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

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

28 January 2016 | analyses__2016_01_28

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 (2016): Correlation between copy number variations of arm-level result and selected clinical features. Broad Institute of MIT and Harvard. doi:10.7908/C1833RD6

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 882 patients, 419 significant findings detected with Q value < 0.25.

1p gain cnv correlated to 'Time to Death', 'YEARS_TO_BIRTH', 'PATHOLOGIC_STAGE', 'PATHOLOGY_T_STAGE', and 'PATHOLOGY_N_STAGE'.
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', 'KARNOFSKY_PERFORMANCE_SCORE', 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', 'HISTOLOGICAL_TYPE', and 'RACE'.
6p gain cnv correlated to 'Time to Death', '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_M_STAGE', 'GENDER', and 'HISTOLOGICAL_TYPE'.
9q gain cnv correlated to 'PATHOLOGIC_STAGE', 'PATHOLOGY_T_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 'Time to Death', '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 'Time to Death', 'PATHOLOGIC_STAGE', 'GENDER', 'KARNOFSKY_PERFORMANCE_SCORE', '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', 'PATHOLOGY_M_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', and 'HISTOLOGICAL_TYPE'.
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', 'PATHOLOGY_N_STAGE', 'HISTOLOGICAL_TYPE', and 'RACE'.
6q loss cnv correlated to 'YEARS_TO_BIRTH', 'PATHOLOGIC_STAGE', 'PATHOLOGY_T_STAGE', 'PATHOLOGY_N_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', 'HISTOLOGICAL_TYPE', and 'RACE'.
18p loss cnv correlated to 'Time to Death', 'PATHOLOGIC_STAGE', 'PATHOLOGY_T_STAGE', 'PATHOLOGY_N_STAGE', 'PATHOLOGY_M_STAGE', and 'YEAR_OF_TOBACCO_SMOKING_ONSET'.
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', 'PATHOLOGY_M_STAGE', and 'HISTOLOGICAL_TYPE'.
20p loss cnv correlated to 'HISTOLOGICAL_TYPE'.
20q loss cnv correlated to 'PATHOLOGY_N_STAGE', '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, 419 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%)	626	0.0708 (0.205)	0.25 (0.484)	0.0337 (0.119)	0.0669 (0.196)	0.00279 (0.0155)	0.013 (0.0538)	0.00574 (0.0284)	1 (1.00)	0.0571 (0.175)	1e-05 (0.000118)	0.992 (1.00)	0.309 (0.546)	0.905 (1.00)	0.0557 (0.174)
17p gain	196 (22%)	686	0.0122 (0.0509)	0.604 (0.843)	1e-05 (0.000118)	1e-05 (0.000118)	0.0184 (0.0718)	0.01 (0.0438)	0.000289 (0.00222)	1 (1.00)	0.611 (0.848)	1e-05 (0.000118)	0.781 (0.989)	0.0967 (0.257)	0.00884 (0.0395)	0.0104 (0.0447)
5p loss	24 (3%)	858	0.0571 (0.175)	0.0017 (0.00996)	1e-05 (0.000118)	1e-05 (0.000118)	0.0176 (0.069)	0.261 (0.499)	0.0816 (0.228)	1 (1.00)	0.247 (0.481)	2e-05 (0.000201)	0.0793 (0.224)	0.333 (0.578)	0.365 (0.607)	0.086 (0.239)
9p loss	192 (22%)	690	3.48e-12 (2e-09)	0.078 (0.221)	1e-05 (0.000118)	1e-05 (0.000118)	0.00318 (0.0171)	0.000125 (0.00106)	0.261 (0.499)	0.378 (0.618)	0.00183 (0.0106)	1e-05 (0.000118)	0.796 (0.997)	0.893 (1.00)	0.014 (0.057)	0.561 (0.801)
9q loss	195 (22%)	687	5.03e-10 (1.44e-07)	0.0619 (0.184)	1e-05 (0.000118)	1e-05 (0.000118)	0.0113 (0.0478)	0.00159 (0.00953)	0.197 (0.416)	0.378 (0.618)	0.00118 (0.00743)	1e-05 (0.000118)	0.974 (1.00)	0.719 (0.936)	0.0115 (0.0483)	1 (1.00)
14q loss	265 (30%)	617	1.07e-09 (2.47e-07)	0.291 (0.532)	1e-05 (0.000118)	1e-05 (0.000118)	0.00607 (0.0297)	4.11e-05 (0.00038)	0.815 (1.00)	0.0959 (0.257)	0.000194 (0.00158)	1e-05 (0.000118)	0.264 (0.503)	0.00516 (0.0258)	0.0208 (0.0797)	0.864 (1.00)
22q loss	107 (12%)	775	0.00104 (0.00677)	0.63 (0.858)	1e-05 (0.000118)	0.00033 (0.00248)	1e-05 (0.000118)	0.0269 (0.0985)	0.0279 (0.102)	1 (1.00)	0.00464 (0.0235)	1e-05 (0.000118)	0.899 (1.00)	0.325 (0.57)	0.588 (0.829)	0.0281 (0.102)
17q gain	222 (25%)	660	0.146 (0.338)	0.335 (0.58)	2e-05 (0.000201)	7e-05 (0.000609)	0.00356 (0.0191)	0.0451 (0.148)	0.0107 (0.0456)	1 (1.00)	0.688 (0.913)	1e-05 (0.000118)	0.884 (1.00)	0.145 (0.338)	0.0118 (0.0496)	0.0341 (0.12)
1q gain	68 (8%)	814	6.31e-06 (0.000118)	0.0416 (0.141)	0.00018 (0.00148)	0.00047 (0.00339)	0.00822 (0.0377)	0.225 (0.453)	0.351 (0.596)	1 (1.00)	0.049 (0.157)	0.00457 (0.0232)	0.282 (0.521)	0.103 (0.267)	0.374 (0.614)	0.763 (0.974)
12p gain	252 (29%)	630	0.102 (0.266)	0.135 (0.322)	0.0583 (0.178)	0.134 (0.321)	0.00852 (0.0388)	0.00873 (0.0391)	0.00562 (0.0279)	1 (1.00)	0.0571 (0.175)	2e-05 (0.000201)	0.797 (0.997)	0.153 (0.349)	0.935 (1.00)	0.0792 (0.224)
2p loss	65 (7%)	817	0.00429 (0.0222)	4.4e-05 (0.000404)	1e-05 (0.000118)	1e-05 (0.000118)	0.16 (0.36)	0.0701 (0.204)	0.135 (0.321)	1 (1.00)	0.0487 (0.157)	1e-05 (0.000118)	0.611 (0.848)	0.96 (1.00)	0.228 (0.456)	0.491 (0.729)
2q loss	63 (7%)	819	0.00297 (0.0162)	2.51e-05 (0.00025)	1e-05 (0.000118)	1e-05 (0.000118)	0.158 (0.357)	0.0701 (0.204)	0.166 (0.365)	1 (1.00)	0.0487 (0.157)	1e-05 (0.000118)	0.331 (0.578)	0.96 (1.00)	0.14 (0.33)	0.491 (0.729)
3p loss	411 (47%)	471	0.00287 (0.0157)	0.818 (1.00)	0.00055 (0.00385)	2e-05 (0.000201)	0.0729 (0.21)	0.817 (1.00)	0.775 (0.984)	0.214 (0.44)	0.0942 (0.254)	1e-05 (0.000118)	0.333 (0.578)	0.0264 (0.0973)	0.00072 (0.00483)	0.428 (0.665)
4p loss	98 (11%)	784	2.36e-11 (9.05e-09)	0.374 (0.614)	1e-05 (0.000118)	1e-05 (0.000118)	0.00158 (0.00953)	0.0145 (0.0588)	0.0538 (0.17)	1 (1.00)	0.157 (0.355)	0.00192 (0.0111)	0.976 (1.00)	0.223 (0.451)	0.131 (0.316)	0.447 (0.68)
5q loss	23 (3%)	859	0.22 (0.448)	0.000448 (0.00328)	8e-05 (0.000691)	4e-05 (0.000373)	0.0488 (0.157)	1 (1.00)	0.176 (0.381)	1 (1.00)	0.859 (1.00)	1e-05 (0.000118)	0.037 (0.128)	0.128 (0.312)	0.47 (0.705)	0.074 (0.213)
11q loss	52 (6%)	830	0.000746 (0.00498)	0.0151 (0.0605)	4e-05 (0.000373)	4e-05 (0.000373)	2e-05 (0.000201)	0.314 (0.552)	0.547 (0.789)	1 (1.00)	0.0432 (0.144)	0.0317 (0.114)	0.536 (0.778)	0.242 (0.475)	0.359 (0.605)	0.723 (0.937)
13q loss	137 (16%)	745	0.0341 (0.12)	0.00011 (0.000942)	1e-05 (0.000118)	1e-05 (0.000118)	0.00757 (0.0353)	0.115 (0.293)	0.0137 (0.0563)	1 (1.00)	0.638 (0.865)	1e-05 (0.000118)	0.933 (1.00)	0.6 (0.84)	0.163 (0.362)	0.641 (0.868)
15q loss	68 (8%)	814	1.98e-05 (0.000201)	0.418 (0.655)	2e-05 (0.000201)	2e-05 (0.000201)	0.00243 (0.0137)	0.0139 (0.0567)	0.592 (0.833)	1 (1.00)	0.0746 (0.213)	0.0668 (0.196)	0.354 (0.599)		0.307 (0.546)	0.352 (0.596)
17q loss	82 (9%)	800	0.00889 (0.0396)	0.000456 (0.00331)	1e-05 (0.000118)	1e-05 (0.000118)	0.12 (0.3)	0.557 (0.798)	0.538 (0.78)	1 (1.00)	0.0283 (0.102)	1e-05 (0.000118)	0.611 (0.848)	0.963 (1.00)	0.0654 (0.193)	0.523 (0.763)
5p gain	238 (27%)	644	0.39 (0.629)	0.000654 (0.00444)	0.00031 (0.00234)	0.00028 (0.00219)	0.912 (1.00)	0.18 (0.386)	0.0906 (0.249)	0.469 (0.705)	0.11 (0.282)	1e-05 (0.000118)	0.88 (1.00)	0.948 (1.00)	0.00026 (0.00206)	0.857 (1.00)
8q gain	103 (12%)	779	0.00853 (0.0388)	0.132 (0.317)	1e-05 (0.000118)	1e-05 (0.000118)	0.00393 (0.0207)	0.0124 (0.0517)	0.911 (1.00)	1 (1.00)	0.308 (0.546)	0.00133 (0.00825)	0.359 (0.605)	0.253 (0.487)	0.154 (0.35)	1 (1.00)
11q gain	55 (6%)	827	0.247 (0.481)	0.0524 (0.166)	0.0346 (0.121)	0.00897 (0.0396)	0.497 (0.735)	0.159 (0.357)	0.3 (0.543)	0.216 (0.443)	0.149 (0.343)	1e-05 (0.000118)	0.0422 (0.142)	0.0498 (0.159)	0.35 (0.596)	0.309 (0.546)
20p gain	233 (26%)	649	0.405 (0.646)	0.43 (0.665)	0.00872 (0.0391)	0.00374 (0.0199)	0.0618 (0.184)	0.0461 (0.151)	0.00114 (0.00728)	0.199 (0.417)	0.849 (1.00)	0.00022 (0.00175)	0.206 (0.427)	0.67 (0.893)	0.307 (0.546)	0.365 (0.607)
20q gain	237 (27%)	645	0.261 (0.499)	0.25 (0.484)	0.00751 (0.0352)	0.00729 (0.0344)	0.0202 (0.0777)	0.0651 (0.192)	0.00282 (0.0156)	0.199 (0.417)	0.849 (1.00)	0.00014 (0.00117)	0.269 (0.507)	0.764 (0.975)	0.157 (0.355)	0.284 (0.522)
xp gain	129 (15%)	753	0.141 (0.331)	0.179 (0.385)	0.0343 (0.12)	0.0614 (0.184)	1 (1.00)	0.25 (0.484)	0.00608 (0.0297)	1 (1.00)	0.108 (0.277)	1e-05 (0.000118)	0.418 (0.655)	0.057 (0.175)	0.033 (0.117)	0.661 (0.888)
xq gain	130 (15%)	752	0.0762 (0.217)	0.27 (0.507)	0.0643 (0.19)	0.113 (0.289)	1 (1.00)	0.178 (0.383)	0.00859 (0.0388)	1 (1.00)	0.074 (0.213)	1e-05 (0.000118)	0.653 (0.879)	0.165 (0.365)	0.0226 (0.0862)	0.662 (0.888)
1q loss	110 (12%)	772	0.0236 (0.0896)	0.00104 (0.00677)	3e-05 (0.000289)	0.00015 (0.00124)	0.488 (0.728)	0.0522 (0.166)	0.235 (0.466)	1 (1.00)	0.557 (0.798)	1e-05 (0.000118)	0.445 (0.68)	0.96 (1.00)	0.248 (0.481)	0.125 (0.309)
4q loss	92 (10%)	790	6.76e-13 (7.76e-10)	0.47 (0.706)	1e-05 (0.000118)	1e-05 (0.000118)	0.00116 (0.00736)	0.000606 (0.00422)	0.414 (0.651)	1 (1.00)	0.136 (0.322)	0.00855 (0.0388)	0.886 (1.00)	0.162 (0.361)	0.0938 (0.254)	0.602 (0.84)
6p loss	171 (19%)	711	0.636 (0.865)	0.0574 (0.176)	1e-05 (0.000118)	1e-05 (0.000118)	0.0542 (0.17)	0.782 (0.989)	0.528 (0.769)	1 (1.00)	0.174 (0.378)	1e-05 (0.000118)	0.367 (0.609)	0.701 (0.922)	0.00039 (0.00289)	0.672 (0.894)
6q loss	206 (23%)	676	0.097 (0.257)	0.0567 (0.175)	3e-05 (0.000289)	2e-05 (0.000201)	0.0442 (0.147)	0.896 (1.00)	0.554 (0.796)	1 (1.00)	0.279 (0.518)	1e-05 (0.000118)	0.142 (0.333)	0.639 (0.866)	0.0007 (0.00473)	0.332 (0.578)
8p loss	161 (18%)	721	0.0148 (0.0596)	0.811 (1.00)	0.0324 (0.115)	0.0371 (0.128)	0.674 (0.895)	0.0402 (0.137)	0.459 (0.694)	1 (1.00)	0.767 (0.977)	1e-05 (0.000118)	0.957 (1.00)	0.666 (0.892)	0.0321 (0.115)	0.138 (0.326)
11p loss	42 (5%)	840	0.00759 (0.0353)	0.0463 (0.151)	0.00142 (0.00867)	0.00113 (0.00725)	0.00063 (0.00436)	0.393 (0.631)	0.738 (0.953)	1 (1.00)	0.372 (0.613)	0.0194 (0.0752)	0.939 (1.00)	0.125 (0.308)	0.499 (0.736)	0.247 (0.481)
18p loss	141 (16%)	741	5.07e-08 (8.31e-06)	0.533 (0.776)	1e-05 (0.000118)	1e-05 (0.000118)	0.0152 (0.0605)	0.0239 (0.0903)	1 (1.00)	1 (1.00)	0.275 (0.513)	0.285 (0.523)	0.176 (0.382)	0.073 (0.21)	0.101 (0.264)	0.181 (0.387)
18q loss	148 (17%)	734	5.6e-07 (8.03e-05)	0.553 (0.796)	1e-05 (0.000118)	1e-05 (0.000118)	0.00366 (0.0195)	0.0378 (0.13)	1 (1.00)	1 (1.00)	0.344 (0.588)	0.499 (0.736)	0.304 (0.546)	0.152 (0.347)	0.059 (0.179)	0.129 (0.314)
19q loss	23 (3%)	859	0.000207 (0.00167)	0.19 (0.402)	0.00031 (0.00234)	2e-05 (0.000201)	5e-05 (0.000452)	0.0881 (0.243)	0.826 (1.00)	1 (1.00)	0.247 (0.481)	0.0005 (0.00357)	0.392 (0.631)	0.18 (0.386)	0.341 (0.584)	1 (1.00)
21q loss	133 (15%)	749	0.89 (1.00)	0.0543 (0.17)	0.00051 (0.00361)	1e-05 (0.000118)	0.00165 (0.00976)	1 (1.00)	0.426 (0.662)	1 (1.00)	0.183 (0.391)	1e-05 (0.000118)	0.447 (0.68)	0.0566 (0.175)	0.119 (0.299)	0.496 (0.733)
1p gain	31 (4%)	851	1.03e-08 (1.97e-06)	0.0808 (0.227)	0.00278 (0.0155)	0.00603 (0.0297)	0.00698 (0.0332)	0.117 (0.297)	0.561 (0.801)	1 (1.00)	0.1 (0.263)	0.515 (0.754)	1 (1.00)		0.392 (0.631)	0.389 (0.629)
3p gain	103 (12%)	779	0.806 (1.00)	0.138 (0.326)	0.0268 (0.0985)	0.0155 (0.0615)	0.0165 (0.0652)	1 (1.00)	0.12 (0.3)	1 (1.00)	0.0893 (0.246)	1e-05 (0.000118)	0.882 (1.00)	0.472 (0.707)	0.369 (0.609)	0.809 (1.00)
5q gain	253 (29%)	629	0.551 (0.794)	0.00195 (0.0112)	0.00144 (0.00875)	0.00634 (0.0307)	0.698 (0.918)	0.189 (0.402)	0.0968 (0.257)	0.507 (0.744)	0.132 (0.317)	1e-05 (0.000118)	0.719 (0.936)	0.869 (1.00)	0.00088 (0.00584)	1 (1.00)
7q gain	371 (42%)	511	0.912 (1.00)	0.224 (0.452)	0.0635 (0.188)	0.973 (1.00)	0.203 (0.422)	0.00437 (0.0224)	8.05e-07 (9.25e-05)	0.0949 (0.256)	0.563 (0.802)	1e-05 (0.000118)	0.408 (0.646)	0.00638 (0.0307)	0.143 (0.333)	0.421 (0.658)
9p gain	26 (3%)	856	0.153 (0.349)	0.614 (0.849)	0.00315 (0.0171)	0.00163 (0.0097)	0.292 (0.533)	0.0581 (0.177)	0.0101 (0.0441)	1 (1.00)	0.0927 (0.252)	2e-05 (0.000201)	0.298 (0.541)		0.394 (0.632)	0.388 (0.629)
11p gain	58 (7%)	824	0.714 (0.934)	0.159 (0.357)	0.00425 (0.0221)	0.00131 (0.00817)	0.224 (0.453)	0.0371 (0.128)	0.665 (0.891)	0.21 (0.433)	0.36 (0.605)	2e-05 (0.000201)	0.0422 (0.142)	0.152 (0.347)	0.34 (0.584)	0.34 (0.584)
14q gain	39 (4%)	843	0.775 (0.984)	0.0426 (0.143)	0.00141 (0.00866)	0.0004 (0.00294)	0.365 (0.607)	0.584 (0.825)	0.488 (0.728)	1 (1.00)	0.229 (0.457)	1e-05 (0.000118)	0.1 (0.263)	0.084 (0.235)	0.242 (0.475)	0.668 (0.892)
16p gain	281 (32%)	601	0.0201 (0.0776)	0.0129 (0.0533)	0.851 (1.00)	0.884 (1.00)	0.409 (0.646)	0.896 (1.00)	0.00212 (0.0121)	0.562 (0.801)	0.813 (1.00)	1e-05 (0.000118)	0.979 (1.00)	0.309 (0.546)	0.0379 (0.13)	0.613 (0.849)
19p gain	74 (8%)	808	0.962 (1.00)	0.708 (0.928)	2e-05 (0.000201)	3e-05 (0.000289)	0.161 (0.36)	0.0107 (0.0457)	0.606 (0.844)	0.216 (0.443)	0.972 (1.00)	1e-05 (0.000118)	0.407 (0.646)	0.126 (0.309)	0.00161 (0.00963)	1 (1.00)
19q gain	78 (9%)	804	0.743 (0.955)	0.776 (0.984)	2e-05 (0.000201)	4e-05 (0.000373)	0.743 (0.955)	0.00274 (0.0153)	0.706 (0.927)	0.204 (0.423)	0.972 (1.00)	1e-05 (0.000118)	0.731 (0.945)	0.202 (0.421)	0.00064 (0.00437)	1 (1.00)
3q loss	119 (13%)	763	0.28 (0.519)	0.0451 (0.148)	0.152 (0.347)	0.0984 (0.26)	0.123 (0.306)	0.54 (0.781)	0.0358 (0.125)	0.0158 (0.0624)	0.725 (0.939)	1e-05 (0.000118)			0.06 (0.181)	0.614 (0.849)
16p loss	18 (2%)	864	6.56e-06 (0.000118)	0.978 (1.00)	0.00896 (0.0396)	0.00029 (0.00222)	0.00097 (0.00636)	0.702 (0.922)	0.617 (0.849)	1 (1.00)		0.0686 (0.2)			1 (1.00)	1 (1.00)
17p loss	111 (13%)	771	0.626 (0.854)	0.00397 (0.0208)	1e-05 (0.000118)	1e-05 (0.000118)	0.0005 (0.00357)	0.169 (0.371)	0.281 (0.519)	1 (1.00)	0.436 (0.672)	1e-05 (0.000118)	0.86 (1.00)	0.837 (1.00)	0.341 (0.584)	1 (1.00)
19p loss	29 (3%)	853	5.51e-05 (0.000495)	0.226 (0.454)	0.0012 (0.00753)	0.00064 (0.00437)	0.025 (0.0927)	0.146 (0.338)	0.844 (1.00)	1 (1.00)	0.247 (0.481)	0.043 (0.143)	0.581 (0.822)		0.49 (0.729)	1 (1.00)
xp loss	114 (13%)	768	0.475 (0.709)	0.000515 (0.00363)	0.00022 (0.00175)	6e-05 (0.00053)	0.00384 (0.0203)	1 (1.00)	0.135 (0.322)	1 (1.00)	0.521 (0.761)	1e-05 (0.000118)	0.697 (0.918)	0.447 (0.68)	0.389 (0.629)	0.303 (0.546)
xq loss	113 (13%)	769	0.2 (0.417)	0.00171 (0.00996)	0.00039 (0.00289)	0.00015 (0.00124)	0.00634 (0.0307)	0.863 (1.00)	0.24 (0.474)	1 (1.00)	0.241 (0.475)	1e-05 (0.000118)	0.986 (1.00)	0.848 (1.00)	0.167 (0.367)	0.3 (0.543)
3q gain	161 (18%)	721	0.301 (0.543)	0.127 (0.311)	0.334 (0.578)	0.152 (0.347)	0.0242 (0.091)	0.0995 (0.262)	0.026 (0.0963)	1 (1.00)	0.492 (0.73)	1e-05 (0.000118)	0.861 (1.00)	0.446 (0.68)	0.0803 (0.226)	0.84 (1.00)
4p gain	47 (5%)	835	0.601 (0.84)	0.0249 (0.0927)	0.0045 (0.023)	0.0072 (0.0342)	0.127 (0.311)	0.584 (0.825)	1 (1.00)	1 (1.00)	0.723 (0.937)	1e-05 (0.000118)	0.162 (0.361)	0.236 (0.467)	0.304 (0.546)	0.457 (0.693)
4q gain	46 (5%)	836	0.273 (0.51)	0.0416 (0.141)	0.0112 (0.0475)	0.0208 (0.0797)	0.097 (0.257)	0.784 (0.992)	0.872 (1.00)	1 (1.00)	0.79 (0.995)	1e-05 (0.000118)	0.305 (0.546)	0.236 (0.467)	0.337 (0.581)	0.437 (0.674)
6p gain	22 (2%)	860	0.0601 (0.181)	0.718 (0.936)	0.00137 (0.00846)	0.00256 (0.0144)	0.004 (0.0209)	0.119 (0.299)	0.364 (0.607)	1 (1.00)	0.789 (0.995)	0.305 (0.546)	0.958 (1.00)	0.792 (0.995)	0.715 (0.935)	0.616 (0.849)
6q gain	16 (2%)	866	0.00434 (0.0223)	0.907 (1.00)	0.0244 (0.0913)	0.0106 (0.0456)	0.0397 (0.136)	0.191 (0.402)	0.599 (0.84)	1 (1.00)	0.789 (0.995)	0.668 (0.892)	0.352 (0.596)	0.622 (0.852)	0.8 (0.999)	1 (1.00)
7p gain	369 (42%)	513	0.572 (0.812)	0.19 (0.402)	0.221 (0.449)	0.969 (1.00)	0.213 (0.438)	0.0242 (0.091)	7.47e-07 (9.25e-05)	0.593 (0.834)	0.402 (0.643)	1e-05 (0.000118)	0.369 (0.609)	0.00638 (0.0307)	0.198 (0.417)	0.421 (0.658)
8p gain	69 (8%)	813	0.389 (0.629)	0.494 (0.731)	2e-05 (0.000201)	2e-05 (0.000201)	0.0545 (0.17)	0.502 (0.737)	1 (1.00)	1 (1.00)	0.792 (0.995)	7e-05 (0.000609)	0.964 (1.00)	0.321 (0.564)	0.284 (0.522)	1 (1.00)
9q gain	24 (3%)	858	0.454 (0.689)	0.671 (0.893)	0.00113 (0.00725)	0.00012 (0.00102)	0.293 (0.534)	1 (1.00)	0.0449 (0.148)	1 (1.00)	0.0927 (0.252)	3e-05 (0.000289)	0.298 (0.541)		0.229 (0.457)	0.365 (0.607)
15q gain	52 (6%)	830	0.264 (0.502)	0.338 (0.583)	0.00095 (0.00627)	0.00311 (0.0169)	0.462 (0.696)	0.474 (0.709)	0.649 (0.874)	1 (1.00)	0.924 (1.00)	1e-05 (0.000118)	0.418 (0.655)	0.0588 (0.178)	0.384 (0.626)	0.269 (0.507)
16q gain	268 (30%)	614	0.00215 (0.0122)	0.0317 (0.114)	0.409 (0.646)	0.692 (0.915)	0.905 (1.00)	0.423 (0.66)	0.0102 (0.0442)	1 (1.00)	0.744 (0.955)	1e-05 (0.000118)	0.616 (0.849)	0.309 (0.546)	0.0958 (0.257)	0.864 (1.00)
1p loss	145 (16%)	737	0.136 (0.322)	0.0108 (0.0461)	6e-05 (0.00053)	5e-05 (0.000452)	0.176 (0.381)	0.119 (0.299)	0.441 (0.679)	1 (1.00)	0.799 (0.999)	1e-05 (0.000118)	0.367 (0.609)	0.253 (0.487)	0.695 (0.918)	0.108 (0.277)
10p loss	133 (15%)	749	0.952 (1.00)	0.0742 (0.213)	1e-05 (0.000118)	2e-05 (0.000201)	0.0915 (0.25)	1 (1.00)	0.69 (0.915)	1 (1.00)	0.558 (0.798)	1e-05 (0.000118)	0.173 (0.378)	0.448 (0.68)	0.368 (0.609)	0.22 (0.448)
10q loss	157 (18%)	725	0.934 (1.00)	0.0296 (0.107)	1e-05 (0.000118)	1e-05 (0.000118)	0.256 (0.491)	1 (1.00)	1 (1.00)	1 (1.00)	0.834 (1.00)	1e-05 (0.000118)	0.173 (0.378)	0.448 (0.68)	0.143 (0.333)	0.262 (0.5)
16q loss	28 (3%)	854	2.23e-06 (0.000118)	0.407 (0.646)	0.00488 (0.0245)	0.00029 (0.00222)	0.00028 (0.00219)	0.72 (0.936)	1 (1.00)	1 (1.00)	0.165 (0.365)	0.112 (0.286)	0.179 (0.385)	0.867 (1.00)	0.875 (1.00)	0.621 (0.852)
13q gain	52 (6%)	830	0.0909 (0.249)	0.309 (0.546)	0.865 (1.00)	0.945 (1.00)	0.352 (0.596)	0.793 (0.995)	0.13 (0.314)	0.0148 (0.0595)	0.759 (0.97)	0.00483 (0.0243)	1 (1.00)	0.876 (1.00)	0.891 (1.00)	0.182 (0.387)
18p gain	54 (6%)	828	0.00923 (0.0404)	0.617 (0.849)	0.501 (0.737)	0.592 (0.833)	1 (1.00)	0.638 (0.865)	0.372 (0.613)	1 (1.00)	0.13 (0.314)	1e-05 (0.000118)	0.265 (0.503)	0.43 (0.665)	0.0758 (0.216)	0.291 (0.532)
18q gain	50 (6%)	832	0.00765 (0.0353)	0.79 (0.995)	0.394 (0.632)	0.429 (0.665)	0.575 (0.815)	0.461 (0.696)	0.283 (0.522)	1 (1.00)	0.0275 (0.1)	1e-05 (0.000118)	0.886 (1.00)	0.43 (0.665)	0.102 (0.266)	0.276 (0.513)
22q gain	64 (7%)	818	0.572 (0.812)	0.357 (0.603)	0.0138 (0.0564)	0.0017 (0.00996)	0.125 (0.309)	0.834 (1.00)	0.411 (0.648)	0.21 (0.433)	0.988 (1.00)	1e-05 (0.000118)	0.716 (0.936)	0.413 (0.65)	0.0941 (0.254)	0.3 (0.543)
20q loss	6 (1%)	876	0.871 (1.00)	0.123 (0.306)	0.109 (0.278)	0.165 (0.365)	0.0873 (0.241)	0.597 (0.838)	1 (1.00)	1 (1.00)		0.00764 (0.0353)			0.648 (0.874)	0.0633 (0.188)
2p gain	120 (14%)	762	0.459 (0.694)	0.332 (0.578)	0.376 (0.616)	0.118 (0.298)	0.0373 (0.129)	0.622 (0.852)	1 (1.00)	0.317 (0.558)	0.146 (0.339)	0.0188 (0.0732)	0.185 (0.393)	0.849 (1.00)	0.691 (0.915)	0.814 (1.00)
2q gain	127 (14%)	755	0.646 (0.874)	0.241 (0.474)	0.523 (0.763)	0.273 (0.51)	0.017 (0.0667)	0.747 (0.958)	0.543 (0.784)	0.345 (0.59)	0.233 (0.463)	0.00909 (0.04)	0.336 (0.581)	0.831 (1.00)	0.723 (0.937)	0.649 (0.874)
10p gain	28 (3%)	854	0.92 (1.00)	0.758 (0.97)	0.168 (0.368)	0.00739 (0.0348)	0.0141 (0.0572)	1 (1.00)	0.541 (0.782)	1 (1.00)	0.625 (0.854)	0.381 (0.621)	0.753 (0.964)		0.147 (0.34)	0.625 (0.854)
10q gain	22 (2%)	860	0.424 (0.661)	0.202 (0.421)	0.267 (0.505)	0.0465 (0.152)	0.0238 (0.0902)	0.74 (0.954)	0.252 (0.486)	1 (1.00)	0.988 (1.00)	0.886 (1.00)			0.13 (0.314)	0.616 (0.849)
21q gain	72 (8%)	810	0.398 (0.638)	0.451 (0.685)	0.387 (0.629)	0.221 (0.449)	1 (1.00)	0.405 (0.646)	0.696 (0.918)	1 (1.00)	0.0417 (0.141)	0.385 (0.627)	0.447 (0.68)	0.627 (0.855)	0.0613 (0.184)	0.77 (0.98)
7p loss	4 (0%)	878	0.0855 (0.238)	0.409 (0.646)	0.269 (0.507)	0.107 (0.277)	0.0477 (0.155)	1 (1.00)	0.308 (0.546)	1 (1.00)		0.362 (0.607)			1 (1.00)	1 (1.00)
7q loss	4 (0%)	878	0.0855 (0.238)	0.409 (0.646)	0.27 (0.507)	0.107 (0.277)	0.0481 (0.155)	1 (1.00)	0.308 (0.546)	1 (1.00)		0.363 (0.607)			1 (1.00)	1 (1.00)
8q loss	83 (9%)	799	0.515 (0.754)	0.205 (0.425)	0.535 (0.777)	0.346 (0.59)	1 (1.00)	1 (1.00)	0.22 (0.448)	1 (1.00)	0.564 (0.802)	1e-05 (0.000118)	0.939 (1.00)		0.269 (0.507)	0.161 (0.36)
12p loss	7 (1%)	875	0.124 (0.308)	0.741 (0.955)	0.147 (0.339)	0.107 (0.277)	0.0479 (0.155)	1 (1.00)	1 (1.00)	1 (1.00)		0.0999 (0.263)			1 (1.00)	1 (1.00)
12q loss	4 (0%)	878	0.998 (1.00)	0.333 (0.578)	0.272 (0.509)	0.0542 (0.17)		1 (1.00)	1 (1.00)	1 (1.00)		0.174 (0.378)			1 (1.00)	1 (1.00)
20p loss	12 (1%)	870	0.444 (0.68)	0.229 (0.457)	0.116 (0.295)	0.129 (0.314)	0.0965 (0.257)	0.658 (0.885)	0.226 (0.454)	1 (1.00)		0.00678 (0.0324)			0.131 (0.316)	0.279 (0.518)

'1p gain' versus 'Time to Death'

P value = 1.03e-08 (logrank test), Q value = 2e-06

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

	nPatients	nDeath	Duration Range (Median), Month
ALL	876	228	0.1 - 194.8 (35.9)
1P GAIN MUTATED	31	20	0.5 - 118.8 (22.3)
1P GAIN WILD-TYPE	845	208	0.1 - 194.8 (36.5)

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

'1p gain' versus 'YEARS_TO_BIRTH'

P value = 0.0808 (Wilcoxon-test), Q value = 0.23

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

	nPatients	Mean (Std.Dev)
ALL	876	60.1 (12.5)
1P GAIN MUTATED	29	63.1 (12.6)
1P GAIN WILD-TYPE	847	60.0 (12.5)

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

'1p gain' versus 'PATHOLOGIC_STAGE'

P value = 0.00278 (Fisher's exact test), Q value = 0.015

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

nPatients	STAGE I	STAGE II	STAGE III	STAGE IV
ALL	454	103	190	104
1P GAIN MUTATED	7	4	13	6
1P GAIN WILD-TYPE	447	99	177	98

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

'1p gain' versus 'PATHOLOGY_T_STAGE'

P value = 0.00603 (Fisher's exact test), Q value = 0.03

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

nPatients	T1	T2	T3	T4
ALL	480	127	258	15
1P GAIN MUTATED	9	4	18	0
1P GAIN WILD-TYPE	471	123	240	15

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

'1p gain' versus 'PATHOLOGY_N_STAGE'

P value = 0.00698 (Fisher's exact test), Q value = 0.033

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

nPatients	N0	N1	N2
ALL	323	44	6
1P GAIN MUTATED	11	6	1
1P GAIN WILD-TYPE	312	38	5

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

'1q gain' versus 'Time to Death'

P value = 6.31e-06 (logrank test), Q value = 0.00012

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

	nPatients	nDeath	Duration Range (Median), Month
ALL	876	228	0.1 - 194.8 (35.9)
1Q GAIN MUTATED	68	32	0.4 - 129.4 (24.8)
1Q GAIN WILD-TYPE	808	196	0.1 - 194.8 (36.7)

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 = 0.0416 (Wilcoxon-test), Q value = 0.14

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

	nPatients	Mean (Std.Dev)
ALL	876	60.1 (12.5)
1Q GAIN MUTATED	66	62.7 (12.1)
1Q GAIN WILD-TYPE	810	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 = 0.00018 (Fisher's exact test), Q value = 0.0015

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

nPatients	STAGE I	STAGE II	STAGE III	STAGE IV
ALL	454	103	190	104
1Q GAIN MUTATED	20	8	27	12
1Q GAIN WILD-TYPE	434	95	163	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 = 0.00047 (Fisher's exact test), Q value = 0.0034

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

nPatients	T1	T2	T3	T4
ALL	480	127	258	15
1Q GAIN MUTATED	23	10	35	0
1Q GAIN WILD-TYPE	457	117	223	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 = 0.00822 (Fisher's exact test), Q value = 0.038

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

nPatients	N0	N1	N2
ALL	323	44	6
1Q GAIN MUTATED	27	9	2
1Q GAIN WILD-TYPE	296	35	4

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 = 0.049 (Wilcoxon-test), Q value = 0.16

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

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

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

'1q gain' versus 'HISTOLOGICAL_TYPE'

P value = 0.00457 (Fisher's exact test), Q value = 0.023

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	288
1Q GAIN MUTATED	0	50	18
1Q GAIN WILD-TYPE	66	478	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 = 0.0373 (Fisher's exact test), Q value = 0.13

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

nPatients	N0	N1	N2
ALL	323	44	6
2P GAIN MUTATED	43	11	2
2P GAIN WILD-TYPE	280	33	4

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

'2p gain' versus 'HISTOLOGICAL_TYPE'

P value = 0.0188 (Fisher's exact test), Q value = 0.073

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	288
2P GAIN MUTATED	2	76	42
2P GAIN WILD-TYPE	64	452	246

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

'2q gain' versus 'PATHOLOGY_N_STAGE'

P value = 0.017 (Fisher's exact test), Q value = 0.067

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

nPatients	N0	N1	N2
ALL	323	44	6
2Q GAIN MUTATED	45	11	3
2Q GAIN WILD-TYPE	278	33	3

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

'2q gain' versus 'HISTOLOGICAL_TYPE'

P value = 0.00909 (Fisher's exact test), Q value = 0.04

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	288
2Q GAIN MUTATED	2	78	47
2Q GAIN WILD-TYPE	64	450	241

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

'3p gain' versus 'PATHOLOGIC_STAGE'

P value = 0.0268 (Fisher's exact test), Q value = 0.098

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

nPatients	STAGE I	STAGE II	STAGE III	STAGE IV
ALL	454	103	190	104
3P GAIN MUTATED	57	16	11	11
3P GAIN WILD-TYPE	397	87	179	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 = 0.0155 (Fisher's exact test), Q value = 0.061

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

nPatients	T1	T2	T3	T4
ALL	480	127	258	15
3P GAIN MUTATED	61	20	18	3
3P GAIN WILD-TYPE	419	107	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 = 0.0165 (Fisher's exact test), Q value = 0.065

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

nPatients	N0	N1	N2
ALL	323	44	6
3P GAIN MUTATED	20	8	1
3P GAIN WILD-TYPE	303	36	5

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

'3p gain' versus 'KARNOFSKY_PERFORMANCE_SCORE'

P value = 0.0893 (Wilcoxon-test), Q value = 0.25

Table S20. Gene #5: '3p gain' versus Clinical Feature #9: 'KARNOFSKY_PERFORMANCE_SCORE'

	nPatients	Mean (Std.Dev)
ALL	143	87.7 (22.8)
3P GAIN MUTATED	26	94.6 (8.1)
3P GAIN WILD-TYPE	117	86.2 (24.6)

Figure S20. Get High-res Image Gene #5: '3p gain' versus Clinical Feature #9: 'KARNOFSKY_PERFORMANCE_SCORE'

'3p gain' versus 'HISTOLOGICAL_TYPE'

P value = 1e-05 (Fisher's exact test), Q value = 0.00012

Table S21. 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	288
3P GAIN MUTATED	9	19	75
3P GAIN WILD-TYPE	57	509	213

Figure S21. Get High-res Image Gene #5: '3p gain' versus Clinical Feature #10: 'HISTOLOGICAL_TYPE'

'3q gain' versus 'PATHOLOGY_N_STAGE'

P value = 0.0242 (Fisher's exact test), Q value = 0.091

Table S22. Gene #6: '3q gain' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

nPatients	N0	N1	N2
ALL	323	44	6
3Q GAIN MUTATED	44	13	1
3Q GAIN WILD-TYPE	279	31	5

Figure S22. Get High-res Image Gene #6: '3q gain' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

'3q gain' versus 'GENDER'

P value = 0.026 (Fisher's exact test), Q value = 0.096

Table S23. Gene #6: '3q gain' versus Clinical Feature #7: 'GENDER'

nPatients	FEMALE	MALE
ALL	292	590
3Q GAIN MUTATED	41	120
3Q GAIN WILD-TYPE	251	470

Figure S23. 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 = 0.00012

Table S24. 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	288
3Q GAIN MUTATED	9	58	94
3Q GAIN WILD-TYPE	57	470	194

Figure S24. Get High-res Image Gene #6: '3q gain' versus Clinical Feature #10: 'HISTOLOGICAL_TYPE'

'3q gain' versus 'RACE'

P value = 0.0803 (Fisher's exact test), Q value = 0.23

Table S25. Gene #6: '3q gain' versus Clinical Feature #13: 'RACE'

nPatients	AMERICAN INDIAN OR ALASKA NATIVE	ASIAN	BLACK OR AFRICAN AMERICAN	WHITE
ALL	2	16	121	719
3Q GAIN MUTATED	2	2	20	128
3Q GAIN WILD-TYPE	0	14	101	591

Figure S25. Get High-res Image Gene #6: '3q gain' versus Clinical Feature #13: 'RACE'

'4p gain' versus 'YEARS_TO_BIRTH'

P value = 0.0249 (Wilcoxon-test), Q value = 0.093

Table S26. Gene #7: '4p gain' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

	nPatients	Mean (Std.Dev)
ALL	876	60.1 (12.5)
4P GAIN MUTATED	46	56.3 (13.3)
4P GAIN WILD-TYPE	830	60.4 (12.4)

Figure S26. Get High-res Image Gene #7: '4p gain' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'4p gain' versus 'PATHOLOGIC_STAGE'

P value = 0.0045 (Fisher's exact test), Q value = 0.023

Table S27. Gene #7: '4p gain' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

nPatients	STAGE I	STAGE II	STAGE III	STAGE IV
ALL	454	103	190	104
4P GAIN MUTATED	18	13	7	8
4P GAIN WILD-TYPE	436	90	183	96

Figure S27. Get High-res Image Gene #7: '4p gain' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

'4p gain' versus 'PATHOLOGY_T_STAGE'

P value = 0.0072 (Fisher's exact test), Q value = 0.034

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

nPatients	T1	T2	T3	T4
ALL	480	127	258	15
4P GAIN MUTATED	18	14	13	2
4P GAIN WILD-TYPE	462	113	245	13

Figure S28. 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 = 0.00012

Table S29. 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	288
4P GAIN MUTATED	24	13	10
4P GAIN WILD-TYPE	42	515	278

Figure S29. Get High-res Image Gene #7: '4p gain' versus Clinical Feature #10: 'HISTOLOGICAL_TYPE'

'4q gain' versus 'YEARS_TO_BIRTH'

P value = 0.0416 (Wilcoxon-test), Q value = 0.14

Table S30. Gene #8: '4q gain' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

	nPatients	Mean (Std.Dev)
ALL	876	60.1 (12.5)
4Q GAIN MUTATED	45	56.6 (13.3)
4Q GAIN WILD-TYPE	831	60.3 (12.5)

Figure S30. Get High-res Image Gene #8: '4q gain' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'4q gain' versus 'PATHOLOGIC_STAGE'

P value = 0.0112 (Fisher's exact test), Q value = 0.047

Table S31. Gene #8: '4q gain' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

nPatients	STAGE I	STAGE II	STAGE III	STAGE IV
ALL	454	103	190	104
4Q GAIN MUTATED	19	13	7	6
4Q GAIN WILD-TYPE	435	90	183	98

Figure S31. Get High-res Image Gene #8: '4q gain' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

'4q gain' versus 'PATHOLOGY_T_STAGE'

P value = 0.0208 (Fisher's exact test), Q value = 0.08

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

nPatients	T1	T2	T3	T4
ALL	480	127	258	15
4Q GAIN MUTATED	19	14	12	1
4Q GAIN WILD-TYPE	461	113	246	14

Figure S32. 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 = 0.00012

Table S33. 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	288
4Q GAIN MUTATED	24	13	9
4Q GAIN WILD-TYPE	42	515	279

Figure S33. Get High-res Image Gene #8: '4q gain' versus Clinical Feature #10: 'HISTOLOGICAL_TYPE'

'5p gain' versus 'YEARS_TO_BIRTH'

P value = 0.000654 (Wilcoxon-test), Q value = 0.0044

Table S34. Gene #9: '5p gain' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

	nPatients	Mean (Std.Dev)
ALL	876	60.1 (12.5)
5P GAIN MUTATED	236	62.7 (12.3)
5P GAIN WILD-TYPE	640	59.2 (12.5)

Figure S34. Get High-res Image Gene #9: '5p gain' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'5p gain' versus 'PATHOLOGIC_STAGE'

P value = 0.00031 (Fisher's exact test), Q value = 0.0023

Table S35. Gene #9: '5p gain' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

nPatients	STAGE I	STAGE II	STAGE III	STAGE IV
ALL	454	103	190	104
5P GAIN MUTATED	102	25	66	42
5P GAIN WILD-TYPE	352	78	124	62

Figure S35. Get High-res Image Gene #9: '5p gain' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

'5p gain' versus 'PATHOLOGY_T_STAGE'

P value = 0.00028 (Fisher's exact test), Q value = 0.0022

Table S36. Gene #9: '5p gain' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

nPatients	T1	T2	T3	T4
ALL	480	127	258	15
5P GAIN MUTATED	106	33	92	7
5P GAIN WILD-TYPE	374	94	166	8

Figure S36. Get High-res Image Gene #9: '5p gain' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

'5p gain' versus 'GENDER'

P value = 0.0906 (Fisher's exact test), Q value = 0.25

Table S37. Gene #9: '5p gain' versus Clinical Feature #7: 'GENDER'

nPatients	FEMALE	MALE
ALL	292	590
5P GAIN MUTATED	68	170
5P GAIN WILD-TYPE	224	420

Figure S37. 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 = 0.00012

Table S38. 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	288
5P GAIN MUTATED	8	195	35
5P GAIN WILD-TYPE	58	333	253

Figure S38. Get High-res Image Gene #9: '5p gain' versus Clinical Feature #10: 'HISTOLOGICAL_TYPE'

'5p gain' versus 'RACE'

P value = 0.00026 (Fisher's exact test), Q value = 0.0021

Table S39. Gene #9: '5p gain' versus Clinical Feature #13: 'RACE'

nPatients	AMERICAN INDIAN OR ALASKA NATIVE	ASIAN	BLACK OR AFRICAN AMERICAN	WHITE
ALL	2	16	121	719
5P GAIN MUTATED	0	4	15	214
5P GAIN WILD-TYPE	2	12	106	505

Figure S39. Get High-res Image Gene #9: '5p gain' versus Clinical Feature #13: 'RACE'

'5q gain' versus 'YEARS_TO_BIRTH'

P value = 0.00195 (Wilcoxon-test), Q value = 0.011

Table S40. Gene #10: '5q gain' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

	nPatients	Mean (Std.Dev)
ALL	876	60.1 (12.5)
5Q GAIN MUTATED	250	62.4 (12.4)
5Q GAIN WILD-TYPE	626	59.3 (12.5)

Figure S40. Get High-res Image Gene #10: '5q gain' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'5q gain' versus 'PATHOLOGIC_STAGE'

P value = 0.00144 (Fisher's exact test), Q value = 0.0087

Table S41. Gene #10: '5q gain' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

nPatients	STAGE I	STAGE II	STAGE III	STAGE IV
ALL	454	103	190	104
5Q GAIN MUTATED	115	25	66	44
5Q GAIN WILD-TYPE	339	78	124	60

Figure S41. Get High-res Image Gene #10: '5q gain' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

'5q gain' versus 'PATHOLOGY_T_STAGE'

P value = 0.00634 (Fisher's exact test), Q value = 0.031

Table S42. Gene #10: '5q gain' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

nPatients	T1	T2	T3	T4
ALL	480	127	258	15
5Q GAIN MUTATED	120	33	94	6
5Q GAIN WILD-TYPE	360	94	164	9

Figure S42. Get High-res Image Gene #10: '5q gain' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

'5q gain' versus 'HISTOLOGICAL_TYPE'

P value = 1e-05 (Fisher's exact test), Q value = 0.00012

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	288
5Q GAIN MUTATED	8	213	32
5Q GAIN WILD-TYPE	58	315	256

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

'5q gain' versus 'RACE'

P value = 0.00088 (Fisher's exact test), Q value = 0.0058

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	16	121	719
5Q GAIN MUTATED	0	4	18	226
5Q GAIN WILD-TYPE	2	12	103	493

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

'6p gain' versus 'Time to Death'

P value = 0.0601 (logrank test), Q value = 0.18

Table S45. Gene #11: '6p gain' versus Clinical Feature #1: 'Time to Death'

	nPatients	nDeath	Duration Range (Median), Month
ALL	876	228	0.1 - 194.8 (35.9)
6P GAIN MUTATED	22	9	1.0 - 113.5 (27.7)
6P GAIN WILD-TYPE	854	219	0.1 - 194.8 (36.0)

Figure S45. Get High-res Image Gene #11: '6p gain' versus Clinical Feature #1: 'Time to Death'

'6p gain' versus 'PATHOLOGIC_STAGE'

P value = 0.00137 (Fisher's exact test), Q value = 0.0085

Table S46. Gene #11: '6p gain' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

nPatients	STAGE I	STAGE II	STAGE III	STAGE IV
ALL	454	103	190	104
6P GAIN MUTATED	6	0	10	6
6P GAIN WILD-TYPE	448	103	180	98

Figure S46. Get High-res Image Gene #11: '6p gain' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

'6p gain' versus 'PATHOLOGY_T_STAGE'

P value = 0.00256 (Fisher's exact test), Q value = 0.014

Table S47. Gene #11: '6p gain' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

nPatients	T1	T2	T3	T4
ALL	480	127	258	15
6P GAIN MUTATED	6	1	14	1
6P GAIN WILD-TYPE	474	126	244	14

Figure S47. Get High-res Image Gene #11: '6p gain' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

'6p gain' versus 'PATHOLOGY_N_STAGE'

P value = 0.004 (Fisher's exact test), Q value = 0.021

Table S48. Gene #11: '6p gain' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

nPatients	N0	N1	N2
ALL	323	44	6
6P GAIN MUTATED	7	6	0
6P GAIN WILD-TYPE	316	38	6

Figure S48. Get High-res Image Gene #11: '6p gain' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

'6q gain' versus 'Time to Death'

P value = 0.00434 (logrank test), Q value = 0.022

Table S49. Gene #12: '6q gain' versus Clinical Feature #1: 'Time to Death'

	nPatients	nDeath	Duration Range (Median), Month
ALL	876	228	0.1 - 194.8 (35.9)
6Q GAIN MUTATED	16	8	6.4 - 113.5 (27.7)
6Q GAIN WILD-TYPE	860	220	0.1 - 194.8 (36.0)

Figure S49. Get High-res Image Gene #12: '6q gain' versus Clinical Feature #1: 'Time to Death'

'6q gain' versus 'PATHOLOGIC_STAGE'

P value = 0.0244 (Fisher's exact test), Q value = 0.091

Table S50. Gene #12: '6q gain' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

nPatients	STAGE I	STAGE II	STAGE III	STAGE IV
ALL	454	103	190	104
6Q GAIN MUTATED	5	0	7	4
6Q GAIN WILD-TYPE	449	103	183	100

Figure S50. Get High-res Image Gene #12: '6q gain' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

'6q gain' versus 'PATHOLOGY_T_STAGE'

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

Table S51. Gene #12: '6q gain' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

nPatients	T1	T2	T3	T4
ALL	480	127	258	15
6Q GAIN MUTATED	5	0	11	0
6Q GAIN WILD-TYPE	475	127	247	15

Figure S51. Get High-res Image Gene #12: '6q gain' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

'6q gain' versus 'PATHOLOGY_N_STAGE'

P value = 0.0397 (Fisher's exact test), Q value = 0.14

Table S52. Gene #12: '6q gain' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

nPatients	N0	N1	N2
ALL	323	44	6
6Q GAIN MUTATED	6	4	0
6Q GAIN WILD-TYPE	317	40	6

Figure S52. Get High-res Image Gene #12: '6q gain' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

'7p gain' versus 'PATHOLOGY_M_STAGE'

P value = 0.0242 (Fisher's exact test), Q value = 0.091

Table S53. Gene #13: '7p gain' versus Clinical Feature #6: 'PATHOLOGY_M_STAGE'

nPatients	0	1
ALL	546	89
7P GAIN MUTATED	193	43
7P GAIN WILD-TYPE	353	46

Figure S53. Get High-res Image Gene #13: '7p gain' versus Clinical Feature #6: 'PATHOLOGY_M_STAGE'

'7p gain' versus 'GENDER'

P value = 7.47e-07 (Fisher's exact test), Q value = 9.2e-05

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

nPatients	FEMALE	MALE
ALL	292	590
7P GAIN MUTATED	88	281
7P GAIN WILD-TYPE	204	309

Figure S54. 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 = 0.00012

Table S55. 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	288
7P GAIN MUTATED	24	173	172
7P GAIN WILD-TYPE	42	355	116

Figure S55. 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 S56. 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 S56. Get High-res Image Gene #13: '7p gain' versus Clinical Feature #12: 'YEAR_OF_TOBACCO_SMOKING_ONSET'

'7q gain' versus 'PATHOLOGIC_STAGE'

P value = 0.0635 (Fisher's exact test), Q value = 0.19

Table S57. Gene #14: '7q gain' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

nPatients	STAGE I	STAGE II	STAGE III	STAGE IV
ALL	454	103	190	104
7Q GAIN MUTATED	191	39	69	54
7Q GAIN WILD-TYPE	263	64	121	50

Figure S57. Get High-res Image Gene #14: '7q gain' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

'7q gain' versus 'PATHOLOGY_M_STAGE'

P value = 0.00437 (Fisher's exact test), Q value = 0.022

Table S58. Gene #14: '7q gain' versus Clinical Feature #6: 'PATHOLOGY_M_STAGE'

nPatients	0	1
ALL	546	89
7Q GAIN MUTATED	192	46
7Q GAIN WILD-TYPE	354	43

Figure S58. Get High-res Image Gene #14: '7q gain' versus Clinical Feature #6: 'PATHOLOGY_M_STAGE'

'7q gain' versus 'GENDER'

P value = 8.05e-07 (Fisher's exact test), Q value = 9.2e-05

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

nPatients	FEMALE	MALE
ALL	292	590
7Q GAIN MUTATED	89	282
7Q GAIN WILD-TYPE	203	308

Figure S59. 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 = 0.00012

Table S60. 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	288
7Q GAIN MUTATED	24	174	173
7Q GAIN WILD-TYPE	42	354	115

Figure S60. 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 S61. 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 S61. Get High-res Image Gene #14: '7q gain' versus Clinical Feature #12: 'YEAR_OF_TOBACCO_SMOKING_ONSET'

'8p gain' versus 'PATHOLOGIC_STAGE'

P value = 2e-05 (Fisher's exact test), Q value = 2e-04

Table S62. Gene #15: '8p gain' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

nPatients	STAGE I	STAGE II	STAGE III	STAGE IV
ALL	454	103	190	104
8P GAIN MUTATED	18	19	19	12
8P GAIN WILD-TYPE	436	84	171	92

Figure S62. Get High-res Image Gene #15: '8p gain' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

'8p gain' versus 'PATHOLOGY_T_STAGE'

P value = 2e-05 (Fisher's exact test), Q value = 2e-04

Table S63. Gene #15: '8p gain' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

nPatients	T1	T2	T3	T4
ALL	480	127	258	15
8P GAIN MUTATED	18	20	30	1
8P GAIN WILD-TYPE	462	107	228	14

Figure S63. Get High-res Image Gene #15: '8p gain' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

'8p gain' versus 'PATHOLOGY_N_STAGE'

P value = 0.0545 (Fisher's exact test), Q value = 0.17

Table S64. Gene #15: '8p gain' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

nPatients	N0	N1	N2
ALL	323	44	6
8P GAIN MUTATED	30	7	2
8P GAIN WILD-TYPE	293	37	4

Figure S64. Get High-res Image Gene #15: '8p gain' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

'8p gain' versus 'HISTOLOGICAL_TYPE'

P value = 7e-05 (Fisher's exact test), Q value = 0.00061

Table S65. 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	288
8P GAIN MUTATED	16	33	20
8P GAIN WILD-TYPE	50	495	268

Figure S65. Get High-res Image Gene #15: '8p gain' versus Clinical Feature #10: 'HISTOLOGICAL_TYPE'

'8q gain' versus 'Time to Death'

P value = 0.00853 (logrank test), Q value = 0.039

Table S66. Gene #16: '8q gain' versus Clinical Feature #1: 'Time to Death'

	nPatients	nDeath	Duration Range (Median), Month
ALL	876	228	0.1 - 194.8 (35.9)
8Q GAIN MUTATED	102	35	0.2 - 153.7 (27.6)
8Q GAIN WILD-TYPE	774	193	0.1 - 194.8 (36.7)

Figure S66. 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 = 0.00012

Table S67. Gene #16: '8q gain' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

nPatients	STAGE I	STAGE II	STAGE III	STAGE IV
ALL	454	103	190	104
8Q GAIN MUTATED	27	23	29	22
8Q GAIN WILD-TYPE	427	80	161	82

Figure S67. 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 = 0.00012

Table S68. Gene #16: '8q gain' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

nPatients	T1	T2	T3	T4
ALL	480	127	258	15
8Q GAIN MUTATED	28	24	48	3
8Q GAIN WILD-TYPE	452	103	210	12

Figure S68. Get High-res Image Gene #16: '8q gain' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

'8q gain' versus 'PATHOLOGY_N_STAGE'

P value = 0.00393 (Fisher's exact test), Q value = 0.021

Table S69. Gene #16: '8q gain' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

nPatients	N0	N1	N2
ALL	323	44	6
8Q GAIN MUTATED	42	12	3
8Q GAIN WILD-TYPE	281	32	3

Figure S69. Get High-res Image Gene #16: '8q gain' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

'8q gain' versus 'PATHOLOGY_M_STAGE'

P value = 0.0124 (Fisher's exact test), Q value = 0.052

Table S70. Gene #16: '8q gain' versus Clinical Feature #6: 'PATHOLOGY_M_STAGE'

nPatients	0	1
ALL	546	89
8Q GAIN MUTATED	57	18
8Q GAIN WILD-TYPE	489	71

Figure S70. Get High-res Image Gene #16: '8q gain' versus Clinical Feature #6: 'PATHOLOGY_M_STAGE'

'8q gain' versus 'HISTOLOGICAL_TYPE'

P value = 0.00133 (Fisher's exact test), Q value = 0.0083

Table S71. 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	288
8Q GAIN MUTATED	17	61	25
8Q GAIN WILD-TYPE	49	467	263

Figure S71. Get High-res Image Gene #16: '8q gain' versus Clinical Feature #10: 'HISTOLOGICAL_TYPE'

'9p gain' versus 'PATHOLOGIC_STAGE'

P value = 0.00315 (Fisher's exact test), Q value = 0.017

Table S72. Gene #17: '9p gain' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

nPatients	STAGE I	STAGE II	STAGE III	STAGE IV
ALL	454	103	190	104
9P GAIN MUTATED	7	9	7	3
9P GAIN WILD-TYPE	447	94	183	101

Figure S72. Get High-res Image Gene #17: '9p gain' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

'9p gain' versus 'PATHOLOGY_T_STAGE'

P value = 0.00163 (Fisher's exact test), Q value = 0.0097

Table S73. Gene #17: '9p gain' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

nPatients	T1	T2	T3	T4
ALL	480	127	258	15
9P GAIN MUTATED	7	9	8	2
9P GAIN WILD-TYPE	473	118	250	13

Figure S73. Get High-res Image Gene #17: '9p gain' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

'9p gain' versus 'PATHOLOGY_M_STAGE'

P value = 0.0581 (Fisher's exact test), Q value = 0.18

Table S74. Gene #17: '9p gain' versus Clinical Feature #6: 'PATHOLOGY_M_STAGE'

nPatients	0	1
ALL	546	89
9P GAIN MUTATED	22	0
9P GAIN WILD-TYPE	524	89

Figure S74. Get High-res Image Gene #17: '9p gain' versus Clinical Feature #6: 'PATHOLOGY_M_STAGE'

'9p gain' versus 'GENDER'

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

Table S75. Gene #17: '9p gain' versus Clinical Feature #7: 'GENDER'

nPatients	FEMALE	MALE
ALL	292	590
9P GAIN MUTATED	15	11
9P GAIN WILD-TYPE	277	579

Figure S75. Get High-res Image Gene #17: '9p gain' versus Clinical Feature #7: 'GENDER'

'9p gain' versus 'HISTOLOGICAL_TYPE'

P value = 2e-05 (Fisher's exact test), Q value = 2e-04

Table S76. 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	288
9P GAIN MUTATED	9	14	3
9P GAIN WILD-TYPE	57	514	285

Figure S76. Get High-res Image Gene #17: '9p gain' versus Clinical Feature #10: 'HISTOLOGICAL_TYPE'

'9q gain' versus 'PATHOLOGIC_STAGE'

P value = 0.00113 (Fisher's exact test), Q value = 0.0072

Table S77. Gene #18: '9q gain' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

nPatients	STAGE I	STAGE II	STAGE III	STAGE IV
ALL	454	103	190	104
9Q GAIN MUTATED	5	8	6	5
9Q GAIN WILD-TYPE	449	95	184	99

Figure S77. Get High-res Image Gene #18: '9q gain' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

'9q gain' versus 'PATHOLOGY_T_STAGE'

P value = 0.00012 (Fisher's exact test), Q value = 0.001

Table S78. Gene #18: '9q gain' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

nPatients	T1	T2	T3	T4
ALL	480	127	258	15
9Q GAIN MUTATED	5	8	8	3
9Q GAIN WILD-TYPE	475	119	250	12

Figure S78. Get High-res Image Gene #18: '9q gain' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

'9q gain' versus 'GENDER'

P value = 0.0449 (Fisher's exact test), Q value = 0.15

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

nPatients	FEMALE	MALE
ALL	292	590
9Q GAIN MUTATED	13	11
9Q GAIN WILD-TYPE	279	579

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

'9q gain' versus 'HISTOLOGICAL_TYPE'

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

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	288
9Q GAIN MUTATED	9	13	2
9Q GAIN WILD-TYPE	57	515	286

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

'10p gain' versus 'PATHOLOGY_T_STAGE'

P value = 0.00739 (Fisher's exact test), Q value = 0.035

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

nPatients	T1	T2	T3	T4
ALL	480	127	258	15
10P GAIN MUTATED	12	7	6	3
10P GAIN WILD-TYPE	468	120	252	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 = 0.0141 (Fisher's exact test), Q value = 0.057

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

nPatients	N0	N1	N2
ALL	323	44	6
10P GAIN MUTATED	7	4	1
10P GAIN WILD-TYPE	316	40	5

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 = 0.0465 (Fisher's exact test), Q value = 0.15

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

nPatients	T1	T2	T3	T4
ALL	480	127	258	15
10Q GAIN MUTATED	11	5	4	2
10Q GAIN WILD-TYPE	469	122	254	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 = 0.0238 (Fisher's exact test), Q value = 0.09

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

nPatients	N0	N1	N2
ALL	323	44	6
10Q GAIN MUTATED	6	3	1
10Q GAIN WILD-TYPE	317	41	5

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

'11p gain' versus 'PATHOLOGIC_STAGE'

P value = 0.00425 (Fisher's exact test), Q value = 0.022

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

nPatients	STAGE I	STAGE II	STAGE III	STAGE IV
ALL	454	103	190	104
11P GAIN MUTATED	18	9	18	12
11P GAIN WILD-TYPE	436	94	172	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 = 0.00131 (Fisher's exact test), Q value = 0.0082

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

nPatients	T1	T2	T3	T4
ALL	480	127	258	15
11P GAIN MUTATED	18	11	28	1
11P GAIN WILD-TYPE	462	116	230	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 = 0.0371 (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	546	89
11P GAIN MUTATED	32	11
11P GAIN WILD-TYPE	514	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 = 2e-05 (Fisher's exact test), Q value = 2e-04

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	288
11P GAIN MUTATED	15	31	12
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 = 0.0422 (Wilcoxon-test), Q value = 0.14

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	8	17.0 (15.3)
11P GAIN WILD-TYPE	98	31.9 (25.2)

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 = 0.0524 (Wilcoxon-test), Q value = 0.17

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

	nPatients	Mean (Std.Dev)
ALL	876	60.1 (12.5)
11Q GAIN MUTATED	55	57.0 (12.8)
11Q GAIN WILD-TYPE	821	60.4 (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 = 0.0346 (Fisher's exact test), Q value = 0.12

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

nPatients	STAGE I	STAGE II	STAGE III	STAGE IV
ALL	454	103	190	104
11Q GAIN MUTATED	19	9	16	10
11Q GAIN WILD-TYPE	435	94	174	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 = 0.00897 (Fisher's exact test), Q value = 0.04

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

nPatients	T1	T2	T3	T4
ALL	480	127	258	15
11Q GAIN MUTATED	19	11	25	0
11Q GAIN WILD-TYPE	461	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 = 0.00012

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	288
11Q GAIN MUTATED	16	29	10
11Q GAIN WILD-TYPE	50	499	278

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 = 0.0583 (Fisher's exact test), Q value = 0.18

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

nPatients	STAGE I	STAGE II	STAGE III	STAGE IV
ALL	454	103	190	104
12P GAIN MUTATED	118	27	54	41
12P GAIN WILD-TYPE	336	76	136	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 = 0.00852 (Fisher's exact test), Q value = 0.039

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

nPatients	N0	N1	N2
ALL	323	44	6
12P GAIN MUTATED	87	21	3
12P GAIN WILD-TYPE	236	23	3

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 = 0.00873 (Fisher's exact test), Q value = 0.039

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

nPatients	0	1
ALL	546	89
12P GAIN MUTATED	129	33
12P GAIN WILD-TYPE	417	56

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

'12p gain' versus 'GENDER'

P value = 0.00562 (Fisher's exact test), Q value = 0.028

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

nPatients	FEMALE	MALE
ALL	292	590
12P GAIN MUTATED	66	186
12P GAIN WILD-TYPE	226	404

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

'12p gain' versus 'KARNOFSKY_PERFORMANCE_SCORE'

P value = 0.0571 (Wilcoxon-test), Q value = 0.18

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

	nPatients	Mean (Std.Dev)
ALL	143	87.7 (22.8)
12P GAIN MUTATED	50	84.2 (26.4)
12P GAIN WILD-TYPE	93	89.6 (20.4)

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 = 2e-04

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	288
12P GAIN MUTATED	19	121	112
12P GAIN WILD-TYPE	47	407	176

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

'12p gain' versus 'ETHNICITY'

P value = 0.0792 (Fisher's exact test), Q value = 0.22

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

nPatients	HISPANIC OR LATINO	NOT HISPANIC OR LATINO
ALL	42	622
12P GAIN MUTATED	7	190
12P GAIN WILD-TYPE	35	432

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

'12q gain' versus 'Time to Death'

P value = 0.0708 (logrank test), Q value = 0.21

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

	nPatients	nDeath	Duration Range (Median), Month
ALL	876	228	0.1 - 194.8 (35.9)
12Q GAIN MUTATED	252	71	0.1 - 194.8 (28.9)
12Q GAIN WILD-TYPE	624	157	0.1 - 149.2 (37.5)

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

'12q gain' versus 'PATHOLOGIC_STAGE'

P value = 0.0337 (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	454	103	190	104
12Q GAIN MUTATED	118	27	57	42
12Q GAIN WILD-TYPE	336	76	133	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 = 0.0669 (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	480	127	258	15
12Q GAIN MUTATED	126	34	87	7
12Q GAIN WILD-TYPE	354	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 = 0.00279 (Fisher's exact test), Q value = 0.015

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

nPatients	N0	N1	N2
ALL	323	44	6
12Q GAIN MUTATED	88	21	4
12Q GAIN WILD-TYPE	235	23	2

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 = 0.013 (Fisher's exact test), Q value = 0.054

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

nPatients	0	1
ALL	546	89
12Q GAIN MUTATED	132	33
12Q GAIN WILD-TYPE	414	56

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

'12q gain' versus 'GENDER'

P value = 0.00574 (Fisher's exact test), Q value = 0.028

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

nPatients	FEMALE	MALE
ALL	292	590
12Q GAIN MUTATED	67	189
12Q GAIN WILD-TYPE	225	401

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

'12q gain' versus 'KARNOFSKY_PERFORMANCE_SCORE'

P value = 0.0571 (Wilcoxon-test), Q value = 0.18

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

	nPatients	Mean (Std.Dev)
ALL	143	87.7 (22.8)
12Q GAIN MUTATED	50	84.2 (26.4)
12Q GAIN WILD-TYPE	93	89.6 (20.4)

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

'12q gain' versus 'HISTOLOGICAL_TYPE'

P value = 1e-05 (Fisher's exact test), Q value = 0.00012

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	288
12Q GAIN MUTATED	21	123	112
12Q GAIN WILD-TYPE	45	405	176

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

'12q gain' versus 'ETHNICITY'

P value = 0.0557 (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	622
12Q GAIN MUTATED	7	193
12Q GAIN WILD-TYPE	35	429

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

'13q gain' versus 'Time to Death'

P value = 0.0909 (logrank test), Q value = 0.25

Table S112. Gene #25: '13q gain' versus Clinical Feature #1: 'Time to Death'

	nPatients	nDeath	Duration Range (Median), Month
ALL	876	228	0.1 - 194.8 (35.9)
13Q GAIN MUTATED	52	8	0.4 - 133.7 (39.8)
13Q GAIN WILD-TYPE	824	220	0.1 - 194.8 (35.5)

Figure S112. Get High-res Image Gene #25: '13q gain' versus Clinical Feature #1: 'Time to Death'

'13q gain' versus 'RADIATION_THERAPY'

P value = 0.0148 (Fisher's exact test), Q value = 0.06

Table S113. Gene #25: '13q gain' versus Clinical Feature #8: 'RADIATION_THERAPY'

nPatients	NO	YES
ALL	408	3
13Q GAIN MUTATED	28	2
13Q GAIN WILD-TYPE	380	1

Figure S113. Get High-res Image Gene #25: '13q gain' versus Clinical Feature #8: 'RADIATION_THERAPY'

'13q gain' versus 'HISTOLOGICAL_TYPE'

P value = 0.00483 (Fisher's exact test), Q value = 0.024

Table S114. 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	288
13Q GAIN MUTATED	2	22	28
13Q GAIN WILD-TYPE	64	506	260

Figure S114. Get High-res Image Gene #25: '13q gain' versus Clinical Feature #10: 'HISTOLOGICAL_TYPE'

'14q gain' versus 'YEARS_TO_BIRTH'

P value = 0.0426 (Wilcoxon-test), Q value = 0.14

Table S115. Gene #26: '14q gain' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

	nPatients	Mean (Std.Dev)
ALL	876	60.1 (12.5)
14Q GAIN MUTATED	38	56.4 (12.4)
14Q GAIN WILD-TYPE	838	60.3 (12.5)

Figure S115. Get High-res Image Gene #26: '14q gain' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'14q gain' versus 'PATHOLOGIC_STAGE'

P value = 0.00141 (Fisher's exact test), Q value = 0.0087

Table S116. Gene #26: '14q gain' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

nPatients	STAGE I	STAGE II	STAGE III	STAGE IV
ALL	454	103	190	104
14Q GAIN MUTATED	12	12	8	7
14Q GAIN WILD-TYPE	442	91	182	97

Figure S116. Get High-res Image Gene #26: '14q gain' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

'14q gain' versus 'PATHOLOGY_T_STAGE'

P value = 4e-04 (Fisher's exact test), Q value = 0.0029

Table S117. Gene #26: '14q gain' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

nPatients	T1	T2	T3	T4
ALL	480	127	258	15
14Q GAIN MUTATED	12	12	12	3
14Q GAIN WILD-TYPE	468	115	246	12

Figure S117. 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 = 0.00012

Table S118. 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	288
14Q GAIN MUTATED	20	16	3
14Q GAIN WILD-TYPE	46	512	285

Figure S118. 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 = 0.23

Table S119. 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 S119. Get High-res Image Gene #26: '14q gain' versus Clinical Feature #12: 'YEAR_OF_TOBACCO_SMOKING_ONSET'

'15q gain' versus 'PATHOLOGIC_STAGE'

P value = 0.00095 (Fisher's exact test), Q value = 0.0063

Table S120. Gene #27: '15q gain' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

nPatients	STAGE I	STAGE II	STAGE III	STAGE IV
ALL	454	103	190	104
15Q GAIN MUTATED	17	15	11	9
15Q GAIN WILD-TYPE	437	88	179	95

Figure S120. Get High-res Image Gene #27: '15q gain' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

'15q gain' versus 'PATHOLOGY_T_STAGE'

P value = 0.00311 (Fisher's exact test), Q value = 0.017

Table S121. Gene #27: '15q gain' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

nPatients	T1	T2	T3	T4
ALL	480	127	258	15
15Q GAIN MUTATED	17	15	19	1
15Q GAIN WILD-TYPE	463	112	239	14

Figure S121. 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 = 0.00012

Table S122. 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	288
15Q GAIN MUTATED	21	26	5
15Q GAIN WILD-TYPE	45	502	283

Figure S122. 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 S123. 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 S123. 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 = 0.0201 (logrank test), Q value = 0.078

Table S124. Gene #28: '16p gain' versus Clinical Feature #1: 'Time to Death'

	nPatients	nDeath	Duration Range (Median), Month
ALL	876	228	0.1 - 194.8 (35.9)
16P GAIN MUTATED	277	56	0.1 - 194.8 (30.7)
16P GAIN WILD-TYPE	599	172	0.1 - 149.2 (36.9)

Figure S124. Get High-res Image Gene #28: '16p gain' versus Clinical Feature #1: 'Time to Death'

'16p gain' versus 'YEARS_TO_BIRTH'

P value = 0.0129 (Wilcoxon-test), Q value = 0.053

Table S125. Gene #28: '16p gain' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

	nPatients	Mean (Std.Dev)
ALL	876	60.1 (12.5)
16P GAIN MUTATED	279	61.6 (12.2)
16P GAIN WILD-TYPE	597	59.5 (12.6)

Figure S125. Get High-res Image Gene #28: '16p gain' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'16p gain' versus 'GENDER'

P value = 0.00212 (Fisher's exact test), Q value = 0.012

Table S126. Gene #28: '16p gain' versus Clinical Feature #7: 'GENDER'

nPatients	FEMALE	MALE
ALL	292	590
16P GAIN MUTATED	73	208
16P GAIN WILD-TYPE	219	382

Figure S126. 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 = 0.00012

Table S127. 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	288
16P GAIN MUTATED	21	107	153
16P GAIN WILD-TYPE	45	421	135

Figure S127. Get High-res Image Gene #28: '16p gain' versus Clinical Feature #10: 'HISTOLOGICAL_TYPE'

'16p gain' versus 'RACE'

P value = 0.0379 (Fisher's exact test), Q value = 0.13

Table S128. Gene #28: '16p gain' versus Clinical Feature #13: 'RACE'

nPatients	AMERICAN INDIAN OR ALASKA NATIVE	ASIAN	BLACK OR AFRICAN AMERICAN	WHITE
ALL	2	16	121	719
16P GAIN MUTATED	2	5	29	238
16P GAIN WILD-TYPE	0	11	92	481

Figure S128. Get High-res Image Gene #28: '16p gain' versus Clinical Feature #13: 'RACE'

'16q gain' versus 'Time to Death'

P value = 0.00215 (logrank test), Q value = 0.012

Table S129. Gene #29: '16q gain' versus Clinical Feature #1: 'Time to Death'

	nPatients	nDeath	Duration Range (Median), Month
ALL	876	228	0.1 - 194.8 (35.9)
16Q GAIN MUTATED	264	49	0.1 - 194.8 (31.4)
16Q GAIN WILD-TYPE	612	179	0.1 - 149.2 (36.5)

Figure S129. Get High-res Image Gene #29: '16q gain' versus Clinical Feature #1: 'Time to Death'

'16q gain' versus 'YEARS_TO_BIRTH'

P value = 0.0317 (Wilcoxon-test), Q value = 0.11

Table S130. Gene #29: '16q gain' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

	nPatients	Mean (Std.Dev)
ALL	876	60.1 (12.5)
16Q GAIN MUTATED	266	61.5 (12.3)
16Q GAIN WILD-TYPE	610	59.6 (12.6)

Figure S130. 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 = 0.044

Table S131. Gene #29: '16q gain' versus Clinical Feature #7: 'GENDER'

nPatients	FEMALE	MALE
ALL	292	590
16Q GAIN MUTATED	72	196
16Q GAIN WILD-TYPE	220	394

Figure S131. 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 = 0.00012

Table S132. 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	288
16Q GAIN MUTATED	21	99	148
16Q GAIN WILD-TYPE	45	429	140

Figure S132. Get High-res Image Gene #29: '16q gain' versus Clinical Feature #10: 'HISTOLOGICAL_TYPE'

'17p gain' versus 'Time to Death'

P value = 0.0122 (logrank test), Q value = 0.051

Table S133. Gene #30: '17p gain' versus Clinical Feature #1: 'Time to Death'

	nPatients	nDeath	Duration Range (Median), Month
ALL	876	228	0.1 - 194.8 (35.9)
17P GAIN MUTATED	193	27	0.1 - 194.8 (25.6)
17P GAIN WILD-TYPE	683	201	0.1 - 153.7 (38.7)

Figure S133. 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 = 0.00012

Table S134. Gene #30: '17p gain' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

nPatients	STAGE I	STAGE II	STAGE III	STAGE IV
ALL	454	103	190	104
17P GAIN MUTATED	131	19	23	6
17P GAIN WILD-TYPE	323	84	167	98

Figure S134. 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 = 0.00012

Table S135. Gene #30: '17p gain' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

nPatients	T1	T2	T3	T4
ALL	480	127	258	15
17P GAIN MUTATED	141	26	26	2
17P GAIN WILD-TYPE	339	101	232	13

Figure S135. Get High-res Image Gene #30: '17p gain' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

'17p gain' versus 'PATHOLOGY_N_STAGE'

P value = 0.0184 (Fisher's exact test), Q value = 0.072

Table S136. Gene #30: '17p gain' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

nPatients	N0	N1	N2
ALL	323	44	6
17P GAIN MUTATED	32	11	0
17P GAIN WILD-TYPE	291	33	6

Figure S136. Get High-res Image Gene #30: '17p gain' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

'17p gain' versus 'PATHOLOGY_M_STAGE'

P value = 0.01 (Fisher's exact test), Q value = 0.044

Table S137. Gene #30: '17p gain' versus Clinical Feature #6: 'PATHOLOGY_M_STAGE'

nPatients	0	1
ALL	546	89
17P GAIN MUTATED	68	3
17P GAIN WILD-TYPE	478	86

Figure S137. Get High-res Image Gene #30: '17p gain' versus Clinical Feature #6: 'PATHOLOGY_M_STAGE'

'17p gain' versus 'GENDER'

P value = 0.000289 (Fisher's exact test), Q value = 0.0022

Table S138. Gene #30: '17p gain' versus Clinical Feature #7: 'GENDER'

nPatients	FEMALE	MALE
ALL	292	590
17P GAIN MUTATED	44	152
17P GAIN WILD-TYPE	248	438

Figure S138. 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 = 0.00012

Table S139. 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	288
17P GAIN MUTATED	0	25	171
17P GAIN WILD-TYPE	66	503	117

Figure S139. Get High-res Image Gene #30: '17p gain' versus Clinical Feature #10: 'HISTOLOGICAL_TYPE'

'17p gain' versus 'RACE'

P value = 0.00884 (Fisher's exact test), Q value = 0.039

Table S140. Gene #30: '17p gain' versus Clinical Feature #13: 'RACE'

nPatients	AMERICAN INDIAN OR ALASKA NATIVE	ASIAN	BLACK OR AFRICAN AMERICAN	WHITE
ALL	2	16	121	719
17P GAIN MUTATED	2	6	33	147
17P GAIN WILD-TYPE	0	10	88	572

Figure S140. Get High-res Image Gene #30: '17p gain' versus Clinical Feature #13: 'RACE'

'17p gain' versus 'ETHNICITY'

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

Table S141. Gene #30: '17p gain' versus Clinical Feature #14: 'ETHNICITY'

nPatients	HISPANIC OR LATINO	NOT HISPANIC OR LATINO
ALL	42	622
17P GAIN MUTATED	4	168
17P GAIN WILD-TYPE	38	454

Figure S141. 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 = 2e-04

Table S142. Gene #31: '17q gain' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

nPatients	STAGE I	STAGE II	STAGE III	STAGE IV
ALL	454	103	190	104
17Q GAIN MUTATED	139	20	33	11
17Q GAIN WILD-TYPE	315	83	157	93

Figure S142. Get High-res Image Gene #31: '17q gain' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

'17q gain' versus 'PATHOLOGY_T_STAGE'

P value = 7e-05 (Fisher's exact test), Q value = 0.00061

Table S143. Gene #31: '17q gain' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

nPatients	T1	T2	T3	T4
ALL	480	127	258	15
17Q GAIN MUTATED	149	28	41	3
17Q GAIN WILD-TYPE	331	99	217	12

Figure S143. Get High-res Image Gene #31: '17q gain' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

'17q gain' versus 'PATHOLOGY_N_STAGE'

P value = 0.00356 (Fisher's exact test), Q value = 0.019

Table S144. Gene #31: '17q gain' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

nPatients	N0	N1	N2
ALL	323	44	6
17Q GAIN MUTATED	42	12	3
17Q GAIN WILD-TYPE	281	32	3

Figure S144. Get High-res Image Gene #31: '17q gain' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

'17q gain' versus 'PATHOLOGY_M_STAGE'

P value = 0.0451 (Fisher's exact test), Q value = 0.15

Table S145. Gene #31: '17q gain' versus Clinical Feature #6: 'PATHOLOGY_M_STAGE'

nPatients	0	1
ALL	546	89
17Q GAIN MUTATED	79	6
17Q GAIN WILD-TYPE	467	83

Figure S145. Get High-res Image Gene #31: '17q gain' versus Clinical Feature #6: 'PATHOLOGY_M_STAGE'

'17q gain' versus 'GENDER'

P value = 0.0107 (Fisher's exact test), Q value = 0.046

Table S146. Gene #31: '17q gain' versus Clinical Feature #7: 'GENDER'

nPatients	FEMALE	MALE
ALL	292	590
17Q GAIN MUTATED	58	164
17Q GAIN WILD-TYPE	234	426

Figure S146. 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 = 0.00012

Table S147. 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	288
17Q GAIN MUTATED	0	32	190
17Q GAIN WILD-TYPE	66	496	98

Figure S147. Get High-res Image Gene #31: '17q gain' versus Clinical Feature #10: 'HISTOLOGICAL_TYPE'

'17q gain' versus 'RACE'

P value = 0.0118 (Fisher's exact test), Q value = 0.05

Table S148. Gene #31: '17q gain' versus Clinical Feature #13: 'RACE'

nPatients	AMERICAN INDIAN OR ALASKA NATIVE	ASIAN	BLACK OR AFRICAN AMERICAN	WHITE
ALL	2	16	121	719
17Q GAIN MUTATED	2	6	38	167
17Q GAIN WILD-TYPE	0	10	83	552

Figure S148. Get High-res Image Gene #31: '17q gain' versus Clinical Feature #13: 'RACE'

'17q gain' versus 'ETHNICITY'

P value = 0.0341 (Fisher's exact test), Q value = 0.12

Table S149. Gene #31: '17q gain' versus Clinical Feature #14: 'ETHNICITY'

nPatients	HISPANIC OR LATINO	NOT HISPANIC OR LATINO
ALL	42	622
17Q GAIN MUTATED	6	185
17Q GAIN WILD-TYPE	36	437

Figure S149. Get High-res Image Gene #31: '17q gain' versus Clinical Feature #14: 'ETHNICITY'

'18p gain' versus 'Time to Death'

P value = 0.00923 (logrank test), Q value = 0.04

Table S150. Gene #32: '18p gain' versus Clinical Feature #1: 'Time to Death'

	nPatients	nDeath	Duration Range (Median), Month
ALL	876	228	0.1 - 194.8 (35.9)
18P GAIN MUTATED	54	7	0.5 - 153.7 (48.9)
18P GAIN WILD-TYPE	822	221	0.1 - 194.8 (34.3)

Figure S150. 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 = 0.00012

Table S151. 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	288
18P GAIN MUTATED	16	25	13
18P GAIN WILD-TYPE	50	503	275

Figure S151. Get High-res Image Gene #32: '18p gain' versus Clinical Feature #10: 'HISTOLOGICAL_TYPE'

'18p gain' versus 'RACE'

P value = 0.0758 (Fisher's exact test), Q value = 0.22

Table S152. Gene #32: '18p gain' versus Clinical Feature #13: 'RACE'

nPatients	AMERICAN INDIAN OR ALASKA NATIVE	ASIAN	BLACK OR AFRICAN AMERICAN	WHITE
ALL	2	16	121	719
18P GAIN MUTATED	0	0	2	50
18P GAIN WILD-TYPE	2	16	119	669

Figure S152. Get High-res Image Gene #32: '18p gain' versus Clinical Feature #13: 'RACE'

'18q gain' versus 'Time to Death'

P value = 0.00765 (logrank test), Q value = 0.035

Table S153. Gene #33: '18q gain' versus Clinical Feature #1: 'Time to Death'

	nPatients	nDeath	Duration Range (Median), Month
ALL	876	228	0.1 - 194.8 (35.9)
18Q GAIN MUTATED	50	6	0.5 - 153.7 (48.9)
18Q GAIN WILD-TYPE	826	222	0.1 - 194.8 (34.6)

Figure S153. Get High-res Image Gene #33: '18q gain' versus Clinical Feature #1: 'Time to Death'

'18q gain' versus 'KARNOFSKY_PERFORMANCE_SCORE'

P value = 0.0275 (Wilcoxon-test), Q value = 0.1

Table S154. Gene #33: '18q gain' versus Clinical Feature #9: 'KARNOFSKY_PERFORMANCE_SCORE'

	nPatients	Mean (Std.Dev)
ALL	143	87.7 (22.8)
18Q GAIN MUTATED	9	97.8 (6.7)
18Q GAIN WILD-TYPE	134	87.0 (23.3)

Figure S154. 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 = 0.00012

Table S155. 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	288
18Q GAIN MUTATED	16	25	9
18Q GAIN WILD-TYPE	50	503	279

Figure S155. Get High-res Image Gene #33: '18q gain' versus Clinical Feature #10: 'HISTOLOGICAL_TYPE'

'19p gain' versus 'PATHOLOGIC_STAGE'

P value = 2e-05 (Fisher's exact test), Q value = 2e-04

Table S156. Gene #34: '19p gain' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

nPatients	STAGE I	STAGE II	STAGE III	STAGE IV
ALL	454	103	190	104
19P GAIN MUTATED	21	16	17	20
19P GAIN WILD-TYPE	433	87	173	84

Figure S156. Get High-res Image Gene #34: '19p gain' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

'19p gain' versus 'PATHOLOGY_T_STAGE'

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

Table S157. Gene #34: '19p gain' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

nPatients	T1	T2	T3	T4
ALL	480	127	258	15
19P GAIN MUTATED	22	16	33	3
19P GAIN WILD-TYPE	458	111	225	12

Figure S157. Get High-res Image Gene #34: '19p gain' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

'19p gain' versus 'PATHOLOGY_M_STAGE'

P value = 0.0107 (Fisher's exact test), Q value = 0.046

Table S158. Gene #34: '19p gain' versus Clinical Feature #6: 'PATHOLOGY_M_STAGE'

nPatients	0	1
ALL	546	89
19P GAIN MUTATED	46	16
19P GAIN WILD-TYPE	500	73

Figure S158. 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 = 0.00012

Table S159. 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	288
19P GAIN MUTATED	20	50	4
19P GAIN WILD-TYPE	46	478	284

Figure S159. Get High-res Image Gene #34: '19p gain' versus Clinical Feature #10: 'HISTOLOGICAL_TYPE'

'19p gain' versus 'RACE'

P value = 0.00161 (Fisher's exact test), Q value = 0.0096

Table S160. Gene #34: '19p gain' versus Clinical Feature #13: 'RACE'

nPatients	AMERICAN INDIAN OR ALASKA NATIVE	ASIAN	BLACK OR AFRICAN AMERICAN	WHITE
ALL	2	16	121	719
19P GAIN MUTATED	0	1	1	72
19P GAIN WILD-TYPE	2	15	120	647

Figure S160. Get High-res Image Gene #34: '19p gain' versus Clinical Feature #13: 'RACE'

'19q gain' versus 'PATHOLOGIC_STAGE'

P value = 2e-05 (Fisher's exact test), Q value = 2e-04

Table S161. Gene #35: '19q gain' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

nPatients	STAGE I	STAGE II	STAGE III	STAGE IV
ALL	454	103	190	104
19Q GAIN MUTATED	22	16	20	20
19Q GAIN WILD-TYPE	432	87	170	84

Figure S161. Get High-res Image Gene #35: '19q gain' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

'19q gain' versus 'PATHOLOGY_T_STAGE'

P value = 4e-05 (Fisher's exact test), Q value = 0.00037

Table S162. Gene #35: '19q gain' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

nPatients	T1	T2	T3	T4
ALL	480	127	258	15
19Q GAIN MUTATED	23	18	35	2
19Q GAIN WILD-TYPE	457	109	223	13

Figure S162. Get High-res Image Gene #35: '19q gain' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

'19q gain' versus 'PATHOLOGY_M_STAGE'

P value = 0.00274 (Fisher's exact test), Q value = 0.015

Table S163. Gene #35: '19q gain' versus Clinical Feature #6: 'PATHOLOGY_M_STAGE'

nPatients	0	1
ALL	546	89
19Q GAIN MUTATED	49	18
19Q GAIN WILD-TYPE	497	71

Figure S163. 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 = 0.00012

Table S164. 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	288
19Q GAIN MUTATED	18	56	4
19Q GAIN WILD-TYPE	48	472	284

Figure S164. Get High-res Image Gene #35: '19q gain' versus Clinical Feature #10: 'HISTOLOGICAL_TYPE'

'19q gain' versus 'RACE'

P value = 0.00064 (Fisher's exact test), Q value = 0.0044

Table S165. Gene #35: '19q gain' versus Clinical Feature #13: 'RACE'

nPatients	AMERICAN INDIAN OR ALASKA NATIVE	ASIAN	BLACK OR AFRICAN AMERICAN	WHITE
ALL	2	16	121	719
19Q GAIN MUTATED	0	1	1	76
19Q GAIN WILD-TYPE	2	15	120	643

Figure S165. Get High-res Image Gene #35: '19q gain' versus Clinical Feature #13: 'RACE'

'20p gain' versus 'PATHOLOGIC_STAGE'

P value = 0.00872 (Fisher's exact test), Q value = 0.039

Table S166. Gene #36: '20p gain' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

nPatients	STAGE I	STAGE II	STAGE III	STAGE IV
ALL	454	103	190	104
20P GAIN MUTATED	99	31	54	38
20P GAIN WILD-TYPE	355	72	136	66

Figure S166. Get High-res Image Gene #36: '20p gain' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

'20p gain' versus 'PATHOLOGY_T_STAGE'

P value = 0.00374 (Fisher's exact test), Q value = 0.02

Table S167. Gene #36: '20p gain' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

nPatients	T1	T2	T3	T4
ALL	480	127	258	15
20P GAIN MUTATED	107	37	81	8
20P GAIN WILD-TYPE	373	90	177	7

Figure S167. Get High-res Image Gene #36: '20p gain' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

'20p gain' versus 'PATHOLOGY_N_STAGE'

P value = 0.0618 (Fisher's exact test), Q value = 0.18

Table S168. Gene #36: '20p gain' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

nPatients	N0	N1	N2
ALL	323	44	6
20P GAIN MUTATED	76	16	3
20P GAIN WILD-TYPE	247	28	3

Figure S168. Get High-res Image Gene #36: '20p gain' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

'20p gain' versus 'PATHOLOGY_M_STAGE'

P value = 0.0461 (Fisher's exact test), Q value = 0.15

Table S169. Gene #36: '20p gain' versus Clinical Feature #6: 'PATHOLOGY_M_STAGE'

nPatients	0	1
ALL	546	89
20P GAIN MUTATED	127	30
20P GAIN WILD-TYPE	419	59

Figure S169. Get High-res Image Gene #36: '20p gain' versus Clinical Feature #6: 'PATHOLOGY_M_STAGE'

'20p gain' versus 'GENDER'

P value = 0.00114 (Fisher's exact test), Q value = 0.0073

Table S170. Gene #36: '20p gain' versus Clinical Feature #7: 'GENDER'

nPatients	FEMALE	MALE
ALL	292	590
20P GAIN MUTATED	57	176
20P GAIN WILD-TYPE	235	414

Figure S170. Get High-res Image Gene #36: '20p gain' versus Clinical Feature #7: 'GENDER'

'20p gain' versus 'HISTOLOGICAL_TYPE'

P value = 0.00022 (Fisher's exact test), Q value = 0.0018

Table S171. 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	288
20P GAIN MUTATED	21	113	99
20P GAIN WILD-TYPE	45	415	189

Figure S171. Get High-res Image Gene #36: '20p gain' versus Clinical Feature #10: 'HISTOLOGICAL_TYPE'

'20q gain' versus 'PATHOLOGIC_STAGE'

P value = 0.00751 (Fisher's exact test), Q value = 0.035

Table S172. Gene #37: '20q gain' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

nPatients	STAGE I	STAGE II	STAGE III	STAGE IV
ALL	454	103	190	104
20Q GAIN MUTATED	100	31	57	38
20Q GAIN WILD-TYPE	354	72	133	66

Figure S172. Get High-res Image Gene #37: '20q gain' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

'20q gain' versus 'PATHOLOGY_T_STAGE'

P value = 0.00729 (Fisher's exact test), Q value = 0.034

Table S173. Gene #37: '20q gain' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

nPatients	T1	T2	T3	T4
ALL	480	127	258	15
20Q GAIN MUTATED	109	37	84	7
20Q GAIN WILD-TYPE	371	90	174	8

Figure S173. Get High-res Image Gene #37: '20q gain' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

'20q gain' versus 'PATHOLOGY_N_STAGE'

P value = 0.0202 (Fisher's exact test), Q value = 0.078

Table S174. Gene #37: '20q gain' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

nPatients	N0	N1	N2
ALL	323	44	6
20Q GAIN MUTATED	77	18	3
20Q GAIN WILD-TYPE	246	26	3

Figure S174. Get High-res Image Gene #37: '20q gain' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

'20q gain' versus 'PATHOLOGY_M_STAGE'

P value = 0.0651 (Fisher's exact test), Q value = 0.19

Table S175. Gene #37: '20q gain' versus Clinical Feature #6: 'PATHOLOGY_M_STAGE'

nPatients	0	1
ALL	546	89
20Q GAIN MUTATED	131	30
20Q GAIN WILD-TYPE	415	59

Figure S175. Get High-res Image Gene #37: '20q gain' versus Clinical Feature #6: 'PATHOLOGY_M_STAGE'

'20q gain' versus 'GENDER'

P value = 0.00282 (Fisher's exact test), Q value = 0.016

Table S176. Gene #37: '20q gain' versus Clinical Feature #7: 'GENDER'

nPatients	FEMALE	MALE
ALL	292	590
20Q GAIN MUTATED	60	177
20Q GAIN WILD-TYPE	232	413

Figure S176. Get High-res Image Gene #37: '20q gain' versus Clinical Feature #7: 'GENDER'

'20q gain' versus 'HISTOLOGICAL_TYPE'

P value = 0.00014 (Fisher's exact test), Q value = 0.0012

Table S177. 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	288
20Q GAIN MUTATED	21	115	101
20Q GAIN WILD-TYPE	45	413	187

Figure S177. Get High-res Image Gene #37: '20q gain' versus Clinical Feature #10: 'HISTOLOGICAL_TYPE'

'21q gain' versus 'KARNOFSKY_PERFORMANCE_SCORE'

P value = 0.0417 (Wilcoxon-test), Q value = 0.14

Table S178. Gene #38: '21q gain' versus Clinical Feature #9: 'KARNOFSKY_PERFORMANCE_SCORE'

	nPatients	Mean (Std.Dev)
ALL	143	87.7 (22.8)
21Q GAIN MUTATED	14	95.7 (9.4)
21Q GAIN WILD-TYPE	129	86.8 (23.6)

Figure S178. Get High-res Image Gene #38: '21q gain' versus Clinical Feature #9: 'KARNOFSKY_PERFORMANCE_SCORE'

'21q gain' versus 'RACE'

P value = 0.0613 (Fisher's exact test), Q value = 0.18

Table S179. Gene #38: '21q gain' versus Clinical Feature #13: 'RACE'

nPatients	AMERICAN INDIAN OR ALASKA NATIVE	ASIAN	BLACK OR AFRICAN AMERICAN	WHITE
ALL	2	16	121	719
21Q GAIN MUTATED	1	1	5	64
21Q GAIN WILD-TYPE	1	15	116	655

Figure S179. Get High-res Image Gene #38: '21q gain' versus Clinical Feature #13: 'RACE'

'22q gain' versus 'PATHOLOGIC_STAGE'

P value = 0.0138 (Fisher's exact test), Q value = 0.056

Table S180. Gene #39: '22q gain' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

nPatients	STAGE I	STAGE II	STAGE III	STAGE IV
ALL	454	103	190	104
22Q GAIN MUTATED	23	13	15	12
22Q GAIN WILD-TYPE	431	90	175	92

Figure S180. Get High-res Image Gene #39: '22q gain' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

'22q gain' versus 'PATHOLOGY_T_STAGE'

P value = 0.0017 (Fisher's exact test), Q value = 0.01

Table S181. Gene #39: '22q gain' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

nPatients	T1	T2	T3	T4
ALL	480	127	258	15
22Q GAIN MUTATED	23	14	23	4
22Q GAIN WILD-TYPE	457	113	235	11

Figure S181. 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 = 0.00012

Table S182. 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	288
22Q GAIN MUTATED	19	40	5
22Q GAIN WILD-TYPE	47	488	283

Figure S182. Get High-res Image Gene #39: '22q gain' versus Clinical Feature #10: 'HISTOLOGICAL_TYPE'

'xp gain' versus 'PATHOLOGIC_STAGE'

P value = 0.0343 (Fisher's exact test), Q value = 0.12

Table S183. Gene #40: 'xp gain' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

nPatients	STAGE I	STAGE II	STAGE III	STAGE IV
ALL	454	103	190	104
XP GAIN MUTATED	74	14	15	16
XP GAIN WILD-TYPE	380	89	175	88

Figure S183. Get High-res Image Gene #40: 'xp gain' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

'xp gain' versus 'PATHOLOGY_T_STAGE'

P value = 0.0614 (Fisher's exact test), Q value = 0.18

Table S184. Gene #40: 'xp gain' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

nPatients	T1	T2	T3	T4
ALL	480	127	258	15
XP GAIN MUTATED	81	19	26	3
XP GAIN WILD-TYPE	399	108	232	12

Figure S184. Get High-res Image Gene #40: 'xp gain' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

'xp gain' versus 'GENDER'

P value = 0.00608 (Fisher's exact test), Q value = 0.03

Table S185. Gene #40: 'xp gain' versus Clinical Feature #7: 'GENDER'

nPatients	FEMALE	MALE
ALL	292	590
XP GAIN MUTATED	29	100
XP GAIN WILD-TYPE	263	490

Figure S185. 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 = 0.00012

Table S186. 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	288
XP GAIN MUTATED	8	33	88
XP GAIN WILD-TYPE	58	495	200

Figure S186. Get High-res Image Gene #40: 'xp gain' versus Clinical Feature #10: 'HISTOLOGICAL_TYPE'

'xp gain' versus 'YEAR_OF_TOBACCO_SMOKING_ONSET'

P value = 0.057 (Wilcoxon-test), Q value = 0.18

Table S187. 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	17	1967.9 (13.8)
XP GAIN WILD-TYPE	57	1975.5 (16.3)

Figure S187. Get High-res Image Gene #40: 'xp gain' versus Clinical Feature #12: 'YEAR_OF_TOBACCO_SMOKING_ONSET'

'xp gain' versus 'RACE'

P value = 0.033 (Fisher's exact test), Q value = 0.12

Table S188. Gene #40: 'xp gain' versus Clinical Feature #13: 'RACE'

nPatients	AMERICAN INDIAN OR ALASKA NATIVE	ASIAN	BLACK OR AFRICAN AMERICAN	WHITE
ALL	2	16	121	719
XP GAIN MUTATED	2	3	19	99
XP GAIN WILD-TYPE	0	13	102	620

Figure S188. Get High-res Image Gene #40: 'xp gain' versus Clinical Feature #13: 'RACE'

'xq gain' versus 'Time to Death'

P value = 0.0762 (logrank test), Q value = 0.22

Table S189. Gene #41: 'xq gain' versus Clinical Feature #1: 'Time to Death'

	nPatients	nDeath	Duration Range (Median), Month
ALL	876	228	0.1 - 194.8 (35.9)
XQ GAIN MUTATED	128	23	0.1 - 194.8 (29.8)
XQ GAIN WILD-TYPE	748	205	0.1 - 153.7 (36.5)

Figure S189. Get High-res Image Gene #41: 'xq gain' versus Clinical Feature #1: 'Time to Death'

'xq gain' versus 'PATHOLOGIC_STAGE'

P value = 0.0643 (Fisher's exact test), Q value = 0.19

Table S190. Gene #41: 'xq gain' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

nPatients	STAGE I	STAGE II	STAGE III	STAGE IV
ALL	454	103	190	104
XQ GAIN MUTATED	74	14	16	15
XQ GAIN WILD-TYPE	380	89	174	89

Figure S190. Get High-res Image Gene #41: 'xq gain' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

'xq gain' versus 'GENDER'

P value = 0.00859 (Fisher's exact test), Q value = 0.039

Table S191. Gene #41: 'xq gain' versus Clinical Feature #7: 'GENDER'

nPatients	FEMALE	MALE
ALL	292	590
XQ GAIN MUTATED	30	100
XQ GAIN WILD-TYPE	262	490

Figure S191. Get High-res Image Gene #41: 'xq gain' versus Clinical Feature #7: 'GENDER'

'xq gain' versus 'KARNOFSKY_PERFORMANCE_SCORE'

P value = 0.074 (Wilcoxon-test), Q value = 0.21

Table S192. Gene #41: 'xq gain' versus Clinical Feature #9: 'KARNOFSKY_PERFORMANCE_SCORE'

	nPatients	Mean (Std.Dev)
ALL	143	87.7 (22.8)
XQ GAIN MUTATED	30	91.7 (19.3)
XQ GAIN WILD-TYPE	113	86.6 (23.6)

Figure S192. Get High-res Image Gene #41: 'xq gain' versus Clinical Feature #9: 'KARNOFSKY_PERFORMANCE_SCORE'

'xq gain' versus 'HISTOLOGICAL_TYPE'

P value = 1e-05 (Fisher's exact test), Q value = 0.00012

Table S193. 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	288
XQ GAIN MUTATED	8	32	90
XQ GAIN WILD-TYPE	58	496	198

Figure S193. Get High-res Image Gene #41: 'xq gain' versus Clinical Feature #10: 'HISTOLOGICAL_TYPE'

'xq gain' versus 'RACE'

P value = 0.0226 (Fisher's exact test), Q value = 0.086

Table S194. Gene #41: 'xq gain' versus Clinical Feature #13: 'RACE'

nPatients	AMERICAN INDIAN OR ALASKA NATIVE	ASIAN	BLACK OR AFRICAN AMERICAN	WHITE
ALL	2	16	121	719
XQ GAIN MUTATED	2	2	22	98
XQ GAIN WILD-TYPE	0	14	99	621

Figure S194. Get High-res Image Gene #41: 'xq gain' versus Clinical Feature #13: 'RACE'

'1p loss' versus 'YEARS_TO_BIRTH'

P value = 0.0108 (Wilcoxon-test), Q value = 0.046

Table S195. Gene #42: '1p loss' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

	nPatients	Mean (Std.Dev)
ALL	876	60.1 (12.5)
1P LOSS MUTATED	145	57.4 (14.0)
1P LOSS WILD-TYPE	731	60.7 (12.1)

Figure S195. 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 S196. Gene #42: '1p loss' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

nPatients	STAGE I	STAGE II	STAGE III	STAGE IV
ALL	454	103	190	104
1P LOSS MUTATED	56	34	32	17
1P LOSS WILD-TYPE	398	69	158	87

Figure S196. Get High-res Image Gene #42: '1p loss' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

'1p loss' versus 'PATHOLOGY_T_STAGE'

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

Table S197. Gene #42: '1p loss' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

nPatients	T1	T2	T3	T4
ALL	480	127	258	15
1P LOSS MUTATED	60	38	42	5
1P LOSS WILD-TYPE	420	89	216	10

Figure S197. 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 = 0.00012

Table S198. 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	288
1P LOSS MUTATED	53	60	32
1P LOSS WILD-TYPE	13	468	256

Figure S198. Get High-res Image Gene #42: '1p loss' versus Clinical Feature #10: 'HISTOLOGICAL_TYPE'

'1q loss' versus 'Time to Death'

P value = 0.0236 (logrank test), Q value = 0.09

Table S199. Gene #43: '1q loss' versus Clinical Feature #1: 'Time to Death'

	nPatients	nDeath	Duration Range (Median), Month
ALL	876	228	0.1 - 194.8 (35.9)
1Q LOSS MUTATED	109	24	0.1 - 153.7 (49.6)
1Q LOSS WILD-TYPE	767	204	0.1 - 194.8 (33.5)

Figure S199. Get High-res Image Gene #43: '1q loss' versus Clinical Feature #1: 'Time to Death'

'1q loss' versus 'YEARS_TO_BIRTH'

P value = 0.00104 (Wilcoxon-test), Q value = 0.0068

Table S200. Gene #43: '1q loss' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

	nPatients	Mean (Std.Dev)
ALL	876	60.1 (12.5)
1Q LOSS MUTATED	110	56.0 (14.0)
1Q LOSS WILD-TYPE	766	60.7 (12.2)

Figure S200. Get High-res Image Gene #43: '1q loss' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'1q loss' versus 'PATHOLOGIC_STAGE'

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

Table S201. Gene #43: '1q loss' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

nPatients	STAGE I	STAGE II	STAGE III	STAGE IV
ALL	454	103	190	104
1Q LOSS MUTATED	44	30	21	11
1Q LOSS WILD-TYPE	410	73	169	93

Figure S201. Get High-res Image Gene #43: '1q loss' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

'1q loss' versus 'PATHOLOGY_T_STAGE'

P value = 0.00015 (Fisher's exact test), Q value = 0.0012

Table S202. Gene #43: '1q loss' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

nPatients	T1	T2	T3	T4
ALL	480	127	258	15
1Q LOSS MUTATED	47	31	28	4
1Q LOSS WILD-TYPE	433	96	230	11

Figure S202. Get High-res Image Gene #43: '1q loss' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

'1q loss' versus 'PATHOLOGY_M_STAGE'

P value = 0.0522 (Fisher's exact test), Q value = 0.17

Table S203. Gene #43: '1q loss' versus Clinical Feature #6: 'PATHOLOGY_M_STAGE'

nPatients	0	1
ALL	546	89
1Q LOSS MUTATED	72	5
1Q LOSS WILD-TYPE	474	84

Figure S203. Get High-res Image Gene #43: '1q loss' versus Clinical Feature #6: 'PATHOLOGY_M_STAGE'

'1q loss' versus 'HISTOLOGICAL_TYPE'

P value = 1e-05 (Fisher's exact test), Q value = 0.00012

Table S204. 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	288
1Q LOSS MUTATED	52	38	20
1Q LOSS WILD-TYPE	14	490	268

Figure S204. Get High-res Image Gene #43: '1q loss' versus Clinical Feature #10: 'HISTOLOGICAL_TYPE'

'2p loss' versus 'Time to Death'

P value = 0.00429 (logrank test), Q value = 0.022

Table S205. Gene #44: '2p loss' versus Clinical Feature #1: 'Time to Death'

	nPatients	nDeath	Duration Range (Median), Month
ALL	876	228	0.1 - 194.8 (35.9)
2P LOSS MUTATED	64	12	2.5 - 153.7 (65.9)
2P LOSS WILD-TYPE	812	216	0.1 - 194.8 (33.3)

Figure S205. Get High-res Image Gene #44: '2p loss' versus Clinical Feature #1: 'Time to Death'

'2p loss' versus 'YEARS_TO_BIRTH'

P value = 4.4e-05 (Wilcoxon-test), Q value = 4e-04

Table S206. Gene #44: '2p loss' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

	nPatients	Mean (Std.Dev)
ALL	876	60.1 (12.5)
2P LOSS MUTATED	64	53.4 (14.2)
2P LOSS WILD-TYPE	812	60.7 (12.2)

Figure S206. 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 = 0.00012

Table S207. Gene #44: '2p loss' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

nPatients	STAGE I	STAGE II	STAGE III	STAGE IV
ALL	454	103	190	104
2P LOSS MUTATED	20	24	14	5
2P LOSS WILD-TYPE	434	79	176	99

Figure S207. Get High-res Image Gene #44: '2p loss' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

'2p loss' versus 'PATHOLOGY_T_STAGE'

P value = 1e-05 (Fisher's exact test), Q value = 0.00012

Table S208. Gene #44: '2p loss' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

nPatients	T1	T2	T3	T4
ALL	480	127	258	15
2P LOSS MUTATED	21	25	18	1
2P LOSS WILD-TYPE	459	102	240	14

Figure S208. 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 S209. Gene #44: '2p loss' versus Clinical Feature #6: 'PATHOLOGY_M_STAGE'

nPatients	0	1
ALL	546	89
2P LOSS MUTATED	42	2
2P LOSS WILD-TYPE	504	87

Figure S209. Get High-res Image Gene #44: '2p loss' versus Clinical Feature #6: 'PATHOLOGY_M_STAGE'

'2p loss' versus 'KARNOFSKY_PERFORMANCE_SCORE'

P value = 0.0487 (Wilcoxon-test), Q value = 0.16

Table S210. Gene #44: '2p loss' versus Clinical Feature #9: 'KARNOFSKY_PERFORMANCE_SCORE'

	nPatients	Mean (Std.Dev)
ALL	143	87.7 (22.8)
2P LOSS MUTATED	9	97.8 (4.4)
2P LOSS WILD-TYPE	134	87.0 (23.3)

Figure S210. 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 = 0.00012

Table S211. 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	288
2P LOSS MUTATED	46	14	5
2P LOSS WILD-TYPE	20	514	283

Figure S211. Get High-res Image Gene #44: '2p loss' versus Clinical Feature #10: 'HISTOLOGICAL_TYPE'

'2q loss' versus 'Time to Death'

P value = 0.00297 (logrank test), Q value = 0.016

Table S212. Gene #45: '2q loss' versus Clinical Feature #1: 'Time to Death'

	nPatients	nDeath	Duration Range (Median), Month
ALL	876	228	0.1 - 194.8 (35.9)
2Q LOSS MUTATED	62	11	2.5 - 153.7 (65.9)
2Q LOSS WILD-TYPE	814	217	0.1 - 194.8 (33.3)

Figure S212. Get High-res Image Gene #45: '2q loss' versus Clinical Feature #1: 'Time to Death'

'2q loss' versus 'YEARS_TO_BIRTH'

P value = 2.51e-05 (Wilcoxon-test), Q value = 0.00025

Table S213. Gene #45: '2q loss' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

	nPatients	Mean (Std.Dev)
ALL	876	60.1 (12.5)
2Q LOSS MUTATED	62	53.0 (14.3)
2Q LOSS WILD-TYPE	814	60.7 (12.2)

Figure S213. 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 = 0.00012

Table S214. Gene #45: '2q loss' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

nPatients	STAGE I	STAGE II	STAGE III	STAGE IV
ALL	454	103	190	104
2Q LOSS MUTATED	19	24	14	5
2Q LOSS WILD-TYPE	435	79	176	99

Figure S214. 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 = 0.00012

Table S215. Gene #45: '2q loss' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

nPatients	T1	T2	T3	T4
ALL	480	127	258	15
2Q LOSS MUTATED	20	24	18	1
2Q LOSS WILD-TYPE	460	103	240	14

Figure S215. Get High-res Image Gene #45: '2q loss' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

'2q loss' versus 'PATHOLOGY_M_STAGE'

P value = 0.0701 (Fisher's exact test), Q value = 0.2

Table S216. Gene #45: '2q loss' versus Clinical Feature #6: 'PATHOLOGY_M_STAGE'

nPatients	0	1
ALL	546	89
2Q LOSS MUTATED	41	2
2Q LOSS WILD-TYPE	505	87

Figure S216. Get High-res Image Gene #45: '2q loss' versus Clinical Feature #6: 'PATHOLOGY_M_STAGE'

'2q loss' versus 'KARNOFSKY_PERFORMANCE_SCORE'

P value = 0.0487 (Wilcoxon-test), Q value = 0.16

Table S217. Gene #45: '2q loss' versus Clinical Feature #9: 'KARNOFSKY_PERFORMANCE_SCORE'

	nPatients	Mean (Std.Dev)
ALL	143	87.7 (22.8)
2Q LOSS MUTATED	9	97.8 (4.4)
2Q LOSS WILD-TYPE	134	87.0 (23.3)

Figure S217. 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 = 0.00012

Table S218. 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	288
2Q LOSS MUTATED	46	14	3
2Q LOSS WILD-TYPE	20	514	285

Figure S218. Get High-res Image Gene #45: '2q loss' versus Clinical Feature #10: 'HISTOLOGICAL_TYPE'

'3p loss' versus 'Time to Death'

P value = 0.00287 (logrank test), Q value = 0.016

Table S219. Gene #46: '3p loss' versus Clinical Feature #1: 'Time to Death'

	nPatients	nDeath	Duration Range (Median), Month
ALL	876	228	0.1 - 194.8 (35.9)
3P LOSS MUTATED	410	134	0.1 - 153.7 (39.7)
3P LOSS WILD-TYPE	466	94	0.1 - 194.8 (30.3)

Figure S219. Get High-res Image Gene #46: '3p loss' versus Clinical Feature #1: 'Time to Death'

'3p loss' versus 'PATHOLOGIC_STAGE'

P value = 0.00055 (Fisher's exact test), Q value = 0.0038

Table S220. Gene #46: '3p loss' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

nPatients	STAGE I	STAGE II	STAGE III	STAGE IV
ALL	454	103	190	104
3P LOSS MUTATED	190	49	112	57
3P LOSS WILD-TYPE	264	54	78	47

Figure S220. Get High-res Image Gene #46: '3p loss' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

'3p loss' versus 'PATHOLOGY_T_STAGE'

P value = 2e-05 (Fisher's exact test), Q value = 2e-04

Table S221. Gene #46: '3p loss' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

nPatients	T1	T2	T3	T4
ALL	480	127	258	15
3P LOSS MUTATED	195	61	151	4
3P LOSS WILD-TYPE	285	66	107	11

Figure S221. Get High-res Image Gene #46: '3p loss' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

'3p loss' versus 'PATHOLOGY_N_STAGE'

P value = 0.0729 (Fisher's exact test), Q value = 0.21

Table S222. Gene #46: '3p loss' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

nPatients	N0	N1	N2
ALL	323	44	6
3P LOSS MUTATED	179	17	2
3P LOSS WILD-TYPE	144	27	4

Figure S222. 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 = 0.00012

Table S223. 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	288
3P LOSS MUTATED	8	381	22
3P LOSS WILD-TYPE	58	147	266

Figure S223. 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 = 0.097

Table S224. 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 S224. Get High-res Image Gene #46: '3p loss' versus Clinical Feature #12: 'YEAR_OF_TOBACCO_SMOKING_ONSET'

'3p loss' versus 'RACE'

P value = 0.00072 (Fisher's exact test), Q value = 0.0048

Table S225. Gene #46: '3p loss' versus Clinical Feature #13: 'RACE'

nPatients	AMERICAN INDIAN OR ALASKA NATIVE	ASIAN	BLACK OR AFRICAN AMERICAN	WHITE
ALL	2	16	121	719
3P LOSS MUTATED	0	6	39	359
3P LOSS WILD-TYPE	2	10	82	360

Figure S225. Get High-res Image Gene #46: '3p loss' versus Clinical Feature #13: 'RACE'

'3q loss' versus 'YEARS_TO_BIRTH'

P value = 0.0451 (Wilcoxon-test), Q value = 0.15

Table S226. Gene #47: '3q loss' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

	nPatients	Mean (Std.Dev)
ALL	876	60.1 (12.5)
3Q LOSS MUTATED	119	62.5 (13.2)
3Q LOSS WILD-TYPE	757	59.8 (12.4)

Figure S226. Get High-res Image Gene #47: '3q loss' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'3q loss' versus 'GENDER'

P value = 0.0358 (Fisher's exact test), Q value = 0.12

Table S227. Gene #47: '3q loss' versus Clinical Feature #7: 'GENDER'

nPatients	FEMALE	MALE
ALL	292	590
3Q LOSS MUTATED	29	90
3Q LOSS WILD-TYPE	263	500

Figure S227. Get High-res Image Gene #47: '3q loss' versus Clinical Feature #7: 'GENDER'

'3q loss' versus 'RADIATION_THERAPY'

P value = 0.0158 (Fisher's exact test), Q value = 0.062

Table S228. Gene #47: '3q loss' versus Clinical Feature #8: 'RADIATION_THERAPY'

nPatients	NO	YES
ALL	408	3
3Q LOSS MUTATED	29	2
3Q LOSS WILD-TYPE	379	1

Figure S228. 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 = 0.00012

Table S229. 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	288
3Q LOSS MUTATED	7	105	7
3Q LOSS WILD-TYPE	59	423	281

Figure S229. Get High-res Image Gene #47: '3q loss' versus Clinical Feature #10: 'HISTOLOGICAL_TYPE'

'3q loss' versus 'RACE'

P value = 0.06 (Fisher's exact test), Q value = 0.18

Table S230. Gene #47: '3q loss' versus Clinical Feature #13: 'RACE'

nPatients	AMERICAN INDIAN OR ALASKA NATIVE	ASIAN	BLACK OR AFRICAN AMERICAN	WHITE
ALL	2	16	121	719
3Q LOSS MUTATED	0	1	8	107
3Q LOSS WILD-TYPE	2	15	113	612

Figure S230. Get High-res Image Gene #47: '3q loss' versus Clinical Feature #13: 'RACE'

'4p loss' versus 'Time to Death'

P value = 2.36e-11 (logrank test), Q value = 9e-09

Table S231. Gene #48: '4p loss' versus Clinical Feature #1: 'Time to Death'

	nPatients	nDeath	Duration Range (Median), Month
ALL	876	228	0.1 - 194.8 (35.9)
4P LOSS MUTATED	98	51	0.5 - 133.7 (31.5)
4P LOSS WILD-TYPE	778	177	0.1 - 194.8 (36.2)

Figure S231. 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 = 0.00012

Table S232. Gene #48: '4p loss' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

nPatients	STAGE I	STAGE II	STAGE III	STAGE IV
ALL	454	103	190	104
4P LOSS MUTATED	25	7	40	23
4P LOSS WILD-TYPE	429	96	150	81

Figure S232. 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 = 0.00012

Table S233. Gene #48: '4p loss' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

nPatients	T1	T2	T3	T4
ALL	480	127	258	15
4P LOSS MUTATED	27	11	55	5
4P LOSS WILD-TYPE	453	116	203	10

Figure S233. Get High-res Image Gene #48: '4p loss' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

'4p loss' versus 'PATHOLOGY_N_STAGE'

P value = 0.00158 (Fisher's exact test), Q value = 0.0095

Table S234. Gene #48: '4p loss' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

nPatients	N0	N1	N2
ALL	323	44	6
4P LOSS MUTATED	36	14	1
4P LOSS WILD-TYPE	287	30	5

Figure S234. Get High-res Image Gene #48: '4p loss' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

'4p loss' versus 'PATHOLOGY_M_STAGE'

P value = 0.0145 (Fisher's exact test), Q value = 0.059

Table S235. Gene #48: '4p loss' versus Clinical Feature #6: 'PATHOLOGY_M_STAGE'

nPatients	0	1
ALL	546	89
4P LOSS MUTATED	61	19
4P LOSS WILD-TYPE	485	70

Figure S235. Get High-res Image Gene #48: '4p loss' versus Clinical Feature #6: 'PATHOLOGY_M_STAGE'

'4p loss' versus 'GENDER'

P value = 0.0538 (Fisher's exact test), Q value = 0.17

Table S236. Gene #48: '4p loss' versus Clinical Feature #7: 'GENDER'

nPatients	FEMALE	MALE
ALL	292	590
4P LOSS MUTATED	41	57
4P LOSS WILD-TYPE	251	533

Figure S236. Get High-res Image Gene #48: '4p loss' versus Clinical Feature #7: 'GENDER'

'4p loss' versus 'HISTOLOGICAL_TYPE'

P value = 0.00192 (Fisher's exact test), Q value = 0.011

Table S237. 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	288
4P LOSS MUTATED	1	72	25
4P LOSS WILD-TYPE	65	456	263

Figure S237. Get High-res Image Gene #48: '4p loss' versus Clinical Feature #10: 'HISTOLOGICAL_TYPE'

'4q loss' versus 'Time to Death'

P value = 6.76e-13 (logrank test), Q value = 7.8e-10

Table S238. Gene #49: '4q loss' versus Clinical Feature #1: 'Time to Death'

	nPatients	nDeath	Duration Range (Median), Month
ALL	876	228	0.1 - 194.8 (35.9)
4Q LOSS MUTATED	92	49	1.0 - 133.7 (22.8)
4Q LOSS WILD-TYPE	784	179	0.1 - 194.8 (36.7)

Figure S238. 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 = 0.00012

Table S239. Gene #49: '4q loss' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

nPatients	STAGE I	STAGE II	STAGE III	STAGE IV
ALL	454	103	190	104
4Q LOSS MUTATED	20	7	37	25
4Q LOSS WILD-TYPE	434	96	153	79

Figure S239. 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 = 0.00012

Table S240. Gene #49: '4q loss' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

nPatients	T1	T2	T3	T4
ALL	480	127	258	15
4Q LOSS MUTATED	22	12	52	6
4Q LOSS WILD-TYPE	458	115	206	9

Figure S240. Get High-res Image Gene #49: '4q loss' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

'4q loss' versus 'PATHOLOGY_N_STAGE'

P value = 0.00116 (Fisher's exact test), Q value = 0.0074

Table S241. Gene #49: '4q loss' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

nPatients	N0	N1	N2
ALL	323	44	6
4Q LOSS MUTATED	31	13	1
4Q LOSS WILD-TYPE	292	31	5

Figure S241. Get High-res Image Gene #49: '4q loss' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

'4q loss' versus 'PATHOLOGY_M_STAGE'

P value = 0.000606 (Fisher's exact test), Q value = 0.0042

Table S242. Gene #49: '4q loss' versus Clinical Feature #6: 'PATHOLOGY_M_STAGE'

nPatients	0	1
ALL	546	89
4Q LOSS MUTATED	54	21
4Q LOSS WILD-TYPE	492	68

Figure S242. Get High-res Image Gene #49: '4q loss' versus Clinical Feature #6: 'PATHOLOGY_M_STAGE'

'4q loss' versus 'HISTOLOGICAL_TYPE'

P value = 0.00855 (Fisher's exact test), Q value = 0.039

Table S243. 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	288
4Q LOSS MUTATED	1	65	26
4Q LOSS WILD-TYPE	65	463	262

Figure S243. Get High-res Image Gene #49: '4q loss' versus Clinical Feature #10: 'HISTOLOGICAL_TYPE'

'5p loss' versus 'Time to Death'

P value = 0.0571 (logrank test), Q value = 0.18

Table S244. Gene #50: '5p loss' versus Clinical Feature #1: 'Time to Death'

	nPatients	nDeath	Duration Range (Median), Month
ALL	876	228	0.1 - 194.8 (35.9)
5P LOSS MUTATED	23	11	2.8 - 153.7 (30.5)
5P LOSS WILD-TYPE	853	217	0.1 - 194.8 (35.9)

Figure S244. Get High-res Image Gene #50: '5p loss' versus Clinical Feature #1: 'Time to Death'

'5p loss' versus 'YEARS_TO_BIRTH'

P value = 0.0017 (Wilcoxon-test), Q value = 0.01

Table S245. Gene #50: '5p loss' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

	nPatients	Mean (Std.Dev)
ALL	876	60.1 (12.5)
5P LOSS MUTATED	24	51.0 (14.1)
5P LOSS WILD-TYPE	852	60.4 (12.4)

Figure S245. 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 = 0.00012

Table S246. Gene #50: '5p loss' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

nPatients	STAGE I	STAGE II	STAGE III	STAGE IV
ALL	454	103	190	104
5P LOSS MUTATED	2	9	5	7
5P LOSS WILD-TYPE	452	94	185	97

Figure S246. 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 = 0.00012

Table S247. Gene #50: '5p loss' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

nPatients	T1	T2	T3	T4
ALL	480	127	258	15
5P LOSS MUTATED	2	10	10	2
5P LOSS WILD-TYPE	478	117	248	13

Figure S247. Get High-res Image Gene #50: '5p loss' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

'5p loss' versus 'PATHOLOGY_N_STAGE'

P value = 0.0176 (Fisher's exact test), Q value = 0.069

Table S248. Gene #50: '5p loss' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

nPatients	N0	N1	N2
ALL	323	44	6
5P LOSS MUTATED	13	3	2
5P LOSS WILD-TYPE	310	41	4

Figure S248. Get High-res Image Gene #50: '5p loss' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

'5p loss' versus 'GENDER'

P value = 0.0816 (Fisher's exact test), Q value = 0.23

Table S249. Gene #50: '5p loss' versus Clinical Feature #7: 'GENDER'

nPatients	FEMALE	MALE
ALL	292	590
5P LOSS MUTATED	12	12
5P LOSS WILD-TYPE	280	578

Figure S249. Get High-res Image Gene #50: '5p loss' versus Clinical Feature #7: 'GENDER'

'5p loss' versus 'HISTOLOGICAL_TYPE'

P value = 2e-05 (Fisher's exact test), Q value = 2e-04

Table S250. 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	288
5P LOSS MUTATED	10	8	6
5P LOSS WILD-TYPE	56	520	282

Figure S250. 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 S251. 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 S251. Get High-res Image Gene #50: '5p loss' versus Clinical Feature #11: 'NUMBER_PACK_YEARS_SMOKED'

'5p loss' versus 'ETHNICITY'

P value = 0.086 (Fisher's exact test), Q value = 0.24

Table S252. Gene #50: '5p loss' versus Clinical Feature #14: 'ETHNICITY'

nPatients	HISPANIC OR LATINO	NOT HISPANIC OR LATINO
ALL	42	622
5P LOSS MUTATED	3	14
5P LOSS WILD-TYPE	39	608

Figure S252. Get High-res Image Gene #50: '5p loss' versus Clinical Feature #14: 'ETHNICITY'

'5q loss' versus 'YEARS_TO_BIRTH'

P value = 0.000448 (Wilcoxon-test), Q value = 0.0033

Table S253. Gene #51: '5q loss' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

	nPatients	Mean (Std.Dev)
ALL	876	60.1 (12.5)
5Q LOSS MUTATED	23	49.4 (15.3)
5Q LOSS WILD-TYPE	853	60.4 (12.3)

Figure S253. Get High-res Image Gene #51: '5q loss' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'5q loss' versus 'PATHOLOGIC_STAGE'

P value = 8e-05 (Fisher's exact test), Q value = 0.00069

Table S254. Gene #51: '5q loss' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

nPatients	STAGE I	STAGE II	STAGE III	STAGE IV
ALL	454	103	190	104
5Q LOSS MUTATED	3	9	6	4
5Q LOSS WILD-TYPE	451	94	184	100

Figure S254. Get High-res Image Gene #51: '5q loss' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

'5q loss' versus 'PATHOLOGY_T_STAGE'

P value = 4e-05 (Fisher's exact test), Q value = 0.00037

Table S255. Gene #51: '5q loss' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

nPatients	T1	T2	T3	T4
ALL	480	127	258	15
5Q LOSS MUTATED	3	9	9	2
5Q LOSS WILD-TYPE	477	118	249	13

Figure S255. Get High-res Image Gene #51: '5q loss' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

'5q loss' versus 'PATHOLOGY_N_STAGE'

P value = 0.0488 (Fisher's exact test), Q value = 0.16

Table S256. Gene #51: '5q loss' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

nPatients	N0	N1	N2
ALL	323	44	6
5Q LOSS MUTATED	11	4	1
5Q LOSS WILD-TYPE	312	40	5

Figure S256. 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 = 0.00012

Table S257. 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	288
5Q LOSS MUTATED	10	6	7
5Q LOSS WILD-TYPE	56	522	281

Figure S257. 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 S258. 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 S258. Get High-res Image Gene #51: '5q loss' versus Clinical Feature #11: 'NUMBER_PACK_YEARS_SMOKED'

'5q loss' versus 'ETHNICITY'

P value = 0.074 (Fisher's exact test), Q value = 0.21

Table S259. Gene #51: '5q loss' versus Clinical Feature #14: 'ETHNICITY'

nPatients	HISPANIC OR LATINO	NOT HISPANIC OR LATINO
ALL	42	622
5Q LOSS MUTATED	3	13
5Q LOSS WILD-TYPE	39	609

Figure S259. Get High-res Image Gene #51: '5q loss' versus Clinical Feature #14: 'ETHNICITY'

'6p loss' versus 'YEARS_TO_BIRTH'

P value = 0.0574 (Wilcoxon-test), Q value = 0.18

Table S260. Gene #52: '6p loss' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

	nPatients	Mean (Std.Dev)
ALL	876	60.1 (12.5)
6P LOSS MUTATED	169	58.0 (14.7)
6P LOSS WILD-TYPE	707	60.7 (11.9)

Figure S260. 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 = 0.00012

Table S261. Gene #52: '6p loss' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

nPatients	STAGE I	STAGE II	STAGE III	STAGE IV
ALL	454	103	190	104
6P LOSS MUTATED	58	36	46	28
6P LOSS WILD-TYPE	396	67	144	76

Figure S261. 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 = 0.00012

Table S262. Gene #52: '6p loss' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

nPatients	T1	T2	T3	T4
ALL	480	127	258	15
6P LOSS MUTATED	61	39	66	5
6P LOSS WILD-TYPE	419	88	192	10

Figure S262. Get High-res Image Gene #52: '6p loss' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

'6p loss' versus 'PATHOLOGY_N_STAGE'

P value = 0.0542 (Fisher's exact test), Q value = 0.17

Table S263. Gene #52: '6p loss' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

nPatients	N0	N1	N2
ALL	323	44	6
6P LOSS MUTATED	73	11	4
6P LOSS WILD-TYPE	250	33	2

Figure S263. Get High-res Image Gene #52: '6p loss' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

'6p loss' versus 'HISTOLOGICAL_TYPE'

P value = 1e-05 (Fisher's exact test), Q value = 0.00012

Table S264. 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	288
6P LOSS MUTATED	50	100	21
6P LOSS WILD-TYPE	16	428	267

Figure S264. Get High-res Image Gene #52: '6p loss' versus Clinical Feature #10: 'HISTOLOGICAL_TYPE'

'6p loss' versus 'RACE'

P value = 0.00039 (Fisher's exact test), Q value = 0.0029

Table S265. Gene #52: '6p loss' versus Clinical Feature #13: 'RACE'

nPatients	AMERICAN INDIAN OR ALASKA NATIVE	ASIAN	BLACK OR AFRICAN AMERICAN	WHITE
ALL	2	16	121	719
6P LOSS MUTATED	0	4	8	152
6P LOSS WILD-TYPE	2	12	113	567

Figure S265. Get High-res Image Gene #52: '6p loss' versus Clinical Feature #13: 'RACE'

'6q loss' versus 'YEARS_TO_BIRTH'

P value = 0.0567 (Wilcoxon-test), Q value = 0.18

Table S266. Gene #53: '6q loss' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

	nPatients	Mean (Std.Dev)
ALL	876	60.1 (12.5)
6Q LOSS MUTATED	204	58.2 (14.1)
6Q LOSS WILD-TYPE	672	60.7 (12.0)

Figure S266. Get High-res Image Gene #53: '6q loss' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'6q loss' versus 'PATHOLOGIC_STAGE'

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

Table S267. Gene #53: '6q loss' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

nPatients	STAGE I	STAGE II	STAGE III	STAGE IV
ALL	454	103	190	104
6Q LOSS MUTATED	81	40	50	32
6Q LOSS WILD-TYPE	373	63	140	72

Figure S267. Get High-res Image Gene #53: '6q loss' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

'6q loss' versus 'PATHOLOGY_T_STAGE'

P value = 2e-05 (Fisher's exact test), Q value = 2e-04

Table S268. Gene #53: '6q loss' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

nPatients	T1	T2	T3	T4
ALL	480	127	258	15
6Q LOSS MUTATED	83	43	73	7
6Q LOSS WILD-TYPE	397	84	185	8

Figure S268. Get High-res Image Gene #53: '6q loss' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

'6q loss' versus 'PATHOLOGY_N_STAGE'

P value = 0.0442 (Fisher's exact test), Q value = 0.15

Table S269. Gene #53: '6q loss' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

nPatients	N0	N1	N2
ALL	323	44	6
6Q LOSS MUTATED	83	15	4
6Q LOSS WILD-TYPE	240	29	2

Figure S269. Get High-res Image Gene #53: '6q loss' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

'6q loss' versus 'HISTOLOGICAL_TYPE'

P value = 1e-05 (Fisher's exact test), Q value = 0.00012

Table S270. 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	288
6Q LOSS MUTATED	51	128	27
6Q LOSS WILD-TYPE	15	400	261

Figure S270. Get High-res Image Gene #53: '6q loss' versus Clinical Feature #10: 'HISTOLOGICAL_TYPE'

'6q loss' versus 'RACE'

P value = 7e-04 (Fisher's exact test), Q value = 0.0047

Table S271. Gene #53: '6q loss' versus Clinical Feature #13: 'RACE'

nPatients	AMERICAN INDIAN OR ALASKA NATIVE	ASIAN	BLACK OR AFRICAN AMERICAN	WHITE
ALL	2	16	121	719
6Q LOSS MUTATED	0	6	13	179
6Q LOSS WILD-TYPE	2	10	108	540

Figure S271. Get High-res Image Gene #53: '6q loss' versus Clinical Feature #13: 'RACE'

'7p loss' versus 'Time to Death'

P value = 0.0855 (logrank test), Q value = 0.24

Table S272. Gene #54: '7p loss' versus Clinical Feature #1: 'Time to Death'

	nPatients	nDeath	Duration Range (Median), Month
ALL	876	228	0.1 - 194.8 (35.9)
7P LOSS MUTATED	4	2	1.4 - 84.9 (9.5)
7P LOSS WILD-TYPE	872	226	0.1 - 194.8 (35.9)

Figure S272. Get High-res Image Gene #54: '7p loss' versus Clinical Feature #1: 'Time to Death'

'7p loss' versus 'PATHOLOGY_N_STAGE'

P value = 0.0477 (Fisher's exact test), Q value = 0.16

Table S273. Gene #54: '7p loss' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

nPatients	N0	N1	N2
ALL	323	44	6
7P LOSS MUTATED	1	2	0
7P LOSS WILD-TYPE	322	42	6

Figure S273. Get High-res Image Gene #54: '7p loss' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

'7q loss' versus 'Time to Death'

P value = 0.0855 (logrank test), Q value = 0.24

Table S274. Gene #55: '7q loss' versus Clinical Feature #1: 'Time to Death'

	nPatients	nDeath	Duration Range (Median), Month
ALL	876	228	0.1 - 194.8 (35.9)
7Q LOSS MUTATED	4	2	1.4 - 84.9 (9.5)
7Q LOSS WILD-TYPE	872	226	0.1 - 194.8 (35.9)

Figure S274. Get High-res Image Gene #55: '7q loss' versus Clinical Feature #1: 'Time to Death'

'7q loss' versus 'PATHOLOGY_N_STAGE'

P value = 0.0481 (Fisher's exact test), Q value = 0.16

Table S275. Gene #55: '7q loss' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

nPatients	N0	N1	N2
ALL	323	44	6
7Q LOSS MUTATED	1	2	0
7Q LOSS WILD-TYPE	322	42	6

Figure S275. Get High-res Image Gene #55: '7q loss' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

'8p loss' versus 'Time to Death'

P value = 0.0148 (logrank test), Q value = 0.06

Table S276. Gene #56: '8p loss' versus Clinical Feature #1: 'Time to Death'

	nPatients	nDeath	Duration Range (Median), Month
ALL	876	228	0.1 - 194.8 (35.9)
8P LOSS MUTATED	161	58	0.1 - 137.1 (40.0)
8P LOSS WILD-TYPE	715	170	0.1 - 194.8 (33.8)

Figure S276. Get High-res Image Gene #56: '8p loss' versus Clinical Feature #1: 'Time to Death'

'8p loss' versus 'PATHOLOGIC_STAGE'

P value = 0.0324 (Fisher's exact test), Q value = 0.12

Table S277. Gene #56: '8p loss' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

nPatients	STAGE I	STAGE II	STAGE III	STAGE IV
ALL	454	103	190	104
8P LOSS MUTATED	69	21	38	28
8P LOSS WILD-TYPE	385	82	152	76

Figure S277. Get High-res Image Gene #56: '8p loss' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

'8p loss' versus 'PATHOLOGY_T_STAGE'

P value = 0.0371 (Fisher's exact test), Q value = 0.13

Table S278. Gene #56: '8p loss' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

nPatients	T1	T2	T3	T4
ALL	480	127	258	15
8P LOSS MUTATED	73	24	60	4
8P LOSS WILD-TYPE	407	103	198	11

Figure S278. Get High-res Image Gene #56: '8p loss' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

'8p loss' versus 'PATHOLOGY_M_STAGE'

P value = 0.0402 (Fisher's exact test), Q value = 0.14

Table S279. Gene #56: '8p loss' versus Clinical Feature #6: 'PATHOLOGY_M_STAGE'

nPatients	0	1
ALL	546	89
8P LOSS MUTATED	116	28
8P LOSS WILD-TYPE	430	61

Figure S279. 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 = 0.00012

Table S280. 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	288
8P LOSS MUTATED	10	135	16
8P LOSS WILD-TYPE	56	393	272

Figure S280. Get High-res Image Gene #56: '8p loss' versus Clinical Feature #10: 'HISTOLOGICAL_TYPE'

'8p loss' versus 'RACE'

P value = 0.0321 (Fisher's exact test), Q value = 0.11

Table S281. Gene #56: '8p loss' versus Clinical Feature #13: 'RACE'

nPatients	AMERICAN INDIAN OR ALASKA NATIVE	ASIAN	BLACK OR AFRICAN AMERICAN	WHITE
ALL	2	16	121	719
8P LOSS MUTATED	0	4	12	143
8P LOSS WILD-TYPE	2	12	109	576

Figure S281. 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 = 0.00012

Table S282. 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	288
8Q LOSS MUTATED	9	65	9
8Q LOSS WILD-TYPE	57	463	279

Figure S282. Get High-res Image Gene #57: '8q loss' versus Clinical Feature #10: 'HISTOLOGICAL_TYPE'

'9p loss' versus 'Time to Death'

P value = 3.48e-12 (logrank test), Q value = 2e-09

Table S283. Gene #58: '9p loss' versus Clinical Feature #1: 'Time to Death'

	nPatients	nDeath	Duration Range (Median), Month
ALL	876	228	0.1 - 194.8 (35.9)
9P LOSS MUTATED	190	89	0.5 - 153.7 (36.5)
9P LOSS WILD-TYPE	686	139	0.1 - 194.8 (35.5)

Figure S283. Get High-res Image Gene #58: '9p loss' versus Clinical Feature #1: 'Time to Death'

'9p loss' versus 'YEARS_TO_BIRTH'

P value = 0.078 (Wilcoxon-test), Q value = 0.22

Table S284. Gene #58: '9p loss' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

	nPatients	Mean (Std.Dev)
ALL	876	60.1 (12.5)
9P LOSS MUTATED	190	61.5 (12.0)
9P LOSS WILD-TYPE	686	59.8 (12.6)

Figure S284. 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 = 0.00012

Table S285. Gene #58: '9p loss' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

nPatients	STAGE I	STAGE II	STAGE III	STAGE IV
ALL	454	103	190	104
9P LOSS MUTATED	64	15	64	44
9P LOSS WILD-TYPE	390	88	126	60

Figure S285. 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 = 0.00012

Table S286. Gene #58: '9p loss' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

nPatients	T1	T2	T3	T4
ALL	480	127	258	15
9P LOSS MUTATED	69	22	94	7
9P LOSS WILD-TYPE	411	105	164	8

Figure S286. Get High-res Image Gene #58: '9p loss' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

'9p loss' versus 'PATHOLOGY_N_STAGE'

P value = 0.00318 (Fisher's exact test), Q value = 0.017

Table S287. Gene #58: '9p loss' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

nPatients	N0	N1	N2
ALL	323	44	6
9P LOSS MUTATED	71	19	3
9P LOSS WILD-TYPE	252	25	3

Figure S287. Get High-res Image Gene #58: '9p loss' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

'9p loss' versus 'PATHOLOGY_M_STAGE'

P value = 0.000125 (Fisher's exact test), Q value = 0.0011

Table S288. Gene #58: '9p loss' versus Clinical Feature #6: 'PATHOLOGY_M_STAGE'

nPatients	0	1
ALL	546	89
9P LOSS MUTATED	124	38
9P LOSS WILD-TYPE	422	51

Figure S288. Get High-res Image Gene #58: '9p loss' versus Clinical Feature #6: 'PATHOLOGY_M_STAGE'

'9p loss' versus 'KARNOFSKY_PERFORMANCE_SCORE'

P value = 0.00183 (Wilcoxon-test), Q value = 0.011

Table S289. Gene #58: '9p loss' versus Clinical Feature #9: 'KARNOFSKY_PERFORMANCE_SCORE'

	nPatients	Mean (Std.Dev)
ALL	143	87.7 (22.8)
9P LOSS MUTATED	28	76.8 (31.7)
9P LOSS WILD-TYPE	115	90.3 (19.2)

Figure S289. 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 = 0.00012

Table S290. 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	288
9P LOSS MUTATED	10	149	33
9P LOSS WILD-TYPE	56	379	255

Figure S290. Get High-res Image Gene #58: '9p loss' versus Clinical Feature #10: 'HISTOLOGICAL_TYPE'

'9p loss' versus 'RACE'

P value = 0.014 (Fisher's exact test), Q value = 0.057

Table S291. Gene #58: '9p loss' versus Clinical Feature #13: 'RACE'

nPatients	AMERICAN INDIAN OR ALASKA NATIVE	ASIAN	BLACK OR AFRICAN AMERICAN	WHITE
ALL	2	16	121	719
9P LOSS MUTATED	0	3	14	170
9P LOSS WILD-TYPE	2	13	107	549

Figure S291. Get High-res Image Gene #58: '9p loss' versus Clinical Feature #13: 'RACE'

'9q loss' versus 'Time to Death'

P value = 5.03e-10 (logrank test), Q value = 1.4e-07

Table S292. Gene #59: '9q loss' versus Clinical Feature #1: 'Time to Death'

	nPatients	nDeath	Duration Range (Median), Month
ALL	876	228	0.1 - 194.8 (35.9)
9Q LOSS MUTATED	193	86	0.5 - 153.7 (36.4)
9Q LOSS WILD-TYPE	683	142	0.1 - 194.8 (35.9)

Figure S292. Get High-res Image Gene #59: '9q loss' versus Clinical Feature #1: 'Time to Death'

'9q loss' versus 'YEARS_TO_BIRTH'

P value = 0.0619 (Wilcoxon-test), Q value = 0.18

Table S293. Gene #59: '9q loss' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

	nPatients	Mean (Std.Dev)
ALL	876	60.1 (12.5)
9Q LOSS MUTATED	193	61.5 (12.2)
9Q LOSS WILD-TYPE	683	59.8 (12.6)

Figure S293. 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 = 0.00012

Table S294. Gene #59: '9q loss' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

nPatients	STAGE I	STAGE II	STAGE III	STAGE IV
ALL	454	103	190	104
9Q LOSS MUTATED	63	19	67	42
9Q LOSS WILD-TYPE	391	84	123	62

Figure S294. 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 = 0.00012

Table S295. Gene #59: '9q loss' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

nPatients	T1	T2	T3	T4
ALL	480	127	258	15
9Q LOSS MUTATED	67	23	99	6
9Q LOSS WILD-TYPE	413	104	159	9

Figure S295. Get High-res Image Gene #59: '9q loss' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

'9q loss' versus 'PATHOLOGY_N_STAGE'

P value = 0.0113 (Fisher's exact test), Q value = 0.048

Table S296. Gene #59: '9q loss' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

nPatients	N0	N1	N2
ALL	323	44	6
9Q LOSS MUTATED	74	18	3
9Q LOSS WILD-TYPE	249	26	3

Figure S296. Get High-res Image Gene #59: '9q loss' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

'9q loss' versus 'PATHOLOGY_M_STAGE'

P value = 0.00159 (Fisher's exact test), Q value = 0.0095

Table S297. Gene #59: '9q loss' versus Clinical Feature #6: 'PATHOLOGY_M_STAGE'

nPatients	0	1
ALL	546	89
9Q LOSS MUTATED	129	36
9Q LOSS WILD-TYPE	417	53

Figure S297. Get High-res Image Gene #59: '9q loss' versus Clinical Feature #6: 'PATHOLOGY_M_STAGE'

'9q loss' versus 'KARNOFSKY_PERFORMANCE_SCORE'

P value = 0.00118 (Wilcoxon-test), Q value = 0.0074

Table S298. Gene #59: '9q loss' versus Clinical Feature #9: 'KARNOFSKY_PERFORMANCE_SCORE'

	nPatients	Mean (Std.Dev)
ALL	143	87.7 (22.8)
9Q LOSS MUTATED	25	74.8 (33.1)
9Q LOSS WILD-TYPE	118	90.4 (19.0)

Figure S298. 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 = 0.00012

Table S299. 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	288
9Q LOSS MUTATED	11	150	34
9Q LOSS WILD-TYPE	55	378	254

Figure S299. Get High-res Image Gene #59: '9q loss' versus Clinical Feature #10: 'HISTOLOGICAL_TYPE'

'9q loss' versus 'RACE'

P value = 0.0115 (Fisher's exact test), Q value = 0.048

Table S300. Gene #59: '9q loss' versus Clinical Feature #13: 'RACE'

nPatients	AMERICAN INDIAN OR ALASKA NATIVE	ASIAN	BLACK OR AFRICAN AMERICAN	WHITE
ALL	2	16	121	719
9Q LOSS MUTATED	0	4	14	172
9Q LOSS WILD-TYPE	2	12	107	547

Figure S300. Get High-res Image Gene #59: '9q loss' versus Clinical Feature #13: 'RACE'

'10p loss' versus 'YEARS_TO_BIRTH'

P value = 0.0742 (Wilcoxon-test), Q value = 0.21

Table S301. Gene #60: '10p loss' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

	nPatients	Mean (Std.Dev)
ALL	876	60.1 (12.5)
10P LOSS MUTATED	132	57.9 (14.6)
10P LOSS WILD-TYPE	744	60.6 (12.1)

Figure S301. 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 = 0.00012

Table S302. Gene #60: '10p loss' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

nPatients	STAGE I	STAGE II	STAGE III	STAGE IV
ALL	454	103	190	104
10P LOSS MUTATED	42	27	43	19
10P LOSS WILD-TYPE	412	76	147	85

Figure S302. Get High-res Image Gene #60: '10p loss' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

'10p loss' versus 'PATHOLOGY_T_STAGE'

P value = 2e-05 (Fisher's exact test), Q value = 2e-04

Table S303. Gene #60: '10p loss' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

nPatients	T1	T2	T3	T4
ALL	480	127	258	15
10P LOSS MUTATED	44	29	55	5
10P LOSS WILD-TYPE	436	98	203	10

Figure S303. 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 = 0.00012

Table S304. 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	288
10P LOSS MUTATED	48	68	17
10P LOSS WILD-TYPE	18	460	271

Figure S304. Get High-res Image Gene #60: '10p loss' versus Clinical Feature #10: 'HISTOLOGICAL_TYPE'

'10q loss' versus 'YEARS_TO_BIRTH'

P value = 0.0296 (Wilcoxon-test), Q value = 0.11

Table S305. Gene #61: '10q loss' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

	nPatients	Mean (Std.Dev)
ALL	876	60.1 (12.5)
10Q LOSS MUTATED	155	57.9 (14.1)
10Q LOSS WILD-TYPE	721	60.6 (12.1)

Figure S305. 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 = 0.00012

Table S306. Gene #61: '10q loss' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

nPatients	STAGE I	STAGE II	STAGE III	STAGE IV
ALL	454	103	190	104
10Q LOSS MUTATED	51	32	49	24
10Q LOSS WILD-TYPE	403	71	141	80

Figure S306. 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 = 0.00012

Table S307. Gene #61: '10q loss' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

nPatients	T1	T2	T3	T4
ALL	480	127	258	15
10Q LOSS MUTATED	53	34	63	7
10Q LOSS WILD-TYPE	427	93	195	8

Figure S307. 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 = 0.00012

Table S308. 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	288
10Q LOSS MUTATED	49	89	19
10Q LOSS WILD-TYPE	17	439	269

Figure S308. Get High-res Image Gene #61: '10q loss' versus Clinical Feature #10: 'HISTOLOGICAL_TYPE'

'11p loss' versus 'Time to Death'

P value = 0.00759 (logrank test), Q value = 0.035

Table S309. Gene #62: '11p loss' versus Clinical Feature #1: 'Time to Death'

	nPatients	nDeath	Duration Range (Median), Month
ALL	876	228	0.1 - 194.8 (35.9)
11P LOSS MUTATED	42	16	1.0 - 102.8 (23.7)
11P LOSS WILD-TYPE	834	212	0.1 - 194.8 (36.5)

Figure S309. Get High-res Image Gene #62: '11p loss' versus Clinical Feature #1: 'Time to Death'

'11p loss' versus 'YEARS_TO_BIRTH'

P value = 0.0463 (Wilcoxon-test), Q value = 0.15

Table S310. Gene #62: '11p loss' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

	nPatients	Mean (Std.Dev)
ALL	876	60.1 (12.5)
11P LOSS MUTATED	41	63.8 (10.9)
11P LOSS WILD-TYPE	835	60.0 (12.6)

Figure S310. Get High-res Image Gene #62: '11p loss' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'11p loss' versus 'PATHOLOGIC_STAGE'

P value = 0.00142 (Fisher's exact test), Q value = 0.0087

Table S311. Gene #62: '11p loss' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

nPatients	STAGE I	STAGE II	STAGE III	STAGE IV
ALL	454	103	190	104
11P LOSS MUTATED	11	10	10	9
11P LOSS WILD-TYPE	443	93	180	95

Figure S311. Get High-res Image Gene #62: '11p loss' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

'11p loss' versus 'PATHOLOGY_T_STAGE'

P value = 0.00113 (Fisher's exact test), Q value = 0.0072

Table S312. Gene #62: '11p loss' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

nPatients	T1	T2	T3	T4
ALL	480	127	258	15
11P LOSS MUTATED	11	10	20	1
11P LOSS WILD-TYPE	469	117	238	14

Figure S312. Get High-res Image Gene #62: '11p loss' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

'11p loss' versus 'PATHOLOGY_N_STAGE'

P value = 0.00063 (Fisher's exact test), Q value = 0.0044

Table S313. Gene #62: '11p loss' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

nPatients	N0	N1	N2
ALL	323	44	6
11P LOSS MUTATED	13	7	2
11P LOSS WILD-TYPE	310	37	4

Figure S313. Get High-res Image Gene #62: '11p loss' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

'11p loss' versus 'HISTOLOGICAL_TYPE'

P value = 0.0194 (Fisher's exact test), Q value = 0.075

Table S314. 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	288
11P LOSS MUTATED	7	18	17
11P LOSS WILD-TYPE	59	510	271

Figure S314. Get High-res Image Gene #62: '11p loss' versus Clinical Feature #10: 'HISTOLOGICAL_TYPE'

'11q loss' versus 'Time to Death'

P value = 0.000746 (logrank test), Q value = 0.005

Table S315. Gene #63: '11q loss' versus Clinical Feature #1: 'Time to Death'

	nPatients	nDeath	Duration Range (Median), Month
ALL	876	228	0.1 - 194.8 (35.9)
11Q LOSS MUTATED	52	21	0.4 - 123.6 (20.6)
11Q LOSS WILD-TYPE	824	207	0.1 - 194.8 (36.8)

Figure S315. Get High-res Image Gene #63: '11q loss' versus Clinical Feature #1: 'Time to Death'

'11q loss' versus 'YEARS_TO_BIRTH'

P value = 0.0151 (Wilcoxon-test), Q value = 0.06

Table S316. Gene #63: '11q loss' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

	nPatients	Mean (Std.Dev)
ALL	876	60.1 (12.5)
11Q LOSS MUTATED	51	63.9 (11.6)
11Q LOSS WILD-TYPE	825	59.9 (12.5)

Figure S316. Get High-res Image Gene #63: '11q loss' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'11q loss' versus 'PATHOLOGIC_STAGE'

P value = 4e-05 (Fisher's exact test), Q value = 0.00037

Table S317. Gene #63: '11q loss' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

nPatients	STAGE I	STAGE II	STAGE III	STAGE IV
ALL	454	103	190	104
11Q LOSS MUTATED	12	9	18	12
11Q LOSS WILD-TYPE	442	94	172	92

Figure S317. 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 = 0.00037

Table S318. Gene #63: '11q loss' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

nPatients	T1	T2	T3	T4
ALL	480	127	258	15
11Q LOSS MUTATED	12	10	29	1
11Q LOSS WILD-TYPE	468	117	229	14

Figure S318. Get High-res Image Gene #63: '11q loss' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

'11q loss' versus 'PATHOLOGY_N_STAGE'

P value = 2e-05 (Fisher's exact test), Q value = 2e-04

Table S319. Gene #63: '11q loss' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

nPatients	N0	N1	N2
ALL	323	44	6
11Q LOSS MUTATED	18	10	3
11Q LOSS WILD-TYPE	305	34	3

Figure S319. Get High-res Image Gene #63: '11q loss' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

'11q loss' versus 'KARNOFSKY_PERFORMANCE_SCORE'

P value = 0.0432 (Wilcoxon-test), Q value = 0.14

Table S320. Gene #63: '11q loss' versus Clinical Feature #9: 'KARNOFSKY_PERFORMANCE_SCORE'

	nPatients	Mean (Std.Dev)
ALL	143	87.7 (22.8)
11Q LOSS MUTATED	13	80.0 (27.4)
11Q LOSS WILD-TYPE	130	88.5 (22.2)

Figure S320. Get High-res Image Gene #63: '11q loss' versus Clinical Feature #9: 'KARNOFSKY_PERFORMANCE_SCORE'

'11q loss' versus 'HISTOLOGICAL_TYPE'

P value = 0.0317 (Fisher's exact test), Q value = 0.11

Table S321. 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	288
11Q LOSS MUTATED	7	23	22
11Q LOSS WILD-TYPE	59	505	266

Figure S321. Get High-res Image Gene #63: '11q loss' versus Clinical Feature #10: 'HISTOLOGICAL_TYPE'

'12p loss' versus 'PATHOLOGY_N_STAGE'

P value = 0.0479 (Fisher's exact test), Q value = 0.16

Table S322. Gene #64: '12p loss' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

nPatients	N0	N1	N2
ALL	323	44	6
12P LOSS MUTATED	1	2	0
12P LOSS WILD-TYPE	322	42	6

Figure S322. Get High-res Image Gene #64: '12p loss' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

'12q loss' versus 'PATHOLOGY_T_STAGE'

P value = 0.0542 (Fisher's exact test), Q value = 0.17

Table S323. Gene #65: '12q loss' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

nPatients	T1	T2	T3	T4
ALL	480	127	258	15
12Q LOSS MUTATED	1	0	2	1
12Q LOSS WILD-TYPE	479	127	256	14

Figure S323. Get High-res Image Gene #65: '12q loss' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

'13q loss' versus 'Time to Death'

P value = 0.0341 (logrank test), Q value = 0.12

Table S324. Gene #66: '13q loss' versus Clinical Feature #1: 'Time to Death'

	nPatients	nDeath	Duration Range (Median), Month
ALL	876	228	0.1 - 194.8 (35.9)
13Q LOSS MUTATED	135	50	0.2 - 153.7 (38.6)
13Q LOSS WILD-TYPE	741	178	0.1 - 194.8 (35.2)

Figure S324. Get High-res Image Gene #66: '13q loss' versus Clinical Feature #1: 'Time to Death'

'13q loss' versus 'YEARS_TO_BIRTH'

P value = 0.00011 (Wilcoxon-test), Q value = 0.00094

Table S325. Gene #66: '13q loss' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

	nPatients	Mean (Std.Dev)
ALL	876	60.1 (12.5)
13Q LOSS MUTATED	137	55.5 (14.9)
13Q LOSS WILD-TYPE	739	61.0 (11.8)

Figure S325. 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 = 0.00012

Table S326. Gene #66: '13q loss' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

nPatients	STAGE I	STAGE II	STAGE III	STAGE IV
ALL	454	103	190	104
13Q LOSS MUTATED	43	21	44	28
13Q LOSS WILD-TYPE	411	82	146	76

Figure S326. 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 = 0.00012

Table S327. Gene #66: '13q loss' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

nPatients	T1	T2	T3	T4
ALL	480	127	258	15
13Q LOSS MUTATED	45	23	60	9
13Q LOSS WILD-TYPE	435	104	198	6

Figure S327. Get High-res Image Gene #66: '13q loss' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

'13q loss' versus 'PATHOLOGY_N_STAGE'

P value = 0.00757 (Fisher's exact test), Q value = 0.035

Table S328. Gene #66: '13q loss' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

nPatients	N0	N1	N2
ALL	323	44	6
13Q LOSS MUTATED	63	14	4
13Q LOSS WILD-TYPE	260	30	2

Figure S328. Get High-res Image Gene #66: '13q loss' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

'13q loss' versus 'GENDER'

P value = 0.0137 (Fisher's exact test), Q value = 0.056

Table S329. Gene #66: '13q loss' versus Clinical Feature #7: 'GENDER'

nPatients	FEMALE	MALE
ALL	292	590
13Q LOSS MUTATED	58	79
13Q LOSS WILD-TYPE	234	511

Figure S329. 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 = 0.00012

Table S330. 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	288
13Q LOSS MUTATED	43	71	23
13Q LOSS WILD-TYPE	23	457	265

Figure S330. Get High-res Image Gene #66: '13q loss' versus Clinical Feature #10: 'HISTOLOGICAL_TYPE'

'14q loss' versus 'Time to Death'

P value = 1.07e-09 (logrank test), Q value = 2.5e-07

Table S331. Gene #67: '14q loss' versus Clinical Feature #1: 'Time to Death'

	nPatients	nDeath	Duration Range (Median), Month
ALL	876	228	0.1 - 194.8 (35.9)
14Q LOSS MUTATED	264	106	0.1 - 133.7 (31.7)
14Q LOSS WILD-TYPE	612	122	0.1 - 194.8 (37.2)

Figure S331. 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 = 0.00012

Table S332. Gene #67: '14q loss' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

nPatients	STAGE I	STAGE II	STAGE III	STAGE IV
ALL	454	103	190	104
14Q LOSS MUTATED	97	29	77	54
14Q LOSS WILD-TYPE	357	74	113	50

Figure S332. 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 = 0.00012

Table S333. Gene #67: '14q loss' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

nPatients	T1	T2	T3	T4
ALL	480	127	258	15
14Q LOSS MUTATED	105	39	117	4
14Q LOSS WILD-TYPE	375	88	141	11

Figure S333. Get High-res Image Gene #67: '14q loss' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

'14q loss' versus 'PATHOLOGY_N_STAGE'

P value = 0.00607 (Fisher's exact test), Q value = 0.03

Table S334. Gene #67: '14q loss' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

nPatients	N0	N1	N2
ALL	323	44	6
14Q LOSS MUTATED	102	23	4
14Q LOSS WILD-TYPE	221	21	2

Figure S334. Get High-res Image Gene #67: '14q loss' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

'14q loss' versus 'PATHOLOGY_M_STAGE'

P value = 4.11e-05 (Fisher's exact test), Q value = 0.00038

Table S335. Gene #67: '14q loss' versus Clinical Feature #6: 'PATHOLOGY_M_STAGE'

nPatients	0	1
ALL	546	89
14Q LOSS MUTATED	175	49
14Q LOSS WILD-TYPE	371	40

Figure S335. Get High-res Image Gene #67: '14q loss' versus Clinical Feature #6: 'PATHOLOGY_M_STAGE'

'14q loss' versus 'KARNOFSKY_PERFORMANCE_SCORE'

P value = 0.000194 (Wilcoxon-test), Q value = 0.0016

Table S336. Gene #67: '14q loss' versus Clinical Feature #9: 'KARNOFSKY_PERFORMANCE_SCORE'

	nPatients	Mean (Std.Dev)
ALL	143	87.7 (22.8)
14Q LOSS MUTATED	34	71.5 (37.0)
14Q LOSS WILD-TYPE	109	92.8 (12.4)

Figure S336. 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 = 0.00012

Table S337. 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	288
14Q LOSS MUTATED	2	216	47
14Q LOSS WILD-TYPE	64	312	241

Figure S337. 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 S338. 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 S338. Get High-res Image Gene #67: '14q loss' versus Clinical Feature #12: 'YEAR_OF_TOBACCO_SMOKING_ONSET'

'14q loss' versus 'RACE'

P value = 0.0208 (Fisher's exact test), Q value = 0.08

Table S339. Gene #67: '14q loss' versus Clinical Feature #13: 'RACE'

nPatients	AMERICAN INDIAN OR ALASKA NATIVE	ASIAN	BLACK OR AFRICAN AMERICAN	WHITE
ALL	2	16	121	719
14Q LOSS MUTATED	0	3	24	231
14Q LOSS WILD-TYPE	2	13	97	488

Figure S339. Get High-res Image Gene #67: '14q loss' versus Clinical Feature #13: 'RACE'

'15q loss' versus 'Time to Death'

P value = 1.98e-05 (logrank test), Q value = 2e-04

Table S340. Gene #68: '15q loss' versus Clinical Feature #1: 'Time to Death'

	nPatients	nDeath	Duration Range (Median), Month
ALL	876	228	0.1 - 194.8 (35.9)
15Q LOSS MUTATED	68	28	0.1 - 99.0 (24.3)
15Q LOSS WILD-TYPE	808	200	0.1 - 194.8 (37.0)

Figure S340. Get High-res Image Gene #68: '15q loss' versus Clinical Feature #1: 'Time to Death'

'15q loss' versus 'PATHOLOGIC_STAGE'

P value = 2e-05 (Fisher's exact test), Q value = 2e-04

Table S341. Gene #68: '15q loss' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

nPatients	STAGE I	STAGE II	STAGE III	STAGE IV
ALL	454	103	190	104
15Q LOSS MUTATED	20	4	23	17
15Q LOSS WILD-TYPE	434	99	167	87

Figure S341. Get High-res Image Gene #68: '15q loss' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

'15q loss' versus 'PATHOLOGY_T_STAGE'

P value = 2e-05 (Fisher's exact test), Q value = 2e-04

Table S342. Gene #68: '15q loss' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

nPatients	T1	T2	T3	T4
ALL	480	127	258	15
15Q LOSS MUTATED	23	5	36	4
15Q LOSS WILD-TYPE	457	122	222	11

Figure S342. Get High-res Image Gene #68: '15q loss' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

'15q loss' versus 'PATHOLOGY_N_STAGE'

P value = 0.00243 (Fisher's exact test), Q value = 0.014

Table S343. Gene #68: '15q loss' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

nPatients	N0	N1	N2
ALL	323	44	6
15Q LOSS MUTATED	22	9	2
15Q LOSS WILD-TYPE	301	35	4

Figure S343. 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 = 0.057

Table S344. Gene #68: '15q loss' versus Clinical Feature #6: 'PATHOLOGY_M_STAGE'

nPatients	0	1
ALL	546	89
15Q LOSS MUTATED	34	13
15Q LOSS WILD-TYPE	512	76

Figure S344. Get High-res Image Gene #68: '15q loss' versus Clinical Feature #6: 'PATHOLOGY_M_STAGE'

'15q loss' versus 'KARNOFSKY_PERFORMANCE_SCORE'

P value = 0.0746 (Wilcoxon-test), Q value = 0.21

Table S345. Gene #68: '15q loss' versus Clinical Feature #9: 'KARNOFSKY_PERFORMANCE_SCORE'

	nPatients	Mean (Std.Dev)
ALL	143	87.7 (22.8)
15Q LOSS MUTATED	13	81.5 (26.7)
15Q LOSS WILD-TYPE	130	88.3 (22.3)

Figure S345. Get High-res Image Gene #68: '15q loss' versus Clinical Feature #9: 'KARNOFSKY_PERFORMANCE_SCORE'

'15q loss' versus 'HISTOLOGICAL_TYPE'

P value = 0.0668 (Fisher's exact test), Q value = 0.2

Table S346. 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	288
15Q LOSS MUTATED	2	36	30
15Q LOSS WILD-TYPE	64	492	258

Figure S346. Get High-res Image Gene #68: '15q loss' versus Clinical Feature #10: 'HISTOLOGICAL_TYPE'

'16p loss' versus 'Time to Death'

P value = 6.56e-06 (logrank test), Q value = 0.00012

Table S347. Gene #69: '16p loss' versus Clinical Feature #1: 'Time to Death'

	nPatients	nDeath	Duration Range (Median), Month
ALL	876	228	0.1 - 194.8 (35.9)
16P LOSS MUTATED	18	11	0.1 - 80.2 (28.3)
16P LOSS WILD-TYPE	858	217	0.1 - 194.8 (36.4)

Figure S347. Get High-res Image Gene #69: '16p loss' versus Clinical Feature #1: 'Time to Death'

'16p loss' versus 'PATHOLOGIC_STAGE'

P value = 0.00896 (Fisher's exact test), Q value = 0.04

Table S348. Gene #69: '16p loss' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

nPatients	STAGE I	STAGE II	STAGE III	STAGE IV
ALL	454	103	190	104
16P LOSS MUTATED	4	2	6	6
16P LOSS WILD-TYPE	450	101	184	98

Figure S348. Get High-res Image Gene #69: '16p loss' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

'16p loss' versus 'PATHOLOGY_T_STAGE'

P value = 0.00029 (Fisher's exact test), Q value = 0.0022

Table S349. Gene #69: '16p loss' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

nPatients	T1	T2	T3	T4
ALL	480	127	258	15
16P LOSS MUTATED	4	2	9	3
16P LOSS WILD-TYPE	476	125	249	12

Figure S349. Get High-res Image Gene #69: '16p loss' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

'16p loss' versus 'PATHOLOGY_N_STAGE'

P value = 0.00097 (Fisher's exact test), Q value = 0.0064

Table S350. Gene #69: '16p loss' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

nPatients	N0	N1	N2
ALL	323	44	6
16P LOSS MUTATED	6	4	2
16P LOSS WILD-TYPE	317	40	4

Figure S350. Get High-res Image Gene #69: '16p loss' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

'16p loss' versus 'HISTOLOGICAL_TYPE'

P value = 0.0686 (Fisher's exact test), Q value = 0.2

Table S351. 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	288
16P LOSS MUTATED	4	10	4
16P LOSS WILD-TYPE	62	518	284

Figure S351. Get High-res Image Gene #69: '16p loss' versus Clinical Feature #10: 'HISTOLOGICAL_TYPE'

'16q loss' versus 'Time to Death'

P value = 2.23e-06 (logrank test), Q value = 0.00012

Table S352. Gene #70: '16q loss' versus Clinical Feature #1: 'Time to Death'

	nPatients	nDeath	Duration Range (Median), Month
ALL	876	228	0.1 - 194.8 (35.9)
16Q LOSS MUTATED	28	16	0.1 - 80.2 (30.8)
16Q LOSS WILD-TYPE	848	212	0.1 - 194.8 (36.2)

Figure S352. Get High-res Image Gene #70: '16q loss' versus Clinical Feature #1: 'Time to Death'

'16q loss' versus 'PATHOLOGIC_STAGE'

P value = 0.00488 (Fisher's exact test), Q value = 0.024

Table S353. Gene #70: '16q loss' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

nPatients	STAGE I	STAGE II	STAGE III	STAGE IV
ALL	454	103	190	104
16Q LOSS MUTATED	7	4	9	8
16Q LOSS WILD-TYPE	447	99	181	96

Figure S353. Get High-res Image Gene #70: '16q loss' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

'16q loss' versus 'PATHOLOGY_T_STAGE'

P value = 0.00029 (Fisher's exact test), Q value = 0.0022

Table S354. Gene #70: '16q loss' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

nPatients	T1	T2	T3	T4
ALL	480	127	258	15
16Q LOSS MUTATED	8	4	12	4
16Q LOSS WILD-TYPE	472	123	246	11

Figure S354. Get High-res Image Gene #70: '16q loss' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

'16q loss' versus 'PATHOLOGY_N_STAGE'

P value = 0.00028 (Fisher's exact test), Q value = 0.0022

Table S355. Gene #70: '16q loss' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

nPatients	N0	N1	N2
ALL	323	44	6
16Q LOSS MUTATED	9	6	2
16Q LOSS WILD-TYPE	314	38	4

Figure S355. Get High-res Image Gene #70: '16q loss' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

'17p loss' versus 'YEARS_TO_BIRTH'

P value = 0.00397 (Wilcoxon-test), Q value = 0.021

Table S356. Gene #71: '17p loss' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

	nPatients	Mean (Std.Dev)
ALL	876	60.1 (12.5)
17P LOSS MUTATED	110	56.4 (14.7)
17P LOSS WILD-TYPE	766	60.7 (12.1)

Figure S356. 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 = 0.00012

Table S357. Gene #71: '17p loss' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

nPatients	STAGE I	STAGE II	STAGE III	STAGE IV
ALL	454	103	190	104
17P LOSS MUTATED	33	30	24	20
17P LOSS WILD-TYPE	421	73	166	84

Figure S357. 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 = 0.00012

Table S358. Gene #71: '17p loss' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

nPatients	T1	T2	T3	T4
ALL	480	127	258	15
17P LOSS MUTATED	34	33	41	3
17P LOSS WILD-TYPE	446	94	217	12

Figure S358. Get High-res Image Gene #71: '17p loss' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

'17p loss' versus 'PATHOLOGY_N_STAGE'

P value = 5e-04 (Fisher's exact test), Q value = 0.0036

Table S359. Gene #71: '17p loss' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

nPatients	N0	N1	N2
ALL	323	44	6
17P LOSS MUTATED	55	4	5
17P LOSS WILD-TYPE	268	40	1

Figure S359. 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 = 0.00012

Table S360. 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	288
17P LOSS MUTATED	50	47	14
17P LOSS WILD-TYPE	16	481	274

Figure S360. Get High-res Image Gene #71: '17p loss' versus Clinical Feature #10: 'HISTOLOGICAL_TYPE'

'17q loss' versus 'Time to Death'

P value = 0.00889 (logrank test), Q value = 0.04

Table S361. Gene #72: '17q loss' versus Clinical Feature #1: 'Time to Death'

	nPatients	nDeath	Duration Range (Median), Month
ALL	876	228	0.1 - 194.8 (35.9)
17Q LOSS MUTATED	81	17	0.4 - 153.7 (59.1)
17Q LOSS WILD-TYPE	795	211	0.1 - 194.8 (32.6)

Figure S361. Get High-res Image Gene #72: '17q loss' versus Clinical Feature #1: 'Time to Death'

'17q loss' versus 'YEARS_TO_BIRTH'

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

Table S362. Gene #72: '17q loss' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

	nPatients	Mean (Std.Dev)
ALL	876	60.1 (12.5)
17Q LOSS MUTATED	82	54.8 (14.9)
17Q LOSS WILD-TYPE	794	60.7 (12.1)

Figure S362. 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 = 0.00012

Table S363. Gene #72: '17q loss' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

nPatients	STAGE I	STAGE II	STAGE III	STAGE IV
ALL	454	103	190	104
17Q LOSS MUTATED	24	27	17	12
17Q LOSS WILD-TYPE	430	76	173	92

Figure S363. 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 = 0.00012

Table S364. Gene #72: '17q loss' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

nPatients	T1	T2	T3	T4
ALL	480	127	258	15
17Q LOSS MUTATED	25	29	26	2
17Q LOSS WILD-TYPE	455	98	232	13

Figure S364. Get High-res Image Gene #72: '17q loss' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

'17q loss' versus 'KARNOFSKY_PERFORMANCE_SCORE'

P value = 0.0283 (Wilcoxon-test), Q value = 0.1

Table S365. Gene #72: '17q loss' versus Clinical Feature #9: 'KARNOFSKY_PERFORMANCE_SCORE'

	nPatients	Mean (Std.Dev)
ALL	143	87.7 (22.8)
17Q LOSS MUTATED	10	98.0 (4.2)
17Q LOSS WILD-TYPE	133	86.9 (23.4)

Figure S365. 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 = 0.00012

Table S366. 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	288
17Q LOSS MUTATED	50	29	3
17Q LOSS WILD-TYPE	16	499	285

Figure S366. Get High-res Image Gene #72: '17q loss' versus Clinical Feature #10: 'HISTOLOGICAL_TYPE'

'17q loss' versus 'RACE'

P value = 0.0654 (Fisher's exact test), Q value = 0.19

Table S367. Gene #72: '17q loss' versus Clinical Feature #13: 'RACE'

nPatients	AMERICAN INDIAN OR ALASKA NATIVE	ASIAN	BLACK OR AFRICAN AMERICAN	WHITE
ALL	2	16	121	719
17Q LOSS MUTATED	0	3	5	71
17Q LOSS WILD-TYPE	2	13	116	648

Figure S367. Get High-res Image Gene #72: '17q loss' versus Clinical Feature #13: 'RACE'

'18p loss' versus 'Time to Death'

P value = 5.07e-08 (logrank test), Q value = 8.3e-06

Table S368. Gene #73: '18p loss' versus Clinical Feature #1: 'Time to Death'

	nPatients	nDeath	Duration Range (Median), Month
ALL	876	228	0.1 - 194.8 (35.9)
18P LOSS MUTATED	139	58	0.4 - 123.6 (25.7)
18P LOSS WILD-TYPE	737	170	0.1 - 194.8 (37.2)

Figure S368. 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 = 0.00012

Table S369. Gene #73: '18p loss' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

nPatients	STAGE I	STAGE II	STAGE III	STAGE IV
ALL	454	103	190	104
18P LOSS MUTATED	45	10	50	31
18P LOSS WILD-TYPE	409	93	140	73

Figure S369. 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 = 0.00012

Table S370. Gene #73: '18p loss' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

nPatients	T1	T2	T3	T4
ALL	480	127	258	15
18P LOSS MUTATED	48	15	71	7
18P LOSS WILD-TYPE	432	112	187	8

Figure S370. Get High-res Image Gene #73: '18p loss' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

'18p loss' versus 'PATHOLOGY_N_STAGE'

P value = 0.0152 (Fisher's exact test), Q value = 0.061

Table S371. Gene #73: '18p loss' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

nPatients	N0	N1	N2
ALL	323	44	6
18P LOSS MUTATED	53	13	3
18P LOSS WILD-TYPE	270	31	3

Figure S371. Get High-res Image Gene #73: '18p loss' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

'18p loss' versus 'PATHOLOGY_M_STAGE'

P value = 0.0239 (Fisher's exact test), Q value = 0.09

Table S372. Gene #73: '18p loss' versus Clinical Feature #6: 'PATHOLOGY_M_STAGE'

nPatients	0	1
ALL	546	89
18P LOSS MUTATED	89	24
18P LOSS WILD-TYPE	457	65

Figure S372. 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 S373. 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 S373. Get High-res Image Gene #73: '18p loss' versus Clinical Feature #12: 'YEAR_OF_TOBACCO_SMOKING_ONSET'

'18q loss' versus 'Time to Death'

P value = 5.6e-07 (logrank test), Q value = 8e-05

Table S374. Gene #74: '18q loss' versus Clinical Feature #1: 'Time to Death'

	nPatients	nDeath	Duration Range (Median), Month
ALL	876	228	0.1 - 194.8 (35.9)
18Q LOSS MUTATED	146	59	0.4 - 123.6 (27.0)
18Q LOSS WILD-TYPE	730	169	0.1 - 194.8 (37.2)

Figure S374. 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 = 0.00012

Table S375. Gene #74: '18q loss' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

nPatients	STAGE I	STAGE II	STAGE III	STAGE IV
ALL	454	103	190	104
18Q LOSS MUTATED	50	11	51	31
18Q LOSS WILD-TYPE	404	92	139	73

Figure S375. 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 = 0.00012

Table S376. Gene #74: '18q loss' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

nPatients	T1	T2	T3	T4
ALL	480	127	258	15
18Q LOSS MUTATED	54	17	70	7
18Q LOSS WILD-TYPE	426	110	188	8

Figure S376. Get High-res Image Gene #74: '18q loss' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

'18q loss' versus 'PATHOLOGY_N_STAGE'

P value = 0.00366 (Fisher's exact test), Q value = 0.02

Table S377. Gene #74: '18q loss' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

nPatients	N0	N1	N2
ALL	323	44	6
18Q LOSS MUTATED	57	16	3
18Q LOSS WILD-TYPE	266	28	3

Figure S377. Get High-res Image Gene #74: '18q loss' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

'18q loss' versus 'PATHOLOGY_M_STAGE'

P value = 0.0378 (Fisher's exact test), Q value = 0.13

Table S378. Gene #74: '18q loss' versus Clinical Feature #6: 'PATHOLOGY_M_STAGE'

nPatients	0	1
ALL	546	89
18Q LOSS MUTATED	93	24
18Q LOSS WILD-TYPE	453	65

Figure S378. Get High-res Image Gene #74: '18q loss' versus Clinical Feature #6: 'PATHOLOGY_M_STAGE'

'18q loss' versus 'RACE'

P value = 0.059 (Fisher's exact test), Q value = 0.18

Table S379. Gene #74: '18q loss' versus Clinical Feature #13: 'RACE'

nPatients	AMERICAN INDIAN OR ALASKA NATIVE	ASIAN	BLACK OR AFRICAN AMERICAN	WHITE
ALL	2	16	121	719
18Q LOSS MUTATED	0	6	14	125
18Q LOSS WILD-TYPE	2	10	107	594

Figure S379. Get High-res Image Gene #74: '18q loss' versus Clinical Feature #13: 'RACE'

'19p loss' versus 'Time to Death'

P value = 5.51e-05 (logrank test), Q value = 0.00049

Table S380. Gene #75: '19p loss' versus Clinical Feature #1: 'Time to Death'

	nPatients	nDeath	Duration Range (Median), Month
ALL	876	228	0.1 - 194.8 (35.9)
19P LOSS MUTATED	29	14	0.9 - 109.9 (19.3)
19P LOSS WILD-TYPE	847	214	0.1 - 194.8 (36.5)

Figure S380. Get High-res Image Gene #75: '19p loss' versus Clinical Feature #1: 'Time to Death'

'19p loss' versus 'PATHOLOGIC_STAGE'

P value = 0.0012 (Fisher's exact test), Q value = 0.0075

Table S381. Gene #75: '19p loss' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

nPatients	STAGE I	STAGE II	STAGE III	STAGE IV
ALL	454	103	190	104
19P LOSS MUTATED	7	1	13	6
19P LOSS WILD-TYPE	447	102	177	98

Figure S381. Get High-res Image Gene #75: '19p loss' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

'19p loss' versus 'PATHOLOGY_T_STAGE'

P value = 0.00064 (Fisher's exact test), Q value = 0.0044

Table S382. Gene #75: '19p loss' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

nPatients	T1	T2	T3	T4
ALL	480	127	258	15
19P LOSS MUTATED	9	2	15	3
19P LOSS WILD-TYPE	471	125	243	12

Figure S382. Get High-res Image Gene #75: '19p loss' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

'19p loss' versus 'PATHOLOGY_N_STAGE'

P value = 0.025 (Fisher's exact test), Q value = 0.093

Table S383. Gene #75: '19p loss' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

nPatients	N0	N1	N2
ALL	323	44	6
19P LOSS MUTATED	8	4	1
19P LOSS WILD-TYPE	315	40	5

Figure S383. Get High-res Image Gene #75: '19p loss' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

'19p loss' versus 'HISTOLOGICAL_TYPE'

P value = 0.043 (Fisher's exact test), Q value = 0.14

Table S384. 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	288
19P LOSS MUTATED	1	12	16
19P LOSS WILD-TYPE	65	516	272

Figure S384. Get High-res Image Gene #75: '19p loss' versus Clinical Feature #10: 'HISTOLOGICAL_TYPE'

'19q loss' versus 'Time to Death'

P value = 0.000207 (logrank test), Q value = 0.0017

Table S385. Gene #76: '19q loss' versus Clinical Feature #1: 'Time to Death'

	nPatients	nDeath	Duration Range (Median), Month
ALL	876	228	0.1 - 194.8 (35.9)
19Q LOSS MUTATED	23	10	0.9 - 96.6 (16.9)
19Q LOSS WILD-TYPE	853	218	0.1 - 194.8 (36.5)

Figure S385. Get High-res Image Gene #76: '19q loss' versus Clinical Feature #1: 'Time to Death'

'19q loss' versus 'PATHOLOGIC_STAGE'

P value = 0.00031 (Fisher's exact test), Q value = 0.0023

Table S386. Gene #76: '19q loss' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

nPatients	STAGE I	STAGE II	STAGE III	STAGE IV
ALL	454	103	190	104
19Q LOSS MUTATED	4	1	11	6
19Q LOSS WILD-TYPE	450	102	179	98

Figure S386. Get High-res Image Gene #76: '19q loss' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

'19q loss' versus 'PATHOLOGY_T_STAGE'

P value = 2e-05 (Fisher's exact test), Q value = 2e-04

Table S387. Gene #76: '19q loss' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

nPatients	T1	T2	T3	T4
ALL	480	127	258	15
19Q LOSS MUTATED	5	1	14	3
19Q LOSS WILD-TYPE	475	126	244	12

Figure S387. Get High-res Image Gene #76: '19q loss' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

'19q loss' versus 'PATHOLOGY_N_STAGE'

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

Table S388. Gene #76: '19q loss' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

nPatients	N0	N1	N2
ALL	323	44	6
19Q LOSS MUTATED	3	5	2
19Q LOSS WILD-TYPE	320	39	4

Figure S388. Get High-res Image Gene #76: '19q loss' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

'19q loss' versus 'PATHOLOGY_M_STAGE'

P value = 0.0881 (Fisher's exact test), Q value = 0.24

Table S389. Gene #76: '19q loss' versus Clinical Feature #6: 'PATHOLOGY_M_STAGE'

nPatients	0	1
ALL	546	89
19Q LOSS MUTATED	5	3
19Q LOSS WILD-TYPE	541	86

Figure S389. Get High-res Image Gene #76: '19q loss' versus Clinical Feature #6: 'PATHOLOGY_M_STAGE'

'19q loss' versus 'HISTOLOGICAL_TYPE'

P value = 5e-04 (Fisher's exact test), Q value = 0.0036

Table S390. 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	288
19Q LOSS MUTATED	3	5	15
19Q LOSS WILD-TYPE	63	523	273

Figure S390. Get High-res Image Gene #76: '19q loss' versus Clinical Feature #10: 'HISTOLOGICAL_TYPE'

'20p loss' versus 'HISTOLOGICAL_TYPE'

P value = 0.00678 (Fisher's exact test), Q value = 0.032

Table S391. 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	288
20P LOSS MUTATED	4	7	1
20P LOSS WILD-TYPE	62	521	287

Figure S391. Get High-res Image Gene #77: '20p loss' versus Clinical Feature #10: 'HISTOLOGICAL_TYPE'

'20q loss' versus 'PATHOLOGY_N_STAGE'

P value = 0.0873 (Fisher's exact test), Q value = 0.24

Table S392. Gene #78: '20q loss' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

nPatients	N0	N1	N2
ALL	323	44	6
20Q LOSS MUTATED	2	0	1
20Q LOSS WILD-TYPE	321	44	5

Figure S392. Get High-res Image Gene #78: '20q loss' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

'20q loss' versus 'HISTOLOGICAL_TYPE'

P value = 0.00764 (Fisher's exact test), Q value = 0.035

Table S393. 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	288
20Q LOSS MUTATED	3	3	0
20Q LOSS WILD-TYPE	63	525	288

Figure S393. 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 S394. Gene #78: '20q loss' versus Clinical Feature #14: 'ETHNICITY'

nPatients	HISPANIC OR LATINO	NOT HISPANIC OR LATINO
ALL	42	622
20Q LOSS MUTATED	1	0
20Q LOSS WILD-TYPE	41	622

Figure S394. Get High-res Image Gene #78: '20q loss' versus Clinical Feature #14: 'ETHNICITY'

'21q loss' versus 'YEARS_TO_BIRTH'

P value = 0.0543 (Wilcoxon-test), Q value = 0.17

Table S395. Gene #79: '21q loss' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

	nPatients	Mean (Std.Dev)
ALL	876	60.1 (12.5)
21Q LOSS MUTATED	132	57.9 (13.5)
21Q LOSS WILD-TYPE	744	60.5 (12.3)

Figure S395. Get High-res Image Gene #79: '21q loss' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'21q loss' versus 'PATHOLOGIC_STAGE'

P value = 0.00051 (Fisher's exact test), Q value = 0.0036

Table S396. Gene #79: '21q loss' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

nPatients	STAGE I	STAGE II	STAGE III	STAGE IV
ALL	454	103	190	104
21Q LOSS MUTATED	47	20	39	22
21Q LOSS WILD-TYPE	407	83	151	82

Figure S396. 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 = 0.00012

Table S397. Gene #79: '21q loss' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

nPatients	T1	T2	T3	T4
ALL	480	127	258	15
21Q LOSS MUTATED	48	24	55	6
21Q LOSS WILD-TYPE	432	103	203	9

Figure S397. Get High-res Image Gene #79: '21q loss' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

'21q loss' versus 'PATHOLOGY_N_STAGE'

P value = 0.00165 (Fisher's exact test), Q value = 0.0098

Table S398. Gene #79: '21q loss' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

nPatients	N0	N1	N2
ALL	323	44	6
21Q LOSS MUTATED	50	13	4
21Q LOSS WILD-TYPE	273	31	2

Figure S398. 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 = 0.00012

Table S399. 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	288
21Q LOSS MUTATED	35	55	43
21Q LOSS WILD-TYPE	31	473	245

Figure S399. 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 = 0.18

Table S400. 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 S400. 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 = 0.00104 (logrank test), Q value = 0.0068

Table S401. Gene #80: '22q loss' versus Clinical Feature #1: 'Time to Death'

	nPatients	nDeath	Duration Range (Median), Month
ALL	876	228	0.1 - 194.8 (35.9)
22Q LOSS MUTATED	106	38	0.9 - 152.0 (26.6)
22Q LOSS WILD-TYPE	770	190	0.1 - 194.8 (37.2)

Figure S401. 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 = 0.00012

Table S402. Gene #80: '22q loss' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

nPatients	STAGE I	STAGE II	STAGE III	STAGE IV
ALL	454	103	190	104
22Q LOSS MUTATED	34	10	39	20
22Q LOSS WILD-TYPE	420	93	151	84

Figure S402. Get High-res Image Gene #80: '22q loss' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

'22q loss' versus 'PATHOLOGY_T_STAGE'

P value = 0.00033 (Fisher's exact test), Q value = 0.0025

Table S403. Gene #80: '22q loss' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

nPatients	T1	T2	T3	T4
ALL	480	127	258	15
22Q LOSS MUTATED	41	14	51	1
22Q LOSS WILD-TYPE	439	113	207	14

Figure S403. Get High-res Image Gene #80: '22q loss' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

'22q loss' versus 'PATHOLOGY_N_STAGE'

P value = 1e-05 (Fisher's exact test), Q value = 0.00012

Table S404. Gene #80: '22q loss' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

nPatients	N0	N1	N2
ALL	323	44	6
22Q LOSS MUTATED	33	16	3
22Q LOSS WILD-TYPE	290	28	3

Figure S404. Get High-res Image Gene #80: '22q loss' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

'22q loss' versus 'PATHOLOGY_M_STAGE'

P value = 0.0269 (Fisher's exact test), Q value = 0.099

Table S405. Gene #80: '22q loss' versus Clinical Feature #6: 'PATHOLOGY_M_STAGE'

nPatients	0	1
ALL	546	89
22Q LOSS MUTATED	53	16
22Q LOSS WILD-TYPE	493	73

Figure S405. Get High-res Image Gene #80: '22q loss' versus Clinical Feature #6: 'PATHOLOGY_M_STAGE'

'22q loss' versus 'GENDER'

P value = 0.0279 (Fisher's exact test), Q value = 0.1

Table S406. Gene #80: '22q loss' versus Clinical Feature #7: 'GENDER'

nPatients	FEMALE	MALE
ALL	292	590
22Q LOSS MUTATED	46	61
22Q LOSS WILD-TYPE	246	529

Figure S406. Get High-res Image Gene #80: '22q loss' versus Clinical Feature #7: 'GENDER'

'22q loss' versus 'KARNOFSKY_PERFORMANCE_SCORE'

P value = 0.00464 (Wilcoxon-test), Q value = 0.023

Table S407. Gene #80: '22q loss' versus Clinical Feature #9: 'KARNOFSKY_PERFORMANCE_SCORE'

	nPatients	Mean (Std.Dev)
ALL	143	87.7 (22.8)
22Q LOSS MUTATED	25	72.8 (35.9)
22Q LOSS WILD-TYPE	118	90.8 (17.5)

Figure S407. 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 = 0.00012

Table S408. 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	288
22Q LOSS MUTATED	8	39	60
22Q LOSS WILD-TYPE	58	489	228

Figure S408. Get High-res Image Gene #80: '22q loss' versus Clinical Feature #10: 'HISTOLOGICAL_TYPE'

'22q loss' versus 'ETHNICITY'

P value = 0.0281 (Fisher's exact test), Q value = 0.1

Table S409. Gene #80: '22q loss' versus Clinical Feature #14: 'ETHNICITY'

nPatients	HISPANIC OR LATINO	NOT HISPANIC OR LATINO
ALL	42	622
22Q LOSS MUTATED	10	72
22Q LOSS WILD-TYPE	32	550

Figure S409. Get High-res Image Gene #80: '22q loss' versus Clinical Feature #14: 'ETHNICITY'

'xp loss' versus 'YEARS_TO_BIRTH'

P value = 0.000515 (Wilcoxon-test), Q value = 0.0036

Table S410. Gene #81: 'xp loss' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

	nPatients	Mean (Std.Dev)
ALL	876	60.1 (12.5)
XP LOSS MUTATED	113	55.7 (14.3)
XP LOSS WILD-TYPE	763	60.8 (12.1)

Figure S410. Get High-res Image Gene #81: 'xp loss' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'xp loss' versus 'PATHOLOGIC_STAGE'

P value = 0.00022 (Fisher's exact test), Q value = 0.0018

Table S411. Gene #81: 'xp loss' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

nPatients	STAGE I	STAGE II	STAGE III	STAGE IV
ALL	454	103	190	104
XP LOSS MUTATED	38	22	34	14
XP LOSS WILD-TYPE	416	81	156	90

Figure S411. Get High-res Image Gene #81: 'xp loss' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

'xp loss' versus 'PATHOLOGY_T_STAGE'

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

Table S412. Gene #81: 'xp loss' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

nPatients	T1	T2	T3	T4
ALL	480	127	258	15
XP LOSS MUTATED	40	25	47	2
XP LOSS WILD-TYPE	440	102	211	13

Figure S412. Get High-res Image Gene #81: 'xp loss' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

'xp loss' versus 'PATHOLOGY_N_STAGE'

P value = 0.00384 (Fisher's exact test), Q value = 0.02

Table S413. Gene #81: 'xp loss' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

nPatients	N0	N1	N2
ALL	323	44	6
XP LOSS MUTATED	39	13	2
XP LOSS WILD-TYPE	284	31	4

Figure S413. 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 = 0.00012

Table S414. 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	288
XP LOSS MUTATED	38	44	32
XP LOSS WILD-TYPE	28	484	256

Figure S414. Get High-res Image Gene #81: 'xp loss' versus Clinical Feature #10: 'HISTOLOGICAL_TYPE'

'xq loss' versus 'YEARS_TO_BIRTH'

P value = 0.00171 (Wilcoxon-test), Q value = 0.01

Table S415. Gene #82: 'xq loss' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

	nPatients	Mean (Std.Dev)
ALL	876	60.1 (12.5)
XQ LOSS MUTATED	112	56.0 (14.4)
XQ LOSS WILD-TYPE	764	60.8 (12.1)

Figure S415. Get High-res Image Gene #82: 'xq loss' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'xq loss' versus 'PATHOLOGIC_STAGE'

P value = 0.00039 (Fisher's exact test), Q value = 0.0029

Table S416. Gene #82: 'xq loss' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

nPatients	STAGE I	STAGE II	STAGE III	STAGE IV
ALL	454	103	190	104
XQ LOSS MUTATED	38	21	33	16
XQ LOSS WILD-TYPE	416	82	157	88

Figure S416. Get High-res Image Gene #82: 'xq loss' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

'xq loss' versus 'PATHOLOGY_T_STAGE'

P value = 0.00015 (Fisher's exact test), Q value = 0.0012

Table S417. Gene #82: 'xq loss' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

nPatients	T1	T2	T3	T4
ALL	480	127	258	15
XQ LOSS MUTATED	40	23	46	4
XQ LOSS WILD-TYPE	440	104	212	11

Figure S417. Get High-res Image Gene #82: 'xq loss' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

'xq loss' versus 'PATHOLOGY_N_STAGE'

P value = 0.00634 (Fisher's exact test), Q value = 0.031

Table S418. Gene #82: 'xq loss' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

nPatients	N0	N1	N2
ALL	323	44	6
XQ LOSS MUTATED	41	13	2
XQ LOSS WILD-TYPE	282	31	4

Figure S418. 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 = 0.00012

Table S419. 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	288
XQ LOSS MUTATED	38	45	30
XQ LOSS WILD-TYPE	28	483	258

Figure S419. 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/22533780/transformed.cor.cli.txt
Clinical data file = /xchip/cga/gdac-prod/tcga-gdac/jobResults/Append_Data/KIPAN-TP/22506733/KIPAN-TP.merged_data.txt
Number of patients = 882
Number of significantly 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)

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