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

Overview

Introduction

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

Summary

Testing the association between copy number variation 39 focal events and 14 clinical features across 881 patients, 255 significant findings detected with Q value < 0.25.

amp_1q32.1 cnv correlated to 'Time to Death', 'YEARS_TO_BIRTH', 'PATHOLOGIC_STAGE', 'PATHOLOGY_T_STAGE', 'PATHOLOGY_N_STAGE', 'KARNOFSKY_PERFORMANCE_SCORE', 'HISTOLOGICAL_TYPE', and 'YEAR_OF_TOBACCO_SMOKING_ONSET'.
amp_2q32.1 cnv correlated to 'PATHOLOGY_N_STAGE' and 'HISTOLOGICAL_TYPE'.
amp_3q26.32 cnv correlated to 'YEARS_TO_BIRTH', 'PATHOLOGY_N_STAGE', 'PATHOLOGY_M_STAGE', 'HISTOLOGICAL_TYPE', and 'RACE'.
amp_5q35.1 cnv correlated to 'PATHOLOGIC_STAGE', 'PATHOLOGY_T_STAGE', 'PATHOLOGY_N_STAGE', 'PATHOLOGY_M_STAGE', 'HISTOLOGICAL_TYPE', and 'RACE'.
amp_7q31.2 cnv correlated to 'PATHOLOGIC_STAGE', 'PATHOLOGY_N_STAGE', 'PATHOLOGY_M_STAGE', 'GENDER', 'RADIATION_THERAPY', 'HISTOLOGICAL_TYPE', and 'YEAR_OF_TOBACCO_SMOKING_ONSET'.
amp_8q24.22 cnv correlated to 'Time to Death', 'YEARS_TO_BIRTH', 'PATHOLOGIC_STAGE', 'PATHOLOGY_T_STAGE', 'PATHOLOGY_N_STAGE', 'PATHOLOGY_M_STAGE', 'HISTOLOGICAL_TYPE', and 'RACE'.
amp_10p14 cnv correlated to 'PATHOLOGIC_STAGE', 'PATHOLOGY_T_STAGE', and 'PATHOLOGY_N_STAGE'.
amp_17q25.2 cnv correlated to 'YEARS_TO_BIRTH', 'PATHOLOGIC_STAGE', 'PATHOLOGY_T_STAGE', 'PATHOLOGY_N_STAGE', 'GENDER', 'HISTOLOGICAL_TYPE', 'YEAR_OF_TOBACCO_SMOKING_ONSET', and 'RACE'.
amp_19p13.2 cnv correlated to 'PATHOLOGIC_STAGE', 'PATHOLOGY_T_STAGE', 'PATHOLOGY_M_STAGE', 'RADIATION_THERAPY', and 'HISTOLOGICAL_TYPE'.
amp_xp22.2 cnv correlated to 'PATHOLOGIC_STAGE', 'GENDER', 'HISTOLOGICAL_TYPE', and 'YEAR_OF_TOBACCO_SMOKING_ONSET'.
amp_xp11.4 cnv correlated to 'PATHOLOGIC_STAGE', 'PATHOLOGY_T_STAGE', 'GENDER', 'HISTOLOGICAL_TYPE', and 'YEAR_OF_TOBACCO_SMOKING_ONSET'.
amp_xq11.2 cnv correlated to 'Time to Death', 'PATHOLOGIC_STAGE', 'PATHOLOGY_T_STAGE', 'GENDER', 'HISTOLOGICAL_TYPE', and 'YEAR_OF_TOBACCO_SMOKING_ONSET'.
amp_xq28 cnv correlated to 'Time to Death', 'PATHOLOGIC_STAGE', 'PATHOLOGY_T_STAGE', 'GENDER', 'KARNOFSKY_PERFORMANCE_SCORE', 'HISTOLOGICAL_TYPE', and 'RACE'.
del_1p36.31 cnv correlated to 'YEARS_TO_BIRTH', 'PATHOLOGIC_STAGE', 'PATHOLOGY_T_STAGE', 'PATHOLOGY_N_STAGE', 'KARNOFSKY_PERFORMANCE_SCORE', and 'HISTOLOGICAL_TYPE'.
del_1p31.1 cnv correlated to 'YEARS_TO_BIRTH', 'PATHOLOGIC_STAGE', 'PATHOLOGY_T_STAGE', 'PATHOLOGY_N_STAGE', 'HISTOLOGICAL_TYPE', and 'ETHNICITY'.
del_1q43 cnv correlated to 'Time to Death', 'YEARS_TO_BIRTH', 'PATHOLOGIC_STAGE', 'PATHOLOGY_T_STAGE', and 'HISTOLOGICAL_TYPE'.
del_2q37.3 cnv correlated to 'Time to Death', 'YEARS_TO_BIRTH', 'PATHOLOGIC_STAGE', 'PATHOLOGY_T_STAGE', 'PATHOLOGY_M_STAGE', 'KARNOFSKY_PERFORMANCE_SCORE', and 'HISTOLOGICAL_TYPE'.
del_3p26.3 cnv correlated to 'Time to Death', 'PATHOLOGIC_STAGE', 'PATHOLOGY_T_STAGE', 'PATHOLOGY_N_STAGE', 'PATHOLOGY_M_STAGE', 'GENDER', 'KARNOFSKY_PERFORMANCE_SCORE', 'HISTOLOGICAL_TYPE', 'YEAR_OF_TOBACCO_SMOKING_ONSET', and 'RACE'.
del_3p21.2 cnv correlated to 'Time to Death', 'PATHOLOGIC_STAGE', 'PATHOLOGY_T_STAGE', 'PATHOLOGY_M_STAGE', 'GENDER', 'KARNOFSKY_PERFORMANCE_SCORE', 'HISTOLOGICAL_TYPE', 'YEAR_OF_TOBACCO_SMOKING_ONSET', and 'RACE'.
del_3p14.1 cnv correlated to 'Time to Death', 'PATHOLOGIC_STAGE', 'PATHOLOGY_T_STAGE', 'HISTOLOGICAL_TYPE', 'YEAR_OF_TOBACCO_SMOKING_ONSET', and 'RACE'.
del_3p12.2 cnv correlated to 'Time to Death', 'PATHOLOGIC_STAGE', 'PATHOLOGY_T_STAGE', 'HISTOLOGICAL_TYPE', 'YEAR_OF_TOBACCO_SMOKING_ONSET', and 'RACE'.
del_4q34.3 cnv correlated to 'Time to Death', 'PATHOLOGIC_STAGE', 'PATHOLOGY_T_STAGE', 'PATHOLOGY_N_STAGE', 'PATHOLOGY_M_STAGE', 'HISTOLOGICAL_TYPE', and 'RACE'.
del_5p15.33 cnv correlated to 'YEARS_TO_BIRTH', 'PATHOLOGIC_STAGE', 'PATHOLOGY_T_STAGE', 'PATHOLOGY_N_STAGE', 'KARNOFSKY_PERFORMANCE_SCORE', and 'HISTOLOGICAL_TYPE'.
del_6q22.31 cnv correlated to 'PATHOLOGIC_STAGE', 'PATHOLOGY_T_STAGE', 'PATHOLOGY_N_STAGE', 'HISTOLOGICAL_TYPE', 'NUMBER_PACK_YEARS_SMOKED', and 'RACE'.
del_6q26 cnv correlated to 'PATHOLOGIC_STAGE', 'PATHOLOGY_T_STAGE', 'PATHOLOGY_N_STAGE', 'HISTOLOGICAL_TYPE', 'NUMBER_PACK_YEARS_SMOKED', and 'RACE'.
del_6q26 cnv correlated to 'PATHOLOGIC_STAGE', 'PATHOLOGY_T_STAGE', 'PATHOLOGY_N_STAGE', 'HISTOLOGICAL_TYPE', 'NUMBER_PACK_YEARS_SMOKED', and 'RACE'.
del_8p23.2 cnv correlated to 'Time to Death', 'PATHOLOGIC_STAGE', 'PATHOLOGY_T_STAGE', 'PATHOLOGY_M_STAGE', 'HISTOLOGICAL_TYPE', and 'RACE'.
del_9p23 cnv correlated to 'Time to Death', 'YEARS_TO_BIRTH', 'PATHOLOGIC_STAGE', 'PATHOLOGY_T_STAGE', 'PATHOLOGY_N_STAGE', 'PATHOLOGY_M_STAGE', 'KARNOFSKY_PERFORMANCE_SCORE', 'HISTOLOGICAL_TYPE', and 'RACE'.
del_9p21.3 cnv correlated to 'Time to Death', 'YEARS_TO_BIRTH', 'PATHOLOGIC_STAGE', 'PATHOLOGY_T_STAGE', 'PATHOLOGY_N_STAGE', 'PATHOLOGY_M_STAGE', 'KARNOFSKY_PERFORMANCE_SCORE', 'HISTOLOGICAL_TYPE', and 'RACE'.
del_10q23.31 cnv correlated to 'YEARS_TO_BIRTH', 'PATHOLOGIC_STAGE', 'PATHOLOGY_T_STAGE', 'HISTOLOGICAL_TYPE', 'NUMBER_PACK_YEARS_SMOKED', and 'RACE'.
del_11q21 cnv correlated to 'Time to Death', 'YEARS_TO_BIRTH', 'PATHOLOGIC_STAGE', 'PATHOLOGY_T_STAGE', 'PATHOLOGY_N_STAGE', 'PATHOLOGY_M_STAGE', 'KARNOFSKY_PERFORMANCE_SCORE', and 'HISTOLOGICAL_TYPE'.
del_11q23.1 cnv correlated to 'Time to Death', 'YEARS_TO_BIRTH', 'PATHOLOGIC_STAGE', 'PATHOLOGY_T_STAGE', 'PATHOLOGY_N_STAGE', 'PATHOLOGY_M_STAGE', 'KARNOFSKY_PERFORMANCE_SCORE', and 'HISTOLOGICAL_TYPE'.
del_13q12.13 cnv correlated to 'Time to Death', 'YEARS_TO_BIRTH', 'PATHOLOGIC_STAGE', 'PATHOLOGY_T_STAGE', 'PATHOLOGY_N_STAGE', 'GENDER', 'HISTOLOGICAL_TYPE', and 'RACE'.
del_13q14.2 cnv correlated to 'Time to Death', 'YEARS_TO_BIRTH', 'PATHOLOGIC_STAGE', 'PATHOLOGY_T_STAGE', 'PATHOLOGY_N_STAGE', 'GENDER', 'HISTOLOGICAL_TYPE', and 'RACE'.
del_14q31.1 cnv correlated to 'Time to Death', 'PATHOLOGIC_STAGE', 'PATHOLOGY_T_STAGE', 'PATHOLOGY_N_STAGE', 'PATHOLOGY_M_STAGE', 'RADIATION_THERAPY', 'KARNOFSKY_PERFORMANCE_SCORE', 'HISTOLOGICAL_TYPE', 'YEAR_OF_TOBACCO_SMOKING_ONSET', and 'RACE'.
del_16q23.3 cnv correlated to 'Time to Death', 'PATHOLOGIC_STAGE', 'PATHOLOGY_T_STAGE', and 'PATHOLOGY_N_STAGE'.
del_18q22.2 cnv correlated to 'Time to Death', 'PATHOLOGIC_STAGE', 'PATHOLOGY_T_STAGE', 'PATHOLOGY_N_STAGE', 'PATHOLOGY_M_STAGE', 'RACE', and 'ETHNICITY'.
del_19p13.3 cnv correlated to 'Time to Death', 'PATHOLOGIC_STAGE', 'PATHOLOGY_T_STAGE', 'PATHOLOGY_N_STAGE', 'PATHOLOGY_M_STAGE', 'KARNOFSKY_PERFORMANCE_SCORE', and 'HISTOLOGICAL_TYPE'.
del_xp22.2 cnv correlated to 'YEARS_TO_BIRTH', 'PATHOLOGIC_STAGE', 'PATHOLOGY_T_STAGE', 'PATHOLOGY_N_STAGE', and 'HISTOLOGICAL_TYPE'.

Results

Overview of the results

Table 1. Get Full Table Overview of the association between significant copy number variation of 39 focal events and 14 clinical features. Shown in the table are P values (Q values). Thresholded by Q value < 0.25, 255 significant findings detected.


		Clinical Features	Time to Death	YEARS TO BIRTH	PATHOLOGIC STAGE	PATHOLOGY T STAGE	PATHOLOGY N STAGE	PATHOLOGY M STAGE	GENDER	RADIATION THERAPY	KARNOFSKY PERFORMANCE SCORE	HISTOLOGICAL TYPE	NUMBER PACK YEARS SMOKED	YEAR OF TOBACCO SMOKING ONSET	RACE	ETHNICITY
	nCNV (%)	nWild-Type	logrank test	Wilcoxon-test	Fisher's exact test	Fisher's exact test	Fisher's exact test	Fisher's exact test	Fisher's exact test	Fisher's exact test	Wilcoxon-test	Fisher's exact test	Wilcoxon-test	Wilcoxon-test	Fisher's exact test	Fisher's exact test
del 3p26 3	489 (56%)	392	0.000307 (0.00158)	0.685 (0.825)	2e-05 (0.00015)	2e-05 (0.00015)	0.0131 (0.0425)	0.105 (0.233)	0.0518 (0.136)	0.278 (0.462)	0.0801 (0.194)	1e-05 (8.4e-05)	0.419 (0.605)	0.0787 (0.191)	1e-05 (8.4e-05)	0.204 (0.373)
del 14q31 1	279 (32%)	602	8.11e-10 (8.86e-08)	0.126 (0.267)	1e-05 (8.4e-05)	1e-05 (8.4e-05)	0.00554 (0.0199)	4.69e-05 (0.000301)	0.591 (0.752)	0.116 (0.249)	0.000186 (0.00103)	1e-05 (8.4e-05)	0.359 (0.554)	0.00978 (0.0328)	0.0226 (0.0679)	1 (1.00)
del 3p21 2	503 (57%)	378	7.07e-07 (5.51e-05)	0.581 (0.743)	1e-05 (8.4e-05)	1e-05 (8.4e-05)	0.13 (0.273)	0.0035 (0.0133)	0.112 (0.244)	0.298 (0.489)	0.0271 (0.0797)	1e-05 (8.4e-05)	0.274 (0.462)	0.042 (0.114)	1e-05 (8.4e-05)	0.75 (0.875)
del 9p23	198 (22%)	683	3.98e-13 (1.09e-10)	0.0277 (0.0809)	1e-05 (8.4e-05)	1e-05 (8.4e-05)	0.0035 (0.0133)	0.000214 (0.00114)	0.347 (0.544)	0.384 (0.569)	0.000649 (0.00313)	1e-05 (8.4e-05)	0.649 (0.794)	0.893 (0.983)	0.0174 (0.0539)	0.847 (0.956)
del 9p21 3	208 (24%)	673	3.33e-16 (1.82e-13)	0.0382 (0.107)	1e-05 (8.4e-05)	1e-05 (8.4e-05)	4e-05 (0.000263)	5.47e-06 (8.4e-05)	0.273 (0.462)	0.395 (0.58)	0.00153 (0.00659)	1e-05 (8.4e-05)	0.88 (0.975)	0.923 (1.00)	0.00624 (0.0221)	1 (1.00)
amp 1q32 1	82 (9%)	799	4.64e-05 (0.000301)	0.034 (0.0962)	4e-05 (0.000263)	6e-05 (0.00036)	0.0261 (0.0769)	0.137 (0.284)	0.538 (0.721)	1 (1.00)	0.0515 (0.136)	0.00297 (0.0118)	0.282 (0.467)	0.103 (0.23)	0.123 (0.262)	0.254 (0.443)
amp 8q24 22	125 (14%)	756	0.00103 (0.00474)	0.034 (0.0962)	1e-05 (8.4e-05)	1e-05 (8.4e-05)	0.0226 (0.0679)	0.0102 (0.0336)	0.539 (0.721)	1 (1.00)	0.225 (0.403)	0.00128 (0.00568)	0.152 (0.304)	0.374 (0.561)	0.0218 (0.0662)	1 (1.00)
amp 17q25 2	244 (28%)	637	0.784 (0.903)	0.0462 (0.124)	0.00056 (0.00275)	0.00273 (0.011)	0.00015 (0.000836)	0.214 (0.387)	0.00078 (0.0037)	1 (1.00)	0.639 (0.787)	1e-05 (8.4e-05)	0.562 (0.738)	0.108 (0.239)	0.0176 (0.054)	0.227 (0.404)
del 11q21	61 (7%)	820	0.000133 (0.00075)	0.00548 (0.0199)	9e-05 (0.000517)	6e-05 (0.00036)	2e-05 (0.00015)	0.0983 (0.226)	0.78 (0.9)	1 (1.00)	0.0973 (0.225)	0.00308 (0.0121)	0.452 (0.642)	0.62 (0.779)	0.398 (0.583)	0.35 (0.545)
del 11q23 1	71 (8%)	810	0.000299 (0.00157)	0.00335 (0.013)	2e-05 (0.00015)	2e-05 (0.00015)	2e-05 (0.00015)	0.111 (0.244)	0.599 (0.758)	0.245 (0.435)	0.0989 (0.227)	0.00461 (0.017)	0.635 (0.785)	0.646 (0.794)	0.265 (0.456)	0.241 (0.429)
del 13q12 13	150 (17%)	731	0.0125 (0.0409)	0.000305 (0.00158)	1e-05 (8.4e-05)	1e-05 (8.4e-05)	0.00389 (0.0146)	0.179 (0.342)	0.00765 (0.0264)	1 (1.00)	0.904 (0.993)	1e-05 (8.4e-05)	0.933 (1.00)	0.6 (0.758)	0.0848 (0.203)	0.378 (0.564)
del 13q14 2	149 (17%)	732	0.0169 (0.0526)	5.79e-05 (0.000359)	1e-05 (8.4e-05)	1e-05 (8.4e-05)	0.03 (0.0868)	0.131 (0.274)	0.00734 (0.0255)	1 (1.00)	0.478 (0.668)	1e-05 (8.4e-05)	0.839 (0.952)	0.542 (0.723)	0.0871 (0.205)	0.822 (0.937)
amp 7q31 2	377 (43%)	504	0.918 (1.00)	0.258 (0.445)	0.0155 (0.0488)	0.83 (0.944)	0.11 (0.243)	0.00201 (0.00837)	7.13e-06 (8.4e-05)	0.102 (0.23)	0.797 (0.917)	1e-05 (8.4e-05)	0.379 (0.564)	0.00994 (0.0331)	0.177 (0.34)	0.199 (0.369)
amp xq28	137 (16%)	744	0.0923 (0.215)	0.39 (0.575)	0.0786 (0.191)	0.067 (0.17)	0.635 (0.785)	0.465 (0.654)	0.00769 (0.0264)	1 (1.00)	0.115 (0.249)	1e-05 (8.4e-05)	0.843 (0.954)	0.341 (0.541)	0.116 (0.249)	0.284 (0.468)
del 2q37 3	111 (13%)	770	0.029 (0.0843)	0.00326 (0.0127)	1e-05 (8.4e-05)	1e-05 (8.4e-05)	0.514 (0.703)	0.085 (0.203)	0.518 (0.707)	1 (1.00)	0.0153 (0.0488)	1e-05 (8.4e-05)	0.49 (0.681)	0.915 (1.00)	0.456 (0.645)	1 (1.00)
del 4q34 3	113 (13%)	768	1.3e-10 (1.77e-08)	0.705 (0.839)	1e-05 (8.4e-05)	1e-05 (8.4e-05)	0.00173 (0.00732)	0.014 (0.0451)	0.749 (0.875)	1 (1.00)	0.261 (0.45)	0.0332 (0.095)	0.348 (0.544)	0.703 (0.839)	0.0496 (0.132)	0.478 (0.668)
del 18q22 2	155 (18%)	726	2.99e-08 (2.72e-06)	0.624 (0.783)	1e-05 (8.4e-05)	1e-05 (8.4e-05)	0.00397 (0.0148)	0.00896 (0.0304)	0.925 (1.00)	1 (1.00)	0.362 (0.555)	0.354 (0.549)	0.454 (0.643)	0.152 (0.304)	0.0557 (0.145)	0.0901 (0.21)
del 19p13 3	43 (5%)	838	5.14e-12 (9.35e-10)	0.411 (0.596)	1e-05 (8.4e-05)	1e-05 (8.4e-05)	6e-05 (0.00036)	0.069 (0.173)	0.619 (0.779)	1 (1.00)	0.00553 (0.0199)	0.00964 (0.0325)	0.15 (0.303)		0.312 (0.509)	0.72 (0.853)
amp 5q35 1	376 (43%)	505	0.157 (0.308)	0.173 (0.337)	2e-05 (0.00015)	0.00344 (0.0132)	0.0382 (0.107)	0.0159 (0.0498)	0.348 (0.544)	0.203 (0.373)	0.165 (0.324)	1e-05 (8.4e-05)	0.77 (0.892)	0.277 (0.462)	5e-05 (0.000314)	1 (1.00)
amp xq11 2	135 (15%)	746	0.0756 (0.186)	0.315 (0.512)	0.0191 (0.0583)	0.0176 (0.054)	0.674 (0.822)	0.562 (0.738)	6.27e-05 (0.000372)	1 (1.00)	0.371 (0.56)	1e-05 (8.4e-05)	0.743 (0.871)	0.0331 (0.095)	0.153 (0.304)	0.522 (0.709)
del 1p36 31	209 (24%)	672	0.122 (0.26)	0.0863 (0.204)	1e-05 (8.4e-05)	1e-05 (8.4e-05)	0.0231 (0.069)	0.422 (0.608)	0.355 (0.549)	0.564 (0.738)	0.101 (0.23)	1e-05 (8.4e-05)	0.402 (0.588)	0.278 (0.462)	0.594 (0.754)	0.336 (0.539)
del 1p31 1	166 (19%)	715	0.555 (0.735)	0.042 (0.114)	4e-05 (0.000263)	3e-05 (0.000218)	0.0861 (0.204)	0.885 (0.978)	0.855 (0.961)	1 (1.00)	0.991 (1.00)	1e-05 (8.4e-05)	0.701 (0.839)	0.537 (0.721)	0.409 (0.594)	0.0888 (0.208)
del 3p14 1	408 (46%)	473	0.000915 (0.00423)	0.986 (1.00)	0.00019 (0.00104)	4e-05 (0.000263)	0.152 (0.304)	0.564 (0.738)	0.251 (0.441)	0.225 (0.403)	0.373 (0.561)	1e-05 (8.4e-05)	0.355 (0.549)	0.0554 (0.145)	0.00036 (0.00184)	0.633 (0.785)
del 3p12 2	336 (38%)	545	0.000231 (0.00122)	0.777 (0.899)	0.0106 (0.0349)	0.00293 (0.0118)	0.342 (0.541)	0.649 (0.794)	0.141 (0.289)	0.148 (0.299)	0.914 (1.00)	1e-05 (8.4e-05)	0.296 (0.487)	0.0829 (0.199)	0.00585 (0.0209)	0.743 (0.871)
del 5p15 33	31 (4%)	850	0.964 (1.00)	0.00433 (0.0161)	0.00143 (0.0062)	0.00062 (0.00302)	0.00814 (0.0278)	0.74 (0.871)	0.174 (0.337)	1 (1.00)	0.103 (0.23)	1e-05 (8.4e-05)	0.537 (0.721)	0.438 (0.629)	0.571 (0.738)	0.142 (0.29)
del 6q22 31	227 (26%)	654	0.565 (0.738)	0.188 (0.359)	9e-05 (0.000517)	4e-05 (0.000263)	0.115 (0.249)	1 (1.00)	0.683 (0.825)	0.576 (0.738)	0.203 (0.373)	1e-05 (8.4e-05)	0.103 (0.23)	0.371 (0.56)	0.00129 (0.00568)	0.256 (0.444)
del 6q26	233 (26%)	648	0.498 (0.684)	0.267 (0.458)	3e-05 (0.000218)	4e-05 (0.000263)	0.04 (0.109)	1 (1.00)	0.57 (0.738)	0.576 (0.738)	0.175 (0.337)	1e-05 (8.4e-05)	0.103 (0.23)	0.371 (0.56)	0.00086 (0.00405)	0.138 (0.285)
del 6q26	234 (27%)	647	0.492 (0.681)	0.274 (0.462)	4e-05 (0.000263)	4e-05 (0.000263)	0.0395 (0.109)	1 (1.00)	0.686 (0.825)	0.575 (0.738)	0.175 (0.337)	1e-05 (8.4e-05)	0.103 (0.23)	0.371 (0.56)	0.00186 (0.00781)	0.189 (0.359)
del 8p23 2	184 (21%)	697	0.000367 (0.00185)	0.633 (0.785)	0.00173 (0.00732)	0.00113 (0.00506)	0.495 (0.681)	0.0255 (0.0756)	0.725 (0.855)	1 (1.00)	0.407 (0.592)	1e-05 (8.4e-05)	0.952 (1.00)	0.725 (0.855)	0.00224 (0.0092)	0.154 (0.304)
del 10q23 31	164 (19%)	717	0.585 (0.746)	0.0762 (0.186)	1e-05 (8.4e-05)	1e-05 (8.4e-05)	0.532 (0.721)	0.888 (0.979)	0.713 (0.847)	1 (1.00)	0.688 (0.826)	1e-05 (8.4e-05)	0.068 (0.172)	0.271 (0.462)	0.0684 (0.172)	0.382 (0.566)
amp 3q26 32	193 (22%)	688	0.208 (0.377)	0.114 (0.249)	0.154 (0.304)	0.195 (0.365)	0.0458 (0.123)	0.0072 (0.0252)	0.194 (0.364)	1 (1.00)	0.48 (0.669)	1e-05 (8.4e-05)	0.571 (0.738)	0.341 (0.541)	0.0562 (0.145)	0.704 (0.839)
amp 19p13 2	98 (11%)	783	0.847 (0.956)	0.376 (0.562)	0.00109 (0.00492)	0.00299 (0.0118)	0.631 (0.785)	0.0154 (0.0488)	0.255 (0.443)	0.0355 (0.1)	0.862 (0.967)	0.00049 (0.00245)	0.337 (0.539)	0.881 (0.975)	0.443 (0.636)	0.8 (0.917)
amp xp11 4	134 (15%)	747	0.343 (0.542)	0.168 (0.327)	0.0153 (0.0488)	0.0602 (0.153)	0.685 (0.825)	0.131 (0.274)	0.000206 (0.00111)	1 (1.00)	0.479 (0.668)	1e-05 (8.4e-05)	0.991 (1.00)	0.0714 (0.178)	0.205 (0.374)	0.522 (0.709)
del 1q43	114 (13%)	767	0.0517 (0.136)	0.00707 (0.0249)	0.0005 (0.00248)	0.00091 (0.00423)	0.494 (0.681)	0.224 (0.403)	0.201 (0.372)	1 (1.00)	0.447 (0.637)	1e-05 (8.4e-05)	0.807 (0.924)	0.567 (0.738)	0.198 (0.368)	0.147 (0.298)
del xp22 2	127 (14%)	754	0.626 (0.784)	0.00138 (0.00603)	9e-05 (0.000517)	0.0001 (0.000569)	0.057 (0.146)	0.868 (0.969)	0.543 (0.723)	1 (1.00)	0.766 (0.89)	1e-05 (8.4e-05)	0.996 (1.00)	0.447 (0.637)	0.191 (0.359)	0.462 (0.651)
amp xp22 2	126 (14%)	755	0.252 (0.441)	0.278 (0.462)	0.0724 (0.179)	0.145 (0.296)	0.684 (0.825)	0.25 (0.44)	0.00216 (0.00893)	1 (1.00)	0.327 (0.528)	1e-05 (8.4e-05)	0.678 (0.825)	0.057 (0.146)	0.319 (0.517)	0.822 (0.937)
del 16q23 3	37 (4%)	844	1.94e-05 (0.00015)	0.537 (0.721)	0.00482 (0.0177)	5e-05 (0.000314)	0.00107 (0.00487)	0.363 (0.555)	1 (1.00)	1 (1.00)	0.339 (0.541)	0.133 (0.276)	0.556 (0.735)	0.867 (0.969)	0.495 (0.681)	1 (1.00)
amp 10p14	34 (4%)	847	0.273 (0.462)	0.333 (0.537)	0.0715 (0.178)	0.00072 (0.00345)	0.0392 (0.109)	0.575 (0.738)	0.853 (0.96)	1 (1.00)	0.14 (0.289)	0.549 (0.73)	0.753 (0.876)		0.19 (0.359)	1 (1.00)
amp 2q32 1	136 (15%)	745	0.877 (0.975)	0.203 (0.373)	0.363 (0.555)	0.312 (0.509)	0.0397 (0.109)	0.876 (0.975)	0.276 (0.462)	0.368 (0.56)	0.25 (0.44)	0.0027 (0.011)	0.974 (1.00)	0.394 (0.579)	0.635 (0.785)	0.654 (0.799)

'amp_1q32.1' versus 'Time to Death'

P value = 4.64e-05 (logrank test), Q value = 3e-04

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

	nPatients	nDeath	Duration Range (Median), Month
ALL	873	228	0.1 - 194.8 (34.5)
AMP PEAK 1(1Q32.1) MUTATED	81	36	0.4 - 129.4 (27.4)
AMP PEAK 1(1Q32.1) WILD-TYPE	792	192	0.1 - 194.8 (35.9)

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

'amp_1q32.1' versus 'YEARS_TO_BIRTH'

P value = 0.034 (Wilcoxon-test), Q value = 0.096

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

	nPatients	Mean (Std.Dev)
ALL	875	60.1 (12.5)
AMP PEAK 1(1Q32.1) MUTATED	80	62.4 (12.2)
AMP PEAK 1(1Q32.1) WILD-TYPE	795	59.9 (12.5)

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

'amp_1q32.1' versus 'PATHOLOGIC_STAGE'

P value = 4e-05 (Fisher's exact test), Q value = 0.00026

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

nPatients	STAGE I	STAGE II	STAGE III	STAGE IV
ALL	455	104	191	104
AMP PEAK 1(1Q32.1) MUTATED	24	10	31	16
AMP PEAK 1(1Q32.1) WILD-TYPE	431	94	160	88

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

'amp_1q32.1' versus 'PATHOLOGY_T_STAGE'

P value = 6e-05 (Fisher's exact test), Q value = 0.00036

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

nPatients	T1	T2	T3	T4
ALL	479	127	258	15
AMP PEAK 1(1Q32.1) MUTATED	27	12	42	1
AMP PEAK 1(1Q32.1) WILD-TYPE	452	115	216	14

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

'amp_1q32.1' versus 'PATHOLOGY_N_STAGE'

P value = 0.0261 (Fisher's exact test), Q value = 0.077

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

nPatients	N0	N1	N2
ALL	322	44	7
AMP PEAK 1(1Q32.1) MUTATED	35	10	2
AMP PEAK 1(1Q32.1) WILD-TYPE	287	34	5

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

'amp_1q32.1' versus 'KARNOFSKY_PERFORMANCE_SCORE'

P value = 0.0515 (Wilcoxon-test), Q value = 0.14

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

	nPatients	Mean (Std.Dev)
ALL	142	87.6 (22.8)
AMP PEAK 1(1Q32.1) MUTATED	11	60.0 (47.7)
AMP PEAK 1(1Q32.1) WILD-TYPE	131	89.9 (17.9)

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

'amp_1q32.1' versus 'HISTOLOGICAL_TYPE'

P value = 0.00297 (Fisher's exact test), Q value = 0.012

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

nPatients	KIDNEY CHROMOPHOBE	KIDNEY CLEAR CELL RENAL CARCINOMA	KIDNEY PAPILLARY RENAL CELL CARCINOMA
ALL	66	528	287
AMP PEAK 1(1Q32.1) MUTATED	1	62	19
AMP PEAK 1(1Q32.1) WILD-TYPE	65	466	268

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

'amp_1q32.1' versus 'YEAR_OF_TOBACCO_SMOKING_ONSET'

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

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

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

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

'amp_2q32.1' versus 'PATHOLOGY_N_STAGE'

P value = 0.0397 (Fisher's exact test), Q value = 0.11

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

nPatients	N0	N1	N2
ALL	322	44	7
AMP PEAK 2(2Q32.1) MUTATED	48	11	3
AMP PEAK 2(2Q32.1) WILD-TYPE	274	33	4

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

'amp_2q32.1' versus 'HISTOLOGICAL_TYPE'

P value = 0.0027 (Fisher's exact test), Q value = 0.011

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

nPatients	KIDNEY CHROMOPHOBE	KIDNEY CLEAR CELL RENAL CARCINOMA	KIDNEY PAPILLARY RENAL CELL CARCINOMA
ALL	66	528	287
AMP PEAK 2(2Q32.1) MUTATED	2	81	53
AMP PEAK 2(2Q32.1) WILD-TYPE	64	447	234

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

'amp_3q26.32' versus 'YEARS_TO_BIRTH'

P value = 0.114 (Wilcoxon-test), Q value = 0.25

Table S11. Gene #3: 'amp_3q26.32' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

	nPatients	Mean (Std.Dev)
ALL	875	60.1 (12.5)
AMP PEAK 3(3Q26.32) MUTATED	190	61.5 (12.0)
AMP PEAK 3(3Q26.32) WILD-TYPE	685	59.7 (12.6)

Figure S11. Get High-res Image Gene #3: 'amp_3q26.32' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'amp_3q26.32' versus 'PATHOLOGY_N_STAGE'

P value = 0.0458 (Fisher's exact test), Q value = 0.12

Table S12. Gene #3: 'amp_3q26.32' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

nPatients	N0	N1	N2
ALL	322	44	7
AMP PEAK 3(3Q26.32) MUTATED	59	15	1
AMP PEAK 3(3Q26.32) WILD-TYPE	263	29	6

Figure S12. Get High-res Image Gene #3: 'amp_3q26.32' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

'amp_3q26.32' versus 'PATHOLOGY_M_STAGE'

P value = 0.0072 (Fisher's exact test), Q value = 0.025

Table S13. Gene #3: 'amp_3q26.32' versus Clinical Feature #6: 'PATHOLOGY_M_STAGE'

nPatients	0	1
ALL	545	89
AMP PEAK 3(3Q26.32) MUTATED	90	26
AMP PEAK 3(3Q26.32) WILD-TYPE	455	63

Figure S13. Get High-res Image Gene #3: 'amp_3q26.32' versus Clinical Feature #6: 'PATHOLOGY_M_STAGE'

'amp_3q26.32' versus 'HISTOLOGICAL_TYPE'

P value = 1e-05 (Fisher's exact test), Q value = 8.4e-05

Table S14. Gene #3: 'amp_3q26.32' versus Clinical Feature #10: 'HISTOLOGICAL_TYPE'

nPatients	KIDNEY CHROMOPHOBE	KIDNEY CLEAR CELL RENAL CARCINOMA	KIDNEY PAPILLARY RENAL CELL CARCINOMA
ALL	66	528	287
AMP PEAK 3(3Q26.32) MUTATED	6	87	100
AMP PEAK 3(3Q26.32) WILD-TYPE	60	441	187

Figure S14. Get High-res Image Gene #3: 'amp_3q26.32' versus Clinical Feature #10: 'HISTOLOGICAL_TYPE'

'amp_3q26.32' versus 'RACE'

P value = 0.0562 (Fisher's exact test), Q value = 0.15

Table S15. Gene #3: 'amp_3q26.32' versus Clinical Feature #13: 'RACE'

nPatients	AMERICAN INDIAN OR ALASKA NATIVE	ASIAN	BLACK OR AFRICAN AMERICAN	WHITE
ALL	2	15	121	719
AMP PEAK 3(3Q26.32) MUTATED	2	1	26	155
AMP PEAK 3(3Q26.32) WILD-TYPE	0	14	95	564

Figure S15. Get High-res Image Gene #3: 'amp_3q26.32' versus Clinical Feature #13: 'RACE'

'amp_5q35.1' versus 'PATHOLOGIC_STAGE'

P value = 2e-05 (Fisher's exact test), Q value = 0.00015

Table S16. Gene #4: 'amp_5q35.1' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

nPatients	STAGE I	STAGE II	STAGE III	STAGE IV
ALL	455	104	191	104
AMP PEAK 4(5Q35.1) MUTATED	173	42	91	66
AMP PEAK 4(5Q35.1) WILD-TYPE	282	62	100	38

Figure S16. Get High-res Image Gene #4: 'amp_5q35.1' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

'amp_5q35.1' versus 'PATHOLOGY_T_STAGE'

P value = 0.00344 (Fisher's exact test), Q value = 0.013

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

nPatients	T1	T2	T3	T4
ALL	479	127	258	15
AMP PEAK 4(5Q35.1) MUTATED	180	56	133	7
AMP PEAK 4(5Q35.1) WILD-TYPE	299	71	125	8

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

'amp_5q35.1' versus 'PATHOLOGY_N_STAGE'

P value = 0.0382 (Fisher's exact test), Q value = 0.11

Table S18. Gene #4: 'amp_5q35.1' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

nPatients	N0	N1	N2
ALL	322	44	7
AMP PEAK 4(5Q35.1) MUTATED	163	14	2
AMP PEAK 4(5Q35.1) WILD-TYPE	159	30	5

Figure S18. Get High-res Image Gene #4: 'amp_5q35.1' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

'amp_5q35.1' versus 'PATHOLOGY_M_STAGE'

P value = 0.0159 (Fisher's exact test), Q value = 0.05

Table S19. Gene #4: 'amp_5q35.1' versus Clinical Feature #6: 'PATHOLOGY_M_STAGE'

nPatients	0	1
ALL	545	89
AMP PEAK 4(5Q35.1) MUTATED	278	58
AMP PEAK 4(5Q35.1) WILD-TYPE	267	31

Figure S19. Get High-res Image Gene #4: 'amp_5q35.1' versus Clinical Feature #6: 'PATHOLOGY_M_STAGE'

'amp_5q35.1' versus 'HISTOLOGICAL_TYPE'

P value = 1e-05 (Fisher's exact test), Q value = 8.4e-05

Table S20. Gene #4: 'amp_5q35.1' versus Clinical Feature #10: 'HISTOLOGICAL_TYPE'

nPatients	KIDNEY CHROMOPHOBE	KIDNEY CLEAR CELL RENAL CARCINOMA	KIDNEY PAPILLARY RENAL CELL CARCINOMA
ALL	66	528	287
AMP PEAK 4(5Q35.1) MUTATED	8	332	36
AMP PEAK 4(5Q35.1) WILD-TYPE	58	196	251

Figure S20. Get High-res Image Gene #4: 'amp_5q35.1' versus Clinical Feature #10: 'HISTOLOGICAL_TYPE'

'amp_5q35.1' versus 'RACE'

P value = 5e-05 (Fisher's exact test), Q value = 0.00031

Table S21. Gene #4: 'amp_5q35.1' versus Clinical Feature #13: 'RACE'

nPatients	AMERICAN INDIAN OR ALASKA NATIVE	ASIAN	BLACK OR AFRICAN AMERICAN	WHITE
ALL	2	15	121	719
AMP PEAK 4(5Q35.1) MUTATED	0	5	31	333
AMP PEAK 4(5Q35.1) WILD-TYPE	2	10	90	386

Figure S21. Get High-res Image Gene #4: 'amp_5q35.1' versus Clinical Feature #13: 'RACE'

'amp_7q31.2' versus 'PATHOLOGIC_STAGE'

P value = 0.0155 (Fisher's exact test), Q value = 0.049

Table S22. Gene #5: 'amp_7q31.2' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

nPatients	STAGE I	STAGE II	STAGE III	STAGE IV
ALL	455	104	191	104
AMP PEAK 5(7Q31.2) MUTATED	194	38	70	57
AMP PEAK 5(7Q31.2) WILD-TYPE	261	66	121	47

Figure S22. Get High-res Image Gene #5: 'amp_7q31.2' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

'amp_7q31.2' versus 'PATHOLOGY_N_STAGE'

P value = 0.11 (Fisher's exact test), Q value = 0.24

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

nPatients	N0	N1	N2
ALL	322	44	7
AMP PEAK 5(7Q31.2) MUTATED	121	21	5
AMP PEAK 5(7Q31.2) WILD-TYPE	201	23	2

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

'amp_7q31.2' versus 'PATHOLOGY_M_STAGE'

P value = 0.00201 (Fisher's exact test), Q value = 0.0084

Table S24. Gene #5: 'amp_7q31.2' versus Clinical Feature #6: 'PATHOLOGY_M_STAGE'

nPatients	0	1
ALL	545	89
AMP PEAK 5(7Q31.2) MUTATED	191	47
AMP PEAK 5(7Q31.2) WILD-TYPE	354	42

Figure S24. Get High-res Image Gene #5: 'amp_7q31.2' versus Clinical Feature #6: 'PATHOLOGY_M_STAGE'

'amp_7q31.2' versus 'GENDER'

P value = 7.13e-06 (Fisher's exact test), Q value = 8.4e-05

Table S25. Gene #5: 'amp_7q31.2' versus Clinical Feature #7: 'GENDER'

nPatients	FEMALE	MALE
ALL	292	589
AMP PEAK 5(7Q31.2) MUTATED	94	283
AMP PEAK 5(7Q31.2) WILD-TYPE	198	306

Figure S25. Get High-res Image Gene #5: 'amp_7q31.2' versus Clinical Feature #7: 'GENDER'

'amp_7q31.2' versus 'RADIATION_THERAPY'

P value = 0.102 (Fisher's exact test), Q value = 0.23

Table S26. Gene #5: 'amp_7q31.2' versus Clinical Feature #8: 'RADIATION_THERAPY'

nPatients	NO	YES
ALL	400	3
AMP PEAK 5(7Q31.2) MUTATED	186	3
AMP PEAK 5(7Q31.2) WILD-TYPE	214	0

Figure S26. Get High-res Image Gene #5: 'amp_7q31.2' versus Clinical Feature #8: 'RADIATION_THERAPY'

'amp_7q31.2' versus 'HISTOLOGICAL_TYPE'

P value = 1e-05 (Fisher's exact test), Q value = 8.4e-05

Table S27. Gene #5: 'amp_7q31.2' versus Clinical Feature #10: 'HISTOLOGICAL_TYPE'

nPatients	KIDNEY CHROMOPHOBE	KIDNEY CLEAR CELL RENAL CARCINOMA	KIDNEY PAPILLARY RENAL CELL CARCINOMA
ALL	66	528	287
AMP PEAK 5(7Q31.2) MUTATED	25	175	177
AMP PEAK 5(7Q31.2) WILD-TYPE	41	353	110

Figure S27. Get High-res Image Gene #5: 'amp_7q31.2' versus Clinical Feature #10: 'HISTOLOGICAL_TYPE'

'amp_7q31.2' versus 'YEAR_OF_TOBACCO_SMOKING_ONSET'

P value = 0.00994 (Wilcoxon-test), Q value = 0.033

Table S28. Gene #5: 'amp_7q31.2' versus Clinical Feature #12: 'YEAR_OF_TOBACCO_SMOKING_ONSET'

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

Figure S28. Get High-res Image Gene #5: 'amp_7q31.2' versus Clinical Feature #12: 'YEAR_OF_TOBACCO_SMOKING_ONSET'

'amp_8q24.22' versus 'Time to Death'

P value = 0.00103 (logrank test), Q value = 0.0047

Table S29. Gene #6: 'amp_8q24.22' versus Clinical Feature #1: 'Time to Death'

	nPatients	nDeath	Duration Range (Median), Month
ALL	873	228	0.1 - 194.8 (34.5)
AMP PEAK 6(8Q24.22) MUTATED	124	45	0.2 - 152.0 (26.7)
AMP PEAK 6(8Q24.22) WILD-TYPE	749	183	0.1 - 194.8 (36.4)

Figure S29. Get High-res Image Gene #6: 'amp_8q24.22' versus Clinical Feature #1: 'Time to Death'

'amp_8q24.22' versus 'YEARS_TO_BIRTH'

P value = 0.034 (Wilcoxon-test), Q value = 0.096

Table S30. Gene #6: 'amp_8q24.22' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

	nPatients	Mean (Std.Dev)
ALL	875	60.1 (12.5)
AMP PEAK 6(8Q24.22) MUTATED	125	62.2 (12.6)
AMP PEAK 6(8Q24.22) WILD-TYPE	750	59.8 (12.5)

Figure S30. Get High-res Image Gene #6: 'amp_8q24.22' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'amp_8q24.22' versus 'PATHOLOGIC_STAGE'

P value = 1e-05 (Fisher's exact test), Q value = 8.4e-05

Table S31. Gene #6: 'amp_8q24.22' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

nPatients	STAGE I	STAGE II	STAGE III	STAGE IV
ALL	455	104	191	104
AMP PEAK 6(8Q24.22) MUTATED	35	23	39	27
AMP PEAK 6(8Q24.22) WILD-TYPE	420	81	152	77

Figure S31. Get High-res Image Gene #6: 'amp_8q24.22' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

'amp_8q24.22' versus 'PATHOLOGY_T_STAGE'

P value = 1e-05 (Fisher's exact test), Q value = 8.4e-05

Table S32. Gene #6: 'amp_8q24.22' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

nPatients	T1	T2	T3	T4
ALL	479	127	258	15
AMP PEAK 6(8Q24.22) MUTATED	36	24	61	4
AMP PEAK 6(8Q24.22) WILD-TYPE	443	103	197	11

Figure S32. Get High-res Image Gene #6: 'amp_8q24.22' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

'amp_8q24.22' versus 'PATHOLOGY_N_STAGE'

P value = 0.0226 (Fisher's exact test), Q value = 0.068

Table S33. Gene #6: 'amp_8q24.22' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

nPatients	N0	N1	N2
ALL	322	44	7
AMP PEAK 6(8Q24.22) MUTATED	53	13	3
AMP PEAK 6(8Q24.22) WILD-TYPE	269	31	4

Figure S33. Get High-res Image Gene #6: 'amp_8q24.22' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

'amp_8q24.22' versus 'PATHOLOGY_M_STAGE'

P value = 0.0102 (Fisher's exact test), Q value = 0.034

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

nPatients	0	1
ALL	545	89
AMP PEAK 6(8Q24.22) MUTATED	74	22
AMP PEAK 6(8Q24.22) WILD-TYPE	471	67

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

'amp_8q24.22' versus 'HISTOLOGICAL_TYPE'

P value = 0.00128 (Fisher's exact test), Q value = 0.0057

Table S35. Gene #6: 'amp_8q24.22' versus Clinical Feature #10: 'HISTOLOGICAL_TYPE'

nPatients	KIDNEY CHROMOPHOBE	KIDNEY CLEAR CELL RENAL CARCINOMA	KIDNEY PAPILLARY RENAL CELL CARCINOMA
ALL	66	528	287
AMP PEAK 6(8Q24.22) MUTATED	18	79	28
AMP PEAK 6(8Q24.22) WILD-TYPE	48	449	259

Figure S35. Get High-res Image Gene #6: 'amp_8q24.22' versus Clinical Feature #10: 'HISTOLOGICAL_TYPE'

'amp_8q24.22' versus 'RACE'

P value = 0.0218 (Fisher's exact test), Q value = 0.066

Table S36. Gene #6: 'amp_8q24.22' versus Clinical Feature #13: 'RACE'

nPatients	AMERICAN INDIAN OR ALASKA NATIVE	ASIAN	BLACK OR AFRICAN AMERICAN	WHITE
ALL	2	15	121	719
AMP PEAK 6(8Q24.22) MUTATED	0	4	8	110
AMP PEAK 6(8Q24.22) WILD-TYPE	2	11	113	609

Figure S36. Get High-res Image Gene #6: 'amp_8q24.22' versus Clinical Feature #13: 'RACE'

'amp_10p14' versus 'PATHOLOGIC_STAGE'

P value = 0.0715 (Fisher's exact test), Q value = 0.18

Table S37. Gene #7: 'amp_10p14' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

nPatients	STAGE I	STAGE II	STAGE III	STAGE IV
ALL	455	104	191	104
AMP PEAK 7(10P14) MUTATED	12	7	6	7
AMP PEAK 7(10P14) WILD-TYPE	443	97	185	97

Figure S37. Get High-res Image Gene #7: 'amp_10p14' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

'amp_10p14' versus 'PATHOLOGY_T_STAGE'

P value = 0.00072 (Fisher's exact test), Q value = 0.0034

Table S38. Gene #7: 'amp_10p14' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

nPatients	T1	T2	T3	T4
ALL	479	127	258	15
AMP PEAK 7(10P14) MUTATED	13	9	8	4
AMP PEAK 7(10P14) WILD-TYPE	466	118	250	11

Figure S38. Get High-res Image Gene #7: 'amp_10p14' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

'amp_10p14' versus 'PATHOLOGY_N_STAGE'

P value = 0.0392 (Fisher's exact test), Q value = 0.11

Table S39. Gene #7: 'amp_10p14' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

nPatients	N0	N1	N2
ALL	322	44	7
AMP PEAK 7(10P14) MUTATED	12	5	1
AMP PEAK 7(10P14) WILD-TYPE	310	39	6

Figure S39. Get High-res Image Gene #7: 'amp_10p14' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

'amp_17q25.2' versus 'YEARS_TO_BIRTH'

P value = 0.0462 (Wilcoxon-test), Q value = 0.12

Table S40. Gene #8: 'amp_17q25.2' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

	nPatients	Mean (Std.Dev)
ALL	875	60.1 (12.5)
AMP PEAK 8(17Q25.2) MUTATED	241	61.5 (12.2)
AMP PEAK 8(17Q25.2) WILD-TYPE	634	59.6 (12.6)

Figure S40. Get High-res Image Gene #8: 'amp_17q25.2' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'amp_17q25.2' versus 'PATHOLOGIC_STAGE'

P value = 0.00056 (Fisher's exact test), Q value = 0.0028

Table S41. Gene #8: 'amp_17q25.2' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

nPatients	STAGE I	STAGE II	STAGE III	STAGE IV
ALL	455	104	191	104
AMP PEAK 8(17Q25.2) MUTATED	146	22	42	16
AMP PEAK 8(17Q25.2) WILD-TYPE	309	82	149	88

Figure S41. Get High-res Image Gene #8: 'amp_17q25.2' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

'amp_17q25.2' versus 'PATHOLOGY_T_STAGE'

P value = 0.00273 (Fisher's exact test), Q value = 0.011

Table S42. Gene #8: 'amp_17q25.2' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

nPatients	T1	T2	T3	T4
ALL	479	127	258	15
AMP PEAK 8(17Q25.2) MUTATED	156	31	52	4
AMP PEAK 8(17Q25.2) WILD-TYPE	323	96	206	11

Figure S42. Get High-res Image Gene #8: 'amp_17q25.2' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

'amp_17q25.2' versus 'PATHOLOGY_N_STAGE'

P value = 0.00015 (Fisher's exact test), Q value = 0.00084

Table S43. Gene #8: 'amp_17q25.2' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

nPatients	N0	N1	N2
ALL	322	44	7
AMP PEAK 8(17Q25.2) MUTATED	47	16	4
AMP PEAK 8(17Q25.2) WILD-TYPE	275	28	3

Figure S43. Get High-res Image Gene #8: 'amp_17q25.2' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

'amp_17q25.2' versus 'GENDER'

P value = 0.00078 (Fisher's exact test), Q value = 0.0037

Table S44. Gene #8: 'amp_17q25.2' versus Clinical Feature #7: 'GENDER'

nPatients	FEMALE	MALE
ALL	292	589
AMP PEAK 8(17Q25.2) MUTATED	60	184
AMP PEAK 8(17Q25.2) WILD-TYPE	232	405

Figure S44. Get High-res Image Gene #8: 'amp_17q25.2' versus Clinical Feature #7: 'GENDER'

'amp_17q25.2' versus 'HISTOLOGICAL_TYPE'

P value = 1e-05 (Fisher's exact test), Q value = 8.4e-05

Table S45. Gene #8: 'amp_17q25.2' versus Clinical Feature #10: 'HISTOLOGICAL_TYPE'

nPatients	KIDNEY CHROMOPHOBE	KIDNEY CLEAR CELL RENAL CARCINOMA	KIDNEY PAPILLARY RENAL CELL CARCINOMA
ALL	66	528	287
AMP PEAK 8(17Q25.2) MUTATED	1	43	200
AMP PEAK 8(17Q25.2) WILD-TYPE	65	485	87

Figure S45. Get High-res Image Gene #8: 'amp_17q25.2' versus Clinical Feature #10: 'HISTOLOGICAL_TYPE'

'amp_17q25.2' versus 'YEAR_OF_TOBACCO_SMOKING_ONSET'

P value = 0.108 (Wilcoxon-test), Q value = 0.24

Table S46. Gene #8: 'amp_17q25.2' versus Clinical Feature #12: 'YEAR_OF_TOBACCO_SMOKING_ONSET'

	nPatients	Mean (Std.Dev)
ALL	74	1973.7 (16.0)
AMP PEAK 8(17Q25.2) MUTATED	37	1971.2 (15.7)
AMP PEAK 8(17Q25.2) WILD-TYPE	37	1976.3 (16.1)

Figure S46. Get High-res Image Gene #8: 'amp_17q25.2' versus Clinical Feature #12: 'YEAR_OF_TOBACCO_SMOKING_ONSET'

'amp_17q25.2' versus 'RACE'

P value = 0.0176 (Fisher's exact test), Q value = 0.054

Table S47. Gene #8: 'amp_17q25.2' versus Clinical Feature #13: 'RACE'

nPatients	AMERICAN INDIAN OR ALASKA NATIVE	ASIAN	BLACK OR AFRICAN AMERICAN	WHITE
ALL	2	15	121	719
AMP PEAK 8(17Q25.2) MUTATED	2	6	41	185
AMP PEAK 8(17Q25.2) WILD-TYPE	0	9	80	534

Figure S47. Get High-res Image Gene #8: 'amp_17q25.2' versus Clinical Feature #13: 'RACE'

'amp_19p13.2' versus 'PATHOLOGIC_STAGE'

P value = 0.00109 (Fisher's exact test), Q value = 0.0049

Table S48. Gene #9: 'amp_19p13.2' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

nPatients	STAGE I	STAGE II	STAGE III	STAGE IV
ALL	455	104	191	104
AMP PEAK 9(19P13.2) MUTATED	35	18	19	20
AMP PEAK 9(19P13.2) WILD-TYPE	420	86	172	84

Figure S48. Get High-res Image Gene #9: 'amp_19p13.2' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

'amp_19p13.2' versus 'PATHOLOGY_T_STAGE'

P value = 0.00299 (Fisher's exact test), Q value = 0.012

Table S49. Gene #9: 'amp_19p13.2' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

nPatients	T1	T2	T3	T4
ALL	479	127	258	15
AMP PEAK 9(19P13.2) MUTATED	38	23	34	3
AMP PEAK 9(19P13.2) WILD-TYPE	441	104	224	12

Figure S49. Get High-res Image Gene #9: 'amp_19p13.2' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

'amp_19p13.2' versus 'PATHOLOGY_M_STAGE'

P value = 0.0154 (Fisher's exact test), Q value = 0.049

Table S50. Gene #9: 'amp_19p13.2' versus Clinical Feature #6: 'PATHOLOGY_M_STAGE'

nPatients	0	1
ALL	545	89
AMP PEAK 9(19P13.2) MUTATED	52	17
AMP PEAK 9(19P13.2) WILD-TYPE	493	72

Figure S50. Get High-res Image Gene #9: 'amp_19p13.2' versus Clinical Feature #6: 'PATHOLOGY_M_STAGE'

'amp_19p13.2' versus 'RADIATION_THERAPY'

P value = 0.0355 (Fisher's exact test), Q value = 0.1

Table S51. Gene #9: 'amp_19p13.2' versus Clinical Feature #8: 'RADIATION_THERAPY'

nPatients	NO	YES
ALL	400	3
AMP PEAK 9(19P13.2) MUTATED	44	2
AMP PEAK 9(19P13.2) WILD-TYPE	356	1

Figure S51. Get High-res Image Gene #9: 'amp_19p13.2' versus Clinical Feature #8: 'RADIATION_THERAPY'

'amp_19p13.2' versus 'HISTOLOGICAL_TYPE'

P value = 0.00049 (Fisher's exact test), Q value = 0.0025

Table S52. Gene #9: 'amp_19p13.2' versus Clinical Feature #10: 'HISTOLOGICAL_TYPE'

nPatients	KIDNEY CHROMOPHOBE	KIDNEY CLEAR CELL RENAL CARCINOMA	KIDNEY PAPILLARY RENAL CELL CARCINOMA
ALL	66	528	287
AMP PEAK 9(19P13.2) MUTATED	18	49	31
AMP PEAK 9(19P13.2) WILD-TYPE	48	479	256

Figure S52. Get High-res Image Gene #9: 'amp_19p13.2' versus Clinical Feature #10: 'HISTOLOGICAL_TYPE'

'amp_xp22.2' versus 'PATHOLOGIC_STAGE'

P value = 0.0724 (Fisher's exact test), Q value = 0.18

Table S53. Gene #10: 'amp_xp22.2' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

nPatients	STAGE I	STAGE II	STAGE III	STAGE IV
ALL	455	104	191	104
AMP PEAK 10(XP22.2) MUTATED	72	15	16	16
AMP PEAK 10(XP22.2) WILD-TYPE	383	89	175	88

Figure S53. Get High-res Image Gene #10: 'amp_xp22.2' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

'amp_xp22.2' versus 'GENDER'

P value = 0.00216 (Fisher's exact test), Q value = 0.0089

Table S54. Gene #10: 'amp_xp22.2' versus Clinical Feature #7: 'GENDER'

nPatients	FEMALE	MALE
ALL	292	589
AMP PEAK 10(XP22.2) MUTATED	27	99
AMP PEAK 10(XP22.2) WILD-TYPE	265	490

Figure S54. Get High-res Image Gene #10: 'amp_xp22.2' versus Clinical Feature #7: 'GENDER'

'amp_xp22.2' versus 'HISTOLOGICAL_TYPE'

P value = 1e-05 (Fisher's exact test), Q value = 8.4e-05

Table S55. Gene #10: 'amp_xp22.2' versus Clinical Feature #10: 'HISTOLOGICAL_TYPE'

nPatients	KIDNEY CHROMOPHOBE	KIDNEY CLEAR CELL RENAL CARCINOMA	KIDNEY PAPILLARY RENAL CELL CARCINOMA
ALL	66	528	287
AMP PEAK 10(XP22.2) MUTATED	7	31	88
AMP PEAK 10(XP22.2) WILD-TYPE	59	497	199

Figure S55. Get High-res Image Gene #10: 'amp_xp22.2' versus Clinical Feature #10: 'HISTOLOGICAL_TYPE'

'amp_xp22.2' versus 'YEAR_OF_TOBACCO_SMOKING_ONSET'

P value = 0.057 (Wilcoxon-test), Q value = 0.15

Table S56. Gene #10: 'amp_xp22.2' versus Clinical Feature #12: 'YEAR_OF_TOBACCO_SMOKING_ONSET'

	nPatients	Mean (Std.Dev)
ALL	74	1973.7 (16.0)
AMP PEAK 10(XP22.2) MUTATED	17	1967.9 (13.8)
AMP PEAK 10(XP22.2) WILD-TYPE	57	1975.5 (16.3)

Figure S56. Get High-res Image Gene #10: 'amp_xp22.2' versus Clinical Feature #12: 'YEAR_OF_TOBACCO_SMOKING_ONSET'

'amp_xp11.4' versus 'PATHOLOGIC_STAGE'

P value = 0.0153 (Fisher's exact test), Q value = 0.049

Table S57. Gene #11: 'amp_xp11.4' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

nPatients	STAGE I	STAGE II	STAGE III	STAGE IV
ALL	455	104	191	104
AMP PEAK 11(XP11.4) MUTATED	78	15	15	17
AMP PEAK 11(XP11.4) WILD-TYPE	377	89	176	87

Figure S57. Get High-res Image Gene #11: 'amp_xp11.4' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

'amp_xp11.4' versus 'PATHOLOGY_T_STAGE'

P value = 0.0602 (Fisher's exact test), Q value = 0.15

Table S58. Gene #11: 'amp_xp11.4' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

nPatients	T1	T2	T3	T4
ALL	479	127	258	15
AMP PEAK 11(XP11.4) MUTATED	82	22	27	3
AMP PEAK 11(XP11.4) WILD-TYPE	397	105	231	12

Figure S58. Get High-res Image Gene #11: 'amp_xp11.4' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

'amp_xp11.4' versus 'GENDER'

P value = 0.000206 (Fisher's exact test), Q value = 0.0011

Table S59. Gene #11: 'amp_xp11.4' versus Clinical Feature #7: 'GENDER'

nPatients	FEMALE	MALE
ALL	292	589
AMP PEAK 11(XP11.4) MUTATED	26	108
AMP PEAK 11(XP11.4) WILD-TYPE	266	481

Figure S59. Get High-res Image Gene #11: 'amp_xp11.4' versus Clinical Feature #7: 'GENDER'

'amp_xp11.4' versus 'HISTOLOGICAL_TYPE'

P value = 1e-05 (Fisher's exact test), Q value = 8.4e-05

Table S60. Gene #11: 'amp_xp11.4' versus Clinical Feature #10: 'HISTOLOGICAL_TYPE'

nPatients	KIDNEY CHROMOPHOBE	KIDNEY CLEAR CELL RENAL CARCINOMA	KIDNEY PAPILLARY RENAL CELL CARCINOMA
ALL	66	528	287
AMP PEAK 11(XP11.4) MUTATED	7	33	94
AMP PEAK 11(XP11.4) WILD-TYPE	59	495	193

Figure S60. Get High-res Image Gene #11: 'amp_xp11.4' versus Clinical Feature #10: 'HISTOLOGICAL_TYPE'

'amp_xp11.4' versus 'YEAR_OF_TOBACCO_SMOKING_ONSET'

P value = 0.0714 (Wilcoxon-test), Q value = 0.18

Table S61. Gene #11: 'amp_xp11.4' versus Clinical Feature #12: 'YEAR_OF_TOBACCO_SMOKING_ONSET'

	nPatients	Mean (Std.Dev)
ALL	74	1973.7 (16.0)
AMP PEAK 11(XP11.4) MUTATED	18	1968.3 (13.5)
AMP PEAK 11(XP11.4) WILD-TYPE	56	1975.5 (16.4)

Figure S61. Get High-res Image Gene #11: 'amp_xp11.4' versus Clinical Feature #12: 'YEAR_OF_TOBACCO_SMOKING_ONSET'

'amp_xq11.2' versus 'Time to Death'

P value = 0.0756 (logrank test), Q value = 0.19

Table S62. Gene #12: 'amp_xq11.2' versus Clinical Feature #1: 'Time to Death'

	nPatients	nDeath	Duration Range (Median), Month
ALL	873	228	0.1 - 194.8 (34.5)
AMP PEAK 12(XQ11.2) MUTATED	132	23	0.1 - 194.8 (28.6)
AMP PEAK 12(XQ11.2) WILD-TYPE	741	205	0.1 - 152.0 (35.9)

Figure S62. Get High-res Image Gene #12: 'amp_xq11.2' versus Clinical Feature #1: 'Time to Death'

'amp_xq11.2' versus 'PATHOLOGIC_STAGE'

P value = 0.0191 (Fisher's exact test), Q value = 0.058

Table S63. Gene #12: 'amp_xq11.2' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

nPatients	STAGE I	STAGE II	STAGE III	STAGE IV
ALL	455	104	191	104
AMP PEAK 12(XQ11.2) MUTATED	80	15	16	13
AMP PEAK 12(XQ11.2) WILD-TYPE	375	89	175	91

Figure S63. Get High-res Image Gene #12: 'amp_xq11.2' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

'amp_xq11.2' versus 'PATHOLOGY_T_STAGE'

P value = 0.0176 (Fisher's exact test), Q value = 0.054

Table S64. Gene #12: 'amp_xq11.2' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

nPatients	T1	T2	T3	T4
ALL	479	127	258	15
AMP PEAK 12(XQ11.2) MUTATED	86	22	25	2
AMP PEAK 12(XQ11.2) WILD-TYPE	393	105	233	13

Figure S64. Get High-res Image Gene #12: 'amp_xq11.2' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

'amp_xq11.2' versus 'GENDER'

P value = 6.27e-05 (Fisher's exact test), Q value = 0.00037

Table S65. Gene #12: 'amp_xq11.2' versus Clinical Feature #7: 'GENDER'

nPatients	FEMALE	MALE
ALL	292	589
AMP PEAK 12(XQ11.2) MUTATED	25	110
AMP PEAK 12(XQ11.2) WILD-TYPE	267	479

Figure S65. Get High-res Image Gene #12: 'amp_xq11.2' versus Clinical Feature #7: 'GENDER'

'amp_xq11.2' versus 'HISTOLOGICAL_TYPE'

P value = 1e-05 (Fisher's exact test), Q value = 8.4e-05

Table S66. Gene #12: 'amp_xq11.2' versus Clinical Feature #10: 'HISTOLOGICAL_TYPE'

nPatients	KIDNEY CHROMOPHOBE	KIDNEY CLEAR CELL RENAL CARCINOMA	KIDNEY PAPILLARY RENAL CELL CARCINOMA
ALL	66	528	287
AMP PEAK 12(XQ11.2) MUTATED	7	29	99
AMP PEAK 12(XQ11.2) WILD-TYPE	59	499	188

Figure S66. Get High-res Image Gene #12: 'amp_xq11.2' versus Clinical Feature #10: 'HISTOLOGICAL_TYPE'

'amp_xq11.2' versus 'YEAR_OF_TOBACCO_SMOKING_ONSET'

P value = 0.0331 (Wilcoxon-test), Q value = 0.095

Table S67. Gene #12: 'amp_xq11.2' versus Clinical Feature #12: 'YEAR_OF_TOBACCO_SMOKING_ONSET'

	nPatients	Mean (Std.Dev)
ALL	74	1973.7 (16.0)
AMP PEAK 12(XQ11.2) MUTATED	18	1966.9 (15.0)
AMP PEAK 12(XQ11.2) WILD-TYPE	56	1975.9 (15.8)

Figure S67. Get High-res Image Gene #12: 'amp_xq11.2' versus Clinical Feature #12: 'YEAR_OF_TOBACCO_SMOKING_ONSET'

'amp_xq28' versus 'Time to Death'

P value = 0.0923 (logrank test), Q value = 0.21

Table S68. Gene #13: 'amp_xq28' versus Clinical Feature #1: 'Time to Death'

	nPatients	nDeath	Duration Range (Median), Month
ALL	873	228	0.1 - 194.8 (34.5)
AMP PEAK 13(XQ28) MUTATED	134	24	0.1 - 194.8 (28.6)
AMP PEAK 13(XQ28) WILD-TYPE	739	204	0.1 - 152.0 (36.2)

Figure S68. Get High-res Image Gene #13: 'amp_xq28' versus Clinical Feature #1: 'Time to Death'

'amp_xq28' versus 'PATHOLOGIC_STAGE'

P value = 0.0786 (Fisher's exact test), Q value = 0.19

Table S69. Gene #13: 'amp_xq28' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

nPatients	STAGE I	STAGE II	STAGE III	STAGE IV
ALL	455	104	191	104
AMP PEAK 13(XQ28) MUTATED	80	13	19	15
AMP PEAK 13(XQ28) WILD-TYPE	375	91	172	89

Figure S69. Get High-res Image Gene #13: 'amp_xq28' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

'amp_xq28' versus 'PATHOLOGY_T_STAGE'

P value = 0.067 (Fisher's exact test), Q value = 0.17

Table S70. Gene #13: 'amp_xq28' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

nPatients	T1	T2	T3	T4
ALL	479	127	258	15
AMP PEAK 13(XQ28) MUTATED	85	21	28	3
AMP PEAK 13(XQ28) WILD-TYPE	394	106	230	12

Figure S70. Get High-res Image Gene #13: 'amp_xq28' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

'amp_xq28' versus 'GENDER'

P value = 0.00769 (Fisher's exact test), Q value = 0.026

Table S71. Gene #13: 'amp_xq28' versus Clinical Feature #7: 'GENDER'

nPatients	FEMALE	MALE
ALL	292	589
AMP PEAK 13(XQ28) MUTATED	32	105
AMP PEAK 13(XQ28) WILD-TYPE	260	484

Figure S71. Get High-res Image Gene #13: 'amp_xq28' versus Clinical Feature #7: 'GENDER'

'amp_xq28' versus 'KARNOFSKY_PERFORMANCE_SCORE'

P value = 0.115 (Wilcoxon-test), Q value = 0.25

Table S72. Gene #13: 'amp_xq28' versus Clinical Feature #9: 'KARNOFSKY_PERFORMANCE_SCORE'

	nPatients	Mean (Std.Dev)
ALL	142	87.6 (22.8)
AMP PEAK 13(XQ28) MUTATED	30	91.7 (19.0)
AMP PEAK 13(XQ28) WILD-TYPE	112	86.5 (23.7)

Figure S72. Get High-res Image Gene #13: 'amp_xq28' versus Clinical Feature #9: 'KARNOFSKY_PERFORMANCE_SCORE'

'amp_xq28' versus 'HISTOLOGICAL_TYPE'

P value = 1e-05 (Fisher's exact test), Q value = 8.4e-05

Table S73. Gene #13: 'amp_xq28' versus Clinical Feature #10: 'HISTOLOGICAL_TYPE'

nPatients	KIDNEY CHROMOPHOBE	KIDNEY CLEAR CELL RENAL CARCINOMA	KIDNEY PAPILLARY RENAL CELL CARCINOMA
ALL	66	528	287
AMP PEAK 13(XQ28) MUTATED	8	38	91
AMP PEAK 13(XQ28) WILD-TYPE	58	490	196

Figure S73. Get High-res Image Gene #13: 'amp_xq28' versus Clinical Feature #10: 'HISTOLOGICAL_TYPE'

'amp_xq28' versus 'RACE'

P value = 0.116 (Fisher's exact test), Q value = 0.25

Table S74. Gene #13: 'amp_xq28' versus Clinical Feature #13: 'RACE'

nPatients	AMERICAN INDIAN OR ALASKA NATIVE	ASIAN	BLACK OR AFRICAN AMERICAN	WHITE
ALL	2	15	121	719
AMP PEAK 13(XQ28) MUTATED	1	2	25	103
AMP PEAK 13(XQ28) WILD-TYPE	1	13	96	616

Figure S74. Get High-res Image Gene #13: 'amp_xq28' versus Clinical Feature #13: 'RACE'

'del_1p36.31' versus 'YEARS_TO_BIRTH'

P value = 0.0863 (Wilcoxon-test), Q value = 0.2

Table S75. Gene #14: 'del_1p36.31' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

	nPatients	Mean (Std.Dev)
ALL	875	60.1 (12.5)
DEL PEAK 1(1P36.31) MUTATED	208	58.5 (13.6)
DEL PEAK 1(1P36.31) WILD-TYPE	667	60.6 (12.1)

Figure S75. Get High-res Image Gene #14: 'del_1p36.31' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'del_1p36.31' versus 'PATHOLOGIC_STAGE'

P value = 1e-05 (Fisher's exact test), Q value = 8.4e-05

Table S76. Gene #14: 'del_1p36.31' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

nPatients	STAGE I	STAGE II	STAGE III	STAGE IV
ALL	455	104	191	104
DEL PEAK 1(1P36.31) MUTATED	73	38	59	31
DEL PEAK 1(1P36.31) WILD-TYPE	382	66	132	73

Figure S76. Get High-res Image Gene #14: 'del_1p36.31' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

'del_1p36.31' versus 'PATHOLOGY_T_STAGE'

P value = 1e-05 (Fisher's exact test), Q value = 8.4e-05

Table S77. Gene #14: 'del_1p36.31' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

nPatients	T1	T2	T3	T4
ALL	479	127	258	15
DEL PEAK 1(1P36.31) MUTATED	80	47	76	6
DEL PEAK 1(1P36.31) WILD-TYPE	399	80	182	9

Figure S77. Get High-res Image Gene #14: 'del_1p36.31' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

'del_1p36.31' versus 'PATHOLOGY_N_STAGE'

P value = 0.0231 (Fisher's exact test), Q value = 0.069

Table S78. Gene #14: 'del_1p36.31' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

nPatients	N0	N1	N2
ALL	322	44	7
DEL PEAK 1(1P36.31) MUTATED	92	20	4
DEL PEAK 1(1P36.31) WILD-TYPE	230	24	3

Figure S78. Get High-res Image Gene #14: 'del_1p36.31' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

'del_1p36.31' versus 'KARNOFSKY_PERFORMANCE_SCORE'

P value = 0.101 (Wilcoxon-test), Q value = 0.23

Table S79. Gene #14: 'del_1p36.31' versus Clinical Feature #9: 'KARNOFSKY_PERFORMANCE_SCORE'

	nPatients	Mean (Std.Dev)
ALL	142	87.6 (22.8)
DEL PEAK 1(1P36.31) MUTATED	33	80.9 (30.2)
DEL PEAK 1(1P36.31) WILD-TYPE	109	89.6 (19.8)

Figure S79. Get High-res Image Gene #14: 'del_1p36.31' versus Clinical Feature #9: 'KARNOFSKY_PERFORMANCE_SCORE'

'del_1p36.31' versus 'HISTOLOGICAL_TYPE'

P value = 1e-05 (Fisher's exact test), Q value = 8.4e-05

Table S80. Gene #14: 'del_1p36.31' versus Clinical Feature #10: 'HISTOLOGICAL_TYPE'

nPatients	KIDNEY CHROMOPHOBE	KIDNEY CLEAR CELL RENAL CARCINOMA	KIDNEY PAPILLARY RENAL CELL CARCINOMA
ALL	66	528	287
DEL PEAK 1(1P36.31) MUTATED	53	102	54
DEL PEAK 1(1P36.31) WILD-TYPE	13	426	233

Figure S80. Get High-res Image Gene #14: 'del_1p36.31' versus Clinical Feature #10: 'HISTOLOGICAL_TYPE'

'del_1p31.1' versus 'YEARS_TO_BIRTH'

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

Table S81. Gene #15: 'del_1p31.1' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

	nPatients	Mean (Std.Dev)
ALL	875	60.1 (12.5)
DEL PEAK 2(1P31.1) MUTATED	166	58.0 (13.9)
DEL PEAK 2(1P31.1) WILD-TYPE	709	60.6 (12.1)

Figure S81. Get High-res Image Gene #15: 'del_1p31.1' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'del_1p31.1' versus 'PATHOLOGIC_STAGE'

P value = 4e-05 (Fisher's exact test), Q value = 0.00026

Table S82. Gene #15: 'del_1p31.1' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

nPatients	STAGE I	STAGE II	STAGE III	STAGE IV
ALL	455	104	191	104
DEL PEAK 2(1P31.1) MUTATED	60	34	42	24
DEL PEAK 2(1P31.1) WILD-TYPE	395	70	149	80

Figure S82. Get High-res Image Gene #15: 'del_1p31.1' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

'del_1p31.1' versus 'PATHOLOGY_T_STAGE'

P value = 3e-05 (Fisher's exact test), Q value = 0.00022

Table S83. Gene #15: 'del_1p31.1' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

nPatients	T1	T2	T3	T4
ALL	479	127	258	15
DEL PEAK 2(1P31.1) MUTATED	66	40	54	6
DEL PEAK 2(1P31.1) WILD-TYPE	413	87	204	9

Figure S83. Get High-res Image Gene #15: 'del_1p31.1' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

'del_1p31.1' versus 'PATHOLOGY_N_STAGE'

P value = 0.0861 (Fisher's exact test), Q value = 0.2

Table S84. Gene #15: 'del_1p31.1' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

nPatients	N0	N1	N2
ALL	322	44	7
DEL PEAK 2(1P31.1) MUTATED	72	15	3
DEL PEAK 2(1P31.1) WILD-TYPE	250	29	4

Figure S84. Get High-res Image Gene #15: 'del_1p31.1' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

'del_1p31.1' versus 'HISTOLOGICAL_TYPE'

P value = 1e-05 (Fisher's exact test), Q value = 8.4e-05

Table S85. Gene #15: 'del_1p31.1' versus Clinical Feature #10: 'HISTOLOGICAL_TYPE'

nPatients	KIDNEY CHROMOPHOBE	KIDNEY CLEAR CELL RENAL CARCINOMA	KIDNEY PAPILLARY RENAL CELL CARCINOMA
ALL	66	528	287
DEL PEAK 2(1P31.1) MUTATED	53	77	36
DEL PEAK 2(1P31.1) WILD-TYPE	13	451	251

Figure S85. Get High-res Image Gene #15: 'del_1p31.1' versus Clinical Feature #10: 'HISTOLOGICAL_TYPE'

'del_1p31.1' versus 'ETHNICITY'

P value = 0.0888 (Fisher's exact test), Q value = 0.21

Table S86. Gene #15: 'del_1p31.1' versus Clinical Feature #14: 'ETHNICITY'

nPatients	HISPANIC OR LATINO	NOT HISPANIC OR LATINO
ALL	42	621
DEL PEAK 2(1P31.1) MUTATED	11	99
DEL PEAK 2(1P31.1) WILD-TYPE	31	522

Figure S86. Get High-res Image Gene #15: 'del_1p31.1' versus Clinical Feature #14: 'ETHNICITY'

'del_1q43' versus 'Time to Death'

P value = 0.0517 (logrank test), Q value = 0.14

Table S87. Gene #16: 'del_1q43' versus Clinical Feature #1: 'Time to Death'

	nPatients	nDeath	Duration Range (Median), Month
ALL	873	228	0.1 - 194.8 (34.5)
DEL PEAK 3(1Q43) MUTATED	113	27	0.1 - 152.0 (49.6)
DEL PEAK 3(1Q43) WILD-TYPE	760	201	0.1 - 194.8 (32.3)

Figure S87. Get High-res Image Gene #16: 'del_1q43' versus Clinical Feature #1: 'Time to Death'

'del_1q43' versus 'YEARS_TO_BIRTH'

P value = 0.00707 (Wilcoxon-test), Q value = 0.025

Table S88. Gene #16: 'del_1q43' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

	nPatients	Mean (Std.Dev)
ALL	875	60.1 (12.5)
DEL PEAK 3(1Q43) MUTATED	114	56.7 (14.5)
DEL PEAK 3(1Q43) WILD-TYPE	761	60.6 (12.1)

Figure S88. Get High-res Image Gene #16: 'del_1q43' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'del_1q43' versus 'PATHOLOGIC_STAGE'

P value = 5e-04 (Fisher's exact test), Q value = 0.0025

Table S89. Gene #16: 'del_1q43' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

nPatients	STAGE I	STAGE II	STAGE III	STAGE IV
ALL	455	104	191	104
DEL PEAK 3(1Q43) MUTATED	46	28	23	13
DEL PEAK 3(1Q43) WILD-TYPE	409	76	168	91

Figure S89. Get High-res Image Gene #16: 'del_1q43' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

'del_1q43' versus 'PATHOLOGY_T_STAGE'

P value = 0.00091 (Fisher's exact test), Q value = 0.0042

Table S90. Gene #16: 'del_1q43' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

nPatients	T1	T2	T3	T4
ALL	479	127	258	15
DEL PEAK 3(1Q43) MUTATED	48	29	33	4
DEL PEAK 3(1Q43) WILD-TYPE	431	98	225	11

Figure S90. Get High-res Image Gene #16: 'del_1q43' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

'del_1q43' versus 'HISTOLOGICAL_TYPE'

P value = 1e-05 (Fisher's exact test), Q value = 8.4e-05

Table S91. Gene #16: 'del_1q43' versus Clinical Feature #10: 'HISTOLOGICAL_TYPE'

nPatients	KIDNEY CHROMOPHOBE	KIDNEY CLEAR CELL RENAL CARCINOMA	KIDNEY PAPILLARY RENAL CELL CARCINOMA
ALL	66	528	287
DEL PEAK 3(1Q43) MUTATED	51	42	21
DEL PEAK 3(1Q43) WILD-TYPE	15	486	266

Figure S91. Get High-res Image Gene #16: 'del_1q43' versus Clinical Feature #10: 'HISTOLOGICAL_TYPE'

'del_2q37.3' versus 'Time to Death'

P value = 0.029 (logrank test), Q value = 0.084

Table S92. Gene #17: 'del_2q37.3' versus Clinical Feature #1: 'Time to Death'

	nPatients	nDeath	Duration Range (Median), Month
ALL	873	228	0.1 - 194.8 (34.5)
DEL PEAK 4(2Q37.3) MUTATED	109	23	0.4 - 152.0 (44.5)
DEL PEAK 4(2Q37.3) WILD-TYPE	764	205	0.1 - 194.8 (31.8)

Figure S92. Get High-res Image Gene #17: 'del_2q37.3' versus Clinical Feature #1: 'Time to Death'

'del_2q37.3' versus 'YEARS_TO_BIRTH'

P value = 0.00326 (Wilcoxon-test), Q value = 0.013

Table S93. Gene #17: 'del_2q37.3' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

	nPatients	Mean (Std.Dev)
ALL	875	60.1 (12.5)
DEL PEAK 4(2Q37.3) MUTATED	110	56.6 (14.1)
DEL PEAK 4(2Q37.3) WILD-TYPE	765	60.6 (12.2)

Figure S93. Get High-res Image Gene #17: 'del_2q37.3' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'del_2q37.3' versus 'PATHOLOGIC_STAGE'

P value = 1e-05 (Fisher's exact test), Q value = 8.4e-05

Table S94. Gene #17: 'del_2q37.3' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

nPatients	STAGE I	STAGE II	STAGE III	STAGE IV
ALL	455	104	191	104
DEL PEAK 4(2Q37.3) MUTATED	38	32	28	11
DEL PEAK 4(2Q37.3) WILD-TYPE	417	72	163	93

Figure S94. Get High-res Image Gene #17: 'del_2q37.3' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

'del_2q37.3' versus 'PATHOLOGY_T_STAGE'

P value = 1e-05 (Fisher's exact test), Q value = 8.4e-05

Table S95. Gene #17: 'del_2q37.3' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

nPatients	T1	T2	T3	T4
ALL	479	127	258	15
DEL PEAK 4(2Q37.3) MUTATED	39	34	35	3
DEL PEAK 4(2Q37.3) WILD-TYPE	440	93	223	12

Figure S95. Get High-res Image Gene #17: 'del_2q37.3' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

'del_2q37.3' versus 'PATHOLOGY_M_STAGE'

P value = 0.085 (Fisher's exact test), Q value = 0.2

Table S96. Gene #17: 'del_2q37.3' versus Clinical Feature #6: 'PATHOLOGY_M_STAGE'

nPatients	0	1
ALL	545	89
DEL PEAK 4(2Q37.3) MUTATED	75	6
DEL PEAK 4(2Q37.3) WILD-TYPE	470	83

Figure S96. Get High-res Image Gene #17: 'del_2q37.3' versus Clinical Feature #6: 'PATHOLOGY_M_STAGE'

'del_2q37.3' versus 'KARNOFSKY_PERFORMANCE_SCORE'

P value = 0.0153 (Wilcoxon-test), Q value = 0.049

Table S97. Gene #17: 'del_2q37.3' versus Clinical Feature #9: 'KARNOFSKY_PERFORMANCE_SCORE'

	nPatients	Mean (Std.Dev)
ALL	142	87.6 (22.8)
DEL PEAK 4(2Q37.3) MUTATED	11	98.2 (4.0)
DEL PEAK 4(2Q37.3) WILD-TYPE	131	86.7 (23.5)

Figure S97. Get High-res Image Gene #17: 'del_2q37.3' versus Clinical Feature #9: 'KARNOFSKY_PERFORMANCE_SCORE'

'del_2q37.3' versus 'HISTOLOGICAL_TYPE'

P value = 1e-05 (Fisher's exact test), Q value = 8.4e-05

Table S98. Gene #17: 'del_2q37.3' versus Clinical Feature #10: 'HISTOLOGICAL_TYPE'

nPatients	KIDNEY CHROMOPHOBE	KIDNEY CLEAR CELL RENAL CARCINOMA	KIDNEY PAPILLARY RENAL CELL CARCINOMA
ALL	66	528	287
DEL PEAK 4(2Q37.3) MUTATED	49	50	12
DEL PEAK 4(2Q37.3) WILD-TYPE	17	478	275

Figure S98. Get High-res Image Gene #17: 'del_2q37.3' versus Clinical Feature #10: 'HISTOLOGICAL_TYPE'

'del_3p26.3' versus 'Time to Death'

P value = 0.000307 (logrank test), Q value = 0.0016

Table S99. Gene #18: 'del_3p26.3' versus Clinical Feature #1: 'Time to Death'

	nPatients	nDeath	Duration Range (Median), Month
ALL	873	228	0.1 - 194.8 (34.5)
DEL PEAK 5(3P26.3) MUTATED	488	159	0.1 - 149.2 (38.4)
DEL PEAK 5(3P26.3) WILD-TYPE	385	69	0.1 - 194.8 (28.8)

Figure S99. Get High-res Image Gene #18: 'del_3p26.3' versus Clinical Feature #1: 'Time to Death'

'del_3p26.3' versus 'PATHOLOGIC_STAGE'

P value = 2e-05 (Fisher's exact test), Q value = 0.00015

Table S100. Gene #18: 'del_3p26.3' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

nPatients	STAGE I	STAGE II	STAGE III	STAGE IV
ALL	455	104	191	104
DEL PEAK 5(3P26.3) MUTATED	228	57	129	74
DEL PEAK 5(3P26.3) WILD-TYPE	227	47	62	30

Figure S100. Get High-res Image Gene #18: 'del_3p26.3' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

'del_3p26.3' versus 'PATHOLOGY_T_STAGE'

P value = 2e-05 (Fisher's exact test), Q value = 0.00015

Table S101. Gene #18: 'del_3p26.3' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

nPatients	T1	T2	T3	T4
ALL	479	127	258	15
DEL PEAK 5(3P26.3) MUTATED	234	71	177	7
DEL PEAK 5(3P26.3) WILD-TYPE	245	56	81	8

Figure S101. Get High-res Image Gene #18: 'del_3p26.3' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

'del_3p26.3' versus 'PATHOLOGY_N_STAGE'

P value = 0.0131 (Fisher's exact test), Q value = 0.043

Table S102. Gene #18: 'del_3p26.3' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

nPatients	N0	N1	N2
ALL	322	44	7
DEL PEAK 5(3P26.3) MUTATED	214	22	2
DEL PEAK 5(3P26.3) WILD-TYPE	108	22	5

Figure S102. Get High-res Image Gene #18: 'del_3p26.3' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

'del_3p26.3' versus 'PATHOLOGY_M_STAGE'

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

Table S103. Gene #18: 'del_3p26.3' versus Clinical Feature #6: 'PATHOLOGY_M_STAGE'

nPatients	0	1
ALL	545	89
DEL PEAK 5(3P26.3) MUTATED	374	69
DEL PEAK 5(3P26.3) WILD-TYPE	171	20

Figure S103. Get High-res Image Gene #18: 'del_3p26.3' versus Clinical Feature #6: 'PATHOLOGY_M_STAGE'

'del_3p26.3' versus 'GENDER'

P value = 0.0518 (Fisher's exact test), Q value = 0.14

Table S104. Gene #18: 'del_3p26.3' versus Clinical Feature #7: 'GENDER'

nPatients	FEMALE	MALE
ALL	292	589
DEL PEAK 5(3P26.3) MUTATED	176	313
DEL PEAK 5(3P26.3) WILD-TYPE	116	276

Figure S104. Get High-res Image Gene #18: 'del_3p26.3' versus Clinical Feature #7: 'GENDER'

'del_3p26.3' versus 'KARNOFSKY_PERFORMANCE_SCORE'

P value = 0.0801 (Wilcoxon-test), Q value = 0.19

Table S105. Gene #18: 'del_3p26.3' versus Clinical Feature #9: 'KARNOFSKY_PERFORMANCE_SCORE'

	nPatients	Mean (Std.Dev)
ALL	142	87.6 (22.8)
DEL PEAK 5(3P26.3) MUTATED	53	82.1 (29.8)
DEL PEAK 5(3P26.3) WILD-TYPE	89	90.9 (16.8)

Figure S105. Get High-res Image Gene #18: 'del_3p26.3' versus Clinical Feature #9: 'KARNOFSKY_PERFORMANCE_SCORE'

'del_3p26.3' versus 'HISTOLOGICAL_TYPE'

P value = 1e-05 (Fisher's exact test), Q value = 8.4e-05

Table S106. Gene #18: 'del_3p26.3' versus Clinical Feature #10: 'HISTOLOGICAL_TYPE'

nPatients	KIDNEY CHROMOPHOBE	KIDNEY CLEAR CELL RENAL CARCINOMA	KIDNEY PAPILLARY RENAL CELL CARCINOMA
ALL	66	528	287
DEL PEAK 5(3P26.3) MUTATED	10	455	24
DEL PEAK 5(3P26.3) WILD-TYPE	56	73	263

Figure S106. Get High-res Image Gene #18: 'del_3p26.3' versus Clinical Feature #10: 'HISTOLOGICAL_TYPE'

'del_3p26.3' versus 'YEAR_OF_TOBACCO_SMOKING_ONSET'

P value = 0.0787 (Wilcoxon-test), Q value = 0.19

Table S107. Gene #18: 'del_3p26.3' versus Clinical Feature #12: 'YEAR_OF_TOBACCO_SMOKING_ONSET'

	nPatients	Mean (Std.Dev)
ALL	74	1973.7 (16.0)
DEL PEAK 5(3P26.3) MUTATED	19	1979.3 (18.0)
DEL PEAK 5(3P26.3) WILD-TYPE	55	1971.8 (14.9)

Figure S107. Get High-res Image Gene #18: 'del_3p26.3' versus Clinical Feature #12: 'YEAR_OF_TOBACCO_SMOKING_ONSET'

'del_3p26.3' versus 'RACE'

P value = 1e-05 (Fisher's exact test), Q value = 8.4e-05

Table S108. Gene #18: 'del_3p26.3' versus Clinical Feature #13: 'RACE'

nPatients	AMERICAN INDIAN OR ALASKA NATIVE	ASIAN	BLACK OR AFRICAN AMERICAN	WHITE
ALL	2	15	121	719
DEL PEAK 5(3P26.3) MUTATED	0	7	43	430
DEL PEAK 5(3P26.3) WILD-TYPE	2	8	78	289

Figure S108. Get High-res Image Gene #18: 'del_3p26.3' versus Clinical Feature #13: 'RACE'

'del_3p21.2' versus 'Time to Death'

P value = 7.07e-07 (logrank test), Q value = 5.5e-05

Table S109. Gene #19: 'del_3p21.2' versus Clinical Feature #1: 'Time to Death'

	nPatients	nDeath	Duration Range (Median), Month
ALL	873	228	0.1 - 194.8 (34.5)
DEL PEAK 6(3P21.2) MUTATED	502	171	0.1 - 149.2 (37.3)
DEL PEAK 6(3P21.2) WILD-TYPE	371	57	0.1 - 194.8 (29.4)

Figure S109. Get High-res Image Gene #19: 'del_3p21.2' versus Clinical Feature #1: 'Time to Death'

'del_3p21.2' versus 'PATHOLOGIC_STAGE'

P value = 1e-05 (Fisher's exact test), Q value = 8.4e-05

Table S110. Gene #19: 'del_3p21.2' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

nPatients	STAGE I	STAGE II	STAGE III	STAGE IV
ALL	455	104	191	104
DEL PEAK 6(3P21.2) MUTATED	228	57	135	81
DEL PEAK 6(3P21.2) WILD-TYPE	227	47	56	23

Figure S110. Get High-res Image Gene #19: 'del_3p21.2' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

'del_3p21.2' versus 'PATHOLOGY_T_STAGE'

P value = 1e-05 (Fisher's exact test), Q value = 8.4e-05

Table S111. Gene #19: 'del_3p21.2' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

nPatients	T1	T2	T3	T4
ALL	479	127	258	15
DEL PEAK 6(3P21.2) MUTATED	234	72	190	7
DEL PEAK 6(3P21.2) WILD-TYPE	245	55	68	8

Figure S111. Get High-res Image Gene #19: 'del_3p21.2' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

'del_3p21.2' versus 'PATHOLOGY_M_STAGE'

P value = 0.0035 (Fisher's exact test), Q value = 0.013

Table S112. Gene #19: 'del_3p21.2' versus Clinical Feature #6: 'PATHOLOGY_M_STAGE'

nPatients	0	1
ALL	545	89
DEL PEAK 6(3P21.2) MUTATED	379	75
DEL PEAK 6(3P21.2) WILD-TYPE	166	14

Figure S112. Get High-res Image Gene #19: 'del_3p21.2' versus Clinical Feature #6: 'PATHOLOGY_M_STAGE'

'del_3p21.2' versus 'GENDER'

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

Table S113. Gene #19: 'del_3p21.2' versus Clinical Feature #7: 'GENDER'

nPatients	FEMALE	MALE
ALL	292	589
DEL PEAK 6(3P21.2) MUTATED	178	325
DEL PEAK 6(3P21.2) WILD-TYPE	114	264

Figure S113. Get High-res Image Gene #19: 'del_3p21.2' versus Clinical Feature #7: 'GENDER'

'del_3p21.2' versus 'KARNOFSKY_PERFORMANCE_SCORE'

P value = 0.0271 (Wilcoxon-test), Q value = 0.08

Table S114. Gene #19: 'del_3p21.2' versus Clinical Feature #9: 'KARNOFSKY_PERFORMANCE_SCORE'

	nPatients	Mean (Std.Dev)
ALL	142	87.6 (22.8)
DEL PEAK 6(3P21.2) MUTATED	56	80.9 (31.0)
DEL PEAK 6(3P21.2) WILD-TYPE	86	92.0 (13.9)

Figure S114. Get High-res Image Gene #19: 'del_3p21.2' versus Clinical Feature #9: 'KARNOFSKY_PERFORMANCE_SCORE'

'del_3p21.2' versus 'HISTOLOGICAL_TYPE'

P value = 1e-05 (Fisher's exact test), Q value = 8.4e-05

Table S115. Gene #19: 'del_3p21.2' versus Clinical Feature #10: 'HISTOLOGICAL_TYPE'

nPatients	KIDNEY CHROMOPHOBE	KIDNEY CLEAR CELL RENAL CARCINOMA	KIDNEY PAPILLARY RENAL CELL CARCINOMA
ALL	66	528	287
DEL PEAK 6(3P21.2) MUTATED	11	465	27
DEL PEAK 6(3P21.2) WILD-TYPE	55	63	260

Figure S115. Get High-res Image Gene #19: 'del_3p21.2' versus Clinical Feature #10: 'HISTOLOGICAL_TYPE'

'del_3p21.2' versus 'YEAR_OF_TOBACCO_SMOKING_ONSET'

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

Table S116. Gene #19: 'del_3p21.2' versus Clinical Feature #12: 'YEAR_OF_TOBACCO_SMOKING_ONSET'

	nPatients	Mean (Std.Dev)
ALL	74	1973.7 (16.0)
DEL PEAK 6(3P21.2) MUTATED	21	1979.4 (17.0)
DEL PEAK 6(3P21.2) WILD-TYPE	53	1971.5 (15.1)

Figure S116. Get High-res Image Gene #19: 'del_3p21.2' versus Clinical Feature #12: 'YEAR_OF_TOBACCO_SMOKING_ONSET'

'del_3p21.2' versus 'RACE'

P value = 1e-05 (Fisher's exact test), Q value = 8.4e-05

Table S117. Gene #19: 'del_3p21.2' versus Clinical Feature #13: 'RACE'

nPatients	AMERICAN INDIAN OR ALASKA NATIVE	ASIAN	BLACK OR AFRICAN AMERICAN	WHITE
ALL	2	15	121	719
DEL PEAK 6(3P21.2) MUTATED	0	8	43	444
DEL PEAK 6(3P21.2) WILD-TYPE	2	7	78	275

Figure S117. Get High-res Image Gene #19: 'del_3p21.2' versus Clinical Feature #13: 'RACE'

'del_3p14.1' versus 'Time to Death'

P value = 0.000915 (logrank test), Q value = 0.0042

Table S118. Gene #20: 'del_3p14.1' versus Clinical Feature #1: 'Time to Death'

	nPatients	nDeath	Duration Range (Median), Month
ALL	873	228	0.1 - 194.8 (34.5)
DEL PEAK 7(3P14.1) MUTATED	408	136	0.1 - 141.7 (38.5)
DEL PEAK 7(3P14.1) WILD-TYPE	465	92	0.1 - 194.8 (30.4)

Figure S118. Get High-res Image Gene #20: 'del_3p14.1' versus Clinical Feature #1: 'Time to Death'

'del_3p14.1' versus 'PATHOLOGIC_STAGE'

P value = 0.00019 (Fisher's exact test), Q value = 0.001

Table S119. Gene #20: 'del_3p14.1' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

nPatients	STAGE I	STAGE II	STAGE III	STAGE IV
ALL	455	104	191	104
DEL PEAK 7(3P14.1) MUTATED	188	49	111	59
DEL PEAK 7(3P14.1) WILD-TYPE	267	55	80	45

Figure S119. Get High-res Image Gene #20: 'del_3p14.1' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

'del_3p14.1' versus 'PATHOLOGY_T_STAGE'

P value = 4e-05 (Fisher's exact test), Q value = 0.00026

Table S120. Gene #20: 'del_3p14.1' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

nPatients	T1	T2	T3	T4
ALL	479	127	258	15
DEL PEAK 7(3P14.1) MUTATED	192	60	151	5
DEL PEAK 7(3P14.1) WILD-TYPE	287	67	107	10

Figure S120. Get High-res Image Gene #20: 'del_3p14.1' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

'del_3p14.1' versus 'HISTOLOGICAL_TYPE'

P value = 1e-05 (Fisher's exact test), Q value = 8.4e-05

Table S121. Gene #20: 'del_3p14.1' versus Clinical Feature #10: 'HISTOLOGICAL_TYPE'

nPatients	KIDNEY CHROMOPHOBE	KIDNEY CLEAR CELL RENAL CARCINOMA	KIDNEY PAPILLARY RENAL CELL CARCINOMA
ALL	66	528	287
DEL PEAK 7(3P14.1) MUTATED	11	373	24
DEL PEAK 7(3P14.1) WILD-TYPE	55	155	263

Figure S121. Get High-res Image Gene #20: 'del_3p14.1' versus Clinical Feature #10: 'HISTOLOGICAL_TYPE'

'del_3p14.1' versus 'YEAR_OF_TOBACCO_SMOKING_ONSET'

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

Table S122. Gene #20: 'del_3p14.1' versus Clinical Feature #12: 'YEAR_OF_TOBACCO_SMOKING_ONSET'

	nPatients	Mean (Std.Dev)
ALL	74	1973.7 (16.0)
DEL PEAK 7(3P14.1) MUTATED	17	1979.9 (18.1)
DEL PEAK 7(3P14.1) WILD-TYPE	57	1971.9 (15.0)

Figure S122. Get High-res Image Gene #20: 'del_3p14.1' versus Clinical Feature #12: 'YEAR_OF_TOBACCO_SMOKING_ONSET'

'del_3p14.1' versus 'RACE'

P value = 0.00036 (Fisher's exact test), Q value = 0.0018

Table S123. Gene #20: 'del_3p14.1' versus Clinical Feature #13: 'RACE'

nPatients	AMERICAN INDIAN OR ALASKA NATIVE	ASIAN	BLACK OR AFRICAN AMERICAN	WHITE
ALL	2	15	121	719
DEL PEAK 7(3P14.1) MUTATED	0	7	37	357
DEL PEAK 7(3P14.1) WILD-TYPE	2	8	84	362

Figure S123. Get High-res Image Gene #20: 'del_3p14.1' versus Clinical Feature #13: 'RACE'

'del_3p12.2' versus 'Time to Death'

P value = 0.000231 (logrank test), Q value = 0.0012

Table S124. Gene #21: 'del_3p12.2' versus Clinical Feature #1: 'Time to Death'

	nPatients	nDeath	Duration Range (Median), Month
ALL	873	228	0.1 - 194.8 (34.5)
DEL PEAK 8(3P12.2) MUTATED	336	117	0.1 - 141.7 (38.5)
DEL PEAK 8(3P12.2) WILD-TYPE	537	111	0.1 - 194.8 (30.7)

Figure S124. Get High-res Image Gene #21: 'del_3p12.2' versus Clinical Feature #1: 'Time to Death'

'del_3p12.2' versus 'PATHOLOGIC_STAGE'

P value = 0.0106 (Fisher's exact test), Q value = 0.035

Table S125. Gene #21: 'del_3p12.2' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

nPatients	STAGE I	STAGE II	STAGE III	STAGE IV
ALL	455	104	191	104
DEL PEAK 8(3P12.2) MUTATED	156	42	88	49
DEL PEAK 8(3P12.2) WILD-TYPE	299	62	103	55

Figure S125. Get High-res Image Gene #21: 'del_3p12.2' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

'del_3p12.2' versus 'PATHOLOGY_T_STAGE'

P value = 0.00293 (Fisher's exact test), Q value = 0.012

Table S126. Gene #21: 'del_3p12.2' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

nPatients	T1	T2	T3	T4
ALL	479	127	258	15
DEL PEAK 8(3P12.2) MUTATED	160	51	121	4
DEL PEAK 8(3P12.2) WILD-TYPE	319	76	137	11

Figure S126. Get High-res Image Gene #21: 'del_3p12.2' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

'del_3p12.2' versus 'HISTOLOGICAL_TYPE'

P value = 1e-05 (Fisher's exact test), Q value = 8.4e-05

Table S127. Gene #21: 'del_3p12.2' versus Clinical Feature #10: 'HISTOLOGICAL_TYPE'

nPatients	KIDNEY CHROMOPHOBE	KIDNEY CLEAR CELL RENAL CARCINOMA	KIDNEY PAPILLARY RENAL CELL CARCINOMA
ALL	66	528	287
DEL PEAK 8(3P12.2) MUTATED	11	305	20
DEL PEAK 8(3P12.2) WILD-TYPE	55	223	267

Figure S127. Get High-res Image Gene #21: 'del_3p12.2' versus Clinical Feature #10: 'HISTOLOGICAL_TYPE'

'del_3p12.2' versus 'YEAR_OF_TOBACCO_SMOKING_ONSET'

P value = 0.0829 (Wilcoxon-test), Q value = 0.2

Table S128. Gene #21: 'del_3p12.2' versus Clinical Feature #12: 'YEAR_OF_TOBACCO_SMOKING_ONSET'

	nPatients	Mean (Std.Dev)
ALL	74	1973.7 (16.0)
DEL PEAK 8(3P12.2) MUTATED	13	1980.2 (17.0)
DEL PEAK 8(3P12.2) WILD-TYPE	61	1972.3 (15.6)

Figure S128. Get High-res Image Gene #21: 'del_3p12.2' versus Clinical Feature #12: 'YEAR_OF_TOBACCO_SMOKING_ONSET'

'del_3p12.2' versus 'RACE'

P value = 0.00585 (Fisher's exact test), Q value = 0.021

Table S129. Gene #21: 'del_3p12.2' versus Clinical Feature #13: 'RACE'

nPatients	AMERICAN INDIAN OR ALASKA NATIVE	ASIAN	BLACK OR AFRICAN AMERICAN	WHITE
ALL	2	15	121	719
DEL PEAK 8(3P12.2) MUTATED	0	6	31	293
DEL PEAK 8(3P12.2) WILD-TYPE	2	9	90	426

Figure S129. Get High-res Image Gene #21: 'del_3p12.2' versus Clinical Feature #13: 'RACE'

'del_4q34.3' versus 'Time to Death'

P value = 1.3e-10 (logrank test), Q value = 1.8e-08

Table S130. Gene #22: 'del_4q34.3' versus Clinical Feature #1: 'Time to Death'

	nPatients	nDeath	Duration Range (Median), Month
ALL	873	228	0.1 - 194.8 (34.5)
DEL PEAK 9(4Q34.3) MUTATED	112	55	0.4 - 133.7 (30.3)
DEL PEAK 9(4Q34.3) WILD-TYPE	761	173	0.1 - 194.8 (35.9)

Figure S130. Get High-res Image Gene #22: 'del_4q34.3' versus Clinical Feature #1: 'Time to Death'

'del_4q34.3' versus 'PATHOLOGIC_STAGE'

P value = 1e-05 (Fisher's exact test), Q value = 8.4e-05

Table S131. Gene #22: 'del_4q34.3' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

nPatients	STAGE I	STAGE II	STAGE III	STAGE IV
ALL	455	104	191	104
DEL PEAK 9(4Q34.3) MUTATED	26	10	48	26
DEL PEAK 9(4Q34.3) WILD-TYPE	429	94	143	78

Figure S131. Get High-res Image Gene #22: 'del_4q34.3' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

'del_4q34.3' versus 'PATHOLOGY_T_STAGE'

P value = 1e-05 (Fisher's exact test), Q value = 8.4e-05

Table S132. Gene #22: 'del_4q34.3' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

nPatients	T1	T2	T3	T4
ALL	479	127	258	15
DEL PEAK 9(4Q34.3) MUTATED	29	15	62	7
DEL PEAK 9(4Q34.3) WILD-TYPE	450	112	196	8

Figure S132. Get High-res Image Gene #22: 'del_4q34.3' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

'del_4q34.3' versus 'PATHOLOGY_N_STAGE'

P value = 0.00173 (Fisher's exact test), Q value = 0.0073

Table S133. Gene #22: 'del_4q34.3' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

nPatients	N0	N1	N2
ALL	322	44	7
DEL PEAK 9(4Q34.3) MUTATED	40	15	1
DEL PEAK 9(4Q34.3) WILD-TYPE	282	29	6

Figure S133. Get High-res Image Gene #22: 'del_4q34.3' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

'del_4q34.3' versus 'PATHOLOGY_M_STAGE'

P value = 0.014 (Fisher's exact test), Q value = 0.045

Table S134. Gene #22: 'del_4q34.3' versus Clinical Feature #6: 'PATHOLOGY_M_STAGE'

nPatients	0	1
ALL	545	89
DEL PEAK 9(4Q34.3) MUTATED	71	21
DEL PEAK 9(4Q34.3) WILD-TYPE	474	68

Figure S134. Get High-res Image Gene #22: 'del_4q34.3' versus Clinical Feature #6: 'PATHOLOGY_M_STAGE'

'del_4q34.3' versus 'HISTOLOGICAL_TYPE'

P value = 0.0332 (Fisher's exact test), Q value = 0.095

Table S135. Gene #22: 'del_4q34.3' versus Clinical Feature #10: 'HISTOLOGICAL_TYPE'

nPatients	KIDNEY CHROMOPHOBE	KIDNEY CLEAR CELL RENAL CARCINOMA	KIDNEY PAPILLARY RENAL CELL CARCINOMA
ALL	66	528	287
DEL PEAK 9(4Q34.3) MUTATED	3	78	32
DEL PEAK 9(4Q34.3) WILD-TYPE	63	450	255

Figure S135. Get High-res Image Gene #22: 'del_4q34.3' versus Clinical Feature #10: 'HISTOLOGICAL_TYPE'

'del_4q34.3' versus 'RACE'

P value = 0.0496 (Fisher's exact test), Q value = 0.13

Table S136. Gene #22: 'del_4q34.3' versus Clinical Feature #13: 'RACE'

nPatients	AMERICAN INDIAN OR ALASKA NATIVE	ASIAN	BLACK OR AFRICAN AMERICAN	WHITE
ALL	2	15	121	719
DEL PEAK 9(4Q34.3) MUTATED	0	4	8	95
DEL PEAK 9(4Q34.3) WILD-TYPE	2	11	113	624

Figure S136. Get High-res Image Gene #22: 'del_4q34.3' versus Clinical Feature #13: 'RACE'

'del_5p15.33' versus 'YEARS_TO_BIRTH'

P value = 0.00433 (Wilcoxon-test), Q value = 0.016

Table S137. Gene #23: 'del_5p15.33' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

	nPatients	Mean (Std.Dev)
ALL	875	60.1 (12.5)
DEL PEAK 10(5P15.33) MUTATED	30	52.4 (14.6)
DEL PEAK 10(5P15.33) WILD-TYPE	845	60.4 (12.4)

Figure S137. Get High-res Image Gene #23: 'del_5p15.33' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'del_5p15.33' versus 'PATHOLOGIC_STAGE'

P value = 0.00143 (Fisher's exact test), Q value = 0.0062

Table S138. Gene #23: 'del_5p15.33' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

nPatients	STAGE I	STAGE II	STAGE III	STAGE IV
ALL	455	104	191	104
DEL PEAK 10(5P15.33) MUTATED	7	9	9	5
DEL PEAK 10(5P15.33) WILD-TYPE	448	95	182	99

Figure S138. Get High-res Image Gene #23: 'del_5p15.33' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

'del_5p15.33' versus 'PATHOLOGY_T_STAGE'

P value = 0.00062 (Fisher's exact test), Q value = 0.003

Table S139. Gene #23: 'del_5p15.33' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

nPatients	T1	T2	T3	T4
ALL	479	127	258	15
DEL PEAK 10(5P15.33) MUTATED	7	11	13	0
DEL PEAK 10(5P15.33) WILD-TYPE	472	116	245	15

Figure S139. Get High-res Image Gene #23: 'del_5p15.33' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

'del_5p15.33' versus 'PATHOLOGY_N_STAGE'

P value = 0.00814 (Fisher's exact test), Q value = 0.028

Table S140. Gene #23: 'del_5p15.33' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

nPatients	N0	N1	N2
ALL	322	44	7
DEL PEAK 10(5P15.33) MUTATED	13	5	2
DEL PEAK 10(5P15.33) WILD-TYPE	309	39	5

Figure S140. Get High-res Image Gene #23: 'del_5p15.33' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

'del_5p15.33' versus 'KARNOFSKY_PERFORMANCE_SCORE'

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

Table S141. Gene #23: 'del_5p15.33' versus Clinical Feature #9: 'KARNOFSKY_PERFORMANCE_SCORE'

	nPatients	Mean (Std.Dev)
ALL	142	87.6 (22.8)
DEL PEAK 10(5P15.33) MUTATED	6	70.0 (38.5)
DEL PEAK 10(5P15.33) WILD-TYPE	136	88.4 (21.8)

Figure S141. Get High-res Image Gene #23: 'del_5p15.33' versus Clinical Feature #9: 'KARNOFSKY_PERFORMANCE_SCORE'

'del_5p15.33' versus 'HISTOLOGICAL_TYPE'

P value = 1e-05 (Fisher's exact test), Q value = 8.4e-05

Table S142. Gene #23: 'del_5p15.33' versus Clinical Feature #10: 'HISTOLOGICAL_TYPE'

nPatients	KIDNEY CHROMOPHOBE	KIDNEY CLEAR CELL RENAL CARCINOMA	KIDNEY PAPILLARY RENAL CELL CARCINOMA
ALL	66	528	287
DEL PEAK 10(5P15.33) MUTATED	10	8	13
DEL PEAK 10(5P15.33) WILD-TYPE	56	520	274

Figure S142. Get High-res Image Gene #23: 'del_5p15.33' versus Clinical Feature #10: 'HISTOLOGICAL_TYPE'

'del_6q22.31' versus 'PATHOLOGIC_STAGE'

P value = 9e-05 (Fisher's exact test), Q value = 0.00052

Table S143. Gene #24: 'del_6q22.31' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

nPatients	STAGE I	STAGE II	STAGE III	STAGE IV
ALL	455	104	191	104
DEL PEAK 11(6Q22.31) MUTATED	93	41	55	36
DEL PEAK 11(6Q22.31) WILD-TYPE	362	63	136	68

Figure S143. Get High-res Image Gene #24: 'del_6q22.31' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

'del_6q22.31' versus 'PATHOLOGY_T_STAGE'

P value = 4e-05 (Fisher's exact test), Q value = 0.00026

Table S144. Gene #24: 'del_6q22.31' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

nPatients	T1	T2	T3	T4
ALL	479	127	258	15
DEL PEAK 11(6Q22.31) MUTATED	95	44	81	7
DEL PEAK 11(6Q22.31) WILD-TYPE	384	83	177	8

Figure S144. Get High-res Image Gene #24: 'del_6q22.31' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

'del_6q22.31' versus 'PATHOLOGY_N_STAGE'

P value = 0.115 (Fisher's exact test), Q value = 0.25

Table S145. Gene #24: 'del_6q22.31' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

nPatients	N0	N1	N2
ALL	322	44	7
DEL PEAK 11(6Q22.31) MUTATED	89	16	4
DEL PEAK 11(6Q22.31) WILD-TYPE	233	28	3

Figure S145. Get High-res Image Gene #24: 'del_6q22.31' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

'del_6q22.31' versus 'HISTOLOGICAL_TYPE'

P value = 1e-05 (Fisher's exact test), Q value = 8.4e-05

Table S146. Gene #24: 'del_6q22.31' versus Clinical Feature #10: 'HISTOLOGICAL_TYPE'

nPatients	KIDNEY CHROMOPHOBE	KIDNEY CLEAR CELL RENAL CARCINOMA	KIDNEY PAPILLARY RENAL CELL CARCINOMA
ALL	66	528	287
DEL PEAK 11(6Q22.31) MUTATED	51	147	29
DEL PEAK 11(6Q22.31) WILD-TYPE	15	381	258

Figure S146. Get High-res Image Gene #24: 'del_6q22.31' versus Clinical Feature #10: 'HISTOLOGICAL_TYPE'

'del_6q22.31' versus 'NUMBER_PACK_YEARS_SMOKED'

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

Table S147. Gene #24: 'del_6q22.31' versus Clinical Feature #11: 'NUMBER_PACK_YEARS_SMOKED'

	nPatients	Mean (Std.Dev)
ALL	106	30.8 (24.9)
DEL PEAK 11(6Q22.31) MUTATED	23	25.0 (20.0)
DEL PEAK 11(6Q22.31) WILD-TYPE	83	32.4 (25.9)

Figure S147. Get High-res Image Gene #24: 'del_6q22.31' versus Clinical Feature #11: 'NUMBER_PACK_YEARS_SMOKED'

'del_6q22.31' versus 'RACE'

P value = 0.00129 (Fisher's exact test), Q value = 0.0057

Table S148. Gene #24: 'del_6q22.31' versus Clinical Feature #13: 'RACE'

nPatients	AMERICAN INDIAN OR ALASKA NATIVE	ASIAN	BLACK OR AFRICAN AMERICAN	WHITE
ALL	2	15	121	719
DEL PEAK 11(6Q22.31) MUTATED	0	6	16	197
DEL PEAK 11(6Q22.31) WILD-TYPE	2	9	105	522

Figure S148. Get High-res Image Gene #24: 'del_6q22.31' versus Clinical Feature #13: 'RACE'

'del_6q26' versus 'PATHOLOGIC_STAGE'

P value = 3e-05 (Fisher's exact test), Q value = 0.00022

Table S149. Gene #25: 'del_6q26' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

nPatients	STAGE I	STAGE II	STAGE III	STAGE IV
ALL	455	104	191	104
DEL PEAK 12(6Q26) MUTATED	94	43	58	35
DEL PEAK 12(6Q26) WILD-TYPE	361	61	133	69

Figure S149. Get High-res Image Gene #25: 'del_6q26' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

'del_6q26' versus 'PATHOLOGY_T_STAGE'

P value = 4e-05 (Fisher's exact test), Q value = 0.00026

Table S150. Gene #25: 'del_6q26' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

nPatients	T1	T2	T3	T4
ALL	479	127	258	15
DEL PEAK 12(6Q26) MUTATED	96	46	85	6
DEL PEAK 12(6Q26) WILD-TYPE	383	81	173	9

Figure S150. Get High-res Image Gene #25: 'del_6q26' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

'del_6q26' versus 'PATHOLOGY_N_STAGE'

P value = 0.04 (Fisher's exact test), Q value = 0.11

Table S151. Gene #25: 'del_6q26' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

nPatients	N0	N1	N2
ALL	322	44	7
DEL PEAK 12(6Q26) MUTATED	94	16	5
DEL PEAK 12(6Q26) WILD-TYPE	228	28	2

Figure S151. Get High-res Image Gene #25: 'del_6q26' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

'del_6q26' versus 'HISTOLOGICAL_TYPE'

P value = 1e-05 (Fisher's exact test), Q value = 8.4e-05

Table S152. Gene #25: 'del_6q26' versus Clinical Feature #10: 'HISTOLOGICAL_TYPE'

nPatients	KIDNEY CHROMOPHOBE	KIDNEY CLEAR CELL RENAL CARCINOMA	KIDNEY PAPILLARY RENAL CELL CARCINOMA
ALL	66	528	287
DEL PEAK 12(6Q26) MUTATED	51	151	31
DEL PEAK 12(6Q26) WILD-TYPE	15	377	256

Figure S152. Get High-res Image Gene #25: 'del_6q26' versus Clinical Feature #10: 'HISTOLOGICAL_TYPE'

'del_6q26' versus 'NUMBER_PACK_YEARS_SMOKED'

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

Table S153. Gene #25: 'del_6q26' versus Clinical Feature #11: 'NUMBER_PACK_YEARS_SMOKED'

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

Figure S153. Get High-res Image Gene #25: 'del_6q26' versus Clinical Feature #11: 'NUMBER_PACK_YEARS_SMOKED'

'del_6q26' versus 'RACE'

P value = 0.00086 (Fisher's exact test), Q value = 0.004

Table S154. Gene #25: 'del_6q26' versus Clinical Feature #13: 'RACE'

nPatients	AMERICAN INDIAN OR ALASKA NATIVE	ASIAN	BLACK OR AFRICAN AMERICAN	WHITE
ALL	2	15	121	719
DEL PEAK 12(6Q26) MUTATED	0	6	16	203
DEL PEAK 12(6Q26) WILD-TYPE	2	9	105	516

Figure S154. Get High-res Image Gene #25: 'del_6q26' versus Clinical Feature #13: 'RACE'

'del_6q26' versus 'PATHOLOGIC_STAGE'

P value = 4e-05 (Fisher's exact test), Q value = 0.00026

Table S155. Gene #26: 'del_6q26' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

nPatients	STAGE I	STAGE II	STAGE III	STAGE IV
ALL	455	104	191	104
DEL PEAK 13(6Q26) MUTATED	95	43	58	35
DEL PEAK 13(6Q26) WILD-TYPE	360	61	133	69

Figure S155. Get High-res Image Gene #26: 'del_6q26' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

'del_6q26' versus 'PATHOLOGY_T_STAGE'

P value = 4e-05 (Fisher's exact test), Q value = 0.00026

Table S156. Gene #26: 'del_6q26' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

nPatients	T1	T2	T3	T4
ALL	479	127	258	15
DEL PEAK 13(6Q26) MUTATED	97	46	85	6
DEL PEAK 13(6Q26) WILD-TYPE	382	81	173	9

Figure S156. Get High-res Image Gene #26: 'del_6q26' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

'del_6q26' versus 'PATHOLOGY_N_STAGE'

P value = 0.0395 (Fisher's exact test), Q value = 0.11

Table S157. Gene #26: 'del_6q26' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

nPatients	N0	N1	N2
ALL	322	44	7
DEL PEAK 13(6Q26) MUTATED	94	16	5
DEL PEAK 13(6Q26) WILD-TYPE	228	28	2

Figure S157. Get High-res Image Gene #26: 'del_6q26' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

'del_6q26' versus 'HISTOLOGICAL_TYPE'

P value = 1e-05 (Fisher's exact test), Q value = 8.4e-05

Table S158. Gene #26: 'del_6q26' versus Clinical Feature #10: 'HISTOLOGICAL_TYPE'

nPatients	KIDNEY CHROMOPHOBE	KIDNEY CLEAR CELL RENAL CARCINOMA	KIDNEY PAPILLARY RENAL CELL CARCINOMA
ALL	66	528	287
DEL PEAK 13(6Q26) MUTATED	51	151	32
DEL PEAK 13(6Q26) WILD-TYPE	15	377	255

Figure S158. Get High-res Image Gene #26: 'del_6q26' versus Clinical Feature #10: 'HISTOLOGICAL_TYPE'

'del_6q26' versus 'NUMBER_PACK_YEARS_SMOKED'

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

Table S159. Gene #26: 'del_6q26' versus Clinical Feature #11: 'NUMBER_PACK_YEARS_SMOKED'

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

Figure S159. Get High-res Image Gene #26: 'del_6q26' versus Clinical Feature #11: 'NUMBER_PACK_YEARS_SMOKED'

'del_6q26' versus 'RACE'

P value = 0.00186 (Fisher's exact test), Q value = 0.0078

Table S160. Gene #26: 'del_6q26' versus Clinical Feature #13: 'RACE'

nPatients	AMERICAN INDIAN OR ALASKA NATIVE	ASIAN	BLACK OR AFRICAN AMERICAN	WHITE
ALL	2	15	121	719
DEL PEAK 13(6Q26) MUTATED	0	6	17	203
DEL PEAK 13(6Q26) WILD-TYPE	2	9	104	516

Figure S160. Get High-res Image Gene #26: 'del_6q26' versus Clinical Feature #13: 'RACE'

'del_8p23.2' versus 'Time to Death'

P value = 0.000367 (logrank test), Q value = 0.0019

Table S161. Gene #27: 'del_8p23.2' versus Clinical Feature #1: 'Time to Death'

	nPatients	nDeath	Duration Range (Median), Month
ALL	873	228	0.1 - 194.8 (34.5)
DEL PEAK 14(8P23.2) MUTATED	184	69	0.1 - 137.1 (36.9)
DEL PEAK 14(8P23.2) WILD-TYPE	689	159	0.1 - 194.8 (34.0)

Figure S161. Get High-res Image Gene #27: 'del_8p23.2' versus Clinical Feature #1: 'Time to Death'

'del_8p23.2' versus 'PATHOLOGIC_STAGE'

P value = 0.00173 (Fisher's exact test), Q value = 0.0073

Table S162. Gene #27: 'del_8p23.2' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

nPatients	STAGE I	STAGE II	STAGE III	STAGE IV
ALL	455	104	191	104
DEL PEAK 14(8P23.2) MUTATED	75	25	47	33
DEL PEAK 14(8P23.2) WILD-TYPE	380	79	144	71

Figure S162. Get High-res Image Gene #27: 'del_8p23.2' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

'del_8p23.2' versus 'PATHOLOGY_T_STAGE'

P value = 0.00113 (Fisher's exact test), Q value = 0.0051

Table S163. Gene #27: 'del_8p23.2' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

nPatients	T1	T2	T3	T4
ALL	479	127	258	15
DEL PEAK 14(8P23.2) MUTATED	78	31	69	6
DEL PEAK 14(8P23.2) WILD-TYPE	401	96	189	9

Figure S163. Get High-res Image Gene #27: 'del_8p23.2' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

'del_8p23.2' versus 'PATHOLOGY_M_STAGE'

P value = 0.0255 (Fisher's exact test), Q value = 0.076

Table S164. Gene #27: 'del_8p23.2' versus Clinical Feature #6: 'PATHOLOGY_M_STAGE'

nPatients	0	1
ALL	545	89
DEL PEAK 14(8P23.2) MUTATED	131	32
DEL PEAK 14(8P23.2) WILD-TYPE	414	57

Figure S164. Get High-res Image Gene #27: 'del_8p23.2' versus Clinical Feature #6: 'PATHOLOGY_M_STAGE'

'del_8p23.2' versus 'HISTOLOGICAL_TYPE'

P value = 1e-05 (Fisher's exact test), Q value = 8.4e-05

Table S165. Gene #27: 'del_8p23.2' versus Clinical Feature #10: 'HISTOLOGICAL_TYPE'

nPatients	KIDNEY CHROMOPHOBE	KIDNEY CLEAR CELL RENAL CARCINOMA	KIDNEY PAPILLARY RENAL CELL CARCINOMA
ALL	66	528	287
DEL PEAK 14(8P23.2) MUTATED	12	154	18
DEL PEAK 14(8P23.2) WILD-TYPE	54	374	269

Figure S165. Get High-res Image Gene #27: 'del_8p23.2' versus Clinical Feature #10: 'HISTOLOGICAL_TYPE'

'del_8p23.2' versus 'RACE'

P value = 0.00224 (Fisher's exact test), Q value = 0.0092

Table S166. Gene #27: 'del_8p23.2' versus Clinical Feature #13: 'RACE'

nPatients	AMERICAN INDIAN OR ALASKA NATIVE	ASIAN	BLACK OR AFRICAN AMERICAN	WHITE
ALL	2	15	121	719
DEL PEAK 14(8P23.2) MUTATED	0	7	14	160
DEL PEAK 14(8P23.2) WILD-TYPE	2	8	107	559

Figure S166. Get High-res Image Gene #27: 'del_8p23.2' versus Clinical Feature #13: 'RACE'

'del_9p23' versus 'Time to Death'

P value = 3.98e-13 (logrank test), Q value = 1.1e-10

Table S167. Gene #28: 'del_9p23' versus Clinical Feature #1: 'Time to Death'

	nPatients	nDeath	Duration Range (Median), Month
ALL	873	228	0.1 - 194.8 (34.5)
DEL PEAK 15(9P23) MUTATED	195	92	0.5 - 141.7 (33.5)
DEL PEAK 15(9P23) WILD-TYPE	678	136	0.1 - 194.8 (34.7)

Figure S167. Get High-res Image Gene #28: 'del_9p23' versus Clinical Feature #1: 'Time to Death'

'del_9p23' versus 'YEARS_TO_BIRTH'

P value = 0.0277 (Wilcoxon-test), Q value = 0.081

Table S168. Gene #28: 'del_9p23' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

	nPatients	Mean (Std.Dev)
ALL	875	60.1 (12.5)
DEL PEAK 15(9P23) MUTATED	196	61.8 (12.0)
DEL PEAK 15(9P23) WILD-TYPE	679	59.7 (12.6)

Figure S168. Get High-res Image Gene #28: 'del_9p23' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'del_9p23' versus 'PATHOLOGIC_STAGE'

P value = 1e-05 (Fisher's exact test), Q value = 8.4e-05

Table S169. Gene #28: 'del_9p23' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

nPatients	STAGE I	STAGE II	STAGE III	STAGE IV
ALL	455	104	191	104
DEL PEAK 15(9P23) MUTATED	64	16	69	46
DEL PEAK 15(9P23) WILD-TYPE	391	88	122	58

Figure S169. Get High-res Image Gene #28: 'del_9p23' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

'del_9p23' versus 'PATHOLOGY_T_STAGE'

P value = 1e-05 (Fisher's exact test), Q value = 8.4e-05

Table S170. Gene #28: 'del_9p23' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

nPatients	T1	T2	T3	T4
ALL	479	127	258	15
DEL PEAK 15(9P23) MUTATED	68	23	100	7
DEL PEAK 15(9P23) WILD-TYPE	411	104	158	8

Figure S170. Get High-res Image Gene #28: 'del_9p23' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

'del_9p23' versus 'PATHOLOGY_N_STAGE'

P value = 0.0035 (Fisher's exact test), Q value = 0.013

Table S171. Gene #28: 'del_9p23' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

nPatients	N0	N1	N2
ALL	322	44	7
DEL PEAK 15(9P23) MUTATED	73	20	3
DEL PEAK 15(9P23) WILD-TYPE	249	24	4

Figure S171. Get High-res Image Gene #28: 'del_9p23' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

'del_9p23' versus 'PATHOLOGY_M_STAGE'

P value = 0.000214 (Fisher's exact test), Q value = 0.0011

Table S172. Gene #28: 'del_9p23' versus Clinical Feature #6: 'PATHOLOGY_M_STAGE'

nPatients	0	1
ALL	545	89
DEL PEAK 15(9P23) MUTATED	126	38
DEL PEAK 15(9P23) WILD-TYPE	419	51

Figure S172. Get High-res Image Gene #28: 'del_9p23' versus Clinical Feature #6: 'PATHOLOGY_M_STAGE'

'del_9p23' versus 'KARNOFSKY_PERFORMANCE_SCORE'

P value = 0.000649 (Wilcoxon-test), Q value = 0.0031

Table S173. Gene #28: 'del_9p23' versus Clinical Feature #9: 'KARNOFSKY_PERFORMANCE_SCORE'

	nPatients	Mean (Std.Dev)
ALL	142	87.6 (22.8)
DEL PEAK 15(9P23) MUTATED	29	74.1 (34.3)
DEL PEAK 15(9P23) WILD-TYPE	113	91.1 (17.4)

Figure S173. Get High-res Image Gene #28: 'del_9p23' versus Clinical Feature #9: 'KARNOFSKY_PERFORMANCE_SCORE'

'del_9p23' versus 'HISTOLOGICAL_TYPE'

P value = 1e-05 (Fisher's exact test), Q value = 8.4e-05

Table S174. Gene #28: 'del_9p23' versus Clinical Feature #10: 'HISTOLOGICAL_TYPE'

nPatients	KIDNEY CHROMOPHOBE	KIDNEY CLEAR CELL RENAL CARCINOMA	KIDNEY PAPILLARY RENAL CELL CARCINOMA
ALL	66	528	287
DEL PEAK 15(9P23) MUTATED	10	152	36
DEL PEAK 15(9P23) WILD-TYPE	56	376	251

Figure S174. Get High-res Image Gene #28: 'del_9p23' versus Clinical Feature #10: 'HISTOLOGICAL_TYPE'

'del_9p23' versus 'RACE'

P value = 0.0174 (Fisher's exact test), Q value = 0.054

Table S175. Gene #28: 'del_9p23' versus Clinical Feature #13: 'RACE'

nPatients	AMERICAN INDIAN OR ALASKA NATIVE	ASIAN	BLACK OR AFRICAN AMERICAN	WHITE
ALL	2	15	121	719
DEL PEAK 15(9P23) MUTATED	0	4	15	173
DEL PEAK 15(9P23) WILD-TYPE	2	11	106	546

Figure S175. Get High-res Image Gene #28: 'del_9p23' versus Clinical Feature #13: 'RACE'

'del_9p21.3' versus 'Time to Death'

P value = 3.33e-16 (logrank test), Q value = 1.8e-13

Table S176. Gene #29: 'del_9p21.3' versus Clinical Feature #1: 'Time to Death'

	nPatients	nDeath	Duration Range (Median), Month
ALL	873	228	0.1 - 194.8 (34.5)
DEL PEAK 16(9P21.3) MUTATED	204	99	0.5 - 141.7 (31.7)
DEL PEAK 16(9P21.3) WILD-TYPE	669	129	0.1 - 194.8 (35.9)

Figure S176. Get High-res Image Gene #29: 'del_9p21.3' versus Clinical Feature #1: 'Time to Death'

'del_9p21.3' versus 'YEARS_TO_BIRTH'

P value = 0.0382 (Wilcoxon-test), Q value = 0.11

Table S177. Gene #29: 'del_9p21.3' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

	nPatients	Mean (Std.Dev)
ALL	875	60.1 (12.5)
DEL PEAK 16(9P21.3) MUTATED	206	61.6 (12.2)
DEL PEAK 16(9P21.3) WILD-TYPE	669	59.7 (12.6)

Figure S177. Get High-res Image Gene #29: 'del_9p21.3' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'del_9p21.3' versus 'PATHOLOGIC_STAGE'

P value = 1e-05 (Fisher's exact test), Q value = 8.4e-05

Table S178. Gene #29: 'del_9p21.3' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

nPatients	STAGE I	STAGE II	STAGE III	STAGE IV
ALL	455	104	191	104
DEL PEAK 16(9P21.3) MUTATED	66	15	74	50
DEL PEAK 16(9P21.3) WILD-TYPE	389	89	117	54

Figure S178. Get High-res Image Gene #29: 'del_9p21.3' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

'del_9p21.3' versus 'PATHOLOGY_T_STAGE'

P value = 1e-05 (Fisher's exact test), Q value = 8.4e-05

Table S179. Gene #29: 'del_9p21.3' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

nPatients	T1	T2	T3	T4
ALL	479	127	258	15
DEL PEAK 16(9P21.3) MUTATED	70	22	108	8
DEL PEAK 16(9P21.3) WILD-TYPE	409	105	150	7

Figure S179. Get High-res Image Gene #29: 'del_9p21.3' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

'del_9p21.3' versus 'PATHOLOGY_N_STAGE'

P value = 4e-05 (Fisher's exact test), Q value = 0.00026

Table S180. Gene #29: 'del_9p21.3' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

nPatients	N0	N1	N2
ALL	322	44	7
DEL PEAK 16(9P21.3) MUTATED	78	25	3
DEL PEAK 16(9P21.3) WILD-TYPE	244	19	4

Figure S180. Get High-res Image Gene #29: 'del_9p21.3' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

'del_9p21.3' versus 'PATHOLOGY_M_STAGE'

P value = 5.47e-06 (Fisher's exact test), Q value = 8.4e-05

Table S181. Gene #29: 'del_9p21.3' versus Clinical Feature #6: 'PATHOLOGY_M_STAGE'

nPatients	0	1
ALL	545	89
DEL PEAK 16(9P21.3) MUTATED	131	43
DEL PEAK 16(9P21.3) WILD-TYPE	414	46

Figure S181. Get High-res Image Gene #29: 'del_9p21.3' versus Clinical Feature #6: 'PATHOLOGY_M_STAGE'

'del_9p21.3' versus 'KARNOFSKY_PERFORMANCE_SCORE'

P value = 0.00153 (Wilcoxon-test), Q value = 0.0066

Table S182. Gene #29: 'del_9p21.3' versus Clinical Feature #9: 'KARNOFSKY_PERFORMANCE_SCORE'

	nPatients	Mean (Std.Dev)
ALL	142	87.6 (22.8)
DEL PEAK 16(9P21.3) MUTATED	30	75.0 (34.0)
DEL PEAK 16(9P21.3) WILD-TYPE	112	91.0 (17.4)

Figure S182. Get High-res Image Gene #29: 'del_9p21.3' versus Clinical Feature #9: 'KARNOFSKY_PERFORMANCE_SCORE'

'del_9p21.3' versus 'HISTOLOGICAL_TYPE'

P value = 1e-05 (Fisher's exact test), Q value = 8.4e-05

Table S183. Gene #29: 'del_9p21.3' versus Clinical Feature #10: 'HISTOLOGICAL_TYPE'

nPatients	KIDNEY CHROMOPHOBE	KIDNEY CLEAR CELL RENAL CARCINOMA	KIDNEY PAPILLARY RENAL CELL CARCINOMA
ALL	66	528	287
DEL PEAK 16(9P21.3) MUTATED	10	159	39
DEL PEAK 16(9P21.3) WILD-TYPE	56	369	248

Figure S183. Get High-res Image Gene #29: 'del_9p21.3' versus Clinical Feature #10: 'HISTOLOGICAL_TYPE'

'del_9p21.3' versus 'RACE'

P value = 0.00624 (Fisher's exact test), Q value = 0.022

Table S184. Gene #29: 'del_9p21.3' versus Clinical Feature #13: 'RACE'

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

Figure S184. Get High-res Image Gene #29: 'del_9p21.3' versus Clinical Feature #13: 'RACE'

'del_10q23.31' versus 'YEARS_TO_BIRTH'

P value = 0.0762 (Wilcoxon-test), Q value = 0.19

Table S185. Gene #30: 'del_10q23.31' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

	nPatients	Mean (Std.Dev)
ALL	875	60.1 (12.5)
DEL PEAK 17(10Q23.31) MUTATED	162	58.3 (14.1)
DEL PEAK 17(10Q23.31) WILD-TYPE	713	60.5 (12.1)

Figure S185. Get High-res Image Gene #30: 'del_10q23.31' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'del_10q23.31' versus 'PATHOLOGIC_STAGE'

P value = 1e-05 (Fisher's exact test), Q value = 8.4e-05

Table S186. Gene #30: 'del_10q23.31' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

nPatients	STAGE I	STAGE II	STAGE III	STAGE IV
ALL	455	104	191	104
DEL PEAK 17(10Q23.31) MUTATED	52	32	53	26
DEL PEAK 17(10Q23.31) WILD-TYPE	403	72	138	78

Figure S186. Get High-res Image Gene #30: 'del_10q23.31' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

'del_10q23.31' versus 'PATHOLOGY_T_STAGE'

P value = 1e-05 (Fisher's exact test), Q value = 8.4e-05

Table S187. Gene #30: 'del_10q23.31' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

nPatients	T1	T2	T3	T4
ALL	479	127	258	15
DEL PEAK 17(10Q23.31) MUTATED	54	33	70	7
DEL PEAK 17(10Q23.31) WILD-TYPE	425	94	188	8

Figure S187. Get High-res Image Gene #30: 'del_10q23.31' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

'del_10q23.31' versus 'HISTOLOGICAL_TYPE'

P value = 1e-05 (Fisher's exact test), Q value = 8.4e-05

Table S188. Gene #30: 'del_10q23.31' versus Clinical Feature #10: 'HISTOLOGICAL_TYPE'

nPatients	KIDNEY CHROMOPHOBE	KIDNEY CLEAR CELL RENAL CARCINOMA	KIDNEY PAPILLARY RENAL CELL CARCINOMA
ALL	66	528	287
DEL PEAK 17(10Q23.31) MUTATED	49	96	19
DEL PEAK 17(10Q23.31) WILD-TYPE	17	432	268

Figure S188. Get High-res Image Gene #30: 'del_10q23.31' versus Clinical Feature #10: 'HISTOLOGICAL_TYPE'

'del_10q23.31' versus 'NUMBER_PACK_YEARS_SMOKED'

P value = 0.068 (Wilcoxon-test), Q value = 0.17

Table S189. Gene #30: 'del_10q23.31' versus Clinical Feature #11: 'NUMBER_PACK_YEARS_SMOKED'

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

Figure S189. Get High-res Image Gene #30: 'del_10q23.31' versus Clinical Feature #11: 'NUMBER_PACK_YEARS_SMOKED'

'del_10q23.31' versus 'RACE'

P value = 0.0684 (Fisher's exact test), Q value = 0.17

Table S190. Gene #30: 'del_10q23.31' versus Clinical Feature #13: 'RACE'

nPatients	AMERICAN INDIAN OR ALASKA NATIVE	ASIAN	BLACK OR AFRICAN AMERICAN	WHITE
ALL	2	15	121	719
DEL PEAK 17(10Q23.31) MUTATED	0	4	13	141
DEL PEAK 17(10Q23.31) WILD-TYPE	2	11	108	578

Figure S190. Get High-res Image Gene #30: 'del_10q23.31' versus Clinical Feature #13: 'RACE'

'del_11q21' versus 'Time to Death'

P value = 0.000133 (logrank test), Q value = 0.00075

Table S191. Gene #31: 'del_11q21' versus Clinical Feature #1: 'Time to Death'

	nPatients	nDeath	Duration Range (Median), Month
ALL	873	228	0.1 - 194.8 (34.5)
DEL PEAK 18(11Q21) MUTATED	60	25	0.4 - 123.6 (20.6)
DEL PEAK 18(11Q21) WILD-TYPE	813	203	0.1 - 194.8 (36.2)

Figure S191. Get High-res Image Gene #31: 'del_11q21' versus Clinical Feature #1: 'Time to Death'

'del_11q21' versus 'YEARS_TO_BIRTH'

P value = 0.00548 (Wilcoxon-test), Q value = 0.02

Table S192. Gene #31: 'del_11q21' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

	nPatients	Mean (Std.Dev)
ALL	875	60.1 (12.5)
DEL PEAK 18(11Q21) MUTATED	60	64.1 (11.0)
DEL PEAK 18(11Q21) WILD-TYPE	815	59.8 (12.6)

Figure S192. Get High-res Image Gene #31: 'del_11q21' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'del_11q21' versus 'PATHOLOGIC_STAGE'

P value = 9e-05 (Fisher's exact test), Q value = 0.00052

Table S193. Gene #31: 'del_11q21' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

nPatients	STAGE I	STAGE II	STAGE III	STAGE IV
ALL	455	104	191	104
DEL PEAK 18(11Q21) MUTATED	16	11	19	14
DEL PEAK 18(11Q21) WILD-TYPE	439	93	172	90

Figure S193. Get High-res Image Gene #31: 'del_11q21' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

'del_11q21' versus 'PATHOLOGY_T_STAGE'

P value = 6e-05 (Fisher's exact test), Q value = 0.00036

Table S194. Gene #31: 'del_11q21' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

nPatients	T1	T2	T3	T4
ALL	479	127	258	15
DEL PEAK 18(11Q21) MUTATED	17	12	31	1
DEL PEAK 18(11Q21) WILD-TYPE	462	115	227	14

Figure S194. Get High-res Image Gene #31: 'del_11q21' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

'del_11q21' versus 'PATHOLOGY_N_STAGE'

P value = 2e-05 (Fisher's exact test), Q value = 0.00015

Table S195. Gene #31: 'del_11q21' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

nPatients	N0	N1	N2
ALL	322	44	7
DEL PEAK 18(11Q21) MUTATED	21	12	3
DEL PEAK 18(11Q21) WILD-TYPE	301	32	4

Figure S195. Get High-res Image Gene #31: 'del_11q21' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

'del_11q21' versus 'PATHOLOGY_M_STAGE'

P value = 0.0983 (Fisher's exact test), Q value = 0.23

Table S196. Gene #31: 'del_11q21' versus Clinical Feature #6: 'PATHOLOGY_M_STAGE'

nPatients	0	1
ALL	545	89
DEL PEAK 18(11Q21) MUTATED	30	9
DEL PEAK 18(11Q21) WILD-TYPE	515	80

Figure S196. Get High-res Image Gene #31: 'del_11q21' versus Clinical Feature #6: 'PATHOLOGY_M_STAGE'

'del_11q21' versus 'KARNOFSKY_PERFORMANCE_SCORE'

P value = 0.0973 (Wilcoxon-test), Q value = 0.23

Table S197. Gene #31: 'del_11q21' versus Clinical Feature #9: 'KARNOFSKY_PERFORMANCE_SCORE'

	nPatients	Mean (Std.Dev)
ALL	142	87.6 (22.8)
DEL PEAK 18(11Q21) MUTATED	14	81.4 (26.8)
DEL PEAK 18(11Q21) WILD-TYPE	128	88.3 (22.3)

Figure S197. Get High-res Image Gene #31: 'del_11q21' versus Clinical Feature #9: 'KARNOFSKY_PERFORMANCE_SCORE'

'del_11q21' versus 'HISTOLOGICAL_TYPE'

P value = 0.00308 (Fisher's exact test), Q value = 0.012

Table S198. Gene #31: 'del_11q21' versus Clinical Feature #10: 'HISTOLOGICAL_TYPE'

nPatients	KIDNEY CHROMOPHOBE	KIDNEY CLEAR CELL RENAL CARCINOMA	KIDNEY PAPILLARY RENAL CELL CARCINOMA
ALL	66	528	287
DEL PEAK 18(11Q21) MUTATED	9	25	27
DEL PEAK 18(11Q21) WILD-TYPE	57	503	260

Figure S198. Get High-res Image Gene #31: 'del_11q21' versus Clinical Feature #10: 'HISTOLOGICAL_TYPE'

'del_11q23.1' versus 'Time to Death'

P value = 0.000299 (logrank test), Q value = 0.0016

Table S199. Gene #32: 'del_11q23.1' versus Clinical Feature #1: 'Time to Death'

	nPatients	nDeath	Duration Range (Median), Month
ALL	873	228	0.1 - 194.8 (34.5)
DEL PEAK 19(11Q23.1) MUTATED	69	28	0.4 - 123.6 (21.6)
DEL PEAK 19(11Q23.1) WILD-TYPE	804	200	0.1 - 194.8 (36.1)

Figure S199. Get High-res Image Gene #32: 'del_11q23.1' versus Clinical Feature #1: 'Time to Death'

'del_11q23.1' versus 'YEARS_TO_BIRTH'

P value = 0.00335 (Wilcoxon-test), Q value = 0.013

Table S200. Gene #32: 'del_11q23.1' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

	nPatients	Mean (Std.Dev)
ALL	875	60.1 (12.5)
DEL PEAK 19(11Q23.1) MUTATED	70	64.0 (10.9)
DEL PEAK 19(11Q23.1) WILD-TYPE	805	59.8 (12.6)

Figure S200. Get High-res Image Gene #32: 'del_11q23.1' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'del_11q23.1' versus 'PATHOLOGIC_STAGE'

P value = 2e-05 (Fisher's exact test), Q value = 0.00015

Table S201. Gene #32: 'del_11q23.1' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

nPatients	STAGE I	STAGE II	STAGE III	STAGE IV
ALL	455	104	191	104
DEL PEAK 19(11Q23.1) MUTATED	18	13	23	16
DEL PEAK 19(11Q23.1) WILD-TYPE	437	91	168	88

Figure S201. Get High-res Image Gene #32: 'del_11q23.1' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

'del_11q23.1' versus 'PATHOLOGY_T_STAGE'

P value = 2e-05 (Fisher's exact test), Q value = 0.00015

Table S202. Gene #32: 'del_11q23.1' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

nPatients	T1	T2	T3	T4
ALL	479	127	258	15
DEL PEAK 19(11Q23.1) MUTATED	19	15	34	3
DEL PEAK 19(11Q23.1) WILD-TYPE	460	112	224	12

Figure S202. Get High-res Image Gene #32: 'del_11q23.1' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

'del_11q23.1' versus 'PATHOLOGY_N_STAGE'

P value = 2e-05 (Fisher's exact test), Q value = 0.00015

Table S203. Gene #32: 'del_11q23.1' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

nPatients	N0	N1	N2
ALL	322	44	7
DEL PEAK 19(11Q23.1) MUTATED	24	12	3
DEL PEAK 19(11Q23.1) WILD-TYPE	298	32	4

Figure S203. Get High-res Image Gene #32: 'del_11q23.1' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

'del_11q23.1' versus 'PATHOLOGY_M_STAGE'

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

Table S204. Gene #32: 'del_11q23.1' versus Clinical Feature #6: 'PATHOLOGY_M_STAGE'

nPatients	0	1
ALL	545	89
DEL PEAK 19(11Q23.1) MUTATED	34	10
DEL PEAK 19(11Q23.1) WILD-TYPE	511	79

Figure S204. Get High-res Image Gene #32: 'del_11q23.1' versus Clinical Feature #6: 'PATHOLOGY_M_STAGE'

'del_11q23.1' versus 'KARNOFSKY_PERFORMANCE_SCORE'

P value = 0.0989 (Wilcoxon-test), Q value = 0.23

Table S205. Gene #32: 'del_11q23.1' versus Clinical Feature #9: 'KARNOFSKY_PERFORMANCE_SCORE'

	nPatients	Mean (Std.Dev)
ALL	142	87.6 (22.8)
DEL PEAK 19(11Q23.1) MUTATED	16	82.5 (25.4)
DEL PEAK 19(11Q23.1) WILD-TYPE	126	88.3 (22.5)

Figure S205. Get High-res Image Gene #32: 'del_11q23.1' versus Clinical Feature #9: 'KARNOFSKY_PERFORMANCE_SCORE'

'del_11q23.1' versus 'HISTOLOGICAL_TYPE'

P value = 0.00461 (Fisher's exact test), Q value = 0.017

Table S206. Gene #32: 'del_11q23.1' versus Clinical Feature #10: 'HISTOLOGICAL_TYPE'

nPatients	KIDNEY CHROMOPHOBE	KIDNEY CLEAR CELL RENAL CARCINOMA	KIDNEY PAPILLARY RENAL CELL CARCINOMA
ALL	66	528	287
DEL PEAK 19(11Q23.1) MUTATED	9	30	32
DEL PEAK 19(11Q23.1) WILD-TYPE	57	498	255

Figure S206. Get High-res Image Gene #32: 'del_11q23.1' versus Clinical Feature #10: 'HISTOLOGICAL_TYPE'

'del_13q12.13' versus 'Time to Death'

P value = 0.0125 (logrank test), Q value = 0.041

Table S207. Gene #33: 'del_13q12.13' versus Clinical Feature #1: 'Time to Death'

	nPatients	nDeath	Duration Range (Median), Month
ALL	873	228	0.1 - 194.8 (34.5)
DEL PEAK 20(13Q12.13) MUTATED	148	56	0.2 - 152.0 (37.7)
DEL PEAK 20(13Q12.13) WILD-TYPE	725	172	0.1 - 194.8 (34.2)

Figure S207. Get High-res Image Gene #33: 'del_13q12.13' versus Clinical Feature #1: 'Time to Death'

'del_13q12.13' versus 'YEARS_TO_BIRTH'

P value = 0.000305 (Wilcoxon-test), Q value = 0.0016

Table S208. Gene #33: 'del_13q12.13' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

	nPatients	Mean (Std.Dev)
ALL	875	60.1 (12.5)
DEL PEAK 20(13Q12.13) MUTATED	150	56.2 (15.1)
DEL PEAK 20(13Q12.13) WILD-TYPE	725	60.9 (11.8)

Figure S208. Get High-res Image Gene #33: 'del_13q12.13' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'del_13q12.13' versus 'PATHOLOGIC_STAGE'

P value = 1e-05 (Fisher's exact test), Q value = 8.4e-05

Table S209. Gene #33: 'del_13q12.13' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

nPatients	STAGE I	STAGE II	STAGE III	STAGE IV
ALL	455	104	191	104
DEL PEAK 20(13Q12.13) MUTATED	46	24	49	29
DEL PEAK 20(13Q12.13) WILD-TYPE	409	80	142	75

Figure S209. Get High-res Image Gene #33: 'del_13q12.13' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

'del_13q12.13' versus 'PATHOLOGY_T_STAGE'

P value = 1e-05 (Fisher's exact test), Q value = 8.4e-05

Table S210. Gene #33: 'del_13q12.13' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

nPatients	T1	T2	T3	T4
ALL	479	127	258	15
DEL PEAK 20(13Q12.13) MUTATED	48	26	67	9
DEL PEAK 20(13Q12.13) WILD-TYPE	431	101	191	6

Figure S210. Get High-res Image Gene #33: 'del_13q12.13' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

'del_13q12.13' versus 'PATHOLOGY_N_STAGE'

P value = 0.00389 (Fisher's exact test), Q value = 0.015

Table S211. Gene #33: 'del_13q12.13' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

nPatients	N0	N1	N2
ALL	322	44	7
DEL PEAK 20(13Q12.13) MUTATED	68	14	5
DEL PEAK 20(13Q12.13) WILD-TYPE	254	30	2

Figure S211. Get High-res Image Gene #33: 'del_13q12.13' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

'del_13q12.13' versus 'GENDER'

P value = 0.00765 (Fisher's exact test), Q value = 0.026

Table S212. Gene #33: 'del_13q12.13' versus Clinical Feature #7: 'GENDER'

nPatients	FEMALE	MALE
ALL	292	589
DEL PEAK 20(13Q12.13) MUTATED	64	86
DEL PEAK 20(13Q12.13) WILD-TYPE	228	503

Figure S212. Get High-res Image Gene #33: 'del_13q12.13' versus Clinical Feature #7: 'GENDER'

'del_13q12.13' versus 'HISTOLOGICAL_TYPE'

P value = 1e-05 (Fisher's exact test), Q value = 8.4e-05

Table S213. Gene #33: 'del_13q12.13' versus Clinical Feature #10: 'HISTOLOGICAL_TYPE'

nPatients	KIDNEY CHROMOPHOBE	KIDNEY CLEAR CELL RENAL CARCINOMA	KIDNEY PAPILLARY RENAL CELL CARCINOMA
ALL	66	528	287
DEL PEAK 20(13Q12.13) MUTATED	44	81	25
DEL PEAK 20(13Q12.13) WILD-TYPE	22	447	262

Figure S213. Get High-res Image Gene #33: 'del_13q12.13' versus Clinical Feature #10: 'HISTOLOGICAL_TYPE'

'del_13q12.13' versus 'RACE'

P value = 0.0848 (Fisher's exact test), Q value = 0.2

Table S214. Gene #33: 'del_13q12.13' versus Clinical Feature #13: 'RACE'

nPatients	AMERICAN INDIAN OR ALASKA NATIVE	ASIAN	BLACK OR AFRICAN AMERICAN	WHITE
ALL	2	15	121	719
DEL PEAK 20(13Q12.13) MUTATED	0	4	12	129
DEL PEAK 20(13Q12.13) WILD-TYPE	2	11	109	590

Figure S214. Get High-res Image Gene #33: 'del_13q12.13' versus Clinical Feature #13: 'RACE'

'del_13q14.2' versus 'Time to Death'

P value = 0.0169 (logrank test), Q value = 0.053

Table S215. Gene #34: 'del_13q14.2' versus Clinical Feature #1: 'Time to Death'

	nPatients	nDeath	Duration Range (Median), Month
ALL	873	228	0.1 - 194.8 (34.5)
DEL PEAK 21(13Q14.2) MUTATED	147	55	0.2 - 152.0 (37.1)
DEL PEAK 21(13Q14.2) WILD-TYPE	726	173	0.1 - 194.8 (34.3)

Figure S215. Get High-res Image Gene #34: 'del_13q14.2' versus Clinical Feature #1: 'Time to Death'

'del_13q14.2' versus 'YEARS_TO_BIRTH'

P value = 5.79e-05 (Wilcoxon-test), Q value = 0.00036

Table S216. Gene #34: 'del_13q14.2' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

	nPatients	Mean (Std.Dev)
ALL	875	60.1 (12.5)
DEL PEAK 21(13Q14.2) MUTATED	149	55.7 (14.9)
DEL PEAK 21(13Q14.2) WILD-TYPE	726	61.0 (11.8)

Figure S216. Get High-res Image Gene #34: 'del_13q14.2' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'del_13q14.2' versus 'PATHOLOGIC_STAGE'

P value = 1e-05 (Fisher's exact test), Q value = 8.4e-05

Table S217. Gene #34: 'del_13q14.2' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

nPatients	STAGE I	STAGE II	STAGE III	STAGE IV
ALL	455	104	191	104
DEL PEAK 21(13Q14.2) MUTATED	46	22	50	30
DEL PEAK 21(13Q14.2) WILD-TYPE	409	82	141	74

Figure S217. Get High-res Image Gene #34: 'del_13q14.2' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

'del_13q14.2' versus 'PATHOLOGY_T_STAGE'

P value = 1e-05 (Fisher's exact test), Q value = 8.4e-05

Table S218. Gene #34: 'del_13q14.2' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

nPatients	T1	T2	T3	T4
ALL	479	127	258	15
DEL PEAK 21(13Q14.2) MUTATED	48	24	68	9
DEL PEAK 21(13Q14.2) WILD-TYPE	431	103	190	6

Figure S218. Get High-res Image Gene #34: 'del_13q14.2' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

'del_13q14.2' versus 'PATHOLOGY_N_STAGE'

P value = 0.03 (Fisher's exact test), Q value = 0.087

Table S219. Gene #34: 'del_13q14.2' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

nPatients	N0	N1	N2
ALL	322	44	7
DEL PEAK 21(13Q14.2) MUTATED	69	14	4
DEL PEAK 21(13Q14.2) WILD-TYPE	253	30	3

Figure S219. Get High-res Image Gene #34: 'del_13q14.2' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

'del_13q14.2' versus 'GENDER'

P value = 0.00734 (Fisher's exact test), Q value = 0.026

Table S220. Gene #34: 'del_13q14.2' versus Clinical Feature #7: 'GENDER'

nPatients	FEMALE	MALE
ALL	292	589
DEL PEAK 21(13Q14.2) MUTATED	64	85
DEL PEAK 21(13Q14.2) WILD-TYPE	228	504

Figure S220. Get High-res Image Gene #34: 'del_13q14.2' versus Clinical Feature #7: 'GENDER'

'del_13q14.2' versus 'HISTOLOGICAL_TYPE'

P value = 1e-05 (Fisher's exact test), Q value = 8.4e-05

Table S221. Gene #34: 'del_13q14.2' versus Clinical Feature #10: 'HISTOLOGICAL_TYPE'

nPatients	KIDNEY CHROMOPHOBE	KIDNEY CLEAR CELL RENAL CARCINOMA	KIDNEY PAPILLARY RENAL CELL CARCINOMA
ALL	66	528	287
DEL PEAK 21(13Q14.2) MUTATED	43	82	24
DEL PEAK 21(13Q14.2) WILD-TYPE	23	446	263

Figure S221. Get High-res Image Gene #34: 'del_13q14.2' versus Clinical Feature #10: 'HISTOLOGICAL_TYPE'

'del_13q14.2' versus 'RACE'

P value = 0.0871 (Fisher's exact test), Q value = 0.2

Table S222. Gene #34: 'del_13q14.2' versus Clinical Feature #13: 'RACE'

nPatients	AMERICAN INDIAN OR ALASKA NATIVE	ASIAN	BLACK OR AFRICAN AMERICAN	WHITE
ALL	2	15	121	719
DEL PEAK 21(13Q14.2) MUTATED	0	4	12	128
DEL PEAK 21(13Q14.2) WILD-TYPE	2	11	109	591

Figure S222. Get High-res Image Gene #34: 'del_13q14.2' versus Clinical Feature #13: 'RACE'

'del_14q31.1' versus 'Time to Death'

P value = 8.11e-10 (logrank test), Q value = 8.9e-08

Table S223. Gene #35: 'del_14q31.1' versus Clinical Feature #1: 'Time to Death'

	nPatients	nDeath	Duration Range (Median), Month
ALL	873	228	0.1 - 194.8 (34.5)
DEL PEAK 22(14Q31.1) MUTATED	278	112	0.1 - 133.7 (32.8)
DEL PEAK 22(14Q31.1) WILD-TYPE	595	116	0.1 - 194.8 (36.4)

Figure S223. Get High-res Image Gene #35: 'del_14q31.1' versus Clinical Feature #1: 'Time to Death'

'del_14q31.1' versus 'PATHOLOGIC_STAGE'

P value = 1e-05 (Fisher's exact test), Q value = 8.4e-05

Table S224. Gene #35: 'del_14q31.1' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

nPatients	STAGE I	STAGE II	STAGE III	STAGE IV
ALL	455	104	191	104
DEL PEAK 22(14Q31.1) MUTATED	104	31	82	56
DEL PEAK 22(14Q31.1) WILD-TYPE	351	73	109	48

Figure S224. Get High-res Image Gene #35: 'del_14q31.1' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

'del_14q31.1' versus 'PATHOLOGY_T_STAGE'

P value = 1e-05 (Fisher's exact test), Q value = 8.4e-05

Table S225. Gene #35: 'del_14q31.1' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

nPatients	T1	T2	T3	T4
ALL	479	127	258	15
DEL PEAK 22(14Q31.1) MUTATED	111	41	122	5
DEL PEAK 22(14Q31.1) WILD-TYPE	368	86	136	10

Figure S225. Get High-res Image Gene #35: 'del_14q31.1' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

'del_14q31.1' versus 'PATHOLOGY_N_STAGE'

P value = 0.00554 (Fisher's exact test), Q value = 0.02

Table S226. Gene #35: 'del_14q31.1' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

nPatients	N0	N1	N2
ALL	322	44	7
DEL PEAK 22(14Q31.1) MUTATED	110	25	4
DEL PEAK 22(14Q31.1) WILD-TYPE	212	19	3

Figure S226. Get High-res Image Gene #35: 'del_14q31.1' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

'del_14q31.1' versus 'PATHOLOGY_M_STAGE'

P value = 4.69e-05 (Fisher's exact test), Q value = 3e-04

Table S227. Gene #35: 'del_14q31.1' versus Clinical Feature #6: 'PATHOLOGY_M_STAGE'

nPatients	0	1
ALL	545	89
DEL PEAK 22(14Q31.1) MUTATED	185	51
DEL PEAK 22(14Q31.1) WILD-TYPE	360	38

Figure S227. Get High-res Image Gene #35: 'del_14q31.1' versus Clinical Feature #6: 'PATHOLOGY_M_STAGE'

'del_14q31.1' versus 'RADIATION_THERAPY'

P value = 0.116 (Fisher's exact test), Q value = 0.25

Table S228. Gene #35: 'del_14q31.1' versus Clinical Feature #8: 'RADIATION_THERAPY'

nPatients	NO	YES
ALL	400	3
DEL PEAK 22(14Q31.1) MUTATED	84	2
DEL PEAK 22(14Q31.1) WILD-TYPE	316	1

Figure S228. Get High-res Image Gene #35: 'del_14q31.1' versus Clinical Feature #8: 'RADIATION_THERAPY'

'del_14q31.1' versus 'KARNOFSKY_PERFORMANCE_SCORE'

P value = 0.000186 (Wilcoxon-test), Q value = 0.001

Table S229. Gene #35: 'del_14q31.1' versus Clinical Feature #9: 'KARNOFSKY_PERFORMANCE_SCORE'

	nPatients	Mean (Std.Dev)
ALL	142	87.6 (22.8)
DEL PEAK 22(14Q31.1) MUTATED	36	71.9 (36.3)
DEL PEAK 22(14Q31.1) WILD-TYPE	106	92.9 (12.1)

Figure S229. Get High-res Image Gene #35: 'del_14q31.1' versus Clinical Feature #9: 'KARNOFSKY_PERFORMANCE_SCORE'

'del_14q31.1' versus 'HISTOLOGICAL_TYPE'

P value = 1e-05 (Fisher's exact test), Q value = 8.4e-05

Table S230. Gene #35: 'del_14q31.1' versus Clinical Feature #10: 'HISTOLOGICAL_TYPE'

nPatients	KIDNEY CHROMOPHOBE	KIDNEY CLEAR CELL RENAL CARCINOMA	KIDNEY PAPILLARY RENAL CELL CARCINOMA
ALL	66	528	287
DEL PEAK 22(14Q31.1) MUTATED	3	228	48
DEL PEAK 22(14Q31.1) WILD-TYPE	63	300	239

Figure S230. Get High-res Image Gene #35: 'del_14q31.1' versus Clinical Feature #10: 'HISTOLOGICAL_TYPE'

'del_14q31.1' versus 'YEAR_OF_TOBACCO_SMOKING_ONSET'

P value = 0.00978 (Wilcoxon-test), Q value = 0.033

Table S231. Gene #35: 'del_14q31.1' versus Clinical Feature #12: 'YEAR_OF_TOBACCO_SMOKING_ONSET'

	nPatients	Mean (Std.Dev)
ALL	74	1973.7 (16.0)
DEL PEAK 22(14Q31.1) MUTATED	15	1983.5 (14.8)
DEL PEAK 22(14Q31.1) WILD-TYPE	59	1971.2 (15.4)

Figure S231. Get High-res Image Gene #35: 'del_14q31.1' versus Clinical Feature #12: 'YEAR_OF_TOBACCO_SMOKING_ONSET'

'del_14q31.1' versus 'RACE'

P value = 0.0226 (Fisher's exact test), Q value = 0.068

Table S232. Gene #35: 'del_14q31.1' versus Clinical Feature #13: 'RACE'

nPatients	AMERICAN INDIAN OR ALASKA NATIVE	ASIAN	BLACK OR AFRICAN AMERICAN	WHITE
ALL	2	15	121	719
DEL PEAK 22(14Q31.1) MUTATED	0	3	26	243
DEL PEAK 22(14Q31.1) WILD-TYPE	2	12	95	476

Figure S232. Get High-res Image Gene #35: 'del_14q31.1' versus Clinical Feature #13: 'RACE'

'del_16q23.3' versus 'Time to Death'

P value = 1.94e-05 (logrank test), Q value = 0.00015

Table S233. Gene #36: 'del_16q23.3' versus Clinical Feature #1: 'Time to Death'

	nPatients	nDeath	Duration Range (Median), Month
ALL	873	228	0.1 - 194.8 (34.5)
DEL PEAK 23(16Q23.3) MUTATED	36	18	0.1 - 90.5 (29.2)
DEL PEAK 23(16Q23.3) WILD-TYPE	837	210	0.1 - 194.8 (35.2)

Figure S233. Get High-res Image Gene #36: 'del_16q23.3' versus Clinical Feature #1: 'Time to Death'

'del_16q23.3' versus 'PATHOLOGIC_STAGE'

P value = 0.00482 (Fisher's exact test), Q value = 0.018

Table S234. Gene #36: 'del_16q23.3' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

nPatients	STAGE I	STAGE II	STAGE III	STAGE IV
ALL	455	104	191	104
DEL PEAK 23(16Q23.3) MUTATED	11	4	12	10
DEL PEAK 23(16Q23.3) WILD-TYPE	444	100	179	94

Figure S234. Get High-res Image Gene #36: 'del_16q23.3' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

'del_16q23.3' versus 'PATHOLOGY_T_STAGE'

P value = 5e-05 (Fisher's exact test), Q value = 0.00031

Table S235. Gene #36: 'del_16q23.3' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

nPatients	T1	T2	T3	T4
ALL	479	127	258	15
DEL PEAK 23(16Q23.3) MUTATED	12	4	16	5
DEL PEAK 23(16Q23.3) WILD-TYPE	467	123	242	10

Figure S235. Get High-res Image Gene #36: 'del_16q23.3' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

'del_16q23.3' versus 'PATHOLOGY_N_STAGE'

P value = 0.00107 (Fisher's exact test), Q value = 0.0049

Table S236. Gene #36: 'del_16q23.3' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

nPatients	N0	N1	N2
ALL	322	44	7
DEL PEAK 23(16Q23.3) MUTATED	13	7	2
DEL PEAK 23(16Q23.3) WILD-TYPE	309	37	5

Figure S236. Get High-res Image Gene #36: 'del_16q23.3' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

'del_18q22.2' versus 'Time to Death'

P value = 2.99e-08 (logrank test), Q value = 2.7e-06

Table S237. Gene #37: 'del_18q22.2' versus Clinical Feature #1: 'Time to Death'

	nPatients	nDeath	Duration Range (Median), Month
ALL	873	228	0.1 - 194.8 (34.5)
DEL PEAK 24(18Q22.2) MUTATED	152	63	0.4 - 123.6 (25.7)
DEL PEAK 24(18Q22.2) WILD-TYPE	721	165	0.1 - 194.8 (37.0)

Figure S237. Get High-res Image Gene #37: 'del_18q22.2' versus Clinical Feature #1: 'Time to Death'

'del_18q22.2' versus 'PATHOLOGIC_STAGE'

P value = 1e-05 (Fisher's exact test), Q value = 8.4e-05

Table S238. Gene #37: 'del_18q22.2' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

nPatients	STAGE I	STAGE II	STAGE III	STAGE IV
ALL	455	104	191	104
DEL PEAK 24(18Q22.2) MUTATED	51	12	55	32
DEL PEAK 24(18Q22.2) WILD-TYPE	404	92	136	72

Figure S238. Get High-res Image Gene #37: 'del_18q22.2' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

'del_18q22.2' versus 'PATHOLOGY_T_STAGE'

P value = 1e-05 (Fisher's exact test), Q value = 8.4e-05

Table S239. Gene #37: 'del_18q22.2' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

nPatients	T1	T2	T3	T4
ALL	479	127	258	15
DEL PEAK 24(18Q22.2) MUTATED	55	18	75	7
DEL PEAK 24(18Q22.2) WILD-TYPE	424	109	183	8

Figure S239. Get High-res Image Gene #37: 'del_18q22.2' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

'del_18q22.2' versus 'PATHOLOGY_N_STAGE'

P value = 0.00397 (Fisher's exact test), Q value = 0.015

Table S240. Gene #37: 'del_18q22.2' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

nPatients	N0	N1	N2
ALL	322	44	7
DEL PEAK 24(18Q22.2) MUTATED	64	16	4
DEL PEAK 24(18Q22.2) WILD-TYPE	258	28	3

Figure S240. Get High-res Image Gene #37: 'del_18q22.2' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

'del_18q22.2' versus 'PATHOLOGY_M_STAGE'

P value = 0.00896 (Fisher's exact test), Q value = 0.03

Table S241. Gene #37: 'del_18q22.2' versus Clinical Feature #6: 'PATHOLOGY_M_STAGE'

nPatients	0	1
ALL	545	89
DEL PEAK 24(18Q22.2) MUTATED	97	27
DEL PEAK 24(18Q22.2) WILD-TYPE	448	62

Figure S241. Get High-res Image Gene #37: 'del_18q22.2' versus Clinical Feature #6: 'PATHOLOGY_M_STAGE'

'del_18q22.2' versus 'RACE'

P value = 0.0557 (Fisher's exact test), Q value = 0.14

Table S242. Gene #37: 'del_18q22.2' versus Clinical Feature #13: 'RACE'

nPatients	AMERICAN INDIAN OR ALASKA NATIVE	ASIAN	BLACK OR AFRICAN AMERICAN	WHITE
ALL	2	15	121	719
DEL PEAK 24(18Q22.2) MUTATED	0	6	15	131
DEL PEAK 24(18Q22.2) WILD-TYPE	2	9	106	588

Figure S242. Get High-res Image Gene #37: 'del_18q22.2' versus Clinical Feature #13: 'RACE'

'del_18q22.2' versus 'ETHNICITY'

P value = 0.0901 (Fisher's exact test), Q value = 0.21

Table S243. Gene #37: 'del_18q22.2' versus Clinical Feature #14: 'ETHNICITY'

nPatients	HISPANIC OR LATINO	NOT HISPANIC OR LATINO
ALL	42	621
DEL PEAK 24(18Q22.2) MUTATED	3	109
DEL PEAK 24(18Q22.2) WILD-TYPE	39	512

Figure S243. Get High-res Image Gene #37: 'del_18q22.2' versus Clinical Feature #14: 'ETHNICITY'

'del_19p13.3' versus 'Time to Death'

P value = 5.14e-12 (logrank test), Q value = 9.3e-10

Table S244. Gene #38: 'del_19p13.3' versus Clinical Feature #1: 'Time to Death'

	nPatients	nDeath	Duration Range (Median), Month
ALL	873	228	0.1 - 194.8 (34.5)
DEL PEAK 25(19P13.3) MUTATED	43	24	0.9 - 109.9 (18.2)
DEL PEAK 25(19P13.3) WILD-TYPE	830	204	0.1 - 194.8 (36.5)

Figure S244. Get High-res Image Gene #38: 'del_19p13.3' versus Clinical Feature #1: 'Time to Death'

'del_19p13.3' versus 'PATHOLOGIC_STAGE'

P value = 1e-05 (Fisher's exact test), Q value = 8.4e-05

Table S245. Gene #38: 'del_19p13.3' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

nPatients	STAGE I	STAGE II	STAGE III	STAGE IV
ALL	455	104	191	104
DEL PEAK 25(19P13.3) MUTATED	10	1	18	11
DEL PEAK 25(19P13.3) WILD-TYPE	445	103	173	93

Figure S245. Get High-res Image Gene #38: 'del_19p13.3' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

'del_19p13.3' versus 'PATHOLOGY_T_STAGE'

P value = 1e-05 (Fisher's exact test), Q value = 8.4e-05

Table S246. Gene #38: 'del_19p13.3' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

nPatients	T1	T2	T3	T4
ALL	479	127	258	15
DEL PEAK 25(19P13.3) MUTATED	12	2	25	4
DEL PEAK 25(19P13.3) WILD-TYPE	467	125	233	11

Figure S246. Get High-res Image Gene #38: 'del_19p13.3' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

'del_19p13.3' versus 'PATHOLOGY_N_STAGE'

P value = 6e-05 (Fisher's exact test), Q value = 0.00036

Table S247. Gene #38: 'del_19p13.3' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

nPatients	N0	N1	N2
ALL	322	44	7
DEL PEAK 25(19P13.3) MUTATED	11	7	3
DEL PEAK 25(19P13.3) WILD-TYPE	311	37	4

Figure S247. Get High-res Image Gene #38: 'del_19p13.3' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

'del_19p13.3' versus 'PATHOLOGY_M_STAGE'

P value = 0.069 (Fisher's exact test), Q value = 0.17

Table S248. Gene #38: 'del_19p13.3' versus Clinical Feature #6: 'PATHOLOGY_M_STAGE'

nPatients	0	1
ALL	545	89
DEL PEAK 25(19P13.3) MUTATED	18	7
DEL PEAK 25(19P13.3) WILD-TYPE	527	82

Figure S248. Get High-res Image Gene #38: 'del_19p13.3' versus Clinical Feature #6: 'PATHOLOGY_M_STAGE'

'del_19p13.3' versus 'KARNOFSKY_PERFORMANCE_SCORE'

P value = 0.00553 (Wilcoxon-test), Q value = 0.02

Table S249. Gene #38: 'del_19p13.3' versus Clinical Feature #9: 'KARNOFSKY_PERFORMANCE_SCORE'

	nPatients	Mean (Std.Dev)
ALL	142	87.6 (22.8)
DEL PEAK 25(19P13.3) MUTATED	12	67.5 (39.3)
DEL PEAK 25(19P13.3) WILD-TYPE	130	89.5 (19.9)

Figure S249. Get High-res Image Gene #38: 'del_19p13.3' versus Clinical Feature #9: 'KARNOFSKY_PERFORMANCE_SCORE'

'del_19p13.3' versus 'HISTOLOGICAL_TYPE'

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

Table S250. Gene #38: 'del_19p13.3' versus Clinical Feature #10: 'HISTOLOGICAL_TYPE'

nPatients	KIDNEY CHROMOPHOBE	KIDNEY CLEAR CELL RENAL CARCINOMA	KIDNEY PAPILLARY RENAL CELL CARCINOMA
ALL	66	528	287
DEL PEAK 25(19P13.3) MUTATED	3	17	23
DEL PEAK 25(19P13.3) WILD-TYPE	63	511	264

Figure S250. Get High-res Image Gene #38: 'del_19p13.3' versus Clinical Feature #10: 'HISTOLOGICAL_TYPE'

'del_xp22.2' versus 'YEARS_TO_BIRTH'

P value = 0.00138 (Wilcoxon-test), Q value = 0.006

Table S251. Gene #39: 'del_xp22.2' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

	nPatients	Mean (Std.Dev)
ALL	875	60.1 (12.5)
DEL PEAK 26(XP22.2) MUTATED	127	56.3 (13.8)
DEL PEAK 26(XP22.2) WILD-TYPE	748	60.8 (12.2)

Figure S251. Get High-res Image Gene #39: 'del_xp22.2' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'del_xp22.2' versus 'PATHOLOGIC_STAGE'

P value = 9e-05 (Fisher's exact test), Q value = 0.00052

Table S252. Gene #39: 'del_xp22.2' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

nPatients	STAGE I	STAGE II	STAGE III	STAGE IV
ALL	455	104	191	104
DEL PEAK 26(XP22.2) MUTATED	43	24	39	15
DEL PEAK 26(XP22.2) WILD-TYPE	412	80	152	89

Figure S252. Get High-res Image Gene #39: 'del_xp22.2' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

'del_xp22.2' versus 'PATHOLOGY_T_STAGE'

P value = 1e-04 (Fisher's exact test), Q value = 0.00057

Table S253. Gene #39: 'del_xp22.2' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

nPatients	T1	T2	T3	T4
ALL	479	127	258	15
DEL PEAK 26(XP22.2) MUTATED	46	27	51	3
DEL PEAK 26(XP22.2) WILD-TYPE	433	100	207	12

Figure S253. Get High-res Image Gene #39: 'del_xp22.2' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

'del_xp22.2' versus 'PATHOLOGY_N_STAGE'

P value = 0.057 (Fisher's exact test), Q value = 0.15

Table S254. Gene #39: 'del_xp22.2' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

nPatients	N0	N1	N2
ALL	322	44	7
DEL PEAK 26(XP22.2) MUTATED	48	12	2
DEL PEAK 26(XP22.2) WILD-TYPE	274	32	5

Figure S254. Get High-res Image Gene #39: 'del_xp22.2' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

'del_xp22.2' versus 'HISTOLOGICAL_TYPE'

P value = 1e-05 (Fisher's exact test), Q value = 8.4e-05

Table S255. Gene #39: 'del_xp22.2' versus Clinical Feature #10: 'HISTOLOGICAL_TYPE'

nPatients	KIDNEY CHROMOPHOBE	KIDNEY CLEAR CELL RENAL CARCINOMA	KIDNEY PAPILLARY RENAL CELL CARCINOMA
ALL	66	528	287
DEL PEAK 26(XP22.2) MUTATED	39	55	33
DEL PEAK 26(XP22.2) WILD-TYPE	27	473	254

Figure S255. Get High-res Image Gene #39: 'del_xp22.2' versus Clinical Feature #10: 'HISTOLOGICAL_TYPE'

Methods & Data

Input

Copy number data file = all_lesions.txt from GISTIC pipeline
Processed Copy number data file = /xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_Correlate_Genomic_Events_Preprocess/KIPAN-TP/19782223/transformed.cor.cli.txt
Clinical data file = /xchip/cga/gdac-prod/tcga-gdac/jobResults/Append_Data/KIPAN-TP/19775252/KIPAN-TP.merged_data.txt
Number of patients = 881
Number of significantly focal cnvs = 39
Number of selected clinical features = 14
Exclude genes that fewer than K tumors have mutations, K = 3

Survival analysis

For survival clinical features, the Kaplan-Meier survival curves of tumors with and without gene mutations were plotted and the statistical significance P values were estimated by logrank test (Bland and Altman 2004) using the 'survdiff' function in R

Fisher's exact test

For binary or multi-class clinical features (nominal or ordinal), two-tailed Fisher's exact tests (Fisher 1922) were used to estimate the P values using the 'fisher.test' function in R

Q value calculation

For multiple hypothesis correction, Q value is the False Discovery Rate (FDR) analogue of the P value (Benjamini and Hochberg 1995), defined as the minimum FDR at which the test may be called significant. We used the 'Benjamini and Hochberg' method of 'p.adjust' function in R to convert P values into Q values.

References

[1] Bland and Altman, Statistics notes: The logrank test, BMJ 328(7447):1073 (2004)

[2] Fisher, R.A., On the interpretation of chi-square from contingency tables, and the calculation of P, Journal of the Royal Statistical Society 85(1):87-94 (1922)

[3] Benjamini and Hochberg, Controlling the false discovery rate: a practical and powerful approach to multiple testing, Journal of the Royal Statistical Society Series B 59:289-300 (1995)

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