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 13 clinical features across 859 patients, 253 significant findings detected with Q value < 0.25.

amp_1q32.1 cnv correlated to 'Time to Death', 'YEARS_TO_BIRTH', 'NEOPLASM_DISEASESTAGE', 'PATHOLOGY_T_STAGE', 'PATHOLOGY_N_STAGE', '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', 'KARNOFSKY_PERFORMANCE_SCORE', 'HISTOLOGICAL_TYPE', and 'RACE'.
amp_5q35.1 cnv correlated to 'NEOPLASM_DISEASESTAGE', 'PATHOLOGY_T_STAGE', 'PATHOLOGY_N_STAGE', 'PATHOLOGY_M_STAGE', 'HISTOLOGICAL_TYPE', and 'RACE'.
amp_7q31.2 cnv correlated to 'NEOPLASM_DISEASESTAGE', 'PATHOLOGY_M_STAGE', 'GENDER', 'HISTOLOGICAL_TYPE', and 'YEAR_OF_TOBACCO_SMOKING_ONSET'.
amp_8q24.22 cnv correlated to 'Time to Death', 'YEARS_TO_BIRTH', 'NEOPLASM_DISEASESTAGE', 'PATHOLOGY_T_STAGE', 'PATHOLOGY_N_STAGE', 'PATHOLOGY_M_STAGE', 'HISTOLOGICAL_TYPE', 'NUMBER_PACK_YEARS_SMOKED', and 'RACE'.
amp_10p14 cnv correlated to 'PATHOLOGY_T_STAGE' and 'PATHOLOGY_N_STAGE'.
amp_17q25.2 cnv correlated to 'YEARS_TO_BIRTH', 'NEOPLASM_DISEASESTAGE', 'PATHOLOGY_T_STAGE', 'PATHOLOGY_N_STAGE', 'GENDER', 'HISTOLOGICAL_TYPE', 'YEAR_OF_TOBACCO_SMOKING_ONSET', and 'RACE'.
amp_19p13.2 cnv correlated to 'NEOPLASM_DISEASESTAGE', 'PATHOLOGY_T_STAGE', 'PATHOLOGY_M_STAGE', and 'HISTOLOGICAL_TYPE'.
amp_xp22.2 cnv correlated to 'NEOPLASM_DISEASESTAGE', 'PATHOLOGY_T_STAGE', 'GENDER', 'KARNOFSKY_PERFORMANCE_SCORE', 'HISTOLOGICAL_TYPE', and 'YEAR_OF_TOBACCO_SMOKING_ONSET'.
amp_xp11.4 cnv correlated to 'NEOPLASM_DISEASESTAGE', 'PATHOLOGY_T_STAGE', 'GENDER', 'KARNOFSKY_PERFORMANCE_SCORE', 'HISTOLOGICAL_TYPE', and 'YEAR_OF_TOBACCO_SMOKING_ONSET'.
amp_xq11.2 cnv correlated to 'Time to Death', 'NEOPLASM_DISEASESTAGE', 'PATHOLOGY_T_STAGE', 'GENDER', 'KARNOFSKY_PERFORMANCE_SCORE', 'HISTOLOGICAL_TYPE', and 'YEAR_OF_TOBACCO_SMOKING_ONSET'.
amp_xq28 cnv correlated to 'Time to Death', 'NEOPLASM_DISEASESTAGE', 'PATHOLOGY_T_STAGE', 'GENDER', 'KARNOFSKY_PERFORMANCE_SCORE', and 'HISTOLOGICAL_TYPE'.
del_1p36.31 cnv correlated to 'YEARS_TO_BIRTH', 'NEOPLASM_DISEASESTAGE', 'PATHOLOGY_T_STAGE', 'PATHOLOGY_N_STAGE', 'KARNOFSKY_PERFORMANCE_SCORE', and 'HISTOLOGICAL_TYPE'.
del_1p31.1 cnv correlated to 'YEARS_TO_BIRTH', 'NEOPLASM_DISEASESTAGE', 'PATHOLOGY_T_STAGE', 'PATHOLOGY_N_STAGE', 'HISTOLOGICAL_TYPE', and 'ETHNICITY'.
del_1q43 cnv correlated to 'Time to Death', 'YEARS_TO_BIRTH', 'NEOPLASM_DISEASESTAGE', 'PATHOLOGY_T_STAGE', and 'HISTOLOGICAL_TYPE'.
del_2q37.3 cnv correlated to 'Time to Death', 'YEARS_TO_BIRTH', 'NEOPLASM_DISEASESTAGE', 'PATHOLOGY_T_STAGE', 'PATHOLOGY_M_STAGE', and 'HISTOLOGICAL_TYPE'.
del_3p26.3 cnv correlated to 'Time to Death', 'NEOPLASM_DISEASESTAGE', 'PATHOLOGY_T_STAGE', 'PATHOLOGY_N_STAGE', 'GENDER', 'HISTOLOGICAL_TYPE', 'YEAR_OF_TOBACCO_SMOKING_ONSET', and 'RACE'.
del_3p21.2 cnv correlated to 'Time to Death', 'NEOPLASM_DISEASESTAGE', 'PATHOLOGY_T_STAGE', 'PATHOLOGY_N_STAGE', 'PATHOLOGY_M_STAGE', 'KARNOFSKY_PERFORMANCE_SCORE', 'HISTOLOGICAL_TYPE', 'YEAR_OF_TOBACCO_SMOKING_ONSET', and 'RACE'.
del_3p14.1 cnv correlated to 'Time to Death', 'NEOPLASM_DISEASESTAGE', 'PATHOLOGY_T_STAGE', 'HISTOLOGICAL_TYPE', 'YEAR_OF_TOBACCO_SMOKING_ONSET', and 'RACE'.
del_3p12.2 cnv correlated to 'Time to Death', 'NEOPLASM_DISEASESTAGE', 'PATHOLOGY_T_STAGE', 'GENDER', 'HISTOLOGICAL_TYPE', 'YEAR_OF_TOBACCO_SMOKING_ONSET', and 'RACE'.
del_4q34.3 cnv correlated to 'Time to Death', 'NEOPLASM_DISEASESTAGE', 'PATHOLOGY_T_STAGE', 'PATHOLOGY_N_STAGE', 'PATHOLOGY_M_STAGE', 'HISTOLOGICAL_TYPE', and 'RACE'.
del_5p15.33 cnv correlated to 'YEARS_TO_BIRTH', 'NEOPLASM_DISEASESTAGE', 'PATHOLOGY_T_STAGE', 'PATHOLOGY_N_STAGE', and 'HISTOLOGICAL_TYPE'.
del_6q22.31 cnv correlated to 'YEARS_TO_BIRTH', 'NEOPLASM_DISEASESTAGE', 'PATHOLOGY_T_STAGE', 'PATHOLOGY_N_STAGE', 'KARNOFSKY_PERFORMANCE_SCORE', 'HISTOLOGICAL_TYPE', and 'RACE'.
del_6q26 cnv correlated to 'NEOPLASM_DISEASESTAGE', 'PATHOLOGY_T_STAGE', 'PATHOLOGY_N_STAGE', 'KARNOFSKY_PERFORMANCE_SCORE', 'HISTOLOGICAL_TYPE', and 'RACE'.
del_6q26 cnv correlated to 'NEOPLASM_DISEASESTAGE', 'PATHOLOGY_T_STAGE', 'PATHOLOGY_N_STAGE', 'KARNOFSKY_PERFORMANCE_SCORE', 'HISTOLOGICAL_TYPE', and 'RACE'.
del_8p23.2 cnv correlated to 'Time to Death', 'NEOPLASM_DISEASESTAGE', 'PATHOLOGY_T_STAGE', 'PATHOLOGY_M_STAGE', 'HISTOLOGICAL_TYPE', and 'RACE'.
del_9p23 cnv correlated to 'Time to Death', 'YEARS_TO_BIRTH', 'NEOPLASM_DISEASESTAGE', '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', 'NEOPLASM_DISEASESTAGE', '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', 'NEOPLASM_DISEASESTAGE', 'PATHOLOGY_T_STAGE', 'HISTOLOGICAL_TYPE', and 'RACE'.
del_11q21 cnv correlated to 'Time to Death', 'YEARS_TO_BIRTH', 'NEOPLASM_DISEASESTAGE', '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', 'NEOPLASM_DISEASESTAGE', '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', 'NEOPLASM_DISEASESTAGE', 'PATHOLOGY_T_STAGE', 'PATHOLOGY_N_STAGE', 'GENDER', 'HISTOLOGICAL_TYPE', and 'RACE'.
del_13q14.2 cnv correlated to 'Time to Death', 'YEARS_TO_BIRTH', 'NEOPLASM_DISEASESTAGE', 'PATHOLOGY_T_STAGE', 'PATHOLOGY_N_STAGE', 'GENDER', 'HISTOLOGICAL_TYPE', and 'RACE'.
del_14q31.1 cnv correlated to 'Time to Death', 'YEARS_TO_BIRTH', 'NEOPLASM_DISEASESTAGE', 'PATHOLOGY_T_STAGE', 'PATHOLOGY_N_STAGE', 'PATHOLOGY_M_STAGE', 'KARNOFSKY_PERFORMANCE_SCORE', 'HISTOLOGICAL_TYPE', 'YEAR_OF_TOBACCO_SMOKING_ONSET', and 'RACE'.
del_16q23.3 cnv correlated to 'Time to Death', 'NEOPLASM_DISEASESTAGE', 'PATHOLOGY_T_STAGE', and 'PATHOLOGY_N_STAGE'.
del_18q22.2 cnv correlated to 'Time to Death', 'NEOPLASM_DISEASESTAGE', 'PATHOLOGY_T_STAGE', 'PATHOLOGY_N_STAGE', 'PATHOLOGY_M_STAGE', 'YEAR_OF_TOBACCO_SMOKING_ONSET', 'RACE', and 'ETHNICITY'.
del_19p13.3 cnv correlated to 'Time to Death', 'NEOPLASM_DISEASESTAGE', 'PATHOLOGY_T_STAGE', 'PATHOLOGY_N_STAGE', 'PATHOLOGY_M_STAGE', 'KARNOFSKY_PERFORMANCE_SCORE', and 'HISTOLOGICAL_TYPE'.
del_xp22.2 cnv correlated to 'YEARS_TO_BIRTH', 'NEOPLASM_DISEASESTAGE', '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 13 clinical features. Shown in the table are P values (Q values). Thresholded by Q value < 0.25, 253 significant findings detected.


		Clinical Features	Time to Death	YEARS TO BIRTH	NEOPLASM DISEASESTAGE	PATHOLOGY T STAGE	PATHOLOGY N STAGE	PATHOLOGY M STAGE	GENDER	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	Wilcoxon-test	Fisher's exact test	Wilcoxon-test	Wilcoxon-test	Fisher's exact test	Fisher's exact test
del 14q31 1	274 (32%)	585	8.67e-09 (8.79e-07)	0.0799 (0.178)	1e-05 (7.57e-05)	1e-05 (7.57e-05)	0.00205 (0.00829)	4.84e-05 (0.000332)	0.699 (0.819)	0.0447 (0.111)	1e-05 (7.57e-05)	0.163 (0.305)	0.00272 (0.0106)	0.011 (0.0346)	1 (1.00)
amp 8q24 22	121 (14%)	738	0.00646 (0.0217)	0.0485 (0.119)	1e-05 (7.57e-05)	1e-05 (7.57e-05)	0.0615 (0.147)	0.00979 (0.0312)	0.533 (0.664)	0.86 (0.932)	0.00092 (0.0042)	0.118 (0.237)	0.149 (0.287)	0.00454 (0.0162)	1 (1.00)
del 3p21 2	499 (58%)	360	7.97e-06 (7.57e-05)	0.683 (0.803)	1e-05 (7.57e-05)	1e-05 (7.57e-05)	0.0986 (0.208)	0.0049 (0.017)	0.143 (0.277)	0.0596 (0.143)	1e-05 (7.57e-05)	0.194 (0.342)	0.0343 (0.0893)	1e-05 (7.57e-05)	0.873 (0.936)
del 9p23	196 (23%)	663	2.91e-11 (4.92e-09)	0.0247 (0.068)	1e-05 (7.57e-05)	1e-05 (7.57e-05)	0.00724 (0.0241)	0.000223 (0.00121)	0.301 (0.453)	0.0204 (0.0586)	1e-05 (7.57e-05)	0.932 (0.966)	0.525 (0.656)	0.0126 (0.0389)	0.704 (0.82)
del 9p21 3	207 (24%)	652	1.12e-14 (5.69e-12)	0.0358 (0.0915)	1e-05 (7.57e-05)	1e-05 (7.57e-05)	0.00013 (0.000758)	9.23e-06 (7.57e-05)	0.177 (0.323)	0.0401 (0.102)	1e-05 (7.57e-05)	0.932 (0.966)	0.525 (0.656)	0.00827 (0.0271)	0.852 (0.927)
amp 17q25 2	232 (27%)	627	0.592 (0.723)	0.0619 (0.147)	0.00052 (0.00251)	0.003 (0.0114)	0.00017 (0.000968)	0.214 (0.366)	0.000821 (0.00382)	0.514 (0.651)	1e-05 (7.57e-05)	0.987 (1.00)	0.0926 (0.197)	0.0121 (0.0379)	0.228 (0.38)
del 3p26 3	486 (57%)	373	0.00113 (0.00513)	0.786 (0.884)	1e-05 (7.57e-05)	2e-05 (0.000149)	0.00885 (0.0288)	0.133 (0.261)	0.0684 (0.159)	0.151 (0.288)	1e-05 (7.57e-05)	0.43 (0.59)	0.0786 (0.175)	1e-05 (7.57e-05)	0.267 (0.423)
del 11q21	60 (7%)	799	0.00196 (0.0082)	0.00478 (0.0167)	0.00026 (0.00136)	0.00041 (0.00206)	0.00019 (0.00106)	0.0998 (0.209)	0.671 (0.793)	0.0624 (0.147)	0.00304 (0.0114)	0.46 (0.619)	0.886 (0.941)	0.418 (0.578)	0.349 (0.504)
del 11q23 1	70 (8%)	789	0.00373 (0.0136)	0.00293 (0.0112)	3e-05 (0.000214)	1e-05 (7.57e-05)	0.00047 (0.00229)	0.112 (0.228)	0.428 (0.59)	0.0253 (0.0686)	0.00361 (0.0134)	0.669 (0.793)	0.927 (0.965)	0.27 (0.426)	0.242 (0.397)
del 13q12 13	148 (17%)	711	0.0323 (0.0845)	0.000423 (0.0021)	1e-05 (7.57e-05)	1e-05 (7.57e-05)	0.0135 (0.041)	0.228 (0.38)	0.0212 (0.0604)	0.316 (0.47)	1e-05 (7.57e-05)	0.751 (0.854)	0.278 (0.432)	0.103 (0.213)	0.377 (0.539)
del 13q14 2	148 (17%)	711	0.0241 (0.0666)	8.11e-05 (0.000501)	1e-05 (7.57e-05)	1e-05 (7.57e-05)	0.015 (0.0449)	0.132 (0.261)	0.0125 (0.0389)	0.379 (0.541)	1e-05 (7.57e-05)	0.914 (0.955)	0.249 (0.407)	0.104 (0.214)	0.66 (0.791)
del 18q22 2	152 (18%)	707	6.48e-07 (5.47e-05)	0.619 (0.749)	1e-05 (7.57e-05)	1e-05 (7.57e-05)	0.0213 (0.0604)	0.00917 (0.0294)	1 (1.00)	0.56 (0.693)	0.318 (0.472)	0.513 (0.651)	0.117 (0.236)	0.0746 (0.171)	0.0894 (0.192)
amp 1q32 1	81 (9%)	778	0.000273 (0.00141)	0.0313 (0.0827)	3e-05 (0.000214)	0.00019 (0.00106)	0.0705 (0.163)	0.137 (0.269)	0.623 (0.752)	0.297 (0.45)	0.00282 (0.0108)	0.336 (0.491)	0.101 (0.212)	0.149 (0.287)	0.259 (0.415)
amp xq11 2	128 (15%)	731	0.0918 (0.196)	0.468 (0.62)	0.00471 (0.0167)	0.00788 (0.0259)	0.894 (0.945)	0.564 (0.695)	0.000237 (0.00127)	0.0254 (0.0686)	1e-05 (7.57e-05)	0.742 (0.847)	0.0193 (0.0556)	0.184 (0.335)	0.661 (0.791)
del 3p12 2	334 (39%)	525	0.00116 (0.00521)	0.813 (0.902)	0.0127 (0.039)	0.00642 (0.0217)	0.515 (0.651)	0.731 (0.841)	0.0884 (0.191)	0.774 (0.874)	1e-05 (7.57e-05)	0.233 (0.385)	0.0826 (0.182)	0.00473 (0.0167)	0.741 (0.847)
del 4q34 3	111 (13%)	748	7.22e-09 (8.79e-07)	0.671 (0.793)	1e-05 (7.57e-05)	1e-05 (7.57e-05)	0.0109 (0.0346)	0.0143 (0.043)	0.83 (0.911)	0.885 (0.941)	0.0318 (0.0836)	0.401 (0.561)	0.665 (0.793)	0.0647 (0.151)	0.482 (0.634)
del 6q22 31	225 (26%)	634	0.383 (0.543)	0.124 (0.248)	0.00013 (0.000758)	4e-05 (0.000278)	0.0357 (0.0915)	1 (1.00)	0.681 (0.803)	0.107 (0.219)	1e-05 (7.57e-05)	0.206 (0.356)	0.22 (0.372)	0.00221 (0.00882)	0.263 (0.42)
del 19p13 3	40 (5%)	819	8.5e-12 (2.16e-09)	0.443 (0.601)	6e-05 (0.00038)	1e-05 (7.57e-05)	0.00022 (0.00121)	0.064 (0.15)	0.864 (0.934)	0.0779 (0.175)	0.0287 (0.0763)	0.464 (0.62)		0.334 (0.49)	0.716 (0.829)
amp 3q26 32	185 (22%)	674	0.414 (0.574)	0.116 (0.236)	0.21 (0.361)	0.185 (0.336)	0.0217 (0.061)	0.00735 (0.0244)	0.187 (0.337)	0.107 (0.219)	1e-05 (7.57e-05)	0.38 (0.541)	0.262 (0.419)	0.0571 (0.138)	0.704 (0.82)
amp 5q35 1	372 (43%)	487	0.189 (0.338)	0.129 (0.256)	0.00012 (0.000724)	0.00911 (0.0294)	0.0235 (0.0656)	0.0161 (0.0467)	0.307 (0.459)	0.514 (0.651)	1e-05 (7.57e-05)	0.431 (0.59)	0.274 (0.428)	3e-05 (0.000214)	0.873 (0.936)
amp xp22 2	121 (14%)	738	0.269 (0.425)	0.392 (0.552)	0.0233 (0.0654)	0.0759 (0.173)	0.896 (0.945)	0.252 (0.409)	0.00494 (0.017)	0.0254 (0.0686)	1e-05 (7.57e-05)	0.826 (0.91)	0.044 (0.11)	0.32 (0.474)	0.821 (0.907)
amp xp11 4	129 (15%)	730	0.236 (0.388)	0.28 (0.434)	0.00376 (0.0136)	0.0259 (0.069)	0.897 (0.945)	0.133 (0.261)	0.000532 (0.00254)	0.0254 (0.0686)	1e-05 (7.57e-05)	0.832 (0.911)	0.0579 (0.139)	0.251 (0.408)	0.522 (0.656)
amp xq28	132 (15%)	727	0.0777 (0.175)	0.46 (0.619)	0.0369 (0.094)	0.0412 (0.104)	0.908 (0.953)	0.466 (0.62)	0.016 (0.0465)	0.00192 (0.00811)	1e-05 (7.57e-05)	0.855 (0.928)	0.267 (0.423)	0.162 (0.304)	0.282 (0.435)
del 1p36 31	203 (24%)	656	0.396 (0.556)	0.0774 (0.175)	1e-05 (7.57e-05)	1e-05 (7.57e-05)	0.0685 (0.159)	0.502 (0.645)	0.496 (0.643)	0.0152 (0.045)	1e-05 (7.57e-05)	0.344 (0.499)	0.327 (0.482)	0.603 (0.732)	0.335 (0.49)
del 1p31 1	161 (19%)	698	0.511 (0.651)	0.0352 (0.091)	4e-05 (0.000278)	5e-05 (0.000334)	0.102 (0.213)	0.885 (0.941)	1 (1.00)	0.229 (0.38)	1e-05 (7.57e-05)	0.473 (0.623)	0.699 (0.819)	0.397 (0.556)	0.0856 (0.186)
del 2q37 3	110 (13%)	749	0.0153 (0.0451)	0.00203 (0.00829)	1e-05 (7.57e-05)	1e-05 (7.57e-05)	0.282 (0.435)	0.0853 (0.186)	0.516 (0.651)	0.955 (0.986)	1e-05 (7.57e-05)	0.559 (0.692)	0.866 (0.934)	0.494 (0.642)	1 (1.00)
del 3p14 1	405 (47%)	454	0.00206 (0.00829)	0.91 (0.953)	0.00023 (0.00124)	6e-05 (0.00038)	0.219 (0.372)	0.565 (0.695)	0.192 (0.341)	0.286 (0.438)	1e-05 (7.57e-05)	0.34 (0.496)	0.055 (0.133)	0.00013 (0.000758)	0.75 (0.854)
del 6q26	230 (27%)	629	0.302 (0.453)	0.187 (0.337)	6e-05 (0.00038)	5e-05 (0.000334)	0.0548 (0.133)	1 (1.00)	0.624 (0.752)	0.086 (0.186)	1e-05 (7.57e-05)	0.206 (0.356)	0.22 (0.372)	0.00126 (0.0056)	0.191 (0.34)
del 6q26	231 (27%)	628	0.298 (0.45)	0.193 (0.341)	8e-05 (0.000501)	6e-05 (0.00038)	0.0549 (0.133)	1 (1.00)	0.807 (0.899)	0.086 (0.186)	1e-05 (7.57e-05)	0.206 (0.356)	0.22 (0.372)	0.00323 (0.012)	0.192 (0.341)
del 8p23 2	181 (21%)	678	0.000909 (0.00419)	0.501 (0.645)	0.00201 (0.00829)	0.00183 (0.0078)	0.47 (0.62)	0.0257 (0.0689)	0.791 (0.887)	0.434 (0.593)	1e-05 (7.57e-05)	0.491 (0.64)	0.524 (0.656)	0.00376 (0.0136)	0.156 (0.295)
amp 7q31 2	364 (42%)	495	0.91 (0.953)	0.376 (0.539)	0.0134 (0.041)	0.793 (0.887)	0.228 (0.38)	0.00198 (0.00821)	7.63e-06 (7.57e-05)	0.292 (0.445)	1e-05 (7.57e-05)	0.411 (0.571)	0.0146 (0.0439)	0.186 (0.337)	0.259 (0.415)
del 1q43	112 (13%)	747	0.0476 (0.118)	0.00276 (0.0107)	0.00037 (0.00188)	0.00154 (0.00662)	0.275 (0.429)	0.17 (0.314)	0.164 (0.305)	0.139 (0.272)	1e-05 (7.57e-05)	0.831 (0.911)	0.601 (0.731)	0.226 (0.38)	0.146 (0.282)
del 5p15 33	31 (4%)	828	0.948 (0.981)	0.00445 (0.016)	0.00148 (0.00647)	0.00057 (0.0027)	0.00573 (0.0196)	0.741 (0.847)	0.176 (0.323)	0.777 (0.875)	1e-05 (7.57e-05)	0.469 (0.62)	0.253 (0.41)	0.575 (0.706)	0.154 (0.291)
del 10q23 31	162 (19%)	697	0.707 (0.822)	0.0425 (0.107)	1e-05 (7.57e-05)	1e-05 (7.57e-05)	0.341 (0.496)	0.888 (0.941)	0.713 (0.827)	0.283 (0.435)	1e-05 (7.57e-05)	0.214 (0.366)	0.223 (0.375)	0.0994 (0.209)	0.385 (0.544)
del xp22 2	123 (14%)	736	0.918 (0.958)	0.00136 (0.006)	0.0001 (0.000611)	0.00025 (0.00132)	0.0948 (0.201)	0.867 (0.934)	0.538 (0.668)	0.718 (0.829)	1e-05 (7.57e-05)	0.813 (0.902)	0.291 (0.445)	0.152 (0.289)	0.46 (0.619)
amp 19p13 2	97 (11%)	762	0.957 (0.986)	0.436 (0.594)	0.00152 (0.00659)	0.00247 (0.00978)	0.593 (0.723)	0.0156 (0.0456)	0.17 (0.314)	0.301 (0.453)	0.00034 (0.00174)	0.404 (0.563)	0.768 (0.87)	0.507 (0.651)	0.803 (0.897)
del 16q23 3	36 (4%)	823	9.39e-06 (7.57e-05)	0.724 (0.834)	0.00647 (0.0217)	0.00014 (0.000807)	0.00046 (0.00226)	0.353 (0.508)	1 (1.00)	0.489 (0.64)	0.151 (0.288)	0.168 (0.313)	0.82 (0.907)	0.439 (0.596)	1 (1.00)
amp 2q32 1	133 (15%)	726	0.843 (0.921)	0.205 (0.356)	0.257 (0.414)	0.385 (0.544)	0.0752 (0.172)	0.876 (0.937)	0.273 (0.428)	0.467 (0.62)	0.00253 (0.00994)	0.85 (0.927)	0.461 (0.619)	0.491 (0.64)	0.656 (0.788)
amp 10p14	33 (4%)	826	0.67 (0.793)	0.311 (0.463)	0.126 (0.252)	0.00061 (0.00286)	0.0809 (0.179)	0.576 (0.706)	1 (1.00)	0.497 (0.643)	0.514 (0.651)	0.764 (0.866)		0.2 (0.351)	1 (1.00)

'amp_1q32.1' versus 'Time to Death'

P value = 0.000273 (logrank test), Q value = 0.0014

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

	nPatients	nDeath	Duration Range (Median), Month
ALL	843	211	0.1 - 194.8 (30.5)
AMP PEAK 1(1Q32.1) MUTATED	80	34	0.4 - 94.7 (26.8)
AMP PEAK 1(1Q32.1) WILD-TYPE	763	177	0.1 - 194.8 (30.7)

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 = 0.0313 (Wilcoxon-test), Q value = 0.083

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

	nPatients	Mean (Std.Dev)
ALL	853	60.1 (12.6)
AMP PEAK 1(1Q32.1) MUTATED	79	62.5 (12.2)
AMP PEAK 1(1Q32.1) WILD-TYPE	774	59.9 (12.6)

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

'amp_1q32.1' versus 'NEOPLASM_DISEASESTAGE'

P value = 3e-05 (Fisher's exact test), Q value = 0.00021

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

nPatients	STAGE I	STAGE II	STAGE III	STAGE IV
ALL	448	103	190	100
AMP PEAK 1(1Q32.1) MUTATED	24	10	32	15
AMP PEAK 1(1Q32.1) WILD-TYPE	424	93	158	85

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

'amp_1q32.1' versus 'PATHOLOGY_T_STAGE'

P value = 0.00019 (Fisher's exact test), Q value = 0.0011

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

nPatients	T1	T2	T3	T4
ALL	462	123	251	15
AMP PEAK 1(1Q32.1) MUTATED	27	12	41	1
AMP PEAK 1(1Q32.1) WILD-TYPE	435	111	210	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 = 0.0705 (Fisher's exact test), Q value = 0.16

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

nPatients	N0	N1	N2
ALL	317	43	6
AMP PEAK 1(1Q32.1) MUTATED	35	10	1
AMP PEAK 1(1Q32.1) WILD-TYPE	282	33	5

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

'amp_1q32.1' versus 'HISTOLOGICAL_TYPE'

P value = 0.00282 (Fisher's exact test), Q value = 0.011

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

nPatients	KIDNEY CHROMOPHOBE	KIDNEY CLEAR CELL RENAL CARCINOMA	KIDNEY PAPILLARY RENAL CELL CARCINOMA
ALL	66	524	269
AMP PEAK 1(1Q32.1) MUTATED	1	62	18
AMP PEAK 1(1Q32.1) WILD-TYPE	65	462	251

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

'amp_1q32.1' versus 'YEAR_OF_TOBACCO_SMOKING_ONSET'

P value = 0.101 (Wilcoxon-test), Q value = 0.21

Table S7. Gene #1: 'amp_1q32.1' versus Clinical Feature #11: 'YEAR_OF_TOBACCO_SMOKING_ONSET'

	nPatients	Mean (Std.Dev)
ALL	67	1973.4 (16.4)
AMP PEAK 1(1Q32.1) MUTATED	3	1989.0 (19.2)
AMP PEAK 1(1Q32.1) WILD-TYPE	64	1972.7 (16.1)

Figure S7. Get High-res Image Gene #1: 'amp_1q32.1' versus Clinical Feature #11: 'YEAR_OF_TOBACCO_SMOKING_ONSET'

'amp_2q32.1' versus 'PATHOLOGY_N_STAGE'

P value = 0.0752 (Fisher's exact test), Q value = 0.17

Table S8. Gene #2: 'amp_2q32.1' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

nPatients	N0	N1	N2
ALL	317	43	6
AMP PEAK 2(2Q32.1) MUTATED	47	11	2
AMP PEAK 2(2Q32.1) WILD-TYPE	270	32	4

Figure S8. Get High-res Image Gene #2: 'amp_2q32.1' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

'amp_2q32.1' versus 'HISTOLOGICAL_TYPE'

P value = 0.00253 (Fisher's exact test), Q value = 0.0099

Table S9. Gene #2: 'amp_2q32.1' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'

nPatients	KIDNEY CHROMOPHOBE	KIDNEY CLEAR CELL RENAL CARCINOMA	KIDNEY PAPILLARY RENAL CELL CARCINOMA
ALL	66	524	269
AMP PEAK 2(2Q32.1) MUTATED	2	80	51
AMP PEAK 2(2Q32.1) WILD-TYPE	64	444	218

Figure S9. Get High-res Image Gene #2: 'amp_2q32.1' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'

'amp_3q26.32' versus 'YEARS_TO_BIRTH'

P value = 0.116 (Wilcoxon-test), Q value = 0.24

Table S10. Gene #3: 'amp_3q26.32' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

	nPatients	Mean (Std.Dev)
ALL	853	60.1 (12.6)
AMP PEAK 3(3Q26.32) MUTATED	182	61.5 (12.1)
AMP PEAK 3(3Q26.32) WILD-TYPE	671	59.7 (12.7)

Figure S10. 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 = 0.0217 (Fisher's exact test), Q value = 0.061

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

nPatients	N0	N1	N2
ALL	317	43	6
AMP PEAK 3(3Q26.32) MUTATED	57	15	0
AMP PEAK 3(3Q26.32) WILD-TYPE	260	28	6

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

'amp_3q26.32' versus 'PATHOLOGY_M_STAGE'

P value = 0.00735 (Fisher's exact test), Q value = 0.024

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

nPatients	0	1
ALL	542	89
AMP PEAK 3(3Q26.32) MUTATED	90	26
AMP PEAK 3(3Q26.32) WILD-TYPE	452	63

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

'amp_3q26.32' versus 'KARNOFSKY_PERFORMANCE_SCORE'

P value = 0.107 (Wilcoxon-test), Q value = 0.22

Table S13. Gene #3: 'amp_3q26.32' versus Clinical Feature #8: 'KARNOFSKY_PERFORMANCE_SCORE'

	nPatients	Mean (Std.Dev)
ALL	115	90.3 (17.6)
AMP PEAK 3(3Q26.32) MUTATED	31	94.8 (6.8)
AMP PEAK 3(3Q26.32) WILD-TYPE	84	88.6 (19.9)

Figure S13. Get High-res Image Gene #3: 'amp_3q26.32' versus Clinical Feature #8: 'KARNOFSKY_PERFORMANCE_SCORE'

'amp_3q26.32' versus 'HISTOLOGICAL_TYPE'

P value = 1e-05 (Fisher's exact test), Q value = 7.6e-05

Table S14. Gene #3: 'amp_3q26.32' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'

nPatients	KIDNEY CHROMOPHOBE	KIDNEY CLEAR CELL RENAL CARCINOMA	KIDNEY PAPILLARY RENAL CELL CARCINOMA
ALL	66	524	269
AMP PEAK 3(3Q26.32) MUTATED	6	86	93
AMP PEAK 3(3Q26.32) WILD-TYPE	60	438	176

Figure S14. Get High-res Image Gene #3: 'amp_3q26.32' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'

'amp_3q26.32' versus 'RACE'

P value = 0.0571 (Fisher's exact test), Q value = 0.14

Table S15. Gene #3: 'amp_3q26.32' versus Clinical Feature #12: 'RACE'

nPatients	AMERICAN INDIAN OR ALASKA NATIVE	ASIAN	BLACK OR AFRICAN AMERICAN	WHITE
ALL	2	15	116	702
AMP PEAK 3(3Q26.32) MUTATED	2	1	24	149
AMP PEAK 3(3Q26.32) WILD-TYPE	0	14	92	553

Figure S15. Get High-res Image Gene #3: 'amp_3q26.32' versus Clinical Feature #12: 'RACE'

'amp_5q35.1' versus 'NEOPLASM_DISEASESTAGE'

P value = 0.00012 (Fisher's exact test), Q value = 0.00072

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

nPatients	STAGE I	STAGE II	STAGE III	STAGE IV
ALL	448	103	190	100
AMP PEAK 4(5Q35.1) MUTATED	172	42	93	62
AMP PEAK 4(5Q35.1) WILD-TYPE	276	61	97	38

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

'amp_5q35.1' versus 'PATHOLOGY_T_STAGE'

P value = 0.00911 (Fisher's exact test), Q value = 0.029

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

nPatients	T1	T2	T3	T4
ALL	462	123	251	15
AMP PEAK 4(5Q35.1) MUTATED	179	55	130	7
AMP PEAK 4(5Q35.1) WILD-TYPE	283	68	121	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 = 0.0235 (Fisher's exact test), Q value = 0.066

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

nPatients	N0	N1	N2
ALL	317	43	6
AMP PEAK 4(5Q35.1) MUTATED	161	14	1
AMP PEAK 4(5Q35.1) WILD-TYPE	156	29	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 = 0.0161 (Fisher's exact test), Q value = 0.047

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

nPatients	0	1
ALL	542	89
AMP PEAK 4(5Q35.1) MUTATED	278	58
AMP PEAK 4(5Q35.1) WILD-TYPE	264	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 = 7.6e-05

Table S20. Gene #4: 'amp_5q35.1' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'

nPatients	KIDNEY CHROMOPHOBE	KIDNEY CLEAR CELL RENAL CARCINOMA	KIDNEY PAPILLARY RENAL CELL CARCINOMA
ALL	66	524	269
AMP PEAK 4(5Q35.1) MUTATED	8	330	34
AMP PEAK 4(5Q35.1) WILD-TYPE	58	194	235

Figure S20. Get High-res Image Gene #4: 'amp_5q35.1' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'

'amp_5q35.1' versus 'RACE'

P value = 3e-05 (Fisher's exact test), Q value = 0.00021

Table S21. Gene #4: 'amp_5q35.1' versus Clinical Feature #12: 'RACE'

nPatients	AMERICAN INDIAN OR ALASKA NATIVE	ASIAN	BLACK OR AFRICAN AMERICAN	WHITE
ALL	2	15	116	702
AMP PEAK 4(5Q35.1) MUTATED	0	5	29	331
AMP PEAK 4(5Q35.1) WILD-TYPE	2	10	87	371

Figure S21. Get High-res Image Gene #4: 'amp_5q35.1' versus Clinical Feature #12: 'RACE'

'amp_7q31.2' versus 'NEOPLASM_DISEASESTAGE'

P value = 0.0134 (Fisher's exact test), Q value = 0.041

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

nPatients	STAGE I	STAGE II	STAGE III	STAGE IV
ALL	448	103	190	100
AMP PEAK 5(7Q31.2) MUTATED	193	37	68	54
AMP PEAK 5(7Q31.2) WILD-TYPE	255	66	122	46

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

'amp_7q31.2' versus 'PATHOLOGY_M_STAGE'

P value = 0.00198 (Fisher's exact test), Q value = 0.0082

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

nPatients	0	1
ALL	542	89
AMP PEAK 5(7Q31.2) MUTATED	189	47
AMP PEAK 5(7Q31.2) WILD-TYPE	353	42

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

'amp_7q31.2' versus 'GENDER'

P value = 7.63e-06 (Fisher's exact test), Q value = 7.6e-05

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

nPatients	FEMALE	MALE
ALL	287	572
AMP PEAK 5(7Q31.2) MUTATED	91	273
AMP PEAK 5(7Q31.2) WILD-TYPE	196	299

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

'amp_7q31.2' versus 'HISTOLOGICAL_TYPE'

P value = 1e-05 (Fisher's exact test), Q value = 7.6e-05

Table S25. Gene #5: 'amp_7q31.2' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'

nPatients	KIDNEY CHROMOPHOBE	KIDNEY CLEAR CELL RENAL CARCINOMA	KIDNEY PAPILLARY RENAL CELL CARCINOMA
ALL	66	524	269
AMP PEAK 5(7Q31.2) MUTATED	25	174	165
AMP PEAK 5(7Q31.2) WILD-TYPE	41	350	104

Figure S25. Get High-res Image Gene #5: 'amp_7q31.2' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'

'amp_7q31.2' versus 'YEAR_OF_TOBACCO_SMOKING_ONSET'

P value = 0.0146 (Wilcoxon-test), Q value = 0.044

Table S26. Gene #5: 'amp_7q31.2' versus Clinical Feature #11: 'YEAR_OF_TOBACCO_SMOKING_ONSET'

	nPatients	Mean (Std.Dev)
ALL	67	1973.4 (16.4)
AMP PEAK 5(7Q31.2) MUTATED	36	1969.0 (15.8)
AMP PEAK 5(7Q31.2) WILD-TYPE	31	1978.5 (15.8)

Figure S26. Get High-res Image Gene #5: 'amp_7q31.2' versus Clinical Feature #11: 'YEAR_OF_TOBACCO_SMOKING_ONSET'

'amp_8q24.22' versus 'Time to Death'

P value = 0.00646 (logrank test), Q value = 0.022

Table S27. Gene #6: 'amp_8q24.22' versus Clinical Feature #1: 'Time to Death'

	nPatients	nDeath	Duration Range (Median), Month
ALL	843	211	0.1 - 194.8 (30.5)
AMP PEAK 6(8Q24.22) MUTATED	120	40	0.2 - 152.0 (25.8)
AMP PEAK 6(8Q24.22) WILD-TYPE	723	171	0.1 - 194.8 (31.2)

Figure S27. 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 = 0.0485 (Wilcoxon-test), Q value = 0.12

Table S28. Gene #6: 'amp_8q24.22' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

	nPatients	Mean (Std.Dev)
ALL	853	60.1 (12.6)
AMP PEAK 6(8Q24.22) MUTATED	121	62.1 (12.7)
AMP PEAK 6(8Q24.22) WILD-TYPE	732	59.8 (12.5)

Figure S28. Get High-res Image Gene #6: 'amp_8q24.22' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'amp_8q24.22' versus 'NEOPLASM_DISEASESTAGE'

P value = 1e-05 (Fisher's exact test), Q value = 7.6e-05

Table S29. Gene #6: 'amp_8q24.22' versus Clinical Feature #3: 'NEOPLASM_DISEASESTAGE'

nPatients	STAGE I	STAGE II	STAGE III	STAGE IV
ALL	448	103	190	100
AMP PEAK 6(8Q24.22) MUTATED	35	22	37	25
AMP PEAK 6(8Q24.22) WILD-TYPE	413	81	153	75

Figure S29. Get High-res Image Gene #6: 'amp_8q24.22' versus Clinical Feature #3: 'NEOPLASM_DISEASESTAGE'

'amp_8q24.22' versus 'PATHOLOGY_T_STAGE'

P value = 1e-05 (Fisher's exact test), Q value = 7.6e-05

Table S30. Gene #6: 'amp_8q24.22' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

nPatients	T1	T2	T3	T4
ALL	462	123	251	15
AMP PEAK 6(8Q24.22) MUTATED	36	23	56	4
AMP PEAK 6(8Q24.22) WILD-TYPE	426	100	195	11

Figure S30. 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 = 0.0615 (Fisher's exact test), Q value = 0.15

Table S31. Gene #6: 'amp_8q24.22' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

nPatients	N0	N1	N2
ALL	317	43	6
AMP PEAK 6(8Q24.22) MUTATED	50	12	2
AMP PEAK 6(8Q24.22) WILD-TYPE	267	31	4

Figure S31. 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 = 0.00979 (Fisher's exact test), Q value = 0.031

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

nPatients	0	1
ALL	542	89
AMP PEAK 6(8Q24.22) MUTATED	73	22
AMP PEAK 6(8Q24.22) WILD-TYPE	469	67

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

'amp_8q24.22' versus 'HISTOLOGICAL_TYPE'

P value = 0.00092 (Fisher's exact test), Q value = 0.0042

Table S33. Gene #6: 'amp_8q24.22' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'

nPatients	KIDNEY CHROMOPHOBE	KIDNEY CLEAR CELL RENAL CARCINOMA	KIDNEY PAPILLARY RENAL CELL CARCINOMA
ALL	66	524	269
AMP PEAK 6(8Q24.22) MUTATED	18	78	25
AMP PEAK 6(8Q24.22) WILD-TYPE	48	446	244

Figure S33. Get High-res Image Gene #6: 'amp_8q24.22' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'

'amp_8q24.22' versus 'NUMBER_PACK_YEARS_SMOKED'

P value = 0.118 (Wilcoxon-test), Q value = 0.24

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

	nPatients	Mean (Std.Dev)
ALL	91	30.8 (26.2)
AMP PEAK 6(8Q24.22) MUTATED	12	20.8 (15.9)
AMP PEAK 6(8Q24.22) WILD-TYPE	79	32.3 (27.2)

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

'amp_8q24.22' versus 'RACE'

P value = 0.00454 (Fisher's exact test), Q value = 0.016

Table S35. Gene #6: 'amp_8q24.22' versus Clinical Feature #12: 'RACE'

nPatients	AMERICAN INDIAN OR ALASKA NATIVE	ASIAN	BLACK OR AFRICAN AMERICAN	WHITE
ALL	2	15	116	702
AMP PEAK 6(8Q24.22) MUTATED	0	4	6	108
AMP PEAK 6(8Q24.22) WILD-TYPE	2	11	110	594

Figure S35. Get High-res Image Gene #6: 'amp_8q24.22' versus Clinical Feature #12: 'RACE'

'amp_10p14' versus 'PATHOLOGY_T_STAGE'

P value = 0.00061 (Fisher's exact test), Q value = 0.0029

Table S36. Gene #7: 'amp_10p14' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

nPatients	T1	T2	T3	T4
ALL	462	123	251	15
AMP PEAK 7(10P14) MUTATED	13	9	7	4
AMP PEAK 7(10P14) WILD-TYPE	449	114	244	11

Figure S36. Get High-res Image Gene #7: 'amp_10p14' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

'amp_10p14' versus 'PATHOLOGY_N_STAGE'

P value = 0.0809 (Fisher's exact test), Q value = 0.18

Table S37. Gene #7: 'amp_10p14' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

nPatients	N0	N1	N2
ALL	317	43	6
AMP PEAK 7(10P14) MUTATED	12	5	0
AMP PEAK 7(10P14) WILD-TYPE	305	38	6

Figure S37. Get High-res Image Gene #7: 'amp_10p14' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

'amp_17q25.2' versus 'YEARS_TO_BIRTH'

P value = 0.0619 (Wilcoxon-test), Q value = 0.15

Table S38. Gene #8: 'amp_17q25.2' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

	nPatients	Mean (Std.Dev)
ALL	853	60.1 (12.6)
AMP PEAK 8(17Q25.2) MUTATED	229	61.4 (12.3)
AMP PEAK 8(17Q25.2) WILD-TYPE	624	59.6 (12.6)

Figure S38. Get High-res Image Gene #8: 'amp_17q25.2' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'amp_17q25.2' versus 'NEOPLASM_DISEASESTAGE'

P value = 0.00052 (Fisher's exact test), Q value = 0.0025

Table S39. Gene #8: 'amp_17q25.2' versus Clinical Feature #3: 'NEOPLASM_DISEASESTAGE'

nPatients	STAGE I	STAGE II	STAGE III	STAGE IV
ALL	448	103	190	100
AMP PEAK 8(17Q25.2) MUTATED	144	21	42	15
AMP PEAK 8(17Q25.2) WILD-TYPE	304	82	148	85

Figure S39. Get High-res Image Gene #8: 'amp_17q25.2' versus Clinical Feature #3: 'NEOPLASM_DISEASESTAGE'

'amp_17q25.2' versus 'PATHOLOGY_T_STAGE'

P value = 0.003 (Fisher's exact test), Q value = 0.011

Table S40. Gene #8: 'amp_17q25.2' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

nPatients	T1	T2	T3	T4
ALL	462	123	251	15
AMP PEAK 8(17Q25.2) MUTATED	148	28	50	4
AMP PEAK 8(17Q25.2) WILD-TYPE	314	95	201	11

Figure S40. 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 = 0.00017 (Fisher's exact test), Q value = 0.00097

Table S41. Gene #8: 'amp_17q25.2' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

nPatients	N0	N1	N2
ALL	317	43	6
AMP PEAK 8(17Q25.2) MUTATED	46	16	3
AMP PEAK 8(17Q25.2) WILD-TYPE	271	27	3

Figure S41. Get High-res Image Gene #8: 'amp_17q25.2' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

'amp_17q25.2' versus 'GENDER'

P value = 0.000821 (Fisher's exact test), Q value = 0.0038

Table S42. Gene #8: 'amp_17q25.2' versus Clinical Feature #7: 'GENDER'

nPatients	FEMALE	MALE
ALL	287	572
AMP PEAK 8(17Q25.2) MUTATED	57	175
AMP PEAK 8(17Q25.2) WILD-TYPE	230	397

Figure S42. 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 = 7.6e-05

Table S43. Gene #8: 'amp_17q25.2' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'

nPatients	KIDNEY CHROMOPHOBE	KIDNEY CLEAR CELL RENAL CARCINOMA	KIDNEY PAPILLARY RENAL CELL CARCINOMA
ALL	66	524	269
AMP PEAK 8(17Q25.2) MUTATED	1	42	189
AMP PEAK 8(17Q25.2) WILD-TYPE	65	482	80

Figure S43. Get High-res Image Gene #8: 'amp_17q25.2' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'

'amp_17q25.2' versus 'YEAR_OF_TOBACCO_SMOKING_ONSET'

P value = 0.0926 (Wilcoxon-test), Q value = 0.2

Table S44. Gene #8: 'amp_17q25.2' versus Clinical Feature #11: 'YEAR_OF_TOBACCO_SMOKING_ONSET'

	nPatients	Mean (Std.Dev)
ALL	67	1973.4 (16.4)
AMP PEAK 8(17Q25.2) MUTATED	33	1970.4 (16.0)
AMP PEAK 8(17Q25.2) WILD-TYPE	34	1976.3 (16.5)

Figure S44. Get High-res Image Gene #8: 'amp_17q25.2' versus Clinical Feature #11: 'YEAR_OF_TOBACCO_SMOKING_ONSET'

'amp_17q25.2' versus 'RACE'

P value = 0.0121 (Fisher's exact test), Q value = 0.038

Table S45. Gene #8: 'amp_17q25.2' versus Clinical Feature #12: 'RACE'

nPatients	AMERICAN INDIAN OR ALASKA NATIVE	ASIAN	BLACK OR AFRICAN AMERICAN	WHITE
ALL	2	15	116	702
AMP PEAK 8(17Q25.2) MUTATED	2	6	39	175
AMP PEAK 8(17Q25.2) WILD-TYPE	0	9	77	527

Figure S45. Get High-res Image Gene #8: 'amp_17q25.2' versus Clinical Feature #12: 'RACE'

'amp_19p13.2' versus 'NEOPLASM_DISEASESTAGE'

P value = 0.00152 (Fisher's exact test), Q value = 0.0066

Table S46. Gene #9: 'amp_19p13.2' versus Clinical Feature #3: 'NEOPLASM_DISEASESTAGE'

nPatients	STAGE I	STAGE II	STAGE III	STAGE IV
ALL	448	103	190	100
AMP PEAK 9(19P13.2) MUTATED	35	18	19	19
AMP PEAK 9(19P13.2) WILD-TYPE	413	85	171	81

Figure S46. Get High-res Image Gene #9: 'amp_19p13.2' versus Clinical Feature #3: 'NEOPLASM_DISEASESTAGE'

'amp_19p13.2' versus 'PATHOLOGY_T_STAGE'

P value = 0.00247 (Fisher's exact test), Q value = 0.0098

Table S47. Gene #9: 'amp_19p13.2' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

nPatients	T1	T2	T3	T4
ALL	462	123	251	15
AMP PEAK 9(19P13.2) MUTATED	37	23	33	3
AMP PEAK 9(19P13.2) WILD-TYPE	425	100	218	12

Figure S47. 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 = 0.0156 (Fisher's exact test), Q value = 0.046

Table S48. Gene #9: 'amp_19p13.2' versus Clinical Feature #6: 'PATHOLOGY_M_STAGE'

nPatients	0	1
ALL	542	89
AMP PEAK 9(19P13.2) MUTATED	52	17
AMP PEAK 9(19P13.2) WILD-TYPE	490	72

Figure S48. Get High-res Image Gene #9: 'amp_19p13.2' versus Clinical Feature #6: 'PATHOLOGY_M_STAGE'

'amp_19p13.2' versus 'HISTOLOGICAL_TYPE'

P value = 0.00034 (Fisher's exact test), Q value = 0.0017

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

nPatients	KIDNEY CHROMOPHOBE	KIDNEY CLEAR CELL RENAL CARCINOMA	KIDNEY PAPILLARY RENAL CELL CARCINOMA
ALL	66	524	269
AMP PEAK 9(19P13.2) MUTATED	18	49	30
AMP PEAK 9(19P13.2) WILD-TYPE	48	475	239

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

'amp_xp22.2' versus 'NEOPLASM_DISEASESTAGE'

P value = 0.0233 (Fisher's exact test), Q value = 0.065

Table S50. Gene #10: 'amp_xp22.2' versus Clinical Feature #3: 'NEOPLASM_DISEASESTAGE'

nPatients	STAGE I	STAGE II	STAGE III	STAGE IV
ALL	448	103	190	100
AMP PEAK 10(XP22.2) MUTATED	72	14	14	15
AMP PEAK 10(XP22.2) WILD-TYPE	376	89	176	85

Figure S50. Get High-res Image Gene #10: 'amp_xp22.2' versus Clinical Feature #3: 'NEOPLASM_DISEASESTAGE'

'amp_xp22.2' versus 'PATHOLOGY_T_STAGE'

P value = 0.0759 (Fisher's exact test), Q value = 0.17

Table S51. Gene #10: 'amp_xp22.2' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

nPatients	T1	T2	T3	T4
ALL	462	123	251	15
AMP PEAK 10(XP22.2) MUTATED	73	19	24	3
AMP PEAK 10(XP22.2) WILD-TYPE	389	104	227	12

Figure S51. Get High-res Image Gene #10: 'amp_xp22.2' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

'amp_xp22.2' versus 'GENDER'

P value = 0.00494 (Fisher's exact test), Q value = 0.017

Table S52. Gene #10: 'amp_xp22.2' versus Clinical Feature #7: 'GENDER'

nPatients	FEMALE	MALE
ALL	287	572
AMP PEAK 10(XP22.2) MUTATED	27	94
AMP PEAK 10(XP22.2) WILD-TYPE	260	478

Figure S52. Get High-res Image Gene #10: 'amp_xp22.2' versus Clinical Feature #7: 'GENDER'

'amp_xp22.2' versus 'KARNOFSKY_PERFORMANCE_SCORE'

P value = 0.0254 (Wilcoxon-test), Q value = 0.069

Table S53. Gene #10: 'amp_xp22.2' versus Clinical Feature #8: 'KARNOFSKY_PERFORMANCE_SCORE'

	nPatients	Mean (Std.Dev)
ALL	115	90.3 (17.6)
AMP PEAK 10(XP22.2) MUTATED	26	92.3 (20.3)
AMP PEAK 10(XP22.2) WILD-TYPE	89	89.7 (16.8)

Figure S53. Get High-res Image Gene #10: 'amp_xp22.2' versus Clinical Feature #8: 'KARNOFSKY_PERFORMANCE_SCORE'

'amp_xp22.2' versus 'HISTOLOGICAL_TYPE'

P value = 1e-05 (Fisher's exact test), Q value = 7.6e-05

Table S54. Gene #10: 'amp_xp22.2' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'

nPatients	KIDNEY CHROMOPHOBE	KIDNEY CLEAR CELL RENAL CARCINOMA	KIDNEY PAPILLARY RENAL CELL CARCINOMA
ALL	66	524	269
AMP PEAK 10(XP22.2) MUTATED	7	30	84
AMP PEAK 10(XP22.2) WILD-TYPE	59	494	185

Figure S54. Get High-res Image Gene #10: 'amp_xp22.2' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'

'amp_xp22.2' versus 'YEAR_OF_TOBACCO_SMOKING_ONSET'

P value = 0.044 (Wilcoxon-test), Q value = 0.11

Table S55. Gene #10: 'amp_xp22.2' versus Clinical Feature #11: 'YEAR_OF_TOBACCO_SMOKING_ONSET'

	nPatients	Mean (Std.Dev)
ALL	67	1973.4 (16.4)
AMP PEAK 10(XP22.2) MUTATED	14	1966.4 (14.1)
AMP PEAK 10(XP22.2) WILD-TYPE	53	1975.3 (16.6)

Figure S55. Get High-res Image Gene #10: 'amp_xp22.2' versus Clinical Feature #11: 'YEAR_OF_TOBACCO_SMOKING_ONSET'

'amp_xp11.4' versus 'NEOPLASM_DISEASESTAGE'

P value = 0.00376 (Fisher's exact test), Q value = 0.014

Table S56. Gene #11: 'amp_xp11.4' versus Clinical Feature #3: 'NEOPLASM_DISEASESTAGE'

nPatients	STAGE I	STAGE II	STAGE III	STAGE IV
ALL	448	103	190	100
AMP PEAK 11(XP11.4) MUTATED	78	14	13	16
AMP PEAK 11(XP11.4) WILD-TYPE	370	89	177	84

Figure S56. Get High-res Image Gene #11: 'amp_xp11.4' versus Clinical Feature #3: 'NEOPLASM_DISEASESTAGE'

'amp_xp11.4' versus 'PATHOLOGY_T_STAGE'

P value = 0.0259 (Fisher's exact test), Q value = 0.069

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

nPatients	T1	T2	T3	T4
ALL	462	123	251	15
AMP PEAK 11(XP11.4) MUTATED	80	20	24	3
AMP PEAK 11(XP11.4) WILD-TYPE	382	103	227	12

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

'amp_xp11.4' versus 'GENDER'

P value = 0.000532 (Fisher's exact test), Q value = 0.0025

Table S58. Gene #11: 'amp_xp11.4' versus Clinical Feature #7: 'GENDER'

nPatients	FEMALE	MALE
ALL	287	572
AMP PEAK 11(XP11.4) MUTATED	26	103
AMP PEAK 11(XP11.4) WILD-TYPE	261	469

Figure S58. Get High-res Image Gene #11: 'amp_xp11.4' versus Clinical Feature #7: 'GENDER'

'amp_xp11.4' versus 'KARNOFSKY_PERFORMANCE_SCORE'

P value = 0.0254 (Wilcoxon-test), Q value = 0.069

Table S59. Gene #11: 'amp_xp11.4' versus Clinical Feature #8: 'KARNOFSKY_PERFORMANCE_SCORE'

	nPatients	Mean (Std.Dev)
ALL	115	90.3 (17.6)
AMP PEAK 11(XP11.4) MUTATED	26	92.3 (20.3)
AMP PEAK 11(XP11.4) WILD-TYPE	89	89.7 (16.8)

Figure S59. Get High-res Image Gene #11: 'amp_xp11.4' versus Clinical Feature #8: 'KARNOFSKY_PERFORMANCE_SCORE'

'amp_xp11.4' versus 'HISTOLOGICAL_TYPE'

P value = 1e-05 (Fisher's exact test), Q value = 7.6e-05

Table S60. Gene #11: 'amp_xp11.4' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'

nPatients	KIDNEY CHROMOPHOBE	KIDNEY CLEAR CELL RENAL CARCINOMA	KIDNEY PAPILLARY RENAL CELL CARCINOMA
ALL	66	524	269
AMP PEAK 11(XP11.4) MUTATED	7	32	90
AMP PEAK 11(XP11.4) WILD-TYPE	59	492	179

Figure S60. Get High-res Image Gene #11: 'amp_xp11.4' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'

'amp_xp11.4' versus 'YEAR_OF_TOBACCO_SMOKING_ONSET'

P value = 0.0579 (Wilcoxon-test), Q value = 0.14

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

	nPatients	Mean (Std.Dev)
ALL	67	1973.4 (16.4)
AMP PEAK 11(XP11.4) MUTATED	15	1966.9 (13.8)
AMP PEAK 11(XP11.4) WILD-TYPE	52	1975.3 (16.8)

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

'amp_xq11.2' versus 'Time to Death'

P value = 0.0918 (logrank test), Q value = 0.2

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

	nPatients	nDeath	Duration Range (Median), Month
ALL	843	211	0.1 - 194.8 (30.5)
AMP PEAK 12(XQ11.2) MUTATED	122	19	0.1 - 194.8 (25.6)
AMP PEAK 12(XQ11.2) WILD-TYPE	721	192	0.1 - 152.0 (31.3)

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

'amp_xq11.2' versus 'NEOPLASM_DISEASESTAGE'

P value = 0.00471 (Fisher's exact test), Q value = 0.017

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

nPatients	STAGE I	STAGE II	STAGE III	STAGE IV
ALL	448	103	190	100
AMP PEAK 12(XQ11.2) MUTATED	80	14	14	12
AMP PEAK 12(XQ11.2) WILD-TYPE	368	89	176	88

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

'amp_xq11.2' versus 'PATHOLOGY_T_STAGE'

P value = 0.00788 (Fisher's exact test), Q value = 0.026

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

nPatients	T1	T2	T3	T4
ALL	462	123	251	15
AMP PEAK 12(XQ11.2) MUTATED	82	20	22	2
AMP PEAK 12(XQ11.2) WILD-TYPE	380	103	229	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 = 0.000237 (Fisher's exact test), Q value = 0.0013

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

nPatients	FEMALE	MALE
ALL	287	572
AMP PEAK 12(XQ11.2) MUTATED	25	103
AMP PEAK 12(XQ11.2) WILD-TYPE	262	469

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

'amp_xq11.2' versus 'KARNOFSKY_PERFORMANCE_SCORE'

P value = 0.0254 (Wilcoxon-test), Q value = 0.069

Table S66. Gene #12: 'amp_xq11.2' versus Clinical Feature #8: 'KARNOFSKY_PERFORMANCE_SCORE'

	nPatients	Mean (Std.Dev)
ALL	115	90.3 (17.6)
AMP PEAK 12(XQ11.2) MUTATED	26	92.3 (20.3)
AMP PEAK 12(XQ11.2) WILD-TYPE	89	89.7 (16.8)

Figure S66. Get High-res Image Gene #12: 'amp_xq11.2' versus Clinical Feature #8: 'KARNOFSKY_PERFORMANCE_SCORE'

'amp_xq11.2' versus 'HISTOLOGICAL_TYPE'

P value = 1e-05 (Fisher's exact test), Q value = 7.6e-05

Table S67. Gene #12: 'amp_xq11.2' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'

nPatients	KIDNEY CHROMOPHOBE	KIDNEY CLEAR CELL RENAL CARCINOMA	KIDNEY PAPILLARY RENAL CELL CARCINOMA
ALL	66	524	269
AMP PEAK 12(XQ11.2) MUTATED	7	28	93
AMP PEAK 12(XQ11.2) WILD-TYPE	59	496	176

Figure S67. Get High-res Image Gene #12: 'amp_xq11.2' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'

'amp_xq11.2' versus 'YEAR_OF_TOBACCO_SMOKING_ONSET'

P value = 0.0193 (Wilcoxon-test), Q value = 0.056

Table S68. Gene #12: 'amp_xq11.2' versus Clinical Feature #11: 'YEAR_OF_TOBACCO_SMOKING_ONSET'

	nPatients	Mean (Std.Dev)
ALL	67	1973.4 (16.4)
AMP PEAK 12(XQ11.2) MUTATED	16	1965.3 (14.8)
AMP PEAK 12(XQ11.2) WILD-TYPE	51	1975.9 (16.2)

Figure S68. Get High-res Image Gene #12: 'amp_xq11.2' versus Clinical Feature #11: 'YEAR_OF_TOBACCO_SMOKING_ONSET'

'amp_xq28' versus 'Time to Death'

P value = 0.0777 (logrank test), Q value = 0.17

Table S69. Gene #13: 'amp_xq28' versus Clinical Feature #1: 'Time to Death'

	nPatients	nDeath	Duration Range (Median), Month
ALL	843	211	0.1 - 194.8 (30.5)
AMP PEAK 13(XQ28) MUTATED	126	20	0.1 - 194.8 (25.5)
AMP PEAK 13(XQ28) WILD-TYPE	717	191	0.1 - 152.0 (31.3)

Figure S69. Get High-res Image Gene #13: 'amp_xq28' versus Clinical Feature #1: 'Time to Death'

'amp_xq28' versus 'NEOPLASM_DISEASESTAGE'

P value = 0.0369 (Fisher's exact test), Q value = 0.094

Table S70. Gene #13: 'amp_xq28' versus Clinical Feature #3: 'NEOPLASM_DISEASESTAGE'

nPatients	STAGE I	STAGE II	STAGE III	STAGE IV
ALL	448	103	190	100
AMP PEAK 13(XQ28) MUTATED	80	12	18	14
AMP PEAK 13(XQ28) WILD-TYPE	368	91	172	86

Figure S70. Get High-res Image Gene #13: 'amp_xq28' versus Clinical Feature #3: 'NEOPLASM_DISEASESTAGE'

'amp_xq28' versus 'PATHOLOGY_T_STAGE'

P value = 0.0412 (Fisher's exact test), Q value = 0.1

Table S71. Gene #13: 'amp_xq28' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

nPatients	T1	T2	T3	T4
ALL	462	123	251	15
AMP PEAK 13(XQ28) MUTATED	83	19	26	3
AMP PEAK 13(XQ28) WILD-TYPE	379	104	225	12

Figure S71. Get High-res Image Gene #13: 'amp_xq28' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

'amp_xq28' versus 'GENDER'

P value = 0.016 (Fisher's exact test), Q value = 0.047

Table S72. Gene #13: 'amp_xq28' versus Clinical Feature #7: 'GENDER'

nPatients	FEMALE	MALE
ALL	287	572
AMP PEAK 13(XQ28) MUTATED	32	100
AMP PEAK 13(XQ28) WILD-TYPE	255	472

Figure S72. Get High-res Image Gene #13: 'amp_xq28' versus Clinical Feature #7: 'GENDER'

'amp_xq28' versus 'KARNOFSKY_PERFORMANCE_SCORE'

P value = 0.00192 (Wilcoxon-test), Q value = 0.0081

Table S73. Gene #13: 'amp_xq28' versus Clinical Feature #8: 'KARNOFSKY_PERFORMANCE_SCORE'

	nPatients	Mean (Std.Dev)
ALL	115	90.3 (17.6)
AMP PEAK 13(XQ28) MUTATED	24	97.1 (5.5)
AMP PEAK 13(XQ28) WILD-TYPE	91	88.5 (19.2)

Figure S73. Get High-res Image Gene #13: 'amp_xq28' versus Clinical Feature #8: 'KARNOFSKY_PERFORMANCE_SCORE'

'amp_xq28' versus 'HISTOLOGICAL_TYPE'

P value = 1e-05 (Fisher's exact test), Q value = 7.6e-05

Table S74. Gene #13: 'amp_xq28' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'

nPatients	KIDNEY CHROMOPHOBE	KIDNEY CLEAR CELL RENAL CARCINOMA	KIDNEY PAPILLARY RENAL CELL CARCINOMA
ALL	66	524	269
AMP PEAK 13(XQ28) MUTATED	8	37	87
AMP PEAK 13(XQ28) WILD-TYPE	58	487	182

Figure S74. Get High-res Image Gene #13: 'amp_xq28' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'

'del_1p36.31' versus 'YEARS_TO_BIRTH'

P value = 0.0774 (Wilcoxon-test), Q value = 0.17

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

	nPatients	Mean (Std.Dev)
ALL	853	60.1 (12.6)
DEL PEAK 1(1P36.31) MUTATED	202	58.4 (13.7)
DEL PEAK 1(1P36.31) WILD-TYPE	651	60.6 (12.2)

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

'del_1p36.31' versus 'NEOPLASM_DISEASESTAGE'

P value = 1e-05 (Fisher's exact test), Q value = 7.6e-05

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

nPatients	STAGE I	STAGE II	STAGE III	STAGE IV
ALL	448	103	190	100
DEL PEAK 1(1P36.31) MUTATED	71	38	60	29
DEL PEAK 1(1P36.31) WILD-TYPE	377	65	130	71

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

'del_1p36.31' versus 'PATHOLOGY_T_STAGE'

P value = 1e-05 (Fisher's exact test), Q value = 7.6e-05

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

nPatients	T1	T2	T3	T4
ALL	462	123	251	15
DEL PEAK 1(1P36.31) MUTATED	77	45	73	6
DEL PEAK 1(1P36.31) WILD-TYPE	385	78	178	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 = 0.0685 (Fisher's exact test), Q value = 0.16

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

nPatients	N0	N1	N2
ALL	317	43	6
DEL PEAK 1(1P36.31) MUTATED	92	19	3
DEL PEAK 1(1P36.31) WILD-TYPE	225	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 = 0.0152 (Wilcoxon-test), Q value = 0.045

Table S79. Gene #14: 'del_1p36.31' versus Clinical Feature #8: 'KARNOFSKY_PERFORMANCE_SCORE'

	nPatients	Mean (Std.Dev)
ALL	115	90.3 (17.6)
DEL PEAK 1(1P36.31) MUTATED	26	86.2 (19.8)
DEL PEAK 1(1P36.31) WILD-TYPE	89	91.5 (16.8)

Figure S79. Get High-res Image Gene #14: 'del_1p36.31' versus Clinical Feature #8: 'KARNOFSKY_PERFORMANCE_SCORE'

'del_1p36.31' versus 'HISTOLOGICAL_TYPE'

P value = 1e-05 (Fisher's exact test), Q value = 7.6e-05

Table S80. Gene #14: 'del_1p36.31' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'

nPatients	KIDNEY CHROMOPHOBE	KIDNEY CLEAR CELL RENAL CARCINOMA	KIDNEY PAPILLARY RENAL CELL CARCINOMA
ALL	66	524	269
DEL PEAK 1(1P36.31) MUTATED	53	101	49
DEL PEAK 1(1P36.31) WILD-TYPE	13	423	220

Figure S80. Get High-res Image Gene #14: 'del_1p36.31' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'

'del_1p31.1' versus 'YEARS_TO_BIRTH'

P value = 0.0352 (Wilcoxon-test), Q value = 0.091

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

	nPatients	Mean (Std.Dev)
ALL	853	60.1 (12.6)
DEL PEAK 2(1P31.1) MUTATED	161	57.8 (13.8)
DEL PEAK 2(1P31.1) WILD-TYPE	692	60.6 (12.2)

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

'del_1p31.1' versus 'NEOPLASM_DISEASESTAGE'

P value = 4e-05 (Fisher's exact test), Q value = 0.00028

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

nPatients	STAGE I	STAGE II	STAGE III	STAGE IV
ALL	448	103	190	100
DEL PEAK 2(1P31.1) MUTATED	59	34	43	22
DEL PEAK 2(1P31.1) WILD-TYPE	389	69	147	78

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

'del_1p31.1' versus 'PATHOLOGY_T_STAGE'

P value = 5e-05 (Fisher's exact test), Q value = 0.00033

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

nPatients	T1	T2	T3	T4
ALL	462	123	251	15
DEL PEAK 2(1P31.1) MUTATED	64	38	52	6
DEL PEAK 2(1P31.1) WILD-TYPE	398	85	199	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 = 0.102 (Fisher's exact test), Q value = 0.21

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

nPatients	N0	N1	N2
ALL	317	43	6
DEL PEAK 2(1P31.1) MUTATED	72	14	3
DEL PEAK 2(1P31.1) WILD-TYPE	245	29	3

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 = 7.6e-05

Table S85. Gene #15: 'del_1p31.1' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'

nPatients	KIDNEY CHROMOPHOBE	KIDNEY CLEAR CELL RENAL CARCINOMA	KIDNEY PAPILLARY RENAL CELL CARCINOMA
ALL	66	524	269
DEL PEAK 2(1P31.1) MUTATED	53	76	32
DEL PEAK 2(1P31.1) WILD-TYPE	13	448	237

Figure S85. Get High-res Image Gene #15: 'del_1p31.1' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'

'del_1p31.1' versus 'ETHNICITY'

P value = 0.0856 (Fisher's exact test), Q value = 0.19

Table S86. Gene #15: 'del_1p31.1' versus Clinical Feature #13: 'ETHNICITY'

nPatients	HISPANIC OR LATINO	NOT HISPANIC OR LATINO
ALL	42	597
DEL PEAK 2(1P31.1) MUTATED	11	94
DEL PEAK 2(1P31.1) WILD-TYPE	31	503

Figure S86. Get High-res Image Gene #15: 'del_1p31.1' versus Clinical Feature #13: 'ETHNICITY'

'del_1q43' versus 'Time to Death'

P value = 0.0476 (logrank test), Q value = 0.12

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

	nPatients	nDeath	Duration Range (Median), Month
ALL	843	211	0.1 - 194.8 (30.5)
DEL PEAK 3(1Q43) MUTATED	111	26	0.1 - 152.0 (47.2)
DEL PEAK 3(1Q43) WILD-TYPE	732	185	0.1 - 194.8 (29.0)

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 = 0.00276 (Wilcoxon-test), Q value = 0.011

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

	nPatients	Mean (Std.Dev)
ALL	853	60.1 (12.6)
DEL PEAK 3(1Q43) MUTATED	112	56.4 (14.3)
DEL PEAK 3(1Q43) WILD-TYPE	741	60.7 (12.2)

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

'del_1q43' versus 'NEOPLASM_DISEASESTAGE'

P value = 0.00037 (Fisher's exact test), Q value = 0.0019

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

nPatients	STAGE I	STAGE II	STAGE III	STAGE IV
ALL	448	103	190	100
DEL PEAK 3(1Q43) MUTATED	46	28	23	11
DEL PEAK 3(1Q43) WILD-TYPE	402	75	167	89

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

'del_1q43' versus 'PATHOLOGY_T_STAGE'

P value = 0.00154 (Fisher's exact test), Q value = 0.0066

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

nPatients	T1	T2	T3	T4
ALL	462	123	251	15
DEL PEAK 3(1Q43) MUTATED	47	28	31	4
DEL PEAK 3(1Q43) WILD-TYPE	415	95	220	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 = 7.6e-05

Table S91. Gene #16: 'del_1q43' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'

nPatients	KIDNEY CHROMOPHOBE	KIDNEY CLEAR CELL RENAL CARCINOMA	KIDNEY PAPILLARY RENAL CELL CARCINOMA
ALL	66	524	269
DEL PEAK 3(1Q43) MUTATED	51	42	19
DEL PEAK 3(1Q43) WILD-TYPE	15	482	250

Figure S91. Get High-res Image Gene #16: 'del_1q43' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'

'del_2q37.3' versus 'Time to Death'

P value = 0.0153 (logrank test), Q value = 0.045

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

	nPatients	nDeath	Duration Range (Median), Month
ALL	843	211	0.1 - 194.8 (30.5)
DEL PEAK 4(2Q37.3) MUTATED	108	21	0.4 - 152.0 (42.7)
DEL PEAK 4(2Q37.3) WILD-TYPE	735	190	0.1 - 194.8 (29.0)

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 = 0.00203 (Wilcoxon-test), Q value = 0.0083

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

	nPatients	Mean (Std.Dev)
ALL	853	60.1 (12.6)
DEL PEAK 4(2Q37.3) MUTATED	109	56.4 (14.0)
DEL PEAK 4(2Q37.3) WILD-TYPE	744	60.6 (12.3)

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

'del_2q37.3' versus 'NEOPLASM_DISEASESTAGE'

P value = 1e-05 (Fisher's exact test), Q value = 7.6e-05

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

nPatients	STAGE I	STAGE II	STAGE III	STAGE IV
ALL	448	103	190	100
DEL PEAK 4(2Q37.3) MUTATED	38	32	28	10
DEL PEAK 4(2Q37.3) WILD-TYPE	410	71	162	90

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

'del_2q37.3' versus 'PATHOLOGY_T_STAGE'

P value = 1e-05 (Fisher's exact test), Q value = 7.6e-05

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

nPatients	T1	T2	T3	T4
ALL	462	123	251	15
DEL PEAK 4(2Q37.3) MUTATED	38	34	34	3
DEL PEAK 4(2Q37.3) WILD-TYPE	424	89	217	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 = 0.0853 (Fisher's exact test), Q value = 0.19

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

nPatients	0	1
ALL	542	89
DEL PEAK 4(2Q37.3) MUTATED	75	6
DEL PEAK 4(2Q37.3) WILD-TYPE	467	83

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

'del_2q37.3' versus 'HISTOLOGICAL_TYPE'

P value = 1e-05 (Fisher's exact test), Q value = 7.6e-05

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

nPatients	KIDNEY CHROMOPHOBE	KIDNEY CLEAR CELL RENAL CARCINOMA	KIDNEY PAPILLARY RENAL CELL CARCINOMA
ALL	66	524	269
DEL PEAK 4(2Q37.3) MUTATED	49	50	11
DEL PEAK 4(2Q37.3) WILD-TYPE	17	474	258

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

'del_3p26.3' versus 'Time to Death'

P value = 0.00113 (logrank test), Q value = 0.0051

Table S98. Gene #18: 'del_3p26.3' versus Clinical Feature #1: 'Time to Death'

	nPatients	nDeath	Duration Range (Median), Month
ALL	843	211	0.1 - 194.8 (30.5)
DEL PEAK 5(3P26.3) MUTATED	485	150	0.1 - 141.7 (36.4)
DEL PEAK 5(3P26.3) WILD-TYPE	358	61	0.1 - 194.8 (25.9)

Figure S98. Get High-res Image Gene #18: 'del_3p26.3' versus Clinical Feature #1: 'Time to Death'

'del_3p26.3' versus 'NEOPLASM_DISEASESTAGE'

P value = 1e-05 (Fisher's exact test), Q value = 7.6e-05

Table S99. Gene #18: 'del_3p26.3' versus Clinical Feature #3: 'NEOPLASM_DISEASESTAGE'

nPatients	STAGE I	STAGE II	STAGE III	STAGE IV
ALL	448	103	190	100
DEL PEAK 5(3P26.3) MUTATED	227	57	131	71
DEL PEAK 5(3P26.3) WILD-TYPE	221	46	59	29

Figure S99. Get High-res Image Gene #18: 'del_3p26.3' versus Clinical Feature #3: 'NEOPLASM_DISEASESTAGE'

'del_3p26.3' versus 'PATHOLOGY_T_STAGE'

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

Table S100. Gene #18: 'del_3p26.3' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

nPatients	T1	T2	T3	T4
ALL	462	123	251	15
DEL PEAK 5(3P26.3) MUTATED	233	71	175	7
DEL PEAK 5(3P26.3) WILD-TYPE	229	52	76	8

Figure S100. 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 = 0.00885 (Fisher's exact test), Q value = 0.029

Table S101. Gene #18: 'del_3p26.3' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

nPatients	N0	N1	N2
ALL	317	43	6
DEL PEAK 5(3P26.3) MUTATED	212	23	1
DEL PEAK 5(3P26.3) WILD-TYPE	105	20	5

Figure S101. Get High-res Image Gene #18: 'del_3p26.3' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

'del_3p26.3' versus 'GENDER'

P value = 0.0684 (Fisher's exact test), Q value = 0.16

Table S102. Gene #18: 'del_3p26.3' versus Clinical Feature #7: 'GENDER'

nPatients	FEMALE	MALE
ALL	287	572
DEL PEAK 5(3P26.3) MUTATED	175	311
DEL PEAK 5(3P26.3) WILD-TYPE	112	261

Figure S102. Get High-res Image Gene #18: 'del_3p26.3' versus Clinical Feature #7: 'GENDER'

'del_3p26.3' versus 'HISTOLOGICAL_TYPE'

P value = 1e-05 (Fisher's exact test), Q value = 7.6e-05

Table S103. Gene #18: 'del_3p26.3' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'

nPatients	KIDNEY CHROMOPHOBE	KIDNEY CLEAR CELL RENAL CARCINOMA	KIDNEY PAPILLARY RENAL CELL CARCINOMA
ALL	66	524	269
DEL PEAK 5(3P26.3) MUTATED	10	453	23
DEL PEAK 5(3P26.3) WILD-TYPE	56	71	246

Figure S103. Get High-res Image Gene #18: 'del_3p26.3' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'

'del_3p26.3' versus 'YEAR_OF_TOBACCO_SMOKING_ONSET'

P value = 0.0786 (Wilcoxon-test), Q value = 0.18

Table S104. Gene #18: 'del_3p26.3' versus Clinical Feature #11: 'YEAR_OF_TOBACCO_SMOKING_ONSET'

	nPatients	Mean (Std.Dev)
ALL	67	1973.4 (16.4)
DEL PEAK 5(3P26.3) MUTATED	17	1979.4 (18.6)
DEL PEAK 5(3P26.3) WILD-TYPE	50	1971.4 (15.3)

Figure S104. Get High-res Image Gene #18: 'del_3p26.3' versus Clinical Feature #11: 'YEAR_OF_TOBACCO_SMOKING_ONSET'

'del_3p26.3' versus 'RACE'

P value = 1e-05 (Fisher's exact test), Q value = 7.6e-05

Table S105. Gene #18: 'del_3p26.3' versus Clinical Feature #12: 'RACE'

nPatients	AMERICAN INDIAN OR ALASKA NATIVE	ASIAN	BLACK OR AFRICAN AMERICAN	WHITE
ALL	2	15	116	702
DEL PEAK 5(3P26.3) MUTATED	0	7	41	429
DEL PEAK 5(3P26.3) WILD-TYPE	2	8	75	273

Figure S105. Get High-res Image Gene #18: 'del_3p26.3' versus Clinical Feature #12: 'RACE'

'del_3p21.2' versus 'Time to Death'

P value = 7.97e-06 (logrank test), Q value = 7.6e-05

Table S106. Gene #19: 'del_3p21.2' versus Clinical Feature #1: 'Time to Death'

	nPatients	nDeath	Duration Range (Median), Month
ALL	843	211	0.1 - 194.8 (30.5)
DEL PEAK 6(3P21.2) MUTATED	498	160	0.1 - 141.7 (35.1)
DEL PEAK 6(3P21.2) WILD-TYPE	345	51	0.1 - 194.8 (26.4)

Figure S106. Get High-res Image Gene #19: 'del_3p21.2' versus Clinical Feature #1: 'Time to Death'

'del_3p21.2' versus 'NEOPLASM_DISEASESTAGE'

P value = 1e-05 (Fisher's exact test), Q value = 7.6e-05

Table S107. Gene #19: 'del_3p21.2' versus Clinical Feature #3: 'NEOPLASM_DISEASESTAGE'

nPatients	STAGE I	STAGE II	STAGE III	STAGE IV
ALL	448	103	190	100
DEL PEAK 6(3P21.2) MUTATED	227	57	137	78
DEL PEAK 6(3P21.2) WILD-TYPE	221	46	53	22

Figure S107. Get High-res Image Gene #19: 'del_3p21.2' versus Clinical Feature #3: 'NEOPLASM_DISEASESTAGE'

'del_3p21.2' versus 'PATHOLOGY_T_STAGE'

P value = 1e-05 (Fisher's exact test), Q value = 7.6e-05

Table S108. Gene #19: 'del_3p21.2' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

nPatients	T1	T2	T3	T4
ALL	462	123	251	15
DEL PEAK 6(3P21.2) MUTATED	233	71	188	7
DEL PEAK 6(3P21.2) WILD-TYPE	229	52	63	8

Figure S108. Get High-res Image Gene #19: 'del_3p21.2' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

'del_3p21.2' versus 'PATHOLOGY_N_STAGE'

P value = 0.0986 (Fisher's exact test), Q value = 0.21

Table S109. Gene #19: 'del_3p21.2' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

nPatients	N0	N1	N2
ALL	317	43	6
DEL PEAK 6(3P21.2) MUTATED	218	26	2
DEL PEAK 6(3P21.2) WILD-TYPE	99	17	4

Figure S109. Get High-res Image Gene #19: 'del_3p21.2' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

'del_3p21.2' versus 'PATHOLOGY_M_STAGE'

P value = 0.0049 (Fisher's exact test), Q value = 0.017

Table S110. Gene #19: 'del_3p21.2' versus Clinical Feature #6: 'PATHOLOGY_M_STAGE'

nPatients	0	1
ALL	542	89
DEL PEAK 6(3P21.2) MUTATED	379	75
DEL PEAK 6(3P21.2) WILD-TYPE	163	14

Figure S110. Get High-res Image Gene #19: 'del_3p21.2' versus Clinical Feature #6: 'PATHOLOGY_M_STAGE'

'del_3p21.2' versus 'KARNOFSKY_PERFORMANCE_SCORE'

P value = 0.0596 (Wilcoxon-test), Q value = 0.14

Table S111. Gene #19: 'del_3p21.2' versus Clinical Feature #8: 'KARNOFSKY_PERFORMANCE_SCORE'

	nPatients	Mean (Std.Dev)
ALL	115	90.3 (17.6)
DEL PEAK 6(3P21.2) MUTATED	48	86.0 (24.0)
DEL PEAK 6(3P21.2) WILD-TYPE	67	93.3 (10.1)

Figure S111. Get High-res Image Gene #19: 'del_3p21.2' versus Clinical Feature #8: 'KARNOFSKY_PERFORMANCE_SCORE'

'del_3p21.2' versus 'HISTOLOGICAL_TYPE'

P value = 1e-05 (Fisher's exact test), Q value = 7.6e-05

Table S112. Gene #19: 'del_3p21.2' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'

nPatients	KIDNEY CHROMOPHOBE	KIDNEY CLEAR CELL RENAL CARCINOMA	KIDNEY PAPILLARY RENAL CELL CARCINOMA
ALL	66	524	269
DEL PEAK 6(3P21.2) MUTATED	11	463	25
DEL PEAK 6(3P21.2) WILD-TYPE	55	61	244

Figure S112. Get High-res Image Gene #19: 'del_3p21.2' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'

'del_3p21.2' versus 'YEAR_OF_TOBACCO_SMOKING_ONSET'

P value = 0.0343 (Wilcoxon-test), Q value = 0.089

Table S113. Gene #19: 'del_3p21.2' versus Clinical Feature #11: 'YEAR_OF_TOBACCO_SMOKING_ONSET'

	nPatients	Mean (Std.Dev)
ALL	67	1973.4 (16.4)
DEL PEAK 6(3P21.2) MUTATED	18	1980.1 (17.8)
DEL PEAK 6(3P21.2) WILD-TYPE	49	1971.0 (15.3)

Figure S113. Get High-res Image Gene #19: 'del_3p21.2' versus Clinical Feature #11: 'YEAR_OF_TOBACCO_SMOKING_ONSET'

'del_3p21.2' versus 'RACE'

P value = 1e-05 (Fisher's exact test), Q value = 7.6e-05

Table S114. Gene #19: 'del_3p21.2' versus Clinical Feature #12: 'RACE'

nPatients	AMERICAN INDIAN OR ALASKA NATIVE	ASIAN	BLACK OR AFRICAN AMERICAN	WHITE
ALL	2	15	116	702
DEL PEAK 6(3P21.2) MUTATED	0	8	41	442
DEL PEAK 6(3P21.2) WILD-TYPE	2	7	75	260

Figure S114. Get High-res Image Gene #19: 'del_3p21.2' versus Clinical Feature #12: 'RACE'

'del_3p14.1' versus 'Time to Death'

P value = 0.00206 (logrank test), Q value = 0.0083

Table S115. Gene #20: 'del_3p14.1' versus Clinical Feature #1: 'Time to Death'

	nPatients	nDeath	Duration Range (Median), Month
ALL	843	211	0.1 - 194.8 (30.5)
DEL PEAK 7(3P14.1) MUTATED	405	128	0.1 - 141.7 (36.4)
DEL PEAK 7(3P14.1) WILD-TYPE	438	83	0.1 - 194.8 (27.1)

Figure S115. Get High-res Image Gene #20: 'del_3p14.1' versus Clinical Feature #1: 'Time to Death'

'del_3p14.1' versus 'NEOPLASM_DISEASESTAGE'

P value = 0.00023 (Fisher's exact test), Q value = 0.0012

Table S116. Gene #20: 'del_3p14.1' versus Clinical Feature #3: 'NEOPLASM_DISEASESTAGE'

nPatients	STAGE I	STAGE II	STAGE III	STAGE IV
ALL	448	103	190	100
DEL PEAK 7(3P14.1) MUTATED	187	49	112	57
DEL PEAK 7(3P14.1) WILD-TYPE	261	54	78	43

Figure S116. Get High-res Image Gene #20: 'del_3p14.1' versus Clinical Feature #3: 'NEOPLASM_DISEASESTAGE'

'del_3p14.1' versus 'PATHOLOGY_T_STAGE'

P value = 6e-05 (Fisher's exact test), Q value = 0.00038

Table S117. Gene #20: 'del_3p14.1' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

nPatients	T1	T2	T3	T4
ALL	462	123	251	15
DEL PEAK 7(3P14.1) MUTATED	191	60	149	5
DEL PEAK 7(3P14.1) WILD-TYPE	271	63	102	10

Figure S117. 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 = 7.6e-05

Table S118. Gene #20: 'del_3p14.1' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'

nPatients	KIDNEY CHROMOPHOBE	KIDNEY CLEAR CELL RENAL CARCINOMA	KIDNEY PAPILLARY RENAL CELL CARCINOMA
ALL	66	524	269
DEL PEAK 7(3P14.1) MUTATED	11	371	23
DEL PEAK 7(3P14.1) WILD-TYPE	55	153	246

Figure S118. Get High-res Image Gene #20: 'del_3p14.1' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'

'del_3p14.1' versus 'YEAR_OF_TOBACCO_SMOKING_ONSET'

P value = 0.055 (Wilcoxon-test), Q value = 0.13

Table S119. Gene #20: 'del_3p14.1' versus Clinical Feature #11: 'YEAR_OF_TOBACCO_SMOKING_ONSET'

	nPatients	Mean (Std.Dev)
ALL	67	1973.4 (16.4)
DEL PEAK 7(3P14.1) MUTATED	15	1980.1 (18.7)
DEL PEAK 7(3P14.1) WILD-TYPE	52	1971.5 (15.3)

Figure S119. Get High-res Image Gene #20: 'del_3p14.1' versus Clinical Feature #11: 'YEAR_OF_TOBACCO_SMOKING_ONSET'

'del_3p14.1' versus 'RACE'

P value = 0.00013 (Fisher's exact test), Q value = 0.00076

Table S120. Gene #20: 'del_3p14.1' versus Clinical Feature #12: 'RACE'

nPatients	AMERICAN INDIAN OR ALASKA NATIVE	ASIAN	BLACK OR AFRICAN AMERICAN	WHITE
ALL	2	15	116	702
DEL PEAK 7(3P14.1) MUTATED	0	7	35	356
DEL PEAK 7(3P14.1) WILD-TYPE	2	8	81	346

Figure S120. Get High-res Image Gene #20: 'del_3p14.1' versus Clinical Feature #12: 'RACE'

'del_3p12.2' versus 'Time to Death'

P value = 0.00116 (logrank test), Q value = 0.0052

Table S121. Gene #21: 'del_3p12.2' versus Clinical Feature #1: 'Time to Death'

	nPatients	nDeath	Duration Range (Median), Month
ALL	843	211	0.1 - 194.8 (30.5)
DEL PEAK 8(3P12.2) MUTATED	334	109	0.1 - 141.7 (36.7)
DEL PEAK 8(3P12.2) WILD-TYPE	509	102	0.1 - 194.8 (27.6)

Figure S121. Get High-res Image Gene #21: 'del_3p12.2' versus Clinical Feature #1: 'Time to Death'

'del_3p12.2' versus 'NEOPLASM_DISEASESTAGE'

P value = 0.0127 (Fisher's exact test), Q value = 0.039

Table S122. Gene #21: 'del_3p12.2' versus Clinical Feature #3: 'NEOPLASM_DISEASESTAGE'

nPatients	STAGE I	STAGE II	STAGE III	STAGE IV
ALL	448	103	190	100
DEL PEAK 8(3P12.2) MUTATED	156	42	89	47
DEL PEAK 8(3P12.2) WILD-TYPE	292	61	101	53

Figure S122. Get High-res Image Gene #21: 'del_3p12.2' versus Clinical Feature #3: 'NEOPLASM_DISEASESTAGE'

'del_3p12.2' versus 'PATHOLOGY_T_STAGE'

P value = 0.00642 (Fisher's exact test), Q value = 0.022

Table S123. Gene #21: 'del_3p12.2' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

nPatients	T1	T2	T3	T4
ALL	462	123	251	15
DEL PEAK 8(3P12.2) MUTATED	160	51	119	4
DEL PEAK 8(3P12.2) WILD-TYPE	302	72	132	11

Figure S123. Get High-res Image Gene #21: 'del_3p12.2' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

'del_3p12.2' versus 'GENDER'

P value = 0.0884 (Fisher's exact test), Q value = 0.19

Table S124. Gene #21: 'del_3p12.2' versus Clinical Feature #7: 'GENDER'

nPatients	FEMALE	MALE
ALL	287	572
DEL PEAK 8(3P12.2) MUTATED	100	234
DEL PEAK 8(3P12.2) WILD-TYPE	187	338

Figure S124. Get High-res Image Gene #21: 'del_3p12.2' versus Clinical Feature #7: 'GENDER'

'del_3p12.2' versus 'HISTOLOGICAL_TYPE'

P value = 1e-05 (Fisher's exact test), Q value = 7.6e-05

Table S125. Gene #21: 'del_3p12.2' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'

nPatients	KIDNEY CHROMOPHOBE	KIDNEY CLEAR CELL RENAL CARCINOMA	KIDNEY PAPILLARY RENAL CELL CARCINOMA
ALL	66	524	269
DEL PEAK 8(3P12.2) MUTATED	11	304	19
DEL PEAK 8(3P12.2) WILD-TYPE	55	220	250

Figure S125. Get High-res Image Gene #21: 'del_3p12.2' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'

'del_3p12.2' versus 'YEAR_OF_TOBACCO_SMOKING_ONSET'

P value = 0.0826 (Wilcoxon-test), Q value = 0.18

Table S126. Gene #21: 'del_3p12.2' versus Clinical Feature #11: 'YEAR_OF_TOBACCO_SMOKING_ONSET'

	nPatients	Mean (Std.Dev)
ALL	67	1973.4 (16.4)
DEL PEAK 8(3P12.2) MUTATED	11	1980.5 (17.8)
DEL PEAK 8(3P12.2) WILD-TYPE	56	1972.0 (15.9)

Figure S126. Get High-res Image Gene #21: 'del_3p12.2' versus Clinical Feature #11: 'YEAR_OF_TOBACCO_SMOKING_ONSET'

'del_3p12.2' versus 'RACE'

P value = 0.00473 (Fisher's exact test), Q value = 0.017

Table S127. Gene #21: 'del_3p12.2' versus Clinical Feature #12: 'RACE'

nPatients	AMERICAN INDIAN OR ALASKA NATIVE	ASIAN	BLACK OR AFRICAN AMERICAN	WHITE
ALL	2	15	116	702
DEL PEAK 8(3P12.2) MUTATED	0	6	30	292
DEL PEAK 8(3P12.2) WILD-TYPE	2	9	86	410

Figure S127. Get High-res Image Gene #21: 'del_3p12.2' versus Clinical Feature #12: 'RACE'

'del_4q34.3' versus 'Time to Death'

P value = 7.22e-09 (logrank test), Q value = 8.8e-07

Table S128. Gene #22: 'del_4q34.3' versus Clinical Feature #1: 'Time to Death'

	nPatients	nDeath	Duration Range (Median), Month
ALL	843	211	0.1 - 194.8 (30.5)
DEL PEAK 9(4Q34.3) MUTATED	110	50	0.1 - 112.8 (22.8)
DEL PEAK 9(4Q34.3) WILD-TYPE	733	161	0.1 - 194.8 (30.6)

Figure S128. Get High-res Image Gene #22: 'del_4q34.3' versus Clinical Feature #1: 'Time to Death'

'del_4q34.3' versus 'NEOPLASM_DISEASESTAGE'

P value = 1e-05 (Fisher's exact test), Q value = 7.6e-05

Table S129. Gene #22: 'del_4q34.3' versus Clinical Feature #3: 'NEOPLASM_DISEASESTAGE'

nPatients	STAGE I	STAGE II	STAGE III	STAGE IV
ALL	448	103	190	100
DEL PEAK 9(4Q34.3) MUTATED	26	10	48	24
DEL PEAK 9(4Q34.3) WILD-TYPE	422	93	142	76

Figure S129. Get High-res Image Gene #22: 'del_4q34.3' versus Clinical Feature #3: 'NEOPLASM_DISEASESTAGE'

'del_4q34.3' versus 'PATHOLOGY_T_STAGE'

P value = 1e-05 (Fisher's exact test), Q value = 7.6e-05

Table S130. Gene #22: 'del_4q34.3' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

nPatients	T1	T2	T3	T4
ALL	462	123	251	15
DEL PEAK 9(4Q34.3) MUTATED	29	14	59	7
DEL PEAK 9(4Q34.3) WILD-TYPE	433	109	192	8

Figure S130. 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 = 0.0109 (Fisher's exact test), Q value = 0.035

Table S131. Gene #22: 'del_4q34.3' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

nPatients	N0	N1	N2
ALL	317	43	6
DEL PEAK 9(4Q34.3) MUTATED	40	13	0
DEL PEAK 9(4Q34.3) WILD-TYPE	277	30	6

Figure S131. 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 = 0.0143 (Fisher's exact test), Q value = 0.043

Table S132. Gene #22: 'del_4q34.3' versus Clinical Feature #6: 'PATHOLOGY_M_STAGE'

nPatients	0	1
ALL	542	89
DEL PEAK 9(4Q34.3) MUTATED	71	21
DEL PEAK 9(4Q34.3) WILD-TYPE	471	68

Figure S132. Get High-res Image Gene #22: 'del_4q34.3' versus Clinical Feature #6: 'PATHOLOGY_M_STAGE'

'del_4q34.3' versus 'HISTOLOGICAL_TYPE'

P value = 0.0318 (Fisher's exact test), Q value = 0.084

Table S133. Gene #22: 'del_4q34.3' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'

nPatients	KIDNEY CHROMOPHOBE	KIDNEY CLEAR CELL RENAL CARCINOMA	KIDNEY PAPILLARY RENAL CELL CARCINOMA
ALL	66	524	269
DEL PEAK 9(4Q34.3) MUTATED	3	78	30
DEL PEAK 9(4Q34.3) WILD-TYPE	63	446	239

Figure S133. Get High-res Image Gene #22: 'del_4q34.3' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'

'del_4q34.3' versus 'RACE'

P value = 0.0647 (Fisher's exact test), Q value = 0.15

Table S134. Gene #22: 'del_4q34.3' versus Clinical Feature #12: 'RACE'

nPatients	AMERICAN INDIAN OR ALASKA NATIVE	ASIAN	BLACK OR AFRICAN AMERICAN	WHITE
ALL	2	15	116	702
DEL PEAK 9(4Q34.3) MUTATED	0	4	8	93
DEL PEAK 9(4Q34.3) WILD-TYPE	2	11	108	609

Figure S134. Get High-res Image Gene #22: 'del_4q34.3' versus Clinical Feature #12: 'RACE'

'del_5p15.33' versus 'YEARS_TO_BIRTH'

P value = 0.00445 (Wilcoxon-test), Q value = 0.016

Table S135. Gene #23: 'del_5p15.33' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

	nPatients	Mean (Std.Dev)
ALL	853	60.1 (12.6)
DEL PEAK 10(5P15.33) MUTATED	30	52.4 (14.6)
DEL PEAK 10(5P15.33) WILD-TYPE	823	60.4 (12.4)

Figure S135. Get High-res Image Gene #23: 'del_5p15.33' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'del_5p15.33' versus 'NEOPLASM_DISEASESTAGE'

P value = 0.00148 (Fisher's exact test), Q value = 0.0065

Table S136. Gene #23: 'del_5p15.33' versus Clinical Feature #3: 'NEOPLASM_DISEASESTAGE'

nPatients	STAGE I	STAGE II	STAGE III	STAGE IV
ALL	448	103	190	100
DEL PEAK 10(5P15.33) MUTATED	7	9	9	5
DEL PEAK 10(5P15.33) WILD-TYPE	441	94	181	95

Figure S136. Get High-res Image Gene #23: 'del_5p15.33' versus Clinical Feature #3: 'NEOPLASM_DISEASESTAGE'

'del_5p15.33' versus 'PATHOLOGY_T_STAGE'

P value = 0.00057 (Fisher's exact test), Q value = 0.0027

Table S137. Gene #23: 'del_5p15.33' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

nPatients	T1	T2	T3	T4
ALL	462	123	251	15
DEL PEAK 10(5P15.33) MUTATED	7	11	13	0
DEL PEAK 10(5P15.33) WILD-TYPE	455	112	238	15

Figure S137. 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 = 0.00573 (Fisher's exact test), Q value = 0.02

Table S138. Gene #23: 'del_5p15.33' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

nPatients	N0	N1	N2
ALL	317	43	6
DEL PEAK 10(5P15.33) MUTATED	13	5	2
DEL PEAK 10(5P15.33) WILD-TYPE	304	38	4

Figure S138. Get High-res Image Gene #23: 'del_5p15.33' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

'del_5p15.33' versus 'HISTOLOGICAL_TYPE'

P value = 1e-05 (Fisher's exact test), Q value = 7.6e-05

Table S139. Gene #23: 'del_5p15.33' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'

nPatients	KIDNEY CHROMOPHOBE	KIDNEY CLEAR CELL RENAL CARCINOMA	KIDNEY PAPILLARY RENAL CELL CARCINOMA
ALL	66	524	269
DEL PEAK 10(5P15.33) MUTATED	10	8	13
DEL PEAK 10(5P15.33) WILD-TYPE	56	516	256

Figure S139. Get High-res Image Gene #23: 'del_5p15.33' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'

'del_6q22.31' versus 'YEARS_TO_BIRTH'

P value = 0.124 (Wilcoxon-test), Q value = 0.25

Table S140. Gene #24: 'del_6q22.31' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

	nPatients	Mean (Std.Dev)
ALL	853	60.1 (12.6)
DEL PEAK 11(6Q22.31) MUTATED	223	58.6 (13.8)
DEL PEAK 11(6Q22.31) WILD-TYPE	630	60.6 (12.1)

Figure S140. Get High-res Image Gene #24: 'del_6q22.31' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'del_6q22.31' versus 'NEOPLASM_DISEASESTAGE'

P value = 0.00013 (Fisher's exact test), Q value = 0.00076

Table S141. Gene #24: 'del_6q22.31' versus Clinical Feature #3: 'NEOPLASM_DISEASESTAGE'

nPatients	STAGE I	STAGE II	STAGE III	STAGE IV
ALL	448	103	190	100
DEL PEAK 11(6Q22.31) MUTATED	93	41	55	35
DEL PEAK 11(6Q22.31) WILD-TYPE	355	62	135	65

Figure S141. Get High-res Image Gene #24: 'del_6q22.31' versus Clinical Feature #3: 'NEOPLASM_DISEASESTAGE'

'del_6q22.31' versus 'PATHOLOGY_T_STAGE'

P value = 4e-05 (Fisher's exact test), Q value = 0.00028

Table S142. Gene #24: 'del_6q22.31' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

nPatients	T1	T2	T3	T4
ALL	462	123	251	15
DEL PEAK 11(6Q22.31) MUTATED	94	44	80	7
DEL PEAK 11(6Q22.31) WILD-TYPE	368	79	171	8

Figure S142. 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 = 0.0357 (Fisher's exact test), Q value = 0.092

Table S143. Gene #24: 'del_6q22.31' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

nPatients	N0	N1	N2
ALL	317	43	6
DEL PEAK 11(6Q22.31) MUTATED	87	17	4
DEL PEAK 11(6Q22.31) WILD-TYPE	230	26	2

Figure S143. Get High-res Image Gene #24: 'del_6q22.31' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

'del_6q22.31' versus 'KARNOFSKY_PERFORMANCE_SCORE'

P value = 0.107 (Wilcoxon-test), Q value = 0.22

Table S144. Gene #24: 'del_6q22.31' versus Clinical Feature #8: 'KARNOFSKY_PERFORMANCE_SCORE'

	nPatients	Mean (Std.Dev)
ALL	115	90.3 (17.6)
DEL PEAK 11(6Q22.31) MUTATED	32	85.6 (24.2)
DEL PEAK 11(6Q22.31) WILD-TYPE	83	92.0 (14.0)

Figure S144. Get High-res Image Gene #24: 'del_6q22.31' versus Clinical Feature #8: 'KARNOFSKY_PERFORMANCE_SCORE'

'del_6q22.31' versus 'HISTOLOGICAL_TYPE'

P value = 1e-05 (Fisher's exact test), Q value = 7.6e-05

Table S145. Gene #24: 'del_6q22.31' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'

nPatients	KIDNEY CHROMOPHOBE	KIDNEY CLEAR CELL RENAL CARCINOMA	KIDNEY PAPILLARY RENAL CELL CARCINOMA
ALL	66	524	269
DEL PEAK 11(6Q22.31) MUTATED	51	147	27
DEL PEAK 11(6Q22.31) WILD-TYPE	15	377	242

Figure S145. Get High-res Image Gene #24: 'del_6q22.31' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'

'del_6q22.31' versus 'RACE'

P value = 0.00221 (Fisher's exact test), Q value = 0.0088

Table S146. Gene #24: 'del_6q22.31' versus Clinical Feature #12: 'RACE'

nPatients	AMERICAN INDIAN OR ALASKA NATIVE	ASIAN	BLACK OR AFRICAN AMERICAN	WHITE
ALL	2	15	116	702
DEL PEAK 11(6Q22.31) MUTATED	0	6	16	195
DEL PEAK 11(6Q22.31) WILD-TYPE	2	9	100	507

Figure S146. Get High-res Image Gene #24: 'del_6q22.31' versus Clinical Feature #12: 'RACE'

'del_6q26' versus 'NEOPLASM_DISEASESTAGE'

P value = 6e-05 (Fisher's exact test), Q value = 0.00038

Table S147. Gene #25: 'del_6q26' versus Clinical Feature #3: 'NEOPLASM_DISEASESTAGE'

nPatients	STAGE I	STAGE II	STAGE III	STAGE IV
ALL	448	103	190	100
DEL PEAK 12(6Q26) MUTATED	94	43	58	34
DEL PEAK 12(6Q26) WILD-TYPE	354	60	132	66

Figure S147. Get High-res Image Gene #25: 'del_6q26' versus Clinical Feature #3: 'NEOPLASM_DISEASESTAGE'

'del_6q26' versus 'PATHOLOGY_T_STAGE'

P value = 5e-05 (Fisher's exact test), Q value = 0.00033

Table S148. Gene #25: 'del_6q26' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

nPatients	T1	T2	T3	T4
ALL	462	123	251	15
DEL PEAK 12(6Q26) MUTATED	95	46	83	6
DEL PEAK 12(6Q26) WILD-TYPE	367	77	168	9

Figure S148. Get High-res Image Gene #25: 'del_6q26' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

'del_6q26' versus 'PATHOLOGY_N_STAGE'

P value = 0.0548 (Fisher's exact test), Q value = 0.13

Table S149. Gene #25: 'del_6q26' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

nPatients	N0	N1	N2
ALL	317	43	6
DEL PEAK 12(6Q26) MUTATED	92	17	4
DEL PEAK 12(6Q26) WILD-TYPE	225	26	2

Figure S149. Get High-res Image Gene #25: 'del_6q26' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

'del_6q26' versus 'KARNOFSKY_PERFORMANCE_SCORE'

P value = 0.086 (Wilcoxon-test), Q value = 0.19

Table S150. Gene #25: 'del_6q26' versus Clinical Feature #8: 'KARNOFSKY_PERFORMANCE_SCORE'

	nPatients	Mean (Std.Dev)
ALL	115	90.3 (17.6)
DEL PEAK 12(6Q26) MUTATED	33	85.8 (23.9)
DEL PEAK 12(6Q26) WILD-TYPE	82	92.1 (14.1)

Figure S150. Get High-res Image Gene #25: 'del_6q26' versus Clinical Feature #8: 'KARNOFSKY_PERFORMANCE_SCORE'

'del_6q26' versus 'HISTOLOGICAL_TYPE'

P value = 1e-05 (Fisher's exact test), Q value = 7.6e-05

Table S151. Gene #25: 'del_6q26' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'

nPatients	KIDNEY CHROMOPHOBE	KIDNEY CLEAR CELL RENAL CARCINOMA	KIDNEY PAPILLARY RENAL CELL CARCINOMA
ALL	66	524	269
DEL PEAK 12(6Q26) MUTATED	51	151	28
DEL PEAK 12(6Q26) WILD-TYPE	15	373	241

Figure S151. Get High-res Image Gene #25: 'del_6q26' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'

'del_6q26' versus 'RACE'

P value = 0.00126 (Fisher's exact test), Q value = 0.0056

Table S152. Gene #25: 'del_6q26' versus Clinical Feature #12: 'RACE'

nPatients	AMERICAN INDIAN OR ALASKA NATIVE	ASIAN	BLACK OR AFRICAN AMERICAN	WHITE
ALL	2	15	116	702
DEL PEAK 12(6Q26) MUTATED	0	6	16	200
DEL PEAK 12(6Q26) WILD-TYPE	2	9	100	502

Figure S152. Get High-res Image Gene #25: 'del_6q26' versus Clinical Feature #12: 'RACE'

'del_6q26' versus 'NEOPLASM_DISEASESTAGE'

P value = 8e-05 (Fisher's exact test), Q value = 5e-04

Table S153. Gene #26: 'del_6q26' versus Clinical Feature #3: 'NEOPLASM_DISEASESTAGE'

nPatients	STAGE I	STAGE II	STAGE III	STAGE IV
ALL	448	103	190	100
DEL PEAK 13(6Q26) MUTATED	95	43	58	34
DEL PEAK 13(6Q26) WILD-TYPE	353	60	132	66

Figure S153. Get High-res Image Gene #26: 'del_6q26' versus Clinical Feature #3: 'NEOPLASM_DISEASESTAGE'

'del_6q26' versus 'PATHOLOGY_T_STAGE'

P value = 6e-05 (Fisher's exact test), Q value = 0.00038

Table S154. Gene #26: 'del_6q26' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

nPatients	T1	T2	T3	T4
ALL	462	123	251	15
DEL PEAK 13(6Q26) MUTATED	96	46	83	6
DEL PEAK 13(6Q26) WILD-TYPE	366	77	168	9

Figure S154. Get High-res Image Gene #26: 'del_6q26' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

'del_6q26' versus 'PATHOLOGY_N_STAGE'

P value = 0.0549 (Fisher's exact test), Q value = 0.13

Table S155. Gene #26: 'del_6q26' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

nPatients	N0	N1	N2
ALL	317	43	6
DEL PEAK 13(6Q26) MUTATED	92	17	4
DEL PEAK 13(6Q26) WILD-TYPE	225	26	2

Figure S155. Get High-res Image Gene #26: 'del_6q26' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

'del_6q26' versus 'KARNOFSKY_PERFORMANCE_SCORE'

P value = 0.086 (Wilcoxon-test), Q value = 0.19

Table S156. Gene #26: 'del_6q26' versus Clinical Feature #8: 'KARNOFSKY_PERFORMANCE_SCORE'

	nPatients	Mean (Std.Dev)
ALL	115	90.3 (17.6)
DEL PEAK 13(6Q26) MUTATED	33	85.8 (23.9)
DEL PEAK 13(6Q26) WILD-TYPE	82	92.1 (14.1)

Figure S156. Get High-res Image Gene #26: 'del_6q26' versus Clinical Feature #8: 'KARNOFSKY_PERFORMANCE_SCORE'

'del_6q26' versus 'HISTOLOGICAL_TYPE'

P value = 1e-05 (Fisher's exact test), Q value = 7.6e-05

Table S157. Gene #26: 'del_6q26' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'

nPatients	KIDNEY CHROMOPHOBE	KIDNEY CLEAR CELL RENAL CARCINOMA	KIDNEY PAPILLARY RENAL CELL CARCINOMA
ALL	66	524	269
DEL PEAK 13(6Q26) MUTATED	51	151	29
DEL PEAK 13(6Q26) WILD-TYPE	15	373	240

Figure S157. Get High-res Image Gene #26: 'del_6q26' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'

'del_6q26' versus 'RACE'

P value = 0.00323 (Fisher's exact test), Q value = 0.012

Table S158. Gene #26: 'del_6q26' versus Clinical Feature #12: 'RACE'

nPatients	AMERICAN INDIAN OR ALASKA NATIVE	ASIAN	BLACK OR AFRICAN AMERICAN	WHITE
ALL	2	15	116	702
DEL PEAK 13(6Q26) MUTATED	0	6	17	200
DEL PEAK 13(6Q26) WILD-TYPE	2	9	99	502

Figure S158. Get High-res Image Gene #26: 'del_6q26' versus Clinical Feature #12: 'RACE'

'del_8p23.2' versus 'Time to Death'

P value = 0.000909 (logrank test), Q value = 0.0042

Table S159. Gene #27: 'del_8p23.2' versus Clinical Feature #1: 'Time to Death'

	nPatients	nDeath	Duration Range (Median), Month
ALL	843	211	0.1 - 194.8 (30.5)
DEL PEAK 14(8P23.2) MUTATED	181	63	0.1 - 137.1 (31.9)
DEL PEAK 14(8P23.2) WILD-TYPE	662	148	0.1 - 194.8 (30.3)

Figure S159. Get High-res Image Gene #27: 'del_8p23.2' versus Clinical Feature #1: 'Time to Death'

'del_8p23.2' versus 'NEOPLASM_DISEASESTAGE'

P value = 0.00201 (Fisher's exact test), Q value = 0.0083

Table S160. Gene #27: 'del_8p23.2' versus Clinical Feature #3: 'NEOPLASM_DISEASESTAGE'

nPatients	STAGE I	STAGE II	STAGE III	STAGE IV
ALL	448	103	190	100
DEL PEAK 14(8P23.2) MUTATED	75	25	48	32
DEL PEAK 14(8P23.2) WILD-TYPE	373	78	142	68

Figure S160. Get High-res Image Gene #27: 'del_8p23.2' versus Clinical Feature #3: 'NEOPLASM_DISEASESTAGE'

'del_8p23.2' versus 'PATHOLOGY_T_STAGE'

P value = 0.00183 (Fisher's exact test), Q value = 0.0078

Table S161. Gene #27: 'del_8p23.2' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

nPatients	T1	T2	T3	T4
ALL	462	123	251	15
DEL PEAK 14(8P23.2) MUTATED	77	30	68	6
DEL PEAK 14(8P23.2) WILD-TYPE	385	93	183	9

Figure S161. 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 = 0.0257 (Fisher's exact test), Q value = 0.069

Table S162. Gene #27: 'del_8p23.2' versus Clinical Feature #6: 'PATHOLOGY_M_STAGE'

nPatients	0	1
ALL	542	89
DEL PEAK 14(8P23.2) MUTATED	131	32
DEL PEAK 14(8P23.2) WILD-TYPE	411	57

Figure S162. 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 = 7.6e-05

Table S163. Gene #27: 'del_8p23.2' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'

nPatients	KIDNEY CHROMOPHOBE	KIDNEY CLEAR CELL RENAL CARCINOMA	KIDNEY PAPILLARY RENAL CELL CARCINOMA
ALL	66	524	269
DEL PEAK 14(8P23.2) MUTATED	12	154	15
DEL PEAK 14(8P23.2) WILD-TYPE	54	370	254

Figure S163. Get High-res Image Gene #27: 'del_8p23.2' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'

'del_8p23.2' versus 'RACE'

P value = 0.00376 (Fisher's exact test), Q value = 0.014

Table S164. Gene #27: 'del_8p23.2' versus Clinical Feature #12: 'RACE'

nPatients	AMERICAN INDIAN OR ALASKA NATIVE	ASIAN	BLACK OR AFRICAN AMERICAN	WHITE
ALL	2	15	116	702
DEL PEAK 14(8P23.2) MUTATED	0	7	14	157
DEL PEAK 14(8P23.2) WILD-TYPE	2	8	102	545

Figure S164. Get High-res Image Gene #27: 'del_8p23.2' versus Clinical Feature #12: 'RACE'

'del_9p23' versus 'Time to Death'

P value = 2.91e-11 (logrank test), Q value = 4.9e-09

Table S165. Gene #28: 'del_9p23' versus Clinical Feature #1: 'Time to Death'

	nPatients	nDeath	Duration Range (Median), Month
ALL	843	211	0.1 - 194.8 (30.5)
DEL PEAK 15(9P23) MUTATED	193	85	0.1 - 141.7 (31.3)
DEL PEAK 15(9P23) WILD-TYPE	650	126	0.1 - 194.8 (30.3)

Figure S165. Get High-res Image Gene #28: 'del_9p23' versus Clinical Feature #1: 'Time to Death'

'del_9p23' versus 'YEARS_TO_BIRTH'

P value = 0.0247 (Wilcoxon-test), Q value = 0.068

Table S166. Gene #28: 'del_9p23' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

	nPatients	Mean (Std.Dev)
ALL	853	60.1 (12.6)
DEL PEAK 15(9P23) MUTATED	194	61.8 (12.0)
DEL PEAK 15(9P23) WILD-TYPE	659	59.6 (12.7)

Figure S166. Get High-res Image Gene #28: 'del_9p23' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'del_9p23' versus 'NEOPLASM_DISEASESTAGE'

P value = 1e-05 (Fisher's exact test), Q value = 7.6e-05

Table S167. Gene #28: 'del_9p23' versus Clinical Feature #3: 'NEOPLASM_DISEASESTAGE'

nPatients	STAGE I	STAGE II	STAGE III	STAGE IV
ALL	448	103	190	100
DEL PEAK 15(9P23) MUTATED	64	16	69	43
DEL PEAK 15(9P23) WILD-TYPE	384	87	121	57

Figure S167. Get High-res Image Gene #28: 'del_9p23' versus Clinical Feature #3: 'NEOPLASM_DISEASESTAGE'

'del_9p23' versus 'PATHOLOGY_T_STAGE'

P value = 1e-05 (Fisher's exact test), Q value = 7.6e-05

Table S168. Gene #28: 'del_9p23' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

nPatients	T1	T2	T3	T4
ALL	462	123	251	15
DEL PEAK 15(9P23) MUTATED	68	23	96	7
DEL PEAK 15(9P23) WILD-TYPE	394	100	155	8

Figure S168. Get High-res Image Gene #28: 'del_9p23' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

'del_9p23' versus 'PATHOLOGY_N_STAGE'

P value = 0.00724 (Fisher's exact test), Q value = 0.024

Table S169. Gene #28: 'del_9p23' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

nPatients	N0	N1	N2
ALL	317	43	6
DEL PEAK 15(9P23) MUTATED	71	19	2
DEL PEAK 15(9P23) WILD-TYPE	246	24	4

Figure S169. Get High-res Image Gene #28: 'del_9p23' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

'del_9p23' versus 'PATHOLOGY_M_STAGE'

P value = 0.000223 (Fisher's exact test), Q value = 0.0012

Table S170. Gene #28: 'del_9p23' versus Clinical Feature #6: 'PATHOLOGY_M_STAGE'

nPatients	0	1
ALL	542	89
DEL PEAK 15(9P23) MUTATED	126	38
DEL PEAK 15(9P23) WILD-TYPE	416	51

Figure S170. Get High-res Image Gene #28: 'del_9p23' versus Clinical Feature #6: 'PATHOLOGY_M_STAGE'

'del_9p23' versus 'KARNOFSKY_PERFORMANCE_SCORE'

P value = 0.0204 (Wilcoxon-test), Q value = 0.059

Table S171. Gene #28: 'del_9p23' versus Clinical Feature #8: 'KARNOFSKY_PERFORMANCE_SCORE'

	nPatients	Mean (Std.Dev)
ALL	115	90.3 (17.6)
DEL PEAK 15(9P23) MUTATED	23	83.0 (27.0)
DEL PEAK 15(9P23) WILD-TYPE	92	92.1 (13.9)

Figure S171. Get High-res Image Gene #28: 'del_9p23' versus Clinical Feature #8: 'KARNOFSKY_PERFORMANCE_SCORE'

'del_9p23' versus 'HISTOLOGICAL_TYPE'

P value = 1e-05 (Fisher's exact test), Q value = 7.6e-05

Table S172. Gene #28: 'del_9p23' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'

nPatients	KIDNEY CHROMOPHOBE	KIDNEY CLEAR CELL RENAL CARCINOMA	KIDNEY PAPILLARY RENAL CELL CARCINOMA
ALL	66	524	269
DEL PEAK 15(9P23) MUTATED	10	151	35
DEL PEAK 15(9P23) WILD-TYPE	56	373	234

Figure S172. Get High-res Image Gene #28: 'del_9p23' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'

'del_9p23' versus 'RACE'

P value = 0.0126 (Fisher's exact test), Q value = 0.039

Table S173. Gene #28: 'del_9p23' versus Clinical Feature #12: 'RACE'

nPatients	AMERICAN INDIAN OR ALASKA NATIVE	ASIAN	BLACK OR AFRICAN AMERICAN	WHITE
ALL	2	15	116	702
DEL PEAK 15(9P23) MUTATED	0	4	14	172
DEL PEAK 15(9P23) WILD-TYPE	2	11	102	530

Figure S173. Get High-res Image Gene #28: 'del_9p23' versus Clinical Feature #12: 'RACE'

'del_9p21.3' versus 'Time to Death'

P value = 1.12e-14 (logrank test), Q value = 5.7e-12

Table S174. Gene #29: 'del_9p21.3' versus Clinical Feature #1: 'Time to Death'

	nPatients	nDeath	Duration Range (Median), Month
ALL	843	211	0.1 - 194.8 (30.5)
DEL PEAK 16(9P21.3) MUTATED	203	93	0.1 - 141.7 (28.9)
DEL PEAK 16(9P21.3) WILD-TYPE	640	118	0.1 - 194.8 (30.7)

Figure S174. 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 = 0.0358 (Wilcoxon-test), Q value = 0.092

Table S175. Gene #29: 'del_9p21.3' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

	nPatients	Mean (Std.Dev)
ALL	853	60.1 (12.6)
DEL PEAK 16(9P21.3) MUTATED	205	61.6 (12.2)
DEL PEAK 16(9P21.3) WILD-TYPE	648	59.6 (12.7)

Figure S175. Get High-res Image Gene #29: 'del_9p21.3' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'del_9p21.3' versus 'NEOPLASM_DISEASESTAGE'

P value = 1e-05 (Fisher's exact test), Q value = 7.6e-05

Table S176. Gene #29: 'del_9p21.3' versus Clinical Feature #3: 'NEOPLASM_DISEASESTAGE'

nPatients	STAGE I	STAGE II	STAGE III	STAGE IV
ALL	448	103	190	100
DEL PEAK 16(9P21.3) MUTATED	66	15	74	48
DEL PEAK 16(9P21.3) WILD-TYPE	382	88	116	52

Figure S176. Get High-res Image Gene #29: 'del_9p21.3' versus Clinical Feature #3: 'NEOPLASM_DISEASESTAGE'

'del_9p21.3' versus 'PATHOLOGY_T_STAGE'

P value = 1e-05 (Fisher's exact test), Q value = 7.6e-05

Table S177. Gene #29: 'del_9p21.3' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

nPatients	T1	T2	T3	T4
ALL	462	123	251	15
DEL PEAK 16(9P21.3) MUTATED	70	22	105	8
DEL PEAK 16(9P21.3) WILD-TYPE	392	101	146	7

Figure S177. 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 = 0.00013 (Fisher's exact test), Q value = 0.00076

Table S178. Gene #29: 'del_9p21.3' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

nPatients	N0	N1	N2
ALL	317	43	6
DEL PEAK 16(9P21.3) MUTATED	77	24	2
DEL PEAK 16(9P21.3) WILD-TYPE	240	19	4

Figure S178. 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 = 9.23e-06 (Fisher's exact test), Q value = 7.6e-05

Table S179. Gene #29: 'del_9p21.3' versus Clinical Feature #6: 'PATHOLOGY_M_STAGE'

nPatients	0	1
ALL	542	89
DEL PEAK 16(9P21.3) MUTATED	131	43
DEL PEAK 16(9P21.3) WILD-TYPE	411	46

Figure S179. 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 = 0.0401 (Wilcoxon-test), Q value = 0.1

Table S180. Gene #29: 'del_9p21.3' versus Clinical Feature #8: 'KARNOFSKY_PERFORMANCE_SCORE'

	nPatients	Mean (Std.Dev)
ALL	115	90.3 (17.6)
DEL PEAK 16(9P21.3) MUTATED	24	83.8 (26.7)
DEL PEAK 16(9P21.3) WILD-TYPE	91	92.0 (14.0)

Figure S180. Get High-res Image Gene #29: 'del_9p21.3' versus Clinical Feature #8: 'KARNOFSKY_PERFORMANCE_SCORE'

'del_9p21.3' versus 'HISTOLOGICAL_TYPE'

P value = 1e-05 (Fisher's exact test), Q value = 7.6e-05

Table S181. Gene #29: 'del_9p21.3' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'

nPatients	KIDNEY CHROMOPHOBE	KIDNEY CLEAR CELL RENAL CARCINOMA	KIDNEY PAPILLARY RENAL CELL CARCINOMA
ALL	66	524	269
DEL PEAK 16(9P21.3) MUTATED	10	159	38
DEL PEAK 16(9P21.3) WILD-TYPE	56	365	231

Figure S181. Get High-res Image Gene #29: 'del_9p21.3' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'

'del_9p21.3' versus 'RACE'

P value = 0.00827 (Fisher's exact test), Q value = 0.027

Table S182. Gene #29: 'del_9p21.3' versus Clinical Feature #12: 'RACE'

nPatients	AMERICAN INDIAN OR ALASKA NATIVE	ASIAN	BLACK OR AFRICAN AMERICAN	WHITE
ALL	2	15	116	702
DEL PEAK 16(9P21.3) MUTATED	0	3	15	184
DEL PEAK 16(9P21.3) WILD-TYPE	2	12	101	518

Figure S182. Get High-res Image Gene #29: 'del_9p21.3' versus Clinical Feature #12: 'RACE'

'del_10q23.31' versus 'YEARS_TO_BIRTH'

P value = 0.0425 (Wilcoxon-test), Q value = 0.11

Table S183. Gene #30: 'del_10q23.31' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

	nPatients	Mean (Std.Dev)
ALL	853	60.1 (12.6)
DEL PEAK 17(10Q23.31) MUTATED	160	58.0 (14.0)
DEL PEAK 17(10Q23.31) WILD-TYPE	693	60.6 (12.2)

Figure S183. Get High-res Image Gene #30: 'del_10q23.31' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'del_10q23.31' versus 'NEOPLASM_DISEASESTAGE'

P value = 1e-05 (Fisher's exact test), Q value = 7.6e-05

Table S184. Gene #30: 'del_10q23.31' versus Clinical Feature #3: 'NEOPLASM_DISEASESTAGE'

nPatients	STAGE I	STAGE II	STAGE III	STAGE IV
ALL	448	103	190	100
DEL PEAK 17(10Q23.31) MUTATED	52	32	53	25
DEL PEAK 17(10Q23.31) WILD-TYPE	396	71	137	75

Figure S184. Get High-res Image Gene #30: 'del_10q23.31' versus Clinical Feature #3: 'NEOPLASM_DISEASESTAGE'

'del_10q23.31' versus 'PATHOLOGY_T_STAGE'

P value = 1e-05 (Fisher's exact test), Q value = 7.6e-05

Table S185. Gene #30: 'del_10q23.31' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

nPatients	T1	T2	T3	T4
ALL	462	123	251	15
DEL PEAK 17(10Q23.31) MUTATED	53	33	69	7
DEL PEAK 17(10Q23.31) WILD-TYPE	409	90	182	8

Figure S185. 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 = 7.6e-05

Table S186. Gene #30: 'del_10q23.31' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'

nPatients	KIDNEY CHROMOPHOBE	KIDNEY CLEAR CELL RENAL CARCINOMA	KIDNEY PAPILLARY RENAL CELL CARCINOMA
ALL	66	524	269
DEL PEAK 17(10Q23.31) MUTATED	49	96	17
DEL PEAK 17(10Q23.31) WILD-TYPE	17	428	252

Figure S186. Get High-res Image Gene #30: 'del_10q23.31' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'

'del_10q23.31' versus 'RACE'

P value = 0.0994 (Fisher's exact test), Q value = 0.21

Table S187. Gene #30: 'del_10q23.31' versus Clinical Feature #12: 'RACE'

nPatients	AMERICAN INDIAN OR ALASKA NATIVE	ASIAN	BLACK OR AFRICAN AMERICAN	WHITE
ALL	2	15	116	702
DEL PEAK 17(10Q23.31) MUTATED	0	4	13	139
DEL PEAK 17(10Q23.31) WILD-TYPE	2	11	103	563

Figure S187. Get High-res Image Gene #30: 'del_10q23.31' versus Clinical Feature #12: 'RACE'

'del_11q21' versus 'Time to Death'

P value = 0.00196 (logrank test), Q value = 0.0082

Table S188. Gene #31: 'del_11q21' versus Clinical Feature #1: 'Time to Death'

	nPatients	nDeath	Duration Range (Median), Month
ALL	843	211	0.1 - 194.8 (30.5)
DEL PEAK 18(11Q21) MUTATED	59	22	0.1 - 123.6 (19.7)
DEL PEAK 18(11Q21) WILD-TYPE	784	189	0.1 - 194.8 (31.1)

Figure S188. Get High-res Image Gene #31: 'del_11q21' versus Clinical Feature #1: 'Time to Death'

'del_11q21' versus 'YEARS_TO_BIRTH'

P value = 0.00478 (Wilcoxon-test), Q value = 0.017

Table S189. Gene #31: 'del_11q21' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

	nPatients	Mean (Std.Dev)
ALL	853	60.1 (12.6)
DEL PEAK 18(11Q21) MUTATED	59	64.2 (11.0)
DEL PEAK 18(11Q21) WILD-TYPE	794	59.8 (12.6)

Figure S189. Get High-res Image Gene #31: 'del_11q21' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'del_11q21' versus 'NEOPLASM_DISEASESTAGE'

P value = 0.00026 (Fisher's exact test), Q value = 0.0014

Table S190. Gene #31: 'del_11q21' versus Clinical Feature #3: 'NEOPLASM_DISEASESTAGE'

nPatients	STAGE I	STAGE II	STAGE III	STAGE IV
ALL	448	103	190	100
DEL PEAK 18(11Q21) MUTATED	16	11	20	12
DEL PEAK 18(11Q21) WILD-TYPE	432	92	170	88

Figure S190. Get High-res Image Gene #31: 'del_11q21' versus Clinical Feature #3: 'NEOPLASM_DISEASESTAGE'

'del_11q21' versus 'PATHOLOGY_T_STAGE'

P value = 0.00041 (Fisher's exact test), Q value = 0.0021

Table S191. Gene #31: 'del_11q21' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

nPatients	T1	T2	T3	T4
ALL	462	123	251	15
DEL PEAK 18(11Q21) MUTATED	17	12	29	1
DEL PEAK 18(11Q21) WILD-TYPE	445	111	222	14

Figure S191. Get High-res Image Gene #31: 'del_11q21' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

'del_11q21' versus 'PATHOLOGY_N_STAGE'

P value = 0.00019 (Fisher's exact test), Q value = 0.0011

Table S192. Gene #31: 'del_11q21' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

nPatients	N0	N1	N2
ALL	317	43	6
DEL PEAK 18(11Q21) MUTATED	21	11	2
DEL PEAK 18(11Q21) WILD-TYPE	296	32	4

Figure S192. Get High-res Image Gene #31: 'del_11q21' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

'del_11q21' versus 'PATHOLOGY_M_STAGE'

P value = 0.0998 (Fisher's exact test), Q value = 0.21

Table S193. Gene #31: 'del_11q21' versus Clinical Feature #6: 'PATHOLOGY_M_STAGE'

nPatients	0	1
ALL	542	89
DEL PEAK 18(11Q21) MUTATED	30	9
DEL PEAK 18(11Q21) WILD-TYPE	512	80

Figure S193. Get High-res Image Gene #31: 'del_11q21' versus Clinical Feature #6: 'PATHOLOGY_M_STAGE'

'del_11q21' versus 'KARNOFSKY_PERFORMANCE_SCORE'

P value = 0.0624 (Wilcoxon-test), Q value = 0.15

Table S194. Gene #31: 'del_11q21' versus Clinical Feature #8: 'KARNOFSKY_PERFORMANCE_SCORE'

	nPatients	Mean (Std.Dev)
ALL	115	90.3 (17.6)
DEL PEAK 18(11Q21) MUTATED	11	89.1 (7.0)
DEL PEAK 18(11Q21) WILD-TYPE	104	90.4 (18.4)

Figure S194. Get High-res Image Gene #31: 'del_11q21' versus Clinical Feature #8: 'KARNOFSKY_PERFORMANCE_SCORE'

'del_11q21' versus 'HISTOLOGICAL_TYPE'

P value = 0.00304 (Fisher's exact test), Q value = 0.011

Table S195. Gene #31: 'del_11q21' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'

nPatients	KIDNEY CHROMOPHOBE	KIDNEY CLEAR CELL RENAL CARCINOMA	KIDNEY PAPILLARY RENAL CELL CARCINOMA
ALL	66	524	269
DEL PEAK 18(11Q21) MUTATED	9	25	26
DEL PEAK 18(11Q21) WILD-TYPE	57	499	243

Figure S195. Get High-res Image Gene #31: 'del_11q21' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'

'del_11q23.1' versus 'Time to Death'

P value = 0.00373 (logrank test), Q value = 0.014

Table S196. Gene #32: 'del_11q23.1' versus Clinical Feature #1: 'Time to Death'

	nPatients	nDeath	Duration Range (Median), Month
ALL	843	211	0.1 - 194.8 (30.5)
DEL PEAK 19(11Q23.1) MUTATED	68	25	0.1 - 123.6 (20.6)
DEL PEAK 19(11Q23.1) WILD-TYPE	775	186	0.1 - 194.8 (30.7)

Figure S196. 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 = 0.00293 (Wilcoxon-test), Q value = 0.011

Table S197. Gene #32: 'del_11q23.1' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

	nPatients	Mean (Std.Dev)
ALL	853	60.1 (12.6)
DEL PEAK 19(11Q23.1) MUTATED	69	64.1 (11.0)
DEL PEAK 19(11Q23.1) WILD-TYPE	784	59.8 (12.6)

Figure S197. Get High-res Image Gene #32: 'del_11q23.1' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'del_11q23.1' versus 'NEOPLASM_DISEASESTAGE'

P value = 3e-05 (Fisher's exact test), Q value = 0.00021

Table S198. Gene #32: 'del_11q23.1' versus Clinical Feature #3: 'NEOPLASM_DISEASESTAGE'

nPatients	STAGE I	STAGE II	STAGE III	STAGE IV
ALL	448	103	190	100
DEL PEAK 19(11Q23.1) MUTATED	18	13	24	14
DEL PEAK 19(11Q23.1) WILD-TYPE	430	90	166	86

Figure S198. Get High-res Image Gene #32: 'del_11q23.1' versus Clinical Feature #3: 'NEOPLASM_DISEASESTAGE'

'del_11q23.1' versus 'PATHOLOGY_T_STAGE'

P value = 1e-05 (Fisher's exact test), Q value = 7.6e-05

Table S199. Gene #32: 'del_11q23.1' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

nPatients	T1	T2	T3	T4
ALL	462	123	251	15
DEL PEAK 19(11Q23.1) MUTATED	19	15	32	3
DEL PEAK 19(11Q23.1) WILD-TYPE	443	108	219	12

Figure S199. 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 = 0.00047 (Fisher's exact test), Q value = 0.0023

Table S200. Gene #32: 'del_11q23.1' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

nPatients	N0	N1	N2
ALL	317	43	6
DEL PEAK 19(11Q23.1) MUTATED	24	11	2
DEL PEAK 19(11Q23.1) WILD-TYPE	293	32	4

Figure S200. 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 = 0.112 (Fisher's exact test), Q value = 0.23

Table S201. Gene #32: 'del_11q23.1' versus Clinical Feature #6: 'PATHOLOGY_M_STAGE'

nPatients	0	1
ALL	542	89
DEL PEAK 19(11Q23.1) MUTATED	34	10
DEL PEAK 19(11Q23.1) WILD-TYPE	508	79

Figure S201. 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 = 0.0253 (Wilcoxon-test), Q value = 0.069

Table S202. Gene #32: 'del_11q23.1' versus Clinical Feature #8: 'KARNOFSKY_PERFORMANCE_SCORE'

	nPatients	Mean (Std.Dev)
ALL	115	90.3 (17.6)
DEL PEAK 19(11Q23.1) MUTATED	12	88.3 (7.2)
DEL PEAK 19(11Q23.1) WILD-TYPE	103	90.5 (18.4)

Figure S202. Get High-res Image Gene #32: 'del_11q23.1' versus Clinical Feature #8: 'KARNOFSKY_PERFORMANCE_SCORE'

'del_11q23.1' versus 'HISTOLOGICAL_TYPE'

P value = 0.00361 (Fisher's exact test), Q value = 0.013

Table S203. Gene #32: 'del_11q23.1' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'

nPatients	KIDNEY CHROMOPHOBE	KIDNEY CLEAR CELL RENAL CARCINOMA	KIDNEY PAPILLARY RENAL CELL CARCINOMA
ALL	66	524	269
DEL PEAK 19(11Q23.1) MUTATED	9	30	31
DEL PEAK 19(11Q23.1) WILD-TYPE	57	494	238

Figure S203. Get High-res Image Gene #32: 'del_11q23.1' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'

'del_13q12.13' versus 'Time to Death'

P value = 0.0323 (logrank test), Q value = 0.085

Table S204. Gene #33: 'del_13q12.13' versus Clinical Feature #1: 'Time to Death'

	nPatients	nDeath	Duration Range (Median), Month
ALL	843	211	0.1 - 194.8 (30.5)
DEL PEAK 20(13Q12.13) MUTATED	146	53	0.1 - 152.0 (36.7)
DEL PEAK 20(13Q12.13) WILD-TYPE	697	158	0.1 - 194.8 (29.5)

Figure S204. 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 = 0.000423 (Wilcoxon-test), Q value = 0.0021

Table S205. Gene #33: 'del_13q12.13' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

	nPatients	Mean (Std.Dev)
ALL	853	60.1 (12.6)
DEL PEAK 20(13Q12.13) MUTATED	148	56.2 (15.2)
DEL PEAK 20(13Q12.13) WILD-TYPE	705	60.9 (11.8)

Figure S205. Get High-res Image Gene #33: 'del_13q12.13' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'del_13q12.13' versus 'NEOPLASM_DISEASESTAGE'

P value = 1e-05 (Fisher's exact test), Q value = 7.6e-05

Table S206. Gene #33: 'del_13q12.13' versus Clinical Feature #3: 'NEOPLASM_DISEASESTAGE'

nPatients	STAGE I	STAGE II	STAGE III	STAGE IV
ALL	448	103	190	100
DEL PEAK 20(13Q12.13) MUTATED	46	24	50	28
DEL PEAK 20(13Q12.13) WILD-TYPE	402	79	140	72

Figure S206. Get High-res Image Gene #33: 'del_13q12.13' versus Clinical Feature #3: 'NEOPLASM_DISEASESTAGE'

'del_13q12.13' versus 'PATHOLOGY_T_STAGE'

P value = 1e-05 (Fisher's exact test), Q value = 7.6e-05

Table S207. Gene #33: 'del_13q12.13' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

nPatients	T1	T2	T3	T4
ALL	462	123	251	15
DEL PEAK 20(13Q12.13) MUTATED	48	26	65	9
DEL PEAK 20(13Q12.13) WILD-TYPE	414	97	186	6

Figure S207. 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 = 0.0135 (Fisher's exact test), Q value = 0.041

Table S208. Gene #33: 'del_13q12.13' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

nPatients	N0	N1	N2
ALL	317	43	6
DEL PEAK 20(13Q12.13) MUTATED	68	14	4
DEL PEAK 20(13Q12.13) WILD-TYPE	249	29	2

Figure S208. Get High-res Image Gene #33: 'del_13q12.13' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

'del_13q12.13' versus 'GENDER'

P value = 0.0212 (Fisher's exact test), Q value = 0.06

Table S209. Gene #33: 'del_13q12.13' versus Clinical Feature #7: 'GENDER'

nPatients	FEMALE	MALE
ALL	287	572
DEL PEAK 20(13Q12.13) MUTATED	62	86
DEL PEAK 20(13Q12.13) WILD-TYPE	225	486

Figure S209. 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 = 7.6e-05

Table S210. Gene #33: 'del_13q12.13' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'

nPatients	KIDNEY CHROMOPHOBE	KIDNEY CLEAR CELL RENAL CARCINOMA	KIDNEY PAPILLARY RENAL CELL CARCINOMA
ALL	66	524	269
DEL PEAK 20(13Q12.13) MUTATED	44	81	23
DEL PEAK 20(13Q12.13) WILD-TYPE	22	443	246

Figure S210. Get High-res Image Gene #33: 'del_13q12.13' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'

'del_13q12.13' versus 'RACE'

P value = 0.103 (Fisher's exact test), Q value = 0.21

Table S211. Gene #33: 'del_13q12.13' versus Clinical Feature #12: 'RACE'

nPatients	AMERICAN INDIAN OR ALASKA NATIVE	ASIAN	BLACK OR AFRICAN AMERICAN	WHITE
ALL	2	15	116	702
DEL PEAK 20(13Q12.13) MUTATED	0	4	12	127
DEL PEAK 20(13Q12.13) WILD-TYPE	2	11	104	575

Figure S211. Get High-res Image Gene #33: 'del_13q12.13' versus Clinical Feature #12: 'RACE'

'del_13q14.2' versus 'Time to Death'

P value = 0.0241 (logrank test), Q value = 0.067

Table S212. Gene #34: 'del_13q14.2' versus Clinical Feature #1: 'Time to Death'

	nPatients	nDeath	Duration Range (Median), Month
ALL	843	211	0.1 - 194.8 (30.5)
DEL PEAK 21(13Q14.2) MUTATED	146	53	0.1 - 152.0 (33.7)
DEL PEAK 21(13Q14.2) WILD-TYPE	697	158	0.1 - 194.8 (29.9)

Figure S212. 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 = 8.11e-05 (Wilcoxon-test), Q value = 5e-04

Table S213. Gene #34: 'del_13q14.2' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

	nPatients	Mean (Std.Dev)
ALL	853	60.1 (12.6)
DEL PEAK 21(13Q14.2) MUTATED	148	55.7 (15.0)
DEL PEAK 21(13Q14.2) WILD-TYPE	705	61.0 (11.8)

Figure S213. Get High-res Image Gene #34: 'del_13q14.2' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'del_13q14.2' versus 'NEOPLASM_DISEASESTAGE'

P value = 1e-05 (Fisher's exact test), Q value = 7.6e-05

Table S214. Gene #34: 'del_13q14.2' versus Clinical Feature #3: 'NEOPLASM_DISEASESTAGE'

nPatients	STAGE I	STAGE II	STAGE III	STAGE IV
ALL	448	103	190	100
DEL PEAK 21(13Q14.2) MUTATED	46	22	51	29
DEL PEAK 21(13Q14.2) WILD-TYPE	402	81	139	71

Figure S214. Get High-res Image Gene #34: 'del_13q14.2' versus Clinical Feature #3: 'NEOPLASM_DISEASESTAGE'

'del_13q14.2' versus 'PATHOLOGY_T_STAGE'

P value = 1e-05 (Fisher's exact test), Q value = 7.6e-05

Table S215. Gene #34: 'del_13q14.2' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

nPatients	T1	T2	T3	T4
ALL	462	123	251	15
DEL PEAK 21(13Q14.2) MUTATED	48	24	67	9
DEL PEAK 21(13Q14.2) WILD-TYPE	414	99	184	6

Figure S215. 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 = 0.015 (Fisher's exact test), Q value = 0.045

Table S216. Gene #34: 'del_13q14.2' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

nPatients	N0	N1	N2
ALL	317	43	6
DEL PEAK 21(13Q14.2) MUTATED	69	14	4
DEL PEAK 21(13Q14.2) WILD-TYPE	248	29	2

Figure S216. Get High-res Image Gene #34: 'del_13q14.2' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

'del_13q14.2' versus 'GENDER'

P value = 0.0125 (Fisher's exact test), Q value = 0.039

Table S217. Gene #34: 'del_13q14.2' versus Clinical Feature #7: 'GENDER'

nPatients	FEMALE	MALE
ALL	287	572
DEL PEAK 21(13Q14.2) MUTATED	63	85
DEL PEAK 21(13Q14.2) WILD-TYPE	224	487

Figure S217. 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 = 7.6e-05

Table S218. Gene #34: 'del_13q14.2' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'

nPatients	KIDNEY CHROMOPHOBE	KIDNEY CLEAR CELL RENAL CARCINOMA	KIDNEY PAPILLARY RENAL CELL CARCINOMA
ALL	66	524	269
DEL PEAK 21(13Q14.2) MUTATED	43	82	23
DEL PEAK 21(13Q14.2) WILD-TYPE	23	442	246

Figure S218. Get High-res Image Gene #34: 'del_13q14.2' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'

'del_13q14.2' versus 'RACE'

P value = 0.104 (Fisher's exact test), Q value = 0.21

Table S219. Gene #34: 'del_13q14.2' versus Clinical Feature #12: 'RACE'

nPatients	AMERICAN INDIAN OR ALASKA NATIVE	ASIAN	BLACK OR AFRICAN AMERICAN	WHITE
ALL	2	15	116	702
DEL PEAK 21(13Q14.2) MUTATED	0	4	12	127
DEL PEAK 21(13Q14.2) WILD-TYPE	2	11	104	575

Figure S219. Get High-res Image Gene #34: 'del_13q14.2' versus Clinical Feature #12: 'RACE'

'del_14q31.1' versus 'Time to Death'

P value = 8.67e-09 (logrank test), Q value = 8.8e-07

Table S220. Gene #35: 'del_14q31.1' versus Clinical Feature #1: 'Time to Death'

	nPatients	nDeath	Duration Range (Median), Month
ALL	843	211	0.1 - 194.8 (30.5)
DEL PEAK 22(14Q31.1) MUTATED	273	103	0.1 - 129.4 (30.5)
DEL PEAK 22(14Q31.1) WILD-TYPE	570	108	0.1 - 194.8 (30.5)

Figure S220. Get High-res Image Gene #35: 'del_14q31.1' versus Clinical Feature #1: 'Time to Death'

'del_14q31.1' versus 'YEARS_TO_BIRTH'

P value = 0.0799 (Wilcoxon-test), Q value = 0.18

Table S221. Gene #35: 'del_14q31.1' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

	nPatients	Mean (Std.Dev)
ALL	853	60.1 (12.6)
DEL PEAK 22(14Q31.1) MUTATED	273	61.3 (12.4)
DEL PEAK 22(14Q31.1) WILD-TYPE	580	59.6 (12.6)

Figure S221. Get High-res Image Gene #35: 'del_14q31.1' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'del_14q31.1' versus 'NEOPLASM_DISEASESTAGE'

P value = 1e-05 (Fisher's exact test), Q value = 7.6e-05

Table S222. Gene #35: 'del_14q31.1' versus Clinical Feature #3: 'NEOPLASM_DISEASESTAGE'

nPatients	STAGE I	STAGE II	STAGE III	STAGE IV
ALL	448	103	190	100
DEL PEAK 22(14Q31.1) MUTATED	103	31	83	54
DEL PEAK 22(14Q31.1) WILD-TYPE	345	72	107	46

Figure S222. Get High-res Image Gene #35: 'del_14q31.1' versus Clinical Feature #3: 'NEOPLASM_DISEASESTAGE'

'del_14q31.1' versus 'PATHOLOGY_T_STAGE'

P value = 1e-05 (Fisher's exact test), Q value = 7.6e-05

Table S223. Gene #35: 'del_14q31.1' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

nPatients	T1	T2	T3	T4
ALL	462	123	251	15
DEL PEAK 22(14Q31.1) MUTATED	110	40	119	5
DEL PEAK 22(14Q31.1) WILD-TYPE	352	83	132	10

Figure S223. 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 = 0.00205 (Fisher's exact test), Q value = 0.0083

Table S224. Gene #35: 'del_14q31.1' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

nPatients	N0	N1	N2
ALL	317	43	6
DEL PEAK 22(14Q31.1) MUTATED	108	26	3
DEL PEAK 22(14Q31.1) WILD-TYPE	209	17	3

Figure S224. 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 = 4.84e-05 (Fisher's exact test), Q value = 0.00033

Table S225. Gene #35: 'del_14q31.1' versus Clinical Feature #6: 'PATHOLOGY_M_STAGE'

nPatients	0	1
ALL	542	89
DEL PEAK 22(14Q31.1) MUTATED	185	51
DEL PEAK 22(14Q31.1) WILD-TYPE	357	38

Figure S225. Get High-res Image Gene #35: 'del_14q31.1' versus Clinical Feature #6: 'PATHOLOGY_M_STAGE'

'del_14q31.1' versus 'KARNOFSKY_PERFORMANCE_SCORE'

P value = 0.0447 (Wilcoxon-test), Q value = 0.11

Table S226. Gene #35: 'del_14q31.1' versus Clinical Feature #8: 'KARNOFSKY_PERFORMANCE_SCORE'

	nPatients	Mean (Std.Dev)
ALL	115	90.3 (17.6)
DEL PEAK 22(14Q31.1) MUTATED	30	82.0 (29.3)
DEL PEAK 22(14Q31.1) WILD-TYPE	85	93.2 (9.5)

Figure S226. Get High-res Image Gene #35: 'del_14q31.1' versus Clinical Feature #8: 'KARNOFSKY_PERFORMANCE_SCORE'

'del_14q31.1' versus 'HISTOLOGICAL_TYPE'

P value = 1e-05 (Fisher's exact test), Q value = 7.6e-05

Table S227. Gene #35: 'del_14q31.1' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'

nPatients	KIDNEY CHROMOPHOBE	KIDNEY CLEAR CELL RENAL CARCINOMA	KIDNEY PAPILLARY RENAL CELL CARCINOMA
ALL	66	524	269
DEL PEAK 22(14Q31.1) MUTATED	3	226	45
DEL PEAK 22(14Q31.1) WILD-TYPE	63	298	224

Figure S227. Get High-res Image Gene #35: 'del_14q31.1' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'

'del_14q31.1' versus 'YEAR_OF_TOBACCO_SMOKING_ONSET'

P value = 0.00272 (Wilcoxon-test), Q value = 0.011

Table S228. Gene #35: 'del_14q31.1' versus Clinical Feature #11: 'YEAR_OF_TOBACCO_SMOKING_ONSET'

	nPatients	Mean (Std.Dev)
ALL	67	1973.4 (16.4)
DEL PEAK 22(14Q31.1) MUTATED	11	1987.4 (14.2)
DEL PEAK 22(14Q31.1) WILD-TYPE	56	1970.7 (15.5)

Figure S228. Get High-res Image Gene #35: 'del_14q31.1' versus Clinical Feature #11: 'YEAR_OF_TOBACCO_SMOKING_ONSET'

'del_14q31.1' versus 'RACE'

P value = 0.011 (Fisher's exact test), Q value = 0.035

Table S229. Gene #35: 'del_14q31.1' versus Clinical Feature #12: 'RACE'

nPatients	AMERICAN INDIAN OR ALASKA NATIVE	ASIAN	BLACK OR AFRICAN AMERICAN	WHITE
ALL	2	15	116	702
DEL PEAK 22(14Q31.1) MUTATED	0	3	24	240
DEL PEAK 22(14Q31.1) WILD-TYPE	2	12	92	462

Figure S229. Get High-res Image Gene #35: 'del_14q31.1' versus Clinical Feature #12: 'RACE'

'del_16q23.3' versus 'Time to Death'

P value = 9.39e-06 (logrank test), Q value = 7.6e-05

Table S230. Gene #36: 'del_16q23.3' versus Clinical Feature #1: 'Time to Death'

	nPatients	nDeath	Duration Range (Median), Month
ALL	843	211	0.1 - 194.8 (30.5)
DEL PEAK 23(16Q23.3) MUTATED	35	18	0.1 - 90.5 (27.6)
DEL PEAK 23(16Q23.3) WILD-TYPE	808	193	0.1 - 194.8 (30.6)

Figure S230. Get High-res Image Gene #36: 'del_16q23.3' versus Clinical Feature #1: 'Time to Death'

'del_16q23.3' versus 'NEOPLASM_DISEASESTAGE'

P value = 0.00647 (Fisher's exact test), Q value = 0.022

Table S231. Gene #36: 'del_16q23.3' versus Clinical Feature #3: 'NEOPLASM_DISEASESTAGE'

nPatients	STAGE I	STAGE II	STAGE III	STAGE IV
ALL	448	103	190	100
DEL PEAK 23(16Q23.3) MUTATED	11	4	11	10
DEL PEAK 23(16Q23.3) WILD-TYPE	437	99	179	90

Figure S231. Get High-res Image Gene #36: 'del_16q23.3' versus Clinical Feature #3: 'NEOPLASM_DISEASESTAGE'

'del_16q23.3' versus 'PATHOLOGY_T_STAGE'

P value = 0.00014 (Fisher's exact test), Q value = 0.00081

Table S232. Gene #36: 'del_16q23.3' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

nPatients	T1	T2	T3	T4
ALL	462	123	251	15
DEL PEAK 23(16Q23.3) MUTATED	12	4	15	5
DEL PEAK 23(16Q23.3) WILD-TYPE	450	119	236	10

Figure S232. 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 = 0.00046 (Fisher's exact test), Q value = 0.0023

Table S233. Gene #36: 'del_16q23.3' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

nPatients	N0	N1	N2
ALL	317	43	6
DEL PEAK 23(16Q23.3) MUTATED	12	7	2
DEL PEAK 23(16Q23.3) WILD-TYPE	305	36	4

Figure S233. 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 = 6.48e-07 (logrank test), Q value = 5.5e-05

Table S234. Gene #37: 'del_18q22.2' versus Clinical Feature #1: 'Time to Death'

	nPatients	nDeath	Duration Range (Median), Month
ALL	843	211	0.1 - 194.8 (30.5)
DEL PEAK 24(18Q22.2) MUTATED	149	59	0.1 - 123.6 (25.6)
DEL PEAK 24(18Q22.2) WILD-TYPE	694	152	0.1 - 194.8 (31.3)

Figure S234. Get High-res Image Gene #37: 'del_18q22.2' versus Clinical Feature #1: 'Time to Death'

'del_18q22.2' versus 'NEOPLASM_DISEASESTAGE'

P value = 1e-05 (Fisher's exact test), Q value = 7.6e-05

Table S235. Gene #37: 'del_18q22.2' versus Clinical Feature #3: 'NEOPLASM_DISEASESTAGE'

nPatients	STAGE I	STAGE II	STAGE III	STAGE IV
ALL	448	103	190	100
DEL PEAK 24(18Q22.2) MUTATED	51	12	55	31
DEL PEAK 24(18Q22.2) WILD-TYPE	397	91	135	69

Figure S235. Get High-res Image Gene #37: 'del_18q22.2' versus Clinical Feature #3: 'NEOPLASM_DISEASESTAGE'

'del_18q22.2' versus 'PATHOLOGY_T_STAGE'

P value = 1e-05 (Fisher's exact test), Q value = 7.6e-05

Table S236. Gene #37: 'del_18q22.2' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

nPatients	T1	T2	T3	T4
ALL	462	123	251	15
DEL PEAK 24(18Q22.2) MUTATED	54	17	73	7
DEL PEAK 24(18Q22.2) WILD-TYPE	408	106	178	8

Figure S236. 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 = 0.0213 (Fisher's exact test), Q value = 0.06

Table S237. Gene #37: 'del_18q22.2' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

nPatients	N0	N1	N2
ALL	317	43	6
DEL PEAK 24(18Q22.2) MUTATED	64	15	3
DEL PEAK 24(18Q22.2) WILD-TYPE	253	28	3

Figure S237. 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 = 0.00917 (Fisher's exact test), Q value = 0.029

Table S238. Gene #37: 'del_18q22.2' versus Clinical Feature #6: 'PATHOLOGY_M_STAGE'

nPatients	0	1
ALL	542	89
DEL PEAK 24(18Q22.2) MUTATED	97	27
DEL PEAK 24(18Q22.2) WILD-TYPE	445	62

Figure S238. Get High-res Image Gene #37: 'del_18q22.2' versus Clinical Feature #6: 'PATHOLOGY_M_STAGE'

'del_18q22.2' versus 'YEAR_OF_TOBACCO_SMOKING_ONSET'

P value = 0.117 (Wilcoxon-test), Q value = 0.24

Table S239. Gene #37: 'del_18q22.2' versus Clinical Feature #11: 'YEAR_OF_TOBACCO_SMOKING_ONSET'

	nPatients	Mean (Std.Dev)
ALL	67	1973.4 (16.4)
DEL PEAK 24(18Q22.2) MUTATED	8	1981.1 (13.2)
DEL PEAK 24(18Q22.2) WILD-TYPE	59	1972.4 (16.6)

Figure S239. Get High-res Image Gene #37: 'del_18q22.2' versus Clinical Feature #11: 'YEAR_OF_TOBACCO_SMOKING_ONSET'

'del_18q22.2' versus 'RACE'

P value = 0.0746 (Fisher's exact test), Q value = 0.17

Table S240. Gene #37: 'del_18q22.2' versus Clinical Feature #12: 'RACE'

nPatients	AMERICAN INDIAN OR ALASKA NATIVE	ASIAN	BLACK OR AFRICAN AMERICAN	WHITE
ALL	2	15	116	702
DEL PEAK 24(18Q22.2) MUTATED	0	6	15	128
DEL PEAK 24(18Q22.2) WILD-TYPE	2	9	101	574

Figure S240. Get High-res Image Gene #37: 'del_18q22.2' versus Clinical Feature #12: 'RACE'

'del_18q22.2' versus 'ETHNICITY'

P value = 0.0894 (Fisher's exact test), Q value = 0.19

Table S241. Gene #37: 'del_18q22.2' versus Clinical Feature #13: 'ETHNICITY'

nPatients	HISPANIC OR LATINO	NOT HISPANIC OR LATINO
ALL	42	597
DEL PEAK 24(18Q22.2) MUTATED	3	106
DEL PEAK 24(18Q22.2) WILD-TYPE	39	491

Figure S241. Get High-res Image Gene #37: 'del_18q22.2' versus Clinical Feature #13: 'ETHNICITY'

'del_19p13.3' versus 'Time to Death'

P value = 8.5e-12 (logrank test), Q value = 2.2e-09

Table S242. Gene #38: 'del_19p13.3' versus Clinical Feature #1: 'Time to Death'

	nPatients	nDeath	Duration Range (Median), Month
ALL	843	211	0.1 - 194.8 (30.5)
DEL PEAK 25(19P13.3) MUTATED	40	21	0.1 - 109.9 (17.5)
DEL PEAK 25(19P13.3) WILD-TYPE	803	190	0.1 - 194.8 (31.3)

Figure S242. Get High-res Image Gene #38: 'del_19p13.3' versus Clinical Feature #1: 'Time to Death'

'del_19p13.3' versus 'NEOPLASM_DISEASESTAGE'

P value = 6e-05 (Fisher's exact test), Q value = 0.00038

Table S243. Gene #38: 'del_19p13.3' versus Clinical Feature #3: 'NEOPLASM_DISEASESTAGE'

nPatients	STAGE I	STAGE II	STAGE III	STAGE IV
ALL	448	103	190	100
DEL PEAK 25(19P13.3) MUTATED	10	1	17	11
DEL PEAK 25(19P13.3) WILD-TYPE	438	102	173	89

Figure S243. Get High-res Image Gene #38: 'del_19p13.3' versus Clinical Feature #3: 'NEOPLASM_DISEASESTAGE'

'del_19p13.3' versus 'PATHOLOGY_T_STAGE'

P value = 1e-05 (Fisher's exact test), Q value = 7.6e-05

Table S244. Gene #38: 'del_19p13.3' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

nPatients	T1	T2	T3	T4
ALL	462	123	251	15
DEL PEAK 25(19P13.3) MUTATED	11	2	23	4
DEL PEAK 25(19P13.3) WILD-TYPE	451	121	228	11

Figure S244. 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 = 0.00022 (Fisher's exact test), Q value = 0.0012

Table S245. Gene #38: 'del_19p13.3' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

nPatients	N0	N1	N2
ALL	317	43	6
DEL PEAK 25(19P13.3) MUTATED	10	7	2
DEL PEAK 25(19P13.3) WILD-TYPE	307	36	4

Figure S245. 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 = 0.064 (Fisher's exact test), Q value = 0.15

Table S246. Gene #38: 'del_19p13.3' versus Clinical Feature #6: 'PATHOLOGY_M_STAGE'

nPatients	0	1
ALL	542	89
DEL PEAK 25(19P13.3) MUTATED	17	7
DEL PEAK 25(19P13.3) WILD-TYPE	525	82

Figure S246. 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 = 0.0779 (Wilcoxon-test), Q value = 0.17

Table S247. Gene #38: 'del_19p13.3' versus Clinical Feature #8: 'KARNOFSKY_PERFORMANCE_SCORE'

	nPatients	Mean (Std.Dev)
ALL	115	90.3 (17.6)
DEL PEAK 25(19P13.3) MUTATED	9	80.0 (30.8)
DEL PEAK 25(19P13.3) WILD-TYPE	106	91.1 (15.9)

Figure S247. Get High-res Image Gene #38: 'del_19p13.3' versus Clinical Feature #8: 'KARNOFSKY_PERFORMANCE_SCORE'

'del_19p13.3' versus 'HISTOLOGICAL_TYPE'

P value = 0.0287 (Fisher's exact test), Q value = 0.076

Table S248. Gene #38: 'del_19p13.3' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'

nPatients	KIDNEY CHROMOPHOBE	KIDNEY CLEAR CELL RENAL CARCINOMA	KIDNEY PAPILLARY RENAL CELL CARCINOMA
ALL	66	524	269
DEL PEAK 25(19P13.3) MUTATED	3	17	20
DEL PEAK 25(19P13.3) WILD-TYPE	63	507	249

Figure S248. Get High-res Image Gene #38: 'del_19p13.3' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'

'del_xp22.2' versus 'YEARS_TO_BIRTH'

P value = 0.00136 (Wilcoxon-test), Q value = 0.006

Table S249. Gene #39: 'del_xp22.2' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

	nPatients	Mean (Std.Dev)
ALL	853	60.1 (12.6)
DEL PEAK 26(XP22.2) MUTATED	123	56.2 (13.9)
DEL PEAK 26(XP22.2) WILD-TYPE	730	60.8 (12.2)

Figure S249. Get High-res Image Gene #39: 'del_xp22.2' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'del_xp22.2' versus 'NEOPLASM_DISEASESTAGE'

P value = 1e-04 (Fisher's exact test), Q value = 0.00061

Table S250. Gene #39: 'del_xp22.2' versus Clinical Feature #3: 'NEOPLASM_DISEASESTAGE'

nPatients	STAGE I	STAGE II	STAGE III	STAGE IV
ALL	448	103	190	100
DEL PEAK 26(XP22.2) MUTATED	43	24	39	14
DEL PEAK 26(XP22.2) WILD-TYPE	405	79	151	86

Figure S250. Get High-res Image Gene #39: 'del_xp22.2' versus Clinical Feature #3: 'NEOPLASM_DISEASESTAGE'

'del_xp22.2' versus 'PATHOLOGY_T_STAGE'

P value = 0.00025 (Fisher's exact test), Q value = 0.0013

Table S251. Gene #39: 'del_xp22.2' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

nPatients	T1	T2	T3	T4
ALL	462	123	251	15
DEL PEAK 26(XP22.2) MUTATED	44	26	49	3
DEL PEAK 26(XP22.2) WILD-TYPE	418	97	202	12

Figure S251. 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 = 0.0948 (Fisher's exact test), Q value = 0.2

Table S252. Gene #39: 'del_xp22.2' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

nPatients	N0	N1	N2
ALL	317	43	6
DEL PEAK 26(XP22.2) MUTATED	48	11	2
DEL PEAK 26(XP22.2) WILD-TYPE	269	32	4

Figure S252. 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 = 7.6e-05

Table S253. Gene #39: 'del_xp22.2' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'

nPatients	KIDNEY CHROMOPHOBE	KIDNEY CLEAR CELL RENAL CARCINOMA	KIDNEY PAPILLARY RENAL CELL CARCINOMA
ALL	66	524	269
DEL PEAK 26(XP22.2) MUTATED	39	55	29
DEL PEAK 26(XP22.2) WILD-TYPE	27	469	240

Figure S253. Get High-res Image Gene #39: 'del_xp22.2' versus Clinical Feature #9: '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/15087107/transformed.cor.cli.txt
Clinical data file = /xchip/cga/gdac-prod/tcga-gdac/jobResults/Append_Data/KIPAN-TP/15081103/KIPAN-TP.merged_data.txt
Number of patients = 859
Number of significantly focal cnvs = 39
Number of selected clinical features = 13
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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