0.269)	0.0134 (0.0563)	0.74 (0.945)	0.00232 (0.0133)	1 (1.00)	0.876 (1.00)	0.833 (1.00)	0.182 (0.391)
21q gain	73 (8%)	808	0.481 (0.714)	0.487 (0.72)	0.349 (0.589)	0.176 (0.386)	1 (1.00)	0.295 (0.543)	0.606 (0.838)	1 (1.00)	0.0394 (0.134)	0.347 (0.586)	0.447 (0.68)	0.627 (0.854)	0.0534 (0.167)	0.773 (0.977)
7p loss	4 (0%)	877	0.089 (0.247)	0.407 (0.644)	0.27 (0.513)	0.109 (0.287)	0.0498 (0.159)	1 (1.00)	0.308 (0.55)	1 (1.00)		0.362 (0.6)			1 (1.00)	1 (1.00)
7q loss	4 (0%)	877	0.089 (0.247)	0.407 (0.644)	0.272 (0.514)	0.109 (0.287)	0.0509 (0.161)	1 (1.00)	0.308 (0.55)	1 (1.00)		0.362 (0.6)			1 (1.00)	1 (1.00)
20q loss	6 (1%)	875	0.857 (1.00)	0.124 (0.315)	0.11 (0.288)	0.168 (0.377)	0.0933 (0.256)	0.598 (0.835)	1 (1.00)	1 (1.00)		0.008 (0.0366)			0.645 (0.865)	0.0633 (0.19)
8q loss	87 (10%)	794	0.837 (1.00)	0.328 (0.572)	0.334 (0.573)	0.18 (0.389)	1 (1.00)	0.601 (0.835)	0.187 (0.398)	1 (1.00)	0.55 (0.788)	1e-05 (0.000109)	0.939 (1.00)		0.152 (0.353)	0.259 (0.501)
12p loss	7 (1%)	874	0.129 (0.319)	0.739 (0.944)	0.148 (0.348)	0.107 (0.284)	0.0506 (0.16)	1 (1.00)	1 (1.00)	1 (1.00)		0.1 (0.269)			1 (1.00)	1 (1.00)
12q loss	4 (0%)	877	0.988 (1.00)	0.332 (0.573)	0.27 (0.513)	0.0549 (0.17)		1 (1.00)	1 (1.00)	1 (1.00)		0.174 (0.384)			1 (1.00)	1 (1.00)
20p loss	12 (1%)	869	0.461 (0.694)	0.231 (0.464)	0.12 (0.307)	0.131 (0.321)	0.106 (0.282)	0.658 (0.877)	0.227 (0.456)	1 (1.00)		0.00667 (0.0315)			0.125 (0.315)	0.28 (0.523)

'1p gain' versus 'Time to Death'

P value = 5.98e-08 (logrank test), Q value = 1.1e-05

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

	nPatients	nDeath	Duration Range (Median), Month
ALL	873	228	0.1 - 194.8 (34.5)
1P GAIN MUTATED	29	18	0.5 - 118.8 (22.3)
1P GAIN WILD-TYPE	844	210	0.1 - 194.8 (35.9)

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

'1p gain' versus 'PATHOLOGIC_STAGE'

P value = 0.00299 (Fisher's exact test), Q value = 0.017

Table S2. Gene #1: '1p gain' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

nPatients	STAGE I	STAGE II	STAGE III	STAGE IV
ALL	455	104	191	104
1P GAIN MUTATED	7	4	12	7
1P GAIN WILD-TYPE	448	100	179	97

Figure S2. Get High-res Image Gene #1: '1p gain' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

'1p gain' versus 'PATHOLOGY_T_STAGE'

P value = 0.00377 (Fisher's exact test), Q value = 0.02

Table S3. Gene #1: '1p gain' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

nPatients	T1	T2	T3	T4
ALL	479	127	258	15
1P GAIN MUTATED	8	4	18	0
1P GAIN WILD-TYPE	471	123	240	15

Figure S3. Get High-res Image Gene #1: '1p gain' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

'1p gain' versus 'PATHOLOGY_N_STAGE'

P value = 0.0298 (Fisher's exact test), Q value = 0.11

Table S4. Gene #1: '1p gain' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

nPatients	N0	N1	N2
ALL	322	44	7
1P GAIN MUTATED	11	5	1
1P GAIN WILD-TYPE	311	39	6

Figure S4. Get High-res Image Gene #1: '1p gain' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

'1p gain' versus 'KARNOFSKY_PERFORMANCE_SCORE'

P value = 0.0252 (Wilcoxon-test), Q value = 0.095

Table S5. Gene #1: '1p gain' versus Clinical Feature #9: 'KARNOFSKY_PERFORMANCE_SCORE'

	nPatients	Mean (Std.Dev)
ALL	142	87.6 (22.8)
1P GAIN MUTATED	6	46.7 (51.3)
1P GAIN WILD-TYPE	136	89.4 (19.2)

Figure S5. Get High-res Image Gene #1: '1p gain' versus Clinical Feature #9: 'KARNOFSKY_PERFORMANCE_SCORE'

'1q gain' versus 'Time to Death'

P value = 2.09e-05 (logrank test), Q value = 0.00021

Table S6. Gene #2: '1q gain' versus Clinical Feature #1: 'Time to Death'

	nPatients	nDeath	Duration Range (Median), Month
ALL	873	228	0.1 - 194.8 (34.5)
1Q GAIN MUTATED	67	31	0.4 - 129.4 (25.4)
1Q GAIN WILD-TYPE	806	197	0.1 - 194.8 (36.0)

Figure S6. Get High-res Image Gene #2: '1q gain' versus Clinical Feature #1: 'Time to Death'

'1q gain' versus 'YEARS_TO_BIRTH'

P value = 0.0431 (Wilcoxon-test), Q value = 0.14

Table S7. Gene #2: '1q gain' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

	nPatients	Mean (Std.Dev)
ALL	875	60.1 (12.5)
1Q GAIN MUTATED	66	62.7 (12.1)
1Q GAIN WILD-TYPE	809	59.9 (12.5)

Figure S7. Get High-res Image Gene #2: '1q gain' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'1q gain' versus 'PATHOLOGIC_STAGE'

P value = 0.00023 (Fisher's exact test), Q value = 0.0018

Table S8. Gene #2: '1q gain' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

nPatients	STAGE I	STAGE II	STAGE III	STAGE IV
ALL	455	104	191	104
1Q GAIN MUTATED	20	9	27	12
1Q GAIN WILD-TYPE	435	95	164	92

Figure S8. Get High-res Image Gene #2: '1q gain' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

'1q gain' versus 'PATHOLOGY_T_STAGE'

P value = 0.00058 (Fisher's exact test), Q value = 0.0042

Table S9. Gene #2: '1q gain' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

nPatients	T1	T2	T3	T4
ALL	479	127	258	15
1Q GAIN MUTATED	23	11	34	0
1Q GAIN WILD-TYPE	456	116	224	15

Figure S9. Get High-res Image Gene #2: '1q gain' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

'1q gain' versus 'PATHOLOGY_N_STAGE'

P value = 0.0561 (Fisher's exact test), Q value = 0.17

Table S10. Gene #2: '1q gain' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

nPatients	N0	N1	N2
ALL	322	44	7
1Q GAIN MUTATED	28	9	1
1Q GAIN WILD-TYPE	294	35	6

Figure S10. Get High-res Image Gene #2: '1q gain' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

'1q gain' versus 'KARNOFSKY_PERFORMANCE_SCORE'

P value = 0.0515 (Wilcoxon-test), Q value = 0.16

Table S11. Gene #2: '1q gain' versus Clinical Feature #9: 'KARNOFSKY_PERFORMANCE_SCORE'

	nPatients	Mean (Std.Dev)
ALL	142	87.6 (22.8)
1Q GAIN MUTATED	11	60.0 (47.7)
1Q GAIN WILD-TYPE	131	89.9 (17.9)

Figure S11. Get High-res Image Gene #2: '1q gain' versus Clinical Feature #9: 'KARNOFSKY_PERFORMANCE_SCORE'

'1q gain' versus 'HISTOLOGICAL_TYPE'

P value = 0.00326 (Fisher's exact test), Q value = 0.017

Table S12. Gene #2: '1q gain' versus Clinical Feature #10: 'HISTOLOGICAL_TYPE'

nPatients	KIDNEY CHROMOPHOBE	KIDNEY CLEAR CELL RENAL CARCINOMA	KIDNEY PAPILLARY RENAL CELL CARCINOMA
ALL	66	528	287
1Q GAIN MUTATED	0	51	17
1Q GAIN WILD-TYPE	66	477	270

Figure S12. Get High-res Image Gene #2: '1q gain' versus Clinical Feature #10: 'HISTOLOGICAL_TYPE'

'2p gain' versus 'PATHOLOGY_N_STAGE'

P value = 0.0436 (Fisher's exact test), Q value = 0.14

Table S13. Gene #3: '2p gain' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

nPatients	N0	N1	N2
ALL	322	44	7
2P GAIN MUTATED	42	11	2
2P GAIN WILD-TYPE	280	33	5

Figure S13. Get High-res Image Gene #3: '2p gain' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

'2p gain' versus 'HISTOLOGICAL_TYPE'

P value = 0.0192 (Fisher's exact test), Q value = 0.076

Table S14. Gene #3: '2p gain' versus Clinical Feature #10: 'HISTOLOGICAL_TYPE'

nPatients	KIDNEY CHROMOPHOBE	KIDNEY CLEAR CELL RENAL CARCINOMA	KIDNEY PAPILLARY RENAL CELL CARCINOMA
ALL	66	528	287
2P GAIN MUTATED	2	75	42
2P GAIN WILD-TYPE	64	453	245

Figure S14. Get High-res Image Gene #3: '2p gain' versus Clinical Feature #10: 'HISTOLOGICAL_TYPE'

'2q gain' versus 'PATHOLOGY_N_STAGE'

P value = 0.022 (Fisher's exact test), Q value = 0.085

Table S15. Gene #4: '2q gain' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

nPatients	N0	N1	N2
ALL	322	44	7
2Q GAIN MUTATED	45	11	3
2Q GAIN WILD-TYPE	277	33	4

Figure S15. Get High-res Image Gene #4: '2q gain' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

'2q gain' versus 'HISTOLOGICAL_TYPE'

P value = 0.00829 (Fisher's exact test), Q value = 0.038

Table S16. Gene #4: '2q gain' versus Clinical Feature #10: 'HISTOLOGICAL_TYPE'

nPatients	KIDNEY CHROMOPHOBE	KIDNEY CLEAR CELL RENAL CARCINOMA	KIDNEY PAPILLARY RENAL CELL CARCINOMA
ALL	66	528	287
2Q GAIN MUTATED	2	78	47
2Q GAIN WILD-TYPE	64	450	240

Figure S16. Get High-res Image Gene #4: '2q gain' versus Clinical Feature #10: 'HISTOLOGICAL_TYPE'

'3p gain' versus 'PATHOLOGIC_STAGE'

P value = 0.0328 (Fisher's exact test), Q value = 0.12

Table S17. Gene #5: '3p gain' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

nPatients	STAGE I	STAGE II	STAGE III	STAGE IV
ALL	455	104	191	104
3P GAIN MUTATED	58	15	11	11
3P GAIN WILD-TYPE	397	89	180	93

Figure S17. Get High-res Image Gene #5: '3p gain' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

'3p gain' versus 'PATHOLOGY_T_STAGE'

P value = 0.0213 (Fisher's exact test), Q value = 0.083

Table S18. Gene #5: '3p gain' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

nPatients	T1	T2	T3	T4
ALL	479	127	258	15
3P GAIN MUTATED	61	19	18	3
3P GAIN WILD-TYPE	418	108	240	12

Figure S18. Get High-res Image Gene #5: '3p gain' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

'3p gain' versus 'PATHOLOGY_N_STAGE'

P value = 0.0258 (Fisher's exact test), Q value = 0.097

Table S19. Gene #5: '3p gain' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

nPatients	N0	N1	N2
ALL	322	44	7
3P GAIN MUTATED	21	8	1
3P GAIN WILD-TYPE	301	36	6

Figure S19. Get High-res Image Gene #5: '3p gain' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

'3p gain' versus 'HISTOLOGICAL_TYPE'

P value = 1e-05 (Fisher's exact test), Q value = 0.00011

Table S20. Gene #5: '3p gain' versus Clinical Feature #10: 'HISTOLOGICAL_TYPE'

nPatients	KIDNEY CHROMOPHOBE	KIDNEY CLEAR CELL RENAL CARCINOMA	KIDNEY PAPILLARY RENAL CELL CARCINOMA
ALL	66	528	287
3P GAIN MUTATED	8	19	75
3P GAIN WILD-TYPE	58	509	212

Figure S20. Get High-res Image Gene #5: '3p gain' versus Clinical Feature #10: 'HISTOLOGICAL_TYPE'

'3q gain' versus 'PATHOLOGY_N_STAGE'

P value = 0.0639 (Fisher's exact test), Q value = 0.19

Table S21. Gene #6: '3q gain' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

nPatients	N0	N1	N2
ALL	322	44	7
3Q GAIN MUTATED	45	12	1
3Q GAIN WILD-TYPE	277	32	6

Figure S21. Get High-res Image Gene #6: '3q gain' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

'3q gain' versus 'GENDER'

P value = 0.0249 (Fisher's exact test), Q value = 0.094

Table S22. Gene #6: '3q gain' versus Clinical Feature #7: 'GENDER'

nPatients	FEMALE	MALE
ALL	292	589
3Q GAIN MUTATED	40	118
3Q GAIN WILD-TYPE	252	471

Figure S22. Get High-res Image Gene #6: '3q gain' versus Clinical Feature #7: 'GENDER'

'3q gain' versus 'HISTOLOGICAL_TYPE'

P value = 1e-05 (Fisher's exact test), Q value = 0.00011

Table S23. Gene #6: '3q gain' versus Clinical Feature #10: 'HISTOLOGICAL_TYPE'

nPatients	KIDNEY CHROMOPHOBE	KIDNEY CLEAR CELL RENAL CARCINOMA	KIDNEY PAPILLARY RENAL CELL CARCINOMA
ALL	66	528	287
3Q GAIN MUTATED	8	56	94
3Q GAIN WILD-TYPE	58	472	193

Figure S23. Get High-res Image Gene #6: '3q gain' versus Clinical Feature #10: 'HISTOLOGICAL_TYPE'

'3q gain' versus 'RACE'

P value = 0.0782 (Fisher's exact test), Q value = 0.22

Table S24. Gene #6: '3q gain' versus Clinical Feature #13: 'RACE'

nPatients	AMERICAN INDIAN OR ALASKA NATIVE	ASIAN	BLACK OR AFRICAN AMERICAN	WHITE
ALL	2	15	121	719
3Q GAIN MUTATED	2	2	20	125
3Q GAIN WILD-TYPE	0	13	101	594

Figure S24. Get High-res Image Gene #6: '3q gain' versus Clinical Feature #13: 'RACE'

'4p gain' versus 'YEARS_TO_BIRTH'

P value = 0.0388 (Wilcoxon-test), Q value = 0.13

Table S25. Gene #7: '4p gain' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

	nPatients	Mean (Std.Dev)
ALL	875	60.1 (12.5)
4P GAIN MUTATED	45	56.5 (13.4)
4P GAIN WILD-TYPE	830	60.3 (12.4)

Figure S25. Get High-res Image Gene #7: '4p gain' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'4p gain' versus 'PATHOLOGIC_STAGE'

P value = 0.0034 (Fisher's exact test), Q value = 0.018

Table S26. Gene #7: '4p gain' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

nPatients	STAGE I	STAGE II	STAGE III	STAGE IV
ALL	455	104	191	104
4P GAIN MUTATED	18	13	6	8
4P GAIN WILD-TYPE	437	91	185	96

Figure S26. Get High-res Image Gene #7: '4p gain' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

'4p gain' versus 'PATHOLOGY_T_STAGE'

P value = 0.00669 (Fisher's exact test), Q value = 0.031

Table S27. Gene #7: '4p gain' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

nPatients	T1	T2	T3	T4
ALL	479	127	258	15
4P GAIN MUTATED	18	14	12	2
4P GAIN WILD-TYPE	461	113	246	13

Figure S27. Get High-res Image Gene #7: '4p gain' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

'4p gain' versus 'HISTOLOGICAL_TYPE'

P value = 1e-05 (Fisher's exact test), Q value = 0.00011

Table S28. Gene #7: '4p gain' versus Clinical Feature #10: 'HISTOLOGICAL_TYPE'

nPatients	KIDNEY CHROMOPHOBE	KIDNEY CLEAR CELL RENAL CARCINOMA	KIDNEY PAPILLARY RENAL CELL CARCINOMA
ALL	66	528	287
4P GAIN MUTATED	23	13	10
4P GAIN WILD-TYPE	43	515	277

Figure S28. Get High-res Image Gene #7: '4p gain' versus Clinical Feature #10: 'HISTOLOGICAL_TYPE'

'4q gain' versus 'YEARS_TO_BIRTH'

P value = 0.0425 (Wilcoxon-test), Q value = 0.14

Table S29. Gene #8: '4q gain' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

	nPatients	Mean (Std.Dev)
ALL	875	60.1 (12.5)
4Q GAIN MUTATED	45	56.6 (13.3)
4Q GAIN WILD-TYPE	830	60.3 (12.4)

Figure S29. Get High-res Image Gene #8: '4q gain' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'4q gain' versus 'PATHOLOGIC_STAGE'

P value = 0.0114 (Fisher's exact test), Q value = 0.049

Table S30. Gene #8: '4q gain' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

nPatients	STAGE I	STAGE II	STAGE III	STAGE IV
ALL	455	104	191	104
4Q GAIN MUTATED	19	13	7	6
4Q GAIN WILD-TYPE	436	91	184	98

Figure S30. Get High-res Image Gene #8: '4q gain' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

'4q gain' versus 'PATHOLOGY_T_STAGE'

P value = 0.0211 (Fisher's exact test), Q value = 0.083

Table S31. Gene #8: '4q gain' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

nPatients	T1	T2	T3	T4
ALL	479	127	258	15
4Q GAIN MUTATED	19	14	12	1
4Q GAIN WILD-TYPE	460	113	246	14

Figure S31. Get High-res Image Gene #8: '4q gain' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

'4q gain' versus 'HISTOLOGICAL_TYPE'

P value = 1e-05 (Fisher's exact test), Q value = 0.00011

Table S32. Gene #8: '4q gain' versus Clinical Feature #10: 'HISTOLOGICAL_TYPE'

nPatients	KIDNEY CHROMOPHOBE	KIDNEY CLEAR CELL RENAL CARCINOMA	KIDNEY PAPILLARY RENAL CELL CARCINOMA
ALL	66	528	287
4Q GAIN MUTATED	24	13	9
4Q GAIN WILD-TYPE	42	515	278

Figure S32. Get High-res Image Gene #8: '4q gain' versus Clinical Feature #10: 'HISTOLOGICAL_TYPE'

'5p gain' versus 'YEARS_TO_BIRTH'

P value = 0.000456 (Wilcoxon-test), Q value = 0.0033

Table S33. Gene #9: '5p gain' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

	nPatients	Mean (Std.Dev)
ALL	875	60.1 (12.5)
5P GAIN MUTATED	235	62.7 (12.3)
5P GAIN WILD-TYPE	640	59.2 (12.5)

Figure S33. Get High-res Image Gene #9: '5p gain' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'5p gain' versus 'PATHOLOGIC_STAGE'

P value = 0.00045 (Fisher's exact test), Q value = 0.0033

Table S34. Gene #9: '5p gain' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

nPatients	STAGE I	STAGE II	STAGE III	STAGE IV
ALL	455	104	191	104
5P GAIN MUTATED	101	27	64	42
5P GAIN WILD-TYPE	354	77	127	62

Figure S34. Get High-res Image Gene #9: '5p gain' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

'5p gain' versus 'PATHOLOGY_T_STAGE'

P value = 0.00071 (Fisher's exact test), Q value = 0.0049

Table S35. Gene #9: '5p gain' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

nPatients	T1	T2	T3	T4
ALL	479	127	258	15
5P GAIN MUTATED	105	35	90	7
5P GAIN WILD-TYPE	374	92	168	8

Figure S35. Get High-res Image Gene #9: '5p gain' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

'5p gain' versus 'GENDER'

P value = 0.044 (Fisher's exact test), Q value = 0.14

Table S36. Gene #9: '5p gain' versus Clinical Feature #7: 'GENDER'

nPatients	FEMALE	MALE
ALL	292	589
5P GAIN MUTATED	66	171
5P GAIN WILD-TYPE	226	418

Figure S36. Get High-res Image Gene #9: '5p gain' versus Clinical Feature #7: 'GENDER'

'5p gain' versus 'HISTOLOGICAL_TYPE'

P value = 1e-05 (Fisher's exact test), Q value = 0.00011

Table S37. Gene #9: '5p gain' versus Clinical Feature #10: 'HISTOLOGICAL_TYPE'

nPatients	KIDNEY CHROMOPHOBE	KIDNEY CLEAR CELL RENAL CARCINOMA	KIDNEY PAPILLARY RENAL CELL CARCINOMA
ALL	66	528	287
5P GAIN MUTATED	8	195	34
5P GAIN WILD-TYPE	58	333	253

Figure S37. Get High-res Image Gene #9: '5p gain' versus Clinical Feature #10: 'HISTOLOGICAL_TYPE'

'5p gain' versus 'RACE'

P value = 0.00021 (Fisher's exact test), Q value = 0.0017

Table S38. Gene #9: '5p gain' versus Clinical Feature #13: 'RACE'

nPatients	AMERICAN INDIAN OR ALASKA NATIVE	ASIAN	BLACK OR AFRICAN AMERICAN	WHITE
ALL	2	15	121	719
5P GAIN MUTATED	0	4	15	213
5P GAIN WILD-TYPE	2	11	106	506

Figure S38. Get High-res Image Gene #9: '5p gain' versus Clinical Feature #13: 'RACE'

'5q gain' versus 'YEARS_TO_BIRTH'

P value = 0.000929 (Wilcoxon-test), Q value = 0.0061

Table S39. Gene #10: '5q gain' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

	nPatients	Mean (Std.Dev)
ALL	875	60.1 (12.5)
5Q GAIN MUTATED	245	62.5 (12.4)
5Q GAIN WILD-TYPE	630	59.2 (12.4)

Figure S39. Get High-res Image Gene #10: '5q gain' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'5q gain' versus 'PATHOLOGIC_STAGE'

P value = 0.00155 (Fisher's exact test), Q value = 0.0093

Table S40. Gene #10: '5q gain' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

nPatients	STAGE I	STAGE II	STAGE III	STAGE IV
ALL	455	104	191	104
5Q GAIN MUTATED	111	27	63	44
5Q GAIN WILD-TYPE	344	77	128	60

Figure S40. Get High-res Image Gene #10: '5q gain' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

'5q gain' versus 'PATHOLOGY_T_STAGE'

P value = 0.00955 (Fisher's exact test), Q value = 0.042

Table S41. Gene #10: '5q gain' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

nPatients	T1	T2	T3	T4
ALL	479	127	258	15
5Q GAIN MUTATED	116	35	91	6
5Q GAIN WILD-TYPE	363	92	167	9

Figure S41. Get High-res Image Gene #10: '5q gain' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

'5q gain' versus 'GENDER'

P value = 0.0802 (Fisher's exact test), Q value = 0.23

Table S42. Gene #10: '5q gain' versus Clinical Feature #7: 'GENDER'

nPatients	FEMALE	MALE
ALL	292	589
5Q GAIN MUTATED	71	177
5Q GAIN WILD-TYPE	221	412

Figure S42. Get High-res Image Gene #10: '5q gain' versus Clinical Feature #7: 'GENDER'

'5q gain' versus 'HISTOLOGICAL_TYPE'

P value = 1e-05 (Fisher's exact test), Q value = 0.00011

Table S43. Gene #10: '5q gain' versus Clinical Feature #10: 'HISTOLOGICAL_TYPE'

nPatients	KIDNEY CHROMOPHOBE	KIDNEY CLEAR CELL RENAL CARCINOMA	KIDNEY PAPILLARY RENAL CELL CARCINOMA
ALL	66	528	287
5Q GAIN MUTATED	8	208	32
5Q GAIN WILD-TYPE	58	320	255

Figure S43. Get High-res Image Gene #10: '5q gain' versus Clinical Feature #10: 'HISTOLOGICAL_TYPE'

'5q gain' versus 'RACE'

P value = 0.00043 (Fisher's exact test), Q value = 0.0032

Table S44. Gene #10: '5q gain' versus Clinical Feature #13: 'RACE'

nPatients	AMERICAN INDIAN OR ALASKA NATIVE	ASIAN	BLACK OR AFRICAN AMERICAN	WHITE
ALL	2	15	121	719
5Q GAIN MUTATED	0	4	17	222
5Q GAIN WILD-TYPE	2	11	104	497

Figure S44. Get High-res Image Gene #10: '5q gain' versus Clinical Feature #13: 'RACE'

'6p gain' versus 'PATHOLOGIC_STAGE'

P value = 0.00262 (Fisher's exact test), Q value = 0.015

Table S45. Gene #11: '6p gain' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

nPatients	STAGE I	STAGE II	STAGE III	STAGE IV
ALL	455	104	191	104
6P GAIN MUTATED	6	0	9	6
6P GAIN WILD-TYPE	449	104	182	98

Figure S45. Get High-res Image Gene #11: '6p gain' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

'6p gain' versus 'PATHOLOGY_T_STAGE'

P value = 0.00493 (Fisher's exact test), Q value = 0.025

Table S46. Gene #11: '6p gain' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

nPatients	T1	T2	T3	T4
ALL	479	127	258	15
6P GAIN MUTATED	6	1	13	1
6P GAIN WILD-TYPE	473	126	245	14

Figure S46. Get High-res Image Gene #11: '6p gain' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

'6p gain' versus 'PATHOLOGY_N_STAGE'

P value = 0.00245 (Fisher's exact test), Q value = 0.014

Table S47. Gene #11: '6p gain' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

nPatients	N0	N1	N2
ALL	322	44	7
6P GAIN MUTATED	6	6	0
6P GAIN WILD-TYPE	316	38	7

Figure S47. Get High-res Image Gene #11: '6p gain' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

'6q gain' versus 'Time to Death'

P value = 0.0127 (logrank test), Q value = 0.054

Table S48. Gene #12: '6q gain' versus Clinical Feature #1: 'Time to Death'

	nPatients	nDeath	Duration Range (Median), Month
ALL	873	228	0.1 - 194.8 (34.5)
6Q GAIN MUTATED	16	8	6.4 - 113.5 (27.7)
6Q GAIN WILD-TYPE	857	220	0.1 - 194.8 (34.9)

Figure S48. Get High-res Image Gene #12: '6q gain' versus Clinical Feature #1: 'Time to Death'

'6q gain' versus 'PATHOLOGIC_STAGE'

P value = 0.0235 (Fisher's exact test), Q value = 0.09

Table S49. Gene #12: '6q gain' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

nPatients	STAGE I	STAGE II	STAGE III	STAGE IV
ALL	455	104	191	104
6Q GAIN MUTATED	5	0	7	4
6Q GAIN WILD-TYPE	450	104	184	100

Figure S49. Get High-res Image Gene #12: '6q gain' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

'6q gain' versus 'PATHOLOGY_T_STAGE'

P value = 0.0516 (Fisher's exact test), Q value = 0.16

Table S50. Gene #12: '6q gain' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

nPatients	T1	T2	T3	T4
ALL	479	127	258	15
6Q GAIN MUTATED	5	1	10	0
6Q GAIN WILD-TYPE	474	126	248	15

Figure S50. Get High-res Image Gene #12: '6q gain' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

'6q gain' versus 'PATHOLOGY_N_STAGE'

P value = 0.00842 (Fisher's exact test), Q value = 0.038

Table S51. Gene #12: '6q gain' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

nPatients	N0	N1	N2
ALL	322	44	7
6Q GAIN MUTATED	5	5	0
6Q GAIN WILD-TYPE	317	39	7

Figure S51. Get High-res Image Gene #12: '6q gain' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

'7p gain' versus 'PATHOLOGY_M_STAGE'

P value = 0.0241 (Fisher's exact test), Q value = 0.092

Table S52. Gene #13: '7p gain' versus Clinical Feature #6: 'PATHOLOGY_M_STAGE'

nPatients	0	1
ALL	545	89
7P GAIN MUTATED	192	43
7P GAIN WILD-TYPE	353	46

Figure S52. Get High-res Image Gene #13: '7p gain' versus Clinical Feature #6: 'PATHOLOGY_M_STAGE'

'7p gain' versus 'GENDER'

P value = 3.51e-07 (Fisher's exact test), Q value = 5e-05

Table S53. Gene #13: '7p gain' versus Clinical Feature #7: 'GENDER'

nPatients	FEMALE	MALE
ALL	292	589
7P GAIN MUTATED	87	281
7P GAIN WILD-TYPE	205	308

Figure S53. Get High-res Image Gene #13: '7p gain' versus Clinical Feature #7: 'GENDER'

'7p gain' versus 'HISTOLOGICAL_TYPE'

P value = 1e-05 (Fisher's exact test), Q value = 0.00011

Table S54. Gene #13: '7p gain' versus Clinical Feature #10: 'HISTOLOGICAL_TYPE'

nPatients	KIDNEY CHROMOPHOBE	KIDNEY CLEAR CELL RENAL CARCINOMA	KIDNEY PAPILLARY RENAL CELL CARCINOMA
ALL	66	528	287
7P GAIN MUTATED	24	172	172
7P GAIN WILD-TYPE	42	356	115

Figure S54. Get High-res Image Gene #13: '7p gain' versus Clinical Feature #10: 'HISTOLOGICAL_TYPE'

'7p gain' versus 'YEAR_OF_TOBACCO_SMOKING_ONSET'

P value = 0.00638 (Wilcoxon-test), Q value = 0.031

Table S55. Gene #13: '7p gain' versus Clinical Feature #12: 'YEAR_OF_TOBACCO_SMOKING_ONSET'

	nPatients	Mean (Std.Dev)
ALL	74	1973.7 (16.0)
7P GAIN MUTATED	38	1968.8 (15.1)
7P GAIN WILD-TYPE	36	1978.9 (15.5)

Figure S55. Get High-res Image Gene #13: '7p gain' versus Clinical Feature #12: 'YEAR_OF_TOBACCO_SMOKING_ONSET'

'7q gain' versus 'PATHOLOGIC_STAGE'

P value = 0.0562 (Fisher's exact test), Q value = 0.17

Table S56. Gene #14: '7q gain' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

nPatients	STAGE I	STAGE II	STAGE III	STAGE IV
ALL	455	104	191	104
7Q GAIN MUTATED	192	38	70	54
7Q GAIN WILD-TYPE	263	66	121	50

Figure S56. Get High-res Image Gene #14: '7q gain' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

'7q gain' versus 'PATHOLOGY_M_STAGE'

P value = 0.00312 (Fisher's exact test), Q value = 0.017

Table S57. Gene #14: '7q gain' versus Clinical Feature #6: 'PATHOLOGY_M_STAGE'

nPatients	0	1
ALL	545	89
7Q GAIN MUTATED	191	46
7Q GAIN WILD-TYPE	354	43

Figure S57. Get High-res Image Gene #14: '7q gain' versus Clinical Feature #6: 'PATHOLOGY_M_STAGE'

'7q gain' versus 'GENDER'

P value = 1.1e-06 (Fisher's exact test), Q value = 1e-04

Table S58. Gene #14: '7q gain' versus Clinical Feature #7: 'GENDER'

nPatients	FEMALE	MALE
ALL	292	589
7Q GAIN MUTATED	89	281
7Q GAIN WILD-TYPE	203	308

Figure S58. Get High-res Image Gene #14: '7q gain' versus Clinical Feature #7: 'GENDER'

'7q gain' versus 'HISTOLOGICAL_TYPE'

P value = 1e-05 (Fisher's exact test), Q value = 0.00011

Table S59. Gene #14: '7q gain' versus Clinical Feature #10: 'HISTOLOGICAL_TYPE'

nPatients	KIDNEY CHROMOPHOBE	KIDNEY CLEAR CELL RENAL CARCINOMA	KIDNEY PAPILLARY RENAL CELL CARCINOMA
ALL	66	528	287
7Q GAIN MUTATED	24	173	173
7Q GAIN WILD-TYPE	42	355	114

Figure S59. Get High-res Image Gene #14: '7q gain' versus Clinical Feature #10: 'HISTOLOGICAL_TYPE'

'7q gain' versus 'YEAR_OF_TOBACCO_SMOKING_ONSET'

P value = 0.00638 (Wilcoxon-test), Q value = 0.031

Table S60. Gene #14: '7q gain' versus Clinical Feature #12: 'YEAR_OF_TOBACCO_SMOKING_ONSET'

	nPatients	Mean (Std.Dev)
ALL	74	1973.7 (16.0)
7Q GAIN MUTATED	38	1968.8 (15.1)
7Q GAIN WILD-TYPE	36	1978.9 (15.5)

Figure S60. Get High-res Image Gene #14: '7q gain' versus Clinical Feature #12: 'YEAR_OF_TOBACCO_SMOKING_ONSET'

'8p gain' versus 'PATHOLOGIC_STAGE'

P value = 1e-05 (Fisher's exact test), Q value = 0.00011

Table S61. Gene #15: '8p gain' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

nPatients	STAGE I	STAGE II	STAGE III	STAGE IV
ALL	455	104	191	104
8P GAIN MUTATED	18	19	16	13
8P GAIN WILD-TYPE	437	85	175	91

Figure S61. Get High-res Image Gene #15: '8p gain' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

'8p gain' versus 'PATHOLOGY_T_STAGE'

P value = 1e-05 (Fisher's exact test), Q value = 0.00011

Table S62. Gene #15: '8p gain' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

nPatients	T1	T2	T3	T4
ALL	479	127	258	15
8P GAIN MUTATED	18	20	28	1
8P GAIN WILD-TYPE	461	107	230	14

Figure S62. Get High-res Image Gene #15: '8p gain' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

'8p gain' versus 'PATHOLOGY_N_STAGE'

P value = 0.073 (Fisher's exact test), Q value = 0.21

Table S63. Gene #15: '8p gain' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

nPatients	N0	N1	N2
ALL	322	44	7
8P GAIN MUTATED	29	7	2
8P GAIN WILD-TYPE	293	37	5

Figure S63. Get High-res Image Gene #15: '8p gain' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

'8p gain' versus 'HISTOLOGICAL_TYPE'

P value = 1e-05 (Fisher's exact test), Q value = 0.00011

Table S64. Gene #15: '8p gain' versus Clinical Feature #10: 'HISTOLOGICAL_TYPE'

nPatients	KIDNEY CHROMOPHOBE	KIDNEY CLEAR CELL RENAL CARCINOMA	KIDNEY PAPILLARY RENAL CELL CARCINOMA
ALL	66	528	287
8P GAIN MUTATED	17	30	20
8P GAIN WILD-TYPE	49	498	267

Figure S64. Get High-res Image Gene #15: '8p gain' versus Clinical Feature #10: 'HISTOLOGICAL_TYPE'

'8q gain' versus 'Time to Death'

P value = 0.0295 (logrank test), Q value = 0.11

Table S65. Gene #16: '8q gain' versus Clinical Feature #1: 'Time to Death'

	nPatients	nDeath	Duration Range (Median), Month
ALL	873	228	0.1 - 194.8 (34.5)
8Q GAIN MUTATED	98	32	0.2 - 152.0 (26.7)
8Q GAIN WILD-TYPE	775	196	0.1 - 194.8 (36.2)

Figure S65. Get High-res Image Gene #16: '8q gain' versus Clinical Feature #1: 'Time to Death'

'8q gain' versus 'PATHOLOGIC_STAGE'

P value = 1e-05 (Fisher's exact test), Q value = 0.00011

Table S66. Gene #16: '8q gain' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

nPatients	STAGE I	STAGE II	STAGE III	STAGE IV
ALL	455	104	191	104
8Q GAIN MUTATED	27	22	29	20
8Q GAIN WILD-TYPE	428	82	162	84

Figure S66. Get High-res Image Gene #16: '8q gain' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

'8q gain' versus 'PATHOLOGY_T_STAGE'

P value = 1e-05 (Fisher's exact test), Q value = 0.00011

Table S67. Gene #16: '8q gain' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

nPatients	T1	T2	T3	T4
ALL	479	127	258	15
8Q GAIN MUTATED	27	23	47	2
8Q GAIN WILD-TYPE	452	104	211	13

Figure S67. Get High-res Image Gene #16: '8q gain' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

'8q gain' versus 'PATHOLOGY_N_STAGE'

P value = 0.0037 (Fisher's exact test), Q value = 0.02

Table S68. Gene #16: '8q gain' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

nPatients	N0	N1	N2
ALL	322	44	7
8Q GAIN MUTATED	39	12	3
8Q GAIN WILD-TYPE	283	32	4

Figure S68. Get High-res Image Gene #16: '8q gain' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

'8q gain' versus 'PATHOLOGY_M_STAGE'

P value = 0.0439 (Fisher's exact test), Q value = 0.14

Table S69. Gene #16: '8q gain' versus Clinical Feature #6: 'PATHOLOGY_M_STAGE'

nPatients	0	1
ALL	545	89
8Q GAIN MUTATED	55	16
8Q GAIN WILD-TYPE	490	73

Figure S69. Get High-res Image Gene #16: '8q gain' versus Clinical Feature #6: 'PATHOLOGY_M_STAGE'

'8q gain' versus 'HISTOLOGICAL_TYPE'

P value = 0.00147 (Fisher's exact test), Q value = 0.0089

Table S70. Gene #16: '8q gain' versus Clinical Feature #10: 'HISTOLOGICAL_TYPE'

nPatients	KIDNEY CHROMOPHOBE	KIDNEY CLEAR CELL RENAL CARCINOMA	KIDNEY PAPILLARY RENAL CELL CARCINOMA
ALL	66	528	287
8Q GAIN MUTATED	17	57	25
8Q GAIN WILD-TYPE	49	471	262

Figure S70. Get High-res Image Gene #16: '8q gain' versus Clinical Feature #10: 'HISTOLOGICAL_TYPE'

'9p gain' versus 'PATHOLOGIC_STAGE'

P value = 0.00375 (Fisher's exact test), Q value = 0.02

Table S71. Gene #17: '9p gain' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

nPatients	STAGE I	STAGE II	STAGE III	STAGE IV
ALL	455	104	191	104
9P GAIN MUTATED	7	9	7	3
9P GAIN WILD-TYPE	448	95	184	101

Figure S71. Get High-res Image Gene #17: '9p gain' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

'9p gain' versus 'PATHOLOGY_T_STAGE'

P value = 0.00521 (Fisher's exact test), Q value = 0.026

Table S72. Gene #17: '9p gain' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

nPatients	T1	T2	T3	T4
ALL	479	127	258	15
9P GAIN MUTATED	7	9	9	1
9P GAIN WILD-TYPE	472	118	249	14

Figure S72. Get High-res Image Gene #17: '9p gain' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

'9p gain' versus 'PATHOLOGY_N_STAGE'

P value = 0.0426 (Fisher's exact test), Q value = 0.14

Table S73. Gene #17: '9p gain' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

nPatients	N0	N1	N2
ALL	322	44	7
9P GAIN MUTATED	13	1	2
9P GAIN WILD-TYPE	309	43	5

Figure S73. Get High-res Image Gene #17: '9p gain' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

'9p gain' versus 'GENDER'

P value = 0.0102 (Fisher's exact test), Q value = 0.045

Table S74. Gene #17: '9p gain' versus Clinical Feature #7: 'GENDER'

nPatients	FEMALE	MALE
ALL	292	589
9P GAIN MUTATED	15	11
9P GAIN WILD-TYPE	277	578

Figure S74. Get High-res Image Gene #17: '9p gain' versus Clinical Feature #7: 'GENDER'

'9p gain' versus 'HISTOLOGICAL_TYPE'

P value = 5e-05 (Fisher's exact test), Q value = 0.00045

Table S75. Gene #17: '9p gain' versus Clinical Feature #10: 'HISTOLOGICAL_TYPE'

nPatients	KIDNEY CHROMOPHOBE	KIDNEY CLEAR CELL RENAL CARCINOMA	KIDNEY PAPILLARY RENAL CELL CARCINOMA
ALL	66	528	287
9P GAIN MUTATED	9	14	3
9P GAIN WILD-TYPE	57	514	284

Figure S75. Get High-res Image Gene #17: '9p gain' versus Clinical Feature #10: 'HISTOLOGICAL_TYPE'

'9q gain' versus 'PATHOLOGIC_STAGE'

P value = 0.00131 (Fisher's exact test), Q value = 0.0081

Table S76. Gene #18: '9q gain' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

nPatients	STAGE I	STAGE II	STAGE III	STAGE IV
ALL	455	104	191	104
9Q GAIN MUTATED	5	8	6	5
9Q GAIN WILD-TYPE	450	96	185	99

Figure S76. Get High-res Image Gene #18: '9q gain' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

'9q gain' versus 'PATHOLOGY_T_STAGE'

P value = 9e-05 (Fisher's exact test), Q value = 0.00078

Table S77. Gene #18: '9q gain' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

nPatients	T1	T2	T3	T4
ALL	479	127	258	15
9Q GAIN MUTATED	5	8	8	3
9Q GAIN WILD-TYPE	474	119	250	12

Figure S77. Get High-res Image Gene #18: '9q gain' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

'9q gain' versus 'PATHOLOGY_N_STAGE'

P value = 0.0425 (Fisher's exact test), Q value = 0.14

Table S78. Gene #18: '9q gain' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

nPatients	N0	N1	N2
ALL	322	44	7
9Q GAIN MUTATED	13	1	2
9Q GAIN WILD-TYPE	309	43	5

Figure S78. Get High-res Image Gene #18: '9q gain' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

'9q gain' versus 'GENDER'

P value = 0.045 (Fisher's exact test), Q value = 0.15

Table S79. Gene #18: '9q gain' versus Clinical Feature #7: 'GENDER'

nPatients	FEMALE	MALE
ALL	292	589
9Q GAIN MUTATED	13	11
9Q GAIN WILD-TYPE	279	578

Figure S79. Get High-res Image Gene #18: '9q gain' versus Clinical Feature #7: 'GENDER'

'9q gain' versus 'HISTOLOGICAL_TYPE'

P value = 2e-05 (Fisher's exact test), Q value = 0.00021

Table S80. Gene #18: '9q gain' versus Clinical Feature #10: 'HISTOLOGICAL_TYPE'

nPatients	KIDNEY CHROMOPHOBE	KIDNEY CLEAR CELL RENAL CARCINOMA	KIDNEY PAPILLARY RENAL CELL CARCINOMA
ALL	66	528	287
9Q GAIN MUTATED	9	13	2
9Q GAIN WILD-TYPE	57	515	285

Figure S80. Get High-res Image Gene #18: '9q gain' versus Clinical Feature #10: 'HISTOLOGICAL_TYPE'

'10p gain' versus 'PATHOLOGY_T_STAGE'

P value = 0.00533 (Fisher's exact test), Q value = 0.026

Table S81. Gene #19: '10p gain' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

nPatients	T1	T2	T3	T4
ALL	479	127	258	15
10P GAIN MUTATED	12	8	7	3
10P GAIN WILD-TYPE	467	119	251	12

Figure S81. Get High-res Image Gene #19: '10p gain' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

'10p gain' versus 'PATHOLOGY_N_STAGE'

P value = 0.0403 (Fisher's exact test), Q value = 0.14

Table S82. Gene #19: '10p gain' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

nPatients	N0	N1	N2
ALL	322	44	7
10P GAIN MUTATED	9	4	1
10P GAIN WILD-TYPE	313	40	6

Figure S82. Get High-res Image Gene #19: '10p gain' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

'10q gain' versus 'PATHOLOGY_T_STAGE'

P value = 0.0714 (Fisher's exact test), Q value = 0.21

Table S83. Gene #20: '10q gain' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

nPatients	T1	T2	T3	T4
ALL	479	127	258	15
10Q GAIN MUTATED	11	5	5	2
10Q GAIN WILD-TYPE	468	122	253	13

Figure S83. Get High-res Image Gene #20: '10q gain' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

'10q gain' versus 'PATHOLOGY_N_STAGE'

P value = 0.0374 (Fisher's exact test), Q value = 0.13

Table S84. Gene #20: '10q gain' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

nPatients	N0	N1	N2
ALL	322	44	7
10Q GAIN MUTATED	7	3	1
10Q GAIN WILD-TYPE	315	41	6

Figure S84. Get High-res Image Gene #20: '10q gain' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

'11p gain' versus 'PATHOLOGIC_STAGE'

P value = 0.00652 (Fisher's exact test), Q value = 0.031

Table S85. Gene #21: '11p gain' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

nPatients	STAGE I	STAGE II	STAGE III	STAGE IV
ALL	455	104	191	104
11P GAIN MUTATED	18	9	17	12
11P GAIN WILD-TYPE	437	95	174	92

Figure S85. Get High-res Image Gene #21: '11p gain' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

'11p gain' versus 'PATHOLOGY_T_STAGE'

P value = 0.00255 (Fisher's exact test), Q value = 0.014

Table S86. Gene #21: '11p gain' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

nPatients	T1	T2	T3	T4
ALL	479	127	258	15
11P GAIN MUTATED	18	11	27	1
11P GAIN WILD-TYPE	461	116	231	14

Figure S86. Get High-res Image Gene #21: '11p gain' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

'11p gain' versus 'PATHOLOGY_M_STAGE'

P value = 0.0373 (Fisher's exact test), Q value = 0.13

Table S87. Gene #21: '11p gain' versus Clinical Feature #6: 'PATHOLOGY_M_STAGE'

nPatients	0	1
ALL	545	89
11P GAIN MUTATED	32	11
11P GAIN WILD-TYPE	513	78

Figure S87. Get High-res Image Gene #21: '11p gain' versus Clinical Feature #6: 'PATHOLOGY_M_STAGE'

'11p gain' versus 'HISTOLOGICAL_TYPE'

P value = 1e-05 (Fisher's exact test), Q value = 0.00011

Table S88. Gene #21: '11p gain' versus Clinical Feature #10: 'HISTOLOGICAL_TYPE'

nPatients	KIDNEY CHROMOPHOBE	KIDNEY CLEAR CELL RENAL CARCINOMA	KIDNEY PAPILLARY RENAL CELL CARCINOMA
ALL	66	528	287
11P GAIN MUTATED	15	31	11
11P GAIN WILD-TYPE	51	497	276

Figure S88. Get High-res Image Gene #21: '11p gain' versus Clinical Feature #10: 'HISTOLOGICAL_TYPE'

'11p gain' versus 'NUMBER_PACK_YEARS_SMOKED'

P value = 0.0636 (Wilcoxon-test), Q value = 0.19

Table S89. Gene #21: '11p gain' versus Clinical Feature #11: 'NUMBER_PACK_YEARS_SMOKED'

	nPatients	Mean (Std.Dev)
ALL	106	30.8 (24.9)
11P GAIN MUTATED	7	17.3 (16.6)
11P GAIN WILD-TYPE	99	31.7 (25.1)

Figure S89. Get High-res Image Gene #21: '11p gain' versus Clinical Feature #11: 'NUMBER_PACK_YEARS_SMOKED'

'11q gain' versus 'YEARS_TO_BIRTH'

P value = 0.0536 (Wilcoxon-test), Q value = 0.17

Table S90. Gene #22: '11q gain' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

	nPatients	Mean (Std.Dev)
ALL	875	60.1 (12.5)
11Q GAIN MUTATED	55	57.0 (12.8)
11Q GAIN WILD-TYPE	820	60.3 (12.5)

Figure S90. Get High-res Image Gene #22: '11q gain' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'11q gain' versus 'PATHOLOGIC_STAGE'

P value = 0.0357 (Fisher's exact test), Q value = 0.13

Table S91. Gene #22: '11q gain' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

nPatients	STAGE I	STAGE II	STAGE III	STAGE IV
ALL	455	104	191	104
11Q GAIN MUTATED	19	9	16	10
11Q GAIN WILD-TYPE	436	95	175	94

Figure S91. Get High-res Image Gene #22: '11q gain' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

'11q gain' versus 'PATHOLOGY_T_STAGE'

P value = 0.0093 (Fisher's exact test), Q value = 0.041

Table S92. Gene #22: '11q gain' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

nPatients	T1	T2	T3	T4
ALL	479	127	258	15
11Q GAIN MUTATED	19	11	25	0
11Q GAIN WILD-TYPE	460	116	233	15

Figure S92. Get High-res Image Gene #22: '11q gain' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

'11q gain' versus 'HISTOLOGICAL_TYPE'

P value = 1e-05 (Fisher's exact test), Q value = 0.00011

Table S93. Gene #22: '11q gain' versus Clinical Feature #10: 'HISTOLOGICAL_TYPE'

nPatients	KIDNEY CHROMOPHOBE	KIDNEY CLEAR CELL RENAL CARCINOMA	KIDNEY PAPILLARY RENAL CELL CARCINOMA
ALL	66	528	287
11Q GAIN MUTATED	16	29	10
11Q GAIN WILD-TYPE	50	499	277

Figure S93. Get High-res Image Gene #22: '11q gain' versus Clinical Feature #10: 'HISTOLOGICAL_TYPE'

'11q gain' versus 'NUMBER_PACK_YEARS_SMOKED'

P value = 0.0422 (Wilcoxon-test), Q value = 0.14

Table S94. Gene #22: '11q gain' versus Clinical Feature #11: 'NUMBER_PACK_YEARS_SMOKED'

	nPatients	Mean (Std.Dev)
ALL	106	30.8 (24.9)
11Q GAIN MUTATED	8	17.0 (15.3)
11Q GAIN WILD-TYPE	98	31.9 (25.2)

Figure S94. Get High-res Image Gene #22: '11q gain' versus Clinical Feature #11: 'NUMBER_PACK_YEARS_SMOKED'

'11q gain' versus 'YEAR_OF_TOBACCO_SMOKING_ONSET'

P value = 0.0498 (Wilcoxon-test), Q value = 0.16

Table S95. Gene #22: '11q gain' versus Clinical Feature #12: 'YEAR_OF_TOBACCO_SMOKING_ONSET'

	nPatients	Mean (Std.Dev)
ALL	74	1973.7 (16.0)
11Q GAIN MUTATED	6	1985.3 (11.3)
11Q GAIN WILD-TYPE	68	1972.7 (16.0)

Figure S95. Get High-res Image Gene #22: '11q gain' versus Clinical Feature #12: 'YEAR_OF_TOBACCO_SMOKING_ONSET'

'12p gain' versus 'PATHOLOGIC_STAGE'

P value = 0.0612 (Fisher's exact test), Q value = 0.19

Table S96. Gene #23: '12p gain' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

nPatients	STAGE I	STAGE II	STAGE III	STAGE IV
ALL	455	104	191	104
12P GAIN MUTATED	118	29	54	41
12P GAIN WILD-TYPE	337	75	137	63

Figure S96. Get High-res Image Gene #23: '12p gain' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

'12p gain' versus 'PATHOLOGY_N_STAGE'

P value = 0.0122 (Fisher's exact test), Q value = 0.052

Table S97. Gene #23: '12p gain' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

nPatients	N0	N1	N2
ALL	322	44	7
12P GAIN MUTATED	87	21	3
12P GAIN WILD-TYPE	235	23	4

Figure S97. Get High-res Image Gene #23: '12p gain' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

'12p gain' versus 'PATHOLOGY_M_STAGE'

P value = 0.00883 (Fisher's exact test), Q value = 0.04

Table S98. Gene #23: '12p gain' versus Clinical Feature #6: 'PATHOLOGY_M_STAGE'

nPatients	0	1
ALL	545	89
12P GAIN MUTATED	129	33
12P GAIN WILD-TYPE	416	56

Figure S98. Get High-res Image Gene #23: '12p gain' versus Clinical Feature #6: 'PATHOLOGY_M_STAGE'

'12p gain' versus 'GENDER'

P value = 0.00558 (Fisher's exact test), Q value = 0.027

Table S99. Gene #23: '12p gain' versus Clinical Feature #7: 'GENDER'

nPatients	FEMALE	MALE
ALL	292	589
12P GAIN MUTATED	66	186
12P GAIN WILD-TYPE	226	403

Figure S99. Get High-res Image Gene #23: '12p gain' versus Clinical Feature #7: 'GENDER'

'12p gain' versus 'KARNOFSKY_PERFORMANCE_SCORE'

P value = 0.0646 (Wilcoxon-test), Q value = 0.19

Table S100. Gene #23: '12p gain' versus Clinical Feature #9: 'KARNOFSKY_PERFORMANCE_SCORE'

	nPatients	Mean (Std.Dev)
ALL	142	87.6 (22.8)
12P GAIN MUTATED	50	84.2 (26.4)
12P GAIN WILD-TYPE	92	89.5 (20.5)

Figure S100. Get High-res Image Gene #23: '12p gain' versus Clinical Feature #9: 'KARNOFSKY_PERFORMANCE_SCORE'

'12p gain' versus 'HISTOLOGICAL_TYPE'

P value = 2e-05 (Fisher's exact test), Q value = 0.00021

Table S101. Gene #23: '12p gain' versus Clinical Feature #10: 'HISTOLOGICAL_TYPE'

nPatients	KIDNEY CHROMOPHOBE	KIDNEY CLEAR CELL RENAL CARCINOMA	KIDNEY PAPILLARY RENAL CELL CARCINOMA
ALL	66	528	287
12P GAIN MUTATED	19	121	112
12P GAIN WILD-TYPE	47	407	175

Figure S101. Get High-res Image Gene #23: '12p gain' versus Clinical Feature #10: 'HISTOLOGICAL_TYPE'

'12p gain' versus 'ETHNICITY'

P value = 0.0568 (Fisher's exact test), Q value = 0.17

Table S102. Gene #23: '12p gain' versus Clinical Feature #14: 'ETHNICITY'

nPatients	HISPANIC OR LATINO	NOT HISPANIC OR LATINO
ALL	42	621
12P GAIN MUTATED	7	190
12P GAIN WILD-TYPE	35	431

Figure S102. Get High-res Image Gene #23: '12p gain' versus Clinical Feature #14: 'ETHNICITY'

'12q gain' versus 'Time to Death'

P value = 0.0636 (logrank test), Q value = 0.19

Table S103. Gene #24: '12q gain' versus Clinical Feature #1: 'Time to Death'

	nPatients	nDeath	Duration Range (Median), Month
ALL	873	228	0.1 - 194.8 (34.5)
12Q GAIN MUTATED	251	71	0.1 - 194.8 (28.2)
12Q GAIN WILD-TYPE	622	157	0.1 - 149.2 (37.3)

Figure S103. Get High-res Image Gene #24: '12q gain' versus Clinical Feature #1: 'Time to Death'

'12q gain' versus 'PATHOLOGIC_STAGE'

P value = 0.035 (Fisher's exact test), Q value = 0.12

Table S104. Gene #24: '12q gain' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

nPatients	STAGE I	STAGE II	STAGE III	STAGE IV
ALL	455	104	191	104
12Q GAIN MUTATED	118	29	57	42
12Q GAIN WILD-TYPE	337	75	134	62

Figure S104. Get High-res Image Gene #24: '12q gain' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

'12q gain' versus 'PATHOLOGY_T_STAGE'

P value = 0.0691 (Fisher's exact test), Q value = 0.2

Table S105. Gene #24: '12q gain' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

nPatients	T1	T2	T3	T4
ALL	479	127	258	15
12Q GAIN MUTATED	126	34	87	7
12Q GAIN WILD-TYPE	353	93	171	8

Figure S105. Get High-res Image Gene #24: '12q gain' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

'12q gain' versus 'PATHOLOGY_N_STAGE'

P value = 0.00551 (Fisher's exact test), Q value = 0.027

Table S106. Gene #24: '12q gain' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

nPatients	N0	N1	N2
ALL	322	44	7
12Q GAIN MUTATED	88	21	4
12Q GAIN WILD-TYPE	234	23	3

Figure S106. Get High-res Image Gene #24: '12q gain' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

'12q gain' versus 'PATHOLOGY_M_STAGE'

P value = 0.0131 (Fisher's exact test), Q value = 0.055

Table S107. Gene #24: '12q gain' versus Clinical Feature #6: 'PATHOLOGY_M_STAGE'

nPatients	0	1
ALL	545	89
12Q GAIN MUTATED	132	33
12Q GAIN WILD-TYPE	413	56

Figure S107. Get High-res Image Gene #24: '12q gain' versus Clinical Feature #6: 'PATHOLOGY_M_STAGE'

'12q gain' versus 'GENDER'

P value = 0.00573 (Fisher's exact test), Q value = 0.028

Table S108. Gene #24: '12q gain' versus Clinical Feature #7: 'GENDER'

nPatients	FEMALE	MALE
ALL	292	589
12Q GAIN MUTATED	67	189
12Q GAIN WILD-TYPE	225	400

Figure S108. Get High-res Image Gene #24: '12q gain' versus Clinical Feature #7: 'GENDER'

'12q gain' versus 'KARNOFSKY_PERFORMANCE_SCORE'

P value = 0.0646 (Wilcoxon-test), Q value = 0.19

Table S109. Gene #24: '12q gain' versus Clinical Feature #9: 'KARNOFSKY_PERFORMANCE_SCORE'

	nPatients	Mean (Std.Dev)
ALL	142	87.6 (22.8)
12Q GAIN MUTATED	50	84.2 (26.4)
12Q GAIN WILD-TYPE	92	89.5 (20.5)

Figure S109. Get High-res Image Gene #24: '12q gain' versus Clinical Feature #9: 'KARNOFSKY_PERFORMANCE_SCORE'

'12q gain' versus 'HISTOLOGICAL_TYPE'

P value = 3e-05 (Fisher's exact test), Q value = 0.00029

Table S110. Gene #24: '12q gain' versus Clinical Feature #10: 'HISTOLOGICAL_TYPE'

nPatients	KIDNEY CHROMOPHOBE	KIDNEY CLEAR CELL RENAL CARCINOMA	KIDNEY PAPILLARY RENAL CELL CARCINOMA
ALL	66	528	287
12Q GAIN MUTATED	21	123	112
12Q GAIN WILD-TYPE	45	405	175

Figure S110. Get High-res Image Gene #24: '12q gain' versus Clinical Feature #10: 'HISTOLOGICAL_TYPE'

'12q gain' versus 'ETHNICITY'

P value = 0.0556 (Fisher's exact test), Q value = 0.17

Table S111. Gene #24: '12q gain' versus Clinical Feature #14: 'ETHNICITY'

nPatients	HISPANIC OR LATINO	NOT HISPANIC OR LATINO
ALL	42	621
12Q GAIN MUTATED	7	193
12Q GAIN WILD-TYPE	35	428

Figure S111. Get High-res Image Gene #24: '12q gain' versus Clinical Feature #14: 'ETHNICITY'

'13q gain' versus 'RADIATION_THERAPY'

P value = 0.0134 (Fisher's exact test), Q value = 0.056

Table S112. Gene #25: '13q gain' versus Clinical Feature #8: 'RADIATION_THERAPY'

nPatients	NO	YES
ALL	400	3
13Q GAIN MUTATED	26	2
13Q GAIN WILD-TYPE	374	1

Figure S112. Get High-res Image Gene #25: '13q gain' versus Clinical Feature #8: 'RADIATION_THERAPY'

'13q gain' versus 'HISTOLOGICAL_TYPE'

P value = 0.00232 (Fisher's exact test), Q value = 0.013

Table S113. Gene #25: '13q gain' versus Clinical Feature #10: 'HISTOLOGICAL_TYPE'

nPatients	KIDNEY CHROMOPHOBE	KIDNEY CLEAR CELL RENAL CARCINOMA	KIDNEY PAPILLARY RENAL CELL CARCINOMA
ALL	66	528	287
13Q GAIN MUTATED	2	22	29
13Q GAIN WILD-TYPE	64	506	258

Figure S113. Get High-res Image Gene #25: '13q gain' versus Clinical Feature #10: 'HISTOLOGICAL_TYPE'

'14q gain' versus 'YEARS_TO_BIRTH'

P value = 0.0435 (Wilcoxon-test), Q value = 0.14

Table S114. Gene #26: '14q gain' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

	nPatients	Mean (Std.Dev)
ALL	875	60.1 (12.5)
14Q GAIN MUTATED	38	56.4 (12.4)
14Q GAIN WILD-TYPE	837	60.3 (12.5)

Figure S114. Get High-res Image Gene #26: '14q gain' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'14q gain' versus 'PATHOLOGIC_STAGE'

P value = 0.00178 (Fisher's exact test), Q value = 0.01

Table S115. Gene #26: '14q gain' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

nPatients	STAGE I	STAGE II	STAGE III	STAGE IV
ALL	455	104	191	104
14Q GAIN MUTATED	12	12	8	7
14Q GAIN WILD-TYPE	443	92	183	97

Figure S115. Get High-res Image Gene #26: '14q gain' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

'14q gain' versus 'PATHOLOGY_T_STAGE'

P value = 0.00045 (Fisher's exact test), Q value = 0.0033

Table S116. Gene #26: '14q gain' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

nPatients	T1	T2	T3	T4
ALL	479	127	258	15
14Q GAIN MUTATED	12	12	12	3
14Q GAIN WILD-TYPE	467	115	246	12

Figure S116. Get High-res Image Gene #26: '14q gain' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

'14q gain' versus 'HISTOLOGICAL_TYPE'

P value = 1e-05 (Fisher's exact test), Q value = 0.00011

Table S117. Gene #26: '14q gain' versus Clinical Feature #10: 'HISTOLOGICAL_TYPE'

nPatients	KIDNEY CHROMOPHOBE	KIDNEY CLEAR CELL RENAL CARCINOMA	KIDNEY PAPILLARY RENAL CELL CARCINOMA
ALL	66	528	287
14Q GAIN MUTATED	20	16	3
14Q GAIN WILD-TYPE	46	512	284

Figure S117. Get High-res Image Gene #26: '14q gain' versus Clinical Feature #10: 'HISTOLOGICAL_TYPE'

'14q gain' versus 'YEAR_OF_TOBACCO_SMOKING_ONSET'

P value = 0.084 (Wilcoxon-test), Q value = 0.24

Table S118. Gene #26: '14q gain' versus Clinical Feature #12: 'YEAR_OF_TOBACCO_SMOKING_ONSET'

	nPatients	Mean (Std.Dev)
ALL	74	1973.7 (16.0)
14Q GAIN MUTATED	3	1989.0 (7.0)
14Q GAIN WILD-TYPE	71	1973.1 (16.0)

Figure S118. Get High-res Image Gene #26: '14q gain' versus Clinical Feature #12: 'YEAR_OF_TOBACCO_SMOKING_ONSET'

'15q gain' versus 'PATHOLOGIC_STAGE'

P value = 0.00091 (Fisher's exact test), Q value = 0.0061

Table S119. Gene #27: '15q gain' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

nPatients	STAGE I	STAGE II	STAGE III	STAGE IV
ALL	455	104	191	104
15Q GAIN MUTATED	17	15	11	9
15Q GAIN WILD-TYPE	438	89	180	95

Figure S119. Get High-res Image Gene #27: '15q gain' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

'15q gain' versus 'PATHOLOGY_T_STAGE'

P value = 0.00321 (Fisher's exact test), Q value = 0.017

Table S120. Gene #27: '15q gain' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

nPatients	T1	T2	T3	T4
ALL	479	127	258	15
15Q GAIN MUTATED	17	15	19	1
15Q GAIN WILD-TYPE	462	112	239	14

Figure S120. Get High-res Image Gene #27: '15q gain' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

'15q gain' versus 'HISTOLOGICAL_TYPE'

P value = 1e-05 (Fisher's exact test), Q value = 0.00011

Table S121. Gene #27: '15q gain' versus Clinical Feature #10: 'HISTOLOGICAL_TYPE'

nPatients	KIDNEY CHROMOPHOBE	KIDNEY CLEAR CELL RENAL CARCINOMA	KIDNEY PAPILLARY RENAL CELL CARCINOMA
ALL	66	528	287
15Q GAIN MUTATED	21	26	5
15Q GAIN WILD-TYPE	45	502	282

Figure S121. Get High-res Image Gene #27: '15q gain' versus Clinical Feature #10: 'HISTOLOGICAL_TYPE'

'15q gain' versus 'YEAR_OF_TOBACCO_SMOKING_ONSET'

P value = 0.0588 (Wilcoxon-test), Q value = 0.18

Table S122. Gene #27: '15q gain' versus Clinical Feature #12: 'YEAR_OF_TOBACCO_SMOKING_ONSET'

	nPatients	Mean (Std.Dev)
ALL	74	1973.7 (16.0)
15Q GAIN MUTATED	4	1987.5 (12.7)
15Q GAIN WILD-TYPE	70	1972.9 (15.9)

Figure S122. Get High-res Image Gene #27: '15q gain' versus Clinical Feature #12: 'YEAR_OF_TOBACCO_SMOKING_ONSET'

'16p gain' versus 'Time to Death'

P value = 0.0206 (logrank test), Q value = 0.081

Table S123. Gene #28: '16p gain' versus Clinical Feature #1: 'Time to Death'

	nPatients	nDeath	Duration Range (Median), Month
ALL	873	228	0.1 - 194.8 (34.5)
16P GAIN MUTATED	276	56	0.1 - 194.8 (30.6)
16P GAIN WILD-TYPE	597	172	0.1 - 149.2 (36.4)

Figure S123. Get High-res Image Gene #28: '16p gain' versus Clinical Feature #1: 'Time to Death'

'16p gain' versus 'YEARS_TO_BIRTH'

P value = 0.0117 (Wilcoxon-test), Q value = 0.05

Table S124. Gene #28: '16p gain' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

	nPatients	Mean (Std.Dev)
ALL	875	60.1 (12.5)
16P GAIN MUTATED	279	61.6 (12.2)
16P GAIN WILD-TYPE	596	59.4 (12.6)

Figure S124. Get High-res Image Gene #28: '16p gain' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'16p gain' versus 'GENDER'

P value = 0.00211 (Fisher's exact test), Q value = 0.012

Table S125. Gene #28: '16p gain' versus Clinical Feature #7: 'GENDER'

nPatients	FEMALE	MALE
ALL	292	589
16P GAIN MUTATED	73	208
16P GAIN WILD-TYPE	219	381

Figure S125. Get High-res Image Gene #28: '16p gain' versus Clinical Feature #7: 'GENDER'

'16p gain' versus 'HISTOLOGICAL_TYPE'

P value = 1e-05 (Fisher's exact test), Q value = 0.00011

Table S126. Gene #28: '16p gain' versus Clinical Feature #10: 'HISTOLOGICAL_TYPE'

nPatients	KIDNEY CHROMOPHOBE	KIDNEY CLEAR CELL RENAL CARCINOMA	KIDNEY PAPILLARY RENAL CELL CARCINOMA
ALL	66	528	287
16P GAIN MUTATED	21	107	153
16P GAIN WILD-TYPE	45	421	134

Figure S126. Get High-res Image Gene #28: '16p gain' versus Clinical Feature #10: 'HISTOLOGICAL_TYPE'

'16p gain' versus 'RACE'

P value = 0.0368 (Fisher's exact test), Q value = 0.13

Table S127. Gene #28: '16p gain' versus Clinical Feature #13: 'RACE'

nPatients	AMERICAN INDIAN OR ALASKA NATIVE	ASIAN	BLACK OR AFRICAN AMERICAN	WHITE
ALL	2	15	121	719
16P GAIN MUTATED	2	5	29	238
16P GAIN WILD-TYPE	0	10	92	481

Figure S127. Get High-res Image Gene #28: '16p gain' versus Clinical Feature #13: 'RACE'

'16q gain' versus 'Time to Death'

P value = 0.00224 (logrank test), Q value = 0.013

Table S128. Gene #29: '16q gain' versus Clinical Feature #1: 'Time to Death'

	nPatients	nDeath	Duration Range (Median), Month
ALL	873	228	0.1 - 194.8 (34.5)
16Q GAIN MUTATED	263	49	0.1 - 194.8 (30.7)
16Q GAIN WILD-TYPE	610	179	0.1 - 149.2 (36.1)

Figure S128. Get High-res Image Gene #29: '16q gain' versus Clinical Feature #1: 'Time to Death'

'16q gain' versus 'YEARS_TO_BIRTH'

P value = 0.0294 (Wilcoxon-test), Q value = 0.11

Table S129. Gene #29: '16q gain' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

	nPatients	Mean (Std.Dev)
ALL	875	60.1 (12.5)
16Q GAIN MUTATED	266	61.5 (12.3)
16Q GAIN WILD-TYPE	609	59.5 (12.6)

Figure S129. Get High-res Image Gene #29: '16q gain' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'16q gain' versus 'GENDER'

P value = 0.0102 (Fisher's exact test), Q value = 0.045

Table S130. Gene #29: '16q gain' versus Clinical Feature #7: 'GENDER'

nPatients	FEMALE	MALE
ALL	292	589
16Q GAIN MUTATED	72	196
16Q GAIN WILD-TYPE	220	393

Figure S130. Get High-res Image Gene #29: '16q gain' versus Clinical Feature #7: 'GENDER'

'16q gain' versus 'HISTOLOGICAL_TYPE'

P value = 1e-05 (Fisher's exact test), Q value = 0.00011

Table S131. Gene #29: '16q gain' versus Clinical Feature #10: 'HISTOLOGICAL_TYPE'

nPatients	KIDNEY CHROMOPHOBE	KIDNEY CLEAR CELL RENAL CARCINOMA	KIDNEY PAPILLARY RENAL CELL CARCINOMA
ALL	66	528	287
16Q GAIN MUTATED	21	99	148
16Q GAIN WILD-TYPE	45	429	139

Figure S131. Get High-res Image Gene #29: '16q gain' versus Clinical Feature #10: 'HISTOLOGICAL_TYPE'

'17p gain' versus 'Time to Death'

P value = 0.0234 (logrank test), Q value = 0.09

Table S132. Gene #30: '17p gain' versus Clinical Feature #1: 'Time to Death'

	nPatients	nDeath	Duration Range (Median), Month
ALL	873	228	0.1 - 194.8 (34.5)
17P GAIN MUTATED	193	28	0.1 - 194.8 (25.4)
17P GAIN WILD-TYPE	680	200	0.1 - 152.0 (38.3)

Figure S132. Get High-res Image Gene #30: '17p gain' versus Clinical Feature #1: 'Time to Death'

'17p gain' versus 'PATHOLOGIC_STAGE'

P value = 1e-05 (Fisher's exact test), Q value = 0.00011

Table S133. Gene #30: '17p gain' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

nPatients	STAGE I	STAGE II	STAGE III	STAGE IV
ALL	455	104	191	104
17P GAIN MUTATED	132	19	23	7
17P GAIN WILD-TYPE	323	85	168	97

Figure S133. Get High-res Image Gene #30: '17p gain' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

'17p gain' versus 'PATHOLOGY_T_STAGE'

P value = 1e-05 (Fisher's exact test), Q value = 0.00011

Table S134. Gene #30: '17p gain' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

nPatients	T1	T2	T3	T4
ALL	479	127	258	15
17P GAIN MUTATED	141	26	27	2
17P GAIN WILD-TYPE	338	101	231	13

Figure S134. Get High-res Image Gene #30: '17p gain' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

'17p gain' versus 'PATHOLOGY_N_STAGE'

P value = 0.0156 (Fisher's exact test), Q value = 0.064

Table S135. Gene #30: '17p gain' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

nPatients	N0	N1	N2
ALL	322	44	7
17P GAIN MUTATED	32	11	1
17P GAIN WILD-TYPE	290	33	6

Figure S135. Get High-res Image Gene #30: '17p gain' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

'17p gain' versus 'PATHOLOGY_M_STAGE'

P value = 0.0101 (Fisher's exact test), Q value = 0.044

Table S136. Gene #30: '17p gain' versus Clinical Feature #6: 'PATHOLOGY_M_STAGE'

nPatients	0	1
ALL	545	89
17P GAIN MUTATED	68	3
17P GAIN WILD-TYPE	477	86

Figure S136. Get High-res Image Gene #30: '17p gain' versus Clinical Feature #6: 'PATHOLOGY_M_STAGE'

'17p gain' versus 'GENDER'

P value = 0.000422 (Fisher's exact test), Q value = 0.0032

Table S137. Gene #30: '17p gain' versus Clinical Feature #7: 'GENDER'

nPatients	FEMALE	MALE
ALL	292	589
17P GAIN MUTATED	45	152
17P GAIN WILD-TYPE	247	437

Figure S137. Get High-res Image Gene #30: '17p gain' versus Clinical Feature #7: 'GENDER'

'17p gain' versus 'HISTOLOGICAL_TYPE'

P value = 1e-05 (Fisher's exact test), Q value = 0.00011

Table S138. Gene #30: '17p gain' versus Clinical Feature #10: 'HISTOLOGICAL_TYPE'

nPatients	KIDNEY CHROMOPHOBE	KIDNEY CLEAR CELL RENAL CARCINOMA	KIDNEY PAPILLARY RENAL CELL CARCINOMA
ALL	66	528	287
17P GAIN MUTATED	0	25	172
17P GAIN WILD-TYPE	66	503	115

Figure S138. Get High-res Image Gene #30: '17p gain' versus Clinical Feature #10: 'HISTOLOGICAL_TYPE'

'17p gain' versus 'RACE'

P value = 0.00721 (Fisher's exact test), Q value = 0.033

Table S139. Gene #30: '17p gain' versus Clinical Feature #13: 'RACE'

nPatients	AMERICAN INDIAN OR ALASKA NATIVE	ASIAN	BLACK OR AFRICAN AMERICAN	WHITE
ALL	2	15	121	719
17P GAIN MUTATED	2	6	33	148
17P GAIN WILD-TYPE	0	9	88	571

Figure S139. Get High-res Image Gene #30: '17p gain' versus Clinical Feature #13: 'RACE'

'17p gain' versus 'ETHNICITY'

P value = 0.0103 (Fisher's exact test), Q value = 0.045

Table S140. Gene #30: '17p gain' versus Clinical Feature #14: 'ETHNICITY'

nPatients	HISPANIC OR LATINO	NOT HISPANIC OR LATINO
ALL	42	621
17P GAIN MUTATED	4	169
17P GAIN WILD-TYPE	38	452

Figure S140. Get High-res Image Gene #30: '17p gain' versus Clinical Feature #14: 'ETHNICITY'

'17q gain' versus 'PATHOLOGIC_STAGE'

P value = 2e-05 (Fisher's exact test), Q value = 0.00021

Table S141. Gene #31: '17q gain' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

nPatients	STAGE I	STAGE II	STAGE III	STAGE IV
ALL	455	104	191	104
17Q GAIN MUTATED	140	20	33	11
17Q GAIN WILD-TYPE	315	84	158	93

Figure S141. Get High-res Image Gene #31: '17q gain' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

'17q gain' versus 'PATHOLOGY_T_STAGE'

P value = 5e-05 (Fisher's exact test), Q value = 0.00045

Table S142. Gene #31: '17q gain' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

nPatients	T1	T2	T3	T4
ALL	479	127	258	15
17Q GAIN MUTATED	149	29	41	2
17Q GAIN WILD-TYPE	330	98	217	13

Figure S142. Get High-res Image Gene #31: '17q gain' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

'17q gain' versus 'PATHOLOGY_N_STAGE'

P value = 0.00153 (Fisher's exact test), Q value = 0.0092

Table S143. Gene #31: '17q gain' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

nPatients	N0	N1	N2
ALL	322	44	7
17Q GAIN MUTATED	43	12	4
17Q GAIN WILD-TYPE	279	32	3

Figure S143. Get High-res Image Gene #31: '17q gain' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

'17q gain' versus 'PATHOLOGY_M_STAGE'

P value = 0.045 (Fisher's exact test), Q value = 0.15

Table S144. Gene #31: '17q gain' versus Clinical Feature #6: 'PATHOLOGY_M_STAGE'

nPatients	0	1
ALL	545	89
17Q GAIN MUTATED	79	6
17Q GAIN WILD-TYPE	466	83

Figure S144. Get High-res Image Gene #31: '17q gain' versus Clinical Feature #6: 'PATHOLOGY_M_STAGE'

'17q gain' versus 'GENDER'

P value = 0.0106 (Fisher's exact test), Q value = 0.046

Table S145. Gene #31: '17q gain' versus Clinical Feature #7: 'GENDER'

nPatients	FEMALE	MALE
ALL	292	589
17Q GAIN MUTATED	58	164
17Q GAIN WILD-TYPE	234	425

Figure S145. Get High-res Image Gene #31: '17q gain' versus Clinical Feature #7: 'GENDER'

'17q gain' versus 'HISTOLOGICAL_TYPE'

P value = 1e-05 (Fisher's exact test), Q value = 0.00011

Table S146. Gene #31: '17q gain' versus Clinical Feature #10: 'HISTOLOGICAL_TYPE'

nPatients	KIDNEY CHROMOPHOBE	KIDNEY CLEAR CELL RENAL CARCINOMA	KIDNEY PAPILLARY RENAL CELL CARCINOMA
ALL	66	528	287
17Q GAIN MUTATED	0	31	191
17Q GAIN WILD-TYPE	66	497	96

Figure S146. Get High-res Image Gene #31: '17q gain' versus Clinical Feature #10: 'HISTOLOGICAL_TYPE'

'17q gain' versus 'RACE'

P value = 0.0097 (Fisher's exact test), Q value = 0.043

Table S147. Gene #31: '17q gain' versus Clinical Feature #13: 'RACE'

nPatients	AMERICAN INDIAN OR ALASKA NATIVE	ASIAN	BLACK OR AFRICAN AMERICAN	WHITE
ALL	2	15	121	719
17Q GAIN MUTATED	2	6	38	167
17Q GAIN WILD-TYPE	0	9	83	552

Figure S147. Get High-res Image Gene #31: '17q gain' versus Clinical Feature #13: 'RACE'

'17q gain' versus 'ETHNICITY'

P value = 0.034 (Fisher's exact test), Q value = 0.12

Table S148. Gene #31: '17q gain' versus Clinical Feature #14: 'ETHNICITY'

nPatients	HISPANIC OR LATINO	NOT HISPANIC OR LATINO
ALL	42	621
17Q GAIN MUTATED	6	186
17Q GAIN WILD-TYPE	36	435

Figure S148. Get High-res Image Gene #31: '17q gain' versus Clinical Feature #14: 'ETHNICITY'

'18p gain' versus 'Time to Death'

P value = 0.0223 (logrank test), Q value = 0.086

Table S149. Gene #32: '18p gain' versus Clinical Feature #1: 'Time to Death'

	nPatients	nDeath	Duration Range (Median), Month
ALL	873	228	0.1 - 194.8 (34.5)
18P GAIN MUTATED	54	8	0.5 - 152.0 (47.7)
18P GAIN WILD-TYPE	819	220	0.1 - 194.8 (33.8)

Figure S149. Get High-res Image Gene #32: '18p gain' versus Clinical Feature #1: 'Time to Death'

'18p gain' versus 'HISTOLOGICAL_TYPE'

P value = 1e-05 (Fisher's exact test), Q value = 0.00011

Table S150. Gene #32: '18p gain' versus Clinical Feature #10: 'HISTOLOGICAL_TYPE'

nPatients	KIDNEY CHROMOPHOBE	KIDNEY CLEAR CELL RENAL CARCINOMA	KIDNEY PAPILLARY RENAL CELL CARCINOMA
ALL	66	528	287
18P GAIN MUTATED	17	25	12
18P GAIN WILD-TYPE	49	503	275

Figure S150. Get High-res Image Gene #32: '18p gain' versus Clinical Feature #10: 'HISTOLOGICAL_TYPE'

'18p gain' versus 'RACE'

P value = 0.0715 (Fisher's exact test), Q value = 0.21

Table S151. Gene #32: '18p gain' versus Clinical Feature #13: 'RACE'

nPatients	AMERICAN INDIAN OR ALASKA NATIVE	ASIAN	BLACK OR AFRICAN AMERICAN	WHITE
ALL	2	15	121	719
18P GAIN MUTATED	0	0	2	51
18P GAIN WILD-TYPE	2	15	119	668

Figure S151. Get High-res Image Gene #32: '18p gain' versus Clinical Feature #13: 'RACE'

'18q gain' versus 'Time to Death'

P value = 0.00698 (logrank test), Q value = 0.032

Table S152. Gene #33: '18q gain' versus Clinical Feature #1: 'Time to Death'

	nPatients	nDeath	Duration Range (Median), Month
ALL	873	228	0.1 - 194.8 (34.5)
18Q GAIN MUTATED	50	6	0.5 - 152.0 (48.9)
18Q GAIN WILD-TYPE	823	222	0.1 - 194.8 (33.5)

Figure S152. Get High-res Image Gene #33: '18q gain' versus Clinical Feature #1: 'Time to Death'

'18q gain' versus 'KARNOFSKY_PERFORMANCE_SCORE'

P value = 0.0262 (Wilcoxon-test), Q value = 0.098

Table S153. Gene #33: '18q gain' versus Clinical Feature #9: 'KARNOFSKY_PERFORMANCE_SCORE'

	nPatients	Mean (Std.Dev)
ALL	142	87.6 (22.8)
18Q GAIN MUTATED	9	97.8 (6.7)
18Q GAIN WILD-TYPE	133	86.9 (23.4)

Figure S153. Get High-res Image Gene #33: '18q gain' versus Clinical Feature #9: 'KARNOFSKY_PERFORMANCE_SCORE'

'18q gain' versus 'HISTOLOGICAL_TYPE'

P value = 1e-05 (Fisher's exact test), Q value = 0.00011

Table S154. Gene #33: '18q gain' versus Clinical Feature #10: 'HISTOLOGICAL_TYPE'

nPatients	KIDNEY CHROMOPHOBE	KIDNEY CLEAR CELL RENAL CARCINOMA	KIDNEY PAPILLARY RENAL CELL CARCINOMA
ALL	66	528	287
18Q GAIN MUTATED	16	25	9
18Q GAIN WILD-TYPE	50	503	278

Figure S154. Get High-res Image Gene #33: '18q gain' versus Clinical Feature #10: 'HISTOLOGICAL_TYPE'

'19p gain' versus 'PATHOLOGIC_STAGE'

P value = 1e-05 (Fisher's exact test), Q value = 0.00011

Table S155. Gene #34: '19p gain' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

nPatients	STAGE I	STAGE II	STAGE III	STAGE IV
ALL	455	104	191	104
19P GAIN MUTATED	21	15	18	21
19P GAIN WILD-TYPE	434	89	173	83

Figure S155. Get High-res Image Gene #34: '19p gain' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

'19p gain' versus 'PATHOLOGY_T_STAGE'

P value = 2e-05 (Fisher's exact test), Q value = 0.00021

Table S156. Gene #34: '19p gain' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

nPatients	T1	T2	T3	T4
ALL	479	127	258	15
19P GAIN MUTATED	22	15	35	3
19P GAIN WILD-TYPE	457	112	223	12

Figure S156. Get High-res Image Gene #34: '19p gain' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

'19p gain' versus 'PATHOLOGY_M_STAGE'

P value = 0.00372 (Fisher's exact test), Q value = 0.02

Table S157. Gene #34: '19p gain' versus Clinical Feature #6: 'PATHOLOGY_M_STAGE'

nPatients	0	1
ALL	545	89
19P GAIN MUTATED	46	17
19P GAIN WILD-TYPE	499	72

Figure S157. Get High-res Image Gene #34: '19p gain' versus Clinical Feature #6: 'PATHOLOGY_M_STAGE'

'19p gain' versus 'HISTOLOGICAL_TYPE'

P value = 1e-05 (Fisher's exact test), Q value = 0.00011

Table S158. Gene #34: '19p gain' versus Clinical Feature #10: 'HISTOLOGICAL_TYPE'

nPatients	KIDNEY CHROMOPHOBE	KIDNEY CLEAR CELL RENAL CARCINOMA	KIDNEY PAPILLARY RENAL CELL CARCINOMA
ALL	66	528	287
19P GAIN MUTATED	19	52	4
19P GAIN WILD-TYPE	47	476	283

Figure S158. Get High-res Image Gene #34: '19p gain' versus Clinical Feature #10: 'HISTOLOGICAL_TYPE'

'19p gain' versus 'RACE'

P value = 0.00103 (Fisher's exact test), Q value = 0.0067

Table S159. Gene #34: '19p gain' versus Clinical Feature #13: 'RACE'

nPatients	AMERICAN INDIAN OR ALASKA NATIVE	ASIAN	BLACK OR AFRICAN AMERICAN	WHITE
ALL	2	15	121	719
19P GAIN MUTATED	0	2	1	72
19P GAIN WILD-TYPE	2	13	120	647

Figure S159. Get High-res Image Gene #34: '19p gain' versus Clinical Feature #13: 'RACE'

'19q gain' versus 'PATHOLOGIC_STAGE'

P value = 1e-05 (Fisher's exact test), Q value = 0.00011

Table S160. Gene #35: '19q gain' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

nPatients	STAGE I	STAGE II	STAGE III	STAGE IV
ALL	455	104	191	104
19Q GAIN MUTATED	22	15	20	21
19Q GAIN WILD-TYPE	433	89	171	83

Figure S160. Get High-res Image Gene #35: '19q gain' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

'19q gain' versus 'PATHOLOGY_T_STAGE'

P value = 6e-05 (Fisher's exact test), Q value = 0.00053

Table S161. Gene #35: '19q gain' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

nPatients	T1	T2	T3	T4
ALL	479	127	258	15
19Q GAIN MUTATED	23	17	36	2
19Q GAIN WILD-TYPE	456	110	222	13

Figure S161. Get High-res Image Gene #35: '19q gain' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

'19q gain' versus 'PATHOLOGY_M_STAGE'

P value = 0.00117 (Fisher's exact test), Q value = 0.0074

Table S162. Gene #35: '19q gain' versus Clinical Feature #6: 'PATHOLOGY_M_STAGE'

nPatients	0	1
ALL	545	89
19Q GAIN MUTATED	48	19
19Q GAIN WILD-TYPE	497	70

Figure S162. Get High-res Image Gene #35: '19q gain' versus Clinical Feature #6: 'PATHOLOGY_M_STAGE'

'19q gain' versus 'HISTOLOGICAL_TYPE'

P value = 1e-05 (Fisher's exact test), Q value = 0.00011

Table S163. Gene #35: '19q gain' versus Clinical Feature #10: 'HISTOLOGICAL_TYPE'

nPatients	KIDNEY CHROMOPHOBE	KIDNEY CLEAR CELL RENAL CARCINOMA	KIDNEY PAPILLARY RENAL CELL CARCINOMA
ALL	66	528	287
19Q GAIN MUTATED	17	57	4
19Q GAIN WILD-TYPE	49	471	283

Figure S163. Get High-res Image Gene #35: '19q gain' versus Clinical Feature #10: 'HISTOLOGICAL_TYPE'

'19q gain' versus 'RACE'

P value = 0.00086 (Fisher's exact test), Q value = 0.0058

Table S164. Gene #35: '19q gain' versus Clinical Feature #13: 'RACE'

nPatients	AMERICAN INDIAN OR ALASKA NATIVE	ASIAN	BLACK OR AFRICAN AMERICAN	WHITE
ALL	2	15	121	719
19Q GAIN MUTATED	0	1	1	76
19Q GAIN WILD-TYPE	2	14	120	643

Figure S164. Get High-res Image Gene #35: '19q gain' versus Clinical Feature #13: 'RACE'

'20p gain' versus 'PATHOLOGIC_STAGE'

P value = 0.00664 (Fisher's exact test), Q value = 0.031

Table S165. Gene #36: '20p gain' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

nPatients	STAGE I	STAGE II	STAGE III	STAGE IV
ALL	455	104	191	104
20P GAIN MUTATED	98	31	55	38
20P GAIN WILD-TYPE	357	73	136	66

Figure S165. Get High-res Image Gene #36: '20p gain' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

'20p gain' versus 'PATHOLOGY_T_STAGE'

P value = 0.00326 (Fisher's exact test), Q value = 0.017

Table S166. Gene #36: '20p gain' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

nPatients	T1	T2	T3	T4
ALL	479	127	258	15
20P GAIN MUTATED	106	37	81	8
20P GAIN WILD-TYPE	373	90	177	7

Figure S166. Get High-res Image Gene #36: '20p gain' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

'20p gain' versus 'PATHOLOGY_N_STAGE'

P value = 0.072 (Fisher's exact test), Q value = 0.21

Table S167. Gene #36: '20p gain' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

nPatients	N0	N1	N2
ALL	322	44	7
20P GAIN MUTATED	75	16	3
20P GAIN WILD-TYPE	247	28	4

Figure S167. Get High-res Image Gene #36: '20p gain' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

'20p gain' versus 'PATHOLOGY_M_STAGE'

P value = 0.0344 (Fisher's exact test), Q value = 0.12

Table S168. Gene #36: '20p gain' versus Clinical Feature #6: 'PATHOLOGY_M_STAGE'

nPatients	0	1
ALL	545	89
20P GAIN MUTATED	126	30
20P GAIN WILD-TYPE	419	59

Figure S168. Get High-res Image Gene #36: '20p gain' versus Clinical Feature #6: 'PATHOLOGY_M_STAGE'

'20p gain' versus 'GENDER'

P value = 0.00115 (Fisher's exact test), Q value = 0.0074

Table S169. Gene #36: '20p gain' versus Clinical Feature #7: 'GENDER'

nPatients	FEMALE	MALE
ALL	292	589
20P GAIN MUTATED	57	175
20P GAIN WILD-TYPE	235	414

Figure S169. Get High-res Image Gene #36: '20p gain' versus Clinical Feature #7: 'GENDER'

'20p gain' versus 'HISTOLOGICAL_TYPE'

P value = 3e-04 (Fisher's exact test), Q value = 0.0023

Table S170. Gene #36: '20p gain' versus Clinical Feature #10: 'HISTOLOGICAL_TYPE'

nPatients	KIDNEY CHROMOPHOBE	KIDNEY CLEAR CELL RENAL CARCINOMA	KIDNEY PAPILLARY RENAL CELL CARCINOMA
ALL	66	528	287
20P GAIN MUTATED	21	113	98
20P GAIN WILD-TYPE	45	415	189

Figure S170. Get High-res Image Gene #36: '20p gain' versus Clinical Feature #10: 'HISTOLOGICAL_TYPE'

'20q gain' versus 'PATHOLOGIC_STAGE'

P value = 0.0052 (Fisher's exact test), Q value = 0.026

Table S171. Gene #37: '20q gain' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

nPatients	STAGE I	STAGE II	STAGE III	STAGE IV
ALL	455	104	191	104
20Q GAIN MUTATED	99	31	58	38
20Q GAIN WILD-TYPE	356	73	133	66

Figure S171. Get High-res Image Gene #37: '20q gain' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

'20q gain' versus 'PATHOLOGY_T_STAGE'

P value = 0.00595 (Fisher's exact test), Q value = 0.029

Table S172. Gene #37: '20q gain' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

nPatients	T1	T2	T3	T4
ALL	479	127	258	15
20Q GAIN MUTATED	108	37	84	7
20Q GAIN WILD-TYPE	371	90	174	8

Figure S172. Get High-res Image Gene #37: '20q gain' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

'20q gain' versus 'PATHOLOGY_N_STAGE'

P value = 0.026 (Fisher's exact test), Q value = 0.097

Table S173. Gene #37: '20q gain' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

nPatients	N0	N1	N2
ALL	322	44	7
20Q GAIN MUTATED	76	18	3
20Q GAIN WILD-TYPE	246	26	4

Figure S173. Get High-res Image Gene #37: '20q gain' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

'20q gain' versus 'PATHOLOGY_M_STAGE'

P value = 0.0645 (Fisher's exact test), Q value = 0.19

Table S174. Gene #37: '20q gain' versus Clinical Feature #6: 'PATHOLOGY_M_STAGE'

nPatients	0	1
ALL	545	89
20Q GAIN MUTATED	130	30
20Q GAIN WILD-TYPE	415	59

Figure S174. Get High-res Image Gene #37: '20q gain' versus Clinical Feature #6: 'PATHOLOGY_M_STAGE'

'20q gain' versus 'GENDER'

P value = 0.00357 (Fisher's exact test), Q value = 0.019

Table S175. Gene #37: '20q gain' versus Clinical Feature #7: 'GENDER'

nPatients	FEMALE	MALE
ALL	292	589
20Q GAIN MUTATED	60	176
20Q GAIN WILD-TYPE	232	413

Figure S175. Get High-res Image Gene #37: '20q gain' versus Clinical Feature #7: 'GENDER'

'20q gain' versus 'HISTOLOGICAL_TYPE'

P value = 2e-04 (Fisher's exact test), Q value = 0.0017

Table S176. Gene #37: '20q gain' versus Clinical Feature #10: 'HISTOLOGICAL_TYPE'

nPatients	KIDNEY CHROMOPHOBE	KIDNEY CLEAR CELL RENAL CARCINOMA	KIDNEY PAPILLARY RENAL CELL CARCINOMA
ALL	66	528	287
20Q GAIN MUTATED	21	115	100
20Q GAIN WILD-TYPE	45	413	187

Figure S176. Get High-res Image Gene #37: '20q gain' versus Clinical Feature #10: 'HISTOLOGICAL_TYPE'

'21q gain' versus 'KARNOFSKY_PERFORMANCE_SCORE'

P value = 0.0394 (Wilcoxon-test), Q value = 0.13

Table S177. Gene #38: '21q gain' versus Clinical Feature #9: 'KARNOFSKY_PERFORMANCE_SCORE'

	nPatients	Mean (Std.Dev)
ALL	142	87.6 (22.8)
21Q GAIN MUTATED	14	95.7 (9.4)
21Q GAIN WILD-TYPE	128	86.7 (23.7)

Figure S177. Get High-res Image Gene #38: '21q gain' versus Clinical Feature #9: 'KARNOFSKY_PERFORMANCE_SCORE'

'21q gain' versus 'RACE'

P value = 0.0534 (Fisher's exact test), Q value = 0.17

Table S178. Gene #38: '21q gain' versus Clinical Feature #13: 'RACE'

nPatients	AMERICAN INDIAN OR ALASKA NATIVE	ASIAN	BLACK OR AFRICAN AMERICAN	WHITE
ALL	2	15	121	719
21Q GAIN MUTATED	1	1	5	65
21Q GAIN WILD-TYPE	1	14	116	654

Figure S178. Get High-res Image Gene #38: '21q gain' versus Clinical Feature #13: 'RACE'

'22q gain' versus 'PATHOLOGIC_STAGE'

P value = 0.0153 (Fisher's exact test), Q value = 0.063

Table S179. Gene #39: '22q gain' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

nPatients	STAGE I	STAGE II	STAGE III	STAGE IV
ALL	455	104	191	104
22Q GAIN MUTATED	23	13	15	12
22Q GAIN WILD-TYPE	432	91	176	92

Figure S179. Get High-res Image Gene #39: '22q gain' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

'22q gain' versus 'PATHOLOGY_T_STAGE'

P value = 0.00173 (Fisher's exact test), Q value = 0.01

Table S180. Gene #39: '22q gain' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

nPatients	T1	T2	T3	T4
ALL	479	127	258	15
22Q GAIN MUTATED	23	14	23	4
22Q GAIN WILD-TYPE	456	113	235	11

Figure S180. Get High-res Image Gene #39: '22q gain' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

'22q gain' versus 'HISTOLOGICAL_TYPE'

P value = 1e-05 (Fisher's exact test), Q value = 0.00011

Table S181. Gene #39: '22q gain' versus Clinical Feature #10: 'HISTOLOGICAL_TYPE'

nPatients	KIDNEY CHROMOPHOBE	KIDNEY CLEAR CELL RENAL CARCINOMA	KIDNEY PAPILLARY RENAL CELL CARCINOMA
ALL	66	528	287
22Q GAIN MUTATED	19	40	5
22Q GAIN WILD-TYPE	47	488	282

Figure S181. Get High-res Image Gene #39: '22q gain' versus Clinical Feature #10: 'HISTOLOGICAL_TYPE'

'xp gain' versus 'PATHOLOGIC_STAGE'

P value = 0.0194 (Fisher's exact test), Q value = 0.077

Table S182. Gene #40: 'xp gain' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

nPatients	STAGE I	STAGE II	STAGE III	STAGE IV
ALL	455	104	191	104
XP GAIN MUTATED	73	12	14	15
XP GAIN WILD-TYPE	382	92	177	89

Figure S182. Get High-res Image Gene #40: 'xp gain' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

'xp gain' versus 'PATHOLOGY_T_STAGE'

P value = 0.0377 (Fisher's exact test), Q value = 0.13

Table S183. Gene #40: 'xp gain' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

nPatients	T1	T2	T3	T4
ALL	479	127	258	15
XP GAIN MUTATED	79	18	24	3
XP GAIN WILD-TYPE	400	109	234	12

Figure S183. Get High-res Image Gene #40: 'xp gain' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

'xp gain' versus 'GENDER'

P value = 0.0073 (Fisher's exact test), Q value = 0.034

Table S184. Gene #40: 'xp gain' versus Clinical Feature #7: 'GENDER'

nPatients	FEMALE	MALE
ALL	292	589
XP GAIN MUTATED	28	96
XP GAIN WILD-TYPE	264	493

Figure S184. Get High-res Image Gene #40: 'xp gain' versus Clinical Feature #7: 'GENDER'

'xp gain' versus 'HISTOLOGICAL_TYPE'

P value = 1e-05 (Fisher's exact test), Q value = 0.00011

Table S185. Gene #40: 'xp gain' versus Clinical Feature #10: 'HISTOLOGICAL_TYPE'

nPatients	KIDNEY CHROMOPHOBE	KIDNEY CLEAR CELL RENAL CARCINOMA	KIDNEY PAPILLARY RENAL CELL CARCINOMA
ALL	66	528	287
XP GAIN MUTATED	7	30	87
XP GAIN WILD-TYPE	59	498	200

Figure S185. Get High-res Image Gene #40: 'xp gain' versus Clinical Feature #10: 'HISTOLOGICAL_TYPE'

'xp gain' versus 'YEAR_OF_TOBACCO_SMOKING_ONSET'

P value = 0.0502 (Wilcoxon-test), Q value = 0.16

Table S186. Gene #40: 'xp gain' versus Clinical Feature #12: 'YEAR_OF_TOBACCO_SMOKING_ONSET'

	nPatients	Mean (Std.Dev)
ALL	74	1973.7 (16.0)
XP GAIN MUTATED	16	1967.7 (14.3)
XP GAIN WILD-TYPE	58	1975.4 (16.1)

Figure S186. Get High-res Image Gene #40: 'xp gain' versus Clinical Feature #12: 'YEAR_OF_TOBACCO_SMOKING_ONSET'

'xp gain' versus 'RACE'

P value = 0.0295 (Fisher's exact test), Q value = 0.11

Table S187. Gene #40: 'xp gain' versus Clinical Feature #13: 'RACE'

nPatients	AMERICAN INDIAN OR ALASKA NATIVE	ASIAN	BLACK OR AFRICAN AMERICAN	WHITE
ALL	2	15	121	719
XP GAIN MUTATED	2	3	17	96
XP GAIN WILD-TYPE	0	12	104	623

Figure S187. Get High-res Image Gene #40: 'xp gain' versus Clinical Feature #13: 'RACE'

'xq gain' versus 'PATHOLOGIC_STAGE'

P value = 0.0203 (Fisher's exact test), Q value = 0.08

Table S188. Gene #41: 'xq gain' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

nPatients	STAGE I	STAGE II	STAGE III	STAGE IV
ALL	455	104	191	104
XQ GAIN MUTATED	73	12	14	15
XQ GAIN WILD-TYPE	382	92	177	89

Figure S188. Get High-res Image Gene #41: 'xq gain' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

'xq gain' versus 'PATHOLOGY_T_STAGE'

P value = 0.0744 (Fisher's exact test), Q value = 0.21

Table S189. Gene #41: 'xq gain' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

nPatients	T1	T2	T3	T4
ALL	479	127	258	15
XQ GAIN MUTATED	79	19	25	2
XQ GAIN WILD-TYPE	400	108	233	13

Figure S189. Get High-res Image Gene #41: 'xq gain' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

'xq gain' versus 'GENDER'

P value = 0.0104 (Fisher's exact test), Q value = 0.045

Table S190. Gene #41: 'xq gain' versus Clinical Feature #7: 'GENDER'

nPatients	FEMALE	MALE
ALL	292	589
XQ GAIN MUTATED	29	96
XQ GAIN WILD-TYPE	263	493

Figure S190. Get High-res Image Gene #41: 'xq gain' versus Clinical Feature #7: 'GENDER'

'xq gain' versus 'HISTOLOGICAL_TYPE'

P value = 1e-05 (Fisher's exact test), Q value = 0.00011

Table S191. Gene #41: 'xq gain' versus Clinical Feature #10: 'HISTOLOGICAL_TYPE'

nPatients	KIDNEY CHROMOPHOBE	KIDNEY CLEAR CELL RENAL CARCINOMA	KIDNEY PAPILLARY RENAL CELL CARCINOMA
ALL	66	528	287
XQ GAIN MUTATED	7	30	88
XQ GAIN WILD-TYPE	59	498	199

Figure S191. Get High-res Image Gene #41: 'xq gain' versus Clinical Feature #10: 'HISTOLOGICAL_TYPE'

'xq gain' versus 'RACE'

P value = 0.0352 (Fisher's exact test), Q value = 0.12

Table S192. Gene #41: 'xq gain' versus Clinical Feature #13: 'RACE'

nPatients	AMERICAN INDIAN OR ALASKA NATIVE	ASIAN	BLACK OR AFRICAN AMERICAN	WHITE
ALL	2	15	121	719
XQ GAIN MUTATED	2	2	19	96
XQ GAIN WILD-TYPE	0	13	102	623

Figure S192. Get High-res Image Gene #41: 'xq gain' versus Clinical Feature #13: 'RACE'

'1p loss' versus 'YEARS_TO_BIRTH'

P value = 0.0183 (Wilcoxon-test), Q value = 0.073

Table S193. Gene #42: '1p loss' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

	nPatients	Mean (Std.Dev)
ALL	875	60.1 (12.5)
1P LOSS MUTATED	145	57.6 (14.1)
1P LOSS WILD-TYPE	730	60.6 (12.1)

Figure S193. Get High-res Image Gene #42: '1p loss' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'1p loss' versus 'PATHOLOGIC_STAGE'

P value = 6e-05 (Fisher's exact test), Q value = 0.00053

Table S194. Gene #42: '1p loss' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

nPatients	STAGE I	STAGE II	STAGE III	STAGE IV
ALL	455	104	191	104
1P LOSS MUTATED	56	34	32	16
1P LOSS WILD-TYPE	399	70	159	88

Figure S194. Get High-res Image Gene #42: '1p loss' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

'1p loss' versus 'PATHOLOGY_T_STAGE'

P value = 1e-05 (Fisher's exact test), Q value = 0.00011

Table S195. Gene #42: '1p loss' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

nPatients	T1	T2	T3	T4
ALL	479	127	258	15
1P LOSS MUTATED	61	38	41	5
1P LOSS WILD-TYPE	418	89	217	10

Figure S195. Get High-res Image Gene #42: '1p loss' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

'1p loss' versus 'HISTOLOGICAL_TYPE'

P value = 1e-05 (Fisher's exact test), Q value = 0.00011

Table S196. Gene #42: '1p loss' versus Clinical Feature #10: 'HISTOLOGICAL_TYPE'

nPatients	KIDNEY CHROMOPHOBE	KIDNEY CLEAR CELL RENAL CARCINOMA	KIDNEY PAPILLARY RENAL CELL CARCINOMA
ALL	66	528	287
1P LOSS MUTATED	53	60	32
1P LOSS WILD-TYPE	13	468	255

Figure S196. Get High-res Image Gene #42: '1p loss' versus Clinical Feature #10: 'HISTOLOGICAL_TYPE'

'1q loss' versus 'Time to Death'

P value = 0.0388 (logrank test), Q value = 0.13

Table S197. Gene #43: '1q loss' versus Clinical Feature #1: 'Time to Death'

	nPatients	nDeath	Duration Range (Median), Month
ALL	873	228	0.1 - 194.8 (34.5)
1Q LOSS MUTATED	109	25	0.1 - 152.0 (49.3)
1Q LOSS WILD-TYPE	764	203	0.1 - 194.8 (32.8)

Figure S197. Get High-res Image Gene #43: '1q loss' versus Clinical Feature #1: 'Time to Death'

'1q loss' versus 'YEARS_TO_BIRTH'

P value = 0.000693 (Wilcoxon-test), Q value = 0.0049

Table S198. Gene #43: '1q loss' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

	nPatients	Mean (Std.Dev)
ALL	875	60.1 (12.5)
1Q LOSS MUTATED	110	55.8 (14.2)
1Q LOSS WILD-TYPE	765	60.7 (12.1)

Figure S198. Get High-res Image Gene #43: '1q loss' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'1q loss' versus 'PATHOLOGIC_STAGE'

P value = 1e-05 (Fisher's exact test), Q value = 0.00011

Table S199. Gene #43: '1q loss' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

nPatients	STAGE I	STAGE II	STAGE III	STAGE IV
ALL	455	104	191	104
1Q LOSS MUTATED	42	30	21	12
1Q LOSS WILD-TYPE	413	74	170	92

Figure S199. Get High-res Image Gene #43: '1q loss' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

'1q loss' versus 'PATHOLOGY_T_STAGE'

P value = 5e-05 (Fisher's exact test), Q value = 0.00045

Table S200. Gene #43: '1q loss' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

nPatients	T1	T2	T3	T4
ALL	479	127	258	15
1Q LOSS MUTATED	45	31	30	4
1Q LOSS WILD-TYPE	434	96	228	11

Figure S200. Get High-res Image Gene #43: '1q loss' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

'1q loss' versus 'HISTOLOGICAL_TYPE'

P value = 1e-05 (Fisher's exact test), Q value = 0.00011

Table S201. Gene #43: '1q loss' versus Clinical Feature #10: 'HISTOLOGICAL_TYPE'

nPatients	KIDNEY CHROMOPHOBE	KIDNEY CLEAR CELL RENAL CARCINOMA	KIDNEY PAPILLARY RENAL CELL CARCINOMA
ALL	66	528	287
1Q LOSS MUTATED	52	37	21
1Q LOSS WILD-TYPE	14	491	266

Figure S201. Get High-res Image Gene #43: '1q loss' versus Clinical Feature #10: 'HISTOLOGICAL_TYPE'

'2p loss' versus 'Time to Death'

P value = 0.00434 (logrank test), Q value = 0.023

Table S202. Gene #44: '2p loss' versus Clinical Feature #1: 'Time to Death'

	nPatients	nDeath	Duration Range (Median), Month
ALL	873	228	0.1 - 194.8 (34.5)
2P LOSS MUTATED	63	12	2.5 - 152.0 (66.5)
2P LOSS WILD-TYPE	810	216	0.1 - 194.8 (31.8)

Figure S202. Get High-res Image Gene #44: '2p loss' versus Clinical Feature #1: 'Time to Death'

'2p loss' versus 'YEARS_TO_BIRTH'

P value = 4.59e-05 (Wilcoxon-test), Q value = 0.00043

Table S203. Gene #44: '2p loss' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

	nPatients	Mean (Std.Dev)
ALL	875	60.1 (12.5)
2P LOSS MUTATED	64	53.4 (14.2)
2P LOSS WILD-TYPE	811	60.7 (12.2)

Figure S203. Get High-res Image Gene #44: '2p loss' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'2p loss' versus 'PATHOLOGIC_STAGE'

P value = 1e-05 (Fisher's exact test), Q value = 0.00011

Table S204. Gene #44: '2p loss' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

nPatients	STAGE I	STAGE II	STAGE III	STAGE IV
ALL	455	104	191	104
2P LOSS MUTATED	20	24	14	5
2P LOSS WILD-TYPE	435	80	177	99

Figure S204. Get High-res Image Gene #44: '2p loss' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

'2p loss' versus 'PATHOLOGY_T_STAGE'

P value = 2e-05 (Fisher's exact test), Q value = 0.00021

Table S205. Gene #44: '2p loss' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

nPatients	T1	T2	T3	T4
ALL	479	127	258	15
2P LOSS MUTATED	21	25	18	1
2P LOSS WILD-TYPE	458	102	240	14

Figure S205. Get High-res Image Gene #44: '2p loss' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

'2p loss' versus 'PATHOLOGY_M_STAGE'

P value = 0.0701 (Fisher's exact test), Q value = 0.2

Table S206. Gene #44: '2p loss' versus Clinical Feature #6: 'PATHOLOGY_M_STAGE'

nPatients	0	1
ALL	545	89
2P LOSS MUTATED	42	2
2P LOSS WILD-TYPE	503	87

Figure S206. Get High-res Image Gene #44: '2p loss' versus Clinical Feature #6: 'PATHOLOGY_M_STAGE'

'2p loss' versus 'KARNOFSKY_PERFORMANCE_SCORE'

P value = 0.0463 (Wilcoxon-test), Q value = 0.15

Table S207. Gene #44: '2p loss' versus Clinical Feature #9: 'KARNOFSKY_PERFORMANCE_SCORE'

	nPatients	Mean (Std.Dev)
ALL	142	87.6 (22.8)
2P LOSS MUTATED	9	97.8 (4.4)
2P LOSS WILD-TYPE	133	86.9 (23.4)

Figure S207. Get High-res Image Gene #44: '2p loss' versus Clinical Feature #9: 'KARNOFSKY_PERFORMANCE_SCORE'

'2p loss' versus 'HISTOLOGICAL_TYPE'

P value = 1e-05 (Fisher's exact test), Q value = 0.00011

Table S208. Gene #44: '2p loss' versus Clinical Feature #10: 'HISTOLOGICAL_TYPE'

nPatients	KIDNEY CHROMOPHOBE	KIDNEY CLEAR CELL RENAL CARCINOMA	KIDNEY PAPILLARY RENAL CELL CARCINOMA
ALL	66	528	287
2P LOSS MUTATED	46	14	5
2P LOSS WILD-TYPE	20	514	282

Figure S208. Get High-res Image Gene #44: '2p loss' versus Clinical Feature #10: 'HISTOLOGICAL_TYPE'

'2q loss' versus 'Time to Death'

P value = 0.00302 (logrank test), Q value = 0.017

Table S209. Gene #45: '2q loss' versus Clinical Feature #1: 'Time to Death'

	nPatients	nDeath	Duration Range (Median), Month
ALL	873	228	0.1 - 194.8 (34.5)
2Q LOSS MUTATED	61	11	2.5 - 152.0 (66.5)
2Q LOSS WILD-TYPE	812	217	0.1 - 194.8 (31.8)

Figure S209. Get High-res Image Gene #45: '2q loss' versus Clinical Feature #1: 'Time to Death'

'2q loss' versus 'YEARS_TO_BIRTH'

P value = 2.61e-05 (Wilcoxon-test), Q value = 0.00027

Table S210. Gene #45: '2q loss' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

	nPatients	Mean (Std.Dev)
ALL	875	60.1 (12.5)
2Q LOSS MUTATED	62	53.0 (14.3)
2Q LOSS WILD-TYPE	813	60.7 (12.2)

Figure S210. Get High-res Image Gene #45: '2q loss' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'2q loss' versus 'PATHOLOGIC_STAGE'

P value = 1e-05 (Fisher's exact test), Q value = 0.00011

Table S211. Gene #45: '2q loss' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

nPatients	STAGE I	STAGE II	STAGE III	STAGE IV
ALL	455	104	191	104
2Q LOSS MUTATED	19	24	14	5
2Q LOSS WILD-TYPE	436	80	177	99

Figure S211. Get High-res Image Gene #45: '2q loss' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

'2q loss' versus 'PATHOLOGY_T_STAGE'

P value = 1e-05 (Fisher's exact test), Q value = 0.00011

Table S212. Gene #45: '2q loss' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

nPatients	T1	T2	T3	T4
ALL	479	127	258	15
2Q LOSS MUTATED	20	24	18	1
2Q LOSS WILD-TYPE	459	103	240	14

Figure S212. Get High-res Image Gene #45: '2q loss' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

'2q loss' versus 'PATHOLOGY_M_STAGE'

P value = 0.07 (Fisher's exact test), Q value = 0.2

Table S213. Gene #45: '2q loss' versus Clinical Feature #6: 'PATHOLOGY_M_STAGE'

nPatients	0	1
ALL	545	89
2Q LOSS MUTATED	41	2
2Q LOSS WILD-TYPE	504	87

Figure S213. Get High-res Image Gene #45: '2q loss' versus Clinical Feature #6: 'PATHOLOGY_M_STAGE'

'2q loss' versus 'KARNOFSKY_PERFORMANCE_SCORE'

P value = 0.0463 (Wilcoxon-test), Q value = 0.15

Table S214. Gene #45: '2q loss' versus Clinical Feature #9: 'KARNOFSKY_PERFORMANCE_SCORE'

	nPatients	Mean (Std.Dev)
ALL	142	87.6 (22.8)
2Q LOSS MUTATED	9	97.8 (4.4)
2Q LOSS WILD-TYPE	133	86.9 (23.4)

Figure S214. Get High-res Image Gene #45: '2q loss' versus Clinical Feature #9: 'KARNOFSKY_PERFORMANCE_SCORE'

'2q loss' versus 'HISTOLOGICAL_TYPE'

P value = 1e-05 (Fisher's exact test), Q value = 0.00011

Table S215. Gene #45: '2q loss' versus Clinical Feature #10: 'HISTOLOGICAL_TYPE'

nPatients	KIDNEY CHROMOPHOBE	KIDNEY CLEAR CELL RENAL CARCINOMA	KIDNEY PAPILLARY RENAL CELL CARCINOMA
ALL	66	528	287
2Q LOSS MUTATED	46	14	3
2Q LOSS WILD-TYPE	20	514	284

Figure S215. Get High-res Image Gene #45: '2q loss' versus Clinical Feature #10: 'HISTOLOGICAL_TYPE'

'3p loss' versus 'Time to Death'

P value = 0.00243 (logrank test), Q value = 0.014

Table S216. Gene #46: '3p loss' versus Clinical Feature #1: 'Time to Death'

	nPatients	nDeath	Duration Range (Median), Month
ALL	873	228	0.1 - 194.8 (34.5)
3P LOSS MUTATED	411	135	0.1 - 141.7 (39.0)
3P LOSS WILD-TYPE	462	93	0.1 - 194.8 (29.7)

Figure S216. Get High-res Image Gene #46: '3p loss' versus Clinical Feature #1: 'Time to Death'

'3p loss' versus 'PATHOLOGIC_STAGE'

P value = 0.00045 (Fisher's exact test), Q value = 0.0033

Table S217. Gene #46: '3p loss' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

nPatients	STAGE I	STAGE II	STAGE III	STAGE IV
ALL	455	104	191	104
3P LOSS MUTATED	191	50	113	57
3P LOSS WILD-TYPE	264	54	78	47

Figure S217. Get High-res Image Gene #46: '3p loss' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

'3p loss' versus 'PATHOLOGY_T_STAGE'

P value = 4e-05 (Fisher's exact test), Q value = 0.00038

Table S218. Gene #46: '3p loss' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

nPatients	T1	T2	T3	T4
ALL	479	127	258	15
3P LOSS MUTATED	195	62	151	4
3P LOSS WILD-TYPE	284	65	107	11

Figure S218. Get High-res Image Gene #46: '3p loss' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

'3p loss' versus 'PATHOLOGY_N_STAGE'

P value = 0.0506 (Fisher's exact test), Q value = 0.16

Table S219. Gene #46: '3p loss' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

nPatients	N0	N1	N2
ALL	322	44	7
3P LOSS MUTATED	178	17	2
3P LOSS WILD-TYPE	144	27	5

Figure S219. Get High-res Image Gene #46: '3p loss' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

'3p loss' versus 'HISTOLOGICAL_TYPE'

P value = 1e-05 (Fisher's exact test), Q value = 0.00011

Table S220. Gene #46: '3p loss' versus Clinical Feature #10: 'HISTOLOGICAL_TYPE'

nPatients	KIDNEY CHROMOPHOBE	KIDNEY CLEAR CELL RENAL CARCINOMA	KIDNEY PAPILLARY RENAL CELL CARCINOMA
ALL	66	528	287
3P LOSS MUTATED	9	381	22
3P LOSS WILD-TYPE	57	147	265

Figure S220. Get High-res Image Gene #46: '3p loss' versus Clinical Feature #10: 'HISTOLOGICAL_TYPE'

'3p loss' versus 'YEAR_OF_TOBACCO_SMOKING_ONSET'

P value = 0.0264 (Wilcoxon-test), Q value = 0.098

Table S221. Gene #46: '3p loss' versus Clinical Feature #12: 'YEAR_OF_TOBACCO_SMOKING_ONSET'

	nPatients	Mean (Std.Dev)
ALL	74	1973.7 (16.0)
3P LOSS MUTATED	16	1981.4 (18.7)
3P LOSS WILD-TYPE	58	1971.6 (14.6)

Figure S221. Get High-res Image Gene #46: '3p loss' versus Clinical Feature #12: 'YEAR_OF_TOBACCO_SMOKING_ONSET'

'3p loss' versus 'RACE'

P value = 0.00068 (Fisher's exact test), Q value = 0.0048

Table S222. Gene #46: '3p loss' versus Clinical Feature #13: 'RACE'

nPatients	AMERICAN INDIAN OR ALASKA NATIVE	ASIAN	BLACK OR AFRICAN AMERICAN	WHITE
ALL	2	15	121	719
3P LOSS MUTATED	0	6	39	360
3P LOSS WILD-TYPE	2	9	82	359

Figure S222. Get High-res Image Gene #46: '3p loss' versus Clinical Feature #13: 'RACE'

'3q loss' versus 'YEARS_TO_BIRTH'

P value = 0.0446 (Wilcoxon-test), Q value = 0.15

Table S223. Gene #47: '3q loss' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

	nPatients	Mean (Std.Dev)
ALL	875	60.1 (12.5)
3Q LOSS MUTATED	124	62.4 (13.1)
3Q LOSS WILD-TYPE	751	59.8 (12.4)

Figure S223. Get High-res Image Gene #47: '3q loss' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'3q loss' versus 'GENDER'

P value = 0.0397 (Fisher's exact test), Q value = 0.13

Table S224. Gene #47: '3q loss' versus Clinical Feature #7: 'GENDER'

nPatients	FEMALE	MALE
ALL	292	589
3Q LOSS MUTATED	31	93
3Q LOSS WILD-TYPE	261	496

Figure S224. Get High-res Image Gene #47: '3q loss' versus Clinical Feature #7: 'GENDER'

'3q loss' versus 'RADIATION_THERAPY'

P value = 0.0164 (Fisher's exact test), Q value = 0.066

Table S225. Gene #47: '3q loss' versus Clinical Feature #8: 'RADIATION_THERAPY'

nPatients	NO	YES
ALL	400	3
3Q LOSS MUTATED	29	2
3Q LOSS WILD-TYPE	371	1

Figure S225. Get High-res Image Gene #47: '3q loss' versus Clinical Feature #8: 'RADIATION_THERAPY'

'3q loss' versus 'HISTOLOGICAL_TYPE'

P value = 1e-05 (Fisher's exact test), Q value = 0.00011

Table S226. Gene #47: '3q loss' versus Clinical Feature #10: 'HISTOLOGICAL_TYPE'

nPatients	KIDNEY CHROMOPHOBE	KIDNEY CLEAR CELL RENAL CARCINOMA	KIDNEY PAPILLARY RENAL CELL CARCINOMA
ALL	66	528	287
3Q LOSS MUTATED	8	109	7
3Q LOSS WILD-TYPE	58	419	280

Figure S226. Get High-res Image Gene #47: '3q loss' versus Clinical Feature #10: 'HISTOLOGICAL_TYPE'

'3q loss' versus 'RACE'

P value = 0.0395 (Fisher's exact test), Q value = 0.13

Table S227. Gene #47: '3q loss' versus Clinical Feature #13: 'RACE'

nPatients	AMERICAN INDIAN OR ALASKA NATIVE	ASIAN	BLACK OR AFRICAN AMERICAN	WHITE
ALL	2	15	121	719
3Q LOSS MUTATED	0	1	8	112
3Q LOSS WILD-TYPE	2	14	113	607

Figure S227. Get High-res Image Gene #47: '3q loss' versus Clinical Feature #13: 'RACE'

'4p loss' versus 'Time to Death'

P value = 5.05e-12 (logrank test), Q value = 1.9e-09

Table S228. Gene #48: '4p loss' versus Clinical Feature #1: 'Time to Death'

	nPatients	nDeath	Duration Range (Median), Month
ALL	873	228	0.1 - 194.8 (34.5)
4P LOSS MUTATED	97	51	0.5 - 133.7 (27.6)
4P LOSS WILD-TYPE	776	177	0.1 - 194.8 (35.5)

Figure S228. Get High-res Image Gene #48: '4p loss' versus Clinical Feature #1: 'Time to Death'

'4p loss' versus 'PATHOLOGIC_STAGE'

P value = 1e-05 (Fisher's exact test), Q value = 0.00011

Table S229. Gene #48: '4p loss' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

nPatients	STAGE I	STAGE II	STAGE III	STAGE IV
ALL	455	104	191	104
4P LOSS MUTATED	25	7	40	23
4P LOSS WILD-TYPE	430	97	151	81

Figure S229. Get High-res Image Gene #48: '4p loss' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

'4p loss' versus 'PATHOLOGY_T_STAGE'

P value = 1e-05 (Fisher's exact test), Q value = 0.00011

Table S230. Gene #48: '4p loss' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

nPatients	T1	T2	T3	T4
ALL	479	127	258	15
4P LOSS MUTATED	27	11	55	5
4P LOSS WILD-TYPE	452	116	203	10

Figure S230. Get High-res Image Gene #48: '4p loss' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

'4p loss' versus 'PATHOLOGY_N_STAGE'

P value = 0.00195 (Fisher's exact test), Q value = 0.011

Table S231. Gene #48: '4p loss' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

nPatients	N0	N1	N2
ALL	322	44	7
4P LOSS MUTATED	36	14	1
4P LOSS WILD-TYPE	286	30	6

Figure S231. Get High-res Image Gene #48: '4p loss' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

'4p loss' versus 'PATHOLOGY_M_STAGE'

P value = 0.0146 (Fisher's exact test), Q value = 0.06

Table S232. Gene #48: '4p loss' versus Clinical Feature #6: 'PATHOLOGY_M_STAGE'

nPatients	0	1
ALL	545	89
4P LOSS MUTATED	61	19
4P LOSS WILD-TYPE	484	70

Figure S232. Get High-res Image Gene #48: '4p loss' versus Clinical Feature #6: 'PATHOLOGY_M_STAGE'

'4p loss' versus 'GENDER'

P value = 0.068 (Fisher's exact test), Q value = 0.2

Table S233. Gene #48: '4p loss' versus Clinical Feature #7: 'GENDER'

nPatients	FEMALE	MALE
ALL	292	589
4P LOSS MUTATED	41	57
4P LOSS WILD-TYPE	251	532

Figure S233. Get High-res Image Gene #48: '4p loss' versus Clinical Feature #7: 'GENDER'

'4p loss' versus 'HISTOLOGICAL_TYPE'

P value = 0.00185 (Fisher's exact test), Q value = 0.011

Table S234. Gene #48: '4p loss' versus Clinical Feature #10: 'HISTOLOGICAL_TYPE'

nPatients	KIDNEY CHROMOPHOBE	KIDNEY CLEAR CELL RENAL CARCINOMA	KIDNEY PAPILLARY RENAL CELL CARCINOMA
ALL	66	528	287
4P LOSS MUTATED	1	72	25
4P LOSS WILD-TYPE	65	456	262

Figure S234. Get High-res Image Gene #48: '4p loss' versus Clinical Feature #10: 'HISTOLOGICAL_TYPE'

'4q loss' versus 'Time to Death'

P value = 9.44e-14 (logrank test), Q value = 1.1e-10

Table S235. Gene #49: '4q loss' versus Clinical Feature #1: 'Time to Death'

	nPatients	nDeath	Duration Range (Median), Month
ALL	873	228	0.1 - 194.8 (34.5)
4Q LOSS MUTATED	91	49	1.0 - 133.7 (20.9)
4Q LOSS WILD-TYPE	782	179	0.1 - 194.8 (36.1)

Figure S235. Get High-res Image Gene #49: '4q loss' versus Clinical Feature #1: 'Time to Death'

'4q loss' versus 'PATHOLOGIC_STAGE'

P value = 1e-05 (Fisher's exact test), Q value = 0.00011

Table S236. Gene #49: '4q loss' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

nPatients	STAGE I	STAGE II	STAGE III	STAGE IV
ALL	455	104	191	104
4Q LOSS MUTATED	20	7	37	25
4Q LOSS WILD-TYPE	435	97	154	79

Figure S236. Get High-res Image Gene #49: '4q loss' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

'4q loss' versus 'PATHOLOGY_T_STAGE'

P value = 1e-05 (Fisher's exact test), Q value = 0.00011

Table S237. Gene #49: '4q loss' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

nPatients	T1	T2	T3	T4
ALL	479	127	258	15
4Q LOSS MUTATED	22	12	52	6
4Q LOSS WILD-TYPE	457	115	206	9

Figure S237. Get High-res Image Gene #49: '4q loss' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

'4q loss' versus 'PATHOLOGY_N_STAGE'

P value = 0.00138 (Fisher's exact test), Q value = 0.0084

Table S238. Gene #49: '4q loss' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

nPatients	N0	N1	N2
ALL	322	44	7
4Q LOSS MUTATED	31	13	1
4Q LOSS WILD-TYPE	291	31	6

Figure S238. Get High-res Image Gene #49: '4q loss' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

'4q loss' versus 'PATHOLOGY_M_STAGE'

P value = 0.000616 (Fisher's exact test), Q value = 0.0044

Table S239. Gene #49: '4q loss' versus Clinical Feature #6: 'PATHOLOGY_M_STAGE'

nPatients	0	1
ALL	545	89
4Q LOSS MUTATED	54	21
4Q LOSS WILD-TYPE	491	68

Figure S239. Get High-res Image Gene #49: '4q loss' versus Clinical Feature #6: 'PATHOLOGY_M_STAGE'

'4q loss' versus 'HISTOLOGICAL_TYPE'

P value = 0.00847 (Fisher's exact test), Q value = 0.038

Table S240. Gene #49: '4q loss' versus Clinical Feature #10: 'HISTOLOGICAL_TYPE'

nPatients	KIDNEY CHROMOPHOBE	KIDNEY CLEAR CELL RENAL CARCINOMA	KIDNEY PAPILLARY RENAL CELL CARCINOMA
ALL	66	528	287
4Q LOSS MUTATED	1	65	26
4Q LOSS WILD-TYPE	65	463	261

Figure S240. Get High-res Image Gene #49: '4q loss' versus Clinical Feature #10: 'HISTOLOGICAL_TYPE'

'4q loss' versus 'RACE'

P value = 0.0785 (Fisher's exact test), Q value = 0.22

Table S241. Gene #49: '4q loss' versus Clinical Feature #13: 'RACE'

nPatients	AMERICAN INDIAN OR ALASKA NATIVE	ASIAN	BLACK OR AFRICAN AMERICAN	WHITE
ALL	2	15	121	719
4Q LOSS MUTATED	0	3	6	77
4Q LOSS WILD-TYPE	2	12	115	642

Figure S241. Get High-res Image Gene #49: '4q loss' versus Clinical Feature #13: 'RACE'

'5p loss' versus 'Time to Death'

P value = 0.052 (logrank test), Q value = 0.16

Table S242. Gene #50: '5p loss' versus Clinical Feature #1: 'Time to Death'

	nPatients	nDeath	Duration Range (Median), Month
ALL	873	228	0.1 - 194.8 (34.5)
5P LOSS MUTATED	23	11	2.8 - 152.0 (24.8)
5P LOSS WILD-TYPE	850	217	0.1 - 194.8 (35.1)

Figure S242. Get High-res Image Gene #50: '5p loss' versus Clinical Feature #1: 'Time to Death'

'5p loss' versus 'YEARS_TO_BIRTH'

P value = 0.00256 (Wilcoxon-test), Q value = 0.014

Table S243. Gene #50: '5p loss' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

	nPatients	Mean (Std.Dev)
ALL	875	60.1 (12.5)
5P LOSS MUTATED	24	51.3 (14.5)
5P LOSS WILD-TYPE	851	60.4 (12.4)

Figure S243. Get High-res Image Gene #50: '5p loss' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'5p loss' versus 'PATHOLOGIC_STAGE'

P value = 1e-05 (Fisher's exact test), Q value = 0.00011

Table S244. Gene #50: '5p loss' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

nPatients	STAGE I	STAGE II	STAGE III	STAGE IV
ALL	455	104	191	104
5P LOSS MUTATED	2	9	5	7
5P LOSS WILD-TYPE	453	95	186	97

Figure S244. Get High-res Image Gene #50: '5p loss' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

'5p loss' versus 'PATHOLOGY_T_STAGE'

P value = 1e-05 (Fisher's exact test), Q value = 0.00011

Table S245. Gene #50: '5p loss' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

nPatients	T1	T2	T3	T4
ALL	479	127	258	15
5P LOSS MUTATED	2	10	10	2
5P LOSS WILD-TYPE	477	117	248	13

Figure S245. Get High-res Image Gene #50: '5p loss' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

'5p loss' versus 'PATHOLOGY_N_STAGE'

P value = 0.0248 (Fisher's exact test), Q value = 0.094

Table S246. Gene #50: '5p loss' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

nPatients	N0	N1	N2
ALL	322	44	7
5P LOSS MUTATED	12	3	2
5P LOSS WILD-TYPE	310	41	5

Figure S246. Get High-res Image Gene #50: '5p loss' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

'5p loss' versus 'GENDER'

P value = 0.045 (Fisher's exact test), Q value = 0.15

Table S247. Gene #50: '5p loss' versus Clinical Feature #7: 'GENDER'

nPatients	FEMALE	MALE
ALL	292	589
5P LOSS MUTATED	13	11
5P LOSS WILD-TYPE	279	578

Figure S247. Get High-res Image Gene #50: '5p loss' versus Clinical Feature #7: 'GENDER'

'5p loss' versus 'HISTOLOGICAL_TYPE'

P value = 1e-05 (Fisher's exact test), Q value = 0.00011

Table S248. Gene #50: '5p loss' versus Clinical Feature #10: 'HISTOLOGICAL_TYPE'

nPatients	KIDNEY CHROMOPHOBE	KIDNEY CLEAR CELL RENAL CARCINOMA	KIDNEY PAPILLARY RENAL CELL CARCINOMA
ALL	66	528	287
5P LOSS MUTATED	10	7	7
5P LOSS WILD-TYPE	56	521	280

Figure S248. Get High-res Image Gene #50: '5p loss' versus Clinical Feature #10: 'HISTOLOGICAL_TYPE'

'5p loss' versus 'NUMBER_PACK_YEARS_SMOKED'

P value = 0.0793 (Wilcoxon-test), Q value = 0.22

Table S249. Gene #50: '5p loss' versus Clinical Feature #11: 'NUMBER_PACK_YEARS_SMOKED'

	nPatients	Mean (Std.Dev)
ALL	106	30.8 (24.9)
5P LOSS MUTATED	5	15.8 (15.7)
5P LOSS WILD-TYPE	101	31.5 (25.0)

Figure S249. Get High-res Image Gene #50: '5p loss' versus Clinical Feature #11: 'NUMBER_PACK_YEARS_SMOKED'

'5p loss' versus 'ETHNICITY'

P value = 0.0863 (Fisher's exact test), Q value = 0.24

Table S250. Gene #50: '5p loss' versus Clinical Feature #14: 'ETHNICITY'

nPatients	HISPANIC OR LATINO	NOT HISPANIC OR LATINO
ALL	42	621
5P LOSS MUTATED	3	14
5P LOSS WILD-TYPE	39	607

Figure S250. Get High-res Image Gene #50: '5p loss' versus Clinical Feature #14: 'ETHNICITY'

'5q loss' versus 'YEARS_TO_BIRTH'

P value = 0.000184 (Wilcoxon-test), Q value = 0.0016

Table S251. Gene #51: '5q loss' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

	nPatients	Mean (Std.Dev)
ALL	875	60.1 (12.5)
5Q LOSS MUTATED	22	48.5 (15.1)
5Q LOSS WILD-TYPE	853	60.4 (12.3)

Figure S251. Get High-res Image Gene #51: '5q loss' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'5q loss' versus 'PATHOLOGIC_STAGE'

P value = 3e-05 (Fisher's exact test), Q value = 0.00029

Table S252. Gene #51: '5q loss' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

nPatients	STAGE I	STAGE II	STAGE III	STAGE IV
ALL	455	104	191	104
5Q LOSS MUTATED	2	9	6	4
5Q LOSS WILD-TYPE	453	95	185	100

Figure S252. Get High-res Image Gene #51: '5q loss' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

'5q loss' versus 'PATHOLOGY_T_STAGE'

P value = 3e-05 (Fisher's exact test), Q value = 0.00029

Table S253. Gene #51: '5q loss' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

nPatients	T1	T2	T3	T4
ALL	479	127	258	15
5Q LOSS MUTATED	2	9	9	2
5Q LOSS WILD-TYPE	477	118	249	13

Figure S253. Get High-res Image Gene #51: '5q loss' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

'5q loss' versus 'PATHOLOGY_N_STAGE'

P value = 0.0495 (Fisher's exact test), Q value = 0.16

Table S254. Gene #51: '5q loss' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

nPatients	N0	N1	N2
ALL	322	44	7
5Q LOSS MUTATED	10	4	1
5Q LOSS WILD-TYPE	312	40	6

Figure S254. Get High-res Image Gene #51: '5q loss' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

'5q loss' versus 'HISTOLOGICAL_TYPE'

P value = 1e-05 (Fisher's exact test), Q value = 0.00011

Table S255. Gene #51: '5q loss' versus Clinical Feature #10: 'HISTOLOGICAL_TYPE'

nPatients	KIDNEY CHROMOPHOBE	KIDNEY CLEAR CELL RENAL CARCINOMA	KIDNEY PAPILLARY RENAL CELL CARCINOMA
ALL	66	528	287
5Q LOSS MUTATED	10	5	7
5Q LOSS WILD-TYPE	56	523	280

Figure S255. Get High-res Image Gene #51: '5q loss' versus Clinical Feature #10: 'HISTOLOGICAL_TYPE'

'5q loss' versus 'NUMBER_PACK_YEARS_SMOKED'

P value = 0.037 (Wilcoxon-test), Q value = 0.13

Table S256. Gene #51: '5q loss' versus Clinical Feature #11: 'NUMBER_PACK_YEARS_SMOKED'

	nPatients	Mean (Std.Dev)
ALL	106	30.8 (24.9)
5Q LOSS MUTATED	4	12.2 (15.6)
5Q LOSS WILD-TYPE	102	31.5 (24.9)

Figure S256. Get High-res Image Gene #51: '5q loss' versus Clinical Feature #11: 'NUMBER_PACK_YEARS_SMOKED'

'5q loss' versus 'ETHNICITY'

P value = 0.0631 (Fisher's exact test), Q value = 0.19

Table S257. Gene #51: '5q loss' versus Clinical Feature #14: 'ETHNICITY'

nPatients	HISPANIC OR LATINO	NOT HISPANIC OR LATINO
ALL	42	621
5Q LOSS MUTATED	3	12
5Q LOSS WILD-TYPE	39	609

Figure S257. Get High-res Image Gene #51: '5q loss' versus Clinical Feature #14: 'ETHNICITY'

'6p loss' versus 'YEARS_TO_BIRTH'

P value = 0.0737 (Wilcoxon-test), Q value = 0.21

Table S258. Gene #52: '6p loss' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

	nPatients	Mean (Std.Dev)
ALL	875	60.1 (12.5)
6P LOSS MUTATED	170	58.1 (14.7)
6P LOSS WILD-TYPE	705	60.6 (11.9)

Figure S258. Get High-res Image Gene #52: '6p loss' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'6p loss' versus 'PATHOLOGIC_STAGE'

P value = 1e-05 (Fisher's exact test), Q value = 0.00011

Table S259. Gene #52: '6p loss' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

nPatients	STAGE I	STAGE II	STAGE III	STAGE IV
ALL	455	104	191	104
6P LOSS MUTATED	59	36	47	28
6P LOSS WILD-TYPE	396	68	144	76

Figure S259. Get High-res Image Gene #52: '6p loss' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

'6p loss' versus 'PATHOLOGY_T_STAGE'

P value = 1e-05 (Fisher's exact test), Q value = 0.00011

Table S260. Gene #52: '6p loss' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

nPatients	T1	T2	T3	T4
ALL	479	127	258	15
6P LOSS MUTATED	61	39	67	5
6P LOSS WILD-TYPE	418	88	191	10

Figure S260. Get High-res Image Gene #52: '6p loss' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

'6p loss' versus 'HISTOLOGICAL_TYPE'

P value = 1e-05 (Fisher's exact test), Q value = 0.00011

Table S261. Gene #52: '6p loss' versus Clinical Feature #10: 'HISTOLOGICAL_TYPE'

nPatients	KIDNEY CHROMOPHOBE	KIDNEY CLEAR CELL RENAL CARCINOMA	KIDNEY PAPILLARY RENAL CELL CARCINOMA
ALL	66	528	287
6P LOSS MUTATED	50	101	21
6P LOSS WILD-TYPE	16	427	266

Figure S261. Get High-res Image Gene #52: '6p loss' versus Clinical Feature #10: 'HISTOLOGICAL_TYPE'

'6p loss' versus 'RACE'

P value = 0.00025 (Fisher's exact test), Q value = 0.002

Table S262. Gene #52: '6p loss' versus Clinical Feature #13: 'RACE'

nPatients	AMERICAN INDIAN OR ALASKA NATIVE	ASIAN	BLACK OR AFRICAN AMERICAN	WHITE
ALL	2	15	121	719
6P LOSS MUTATED	0	4	8	153
6P LOSS WILD-TYPE	2	11	113	566

Figure S262. Get High-res Image Gene #52: '6p loss' versus Clinical Feature #13: 'RACE'

'6q loss' versus 'YEARS_TO_BIRTH'

P value = 0.0738 (Wilcoxon-test), Q value = 0.21

Table S263. Gene #53: '6q loss' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

	nPatients	Mean (Std.Dev)
ALL	875	60.1 (12.5)
6Q LOSS MUTATED	204	58.3 (14.1)
6Q LOSS WILD-TYPE	671	60.7 (11.9)

Figure S263. Get High-res Image Gene #53: '6q loss' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'6q loss' versus 'PATHOLOGIC_STAGE'

P value = 6e-05 (Fisher's exact test), Q value = 0.00053

Table S264. Gene #53: '6q loss' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

nPatients	STAGE I	STAGE II	STAGE III	STAGE IV
ALL	455	104	191	104
6Q LOSS MUTATED	82	40	50	32
6Q LOSS WILD-TYPE	373	64	141	72

Figure S264. Get High-res Image Gene #53: '6q loss' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

'6q loss' versus 'PATHOLOGY_T_STAGE'

P value = 3e-05 (Fisher's exact test), Q value = 0.00029

Table S265. Gene #53: '6q loss' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

nPatients	T1	T2	T3	T4
ALL	479	127	258	15
6Q LOSS MUTATED	83	42	74	7
6Q LOSS WILD-TYPE	396	85	184	8

Figure S265. Get High-res Image Gene #53: '6q loss' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

'6q loss' versus 'HISTOLOGICAL_TYPE'

P value = 1e-05 (Fisher's exact test), Q value = 0.00011

Table S266. Gene #53: '6q loss' versus Clinical Feature #10: 'HISTOLOGICAL_TYPE'

nPatients	KIDNEY CHROMOPHOBE	KIDNEY CLEAR CELL RENAL CARCINOMA	KIDNEY PAPILLARY RENAL CELL CARCINOMA
ALL	66	528	287
6Q LOSS MUTATED	51	129	26
6Q LOSS WILD-TYPE	15	399	261

Figure S266. Get High-res Image Gene #53: '6q loss' versus Clinical Feature #10: 'HISTOLOGICAL_TYPE'

'6q loss' versus 'RACE'

P value = 0.00022 (Fisher's exact test), Q value = 0.0018

Table S267. Gene #53: '6q loss' versus Clinical Feature #13: 'RACE'

nPatients	AMERICAN INDIAN OR ALASKA NATIVE	ASIAN	BLACK OR AFRICAN AMERICAN	WHITE
ALL	2	15	121	719
6Q LOSS MUTATED	0	6	12	180
6Q LOSS WILD-TYPE	2	9	109	539

Figure S267. Get High-res Image Gene #53: '6q loss' versus Clinical Feature #13: 'RACE'

'7p loss' versus 'Time to Death'

P value = 0.089 (logrank test), Q value = 0.25

Table S268. Gene #54: '7p loss' versus Clinical Feature #1: 'Time to Death'

	nPatients	nDeath	Duration Range (Median), Month
ALL	873	228	0.1 - 194.8 (34.5)
7P LOSS MUTATED	4	2	1.4 - 84.9 (9.5)
7P LOSS WILD-TYPE	869	226	0.1 - 194.8 (34.9)

Figure S268. Get High-res Image Gene #54: '7p loss' versus Clinical Feature #1: 'Time to Death'

'7p loss' versus 'PATHOLOGY_N_STAGE'

P value = 0.0498 (Fisher's exact test), Q value = 0.16

Table S269. Gene #54: '7p loss' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

nPatients	N0	N1	N2
ALL	322	44	7
7P LOSS MUTATED	1	2	0
7P LOSS WILD-TYPE	321	42	7

Figure S269. Get High-res Image Gene #54: '7p loss' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

'7q loss' versus 'Time to Death'

P value = 0.089 (logrank test), Q value = 0.25

Table S270. Gene #55: '7q loss' versus Clinical Feature #1: 'Time to Death'

	nPatients	nDeath	Duration Range (Median), Month
ALL	873	228	0.1 - 194.8 (34.5)
7Q LOSS MUTATED	4	2	1.4 - 84.9 (9.5)
7Q LOSS WILD-TYPE	869	226	0.1 - 194.8 (34.9)

Figure S270. Get High-res Image Gene #55: '7q loss' versus Clinical Feature #1: 'Time to Death'

'7q loss' versus 'PATHOLOGY_N_STAGE'

P value = 0.0509 (Fisher's exact test), Q value = 0.16

Table S271. Gene #55: '7q loss' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

nPatients	N0	N1	N2
ALL	322	44	7
7Q LOSS MUTATED	1	2	0
7Q LOSS WILD-TYPE	321	42	7

Figure S271. Get High-res Image Gene #55: '7q loss' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

'8p loss' versus 'Time to Death'

P value = 0.0151 (logrank test), Q value = 0.062

Table S272. Gene #56: '8p loss' versus Clinical Feature #1: 'Time to Death'

	nPatients	nDeath	Duration Range (Median), Month
ALL	873	228	0.1 - 194.8 (34.5)
8P LOSS MUTATED	164	59	0.1 - 137.1 (39.2)
8P LOSS WILD-TYPE	709	169	0.1 - 194.8 (33.2)

Figure S272. Get High-res Image Gene #56: '8p loss' versus Clinical Feature #1: 'Time to Death'

'8p loss' versus 'PATHOLOGIC_STAGE'

P value = 0.0236 (Fisher's exact test), Q value = 0.09

Table S273. Gene #56: '8p loss' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

nPatients	STAGE I	STAGE II	STAGE III	STAGE IV
ALL	455	104	191	104
8P LOSS MUTATED	70	21	42	28
8P LOSS WILD-TYPE	385	83	149	76

Figure S273. Get High-res Image Gene #56: '8p loss' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

'8p loss' versus 'PATHOLOGY_T_STAGE'

P value = 0.0158 (Fisher's exact test), Q value = 0.064

Table S274. Gene #56: '8p loss' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

nPatients	T1	T2	T3	T4
ALL	479	127	258	15
8P LOSS MUTATED	73	24	63	4
8P LOSS WILD-TYPE	406	103	195	11

Figure S274. Get High-res Image Gene #56: '8p loss' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

'8p loss' versus 'PATHOLOGY_M_STAGE'

P value = 0.0572 (Fisher's exact test), Q value = 0.17

Table S275. Gene #56: '8p loss' versus Clinical Feature #6: 'PATHOLOGY_M_STAGE'

nPatients	0	1
ALL	545	89
8P LOSS MUTATED	119	28
8P LOSS WILD-TYPE	426	61

Figure S275. Get High-res Image Gene #56: '8p loss' versus Clinical Feature #6: 'PATHOLOGY_M_STAGE'

'8p loss' versus 'HISTOLOGICAL_TYPE'

P value = 1e-05 (Fisher's exact test), Q value = 0.00011

Table S276. Gene #56: '8p loss' versus Clinical Feature #10: 'HISTOLOGICAL_TYPE'

nPatients	KIDNEY CHROMOPHOBE	KIDNEY CLEAR CELL RENAL CARCINOMA	KIDNEY PAPILLARY RENAL CELL CARCINOMA
ALL	66	528	287
8P LOSS MUTATED	10	138	16
8P LOSS WILD-TYPE	56	390	271

Figure S276. Get High-res Image Gene #56: '8p loss' versus Clinical Feature #10: 'HISTOLOGICAL_TYPE'

'8p loss' versus 'RACE'

P value = 0.00498 (Fisher's exact test), Q value = 0.025

Table S277. Gene #56: '8p loss' versus Clinical Feature #13: 'RACE'

nPatients	AMERICAN INDIAN OR ALASKA NATIVE	ASIAN	BLACK OR AFRICAN AMERICAN	WHITE
ALL	2	15	121	719
8P LOSS MUTATED	0	6	12	144
8P LOSS WILD-TYPE	2	9	109	575

Figure S277. Get High-res Image Gene #56: '8p loss' versus Clinical Feature #13: 'RACE'

'8q loss' versus 'HISTOLOGICAL_TYPE'

P value = 1e-05 (Fisher's exact test), Q value = 0.00011

Table S278. Gene #57: '8q loss' versus Clinical Feature #10: 'HISTOLOGICAL_TYPE'

nPatients	KIDNEY CHROMOPHOBE	KIDNEY CLEAR CELL RENAL CARCINOMA	KIDNEY PAPILLARY RENAL CELL CARCINOMA
ALL	66	528	287
8Q LOSS MUTATED	9	69	9
8Q LOSS WILD-TYPE	57	459	278

Figure S278. Get High-res Image Gene #57: '8q loss' versus Clinical Feature #10: 'HISTOLOGICAL_TYPE'

'9p loss' versus 'Time to Death'

P value = 2.75e-12 (logrank test), Q value = 1.6e-09

Table S279. Gene #58: '9p loss' versus Clinical Feature #1: 'Time to Death'

	nPatients	nDeath	Duration Range (Median), Month
ALL	873	228	0.1 - 194.8 (34.5)
9P LOSS MUTATED	189	89	0.5 - 141.7 (36.2)
9P LOSS WILD-TYPE	684	139	0.1 - 194.8 (34.4)

Figure S279. Get High-res Image Gene #58: '9p loss' versus Clinical Feature #1: 'Time to Death'

'9p loss' versus 'YEARS_TO_BIRTH'

P value = 0.079 (Wilcoxon-test), Q value = 0.22

Table S280. Gene #58: '9p loss' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

	nPatients	Mean (Std.Dev)
ALL	875	60.1 (12.5)
9P LOSS MUTATED	190	61.4 (12.0)
9P LOSS WILD-TYPE	685	59.8 (12.6)

Figure S280. Get High-res Image Gene #58: '9p loss' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'9p loss' versus 'PATHOLOGIC_STAGE'

P value = 1e-05 (Fisher's exact test), Q value = 0.00011

Table S281. Gene #58: '9p loss' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

nPatients	STAGE I	STAGE II	STAGE III	STAGE IV
ALL	455	104	191	104
9P LOSS MUTATED	65	15	65	44
9P LOSS WILD-TYPE	390	89	126	60

Figure S281. Get High-res Image Gene #58: '9p loss' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

'9p loss' versus 'PATHOLOGY_T_STAGE'

P value = 1e-05 (Fisher's exact test), Q value = 0.00011

Table S282. Gene #58: '9p loss' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

nPatients	T1	T2	T3	T4
ALL	479	127	258	15
9P LOSS MUTATED	69	22	93	8
9P LOSS WILD-TYPE	410	105	165	7

Figure S282. Get High-res Image Gene #58: '9p loss' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

'9p loss' versus 'PATHOLOGY_N_STAGE'

P value = 0.00502 (Fisher's exact test), Q value = 0.025

Table S283. Gene #58: '9p loss' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

nPatients	N0	N1	N2
ALL	322	44	7
9P LOSS MUTATED	71	19	3
9P LOSS WILD-TYPE	251	25	4

Figure S283. Get High-res Image Gene #58: '9p loss' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

'9p loss' versus 'PATHOLOGY_M_STAGE'

P value = 0.000356 (Fisher's exact test), Q value = 0.0027

Table S284. Gene #58: '9p loss' versus Clinical Feature #6: 'PATHOLOGY_M_STAGE'

nPatients	0	1
ALL	545	89
9P LOSS MUTATED	125	37
9P LOSS WILD-TYPE	420	52

Figure S284. Get High-res Image Gene #58: '9p loss' versus Clinical Feature #6: 'PATHOLOGY_M_STAGE'

'9p loss' versus 'KARNOFSKY_PERFORMANCE_SCORE'

P value = 0.00208 (Wilcoxon-test), Q value = 0.012

Table S285. Gene #58: '9p loss' versus Clinical Feature #9: 'KARNOFSKY_PERFORMANCE_SCORE'

	nPatients	Mean (Std.Dev)
ALL	142	87.6 (22.8)
9P LOSS MUTATED	28	76.8 (31.7)
9P LOSS WILD-TYPE	114	90.3 (19.3)

Figure S285. Get High-res Image Gene #58: '9p loss' versus Clinical Feature #9: 'KARNOFSKY_PERFORMANCE_SCORE'

'9p loss' versus 'HISTOLOGICAL_TYPE'

P value = 1e-05 (Fisher's exact test), Q value = 0.00011

Table S286. Gene #58: '9p loss' versus Clinical Feature #10: 'HISTOLOGICAL_TYPE'

nPatients	KIDNEY CHROMOPHOBE	KIDNEY CLEAR CELL RENAL CARCINOMA	KIDNEY PAPILLARY RENAL CELL CARCINOMA
ALL	66	528	287
9P LOSS MUTATED	10	149	33
9P LOSS WILD-TYPE	56	379	254

Figure S286. Get High-res Image Gene #58: '9p loss' versus Clinical Feature #10: 'HISTOLOGICAL_TYPE'

'9p loss' versus 'RACE'

P value = 0.0134 (Fisher's exact test), Q value = 0.056

Table S287. Gene #58: '9p loss' versus Clinical Feature #13: 'RACE'

nPatients	AMERICAN INDIAN OR ALASKA NATIVE	ASIAN	BLACK OR AFRICAN AMERICAN	WHITE
ALL	2	15	121	719
9P LOSS MUTATED	0	3	14	170
9P LOSS WILD-TYPE	2	12	107	549

Figure S287. Get High-res Image Gene #58: '9p loss' versus Clinical Feature #13: 'RACE'

'9q loss' versus 'Time to Death'

P value = 3.54e-10 (logrank test), Q value = 1e-07

Table S288. Gene #59: '9q loss' versus Clinical Feature #1: 'Time to Death'

	nPatients	nDeath	Duration Range (Median), Month
ALL	873	228	0.1 - 194.8 (34.5)
9Q LOSS MUTATED	191	86	0.5 - 141.7 (36.2)
9Q LOSS WILD-TYPE	682	142	0.1 - 194.8 (34.3)

Figure S288. Get High-res Image Gene #59: '9q loss' versus Clinical Feature #1: 'Time to Death'

'9q loss' versus 'YEARS_TO_BIRTH'

P value = 0.0734 (Wilcoxon-test), Q value = 0.21

Table S289. Gene #59: '9q loss' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

	nPatients	Mean (Std.Dev)
ALL	875	60.1 (12.5)
9Q LOSS MUTATED	192	61.4 (12.2)
9Q LOSS WILD-TYPE	683	59.8 (12.6)

Figure S289. Get High-res Image Gene #59: '9q loss' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'9q loss' versus 'PATHOLOGIC_STAGE'

P value = 1e-05 (Fisher's exact test), Q value = 0.00011

Table S290. Gene #59: '9q loss' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

nPatients	STAGE I	STAGE II	STAGE III	STAGE IV
ALL	455	104	191	104
9Q LOSS MUTATED	63	19	68	42
9Q LOSS WILD-TYPE	392	85	123	62

Figure S290. Get High-res Image Gene #59: '9q loss' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

'9q loss' versus 'PATHOLOGY_T_STAGE'

P value = 1e-05 (Fisher's exact test), Q value = 0.00011

Table S291. Gene #59: '9q loss' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

nPatients	T1	T2	T3	T4
ALL	479	127	258	15
9Q LOSS MUTATED	66	23	99	6
9Q LOSS WILD-TYPE	413	104	159	9

Figure S291. Get High-res Image Gene #59: '9q loss' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

'9q loss' versus 'PATHOLOGY_N_STAGE'

P value = 0.0146 (Fisher's exact test), Q value = 0.06

Table S292. Gene #59: '9q loss' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

nPatients	N0	N1	N2
ALL	322	44	7
9Q LOSS MUTATED	73	18	3
9Q LOSS WILD-TYPE	249	26	4

Figure S292. Get High-res Image Gene #59: '9q loss' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

'9q loss' versus 'PATHOLOGY_M_STAGE'

P value = 0.00107 (Fisher's exact test), Q value = 0.0069

Table S293. Gene #59: '9q loss' versus Clinical Feature #6: 'PATHOLOGY_M_STAGE'

nPatients	0	1
ALL	545	89
9Q LOSS MUTATED	128	36
9Q LOSS WILD-TYPE	417	53

Figure S293. Get High-res Image Gene #59: '9q loss' versus Clinical Feature #6: 'PATHOLOGY_M_STAGE'

'9q loss' versus 'KARNOFSKY_PERFORMANCE_SCORE'

P value = 0.00132 (Wilcoxon-test), Q value = 0.0082

Table S294. Gene #59: '9q loss' versus Clinical Feature #9: 'KARNOFSKY_PERFORMANCE_SCORE'

	nPatients	Mean (Std.Dev)
ALL	142	87.6 (22.8)
9Q LOSS MUTATED	25	74.8 (33.1)
9Q LOSS WILD-TYPE	117	90.3 (19.1)

Figure S294. Get High-res Image Gene #59: '9q loss' versus Clinical Feature #9: 'KARNOFSKY_PERFORMANCE_SCORE'

'9q loss' versus 'HISTOLOGICAL_TYPE'

P value = 1e-05 (Fisher's exact test), Q value = 0.00011

Table S295. Gene #59: '9q loss' versus Clinical Feature #10: 'HISTOLOGICAL_TYPE'

nPatients	KIDNEY CHROMOPHOBE	KIDNEY CLEAR CELL RENAL CARCINOMA	KIDNEY PAPILLARY RENAL CELL CARCINOMA
ALL	66	528	287
9Q LOSS MUTATED	11	150	33
9Q LOSS WILD-TYPE	55	378	254

Figure S295. Get High-res Image Gene #59: '9q loss' versus Clinical Feature #10: 'HISTOLOGICAL_TYPE'

'9q loss' versus 'RACE'

P value = 0.0113 (Fisher's exact test), Q value = 0.048

Table S296. Gene #59: '9q loss' versus Clinical Feature #13: 'RACE'

nPatients	AMERICAN INDIAN OR ALASKA NATIVE	ASIAN	BLACK OR AFRICAN AMERICAN	WHITE
ALL	2	15	121	719
9Q LOSS MUTATED	0	3	14	172
9Q LOSS WILD-TYPE	2	12	107	547

Figure S296. Get High-res Image Gene #59: '9q loss' versus Clinical Feature #13: 'RACE'

'10p loss' versus 'YEARS_TO_BIRTH'

P value = 0.0621 (Wilcoxon-test), Q value = 0.19

Table S297. Gene #60: '10p loss' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

	nPatients	Mean (Std.Dev)
ALL	875	60.1 (12.5)
10P LOSS MUTATED	130	57.7 (14.6)
10P LOSS WILD-TYPE	745	60.6 (12.1)

Figure S297. Get High-res Image Gene #60: '10p loss' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'10p loss' versus 'PATHOLOGIC_STAGE'

P value = 1e-05 (Fisher's exact test), Q value = 0.00011

Table S298. Gene #60: '10p loss' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

nPatients	STAGE I	STAGE II	STAGE III	STAGE IV
ALL	455	104	191	104
10P LOSS MUTATED	42	26	42	19
10P LOSS WILD-TYPE	413	78	149	85

Figure S298. Get High-res Image Gene #60: '10p loss' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

'10p loss' versus 'PATHOLOGY_T_STAGE'

P value = 1e-05 (Fisher's exact test), Q value = 0.00011

Table S299. Gene #60: '10p loss' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

nPatients	T1	T2	T3	T4
ALL	479	127	258	15
10P LOSS MUTATED	44	28	54	5
10P LOSS WILD-TYPE	435	99	204	10

Figure S299. Get High-res Image Gene #60: '10p loss' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

'10p loss' versus 'HISTOLOGICAL_TYPE'

P value = 1e-05 (Fisher's exact test), Q value = 0.00011

Table S300. Gene #60: '10p loss' versus Clinical Feature #10: 'HISTOLOGICAL_TYPE'

nPatients	KIDNEY CHROMOPHOBE	KIDNEY CLEAR CELL RENAL CARCINOMA	KIDNEY PAPILLARY RENAL CELL CARCINOMA
ALL	66	528	287
10P LOSS MUTATED	48	67	16
10P LOSS WILD-TYPE	18	461	271

Figure S300. Get High-res Image Gene #60: '10p loss' versus Clinical Feature #10: 'HISTOLOGICAL_TYPE'

'10q loss' versus 'YEARS_TO_BIRTH'

P value = 0.035 (Wilcoxon-test), Q value = 0.12

Table S301. Gene #61: '10q loss' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

	nPatients	Mean (Std.Dev)
ALL	875	60.1 (12.5)
10Q LOSS MUTATED	154	57.9 (14.2)
10Q LOSS WILD-TYPE	721	60.6 (12.1)

Figure S301. Get High-res Image Gene #61: '10q loss' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'10q loss' versus 'PATHOLOGIC_STAGE'

P value = 1e-05 (Fisher's exact test), Q value = 0.00011

Table S302. Gene #61: '10q loss' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

nPatients	STAGE I	STAGE II	STAGE III	STAGE IV
ALL	455	104	191	104
10Q LOSS MUTATED	51	32	48	24
10Q LOSS WILD-TYPE	404	72	143	80

Figure S302. Get High-res Image Gene #61: '10q loss' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

'10q loss' versus 'PATHOLOGY_T_STAGE'

P value = 1e-05 (Fisher's exact test), Q value = 0.00011

Table S303. Gene #61: '10q loss' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

nPatients	T1	T2	T3	T4
ALL	479	127	258	15
10Q LOSS MUTATED	53	34	62	7
10Q LOSS WILD-TYPE	426	93	196	8

Figure S303. Get High-res Image Gene #61: '10q loss' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

'10q loss' versus 'HISTOLOGICAL_TYPE'

P value = 1e-05 (Fisher's exact test), Q value = 0.00011

Table S304. Gene #61: '10q loss' versus Clinical Feature #10: 'HISTOLOGICAL_TYPE'

nPatients	KIDNEY CHROMOPHOBE	KIDNEY CLEAR CELL RENAL CARCINOMA	KIDNEY PAPILLARY RENAL CELL CARCINOMA
ALL	66	528	287
10Q LOSS MUTATED	49	89	18
10Q LOSS WILD-TYPE	17	439	269

Figure S304. Get High-res Image Gene #61: '10q loss' versus Clinical Feature #10: 'HISTOLOGICAL_TYPE'

'11p loss' versus 'Time to Death'

P value = 0.00492 (logrank test), Q value = 0.025

Table S305. Gene #62: '11p loss' versus Clinical Feature #1: 'Time to Death'

	nPatients	nDeath	Duration Range (Median), Month
ALL	873	228	0.1 - 194.8 (34.5)
11P LOSS MUTATED	42	16	1.0 - 102.8 (21.6)
11P LOSS WILD-TYPE	831	212	0.1 - 194.8 (35.9)

Figure S305. Get High-res Image Gene #62: '11p loss' versus Clinical Feature #1: 'Time to Death'

'11p loss' versus 'YEARS_TO_BIRTH'

P value = 0.0337 (Wilcoxon-test), Q value = 0.12

Table S306. Gene #62: '11p loss' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

	nPatients	Mean (Std.Dev)
ALL	875	60.1 (12.5)
11P LOSS MUTATED	42	63.9 (10.8)
11P LOSS WILD-TYPE	833	59.9 (12.6)

Figure S306. Get High-res Image Gene #62: '11p loss' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'11p loss' versus 'PATHOLOGIC_STAGE'

P value = 0.00129 (Fisher's exact test), Q value = 0.008

Table S307. Gene #62: '11p loss' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

nPatients	STAGE I	STAGE II	STAGE III	STAGE IV
ALL	455	104	191	104
11P LOSS MUTATED	11	10	11	9
11P LOSS WILD-TYPE	444	94	180	95

Figure S307. Get High-res Image Gene #62: '11p loss' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

'11p loss' versus 'PATHOLOGY_T_STAGE'

P value = 0.00078 (Fisher's exact test), Q value = 0.0053

Table S308. Gene #62: '11p loss' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

nPatients	T1	T2	T3	T4
ALL	479	127	258	15
11P LOSS MUTATED	11	10	21	1
11P LOSS WILD-TYPE	468	117	237	14

Figure S308. Get High-res Image Gene #62: '11p loss' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

'11p loss' versus 'PATHOLOGY_N_STAGE'

P value = 0.00107 (Fisher's exact test), Q value = 0.0069

Table S309. Gene #62: '11p loss' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

nPatients	N0	N1	N2
ALL	322	44	7
11P LOSS MUTATED	13	7	2
11P LOSS WILD-TYPE	309	37	5

Figure S309. Get High-res Image Gene #62: '11p loss' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

'11p loss' versus 'HISTOLOGICAL_TYPE'

P value = 0.0161 (Fisher's exact test), Q value = 0.065

Table S310. Gene #62: '11p loss' versus Clinical Feature #10: 'HISTOLOGICAL_TYPE'

nPatients	KIDNEY CHROMOPHOBE	KIDNEY CLEAR CELL RENAL CARCINOMA	KIDNEY PAPILLARY RENAL CELL CARCINOMA
ALL	66	528	287
11P LOSS MUTATED	7	18	18
11P LOSS WILD-TYPE	59	510	269

Figure S310. Get High-res Image Gene #62: '11p loss' versus Clinical Feature #10: 'HISTOLOGICAL_TYPE'

'11q loss' versus 'Time to Death'

P value = 0.000416 (logrank test), Q value = 0.0032

Table S311. Gene #63: '11q loss' versus Clinical Feature #1: 'Time to Death'

	nPatients	nDeath	Duration Range (Median), Month
ALL	873	228	0.1 - 194.8 (34.5)
11Q LOSS MUTATED	51	21	0.4 - 123.6 (19.7)
11Q LOSS WILD-TYPE	822	207	0.1 - 194.8 (36.1)

Figure S311. Get High-res Image Gene #63: '11q loss' versus Clinical Feature #1: 'Time to Death'

'11q loss' versus 'YEARS_TO_BIRTH'

P value = 0.0146 (Wilcoxon-test), Q value = 0.06

Table S312. Gene #63: '11q loss' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

	nPatients	Mean (Std.Dev)
ALL	875	60.1 (12.5)
11Q LOSS MUTATED	51	63.9 (11.6)
11Q LOSS WILD-TYPE	824	59.9 (12.5)

Figure S312. Get High-res Image Gene #63: '11q loss' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'11q loss' versus 'PATHOLOGIC_STAGE'

P value = 9e-05 (Fisher's exact test), Q value = 0.00078

Table S313. Gene #63: '11q loss' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

nPatients	STAGE I	STAGE II	STAGE III	STAGE IV
ALL	455	104	191	104
11Q LOSS MUTATED	12	9	18	12
11Q LOSS WILD-TYPE	443	95	173	92

Figure S313. Get High-res Image Gene #63: '11q loss' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

'11q loss' versus 'PATHOLOGY_T_STAGE'

P value = 4e-05 (Fisher's exact test), Q value = 0.00038

Table S314. Gene #63: '11q loss' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

nPatients	T1	T2	T3	T4
ALL	479	127	258	15
11Q LOSS MUTATED	12	10	29	1
11Q LOSS WILD-TYPE	467	117	229	14

Figure S314. Get High-res Image Gene #63: '11q loss' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

'11q loss' versus 'PATHOLOGY_N_STAGE'

P value = 5e-05 (Fisher's exact test), Q value = 0.00045

Table S315. Gene #63: '11q loss' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

nPatients	N0	N1	N2
ALL	322	44	7
11Q LOSS MUTATED	18	10	3
11Q LOSS WILD-TYPE	304	34	4

Figure S315. Get High-res Image Gene #63: '11q loss' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

'11q loss' versus 'KARNOFSKY_PERFORMANCE_SCORE'

P value = 0.0459 (Wilcoxon-test), Q value = 0.15

Table S316. Gene #63: '11q loss' versus Clinical Feature #9: 'KARNOFSKY_PERFORMANCE_SCORE'

	nPatients	Mean (Std.Dev)
ALL	142	87.6 (22.8)
11Q LOSS MUTATED	13	80.0 (27.4)
11Q LOSS WILD-TYPE	129	88.4 (22.3)

Figure S316. Get High-res Image Gene #63: '11q loss' versus Clinical Feature #9: 'KARNOFSKY_PERFORMANCE_SCORE'

'11q loss' versus 'HISTOLOGICAL_TYPE'

P value = 0.0316 (Fisher's exact test), Q value = 0.11

Table S317. Gene #63: '11q loss' versus Clinical Feature #10: 'HISTOLOGICAL_TYPE'

nPatients	KIDNEY CHROMOPHOBE	KIDNEY CLEAR CELL RENAL CARCINOMA	KIDNEY PAPILLARY RENAL CELL CARCINOMA
ALL	66	528	287
11Q LOSS MUTATED	7	23	22
11Q LOSS WILD-TYPE	59	505	265

Figure S317. Get High-res Image Gene #63: '11q loss' versus Clinical Feature #10: 'HISTOLOGICAL_TYPE'

'12p loss' versus 'PATHOLOGY_N_STAGE'

P value = 0.0506 (Fisher's exact test), Q value = 0.16

Table S318. Gene #64: '12p loss' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

nPatients	N0	N1	N2
ALL	322	44	7
12P LOSS MUTATED	1	2	0
12P LOSS WILD-TYPE	321	42	7

Figure S318. Get High-res Image Gene #64: '12p loss' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

'12q loss' versus 'PATHOLOGY_T_STAGE'

P value = 0.0549 (Fisher's exact test), Q value = 0.17

Table S319. Gene #65: '12q loss' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

nPatients	T1	T2	T3	T4
ALL	479	127	258	15
12Q LOSS MUTATED	1	0	2	1
12Q LOSS WILD-TYPE	478	127	256	14

Figure S319. Get High-res Image Gene #65: '12q loss' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

'13q loss' versus 'Time to Death'

P value = 0.0366 (logrank test), Q value = 0.13

Table S320. Gene #66: '13q loss' versus Clinical Feature #1: 'Time to Death'

	nPatients	nDeath	Duration Range (Median), Month
ALL	873	228	0.1 - 194.8 (34.5)
13Q LOSS MUTATED	135	50	0.2 - 152.0 (38.6)
13Q LOSS WILD-TYPE	738	178	0.1 - 194.8 (34.2)

Figure S320. Get High-res Image Gene #66: '13q loss' versus Clinical Feature #1: 'Time to Death'

'13q loss' versus 'YEARS_TO_BIRTH'

P value = 0.000117 (Wilcoxon-test), Q value = 0.001

Table S321. Gene #66: '13q loss' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

	nPatients	Mean (Std.Dev)
ALL	875	60.1 (12.5)
13Q LOSS MUTATED	137	55.5 (14.9)
13Q LOSS WILD-TYPE	738	61.0 (11.8)

Figure S321. Get High-res Image Gene #66: '13q loss' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'13q loss' versus 'PATHOLOGIC_STAGE'

P value = 1e-05 (Fisher's exact test), Q value = 0.00011

Table S322. Gene #66: '13q loss' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

nPatients	STAGE I	STAGE II	STAGE III	STAGE IV
ALL	455	104	191	104
13Q LOSS MUTATED	43	21	44	28
13Q LOSS WILD-TYPE	412	83	147	76

Figure S322. Get High-res Image Gene #66: '13q loss' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

'13q loss' versus 'PATHOLOGY_T_STAGE'

P value = 1e-05 (Fisher's exact test), Q value = 0.00011

Table S323. Gene #66: '13q loss' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

nPatients	T1	T2	T3	T4
ALL	479	127	258	15
13Q LOSS MUTATED	45	23	60	9
13Q LOSS WILD-TYPE	434	104	198	6

Figure S323. Get High-res Image Gene #66: '13q loss' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

'13q loss' versus 'PATHOLOGY_N_STAGE'

P value = 0.0164 (Fisher's exact test), Q value = 0.066

Table S324. Gene #66: '13q loss' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

nPatients	N0	N1	N2
ALL	322	44	7
13Q LOSS MUTATED	63	14	4
13Q LOSS WILD-TYPE	259	30	3

Figure S324. Get High-res Image Gene #66: '13q loss' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

'13q loss' versus 'GENDER'

P value = 0.0175 (Fisher's exact test), Q value = 0.07

Table S325. Gene #66: '13q loss' versus Clinical Feature #7: 'GENDER'

nPatients	FEMALE	MALE
ALL	292	589
13Q LOSS MUTATED	58	79
13Q LOSS WILD-TYPE	234	510

Figure S325. Get High-res Image Gene #66: '13q loss' versus Clinical Feature #7: 'GENDER'

'13q loss' versus 'HISTOLOGICAL_TYPE'

P value = 1e-05 (Fisher's exact test), Q value = 0.00011

Table S326. Gene #66: '13q loss' versus Clinical Feature #10: 'HISTOLOGICAL_TYPE'

nPatients	KIDNEY CHROMOPHOBE	KIDNEY CLEAR CELL RENAL CARCINOMA	KIDNEY PAPILLARY RENAL CELL CARCINOMA
ALL	66	528	287
13Q LOSS MUTATED	43	71	23
13Q LOSS WILD-TYPE	23	457	264

Figure S326. Get High-res Image Gene #66: '13q loss' versus Clinical Feature #10: 'HISTOLOGICAL_TYPE'

'14q loss' versus 'Time to Death'

P value = 1.38e-09 (logrank test), Q value = 3.2e-07

Table S327. Gene #67: '14q loss' versus Clinical Feature #1: 'Time to Death'

	nPatients	nDeath	Duration Range (Median), Month
ALL	873	228	0.1 - 194.8 (34.5)
14Q LOSS MUTATED	264	106	0.1 - 133.7 (31.5)
14Q LOSS WILD-TYPE	609	122	0.1 - 194.8 (36.5)

Figure S327. Get High-res Image Gene #67: '14q loss' versus Clinical Feature #1: 'Time to Death'

'14q loss' versus 'PATHOLOGIC_STAGE'

P value = 1e-05 (Fisher's exact test), Q value = 0.00011

Table S328. Gene #67: '14q loss' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

nPatients	STAGE I	STAGE II	STAGE III	STAGE IV
ALL	455	104	191	104
14Q LOSS MUTATED	98	29	78	54
14Q LOSS WILD-TYPE	357	75	113	50

Figure S328. Get High-res Image Gene #67: '14q loss' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

'14q loss' versus 'PATHOLOGY_T_STAGE'

P value = 1e-05 (Fisher's exact test), Q value = 0.00011

Table S329. Gene #67: '14q loss' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

nPatients	T1	T2	T3	T4
ALL	479	127	258	15
14Q LOSS MUTATED	105	39	117	4
14Q LOSS WILD-TYPE	374	88	141	11

Figure S329. Get High-res Image Gene #67: '14q loss' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

'14q loss' versus 'PATHOLOGY_N_STAGE'

P value = 0.00926 (Fisher's exact test), Q value = 0.041

Table S330. Gene #67: '14q loss' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

nPatients	N0	N1	N2
ALL	322	44	7
14Q LOSS MUTATED	102	23	4
14Q LOSS WILD-TYPE	220	21	3

Figure S330. Get High-res Image Gene #67: '14q loss' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

'14q loss' versus 'PATHOLOGY_M_STAGE'

P value = 4.21e-05 (Fisher's exact test), Q value = 4e-04

Table S331. Gene #67: '14q loss' versus Clinical Feature #6: 'PATHOLOGY_M_STAGE'

nPatients	0	1
ALL	545	89
14Q LOSS MUTATED	175	49
14Q LOSS WILD-TYPE	370	40

Figure S331. Get High-res Image Gene #67: '14q loss' versus Clinical Feature #6: 'PATHOLOGY_M_STAGE'

'14q loss' versus 'KARNOFSKY_PERFORMANCE_SCORE'

P value = 0.000225 (Wilcoxon-test), Q value = 0.0018

Table S332. Gene #67: '14q loss' versus Clinical Feature #9: 'KARNOFSKY_PERFORMANCE_SCORE'

	nPatients	Mean (Std.Dev)
ALL	142	87.6 (22.8)
14Q LOSS MUTATED	34	71.5 (37.0)
14Q LOSS WILD-TYPE	108	92.7 (12.4)

Figure S332. Get High-res Image Gene #67: '14q loss' versus Clinical Feature #9: 'KARNOFSKY_PERFORMANCE_SCORE'

'14q loss' versus 'HISTOLOGICAL_TYPE'

P value = 1e-05 (Fisher's exact test), Q value = 0.00011

Table S333. Gene #67: '14q loss' versus Clinical Feature #10: 'HISTOLOGICAL_TYPE'

nPatients	KIDNEY CHROMOPHOBE	KIDNEY CLEAR CELL RENAL CARCINOMA	KIDNEY PAPILLARY RENAL CELL CARCINOMA
ALL	66	528	287
14Q LOSS MUTATED	2	216	47
14Q LOSS WILD-TYPE	64	312	240

Figure S333. Get High-res Image Gene #67: '14q loss' versus Clinical Feature #10: 'HISTOLOGICAL_TYPE'

'14q loss' versus 'YEAR_OF_TOBACCO_SMOKING_ONSET'

P value = 0.00516 (Wilcoxon-test), Q value = 0.026

Table S334. Gene #67: '14q loss' versus Clinical Feature #12: 'YEAR_OF_TOBACCO_SMOKING_ONSET'

	nPatients	Mean (Std.Dev)
ALL	74	1973.7 (16.0)
14Q LOSS MUTATED	14	1984.8 (14.5)
14Q LOSS WILD-TYPE	60	1971.2 (15.3)

Figure S334. Get High-res Image Gene #67: '14q loss' versus Clinical Feature #12: 'YEAR_OF_TOBACCO_SMOKING_ONSET'

'14q loss' versus 'RACE'

P value = 0.0227 (Fisher's exact test), Q value = 0.088

Table S335. Gene #67: '14q loss' versus Clinical Feature #13: 'RACE'

nPatients	AMERICAN INDIAN OR ALASKA NATIVE	ASIAN	BLACK OR AFRICAN AMERICAN	WHITE
ALL	2	15	121	719
14Q LOSS MUTATED	0	3	24	231
14Q LOSS WILD-TYPE	2	12	97	488

Figure S335. Get High-res Image Gene #67: '14q loss' versus Clinical Feature #13: 'RACE'

'15q loss' versus 'Time to Death'

P value = 2.86e-05 (logrank test), Q value = 0.00029

Table S336. Gene #68: '15q loss' versus Clinical Feature #1: 'Time to Death'

	nPatients	nDeath	Duration Range (Median), Month
ALL	873	228	0.1 - 194.8 (34.5)
15Q LOSS MUTATED	68	28	0.1 - 194.8 (22.3)
15Q LOSS WILD-TYPE	805	200	0.1 - 152.0 (36.5)

Figure S336. Get High-res Image Gene #68: '15q loss' versus Clinical Feature #1: 'Time to Death'

'15q loss' versus 'PATHOLOGIC_STAGE'

P value = 1e-05 (Fisher's exact test), Q value = 0.00011

Table S337. Gene #68: '15q loss' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

nPatients	STAGE I	STAGE II	STAGE III	STAGE IV
ALL	455	104	191	104
15Q LOSS MUTATED	20	4	23	18
15Q LOSS WILD-TYPE	435	100	168	86

Figure S337. Get High-res Image Gene #68: '15q loss' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

'15q loss' versus 'PATHOLOGY_T_STAGE'

P value = 1e-05 (Fisher's exact test), Q value = 0.00011

Table S338. Gene #68: '15q loss' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

nPatients	T1	T2	T3	T4
ALL	479	127	258	15
15Q LOSS MUTATED	23	5	36	5
15Q LOSS WILD-TYPE	456	122	222	10

Figure S338. Get High-res Image Gene #68: '15q loss' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

'15q loss' versus 'PATHOLOGY_N_STAGE'

P value = 0.00097 (Fisher's exact test), Q value = 0.0064

Table S339. Gene #68: '15q loss' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

nPatients	N0	N1	N2
ALL	322	44	7
15Q LOSS MUTATED	22	10	2
15Q LOSS WILD-TYPE	300	34	5

Figure S339. Get High-res Image Gene #68: '15q loss' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

'15q loss' versus 'PATHOLOGY_M_STAGE'

P value = 0.0139 (Fisher's exact test), Q value = 0.058

Table S340. Gene #68: '15q loss' versus Clinical Feature #6: 'PATHOLOGY_M_STAGE'

nPatients	0	1
ALL	545	89
15Q LOSS MUTATED	34	13
15Q LOSS WILD-TYPE	511	76

Figure S340. Get High-res Image Gene #68: '15q loss' versus Clinical Feature #6: 'PATHOLOGY_M_STAGE'

'15q loss' versus 'KARNOFSKY_PERFORMANCE_SCORE'

P value = 0.0791 (Wilcoxon-test), Q value = 0.22

Table S341. Gene #68: '15q loss' versus Clinical Feature #9: 'KARNOFSKY_PERFORMANCE_SCORE'

	nPatients	Mean (Std.Dev)
ALL	142	87.6 (22.8)
15Q LOSS MUTATED	13	81.5 (26.7)
15Q LOSS WILD-TYPE	129	88.2 (22.4)

Figure S341. Get High-res Image Gene #68: '15q loss' versus Clinical Feature #9: 'KARNOFSKY_PERFORMANCE_SCORE'

'15q loss' versus 'HISTOLOGICAL_TYPE'

P value = 0.046 (Fisher's exact test), Q value = 0.15

Table S342. Gene #68: '15q loss' versus Clinical Feature #10: 'HISTOLOGICAL_TYPE'

nPatients	KIDNEY CHROMOPHOBE	KIDNEY CLEAR CELL RENAL CARCINOMA	KIDNEY PAPILLARY RENAL CELL CARCINOMA
ALL	66	528	287
15Q LOSS MUTATED	2	36	31
15Q LOSS WILD-TYPE	64	492	256

Figure S342. Get High-res Image Gene #68: '15q loss' versus Clinical Feature #10: 'HISTOLOGICAL_TYPE'

'16p loss' versus 'Time to Death'

P value = 6.06e-07 (logrank test), Q value = 6.3e-05

Table S343. Gene #69: '16p loss' versus Clinical Feature #1: 'Time to Death'

	nPatients	nDeath	Duration Range (Median), Month
ALL	873	228	0.1 - 194.8 (34.5)
16P LOSS MUTATED	17	11	0.1 - 80.2 (28.1)
16P LOSS WILD-TYPE	856	217	0.1 - 194.8 (35.5)

Figure S343. Get High-res Image Gene #69: '16p loss' versus Clinical Feature #1: 'Time to Death'

'16p loss' versus 'PATHOLOGIC_STAGE'

P value = 0.00851 (Fisher's exact test), Q value = 0.038

Table S344. Gene #69: '16p loss' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

nPatients	STAGE I	STAGE II	STAGE III	STAGE IV
ALL	455	104	191	104
16P LOSS MUTATED	4	2	6	6
16P LOSS WILD-TYPE	451	102	185	98

Figure S344. Get High-res Image Gene #69: '16p loss' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

'16p loss' versus 'PATHOLOGY_T_STAGE'

P value = 0.00042 (Fisher's exact test), Q value = 0.0032

Table S345. Gene #69: '16p loss' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

nPatients	T1	T2	T3	T4
ALL	479	127	258	15
16P LOSS MUTATED	4	2	9	3
16P LOSS WILD-TYPE	475	125	249	12

Figure S345. Get High-res Image Gene #69: '16p loss' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

'16p loss' versus 'PATHOLOGY_N_STAGE'

P value = 0.00127 (Fisher's exact test), Q value = 0.008

Table S346. Gene #69: '16p loss' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

nPatients	N0	N1	N2
ALL	322	44	7
16P LOSS MUTATED	6	4	2
16P LOSS WILD-TYPE	316	40	5

Figure S346. Get High-res Image Gene #69: '16p loss' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

'16p loss' versus 'HISTOLOGICAL_TYPE'

P value = 0.0689 (Fisher's exact test), Q value = 0.2

Table S347. Gene #69: '16p loss' versus Clinical Feature #10: 'HISTOLOGICAL_TYPE'

nPatients	KIDNEY CHROMOPHOBE	KIDNEY CLEAR CELL RENAL CARCINOMA	KIDNEY PAPILLARY RENAL CELL CARCINOMA
ALL	66	528	287
16P LOSS MUTATED	4	10	4
16P LOSS WILD-TYPE	62	518	283

Figure S347. Get High-res Image Gene #69: '16p loss' versus Clinical Feature #10: 'HISTOLOGICAL_TYPE'

'16q loss' versus 'Time to Death'

P value = 4.99e-07 (logrank test), Q value = 6.3e-05

Table S348. Gene #70: '16q loss' versus Clinical Feature #1: 'Time to Death'

	nPatients	nDeath	Duration Range (Median), Month
ALL	873	228	0.1 - 194.8 (34.5)
16Q LOSS MUTATED	27	16	0.1 - 80.2 (30.2)
16Q LOSS WILD-TYPE	846	212	0.1 - 194.8 (35.1)

Figure S348. Get High-res Image Gene #70: '16q loss' versus Clinical Feature #1: 'Time to Death'

'16q loss' versus 'PATHOLOGIC_STAGE'

P value = 0.00502 (Fisher's exact test), Q value = 0.025

Table S349. Gene #70: '16q loss' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

nPatients	STAGE I	STAGE II	STAGE III	STAGE IV
ALL	455	104	191	104
16Q LOSS MUTATED	7	4	9	8
16Q LOSS WILD-TYPE	448	100	182	96

Figure S349. Get High-res Image Gene #70: '16q loss' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

'16q loss' versus 'PATHOLOGY_T_STAGE'

P value = 0.00027 (Fisher's exact test), Q value = 0.0021

Table S350. Gene #70: '16q loss' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

nPatients	T1	T2	T3	T4
ALL	479	127	258	15
16Q LOSS MUTATED	8	4	12	4
16Q LOSS WILD-TYPE	471	123	246	11

Figure S350. Get High-res Image Gene #70: '16q loss' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

'16q loss' versus 'PATHOLOGY_N_STAGE'

P value = 0.00042 (Fisher's exact test), Q value = 0.0032

Table S351. Gene #70: '16q loss' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

nPatients	N0	N1	N2
ALL	322	44	7
16Q LOSS MUTATED	9	6	2
16Q LOSS WILD-TYPE	313	38	5

Figure S351. Get High-res Image Gene #70: '16q loss' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

'17p loss' versus 'YEARS_TO_BIRTH'

P value = 0.00319 (Wilcoxon-test), Q value = 0.017

Table S352. Gene #71: '17p loss' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

	nPatients	Mean (Std.Dev)
ALL	875	60.1 (12.5)
17P LOSS MUTATED	108	56.3 (14.7)
17P LOSS WILD-TYPE	767	60.7 (12.1)

Figure S352. Get High-res Image Gene #71: '17p loss' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'17p loss' versus 'PATHOLOGIC_STAGE'

P value = 1e-05 (Fisher's exact test), Q value = 0.00011

Table S353. Gene #71: '17p loss' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

nPatients	STAGE I	STAGE II	STAGE III	STAGE IV
ALL	455	104	191	104
17P LOSS MUTATED	32	30	25	19
17P LOSS WILD-TYPE	423	74	166	85

Figure S353. Get High-res Image Gene #71: '17p loss' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

'17p loss' versus 'PATHOLOGY_T_STAGE'

P value = 1e-05 (Fisher's exact test), Q value = 0.00011

Table S354. Gene #71: '17p loss' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

nPatients	T1	T2	T3	T4
ALL	479	127	258	15
17P LOSS MUTATED	33	33	40	3
17P LOSS WILD-TYPE	446	94	218	12

Figure S354. Get High-res Image Gene #71: '17p loss' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

'17p loss' versus 'PATHOLOGY_N_STAGE'

P value = 0.00128 (Fisher's exact test), Q value = 0.008

Table S355. Gene #71: '17p loss' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

nPatients	N0	N1	N2
ALL	322	44	7
17P LOSS MUTATED	54	4	5
17P LOSS WILD-TYPE	268	40	2

Figure S355. Get High-res Image Gene #71: '17p loss' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

'17p loss' versus 'HISTOLOGICAL_TYPE'

P value = 1e-05 (Fisher's exact test), Q value = 0.00011

Table S356. Gene #71: '17p loss' versus Clinical Feature #10: 'HISTOLOGICAL_TYPE'

nPatients	KIDNEY CHROMOPHOBE	KIDNEY CLEAR CELL RENAL CARCINOMA	KIDNEY PAPILLARY RENAL CELL CARCINOMA
ALL	66	528	287
17P LOSS MUTATED	50	47	12
17P LOSS WILD-TYPE	16	481	275

Figure S356. Get High-res Image Gene #71: '17p loss' versus Clinical Feature #10: 'HISTOLOGICAL_TYPE'

'17q loss' versus 'Time to Death'

P value = 0.00754 (logrank test), Q value = 0.035

Table S357. Gene #72: '17q loss' versus Clinical Feature #1: 'Time to Death'

	nPatients	nDeath	Duration Range (Median), Month
ALL	873	228	0.1 - 194.8 (34.5)
17Q LOSS MUTATED	80	17	0.4 - 152.0 (60.7)
17Q LOSS WILD-TYPE	793	211	0.1 - 194.8 (31.3)

Figure S357. Get High-res Image Gene #72: '17q loss' versus Clinical Feature #1: 'Time to Death'

'17q loss' versus 'YEARS_TO_BIRTH'

P value = 0.000261 (Wilcoxon-test), Q value = 0.0021

Table S358. Gene #72: '17q loss' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

	nPatients	Mean (Std.Dev)
ALL	875	60.1 (12.5)
17Q LOSS MUTATED	81	54.6 (14.8)
17Q LOSS WILD-TYPE	794	60.7 (12.1)

Figure S358. Get High-res Image Gene #72: '17q loss' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'17q loss' versus 'PATHOLOGIC_STAGE'

P value = 1e-05 (Fisher's exact test), Q value = 0.00011

Table S359. Gene #72: '17q loss' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

nPatients	STAGE I	STAGE II	STAGE III	STAGE IV
ALL	455	104	191	104
17Q LOSS MUTATED	23	27	18	12
17Q LOSS WILD-TYPE	432	77	173	92

Figure S359. Get High-res Image Gene #72: '17q loss' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

'17q loss' versus 'PATHOLOGY_T_STAGE'

P value = 1e-05 (Fisher's exact test), Q value = 0.00011

Table S360. Gene #72: '17q loss' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

nPatients	T1	T2	T3	T4
ALL	479	127	258	15
17Q LOSS MUTATED	24	28	26	3
17Q LOSS WILD-TYPE	455	99	232	12

Figure S360. Get High-res Image Gene #72: '17q loss' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

'17q loss' versus 'KARNOFSKY_PERFORMANCE_SCORE'

P value = 0.00699 (Wilcoxon-test), Q value = 0.032

Table S361. Gene #72: '17q loss' versus Clinical Feature #9: 'KARNOFSKY_PERFORMANCE_SCORE'

	nPatients	Mean (Std.Dev)
ALL	142	87.6 (22.8)
17Q LOSS MUTATED	10	99.0 (3.2)
17Q LOSS WILD-TYPE	132	86.7 (23.4)

Figure S361. Get High-res Image Gene #72: '17q loss' versus Clinical Feature #9: 'KARNOFSKY_PERFORMANCE_SCORE'

'17q loss' versus 'HISTOLOGICAL_TYPE'

P value = 1e-05 (Fisher's exact test), Q value = 0.00011

Table S362. Gene #72: '17q loss' versus Clinical Feature #10: 'HISTOLOGICAL_TYPE'

nPatients	KIDNEY CHROMOPHOBE	KIDNEY CLEAR CELL RENAL CARCINOMA	KIDNEY PAPILLARY RENAL CELL CARCINOMA
ALL	66	528	287
17Q LOSS MUTATED	50	30	1
17Q LOSS WILD-TYPE	16	498	286

Figure S362. Get High-res Image Gene #72: '17q loss' versus Clinical Feature #10: 'HISTOLOGICAL_TYPE'

'18p loss' versus 'Time to Death'

P value = 3.28e-07 (logrank test), Q value = 5e-05

Table S363. Gene #73: '18p loss' versus Clinical Feature #1: 'Time to Death'

	nPatients	nDeath	Duration Range (Median), Month
ALL	873	228	0.1 - 194.8 (34.5)
18P LOSS MUTATED	139	57	0.4 - 123.6 (25.7)
18P LOSS WILD-TYPE	734	171	0.1 - 194.8 (37.0)

Figure S363. Get High-res Image Gene #73: '18p loss' versus Clinical Feature #1: 'Time to Death'

'18p loss' versus 'PATHOLOGIC_STAGE'

P value = 1e-05 (Fisher's exact test), Q value = 0.00011

Table S364. Gene #73: '18p loss' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

nPatients	STAGE I	STAGE II	STAGE III	STAGE IV
ALL	455	104	191	104
18P LOSS MUTATED	45	11	51	30
18P LOSS WILD-TYPE	410	93	140	74

Figure S364. Get High-res Image Gene #73: '18p loss' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

'18p loss' versus 'PATHOLOGY_T_STAGE'

P value = 1e-05 (Fisher's exact test), Q value = 0.00011

Table S365. Gene #73: '18p loss' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

nPatients	T1	T2	T3	T4
ALL	479	127	258	15
18P LOSS MUTATED	48	16	72	6
18P LOSS WILD-TYPE	431	111	186	9

Figure S365. Get High-res Image Gene #73: '18p loss' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

'18p loss' versus 'PATHOLOGY_N_STAGE'

P value = 0.00689 (Fisher's exact test), Q value = 0.032

Table S366. Gene #73: '18p loss' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

nPatients	N0	N1	N2
ALL	322	44	7
18P LOSS MUTATED	54	13	4
18P LOSS WILD-TYPE	268	31	3

Figure S366. Get High-res Image Gene #73: '18p loss' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

'18p loss' versus 'PATHOLOGY_M_STAGE'

P value = 0.0256 (Fisher's exact test), Q value = 0.096

Table S367. Gene #73: '18p loss' versus Clinical Feature #6: 'PATHOLOGY_M_STAGE'

nPatients	0	1
ALL	545	89
18P LOSS MUTATED	91	24
18P LOSS WILD-TYPE	454	65

Figure S367. Get High-res Image Gene #73: '18p loss' versus Clinical Feature #6: 'PATHOLOGY_M_STAGE'

'18p loss' versus 'YEAR_OF_TOBACCO_SMOKING_ONSET'

P value = 0.073 (Wilcoxon-test), Q value = 0.21

Table S368. Gene #73: '18p loss' versus Clinical Feature #12: 'YEAR_OF_TOBACCO_SMOKING_ONSET'

	nPatients	Mean (Std.Dev)
ALL	74	1973.7 (16.0)
18P LOSS MUTATED	7	1983.1 (12.8)
18P LOSS WILD-TYPE	67	1972.7 (16.0)

Figure S368. Get High-res Image Gene #73: '18p loss' versus Clinical Feature #12: 'YEAR_OF_TOBACCO_SMOKING_ONSET'

'18p loss' versus 'RACE'

P value = 0.0867 (Fisher's exact test), Q value = 0.24

Table S369. Gene #73: '18p loss' versus Clinical Feature #13: 'RACE'

nPatients	AMERICAN INDIAN OR ALASKA NATIVE	ASIAN	BLACK OR AFRICAN AMERICAN	WHITE
ALL	2	15	121	719
18P LOSS MUTATED	0	5	13	121
18P LOSS WILD-TYPE	2	10	108	598

Figure S369. Get High-res Image Gene #73: '18p loss' versus Clinical Feature #13: 'RACE'

'18q loss' versus 'Time to Death'

P value = 5.88e-07 (logrank test), Q value = 6.3e-05

Table S370. Gene #74: '18q loss' versus Clinical Feature #1: 'Time to Death'

	nPatients	nDeath	Duration Range (Median), Month
ALL	873	228	0.1 - 194.8 (34.5)
18Q LOSS MUTATED	146	59	0.4 - 123.6 (25.8)
18Q LOSS WILD-TYPE	727	169	0.1 - 194.8 (37.0)

Figure S370. Get High-res Image Gene #74: '18q loss' versus Clinical Feature #1: 'Time to Death'

'18q loss' versus 'PATHOLOGIC_STAGE'

P value = 1e-05 (Fisher's exact test), Q value = 0.00011

Table S371. Gene #74: '18q loss' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

nPatients	STAGE I	STAGE II	STAGE III	STAGE IV
ALL	455	104	191	104
18Q LOSS MUTATED	50	12	51	31
18Q LOSS WILD-TYPE	405	92	140	73

Figure S371. Get High-res Image Gene #74: '18q loss' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

'18q loss' versus 'PATHOLOGY_T_STAGE'

P value = 1e-05 (Fisher's exact test), Q value = 0.00011

Table S372. Gene #74: '18q loss' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

nPatients	T1	T2	T3	T4
ALL	479	127	258	15
18Q LOSS MUTATED	54	18	70	7
18Q LOSS WILD-TYPE	425	109	188	8

Figure S372. Get High-res Image Gene #74: '18q loss' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

'18q loss' versus 'PATHOLOGY_N_STAGE'

P value = 0.00155 (Fisher's exact test), Q value = 0.0093

Table S373. Gene #74: '18q loss' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

nPatients	N0	N1	N2
ALL	322	44	7
18Q LOSS MUTATED	58	16	4
18Q LOSS WILD-TYPE	264	28	3

Figure S373. Get High-res Image Gene #74: '18q loss' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

'18q loss' versus 'PATHOLOGY_M_STAGE'

P value = 0.0388 (Fisher's exact test), Q value = 0.13

Table S374. Gene #74: '18q loss' versus Clinical Feature #6: 'PATHOLOGY_M_STAGE'

nPatients	0	1
ALL	545	89
18Q LOSS MUTATED	94	24
18Q LOSS WILD-TYPE	451	65

Figure S374. Get High-res Image Gene #74: '18q loss' versus Clinical Feature #6: 'PATHOLOGY_M_STAGE'

'18q loss' versus 'RACE'

P value = 0.0422 (Fisher's exact test), Q value = 0.14

Table S375. Gene #74: '18q loss' versus Clinical Feature #13: 'RACE'

nPatients	AMERICAN INDIAN OR ALASKA NATIVE	ASIAN	BLACK OR AFRICAN AMERICAN	WHITE
ALL	2	15	121	719
18Q LOSS MUTATED	0	6	14	126
18Q LOSS WILD-TYPE	2	9	107	593

Figure S375. Get High-res Image Gene #74: '18q loss' versus Clinical Feature #13: 'RACE'

'19p loss' versus 'Time to Death'

P value = 0.00074 (logrank test), Q value = 0.0051

Table S376. Gene #75: '19p loss' versus Clinical Feature #1: 'Time to Death'

	nPatients	nDeath	Duration Range (Median), Month
ALL	873	228	0.1 - 194.8 (34.5)
19P LOSS MUTATED	27	12	0.9 - 109.9 (19.3)
19P LOSS WILD-TYPE	846	216	0.1 - 194.8 (35.9)

Figure S376. Get High-res Image Gene #75: '19p loss' versus Clinical Feature #1: 'Time to Death'

'19p loss' versus 'PATHOLOGIC_STAGE'

P value = 0.00482 (Fisher's exact test), Q value = 0.025

Table S377. Gene #75: '19p loss' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

nPatients	STAGE I	STAGE II	STAGE III	STAGE IV
ALL	455	104	191	104
19P LOSS MUTATED	7	1	12	5
19P LOSS WILD-TYPE	448	103	179	99

Figure S377. Get High-res Image Gene #75: '19p loss' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

'19p loss' versus 'PATHOLOGY_T_STAGE'

P value = 0.00164 (Fisher's exact test), Q value = 0.0098

Table S378. Gene #75: '19p loss' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

nPatients	T1	T2	T3	T4
ALL	479	127	258	15
19P LOSS MUTATED	9	2	13	3
19P LOSS WILD-TYPE	470	125	245	12

Figure S378. Get High-res Image Gene #75: '19p loss' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

'19p loss' versus 'PATHOLOGY_N_STAGE'

P value = 0.0377 (Fisher's exact test), Q value = 0.13

Table S379. Gene #75: '19p loss' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

nPatients	N0	N1	N2
ALL	322	44	7
19P LOSS MUTATED	7	3	1
19P LOSS WILD-TYPE	315	41	6

Figure S379. Get High-res Image Gene #75: '19p loss' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

'19p loss' versus 'HISTOLOGICAL_TYPE'

P value = 0.0135 (Fisher's exact test), Q value = 0.056

Table S380. Gene #75: '19p loss' versus Clinical Feature #10: 'HISTOLOGICAL_TYPE'

nPatients	KIDNEY CHROMOPHOBE	KIDNEY CLEAR CELL RENAL CARCINOMA	KIDNEY PAPILLARY RENAL CELL CARCINOMA
ALL	66	528	287
19P LOSS MUTATED	1	10	16
19P LOSS WILD-TYPE	65	518	271

Figure S380. Get High-res Image Gene #75: '19p loss' versus Clinical Feature #10: 'HISTOLOGICAL_TYPE'

'19q loss' versus 'Time to Death'

P value = 0.00121 (logrank test), Q value = 0.0077

Table S381. Gene #76: '19q loss' versus Clinical Feature #1: 'Time to Death'

	nPatients	nDeath	Duration Range (Median), Month
ALL	873	228	0.1 - 194.8 (34.5)
19Q LOSS MUTATED	22	9	0.9 - 96.6 (17.6)
19Q LOSS WILD-TYPE	851	219	0.1 - 194.8 (35.9)

Figure S381. Get High-res Image Gene #76: '19q loss' versus Clinical Feature #1: 'Time to Death'

'19q loss' versus 'PATHOLOGIC_STAGE'

P value = 7e-04 (Fisher's exact test), Q value = 0.0049

Table S382. Gene #76: '19q loss' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

nPatients	STAGE I	STAGE II	STAGE III	STAGE IV
ALL	455	104	191	104
19Q LOSS MUTATED	4	1	11	5
19Q LOSS WILD-TYPE	451	103	180	99

Figure S382. Get High-res Image Gene #76: '19q loss' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

'19q loss' versus 'PATHOLOGY_T_STAGE'

P value = 4e-05 (Fisher's exact test), Q value = 0.00038

Table S383. Gene #76: '19q loss' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

nPatients	T1	T2	T3	T4
ALL	479	127	258	15
19Q LOSS MUTATED	5	1	13	3
19Q LOSS WILD-TYPE	474	126	245	12

Figure S383. Get High-res Image Gene #76: '19q loss' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

'19q loss' versus 'PATHOLOGY_N_STAGE'

P value = 0.00011 (Fisher's exact test), Q value = 0.00095

Table S384. Gene #76: '19q loss' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

nPatients	N0	N1	N2
ALL	322	44	7
19Q LOSS MUTATED	3	4	2
19Q LOSS WILD-TYPE	319	40	5

Figure S384. Get High-res Image Gene #76: '19q loss' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

'19q loss' versus 'HISTOLOGICAL_TYPE'

P value = 0.00021 (Fisher's exact test), Q value = 0.0017

Table S385. Gene #76: '19q loss' versus Clinical Feature #10: 'HISTOLOGICAL_TYPE'

nPatients	KIDNEY CHROMOPHOBE	KIDNEY CLEAR CELL RENAL CARCINOMA	KIDNEY PAPILLARY RENAL CELL CARCINOMA
ALL	66	528	287
19Q LOSS MUTATED	3	4	15
19Q LOSS WILD-TYPE	63	524	272

Figure S385. Get High-res Image Gene #76: '19q loss' versus Clinical Feature #10: 'HISTOLOGICAL_TYPE'

'20p loss' versus 'HISTOLOGICAL_TYPE'

P value = 0.00667 (Fisher's exact test), Q value = 0.031

Table S386. Gene #77: '20p loss' versus Clinical Feature #10: 'HISTOLOGICAL_TYPE'

nPatients	KIDNEY CHROMOPHOBE	KIDNEY CLEAR CELL RENAL CARCINOMA	KIDNEY PAPILLARY RENAL CELL CARCINOMA
ALL	66	528	287
20P LOSS MUTATED	4	7	1
20P LOSS WILD-TYPE	62	521	286

Figure S386. Get High-res Image Gene #77: '20p loss' versus Clinical Feature #10: 'HISTOLOGICAL_TYPE'

'20q loss' versus 'HISTOLOGICAL_TYPE'

P value = 0.008 (Fisher's exact test), Q value = 0.037

Table S387. Gene #78: '20q loss' versus Clinical Feature #10: 'HISTOLOGICAL_TYPE'

nPatients	KIDNEY CHROMOPHOBE	KIDNEY CLEAR CELL RENAL CARCINOMA	KIDNEY PAPILLARY RENAL CELL CARCINOMA
ALL	66	528	287
20Q LOSS MUTATED	3	3	0
20Q LOSS WILD-TYPE	63	525	287

Figure S387. Get High-res Image Gene #78: '20q loss' versus Clinical Feature #10: 'HISTOLOGICAL_TYPE'

'20q loss' versus 'ETHNICITY'

P value = 0.0633 (Fisher's exact test), Q value = 0.19

Table S388. Gene #78: '20q loss' versus Clinical Feature #14: 'ETHNICITY'

nPatients	HISPANIC OR LATINO	NOT HISPANIC OR LATINO
ALL	42	621
20Q LOSS MUTATED	1	0
20Q LOSS WILD-TYPE	41	621

Figure S388. Get High-res Image Gene #78: '20q loss' versus Clinical Feature #14: 'ETHNICITY'

'21q loss' versus 'YEARS_TO_BIRTH'

P value = 0.0566 (Wilcoxon-test), Q value = 0.17

Table S389. Gene #79: '21q loss' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

	nPatients	Mean (Std.Dev)
ALL	875	60.1 (12.5)
21Q LOSS MUTATED	132	57.9 (13.5)
21Q LOSS WILD-TYPE	743	60.5 (12.3)

Figure S389. Get High-res Image Gene #79: '21q loss' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'21q loss' versus 'PATHOLOGIC_STAGE'

P value = 8e-04 (Fisher's exact test), Q value = 0.0054

Table S390. Gene #79: '21q loss' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

nPatients	STAGE I	STAGE II	STAGE III	STAGE IV
ALL	455	104	191	104
21Q LOSS MUTATED	48	20	39	22
21Q LOSS WILD-TYPE	407	84	152	82

Figure S390. Get High-res Image Gene #79: '21q loss' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

'21q loss' versus 'PATHOLOGY_T_STAGE'

P value = 1e-05 (Fisher's exact test), Q value = 0.00011

Table S391. Gene #79: '21q loss' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

nPatients	T1	T2	T3	T4
ALL	479	127	258	15
21Q LOSS MUTATED	48	24	55	6
21Q LOSS WILD-TYPE	431	103	203	9

Figure S391. Get High-res Image Gene #79: '21q loss' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

'21q loss' versus 'PATHOLOGY_N_STAGE'

P value = 0.00319 (Fisher's exact test), Q value = 0.017

Table S392. Gene #79: '21q loss' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

nPatients	N0	N1	N2
ALL	322	44	7
21Q LOSS MUTATED	50	13	4
21Q LOSS WILD-TYPE	272	31	3

Figure S392. Get High-res Image Gene #79: '21q loss' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

'21q loss' versus 'HISTOLOGICAL_TYPE'

P value = 1e-05 (Fisher's exact test), Q value = 0.00011

Table S393. Gene #79: '21q loss' versus Clinical Feature #10: 'HISTOLOGICAL_TYPE'

nPatients	KIDNEY CHROMOPHOBE	KIDNEY CLEAR CELL RENAL CARCINOMA	KIDNEY PAPILLARY RENAL CELL CARCINOMA
ALL	66	528	287
21Q LOSS MUTATED	35	55	43
21Q LOSS WILD-TYPE	31	473	244

Figure S393. Get High-res Image Gene #79: '21q loss' versus Clinical Feature #10: 'HISTOLOGICAL_TYPE'

'21q loss' versus 'YEAR_OF_TOBACCO_SMOKING_ONSET'

P value = 0.0566 (Wilcoxon-test), Q value = 0.17

Table S394. Gene #79: '21q loss' versus Clinical Feature #12: 'YEAR_OF_TOBACCO_SMOKING_ONSET'

	nPatients	Mean (Std.Dev)
ALL	74	1973.7 (16.0)
21Q LOSS MUTATED	10	1982.2 (12.9)
21Q LOSS WILD-TYPE	64	1972.4 (16.1)

Figure S394. Get High-res Image Gene #79: '21q loss' versus Clinical Feature #12: 'YEAR_OF_TOBACCO_SMOKING_ONSET'

'22q loss' versus 'Time to Death'

P value = 0.000828 (logrank test), Q value = 0.0056

Table S395. Gene #80: '22q loss' versus Clinical Feature #1: 'Time to Death'

	nPatients	nDeath	Duration Range (Median), Month
ALL	873	228	0.1 - 194.8 (34.5)
22Q LOSS MUTATED	106	38	0.9 - 152.0 (25.9)
22Q LOSS WILD-TYPE	767	190	0.1 - 194.8 (36.9)

Figure S395. Get High-res Image Gene #80: '22q loss' versus Clinical Feature #1: 'Time to Death'

'22q loss' versus 'PATHOLOGIC_STAGE'

P value = 1e-05 (Fisher's exact test), Q value = 0.00011

Table S396. Gene #80: '22q loss' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

nPatients	STAGE I	STAGE II	STAGE III	STAGE IV
ALL	455	104	191	104
22Q LOSS MUTATED	34	10	39	20
22Q LOSS WILD-TYPE	421	94	152	84

Figure S396. Get High-res Image Gene #80: '22q loss' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

'22q loss' versus 'PATHOLOGY_T_STAGE'

P value = 0.00021 (Fisher's exact test), Q value = 0.0017

Table S397. Gene #80: '22q loss' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

nPatients	T1	T2	T3	T4
ALL	479	127	258	15
22Q LOSS MUTATED	41	14	51	1
22Q LOSS WILD-TYPE	438	113	207	14

Figure S397. Get High-res Image Gene #80: '22q loss' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

'22q loss' versus 'PATHOLOGY_N_STAGE'

P value = 2e-05 (Fisher's exact test), Q value = 0.00021

Table S398. Gene #80: '22q loss' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

nPatients	N0	N1	N2
ALL	322	44	7
22Q LOSS MUTATED	33	16	3
22Q LOSS WILD-TYPE	289	28	4

Figure S398. Get High-res Image Gene #80: '22q loss' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

'22q loss' versus 'PATHOLOGY_M_STAGE'

P value = 0.0271 (Fisher's exact test), Q value = 0.1

Table S399. Gene #80: '22q loss' versus Clinical Feature #6: 'PATHOLOGY_M_STAGE'

nPatients	0	1
ALL	545	89
22Q LOSS MUTATED	53	16
22Q LOSS WILD-TYPE	492	73

Figure S399. Get High-res Image Gene #80: '22q loss' versus Clinical Feature #6: 'PATHOLOGY_M_STAGE'

'22q loss' versus 'GENDER'

P value = 0.028 (Fisher's exact test), Q value = 0.1

Table S400. Gene #80: '22q loss' versus Clinical Feature #7: 'GENDER'

nPatients	FEMALE	MALE
ALL	292	589
22Q LOSS MUTATED	46	61
22Q LOSS WILD-TYPE	246	528

Figure S400. Get High-res Image Gene #80: '22q loss' versus Clinical Feature #7: 'GENDER'

'22q loss' versus 'KARNOFSKY_PERFORMANCE_SCORE'

P value = 0.00515 (Wilcoxon-test), Q value = 0.026

Table S401. Gene #80: '22q loss' versus Clinical Feature #9: 'KARNOFSKY_PERFORMANCE_SCORE'

	nPatients	Mean (Std.Dev)
ALL	142	87.6 (22.8)
22Q LOSS MUTATED	25	72.8 (35.9)
22Q LOSS WILD-TYPE	117	90.8 (17.6)

Figure S401. Get High-res Image Gene #80: '22q loss' versus Clinical Feature #9: 'KARNOFSKY_PERFORMANCE_SCORE'

'22q loss' versus 'HISTOLOGICAL_TYPE'

P value = 1e-05 (Fisher's exact test), Q value = 0.00011

Table S402. Gene #80: '22q loss' versus Clinical Feature #10: 'HISTOLOGICAL_TYPE'

nPatients	KIDNEY CHROMOPHOBE	KIDNEY CLEAR CELL RENAL CARCINOMA	KIDNEY PAPILLARY RENAL CELL CARCINOMA
ALL	66	528	287
22Q LOSS MUTATED	8	39	60
22Q LOSS WILD-TYPE	58	489	227

Figure S402. Get High-res Image Gene #80: '22q loss' versus Clinical Feature #10: 'HISTOLOGICAL_TYPE'

'22q loss' versus 'ETHNICITY'

P value = 0.0283 (Fisher's exact test), Q value = 0.1

Table S403. Gene #80: '22q loss' versus Clinical Feature #14: 'ETHNICITY'

nPatients	HISPANIC OR LATINO	NOT HISPANIC OR LATINO
ALL	42	621
22Q LOSS MUTATED	10	72
22Q LOSS WILD-TYPE	32	549

Figure S403. Get High-res Image Gene #80: '22q loss' versus Clinical Feature #14: 'ETHNICITY'

'xp loss' versus 'YEARS_TO_BIRTH'

P value = 0.000927 (Wilcoxon-test), Q value = 0.0061

Table S404. Gene #81: 'xp loss' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

	nPatients	Mean (Std.Dev)
ALL	875	60.1 (12.5)
XP LOSS MUTATED	117	55.9 (14.2)
XP LOSS WILD-TYPE	758	60.8 (12.1)

Figure S404. Get High-res Image Gene #81: 'xp loss' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'xp loss' versus 'PATHOLOGIC_STAGE'

P value = 0.00051 (Fisher's exact test), Q value = 0.0037

Table S405. Gene #81: 'xp loss' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

nPatients	STAGE I	STAGE II	STAGE III	STAGE IV
ALL	455	104	191	104
XP LOSS MUTATED	41	22	35	15
XP LOSS WILD-TYPE	414	82	156	89

Figure S405. Get High-res Image Gene #81: 'xp loss' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

'xp loss' versus 'PATHOLOGY_T_STAGE'

P value = 0.00015 (Fisher's exact test), Q value = 0.0013

Table S406. Gene #81: 'xp loss' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

nPatients	T1	T2	T3	T4
ALL	479	127	258	15
XP LOSS MUTATED	42	25	49	2
XP LOSS WILD-TYPE	437	102	209	13

Figure S406. Get High-res Image Gene #81: 'xp loss' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

'xp loss' versus 'PATHOLOGY_N_STAGE'

P value = 0.00611 (Fisher's exact test), Q value = 0.029

Table S407. Gene #81: 'xp loss' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

nPatients	N0	N1	N2
ALL	322	44	7
XP LOSS MUTATED	40	13	2
XP LOSS WILD-TYPE	282	31	5

Figure S407. Get High-res Image Gene #81: 'xp loss' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

'xp loss' versus 'HISTOLOGICAL_TYPE'

P value = 1e-05 (Fisher's exact test), Q value = 0.00011

Table S408. Gene #81: 'xp loss' versus Clinical Feature #10: 'HISTOLOGICAL_TYPE'

nPatients	KIDNEY CHROMOPHOBE	KIDNEY CLEAR CELL RENAL CARCINOMA	KIDNEY PAPILLARY RENAL CELL CARCINOMA
ALL	66	528	287
XP LOSS MUTATED	38	47	33
XP LOSS WILD-TYPE	28	481	254

Figure S408. Get High-res Image Gene #81: 'xp loss' versus Clinical Feature #10: 'HISTOLOGICAL_TYPE'

'xq loss' versus 'YEARS_TO_BIRTH'

P value = 0.00135 (Wilcoxon-test), Q value = 0.0083

Table S409. Gene #82: 'xq loss' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

	nPatients	Mean (Std.Dev)
ALL	875	60.1 (12.5)
XQ LOSS MUTATED	115	56.0 (14.2)
XQ LOSS WILD-TYPE	760	60.8 (12.1)

Figure S409. Get High-res Image Gene #82: 'xq loss' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'xq loss' versus 'PATHOLOGIC_STAGE'

P value = 0.00076 (Fisher's exact test), Q value = 0.0052

Table S410. Gene #82: 'xq loss' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

nPatients	STAGE I	STAGE II	STAGE III	STAGE IV
ALL	455	104	191	104
XQ LOSS MUTATED	41	21	35	15
XQ LOSS WILD-TYPE	414	83	156	89

Figure S410. Get High-res Image Gene #82: 'xq loss' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

'xq loss' versus 'PATHOLOGY_T_STAGE'

P value = 0.00033 (Fisher's exact test), Q value = 0.0026

Table S411. Gene #82: 'xq loss' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

nPatients	T1	T2	T3	T4
ALL	479	127	258	15
XQ LOSS MUTATED	42	23	48	3
XQ LOSS WILD-TYPE	437	104	210	12

Figure S411. Get High-res Image Gene #82: 'xq loss' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

'xq loss' versus 'PATHOLOGY_N_STAGE'

P value = 0.00566 (Fisher's exact test), Q value = 0.028

Table S412. Gene #82: 'xq loss' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

nPatients	N0	N1	N2
ALL	322	44	7
XQ LOSS MUTATED	40	13	2
XQ LOSS WILD-TYPE	282	31	5

Figure S412. Get High-res Image Gene #82: 'xq loss' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

'xq loss' versus 'HISTOLOGICAL_TYPE'

P value = 1e-05 (Fisher's exact test), Q value = 0.00011

Table S413. Gene #82: 'xq loss' versus Clinical Feature #10: 'HISTOLOGICAL_TYPE'

nPatients	KIDNEY CHROMOPHOBE	KIDNEY CLEAR CELL RENAL CARCINOMA	KIDNEY PAPILLARY RENAL CELL CARCINOMA
ALL	66	528	287
XQ LOSS MUTATED	38	46	32
XQ LOSS WILD-TYPE	28	482	255

Figure S413. Get High-res Image Gene #82: 'xq loss' versus Clinical Feature #10: 'HISTOLOGICAL_TYPE'

Methods & Data

Input

Copy number data file = broad_values_by_arm.txt from GISTIC pipeline
Processed Copy number data file = /xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_Correlate_Genomic_Events_Preprocess/KIPAN-TP/19782227/transformed.cor.cli.txt
Clinical data file = /xchip/cga/gdac-prod/tcga-gdac/jobResults/Append_Data/KIPAN-TP/19775252/KIPAN-TP.merged_data.txt
Number of patients = 881
Number of significantly arm-level cnvs = 82
Number of selected clinical features = 14
Exclude regions 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.

Download Results

In addition to the links below, the full results of the analysis summarized in this report can also be downloaded programmatically using firehose_get, or interactively from either the Broad GDAC website or TCGA Data Coordination Center Portal.

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)

Made with Nozzle