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

Prostate Adenocarcinoma (Primary solid tumor)

21 August 2015 | analyses__2015_08_21

Maintainer Information

Citation Information

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

Cite as Broad Institute TCGA Genome Data Analysis Center (2015): Correlation between copy number variations of arm-level result and selected clinical features. Broad Institute of MIT and Harvard. doi:10.7908/C10V8C1Q

Overview

Introduction

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

Summary

Testing the association between copy number variation 80 arm-level events and 11 clinical features across 491 patients, 316 significant findings detected with Q value < 0.25.

1p gain cnv correlated to 'PATHOLOGY_T_STAGE', 'RADIATION_THERAPY', and 'GLEASON_SCORE'.
1q gain cnv correlated to 'PATHOLOGY_T_STAGE', 'RADIATION_THERAPY', and 'GLEASON_SCORE'.
2p gain cnv correlated to 'PSA_VALUE'.
2q gain cnv correlated to 'PSA_VALUE'.
3p gain cnv correlated to 'YEARS_TO_BIRTH', 'PATHOLOGY_T_STAGE', 'PATHOLOGY_N_STAGE', 'RESIDUAL_TUMOR', 'NUMBER_OF_LYMPH_NODES', and 'GLEASON_SCORE'.
3q gain cnv correlated to 'YEARS_TO_BIRTH', 'PATHOLOGY_T_STAGE', 'PATHOLOGY_N_STAGE', 'RESIDUAL_TUMOR', 'NUMBER_OF_LYMPH_NODES', 'GLEASON_SCORE', and 'PSA_VALUE'.
5p gain cnv correlated to 'YEARS_TO_BIRTH', 'PATHOLOGY_T_STAGE', 'PATHOLOGY_N_STAGE', 'RADIATION_THERAPY', 'RESIDUAL_TUMOR', 'NUMBER_OF_LYMPH_NODES', and 'GLEASON_SCORE'.
5q gain cnv correlated to 'YEARS_TO_BIRTH', 'PATHOLOGY_T_STAGE', 'PATHOLOGY_N_STAGE', 'RESIDUAL_TUMOR', 'NUMBER_OF_LYMPH_NODES', and 'GLEASON_SCORE'.
6p gain cnv correlated to 'Time to Death', 'PATHOLOGY_N_STAGE', 'NUMBER_OF_LYMPH_NODES', and 'GLEASON_SCORE'.
6q gain cnv correlated to 'YEARS_TO_BIRTH', 'PATHOLOGY_N_STAGE', 'NUMBER_OF_LYMPH_NODES', and 'GLEASON_SCORE'.
7p gain cnv correlated to 'YEARS_TO_BIRTH', 'PATHOLOGY_T_STAGE', 'RESIDUAL_TUMOR', and 'GLEASON_SCORE'.
7q gain cnv correlated to 'YEARS_TO_BIRTH', 'PATHOLOGY_T_STAGE', 'RESIDUAL_TUMOR', and 'GLEASON_SCORE'.
8p gain cnv correlated to 'YEARS_TO_BIRTH', 'PATHOLOGY_T_STAGE', 'RESIDUAL_TUMOR', and 'GLEASON_SCORE'.
8q gain cnv correlated to 'PATHOLOGY_T_STAGE', 'RESIDUAL_TUMOR', 'GLEASON_SCORE', and 'PSA_VALUE'.
9p gain cnv correlated to 'YEARS_TO_BIRTH', 'PATHOLOGY_T_STAGE', 'PATHOLOGY_N_STAGE', 'RESIDUAL_TUMOR', 'NUMBER_OF_LYMPH_NODES', and 'GLEASON_SCORE'.
9q gain cnv correlated to 'YEARS_TO_BIRTH', 'PATHOLOGY_T_STAGE', 'PATHOLOGY_N_STAGE', 'RESIDUAL_TUMOR', 'NUMBER_OF_LYMPH_NODES', and 'GLEASON_SCORE'.
10p gain cnv correlated to 'PATHOLOGY_N_STAGE', 'NUMBER_OF_LYMPH_NODES', and 'GLEASON_SCORE'.
10q gain cnv correlated to 'GLEASON_SCORE'.
11p gain cnv correlated to 'YEARS_TO_BIRTH', 'PATHOLOGY_T_STAGE', 'PATHOLOGY_N_STAGE', 'RESIDUAL_TUMOR', 'NUMBER_OF_LYMPH_NODES', and 'GLEASON_SCORE'.
11q gain cnv correlated to 'YEARS_TO_BIRTH', 'PATHOLOGY_T_STAGE', 'PATHOLOGY_N_STAGE', 'RESIDUAL_TUMOR', 'NUMBER_OF_LYMPH_NODES', and 'GLEASON_SCORE'.
12p gain cnv correlated to 'YEARS_TO_BIRTH', 'PATHOLOGY_T_STAGE', 'PATHOLOGY_N_STAGE', 'RADIATION_THERAPY', 'RESIDUAL_TUMOR', 'NUMBER_OF_LYMPH_NODES', and 'GLEASON_SCORE'.
12q gain cnv correlated to 'YEARS_TO_BIRTH', 'PATHOLOGY_T_STAGE', 'PATHOLOGY_N_STAGE', 'RADIATION_THERAPY', 'RESIDUAL_TUMOR', 'NUMBER_OF_LYMPH_NODES', and 'GLEASON_SCORE'.
14q gain cnv correlated to 'YEARS_TO_BIRTH', 'RADIATION_THERAPY', 'RESIDUAL_TUMOR', and 'GLEASON_SCORE'.
16p gain cnv correlated to 'PATHOLOGY_T_STAGE', 'PATHOLOGY_N_STAGE', 'NUMBER_OF_LYMPH_NODES', and 'GLEASON_SCORE'.
16q gain cnv correlated to 'YEARS_TO_BIRTH' and 'GLEASON_SCORE'.
17p gain cnv correlated to 'PATHOLOGY_T_STAGE', 'PATHOLOGY_N_STAGE', 'RADIATION_THERAPY', 'NUMBER_OF_LYMPH_NODES', and 'GLEASON_SCORE'.
17q gain cnv correlated to 'PATHOLOGY_T_STAGE', 'PATHOLOGY_N_STAGE', 'NUMBER_OF_LYMPH_NODES', and 'GLEASON_SCORE'.
18p gain cnv correlated to 'YEARS_TO_BIRTH', 'PATHOLOGY_T_STAGE', 'PATHOLOGY_N_STAGE', and 'NUMBER_OF_LYMPH_NODES'.
18q gain cnv correlated to 'YEARS_TO_BIRTH' and 'PATHOLOGY_T_STAGE'.
19p gain cnv correlated to 'PATHOLOGY_T_STAGE', 'PATHOLOGY_N_STAGE', 'NUMBER_OF_LYMPH_NODES', and 'GLEASON_SCORE'.
19q gain cnv correlated to 'PATHOLOGY_T_STAGE', 'PATHOLOGY_N_STAGE', 'NUMBER_OF_LYMPH_NODES', and 'GLEASON_SCORE'.
20p gain cnv correlated to 'YEARS_TO_BIRTH', 'PATHOLOGY_T_STAGE', 'PATHOLOGY_N_STAGE', 'NUMBER_OF_LYMPH_NODES', and 'GLEASON_SCORE'.
20q gain cnv correlated to 'YEARS_TO_BIRTH', 'PATHOLOGY_T_STAGE', 'PATHOLOGY_N_STAGE', 'RADIATION_THERAPY', 'NUMBER_OF_LYMPH_NODES', and 'GLEASON_SCORE'.
21q gain cnv correlated to 'YEARS_TO_BIRTH', 'PATHOLOGY_T_STAGE', 'PATHOLOGY_N_STAGE', 'NUMBER_OF_LYMPH_NODES', and 'GLEASON_SCORE'.
22q gain cnv correlated to 'GLEASON_SCORE'.
xp gain cnv correlated to 'PATHOLOGY_T_STAGE', 'RESIDUAL_TUMOR', and 'GLEASON_SCORE'.
xq gain cnv correlated to 'PATHOLOGY_T_STAGE', 'RESIDUAL_TUMOR', and 'GLEASON_SCORE'.
1p loss cnv correlated to 'PATHOLOGY_T_STAGE', 'RADIATION_THERAPY', and 'GLEASON_SCORE'.
1q loss cnv correlated to 'RESIDUAL_TUMOR', 'NUMBER_OF_LYMPH_NODES', and 'GLEASON_SCORE'.
2p loss cnv correlated to 'YEARS_TO_BIRTH', 'PATHOLOGY_T_STAGE', and 'GLEASON_SCORE'.
2q loss cnv correlated to 'YEARS_TO_BIRTH', 'PATHOLOGY_T_STAGE', and 'GLEASON_SCORE'.
3p loss cnv correlated to 'GLEASON_SCORE'.
3q loss cnv correlated to 'GLEASON_SCORE'.
4p loss cnv correlated to 'YEARS_TO_BIRTH', 'PATHOLOGY_T_STAGE', 'PATHOLOGY_N_STAGE', 'RADIATION_THERAPY', 'RESIDUAL_TUMOR', 'NUMBER_OF_LYMPH_NODES', and 'GLEASON_SCORE'.
4q loss cnv correlated to 'PATHOLOGY_T_STAGE', 'PATHOLOGY_N_STAGE', 'RADIATION_THERAPY', 'RESIDUAL_TUMOR', 'NUMBER_OF_LYMPH_NODES', and 'GLEASON_SCORE'.
5p loss cnv correlated to 'PATHOLOGY_T_STAGE', 'RADIATION_THERAPY', 'RESIDUAL_TUMOR', and 'GLEASON_SCORE'.
5q loss cnv correlated to 'PATHOLOGY_T_STAGE', 'PATHOLOGY_N_STAGE', 'RADIATION_THERAPY', 'NUMBER_OF_LYMPH_NODES', and 'GLEASON_SCORE'.
6p loss cnv correlated to 'PATHOLOGY_T_STAGE', 'PATHOLOGY_N_STAGE', 'NUMBER_OF_LYMPH_NODES', and 'GLEASON_SCORE'.
6q loss cnv correlated to 'Time to Death', 'PATHOLOGY_T_STAGE', 'PATHOLOGY_N_STAGE', 'RADIATION_THERAPY', 'NUMBER_OF_LYMPH_NODES', and 'GLEASON_SCORE'.
8p loss cnv correlated to 'PATHOLOGY_T_STAGE' and 'NUMBER_OF_LYMPH_NODES'.
8q loss cnv correlated to 'Time to Death', 'PATHOLOGY_T_STAGE', 'PATHOLOGY_N_STAGE', 'RADIATION_THERAPY', 'NUMBER_OF_LYMPH_NODES', and 'GLEASON_SCORE'.
9p loss cnv correlated to 'PATHOLOGY_T_STAGE', 'PATHOLOGY_N_STAGE', 'NUMBER_OF_LYMPH_NODES', and 'GLEASON_SCORE'.
9q loss cnv correlated to 'GLEASON_SCORE'.
10p loss cnv correlated to 'PATHOLOGY_T_STAGE', 'PATHOLOGY_N_STAGE', 'RESIDUAL_TUMOR', 'NUMBER_OF_LYMPH_NODES', and 'GLEASON_SCORE'.
10q loss cnv correlated to 'PATHOLOGY_T_STAGE', 'PATHOLOGY_N_STAGE', 'RESIDUAL_TUMOR', 'NUMBER_OF_LYMPH_NODES', and 'GLEASON_SCORE'.
11p loss cnv correlated to 'Time to Death', 'PATHOLOGY_T_STAGE', and 'GLEASON_SCORE'.
11q loss cnv correlated to 'PATHOLOGY_T_STAGE' and 'GLEASON_SCORE'.
12p loss cnv correlated to 'PATHOLOGY_T_STAGE', 'PATHOLOGY_N_STAGE', 'NUMBER_OF_LYMPH_NODES', and 'GLEASON_SCORE'.
12q loss cnv correlated to 'PATHOLOGY_N_STAGE', 'NUMBER_OF_LYMPH_NODES', and 'GLEASON_SCORE'.
13q loss cnv correlated to 'YEARS_TO_BIRTH', 'PATHOLOGY_T_STAGE', 'PATHOLOGY_N_STAGE', 'RESIDUAL_TUMOR', 'NUMBER_OF_LYMPH_NODES', and 'GLEASON_SCORE'.
14q loss cnv correlated to 'PATHOLOGY_T_STAGE', 'PATHOLOGY_N_STAGE', 'RESIDUAL_TUMOR', 'NUMBER_OF_LYMPH_NODES', and 'GLEASON_SCORE'.
15q loss cnv correlated to 'YEARS_TO_BIRTH', 'PATHOLOGY_T_STAGE', 'PATHOLOGY_N_STAGE', 'NUMBER_OF_LYMPH_NODES', and 'GLEASON_SCORE'.
16p loss cnv correlated to 'GLEASON_SCORE'.
16q loss cnv correlated to 'PATHOLOGY_T_STAGE', 'PATHOLOGY_N_STAGE', 'RESIDUAL_TUMOR', 'NUMBER_OF_LYMPH_NODES', and 'GLEASON_SCORE'.
17p loss cnv correlated to 'PATHOLOGY_T_STAGE', 'PATHOLOGY_N_STAGE', 'RESIDUAL_TUMOR', 'NUMBER_OF_LYMPH_NODES', 'GLEASON_SCORE', and 'PSA_VALUE'.
17q loss cnv correlated to 'Time to Death', 'PATHOLOGY_T_STAGE', 'RESIDUAL_TUMOR', and 'GLEASON_SCORE'.
18p loss cnv correlated to 'PATHOLOGY_T_STAGE', 'RADIATION_THERAPY', 'RESIDUAL_TUMOR', 'NUMBER_OF_LYMPH_NODES', and 'GLEASON_SCORE'.
18q loss cnv correlated to 'PATHOLOGY_T_STAGE', 'PATHOLOGY_N_STAGE', 'RADIATION_THERAPY', 'RESIDUAL_TUMOR', 'NUMBER_OF_LYMPH_NODES', and 'GLEASON_SCORE'.
19p loss cnv correlated to 'YEARS_TO_BIRTH' and 'GLEASON_SCORE'.
19q loss cnv correlated to 'YEARS_TO_BIRTH' and 'GLEASON_SCORE'.
20p loss cnv correlated to 'PATHOLOGY_T_STAGE', 'PATHOLOGY_N_STAGE', 'RADIATION_THERAPY', and 'NUMBER_OF_LYMPH_NODES'.
20q loss cnv correlated to 'PATHOLOGY_T_STAGE'.
21q loss cnv correlated to 'PATHOLOGY_T_STAGE', 'PATHOLOGY_N_STAGE', 'NUMBER_OF_LYMPH_NODES', and 'GLEASON_SCORE'.
22q loss cnv correlated to 'PATHOLOGY_T_STAGE', 'PATHOLOGY_N_STAGE', 'RADIATION_THERAPY', 'RESIDUAL_TUMOR', 'NUMBER_OF_LYMPH_NODES', 'GLEASON_SCORE', and 'PSA_VALUE'.
xp loss cnv correlated to 'Time to Death', 'YEARS_TO_BIRTH', 'PATHOLOGY_T_STAGE', 'PATHOLOGY_N_STAGE', 'RADIATION_THERAPY', 'NUMBER_OF_LYMPH_NODES', 'GLEASON_SCORE', and 'PSA_VALUE'.
xq loss cnv correlated to 'Time to Death', 'YEARS_TO_BIRTH', 'PATHOLOGY_T_STAGE', 'PATHOLOGY_N_STAGE', 'RADIATION_THERAPY', 'NUMBER_OF_LYMPH_NODES', 'GLEASON_SCORE', and 'PSA_VALUE'.

Results

Overview of the results

Table 1. Get Full Table Overview of the association between significant copy number variation of 80 arm-level events and 11 clinical features. Shown in the table are P values (Q values). Thresholded by Q value < 0.25, 316 significant findings detected.


		Clinical Features	Time to Death	YEARS TO BIRTH	PATHOLOGY T STAGE	PATHOLOGY N STAGE	RADIATION THERAPY	HISTOLOGICAL TYPE	RESIDUAL TUMOR	NUMBER OF LYMPH NODES	GLEASON SCORE	PSA VALUE	RACE
	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	Wilcoxon-test	Wilcoxon-test	Fisher's exact test
xp loss	38 (8%)	453	0.0575 (0.178)	0.0733 (0.217)	0.0112 (0.0528)	0.023 (0.0868)	0.033 (0.116)	0.296 (0.555)	0.572 (0.844)	0.00782 (0.04)	1.45e-06 (7.97e-05)	0.0172 (0.0743)	0.386 (0.658)
xq loss	38 (8%)	453	0.0575 (0.178)	0.0733 (0.217)	0.0117 (0.0546)	0.023 (0.0868)	0.033 (0.116)	0.296 (0.555)	0.575 (0.846)	0.00782 (0.04)	1.45e-06 (7.97e-05)	0.0172 (0.0743)	0.386 (0.658)
3q gain	53 (11%)	438	0.0937 (0.258)	0.00513 (0.0307)	5e-05 (0.00102)	0.0351 (0.121)	0.161 (0.381)	0.184 (0.414)	0.0273 (0.101)	0.00901 (0.0448)	1e-08 (2.95e-06)	0.0287 (0.105)	0.634 (0.895)
5p gain	23 (5%)	468	0.397 (0.672)	0.00181 (0.0151)	0.00018 (0.00283)	0.00247 (0.0191)	0.0269 (0.1)	0.494 (0.776)	0.0183 (0.0759)	5.17e-05 (0.00103)	1.77e-06 (9.19e-05)	0.351 (0.627)
12p gain	13 (3%)	478	0.556 (0.826)	0.0159 (0.07)	0.00603 (0.0343)	0.0218 (0.0837)	0.0432 (0.143)	1 (1.00)	0.00286 (0.0211)	0.0134 (0.061)	2.03e-05 (0.000511)	0.337 (0.61)
12q gain	16 (3%)	475	0.553 (0.825)	0.0855 (0.243)	0.00663 (0.036)	0.0185 (0.0761)	0.00508 (0.0306)	1 (1.00)	6e-05 (0.00112)	0.00786 (0.04)	1.19e-05 (0.000362)	0.675 (0.921)
4p loss	24 (5%)	467	0.552 (0.825)	0.0735 (0.217)	0.0119 (0.0552)	4.87e-05 (0.00102)	0.0539 (0.171)	0.509 (0.784)	0.00919 (0.0454)	2.28e-06 (0.000106)	3.09e-07 (2.47e-05)	0.902 (1.00)	1 (1.00)
22q loss	47 (10%)	444	0.218 (0.459)	0.476 (0.757)	3e-05 (0.000695)	0.000733 (0.00785)	0.011 (0.0525)	0.634 (0.895)	0.00893 (0.0446)	0.000482 (0.00589)	3.31e-08 (4.4e-06)	0.0752 (0.219)	0.493 (0.776)
3p gain	39 (8%)	452	0.274 (0.535)	0.00172 (0.0144)	0.00223 (0.018)	0.0449 (0.147)	0.167 (0.386)	0.0915 (0.253)	0.061 (0.187)	0.00694 (0.0366)	5.1e-08 (5.01e-06)	0.328 (0.603)	0.529 (0.808)
5q gain	12 (2%)	479	0.667 (0.913)	0.000169 (0.00271)	0.00878 (0.0442)	0.00683 (0.0362)	1 (1.00)	1 (1.00)	0.0226 (0.0861)	0.00028 (0.00391)	0.00191 (0.0157)	0.179 (0.405)
9p gain	33 (7%)	458	0.791 (1.00)	0.00505 (0.0306)	6e-05 (0.00112)	0.000316 (0.00422)	0.16 (0.381)	0.241 (0.487)	0.0204 (0.0796)	0.000223 (0.00328)	2.23e-06 (0.000106)	0.581 (0.847)	0.348 (0.623)
9q gain	49 (10%)	442	0.967 (1.00)	0.0181 (0.0757)	2e-05 (0.000511)	4.99e-06 (0.000176)	0.161 (0.381)	0.155 (0.371)	0.0148 (0.0667)	8.05e-07 (5.06e-05)	1.83e-08 (3.23e-06)	0.923 (1.00)	0.46 (0.739)
11p gain	25 (5%)	466	0.548 (0.821)	0.0461 (0.149)	0.00282 (0.021)	0.00133 (0.0119)	0.224 (0.467)	1 (1.00)	0.0239 (0.0898)	0.00162 (0.0138)	7.09e-05 (0.0013)	0.207 (0.45)	0.26 (0.514)
11q gain	28 (6%)	463	0.508 (0.784)	0.0516 (0.164)	0.00437 (0.0284)	0.0011 (0.0106)	0.378 (0.654)	1 (1.00)	0.0367 (0.126)	0.000937 (0.00959)	1.09e-05 (0.000344)	0.499 (0.781)	0.264 (0.52)
20q gain	27 (5%)	464	0.49 (0.773)	0.00574 (0.0334)	0.00146 (0.0128)	0.0299 (0.108)	0.0634 (0.193)	1 (1.00)	0.112 (0.293)	0.0202 (0.0795)	0.000339 (0.00445)	0.284 (0.544)	1 (1.00)
4q loss	16 (3%)	475	0.635 (0.895)	0.179 (0.405)	0.018 (0.0757)	0.00338 (0.0236)	0.0109 (0.0523)	0.375 (0.654)	0.0347 (0.12)	0.000502 (0.00605)	2.9e-06 (0.000122)	0.423 (0.706)	1 (1.00)
6q loss	39 (8%)	452	0.0514 (0.164)	0.536 (0.814)	0.00108 (0.0106)	0.00314 (0.0228)	0.0149 (0.0668)	0.616 (0.874)	0.2 (0.438)	0.00129 (0.0117)	7.94e-09 (2.95e-06)	0.581 (0.847)	0.125 (0.315)
8q loss	24 (5%)	467	0.00438 (0.0284)	0.783 (1.00)	0.00074 (0.00785)	0.0421 (0.14)	0.0883 (0.249)	1 (1.00)	0.497 (0.779)	0.0084 (0.0425)	0.0853 (0.243)	0.99 (1.00)	1 (1.00)
13q loss	77 (16%)	414	0.696 (0.935)	0.082 (0.236)	0.0008 (0.00838)	0.0112 (0.0528)	0.702 (0.938)	0.707 (0.94)	0.0361 (0.124)	0.00318 (0.0228)	3.23e-11 (2.84e-08)	0.215 (0.459)	0.438 (0.721)
17p loss	75 (15%)	416	0.856 (1.00)	0.372 (0.652)	0.00106 (0.0106)	0.0104 (0.0501)	0.232 (0.478)	0.706 (0.94)	0.0567 (0.177)	0.00152 (0.0133)	4.98e-06 (0.000176)	0.0413 (0.139)	0.701 (0.938)
18q loss	100 (20%)	391	0.667 (0.913)	0.375 (0.654)	0.00111 (0.0106)	0.000371 (0.00479)	0.0206 (0.0804)	1 (1.00)	5e-05 (0.00102)	0.000116 (0.00196)	1.74e-08 (3.23e-06)	0.218 (0.459)	0.755 (0.974)
17p gain	8 (2%)	483	0.747 (0.969)	0.361 (0.639)	0.0183 (0.0759)	0.00659 (0.036)	0.0739 (0.218)	1 (1.00)	0.795 (1.00)	0.00119 (0.0113)	0.0544 (0.171)	0.968 (1.00)
20p gain	25 (5%)	466	0.271 (0.532)	0.0545 (0.171)	0.0109 (0.0523)	0.0421 (0.14)	0.102 (0.273)	1 (1.00)	0.396 (0.671)	0.0278 (0.102)	0.00105 (0.0106)	0.172 (0.397)
21q gain	20 (4%)	471	0.376 (0.654)	0.00612 (0.0343)	0.0156 (0.0689)	0.0174 (0.0743)	1 (1.00)	0.446 (0.729)	0.106 (0.282)	0.0117 (0.0546)	0.000128 (0.00213)	0.764 (0.981)	1 (1.00)
5q loss	22 (4%)	469	0.582 (0.847)	0.882 (1.00)	3e-05 (0.000695)	0.00158 (0.0137)	0.00655 (0.036)	1 (1.00)	0.117 (0.301)	0.00021 (0.00319)	5.46e-07 (4e-05)	0.653 (0.907)	1 (1.00)
10p loss	41 (8%)	450	0.769 (0.986)	0.13 (0.325)	2e-05 (0.000511)	0.0003 (0.00413)	0.222 (0.463)	1 (1.00)	0.0177 (0.0749)	2.21e-05 (0.000541)	2.68e-06 (0.000118)	0.411 (0.691)	1 (1.00)
10q loss	43 (9%)	448	0.795 (1.00)	0.273 (0.535)	0.00019 (0.00293)	0.000384 (0.00483)	0.222 (0.463)	1 (1.00)	0.00611 (0.0343)	3.91e-05 (0.000882)	3.5e-08 (4.4e-06)	0.578 (0.847)	0.585 (0.849)
14q loss	25 (5%)	466	0.38 (0.654)	0.0999 (0.271)	0.00054 (0.00625)	0.0299 (0.108)	1 (1.00)	0.524 (0.802)	0.0165 (0.0722)	0.0312 (0.112)	0.000376 (0.00479)	0.136 (0.336)	1 (1.00)
15q loss	36 (7%)	455	0.843 (1.00)	0.0192 (0.0782)	1e-05 (0.000326)	0.00352 (0.0239)	0.175 (0.403)	1 (1.00)	0.185 (0.415)	0.00132 (0.0118)	1.4e-05 (0.000412)	0.237 (0.484)	1 (1.00)
16q loss	106 (22%)	385	0.358 (0.635)	0.273 (0.535)	0.00246 (0.0191)	0.071 (0.212)	0.605 (0.867)	1 (1.00)	0.0177 (0.0749)	0.0406 (0.137)	4.42e-06 (0.000169)	0.381 (0.654)	1 (1.00)
18p loss	67 (14%)	424	0.348 (0.623)	0.296 (0.555)	0.00622 (0.0346)	0.111 (0.292)	0.0887 (0.249)	0.42 (0.703)	0.00493 (0.0301)	0.0857 (0.243)	6.43e-07 (4.35e-05)	0.6 (0.867)	0.703 (0.938)
6p gain	10 (2%)	481	0.046 (0.149)	0.33 (0.604)	0.182 (0.41)	0.0218 (0.0837)	0.101 (0.272)	1 (1.00)	0.218 (0.459)	0.0152 (0.0676)	0.0302 (0.109)	0.329 (0.603)
6q gain	6 (1%)	485	0.714 (0.944)	0.0715 (0.213)	0.48 (0.761)	0.0785 (0.227)	0.13 (0.325)	1 (1.00)	0.236 (0.483)	0.0443 (0.146)	0.0895 (0.249)	0.762 (0.979)
7p gain	101 (21%)	390	0.11 (0.291)	0.0102 (0.0496)	0.0325 (0.116)	0.439 (0.721)	0.38 (0.654)	0.745 (0.969)	0.00476 (0.0301)	0.338 (0.61)	8.43e-05 (0.00151)	0.712 (0.944)	1 (1.00)
7q gain	94 (19%)	397	0.125 (0.315)	0.0174 (0.0743)	0.0874 (0.247)	0.874 (1.00)	0.467 (0.746)	1 (1.00)	0.00262 (0.02)	0.812 (1.00)	0.000253 (0.00359)	0.857 (1.00)	1 (1.00)
8p gain	71 (14%)	420	0.696 (0.935)	0.0099 (0.0484)	0.00713 (0.0373)	0.614 (0.874)	0.322 (0.593)	0.238 (0.484)	0.00526 (0.0313)	0.738 (0.962)	3e-07 (2.47e-05)	0.0912 (0.253)	0.66 (0.912)
8q gain	123 (25%)	368	0.709 (0.94)	0.101 (0.272)	0.00015 (0.00244)	0.158 (0.378)	0.249 (0.496)	0.534 (0.812)	0.00424 (0.0281)	0.135 (0.336)	5.12e-08 (5.01e-06)	0.0378 (0.129)	0.733 (0.957)
14q gain	10 (2%)	481	0.402 (0.678)	0.0293 (0.107)	0.795 (1.00)	0.218 (0.459)	0.00272 (0.0205)	0.253 (0.502)	0.0452 (0.147)	0.207 (0.45)	0.00352 (0.0239)	0.428 (0.712)
16p gain	31 (6%)	460	0.246 (0.492)	0.179 (0.405)	0.00082 (0.00849)	0.00163 (0.0138)	0.378 (0.654)	0.604 (0.867)	0.28 (0.542)	0.000714 (0.00776)	6.44e-06 (0.000218)	0.148 (0.357)	1 (1.00)
17q gain	11 (2%)	480	0.72 (0.948)	0.221 (0.463)	0.00461 (0.0296)	0.00683 (0.0362)	0.164 (0.385)	1 (1.00)	0.844 (1.00)	0.00238 (0.0191)	0.0691 (0.209)	0.547 (0.821)
18p gain	18 (4%)	473	0.578 (0.847)	0.00428 (0.0281)	0.00316 (0.0228)	0.00338 (0.0236)	1 (1.00)	1 (1.00)	0.82 (1.00)	0.00264 (0.02)	0.13 (0.325)	0.722 (0.949)	1 (1.00)
19p gain	11 (2%)	480	0.638 (0.896)	0.303 (0.567)	0.00059 (0.00657)	0.00683 (0.0362)	0.644 (0.897)	1 (1.00)	0.141 (0.345)	0.00345 (0.0237)	0.000556 (0.00628)	0.832 (1.00)
19q gain	11 (2%)	480	0.616 (0.874)	0.238 (0.484)	0.00052 (0.0061)	0.00683 (0.0362)	1 (1.00)	1 (1.00)	0.14 (0.345)	0.00345 (0.0237)	0.000556 (0.00628)	0.951 (1.00)	1 (1.00)
5p loss	12 (2%)	479	0.729 (0.955)	0.836 (1.00)	0.00046 (0.0057)	0.124 (0.315)	0.0049 (0.0301)	1 (1.00)	0.0626 (0.191)	0.144 (0.351)	5.31e-05 (0.00104)	0.211 (0.455)	1 (1.00)
6p loss	25 (5%)	466	0.278 (0.538)	0.947 (1.00)	0.00067 (0.00737)	0.00247 (0.0191)	0.189 (0.421)	1 (1.00)	0.14 (0.345)	0.00125 (0.0116)	3.22e-06 (0.000129)	0.197 (0.435)	0.307 (0.569)
9p loss	21 (4%)	470	0.405 (0.682)	0.351 (0.627)	0.0184 (0.0759)	0.0701 (0.211)	0.49 (0.773)	1 (1.00)	0.919 (1.00)	0.0202 (0.0795)	0.00571 (0.0334)	0.543 (0.821)	1 (1.00)
12p loss	48 (10%)	443	0.355 (0.631)	0.451 (0.73)	0.0049 (0.0301)	0.00109 (0.0106)	0.636 (0.895)	0.38 (0.654)	0.291 (0.552)	0.00051 (0.00606)	0.000243 (0.00351)	0.112 (0.293)	1 (1.00)
17q loss	20 (4%)	471	0.0683 (0.207)	0.547 (0.821)	0.0199 (0.0787)	0.365 (0.643)	1 (1.00)	1 (1.00)	0.0338 (0.118)	0.327 (0.602)	0.00318 (0.0228)	0.572 (0.844)	1 (1.00)
20p loss	19 (4%)	472	0.197 (0.435)	0.801 (1.00)	0.0447 (0.147)	0.022 (0.0843)	0.0578 (0.178)	1 (1.00)	1 (1.00)	0.00484 (0.0301)	0.368 (0.649)	0.887 (1.00)	0.347 (0.623)
21q loss	24 (5%)	467	0.582 (0.847)	0.731 (0.956)	0.00211 (0.0172)	0.00371 (0.0249)	0.524 (0.802)	0.509 (0.784)	0.307 (0.569)	0.00124 (0.0116)	0.000309 (0.00419)	0.216 (0.459)	1 (1.00)
1p gain	16 (3%)	475	0.599 (0.867)	0.146 (0.355)	2e-05 (0.000511)	0.166 (0.386)	0.00761 (0.0396)	1 (1.00)	0.099 (0.27)	0.165 (0.386)	0.000101 (0.00174)	0.288 (0.547)	1 (1.00)
1q gain	26 (5%)	465	0.5 (0.782)	0.2 (0.438)	5e-05 (0.00102)	0.104 (0.279)	0.0328 (0.116)	0.538 (0.815)	0.125 (0.315)	0.0958 (0.263)	9.19e-05 (0.00162)	0.662 (0.913)	1 (1.00)
10p gain	14 (3%)	477	0.461 (0.74)	0.196 (0.435)	0.389 (0.662)	0.0702 (0.211)	1 (1.00)	0.337 (0.61)	0.171 (0.396)	0.0758 (0.22)	0.00576 (0.0334)	0.442 (0.725)	1 (1.00)
xp gain	7 (1%)	484	0.758 (0.976)	0.204 (0.444)	0.0198 (0.0787)	0.12 (0.306)	0.572 (0.844)	1 (1.00)	0.00552 (0.0326)	0.177 (0.403)	0.00489 (0.0301)	0.805 (1.00)
xq gain	7 (1%)	484	0.758 (0.976)	0.204 (0.444)	0.0193 (0.0782)	0.12 (0.306)	0.572 (0.844)	1 (1.00)	0.00582 (0.0335)	0.177 (0.403)	0.00489 (0.0301)	0.805 (1.00)
1p loss	22 (4%)	469	0.523 (0.802)	0.538 (0.815)	0.0247 (0.0926)	0.244 (0.492)	0.0436 (0.144)	1 (1.00)	0.434 (0.717)	0.166 (0.386)	1.79e-05 (0.000509)	0.294 (0.555)	1 (1.00)
1q loss	6 (1%)	485	0.746 (0.969)	0.667 (0.913)	0.195 (0.432)	0.229 (0.476)	0.506 (0.784)	1 (1.00)	0.0565 (0.177)	0.0749 (0.219)	0.0895 (0.249)	0.371 (0.651)
2p loss	15 (3%)	476	0.546 (0.821)	0.00247 (0.0191)	0.00983 (0.0483)	1 (1.00)	1 (1.00)	1 (1.00)	0.0987 (0.27)	0.684 (0.93)	0.089 (0.249)	0.414 (0.694)
2q loss	18 (4%)	473	0.612 (0.874)	0.0196 (0.0783)	0.0194 (0.0783)	0.749 (0.97)	1 (1.00)	1 (1.00)	0.118 (0.303)	0.53 (0.808)	0.0195 (0.0783)	0.688 (0.931)
11p loss	8 (2%)	483	0.00635 (0.0352)	0.307 (0.569)	0.0753 (0.219)	1 (1.00)	1 (1.00)	1 (1.00)	0.146 (0.355)	0.714 (0.944)	0.0191 (0.0782)	0.999 (1.00)
12q loss	20 (4%)	471	0.548 (0.821)	0.94 (1.00)	0.11 (0.291)	0.0174 (0.0743)	1 (1.00)	1 (1.00)	0.24 (0.487)	0.0146 (0.066)	0.00129 (0.0117)	0.451 (0.73)	1 (1.00)
16q gain	8 (2%)	483	0.795 (1.00)	0.00765 (0.0396)	0.286 (0.546)	1 (1.00)	0.23 (0.476)	1 (1.00)	1 (1.00)	0.81 (1.00)	0.0826 (0.237)	0.939 (1.00)	1 (1.00)
18q gain	9 (2%)	482	0.665 (0.913)	0.0488 (0.157)	0.0341 (0.118)	0.218 (0.459)	1 (1.00)	1 (1.00)	1 (1.00)	0.385 (0.658)	0.43 (0.713)	0.908 (1.00)
8p loss	167 (34%)	324	0.38 (0.654)	0.508 (0.784)	0.00022 (0.00328)	0.146 (0.355)	0.881 (1.00)	1 (1.00)	0.427 (0.711)	0.0819 (0.236)	0.726 (0.954)	0.286 (0.546)	0.162 (0.381)
11q loss	5 (1%)	486	0.896 (1.00)	0.337 (0.61)	0.0273 (0.101)	0.334 (0.609)	1 (1.00)	1 (1.00)	0.101 (0.272)		0.0335 (0.118)	0.696 (0.935)
19p loss	17 (3%)	474	0.602 (0.867)	0.0123 (0.0561)	0.15 (0.36)	1 (1.00)	1 (1.00)	1 (1.00)	0.449 (0.73)	0.94 (1.00)	0.0382 (0.129)	0.464 (0.743)	1 (1.00)
19q loss	17 (3%)	474	0.602 (0.867)	0.0123 (0.0561)	0.15 (0.36)	1 (1.00)	1 (1.00)	1 (1.00)	0.451 (0.73)	0.94 (1.00)	0.0382 (0.129)	0.464 (0.743)	1 (1.00)
2p gain	10 (2%)	481	0.69 (0.933)	0.706 (0.94)	1 (1.00)	1 (1.00)	1 (1.00)	1 (1.00)	0.364 (0.643)	0.992 (1.00)	0.116 (0.3)	0.0251 (0.0935)
2q gain	7 (1%)	484	0.791 (1.00)	0.413 (0.693)	0.747 (0.969)	1 (1.00)	0.506 (0.784)	1 (1.00)	0.237 (0.484)	0.819 (1.00)	0.277 (0.538)	0.00605 (0.0343)
10q gain	13 (3%)	478	0.452 (0.73)	0.814 (1.00)	0.439 (0.721)	0.246 (0.492)	0.373 (0.652)	0.317 (0.585)	0.149 (0.358)	0.165 (0.386)	0.0516 (0.164)	0.185 (0.415)	1 (1.00)
22q gain	4 (1%)	487	0.794 (1.00)	0.434 (0.717)	0.679 (0.925)	0.558 (0.827)	0.431 (0.714)	1 (1.00)	0.658 (0.911)	0.609 (0.871)	0.0217 (0.0837)	0.242 (0.489)
3p loss	9 (2%)	482	0.649 (0.904)	0.772 (0.987)	0.252 (0.502)	0.167 (0.386)	0.282 (0.544)	1 (1.00)	0.218 (0.459)	0.138 (0.341)	0.00333 (0.0236)	0.126 (0.318)
3q loss	5 (1%)	486	0.686 (0.93)	0.292 (0.552)	0.686 (0.93)	0.59 (0.855)	0.506 (0.784)	1 (1.00)	0.339 (0.611)	0.277 (0.538)	0.00384 (0.0256)	0.212 (0.455)
9q loss	10 (2%)	481	0.691 (0.933)	0.656 (0.909)	0.115 (0.299)	0.218 (0.459)	1 (1.00)	1 (1.00)	0.64 (0.897)	0.192 (0.427)	0.0151 (0.0676)	0.256 (0.506)	1 (1.00)
16p loss	32 (7%)	459	0.451 (0.73)	0.91 (1.00)	0.519 (0.799)	0.447 (0.729)	0.554 (0.825)	0.614 (0.874)	0.306 (0.569)	0.284 (0.544)	0.0577 (0.178)	0.898 (1.00)	1 (1.00)
20q loss	9 (2%)	482	0.728 (0.954)	0.245 (0.492)	0.048 (0.155)	0.643 (0.897)	0.282 (0.544)	1 (1.00)	0.815 (1.00)	0.655 (0.909)	0.114 (0.298)	0.96 (1.00)	1 (1.00)
4p gain	8 (2%)	483	0.67 (0.915)	0.122 (0.31)	0.284 (0.544)	0.643 (0.897)	1 (1.00)	1 (1.00)	0.795 (1.00)	0.789 (1.00)	0.717 (0.947)	0.476 (0.757)	1 (1.00)
4q gain	10 (2%)	481	0.663 (0.913)	0.204 (0.444)	0.179 (0.405)	0.0915 (0.253)	0.334 (0.609)	0.253 (0.502)	0.546 (0.821)	0.116 (0.3)	0.576 (0.846)	0.23 (0.476)
13q gain	8 (2%)	483	0.476 (0.757)	0.456 (0.734)	0.208 (0.45)	0.617 (0.875)	0.604 (0.867)	0.208 (0.45)	0.485 (0.767)	0.639 (0.896)	0.699 (0.938)	0.231 (0.476)
15q gain	6 (1%)	485	0.753 (0.973)	0.923 (1.00)	1 (1.00)	0.305 (0.569)	0.506 (0.784)	1 (1.00)	1 (1.00)	0.394 (0.669)	0.108 (0.288)	0.353 (0.628)

'1p gain' versus 'PATHOLOGY_T_STAGE'

P value = 2e-05 (Fisher's exact test), Q value = 0.00051

Table S1. Gene #1: '1p gain' versus Clinical Feature #3: 'PATHOLOGY_T_STAGE'

nPatients	T2	T3	T4
ALL	188	287	10
1P GAIN MUTATED	0	13	3
1P GAIN WILD-TYPE	188	274	7

Figure S1. Get High-res Image Gene #1: '1p gain' versus Clinical Feature #3: 'PATHOLOGY_T_STAGE'

'1p gain' versus 'RADIATION_THERAPY'

P value = 0.00761 (Fisher's exact test), Q value = 0.04

Table S2. Gene #1: '1p gain' versus Clinical Feature #5: 'RADIATION_THERAPY'

nPatients	NO	YES
ALL	378	57
1P GAIN MUTATED	9	6
1P GAIN WILD-TYPE	369	51

Figure S2. Get High-res Image Gene #1: '1p gain' versus Clinical Feature #5: 'RADIATION_THERAPY'

'1p gain' versus 'GLEASON_SCORE'

P value = 0.000101 (Wilcoxon-test), Q value = 0.0017

Table S3. Gene #1: '1p gain' versus Clinical Feature #9: 'GLEASON_SCORE'

	nPatients	Mean (Std.Dev)
ALL	491	7.6 (1.0)
1P GAIN MUTATED	16	8.6 (0.9)
1P GAIN WILD-TYPE	475	7.6 (1.0)

Figure S3. Get High-res Image Gene #1: '1p gain' versus Clinical Feature #9: 'GLEASON_SCORE'

'1q gain' versus 'PATHOLOGY_T_STAGE'

P value = 5e-05 (Fisher's exact test), Q value = 0.001

Table S4. Gene #2: '1q gain' versus Clinical Feature #3: 'PATHOLOGY_T_STAGE'

nPatients	T2	T3	T4
ALL	188	287	10
1Q GAIN MUTATED	2	21	3
1Q GAIN WILD-TYPE	186	266	7

Figure S4. Get High-res Image Gene #2: '1q gain' versus Clinical Feature #3: 'PATHOLOGY_T_STAGE'

'1q gain' versus 'RADIATION_THERAPY'

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

Table S5. Gene #2: '1q gain' versus Clinical Feature #5: 'RADIATION_THERAPY'

nPatients	NO	YES
ALL	378	57
1Q GAIN MUTATED	18	7
1Q GAIN WILD-TYPE	360	50

Figure S5. Get High-res Image Gene #2: '1q gain' versus Clinical Feature #5: 'RADIATION_THERAPY'

'1q gain' versus 'GLEASON_SCORE'

P value = 9.19e-05 (Wilcoxon-test), Q value = 0.0016

Table S6. Gene #2: '1q gain' versus Clinical Feature #9: 'GLEASON_SCORE'

	nPatients	Mean (Std.Dev)
ALL	491	7.6 (1.0)
1Q GAIN MUTATED	26	8.4 (0.9)
1Q GAIN WILD-TYPE	465	7.6 (1.0)

Figure S6. Get High-res Image Gene #2: '1q gain' versus Clinical Feature #9: 'GLEASON_SCORE'

'2p gain' versus 'PSA_VALUE'

P value = 0.0251 (Wilcoxon-test), Q value = 0.094

Table S7. Gene #3: '2p gain' versus Clinical Feature #10: 'PSA_VALUE'

	nPatients	Mean (Std.Dev)
ALL	434	1.8 (16.0)
2P GAIN MUTATED	7	2.0 (2.7)
2P GAIN WILD-TYPE	427	1.8 (16.1)

Figure S7. Get High-res Image Gene #3: '2p gain' versus Clinical Feature #10: 'PSA_VALUE'

'2q gain' versus 'PSA_VALUE'

P value = 0.00605 (Wilcoxon-test), Q value = 0.034

Table S8. Gene #4: '2q gain' versus Clinical Feature #10: 'PSA_VALUE'

	nPatients	Mean (Std.Dev)
ALL	434	1.8 (16.0)
2Q GAIN MUTATED	5	2.6 (3.0)
2Q GAIN WILD-TYPE	429	1.8 (16.1)

Figure S8. Get High-res Image Gene #4: '2q gain' versus Clinical Feature #10: 'PSA_VALUE'

'3p gain' versus 'YEARS_TO_BIRTH'

P value = 0.00172 (Wilcoxon-test), Q value = 0.014

Table S9. Gene #5: '3p gain' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

	nPatients	Mean (Std.Dev)
ALL	480	61.0 (6.8)
3P GAIN MUTATED	37	64.4 (5.6)
3P GAIN WILD-TYPE	443	60.7 (6.8)

Figure S9. Get High-res Image Gene #5: '3p gain' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'3p gain' versus 'PATHOLOGY_T_STAGE'

P value = 0.00223 (Fisher's exact test), Q value = 0.018

Table S10. Gene #5: '3p gain' versus Clinical Feature #3: 'PATHOLOGY_T_STAGE'

nPatients	T2	T3	T4
ALL	188	287	10
3P GAIN MUTATED	7	29	3
3P GAIN WILD-TYPE	181	258	7

Figure S10. Get High-res Image Gene #5: '3p gain' versus Clinical Feature #3: 'PATHOLOGY_T_STAGE'

'3p gain' versus 'PATHOLOGY_N_STAGE'

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

Table S11. Gene #5: '3p gain' versus Clinical Feature #4: 'PATHOLOGY_N_STAGE'

nPatients	0	1
ALL	342	77
3P GAIN MUTATED	26	12
3P GAIN WILD-TYPE	316	65

Figure S11. Get High-res Image Gene #5: '3p gain' versus Clinical Feature #4: 'PATHOLOGY_N_STAGE'

'3p gain' versus 'RESIDUAL_TUMOR'

P value = 0.061 (Fisher's exact test), Q value = 0.19

Table S12. Gene #5: '3p gain' versus Clinical Feature #7: 'RESIDUAL_TUMOR'

nPatients	R0	R1	R2	RX
ALL	312	143	5	15
3P GAIN MUTATED	18	17	1	1
3P GAIN WILD-TYPE	294	126	4	14

Figure S12. Get High-res Image Gene #5: '3p gain' versus Clinical Feature #7: 'RESIDUAL_TUMOR'

'3p gain' versus 'NUMBER_OF_LYMPH_NODES'

P value = 0.00694 (Wilcoxon-test), Q value = 0.037

Table S13. Gene #5: '3p gain' versus Clinical Feature #8: 'NUMBER_OF_LYMPH_NODES'

	nPatients	Mean (Std.Dev)
ALL	401	0.4 (1.4)
3P GAIN MUTATED	34	1.1 (2.0)
3P GAIN WILD-TYPE	367	0.4 (1.3)

Figure S13. Get High-res Image Gene #5: '3p gain' versus Clinical Feature #8: 'NUMBER_OF_LYMPH_NODES'

'3p gain' versus 'GLEASON_SCORE'

P value = 5.1e-08 (Wilcoxon-test), Q value = 5e-06

Table S14. Gene #5: '3p gain' versus Clinical Feature #9: 'GLEASON_SCORE'

	nPatients	Mean (Std.Dev)
ALL	491	7.6 (1.0)
3P GAIN MUTATED	39	8.5 (0.9)
3P GAIN WILD-TYPE	452	7.5 (1.0)

Figure S14. Get High-res Image Gene #5: '3p gain' versus Clinical Feature #9: 'GLEASON_SCORE'

'3q gain' versus 'YEARS_TO_BIRTH'

P value = 0.00513 (Wilcoxon-test), Q value = 0.031

Table S15. Gene #6: '3q gain' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

	nPatients	Mean (Std.Dev)
ALL	480	61.0 (6.8)
3Q GAIN MUTATED	51	63.5 (6.0)
3Q GAIN WILD-TYPE	429	60.7 (6.8)

Figure S15. Get High-res Image Gene #6: '3q gain' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'3q gain' versus 'PATHOLOGY_T_STAGE'

P value = 5e-05 (Fisher's exact test), Q value = 0.001

Table S16. Gene #6: '3q gain' versus Clinical Feature #3: 'PATHOLOGY_T_STAGE'

nPatients	T2	T3	T4
ALL	188	287	10
3Q GAIN MUTATED	8	41	4
3Q GAIN WILD-TYPE	180	246	6

Figure S16. Get High-res Image Gene #6: '3q gain' versus Clinical Feature #3: 'PATHOLOGY_T_STAGE'

'3q gain' versus 'PATHOLOGY_N_STAGE'

P value = 0.0351 (Fisher's exact test), Q value = 0.12

Table S17. Gene #6: '3q gain' versus Clinical Feature #4: 'PATHOLOGY_N_STAGE'

nPatients	0	1
ALL	342	77
3Q GAIN MUTATED	36	15
3Q GAIN WILD-TYPE	306	62

Figure S17. Get High-res Image Gene #6: '3q gain' versus Clinical Feature #4: 'PATHOLOGY_N_STAGE'

'3q gain' versus 'RESIDUAL_TUMOR'

P value = 0.0273 (Fisher's exact test), Q value = 0.1

Table S18. Gene #6: '3q gain' versus Clinical Feature #7: 'RESIDUAL_TUMOR'

nPatients	R0	R1	R2	RX
ALL	312	143	5	15
3Q GAIN MUTATED	25	24	1	1
3Q GAIN WILD-TYPE	287	119	4	14

Figure S18. Get High-res Image Gene #6: '3q gain' versus Clinical Feature #7: 'RESIDUAL_TUMOR'

'3q gain' versus 'NUMBER_OF_LYMPH_NODES'

P value = 0.00901 (Wilcoxon-test), Q value = 0.045

Table S19. Gene #6: '3q gain' versus Clinical Feature #8: 'NUMBER_OF_LYMPH_NODES'

	nPatients	Mean (Std.Dev)
ALL	401	0.4 (1.4)
3Q GAIN MUTATED	46	0.9 (1.9)
3Q GAIN WILD-TYPE	355	0.4 (1.3)

Figure S19. Get High-res Image Gene #6: '3q gain' versus Clinical Feature #8: 'NUMBER_OF_LYMPH_NODES'

'3q gain' versus 'GLEASON_SCORE'

P value = 1e-08 (Wilcoxon-test), Q value = 2.9e-06

Table S20. Gene #6: '3q gain' versus Clinical Feature #9: 'GLEASON_SCORE'

	nPatients	Mean (Std.Dev)
ALL	491	7.6 (1.0)
3Q GAIN MUTATED	53	8.4 (0.9)
3Q GAIN WILD-TYPE	438	7.5 (1.0)

Figure S20. Get High-res Image Gene #6: '3q gain' versus Clinical Feature #9: 'GLEASON_SCORE'

'3q gain' versus 'PSA_VALUE'

P value = 0.0287 (Wilcoxon-test), Q value = 0.1

Table S21. Gene #6: '3q gain' versus Clinical Feature #10: 'PSA_VALUE'

	nPatients	Mean (Std.Dev)
ALL	434	1.8 (16.0)
3Q GAIN MUTATED	44	2.3 (7.7)
3Q GAIN WILD-TYPE	390	1.7 (16.7)

Figure S21. Get High-res Image Gene #6: '3q gain' versus Clinical Feature #10: 'PSA_VALUE'

'5p gain' versus 'YEARS_TO_BIRTH'

P value = 0.00181 (Wilcoxon-test), Q value = 0.015

Table S22. Gene #9: '5p gain' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

	nPatients	Mean (Std.Dev)
ALL	480	61.0 (6.8)
5P GAIN MUTATED	23	65.3 (5.5)
5P GAIN WILD-TYPE	457	60.8 (6.8)

Figure S22. Get High-res Image Gene #9: '5p gain' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'5p gain' versus 'PATHOLOGY_T_STAGE'

P value = 0.00018 (Fisher's exact test), Q value = 0.0028

Table S23. Gene #9: '5p gain' versus Clinical Feature #3: 'PATHOLOGY_T_STAGE'

nPatients	T2	T3	T4
ALL	188	287	10
5P GAIN MUTATED	1	20	2
5P GAIN WILD-TYPE	187	267	8

Figure S23. Get High-res Image Gene #9: '5p gain' versus Clinical Feature #3: 'PATHOLOGY_T_STAGE'

'5p gain' versus 'PATHOLOGY_N_STAGE'

P value = 0.00247 (Fisher's exact test), Q value = 0.019

Table S24. Gene #9: '5p gain' versus Clinical Feature #4: 'PATHOLOGY_N_STAGE'

nPatients	0	1
ALL	342	77
5P GAIN MUTATED	12	10
5P GAIN WILD-TYPE	330	67

Figure S24. Get High-res Image Gene #9: '5p gain' versus Clinical Feature #4: 'PATHOLOGY_N_STAGE'

'5p gain' versus 'RADIATION_THERAPY'

P value = 0.0269 (Fisher's exact test), Q value = 0.1

Table S25. Gene #9: '5p gain' versus Clinical Feature #5: 'RADIATION_THERAPY'

nPatients	NO	YES
ALL	378	57
5P GAIN MUTATED	13	6
5P GAIN WILD-TYPE	365	51

Figure S25. Get High-res Image Gene #9: '5p gain' versus Clinical Feature #5: 'RADIATION_THERAPY'

'5p gain' versus 'RESIDUAL_TUMOR'

P value = 0.0183 (Fisher's exact test), Q value = 0.076

Table S26. Gene #9: '5p gain' versus Clinical Feature #7: 'RESIDUAL_TUMOR'

nPatients	R0	R1	R2	RX
ALL	312	143	5	15
5P GAIN MUTATED	9	12	1	1
5P GAIN WILD-TYPE	303	131	4	14

Figure S26. Get High-res Image Gene #9: '5p gain' versus Clinical Feature #7: 'RESIDUAL_TUMOR'

'5p gain' versus 'NUMBER_OF_LYMPH_NODES'

P value = 5.17e-05 (Wilcoxon-test), Q value = 0.001

Table S27. Gene #9: '5p gain' versus Clinical Feature #8: 'NUMBER_OF_LYMPH_NODES'

	nPatients	Mean (Std.Dev)
ALL	401	0.4 (1.4)
5P GAIN MUTATED	19	1.7 (2.6)
5P GAIN WILD-TYPE	382	0.4 (1.2)

Figure S27. Get High-res Image Gene #9: '5p gain' versus Clinical Feature #8: 'NUMBER_OF_LYMPH_NODES'

'5p gain' versus 'GLEASON_SCORE'

P value = 1.77e-06 (Wilcoxon-test), Q value = 9.2e-05

Table S28. Gene #9: '5p gain' versus Clinical Feature #9: 'GLEASON_SCORE'

	nPatients	Mean (Std.Dev)
ALL	491	7.6 (1.0)
5P GAIN MUTATED	23	8.6 (0.8)
5P GAIN WILD-TYPE	468	7.6 (1.0)

Figure S28. Get High-res Image Gene #9: '5p gain' versus Clinical Feature #9: 'GLEASON_SCORE'

'5q gain' versus 'YEARS_TO_BIRTH'

P value = 0.000169 (Wilcoxon-test), Q value = 0.0027

Table S29. Gene #10: '5q gain' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

	nPatients	Mean (Std.Dev)
ALL	480	61.0 (6.8)
5Q GAIN MUTATED	12	68.1 (3.8)
5Q GAIN WILD-TYPE	468	60.8 (6.8)

Figure S29. Get High-res Image Gene #10: '5q gain' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'5q gain' versus 'PATHOLOGY_T_STAGE'

P value = 0.00878 (Fisher's exact test), Q value = 0.044

Table S30. Gene #10: '5q gain' versus Clinical Feature #3: 'PATHOLOGY_T_STAGE'

nPatients	T2	T3	T4
ALL	188	287	10
5Q GAIN MUTATED	0	12	0
5Q GAIN WILD-TYPE	188	275	10

Figure S30. Get High-res Image Gene #10: '5q gain' versus Clinical Feature #3: 'PATHOLOGY_T_STAGE'

'5q gain' versus 'PATHOLOGY_N_STAGE'

P value = 0.00683 (Fisher's exact test), Q value = 0.036

Table S31. Gene #10: '5q gain' versus Clinical Feature #4: 'PATHOLOGY_N_STAGE'

nPatients	0	1
ALL	342	77
5Q GAIN MUTATED	5	6
5Q GAIN WILD-TYPE	337	71

Figure S31. Get High-res Image Gene #10: '5q gain' versus Clinical Feature #4: 'PATHOLOGY_N_STAGE'

'5q gain' versus 'RESIDUAL_TUMOR'

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

Table S32. Gene #10: '5q gain' versus Clinical Feature #7: 'RESIDUAL_TUMOR'

nPatients	R0	R1	R2	RX
ALL	312	143	5	15
5Q GAIN MUTATED	4	6	1	1
5Q GAIN WILD-TYPE	308	137	4	14

Figure S32. Get High-res Image Gene #10: '5q gain' versus Clinical Feature #7: 'RESIDUAL_TUMOR'

'5q gain' versus 'NUMBER_OF_LYMPH_NODES'

P value = 0.00028 (Wilcoxon-test), Q value = 0.0039

Table S33. Gene #10: '5q gain' versus Clinical Feature #8: 'NUMBER_OF_LYMPH_NODES'

	nPatients	Mean (Std.Dev)
ALL	401	0.4 (1.4)
5Q GAIN MUTATED	10	2.3 (3.0)
5Q GAIN WILD-TYPE	391	0.4 (1.3)

Figure S33. Get High-res Image Gene #10: '5q gain' versus Clinical Feature #8: 'NUMBER_OF_LYMPH_NODES'

'5q gain' versus 'GLEASON_SCORE'

P value = 0.00191 (Wilcoxon-test), Q value = 0.016

Table S34. Gene #10: '5q gain' versus Clinical Feature #9: 'GLEASON_SCORE'

	nPatients	Mean (Std.Dev)
ALL	491	7.6 (1.0)
5Q GAIN MUTATED	12	8.5 (0.8)
5Q GAIN WILD-TYPE	479	7.6 (1.0)

Figure S34. Get High-res Image Gene #10: '5q gain' versus Clinical Feature #9: 'GLEASON_SCORE'

'6p gain' versus 'Time to Death'

P value = 0.046 (logrank test), Q value = 0.15

Table S35. Gene #11: '6p gain' versus Clinical Feature #1: 'Time to Death'

	nPatients	nDeath	Duration Range (Median), Month
ALL	489	9	0.7 - 165.2 (28.8)
6P GAIN MUTATED	10	1	4.3 - 109.2 (37.4)
6P GAIN WILD-TYPE	479	8	0.7 - 165.2 (28.8)

Figure S35. Get High-res Image Gene #11: '6p gain' versus Clinical Feature #1: 'Time to Death'

'6p gain' versus 'PATHOLOGY_N_STAGE'

P value = 0.0218 (Fisher's exact test), Q value = 0.084

Table S36. Gene #11: '6p gain' versus Clinical Feature #4: 'PATHOLOGY_N_STAGE'

nPatients	0	1
ALL	342	77
6P GAIN MUTATED	5	5
6P GAIN WILD-TYPE	337	72

Figure S36. Get High-res Image Gene #11: '6p gain' versus Clinical Feature #4: 'PATHOLOGY_N_STAGE'

'6p gain' versus 'NUMBER_OF_LYMPH_NODES'

P value = 0.0152 (Wilcoxon-test), Q value = 0.068

Table S37. Gene #11: '6p gain' versus Clinical Feature #8: 'NUMBER_OF_LYMPH_NODES'

	nPatients	Mean (Std.Dev)
ALL	401	0.4 (1.4)
6P GAIN MUTATED	10	0.8 (1.0)
6P GAIN WILD-TYPE	391	0.4 (1.4)

Figure S37. Get High-res Image Gene #11: '6p gain' versus Clinical Feature #8: 'NUMBER_OF_LYMPH_NODES'

'6p gain' versus 'GLEASON_SCORE'

P value = 0.0302 (Wilcoxon-test), Q value = 0.11

Table S38. Gene #11: '6p gain' versus Clinical Feature #9: 'GLEASON_SCORE'

	nPatients	Mean (Std.Dev)
ALL	491	7.6 (1.0)
6P GAIN MUTATED	10	8.3 (0.9)
6P GAIN WILD-TYPE	481	7.6 (1.0)

Figure S38. Get High-res Image Gene #11: '6p gain' versus Clinical Feature #9: 'GLEASON_SCORE'

'6q gain' versus 'YEARS_TO_BIRTH'

P value = 0.0715 (Wilcoxon-test), Q value = 0.21

Table S39. Gene #12: '6q gain' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

	nPatients	Mean (Std.Dev)
ALL	480	61.0 (6.8)
6Q GAIN MUTATED	5	66.6 (5.0)
6Q GAIN WILD-TYPE	475	60.9 (6.8)

Figure S39. Get High-res Image Gene #12: '6q gain' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'6q gain' versus 'PATHOLOGY_N_STAGE'

P value = 0.0785 (Fisher's exact test), Q value = 0.23

Table S40. Gene #12: '6q gain' versus Clinical Feature #4: 'PATHOLOGY_N_STAGE'

nPatients	0	1
ALL	342	77
6Q GAIN MUTATED	3	3
6Q GAIN WILD-TYPE	339	74

Figure S40. Get High-res Image Gene #12: '6q gain' versus Clinical Feature #4: 'PATHOLOGY_N_STAGE'

'6q gain' versus 'NUMBER_OF_LYMPH_NODES'

P value = 0.0443 (Wilcoxon-test), Q value = 0.15

Table S41. Gene #12: '6q gain' versus Clinical Feature #8: 'NUMBER_OF_LYMPH_NODES'

	nPatients	Mean (Std.Dev)
ALL	401	0.4 (1.4)
6Q GAIN MUTATED	6	1.0 (1.3)
6Q GAIN WILD-TYPE	395	0.4 (1.4)

Figure S41. Get High-res Image Gene #12: '6q gain' versus Clinical Feature #8: 'NUMBER_OF_LYMPH_NODES'

'6q gain' versus 'GLEASON_SCORE'

P value = 0.0895 (Wilcoxon-test), Q value = 0.25

Table S42. Gene #12: '6q gain' versus Clinical Feature #9: 'GLEASON_SCORE'

	nPatients	Mean (Std.Dev)
ALL	491	7.6 (1.0)
6Q GAIN MUTATED	6	8.3 (1.0)
6Q GAIN WILD-TYPE	485	7.6 (1.0)

Figure S42. Get High-res Image Gene #12: '6q gain' versus Clinical Feature #9: 'GLEASON_SCORE'

'7p gain' versus 'YEARS_TO_BIRTH'

P value = 0.0102 (Wilcoxon-test), Q value = 0.05

Table S43. Gene #13: '7p gain' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

	nPatients	Mean (Std.Dev)
ALL	480	61.0 (6.8)
7P GAIN MUTATED	99	62.4 (6.6)
7P GAIN WILD-TYPE	381	60.6 (6.8)

Figure S43. Get High-res Image Gene #13: '7p gain' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'7p gain' versus 'PATHOLOGY_T_STAGE'

P value = 0.0325 (Fisher's exact test), Q value = 0.12

Table S44. Gene #13: '7p gain' versus Clinical Feature #3: 'PATHOLOGY_T_STAGE'

nPatients	T2	T3	T4
ALL	188	287	10
7P GAIN MUTATED	29	71	1
7P GAIN WILD-TYPE	159	216	9

Figure S44. Get High-res Image Gene #13: '7p gain' versus Clinical Feature #3: 'PATHOLOGY_T_STAGE'

'7p gain' versus 'RESIDUAL_TUMOR'

P value = 0.00476 (Fisher's exact test), Q value = 0.03

Table S45. Gene #13: '7p gain' versus Clinical Feature #7: 'RESIDUAL_TUMOR'

nPatients	R0	R1	R2	RX
ALL	312	143	5	15
7P GAIN MUTATED	50	43	1	4
7P GAIN WILD-TYPE	262	100	4	11

Figure S45. Get High-res Image Gene #13: '7p gain' versus Clinical Feature #7: 'RESIDUAL_TUMOR'

'7p gain' versus 'GLEASON_SCORE'

P value = 8.43e-05 (Wilcoxon-test), Q value = 0.0015

Table S46. Gene #13: '7p gain' versus Clinical Feature #9: 'GLEASON_SCORE'

	nPatients	Mean (Std.Dev)
ALL	491	7.6 (1.0)
7P GAIN MUTATED	101	8.0 (1.1)
7P GAIN WILD-TYPE	390	7.5 (1.0)

Figure S46. Get High-res Image Gene #13: '7p gain' versus Clinical Feature #9: 'GLEASON_SCORE'

'7q gain' versus 'YEARS_TO_BIRTH'

P value = 0.0174 (Wilcoxon-test), Q value = 0.074

Table S47. Gene #14: '7q gain' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

	nPatients	Mean (Std.Dev)
ALL	480	61.0 (6.8)
7Q GAIN MUTATED	92	62.3 (6.8)
7Q GAIN WILD-TYPE	388	60.7 (6.8)

Figure S47. Get High-res Image Gene #14: '7q gain' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'7q gain' versus 'PATHOLOGY_T_STAGE'

P value = 0.0874 (Fisher's exact test), Q value = 0.25

Table S48. Gene #14: '7q gain' versus Clinical Feature #3: 'PATHOLOGY_T_STAGE'

nPatients	T2	T3	T4
ALL	188	287	10
7Q GAIN MUTATED	28	65	1
7Q GAIN WILD-TYPE	160	222	9

Figure S48. Get High-res Image Gene #14: '7q gain' versus Clinical Feature #3: 'PATHOLOGY_T_STAGE'

'7q gain' versus 'RESIDUAL_TUMOR'

P value = 0.00262 (Fisher's exact test), Q value = 0.02

Table S49. Gene #14: '7q gain' versus Clinical Feature #7: 'RESIDUAL_TUMOR'

nPatients	R0	R1	R2	RX
ALL	312	143	5	15
7Q GAIN MUTATED	45	41	1	4
7Q GAIN WILD-TYPE	267	102	4	11

Figure S49. Get High-res Image Gene #14: '7q gain' versus Clinical Feature #7: 'RESIDUAL_TUMOR'

'7q gain' versus 'GLEASON_SCORE'

P value = 0.000253 (Wilcoxon-test), Q value = 0.0036

Table S50. Gene #14: '7q gain' versus Clinical Feature #9: 'GLEASON_SCORE'

	nPatients	Mean (Std.Dev)
ALL	491	7.6 (1.0)
7Q GAIN MUTATED	94	8.0 (1.1)
7Q GAIN WILD-TYPE	397	7.5 (1.0)

Figure S50. Get High-res Image Gene #14: '7q gain' versus Clinical Feature #9: 'GLEASON_SCORE'

'8p gain' versus 'YEARS_TO_BIRTH'

P value = 0.0099 (Wilcoxon-test), Q value = 0.048

Table S51. Gene #15: '8p gain' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

	nPatients	Mean (Std.Dev)
ALL	480	61.0 (6.8)
8P GAIN MUTATED	71	62.7 (6.5)
8P GAIN WILD-TYPE	409	60.7 (6.8)

Figure S51. Get High-res Image Gene #15: '8p gain' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'8p gain' versus 'PATHOLOGY_T_STAGE'

P value = 0.00713 (Fisher's exact test), Q value = 0.037

Table S52. Gene #15: '8p gain' versus Clinical Feature #3: 'PATHOLOGY_T_STAGE'

nPatients	T2	T3	T4
ALL	188	287	10
8P GAIN MUTATED	17	51	3
8P GAIN WILD-TYPE	171	236	7

Figure S52. Get High-res Image Gene #15: '8p gain' versus Clinical Feature #3: 'PATHOLOGY_T_STAGE'

'8p gain' versus 'RESIDUAL_TUMOR'

P value = 0.00526 (Fisher's exact test), Q value = 0.031

Table S53. Gene #15: '8p gain' versus Clinical Feature #7: 'RESIDUAL_TUMOR'

nPatients	R0	R1	R2	RX
ALL	312	143	5	15
8P GAIN MUTATED	34	33	1	1
8P GAIN WILD-TYPE	278	110	4	14

Figure S53. Get High-res Image Gene #15: '8p gain' versus Clinical Feature #7: 'RESIDUAL_TUMOR'

'8p gain' versus 'GLEASON_SCORE'

P value = 3e-07 (Wilcoxon-test), Q value = 2.5e-05

Table S54. Gene #15: '8p gain' versus Clinical Feature #9: 'GLEASON_SCORE'

	nPatients	Mean (Std.Dev)
ALL	491	7.6 (1.0)
8P GAIN MUTATED	71	8.2 (1.0)
8P GAIN WILD-TYPE	420	7.5 (1.0)

Figure S54. Get High-res Image Gene #15: '8p gain' versus Clinical Feature #9: 'GLEASON_SCORE'

'8q gain' versus 'PATHOLOGY_T_STAGE'

P value = 0.00015 (Fisher's exact test), Q value = 0.0024

Table S55. Gene #16: '8q gain' versus Clinical Feature #3: 'PATHOLOGY_T_STAGE'

nPatients	T2	T3	T4
ALL	188	287	10
8Q GAIN MUTATED	29	90	3
8Q GAIN WILD-TYPE	159	197	7

Figure S55. Get High-res Image Gene #16: '8q gain' versus Clinical Feature #3: 'PATHOLOGY_T_STAGE'

'8q gain' versus 'RESIDUAL_TUMOR'

P value = 0.00424 (Fisher's exact test), Q value = 0.028

Table S56. Gene #16: '8q gain' versus Clinical Feature #7: 'RESIDUAL_TUMOR'

nPatients	R0	R1	R2	RX
ALL	312	143	5	15
8Q GAIN MUTATED	62	50	1	5
8Q GAIN WILD-TYPE	250	93	4	10

Figure S56. Get High-res Image Gene #16: '8q gain' versus Clinical Feature #7: 'RESIDUAL_TUMOR'

'8q gain' versus 'GLEASON_SCORE'

P value = 5.12e-08 (Wilcoxon-test), Q value = 5e-06

Table S57. Gene #16: '8q gain' versus Clinical Feature #9: 'GLEASON_SCORE'

	nPatients	Mean (Std.Dev)
ALL	491	7.6 (1.0)
8Q GAIN MUTATED	123	8.0 (1.0)
8Q GAIN WILD-TYPE	368	7.5 (1.0)

Figure S57. Get High-res Image Gene #16: '8q gain' versus Clinical Feature #9: 'GLEASON_SCORE'

'8q gain' versus 'PSA_VALUE'

P value = 0.0378 (Wilcoxon-test), Q value = 0.13

Table S58. Gene #16: '8q gain' versus Clinical Feature #10: 'PSA_VALUE'

	nPatients	Mean (Std.Dev)
ALL	434	1.8 (16.0)
8Q GAIN MUTATED	104	4.4 (31.8)
8Q GAIN WILD-TYPE	330	1.0 (4.1)

Figure S58. Get High-res Image Gene #16: '8q gain' versus Clinical Feature #10: 'PSA_VALUE'

'9p gain' versus 'YEARS_TO_BIRTH'

P value = 0.00505 (Wilcoxon-test), Q value = 0.031

Table S59. Gene #17: '9p gain' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

	nPatients	Mean (Std.Dev)
ALL	480	61.0 (6.8)
9P GAIN MUTATED	33	64.3 (5.9)
9P GAIN WILD-TYPE	447	60.7 (6.8)

Figure S59. Get High-res Image Gene #17: '9p gain' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'9p gain' versus 'PATHOLOGY_T_STAGE'

P value = 6e-05 (Fisher's exact test), Q value = 0.0011

Table S60. Gene #17: '9p gain' versus Clinical Feature #3: 'PATHOLOGY_T_STAGE'

nPatients	T2	T3	T4
ALL	188	287	10
9P GAIN MUTATED	2	29	1
9P GAIN WILD-TYPE	186	258	9

Figure S60. Get High-res Image Gene #17: '9p gain' versus Clinical Feature #3: 'PATHOLOGY_T_STAGE'

'9p gain' versus 'PATHOLOGY_N_STAGE'

P value = 0.000316 (Fisher's exact test), Q value = 0.0042

Table S61. Gene #17: '9p gain' versus Clinical Feature #4: 'PATHOLOGY_N_STAGE'

nPatients	0	1
ALL	342	77
9P GAIN MUTATED	17	14
9P GAIN WILD-TYPE	325	63

Figure S61. Get High-res Image Gene #17: '9p gain' versus Clinical Feature #4: 'PATHOLOGY_N_STAGE'

'9p gain' versus 'RESIDUAL_TUMOR'

P value = 0.0204 (Fisher's exact test), Q value = 0.08

Table S62. Gene #17: '9p gain' versus Clinical Feature #7: 'RESIDUAL_TUMOR'

nPatients	R0	R1	R2	RX
ALL	312	143	5	15
9P GAIN MUTATED	14	16	1	0
9P GAIN WILD-TYPE	298	127	4	15

Figure S62. Get High-res Image Gene #17: '9p gain' versus Clinical Feature #7: 'RESIDUAL_TUMOR'

'9p gain' versus 'NUMBER_OF_LYMPH_NODES'

P value = 0.000223 (Wilcoxon-test), Q value = 0.0033

Table S63. Gene #17: '9p gain' versus Clinical Feature #8: 'NUMBER_OF_LYMPH_NODES'

	nPatients	Mean (Std.Dev)
ALL	401	0.4 (1.4)
9P GAIN MUTATED	31	0.8 (1.4)
9P GAIN WILD-TYPE	370	0.4 (1.4)

Figure S63. Get High-res Image Gene #17: '9p gain' versus Clinical Feature #8: 'NUMBER_OF_LYMPH_NODES'

'9p gain' versus 'GLEASON_SCORE'

P value = 2.23e-06 (Wilcoxon-test), Q value = 0.00011

Table S64. Gene #17: '9p gain' versus Clinical Feature #9: 'GLEASON_SCORE'

	nPatients	Mean (Std.Dev)
ALL	491	7.6 (1.0)
9P GAIN MUTATED	33	8.4 (0.9)
9P GAIN WILD-TYPE	458	7.5 (1.0)

Figure S64. Get High-res Image Gene #17: '9p gain' versus Clinical Feature #9: 'GLEASON_SCORE'

'9q gain' versus 'YEARS_TO_BIRTH'

P value = 0.0181 (Wilcoxon-test), Q value = 0.076

Table S65. Gene #18: '9q gain' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

	nPatients	Mean (Std.Dev)
ALL	480	61.0 (6.8)
9Q GAIN MUTATED	49	63.3 (5.9)
9Q GAIN WILD-TYPE	431	60.7 (6.9)

Figure S65. Get High-res Image Gene #18: '9q gain' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'9q gain' versus 'PATHOLOGY_T_STAGE'

P value = 2e-05 (Fisher's exact test), Q value = 0.00051

Table S66. Gene #18: '9q gain' versus Clinical Feature #3: 'PATHOLOGY_T_STAGE'

nPatients	T2	T3	T4
ALL	188	287	10
9Q GAIN MUTATED	4	42	2
9Q GAIN WILD-TYPE	184	245	8

Figure S66. Get High-res Image Gene #18: '9q gain' versus Clinical Feature #3: 'PATHOLOGY_T_STAGE'

'9q gain' versus 'PATHOLOGY_N_STAGE'

P value = 4.99e-06 (Fisher's exact test), Q value = 0.00018

Table S67. Gene #18: '9q gain' versus Clinical Feature #4: 'PATHOLOGY_N_STAGE'

nPatients	0	1
ALL	342	77
9Q GAIN MUTATED	25	21
9Q GAIN WILD-TYPE	317	56

Figure S67. Get High-res Image Gene #18: '9q gain' versus Clinical Feature #4: 'PATHOLOGY_N_STAGE'

'9q gain' versus 'RESIDUAL_TUMOR'

P value = 0.0148 (Fisher's exact test), Q value = 0.067

Table S68. Gene #18: '9q gain' versus Clinical Feature #7: 'RESIDUAL_TUMOR'

nPatients	R0	R1	R2	RX
ALL	312	143	5	15
9Q GAIN MUTATED	22	23	1	1
9Q GAIN WILD-TYPE	290	120	4	14

Figure S68. Get High-res Image Gene #18: '9q gain' versus Clinical Feature #7: 'RESIDUAL_TUMOR'

'9q gain' versus 'NUMBER_OF_LYMPH_NODES'

P value = 8.05e-07 (Wilcoxon-test), Q value = 5.1e-05

Table S69. Gene #18: '9q gain' versus Clinical Feature #8: 'NUMBER_OF_LYMPH_NODES'

	nPatients	Mean (Std.Dev)
ALL	401	0.4 (1.4)
9Q GAIN MUTATED	46	1.3 (2.6)
9Q GAIN WILD-TYPE	355	0.3 (1.1)

Figure S69. Get High-res Image Gene #18: '9q gain' versus Clinical Feature #8: 'NUMBER_OF_LYMPH_NODES'

'9q gain' versus 'GLEASON_SCORE'

P value = 1.83e-08 (Wilcoxon-test), Q value = 3.2e-06

Table S70. Gene #18: '9q gain' versus Clinical Feature #9: 'GLEASON_SCORE'

	nPatients	Mean (Std.Dev)
ALL	491	7.6 (1.0)
9Q GAIN MUTATED	49	8.4 (0.9)
9Q GAIN WILD-TYPE	442	7.5 (1.0)

Figure S70. Get High-res Image Gene #18: '9q gain' versus Clinical Feature #9: 'GLEASON_SCORE'

'10p gain' versus 'PATHOLOGY_N_STAGE'

P value = 0.0702 (Fisher's exact test), Q value = 0.21

Table S71. Gene #19: '10p gain' versus Clinical Feature #4: 'PATHOLOGY_N_STAGE'

nPatients	0	1
ALL	342	77
10P GAIN MUTATED	8	5
10P GAIN WILD-TYPE	334	72

Figure S71. Get High-res Image Gene #19: '10p gain' versus Clinical Feature #4: 'PATHOLOGY_N_STAGE'

'10p gain' versus 'NUMBER_OF_LYMPH_NODES'

P value = 0.0758 (Wilcoxon-test), Q value = 0.22

Table S72. Gene #19: '10p gain' versus Clinical Feature #8: 'NUMBER_OF_LYMPH_NODES'

	nPatients	Mean (Std.Dev)
ALL	401	0.4 (1.4)
10P GAIN MUTATED	13	1.2 (3.0)
10P GAIN WILD-TYPE	388	0.4 (1.3)

Figure S72. Get High-res Image Gene #19: '10p gain' versus Clinical Feature #8: 'NUMBER_OF_LYMPH_NODES'

'10p gain' versus 'GLEASON_SCORE'

P value = 0.00576 (Wilcoxon-test), Q value = 0.033

Table S73. Gene #19: '10p gain' versus Clinical Feature #9: 'GLEASON_SCORE'

	nPatients	Mean (Std.Dev)
ALL	491	7.6 (1.0)
10P GAIN MUTATED	14	8.4 (0.9)
10P GAIN WILD-TYPE	477	7.6 (1.0)

Figure S73. Get High-res Image Gene #19: '10p gain' versus Clinical Feature #9: 'GLEASON_SCORE'

'10q gain' versus 'GLEASON_SCORE'

P value = 0.0516 (Wilcoxon-test), Q value = 0.16

Table S74. Gene #20: '10q gain' versus Clinical Feature #9: 'GLEASON_SCORE'

	nPatients	Mean (Std.Dev)
ALL	491	7.6 (1.0)
10Q GAIN MUTATED	13	8.2 (1.0)
10Q GAIN WILD-TYPE	478	7.6 (1.0)

Figure S74. Get High-res Image Gene #20: '10q gain' versus Clinical Feature #9: 'GLEASON_SCORE'

'11p gain' versus 'YEARS_TO_BIRTH'

P value = 0.0461 (Wilcoxon-test), Q value = 0.15

Table S75. Gene #21: '11p gain' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

	nPatients	Mean (Std.Dev)
ALL	480	61.0 (6.8)
11P GAIN MUTATED	25	63.3 (6.4)
11P GAIN WILD-TYPE	455	60.8 (6.8)

Figure S75. Get High-res Image Gene #21: '11p gain' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'11p gain' versus 'PATHOLOGY_T_STAGE'

P value = 0.00282 (Fisher's exact test), Q value = 0.021

Table S76. Gene #21: '11p gain' versus Clinical Feature #3: 'PATHOLOGY_T_STAGE'

nPatients	T2	T3	T4
ALL	188	287	10
11P GAIN MUTATED	3	20	2
11P GAIN WILD-TYPE	185	267	8

Figure S76. Get High-res Image Gene #21: '11p gain' versus Clinical Feature #3: 'PATHOLOGY_T_STAGE'

'11p gain' versus 'PATHOLOGY_N_STAGE'

P value = 0.00133 (Fisher's exact test), Q value = 0.012

Table S77. Gene #21: '11p gain' versus Clinical Feature #4: 'PATHOLOGY_N_STAGE'

nPatients	0	1
ALL	342	77
11P GAIN MUTATED	13	11
11P GAIN WILD-TYPE	329	66

Figure S77. Get High-res Image Gene #21: '11p gain' versus Clinical Feature #4: 'PATHOLOGY_N_STAGE'

'11p gain' versus 'RESIDUAL_TUMOR'

P value = 0.0239 (Fisher's exact test), Q value = 0.09

Table S78. Gene #21: '11p gain' versus Clinical Feature #7: 'RESIDUAL_TUMOR'

nPatients	R0	R1	R2	RX
ALL	312	143	5	15
11P GAIN MUTATED	10	13	0	2
11P GAIN WILD-TYPE	302	130	5	13

Figure S78. Get High-res Image Gene #21: '11p gain' versus Clinical Feature #7: 'RESIDUAL_TUMOR'

'11p gain' versus 'NUMBER_OF_LYMPH_NODES'

P value = 0.00162 (Wilcoxon-test), Q value = 0.014

Table S79. Gene #21: '11p gain' versus Clinical Feature #8: 'NUMBER_OF_LYMPH_NODES'

	nPatients	Mean (Std.Dev)
ALL	401	0.4 (1.4)
11P GAIN MUTATED	24	0.8 (1.5)
11P GAIN WILD-TYPE	377	0.4 (1.4)

Figure S79. Get High-res Image Gene #21: '11p gain' versus Clinical Feature #8: 'NUMBER_OF_LYMPH_NODES'

'11p gain' versus 'GLEASON_SCORE'

P value = 7.09e-05 (Wilcoxon-test), Q value = 0.0013

Table S80. Gene #21: '11p gain' versus Clinical Feature #9: 'GLEASON_SCORE'

	nPatients	Mean (Std.Dev)
ALL	491	7.6 (1.0)
11P GAIN MUTATED	25	8.4 (1.0)
11P GAIN WILD-TYPE	466	7.6 (1.0)

Figure S80. Get High-res Image Gene #21: '11p gain' versus Clinical Feature #9: 'GLEASON_SCORE'

'11q gain' versus 'YEARS_TO_BIRTH'

P value = 0.0516 (Wilcoxon-test), Q value = 0.16

Table S81. Gene #22: '11q gain' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

	nPatients	Mean (Std.Dev)
ALL	480	61.0 (6.8)
11Q GAIN MUTATED	28	63.2 (6.4)
11Q GAIN WILD-TYPE	452	60.8 (6.8)

Figure S81. Get High-res Image Gene #22: '11q gain' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'11q gain' versus 'PATHOLOGY_T_STAGE'

P value = 0.00437 (Fisher's exact test), Q value = 0.028

Table S82. Gene #22: '11q gain' versus Clinical Feature #3: 'PATHOLOGY_T_STAGE'

nPatients	T2	T3	T4
ALL	188	287	10
11Q GAIN MUTATED	4	22	2
11Q GAIN WILD-TYPE	184	265	8

Figure S82. Get High-res Image Gene #22: '11q gain' versus Clinical Feature #3: 'PATHOLOGY_T_STAGE'

'11q gain' versus 'PATHOLOGY_N_STAGE'

P value = 0.0011 (Fisher's exact test), Q value = 0.011

Table S83. Gene #22: '11q gain' versus Clinical Feature #4: 'PATHOLOGY_N_STAGE'

nPatients	0	1
ALL	342	77
11Q GAIN MUTATED	15	12
11Q GAIN WILD-TYPE	327	65

Figure S83. Get High-res Image Gene #22: '11q gain' versus Clinical Feature #4: 'PATHOLOGY_N_STAGE'

'11q gain' versus 'RESIDUAL_TUMOR'

P value = 0.0367 (Fisher's exact test), Q value = 0.13

Table S84. Gene #22: '11q gain' versus Clinical Feature #7: 'RESIDUAL_TUMOR'

nPatients	R0	R1	R2	RX
ALL	312	143	5	15
11Q GAIN MUTATED	12	14	0	2
11Q GAIN WILD-TYPE	300	129	5	13

Figure S84. Get High-res Image Gene #22: '11q gain' versus Clinical Feature #7: 'RESIDUAL_TUMOR'

'11q gain' versus 'NUMBER_OF_LYMPH_NODES'

P value = 0.000937 (Wilcoxon-test), Q value = 0.0096

Table S85. Gene #22: '11q gain' versus Clinical Feature #8: 'NUMBER_OF_LYMPH_NODES'

	nPatients	Mean (Std.Dev)
ALL	401	0.4 (1.4)
11Q GAIN MUTATED	26	0.8 (1.5)
11Q GAIN WILD-TYPE	375	0.4 (1.4)

Figure S85. Get High-res Image Gene #22: '11q gain' versus Clinical Feature #8: 'NUMBER_OF_LYMPH_NODES'

'11q gain' versus 'GLEASON_SCORE'

P value = 1.09e-05 (Wilcoxon-test), Q value = 0.00034

Table S86. Gene #22: '11q gain' versus Clinical Feature #9: 'GLEASON_SCORE'

	nPatients	Mean (Std.Dev)
ALL	491	7.6 (1.0)
11Q GAIN MUTATED	28	8.5 (1.0)
11Q GAIN WILD-TYPE	463	7.6 (1.0)

Figure S86. Get High-res Image Gene #22: '11q gain' versus Clinical Feature #9: 'GLEASON_SCORE'

'12p gain' versus 'YEARS_TO_BIRTH'

P value = 0.0159 (Wilcoxon-test), Q value = 0.07

Table S87. Gene #23: '12p gain' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

	nPatients	Mean (Std.Dev)
ALL	480	61.0 (6.8)
12P GAIN MUTATED	13	65.6 (5.8)
12P GAIN WILD-TYPE	467	60.8 (6.8)

Figure S87. Get High-res Image Gene #23: '12p gain' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'12p gain' versus 'PATHOLOGY_T_STAGE'

P value = 0.00603 (Fisher's exact test), Q value = 0.034

Table S88. Gene #23: '12p gain' versus Clinical Feature #3: 'PATHOLOGY_T_STAGE'

nPatients	T2	T3	T4
ALL	188	287	10
12P GAIN MUTATED	0	13	0
12P GAIN WILD-TYPE	188	274	10

Figure S88. Get High-res Image Gene #23: '12p gain' versus Clinical Feature #3: 'PATHOLOGY_T_STAGE'

'12p gain' versus 'PATHOLOGY_N_STAGE'

P value = 0.0218 (Fisher's exact test), Q value = 0.084

Table S89. Gene #23: '12p gain' versus Clinical Feature #4: 'PATHOLOGY_N_STAGE'

nPatients	0	1
ALL	342	77
12P GAIN MUTATED	5	5
12P GAIN WILD-TYPE	337	72

Figure S89. Get High-res Image Gene #23: '12p gain' versus Clinical Feature #4: 'PATHOLOGY_N_STAGE'

'12p gain' versus 'RADIATION_THERAPY'

P value = 0.0432 (Fisher's exact test), Q value = 0.14

Table S90. Gene #23: '12p gain' versus Clinical Feature #5: 'RADIATION_THERAPY'

nPatients	NO	YES
ALL	378	57
12P GAIN MUTATED	7	4
12P GAIN WILD-TYPE	371	53

Figure S90. Get High-res Image Gene #23: '12p gain' versus Clinical Feature #5: 'RADIATION_THERAPY'

'12p gain' versus 'RESIDUAL_TUMOR'

P value = 0.00286 (Fisher's exact test), Q value = 0.021

Table S91. Gene #23: '12p gain' versus Clinical Feature #7: 'RESIDUAL_TUMOR'

nPatients	R0	R1	R2	RX
ALL	312	143	5	15
12P GAIN MUTATED	3	9	1	0
12P GAIN WILD-TYPE	309	134	4	15

Figure S91. Get High-res Image Gene #23: '12p gain' versus Clinical Feature #7: 'RESIDUAL_TUMOR'

'12p gain' versus 'NUMBER_OF_LYMPH_NODES'

P value = 0.0134 (Wilcoxon-test), Q value = 0.061

Table S92. Gene #23: '12p gain' versus Clinical Feature #8: 'NUMBER_OF_LYMPH_NODES'

	nPatients	Mean (Std.Dev)
ALL	401	0.4 (1.4)
12P GAIN MUTATED	10	1.2 (2.1)
12P GAIN WILD-TYPE	391	0.4 (1.3)

Figure S92. Get High-res Image Gene #23: '12p gain' versus Clinical Feature #8: 'NUMBER_OF_LYMPH_NODES'

'12p gain' versus 'GLEASON_SCORE'

P value = 2.03e-05 (Wilcoxon-test), Q value = 0.00051

Table S93. Gene #23: '12p gain' versus Clinical Feature #9: 'GLEASON_SCORE'

	nPatients	Mean (Std.Dev)
ALL	491	7.6 (1.0)
12P GAIN MUTATED	13	8.8 (0.7)
12P GAIN WILD-TYPE	478	7.6 (1.0)

Figure S93. Get High-res Image Gene #23: '12p gain' versus Clinical Feature #9: 'GLEASON_SCORE'

'12q gain' versus 'YEARS_TO_BIRTH'

P value = 0.0855 (Wilcoxon-test), Q value = 0.24

Table S94. Gene #24: '12q gain' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

	nPatients	Mean (Std.Dev)
ALL	480	61.0 (6.8)
12Q GAIN MUTATED	16	64.1 (6.1)
12Q GAIN WILD-TYPE	464	60.9 (6.8)

Figure S94. Get High-res Image Gene #24: '12q gain' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'12q gain' versus 'PATHOLOGY_T_STAGE'

P value = 0.00663 (Fisher's exact test), Q value = 0.036

Table S95. Gene #24: '12q gain' versus Clinical Feature #3: 'PATHOLOGY_T_STAGE'

nPatients	T2	T3	T4
ALL	188	287	10
12Q GAIN MUTATED	1	14	1
12Q GAIN WILD-TYPE	187	273	9

Figure S95. Get High-res Image Gene #24: '12q gain' versus Clinical Feature #3: 'PATHOLOGY_T_STAGE'

'12q gain' versus 'PATHOLOGY_N_STAGE'

P value = 0.0185 (Fisher's exact test), Q value = 0.076

Table S96. Gene #24: '12q gain' versus Clinical Feature #4: 'PATHOLOGY_N_STAGE'

nPatients	0	1
ALL	342	77
12Q GAIN MUTATED	7	6
12Q GAIN WILD-TYPE	335	71

Figure S96. Get High-res Image Gene #24: '12q gain' versus Clinical Feature #4: 'PATHOLOGY_N_STAGE'

'12q gain' versus 'RADIATION_THERAPY'

P value = 0.00508 (Fisher's exact test), Q value = 0.031

Table S97. Gene #24: '12q gain' versus Clinical Feature #5: 'RADIATION_THERAPY'

nPatients	NO	YES
ALL	378	57
12Q GAIN MUTATED	8	6
12Q GAIN WILD-TYPE	370	51

Figure S97. Get High-res Image Gene #24: '12q gain' versus Clinical Feature #5: 'RADIATION_THERAPY'

'12q gain' versus 'RESIDUAL_TUMOR'

P value = 6e-05 (Fisher's exact test), Q value = 0.0011

Table S98. Gene #24: '12q gain' versus Clinical Feature #7: 'RESIDUAL_TUMOR'

nPatients	R0	R1	R2	RX
ALL	312	143	5	15
12Q GAIN MUTATED	2	13	1	0
12Q GAIN WILD-TYPE	310	130	4	15

Figure S98. Get High-res Image Gene #24: '12q gain' versus Clinical Feature #7: 'RESIDUAL_TUMOR'

'12q gain' versus 'NUMBER_OF_LYMPH_NODES'

P value = 0.00786 (Wilcoxon-test), Q value = 0.04

Table S99. Gene #24: '12q gain' versus Clinical Feature #8: 'NUMBER_OF_LYMPH_NODES'

	nPatients	Mean (Std.Dev)
ALL	401	0.4 (1.4)
12Q GAIN MUTATED	12	1.1 (2.0)
12Q GAIN WILD-TYPE	389	0.4 (1.3)

Figure S99. Get High-res Image Gene #24: '12q gain' versus Clinical Feature #8: 'NUMBER_OF_LYMPH_NODES'

'12q gain' versus 'GLEASON_SCORE'

P value = 1.19e-05 (Wilcoxon-test), Q value = 0.00036

Table S100. Gene #24: '12q gain' versus Clinical Feature #9: 'GLEASON_SCORE'

	nPatients	Mean (Std.Dev)
ALL	491	7.6 (1.0)
12Q GAIN MUTATED	16	8.8 (0.8)
12Q GAIN WILD-TYPE	475	7.6 (1.0)

Figure S100. Get High-res Image Gene #24: '12q gain' versus Clinical Feature #9: 'GLEASON_SCORE'

'14q gain' versus 'YEARS_TO_BIRTH'

P value = 0.0293 (Wilcoxon-test), Q value = 0.11

Table S101. Gene #26: '14q gain' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

	nPatients	Mean (Std.Dev)
ALL	480	61.0 (6.8)
14Q GAIN MUTATED	10	65.2 (5.4)
14Q GAIN WILD-TYPE	470	60.9 (6.8)

Figure S101. Get High-res Image Gene #26: '14q gain' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'14q gain' versus 'RADIATION_THERAPY'

P value = 0.00272 (Fisher's exact test), Q value = 0.02

Table S102. Gene #26: '14q gain' versus Clinical Feature #5: 'RADIATION_THERAPY'

nPatients	NO	YES
ALL	378	57
14Q GAIN MUTATED	4	5
14Q GAIN WILD-TYPE	374	52

Figure S102. Get High-res Image Gene #26: '14q gain' versus Clinical Feature #5: 'RADIATION_THERAPY'

'14q gain' versus 'RESIDUAL_TUMOR'

P value = 0.0452 (Fisher's exact test), Q value = 0.15

Table S103. Gene #26: '14q gain' versus Clinical Feature #7: 'RESIDUAL_TUMOR'

nPatients	R0	R1	R2	RX
ALL	312	143	5	15
14Q GAIN MUTATED	3	6	0	1
14Q GAIN WILD-TYPE	309	137	5	14

Figure S103. Get High-res Image Gene #26: '14q gain' versus Clinical Feature #7: 'RESIDUAL_TUMOR'

'14q gain' versus 'GLEASON_SCORE'

P value = 0.00352 (Wilcoxon-test), Q value = 0.024

Table S104. Gene #26: '14q gain' versus Clinical Feature #9: 'GLEASON_SCORE'

	nPatients	Mean (Std.Dev)
ALL	491	7.6 (1.0)
14Q GAIN MUTATED	10	8.5 (0.7)
14Q GAIN WILD-TYPE	481	7.6 (1.0)

Figure S104. Get High-res Image Gene #26: '14q gain' versus Clinical Feature #9: 'GLEASON_SCORE'

'16p gain' versus 'PATHOLOGY_T_STAGE'

P value = 0.00082 (Fisher's exact test), Q value = 0.0085

Table S105. Gene #28: '16p gain' versus Clinical Feature #3: 'PATHOLOGY_T_STAGE'

nPatients	T2	T3	T4
ALL	188	287	10
16P GAIN MUTATED	3	27	1
16P GAIN WILD-TYPE	185	260	9

Figure S105. Get High-res Image Gene #28: '16p gain' versus Clinical Feature #3: 'PATHOLOGY_T_STAGE'

'16p gain' versus 'PATHOLOGY_N_STAGE'

P value = 0.00163 (Fisher's exact test), Q value = 0.014

Table S106. Gene #28: '16p gain' versus Clinical Feature #4: 'PATHOLOGY_N_STAGE'

nPatients	0	1
ALL	342	77
16P GAIN MUTATED	16	12
16P GAIN WILD-TYPE	326	65

Figure S106. Get High-res Image Gene #28: '16p gain' versus Clinical Feature #4: 'PATHOLOGY_N_STAGE'

'16p gain' versus 'NUMBER_OF_LYMPH_NODES'

P value = 0.000714 (Wilcoxon-test), Q value = 0.0078

Table S107. Gene #28: '16p gain' versus Clinical Feature #8: 'NUMBER_OF_LYMPH_NODES'

	nPatients	Mean (Std.Dev)
ALL	401	0.4 (1.4)
16P GAIN MUTATED	26	0.8 (1.6)
16P GAIN WILD-TYPE	375	0.4 (1.3)

Figure S107. Get High-res Image Gene #28: '16p gain' versus Clinical Feature #8: 'NUMBER_OF_LYMPH_NODES'

'16p gain' versus 'GLEASON_SCORE'

P value = 6.44e-06 (Wilcoxon-test), Q value = 0.00022

Table S108. Gene #28: '16p gain' versus Clinical Feature #9: 'GLEASON_SCORE'

	nPatients	Mean (Std.Dev)
ALL	491	7.6 (1.0)
16P GAIN MUTATED	31	8.5 (1.0)
16P GAIN WILD-TYPE	460	7.5 (1.0)

Figure S108. Get High-res Image Gene #28: '16p gain' versus Clinical Feature #9: 'GLEASON_SCORE'

'16q gain' versus 'YEARS_TO_BIRTH'

P value = 0.00765 (Wilcoxon-test), Q value = 0.04

Table S109. Gene #29: '16q gain' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

	nPatients	Mean (Std.Dev)
ALL	480	61.0 (6.8)
16Q GAIN MUTATED	8	66.9 (3.6)
16Q GAIN WILD-TYPE	472	60.9 (6.8)

Figure S109. Get High-res Image Gene #29: '16q gain' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'16q gain' versus 'GLEASON_SCORE'

P value = 0.0826 (Wilcoxon-test), Q value = 0.24

Table S110. Gene #29: '16q gain' versus Clinical Feature #9: 'GLEASON_SCORE'

	nPatients	Mean (Std.Dev)
ALL	491	7.6 (1.0)
16Q GAIN MUTATED	8	8.2 (1.0)
16Q GAIN WILD-TYPE	483	7.6 (1.0)

Figure S110. Get High-res Image Gene #29: '16q gain' versus Clinical Feature #9: 'GLEASON_SCORE'

'17p gain' versus 'PATHOLOGY_T_STAGE'

P value = 0.0183 (Fisher's exact test), Q value = 0.076

Table S111. Gene #30: '17p gain' versus Clinical Feature #3: 'PATHOLOGY_T_STAGE'

nPatients	T2	T3	T4
ALL	188	287	10
17P GAIN MUTATED	0	7	1
17P GAIN WILD-TYPE	188	280	9

Figure S111. Get High-res Image Gene #30: '17p gain' versus Clinical Feature #3: 'PATHOLOGY_T_STAGE'

'17p gain' versus 'PATHOLOGY_N_STAGE'

P value = 0.00659 (Fisher's exact test), Q value = 0.036

Table S112. Gene #30: '17p gain' versus Clinical Feature #4: 'PATHOLOGY_N_STAGE'

nPatients	0	1
ALL	342	77
17P GAIN MUTATED	3	5
17P GAIN WILD-TYPE	339	72

Figure S112. Get High-res Image Gene #30: '17p gain' versus Clinical Feature #4: 'PATHOLOGY_N_STAGE'

'17p gain' versus 'RADIATION_THERAPY'

P value = 0.0739 (Fisher's exact test), Q value = 0.22

Table S113. Gene #30: '17p gain' versus Clinical Feature #5: 'RADIATION_THERAPY'

nPatients	NO	YES
ALL	378	57
17P GAIN MUTATED	5	3
17P GAIN WILD-TYPE	373	54

Figure S113. Get High-res Image Gene #30: '17p gain' versus Clinical Feature #5: 'RADIATION_THERAPY'

'17p gain' versus 'NUMBER_OF_LYMPH_NODES'

P value = 0.00119 (Wilcoxon-test), Q value = 0.011

Table S114. Gene #30: '17p gain' versus Clinical Feature #8: 'NUMBER_OF_LYMPH_NODES'

	nPatients	Mean (Std.Dev)
ALL	401	0.4 (1.4)
17P GAIN MUTATED	8	2.1 (3.7)
17P GAIN WILD-TYPE	393	0.4 (1.3)

Figure S114. Get High-res Image Gene #30: '17p gain' versus Clinical Feature #8: 'NUMBER_OF_LYMPH_NODES'

'17p gain' versus 'GLEASON_SCORE'

P value = 0.0544 (Wilcoxon-test), Q value = 0.17

Table S115. Gene #30: '17p gain' versus Clinical Feature #9: 'GLEASON_SCORE'

	nPatients	Mean (Std.Dev)
ALL	491	7.6 (1.0)
17P GAIN MUTATED	8	8.4 (1.2)
17P GAIN WILD-TYPE	483	7.6 (1.0)

Figure S115. Get High-res Image Gene #30: '17p gain' versus Clinical Feature #9: 'GLEASON_SCORE'

'17q gain' versus 'PATHOLOGY_T_STAGE'

P value = 0.00461 (Fisher's exact test), Q value = 0.03

Table S116. Gene #31: '17q gain' versus Clinical Feature #3: 'PATHOLOGY_T_STAGE'

nPatients	T2	T3	T4
ALL	188	287	10
17Q GAIN MUTATED	0	10	1
17Q GAIN WILD-TYPE	188	277	9

Figure S116. Get High-res Image Gene #31: '17q gain' versus Clinical Feature #3: 'PATHOLOGY_T_STAGE'

'17q gain' versus 'PATHOLOGY_N_STAGE'

P value = 0.00683 (Fisher's exact test), Q value = 0.036

Table S117. Gene #31: '17q gain' versus Clinical Feature #4: 'PATHOLOGY_N_STAGE'

nPatients	0	1
ALL	342	77
17Q GAIN MUTATED	5	6
17Q GAIN WILD-TYPE	337	71

Figure S117. Get High-res Image Gene #31: '17q gain' versus Clinical Feature #4: 'PATHOLOGY_N_STAGE'

'17q gain' versus 'NUMBER_OF_LYMPH_NODES'

P value = 0.00238 (Wilcoxon-test), Q value = 0.019

Table S118. Gene #31: '17q gain' versus Clinical Feature #8: 'NUMBER_OF_LYMPH_NODES'

	nPatients	Mean (Std.Dev)
ALL	401	0.4 (1.4)
17Q GAIN MUTATED	11	1.6 (3.2)
17Q GAIN WILD-TYPE	390	0.4 (1.3)

Figure S118. Get High-res Image Gene #31: '17q gain' versus Clinical Feature #8: 'NUMBER_OF_LYMPH_NODES'

'17q gain' versus 'GLEASON_SCORE'

P value = 0.0691 (Wilcoxon-test), Q value = 0.21

Table S119. Gene #31: '17q gain' versus Clinical Feature #9: 'GLEASON_SCORE'

	nPatients	Mean (Std.Dev)
ALL	491	7.6 (1.0)
17Q GAIN MUTATED	11	8.2 (1.1)
17Q GAIN WILD-TYPE	480	7.6 (1.0)

Figure S119. Get High-res Image Gene #31: '17q gain' versus Clinical Feature #9: 'GLEASON_SCORE'

'18p gain' versus 'YEARS_TO_BIRTH'

P value = 0.00428 (Wilcoxon-test), Q value = 0.028

Table S120. Gene #32: '18p gain' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

	nPatients	Mean (Std.Dev)
ALL	480	61.0 (6.8)
18P GAIN MUTATED	18	65.4 (6.0)
18P GAIN WILD-TYPE	462	60.8 (6.8)

Figure S120. Get High-res Image Gene #32: '18p gain' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'18p gain' versus 'PATHOLOGY_T_STAGE'

P value = 0.00316 (Fisher's exact test), Q value = 0.023

Table S121. Gene #32: '18p gain' versus Clinical Feature #3: 'PATHOLOGY_T_STAGE'

nPatients	T2	T3	T4
ALL	188	287	10
18P GAIN MUTATED	1	16	1
18P GAIN WILD-TYPE	187	271	9

Figure S121. Get High-res Image Gene #32: '18p gain' versus Clinical Feature #3: 'PATHOLOGY_T_STAGE'

'18p gain' versus 'PATHOLOGY_N_STAGE'

P value = 0.00338 (Fisher's exact test), Q value = 0.024

Table S122. Gene #32: '18p gain' versus Clinical Feature #4: 'PATHOLOGY_N_STAGE'

nPatients	0	1
ALL	342	77
18P GAIN MUTATED	8	8
18P GAIN WILD-TYPE	334	69

Figure S122. Get High-res Image Gene #32: '18p gain' versus Clinical Feature #4: 'PATHOLOGY_N_STAGE'

'18p gain' versus 'NUMBER_OF_LYMPH_NODES'

P value = 0.00264 (Wilcoxon-test), Q value = 0.02

Table S123. Gene #32: '18p gain' versus Clinical Feature #8: 'NUMBER_OF_LYMPH_NODES'

	nPatients	Mean (Std.Dev)
ALL	401	0.4 (1.4)
18P GAIN MUTATED	16	1.2 (2.7)
18P GAIN WILD-TYPE	385	0.4 (1.3)

Figure S123. Get High-res Image Gene #32: '18p gain' versus Clinical Feature #8: 'NUMBER_OF_LYMPH_NODES'

'18q gain' versus 'YEARS_TO_BIRTH'

P value = 0.0488 (Wilcoxon-test), Q value = 0.16

Table S124. Gene #33: '18q gain' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

	nPatients	Mean (Std.Dev)
ALL	480	61.0 (6.8)
18Q GAIN MUTATED	9	64.9 (3.0)
18Q GAIN WILD-TYPE	471	60.9 (6.8)

Figure S124. Get High-res Image Gene #33: '18q gain' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'18q gain' versus 'PATHOLOGY_T_STAGE'

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

Table S125. Gene #33: '18q gain' versus Clinical Feature #3: 'PATHOLOGY_T_STAGE'

nPatients	T2	T3	T4
ALL	188	287	10
18Q GAIN MUTATED	0	9	0
18Q GAIN WILD-TYPE	188	278	10

Figure S125. Get High-res Image Gene #33: '18q gain' versus Clinical Feature #3: 'PATHOLOGY_T_STAGE'

'19p gain' versus 'PATHOLOGY_T_STAGE'

P value = 0.00059 (Fisher's exact test), Q value = 0.0066

Table S126. Gene #34: '19p gain' versus Clinical Feature #3: 'PATHOLOGY_T_STAGE'

nPatients	T2	T3	T4
ALL	188	287	10
19P GAIN MUTATED	0	9	2
19P GAIN WILD-TYPE	188	278	8

Figure S126. Get High-res Image Gene #34: '19p gain' versus Clinical Feature #3: 'PATHOLOGY_T_STAGE'

'19p gain' versus 'PATHOLOGY_N_STAGE'

P value = 0.00683 (Fisher's exact test), Q value = 0.036

Table S127. Gene #34: '19p gain' versus Clinical Feature #4: 'PATHOLOGY_N_STAGE'

nPatients	0	1
ALL	342	77
19P GAIN MUTATED	5	6
19P GAIN WILD-TYPE	337	71

Figure S127. Get High-res Image Gene #34: '19p gain' versus Clinical Feature #4: 'PATHOLOGY_N_STAGE'

'19p gain' versus 'NUMBER_OF_LYMPH_NODES'

P value = 0.00345 (Wilcoxon-test), Q value = 0.024

Table S128. Gene #34: '19p gain' versus Clinical Feature #8: 'NUMBER_OF_LYMPH_NODES'

	nPatients	Mean (Std.Dev)
ALL	401	0.4 (1.4)
19P GAIN MUTATED	11	1.3 (2.3)
19P GAIN WILD-TYPE	390	0.4 (1.3)

Figure S128. Get High-res Image Gene #34: '19p gain' versus Clinical Feature #8: 'NUMBER_OF_LYMPH_NODES'

'19p gain' versus 'GLEASON_SCORE'

P value = 0.000556 (Wilcoxon-test), Q value = 0.0063

Table S129. Gene #34: '19p gain' versus Clinical Feature #9: 'GLEASON_SCORE'

	nPatients	Mean (Std.Dev)
ALL	491	7.6 (1.0)
19P GAIN MUTATED	11	8.7 (0.9)
19P GAIN WILD-TYPE	480	7.6 (1.0)

Figure S129. Get High-res Image Gene #34: '19p gain' versus Clinical Feature #9: 'GLEASON_SCORE'

'19q gain' versus 'PATHOLOGY_T_STAGE'

P value = 0.00052 (Fisher's exact test), Q value = 0.0061

Table S130. Gene #35: '19q gain' versus Clinical Feature #3: 'PATHOLOGY_T_STAGE'

nPatients	T2	T3	T4
ALL	188	287	10
19Q GAIN MUTATED	0	9	2
19Q GAIN WILD-TYPE	188	278	8

Figure S130. Get High-res Image Gene #35: '19q gain' versus Clinical Feature #3: 'PATHOLOGY_T_STAGE'

'19q gain' versus 'PATHOLOGY_N_STAGE'

P value = 0.00683 (Fisher's exact test), Q value = 0.036

Table S131. Gene #35: '19q gain' versus Clinical Feature #4: 'PATHOLOGY_N_STAGE'

nPatients	0	1
ALL	342	77
19Q GAIN MUTATED	5	6
19Q GAIN WILD-TYPE	337	71

Figure S131. Get High-res Image Gene #35: '19q gain' versus Clinical Feature #4: 'PATHOLOGY_N_STAGE'

'19q gain' versus 'NUMBER_OF_LYMPH_NODES'

P value = 0.00345 (Wilcoxon-test), Q value = 0.024

Table S132. Gene #35: '19q gain' versus Clinical Feature #8: 'NUMBER_OF_LYMPH_NODES'

	nPatients	Mean (Std.Dev)
ALL	401	0.4 (1.4)
19Q GAIN MUTATED	11	1.3 (2.3)
19Q GAIN WILD-TYPE	390	0.4 (1.3)

Figure S132. Get High-res Image Gene #35: '19q gain' versus Clinical Feature #8: 'NUMBER_OF_LYMPH_NODES'

'19q gain' versus 'GLEASON_SCORE'

P value = 0.000556 (Wilcoxon-test), Q value = 0.0063

Table S133. Gene #35: '19q gain' versus Clinical Feature #9: 'GLEASON_SCORE'

	nPatients	Mean (Std.Dev)
ALL	491	7.6 (1.0)
19Q GAIN MUTATED	11	8.7 (0.9)
19Q GAIN WILD-TYPE	480	7.6 (1.0)

Figure S133. Get High-res Image Gene #35: '19q gain' versus Clinical Feature #9: 'GLEASON_SCORE'

'20p gain' versus 'YEARS_TO_BIRTH'

P value = 0.0545 (Wilcoxon-test), Q value = 0.17

Table S134. Gene #36: '20p gain' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

	nPatients	Mean (Std.Dev)
ALL	480	61.0 (6.8)
20P GAIN MUTATED	24	63.4 (4.7)
20P GAIN WILD-TYPE	456	60.8 (6.9)

Figure S134. Get High-res Image Gene #36: '20p gain' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'20p gain' versus 'PATHOLOGY_T_STAGE'

P value = 0.0109 (Fisher's exact test), Q value = 0.052

Table S135. Gene #36: '20p gain' versus Clinical Feature #3: 'PATHOLOGY_T_STAGE'

nPatients	T2	T3	T4
ALL	188	287	10
20P GAIN MUTATED	3	20	1
20P GAIN WILD-TYPE	185	267	9

Figure S135. Get High-res Image Gene #36: '20p gain' versus Clinical Feature #3: 'PATHOLOGY_T_STAGE'

'20p gain' versus 'PATHOLOGY_N_STAGE'

P value = 0.0421 (Fisher's exact test), Q value = 0.14

Table S136. Gene #36: '20p gain' versus Clinical Feature #4: 'PATHOLOGY_N_STAGE'

nPatients	0	1
ALL	342	77
20P GAIN MUTATED	14	8
20P GAIN WILD-TYPE	328	69

Figure S136. Get High-res Image Gene #36: '20p gain' versus Clinical Feature #4: 'PATHOLOGY_N_STAGE'

'20p gain' versus 'NUMBER_OF_LYMPH_NODES'

P value = 0.0278 (Wilcoxon-test), Q value = 0.1

Table S137. Gene #36: '20p gain' versus Clinical Feature #8: 'NUMBER_OF_LYMPH_NODES'

	nPatients	Mean (Std.Dev)
ALL	401	0.4 (1.4)
20P GAIN MUTATED	21	0.8 (1.4)
20P GAIN WILD-TYPE	380	0.4 (1.4)

Figure S137. Get High-res Image Gene #36: '20p gain' versus Clinical Feature #8: 'NUMBER_OF_LYMPH_NODES'

'20p gain' versus 'GLEASON_SCORE'

P value = 0.00105 (Wilcoxon-test), Q value = 0.011

Table S138. Gene #36: '20p gain' versus Clinical Feature #9: 'GLEASON_SCORE'

	nPatients	Mean (Std.Dev)
ALL	491	7.6 (1.0)
20P GAIN MUTATED	25	8.3 (1.2)
20P GAIN WILD-TYPE	466	7.6 (1.0)

Figure S138. Get High-res Image Gene #36: '20p gain' versus Clinical Feature #9: 'GLEASON_SCORE'

'20q gain' versus 'YEARS_TO_BIRTH'

P value = 0.00574 (Wilcoxon-test), Q value = 0.033

Table S139. Gene #37: '20q gain' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

	nPatients	Mean (Std.Dev)
ALL	480	61.0 (6.8)
20Q GAIN MUTATED	26	64.3 (4.5)
20Q GAIN WILD-TYPE	454	60.8 (6.9)

Figure S139. Get High-res Image Gene #37: '20q gain' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'20q gain' versus 'PATHOLOGY_T_STAGE'

P value = 0.00146 (Fisher's exact test), Q value = 0.013

Table S140. Gene #37: '20q gain' versus Clinical Feature #3: 'PATHOLOGY_T_STAGE'

nPatients	T2	T3	T4
ALL	188	287	10
20Q GAIN MUTATED	3	22	2
20Q GAIN WILD-TYPE	185	265	8

Figure S140. Get High-res Image Gene #37: '20q gain' versus Clinical Feature #3: 'PATHOLOGY_T_STAGE'

'20q gain' versus 'PATHOLOGY_N_STAGE'

P value = 0.0299 (Fisher's exact test), Q value = 0.11

Table S141. Gene #37: '20q gain' versus Clinical Feature #4: 'PATHOLOGY_N_STAGE'

nPatients	0	1
ALL	342	77
20Q GAIN MUTATED	16	9
20Q GAIN WILD-TYPE	326	68

Figure S141. Get High-res Image Gene #37: '20q gain' versus Clinical Feature #4: 'PATHOLOGY_N_STAGE'

'20q gain' versus 'RADIATION_THERAPY'

P value = 0.0634 (Fisher's exact test), Q value = 0.19

Table S142. Gene #37: '20q gain' versus Clinical Feature #5: 'RADIATION_THERAPY'

nPatients	NO	YES
ALL	378	57
20Q GAIN MUTATED	19	7
20Q GAIN WILD-TYPE	359	50

Figure S142. Get High-res Image Gene #37: '20q gain' versus Clinical Feature #5: 'RADIATION_THERAPY'

'20q gain' versus 'NUMBER_OF_LYMPH_NODES'

P value = 0.0202 (Wilcoxon-test), Q value = 0.079

Table S143. Gene #37: '20q gain' versus Clinical Feature #8: 'NUMBER_OF_LYMPH_NODES'

	nPatients	Mean (Std.Dev)
ALL	401	0.4 (1.4)
20Q GAIN MUTATED	24	0.8 (1.4)
20Q GAIN WILD-TYPE	377	0.4 (1.4)

Figure S143. Get High-res Image Gene #37: '20q gain' versus Clinical Feature #8: 'NUMBER_OF_LYMPH_NODES'

'20q gain' versus 'GLEASON_SCORE'

P value = 0.000339 (Wilcoxon-test), Q value = 0.0044

Table S144. Gene #37: '20q gain' versus Clinical Feature #9: 'GLEASON_SCORE'

	nPatients	Mean (Std.Dev)
ALL	491	7.6 (1.0)
20Q GAIN MUTATED	27	8.3 (1.1)
20Q GAIN WILD-TYPE	464	7.6 (1.0)

Figure S144. Get High-res Image Gene #37: '20q gain' versus Clinical Feature #9: 'GLEASON_SCORE'

'21q gain' versus 'YEARS_TO_BIRTH'

P value = 0.00612 (Wilcoxon-test), Q value = 0.034

Table S145. Gene #38: '21q gain' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

	nPatients	Mean (Std.Dev)
ALL	480	61.0 (6.8)
21Q GAIN MUTATED	20	65.0 (5.5)
21Q GAIN WILD-TYPE	460	60.8 (6.8)

Figure S145. Get High-res Image Gene #38: '21q gain' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'21q gain' versus 'PATHOLOGY_T_STAGE'

P value = 0.0156 (Fisher's exact test), Q value = 0.069

Table S146. Gene #38: '21q gain' versus Clinical Feature #3: 'PATHOLOGY_T_STAGE'

nPatients	T2	T3	T4
ALL	188	287	10
21Q GAIN MUTATED	2	18	0
21Q GAIN WILD-TYPE	186	269	10

Figure S146. Get High-res Image Gene #38: '21q gain' versus Clinical Feature #3: 'PATHOLOGY_T_STAGE'

'21q gain' versus 'PATHOLOGY_N_STAGE'

P value = 0.0174 (Fisher's exact test), Q value = 0.074

Table S147. Gene #38: '21q gain' versus Clinical Feature #4: 'PATHOLOGY_N_STAGE'

nPatients	0	1
ALL	342	77
21Q GAIN MUTATED	12	8
21Q GAIN WILD-TYPE	330	69

Figure S147. Get High-res Image Gene #38: '21q gain' versus Clinical Feature #4: 'PATHOLOGY_N_STAGE'

'21q gain' versus 'NUMBER_OF_LYMPH_NODES'

P value = 0.0117 (Wilcoxon-test), Q value = 0.055

Table S148. Gene #38: '21q gain' versus Clinical Feature #8: 'NUMBER_OF_LYMPH_NODES'

	nPatients	Mean (Std.Dev)
ALL	401	0.4 (1.4)
21Q GAIN MUTATED	20	1.2 (2.3)
21Q GAIN WILD-TYPE	381	0.4 (1.3)

Figure S148. Get High-res Image Gene #38: '21q gain' versus Clinical Feature #8: 'NUMBER_OF_LYMPH_NODES'

'21q gain' versus 'GLEASON_SCORE'

P value = 0.000128 (Wilcoxon-test), Q value = 0.0021

Table S149. Gene #38: '21q gain' versus Clinical Feature #9: 'GLEASON_SCORE'

	nPatients	Mean (Std.Dev)
ALL	491	7.6 (1.0)
21Q GAIN MUTATED	20	8.5 (0.9)
21Q GAIN WILD-TYPE	471	7.6 (1.0)

Figure S149. Get High-res Image Gene #38: '21q gain' versus Clinical Feature #9: 'GLEASON_SCORE'

'22q gain' versus 'GLEASON_SCORE'

P value = 0.0217 (Wilcoxon-test), Q value = 0.084

Table S150. Gene #39: '22q gain' versus Clinical Feature #9: 'GLEASON_SCORE'

	nPatients	Mean (Std.Dev)
ALL	491	7.6 (1.0)
22Q GAIN MUTATED	4	8.8 (0.5)
22Q GAIN WILD-TYPE	487	7.6 (1.0)

Figure S150. Get High-res Image Gene #39: '22q gain' versus Clinical Feature #9: 'GLEASON_SCORE'

'xp gain' versus 'PATHOLOGY_T_STAGE'

P value = 0.0198 (Fisher's exact test), Q value = 0.079

Table S151. Gene #40: 'xp gain' versus Clinical Feature #3: 'PATHOLOGY_T_STAGE'

nPatients	T2	T3	T4
ALL	188	287	10
XP GAIN MUTATED	0	6	1
XP GAIN WILD-TYPE	188	281	9

Figure S151. Get High-res Image Gene #40: 'xp gain' versus Clinical Feature #3: 'PATHOLOGY_T_STAGE'

'xp gain' versus 'RESIDUAL_TUMOR'

P value = 0.00552 (Fisher's exact test), Q value = 0.033

Table S152. Gene #40: 'xp gain' versus Clinical Feature #7: 'RESIDUAL_TUMOR'

nPatients	R0	R1	R2	RX
ALL	312	143	5	15
XP GAIN MUTATED	1	5	1	0
XP GAIN WILD-TYPE	311	138	4	15

Figure S152. Get High-res Image Gene #40: 'xp gain' versus Clinical Feature #7: 'RESIDUAL_TUMOR'

'xp gain' versus 'GLEASON_SCORE'

P value = 0.00489 (Wilcoxon-test), Q value = 0.03

Table S153. Gene #40: 'xp gain' versus Clinical Feature #9: 'GLEASON_SCORE'

	nPatients	Mean (Std.Dev)
ALL	491	7.6 (1.0)
XP GAIN MUTATED	7	8.7 (0.8)
XP GAIN WILD-TYPE	484	7.6 (1.0)

Figure S153. Get High-res Image Gene #40: 'xp gain' versus Clinical Feature #9: 'GLEASON_SCORE'

'xq gain' versus 'PATHOLOGY_T_STAGE'

P value = 0.0193 (Fisher's exact test), Q value = 0.078

Table S154. Gene #41: 'xq gain' versus Clinical Feature #3: 'PATHOLOGY_T_STAGE'

nPatients	T2	T3	T4
ALL	188	287	10
XQ GAIN MUTATED	0	6	1
XQ GAIN WILD-TYPE	188	281	9

Figure S154. Get High-res Image Gene #41: 'xq gain' versus Clinical Feature #3: 'PATHOLOGY_T_STAGE'

'xq gain' versus 'RESIDUAL_TUMOR'

P value = 0.00582 (Fisher's exact test), Q value = 0.033

Table S155. Gene #41: 'xq gain' versus Clinical Feature #7: 'RESIDUAL_TUMOR'

nPatients	R0	R1	R2	RX
ALL	312	143	5	15
XQ GAIN MUTATED	1	5	1	0
XQ GAIN WILD-TYPE	311	138	4	15

Figure S155. Get High-res Image Gene #41: 'xq gain' versus Clinical Feature #7: 'RESIDUAL_TUMOR'

'xq gain' versus 'GLEASON_SCORE'

P value = 0.00489 (Wilcoxon-test), Q value = 0.03

Table S156. Gene #41: 'xq gain' versus Clinical Feature #9: 'GLEASON_SCORE'

	nPatients	Mean (Std.Dev)
ALL	491	7.6 (1.0)
XQ GAIN MUTATED	7	8.7 (0.8)
XQ GAIN WILD-TYPE	484	7.6 (1.0)

Figure S156. Get High-res Image Gene #41: 'xq gain' versus Clinical Feature #9: 'GLEASON_SCORE'

'1p loss' versus 'PATHOLOGY_T_STAGE'

P value = 0.0247 (Fisher's exact test), Q value = 0.093

Table S157. Gene #42: '1p loss' versus Clinical Feature #3: 'PATHOLOGY_T_STAGE'

nPatients	T2	T3	T4
ALL	188	287	10
1P LOSS MUTATED	3	18	1
1P LOSS WILD-TYPE	185	269	9

Figure S157. Get High-res Image Gene #42: '1p loss' versus Clinical Feature #3: 'PATHOLOGY_T_STAGE'

'1p loss' versus 'RADIATION_THERAPY'

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

Table S158. Gene #42: '1p loss' versus Clinical Feature #5: 'RADIATION_THERAPY'

nPatients	NO	YES
ALL	378	57
1P LOSS MUTATED	15	6
1P LOSS WILD-TYPE	363	51

Figure S158. Get High-res Image Gene #42: '1p loss' versus Clinical Feature #5: 'RADIATION_THERAPY'

'1p loss' versus 'GLEASON_SCORE'

P value = 1.79e-05 (Wilcoxon-test), Q value = 0.00051

Table S159. Gene #42: '1p loss' versus Clinical Feature #9: 'GLEASON_SCORE'

	nPatients	Mean (Std.Dev)
ALL	491	7.6 (1.0)
1P LOSS MUTATED	22	8.5 (0.9)
1P LOSS WILD-TYPE	469	7.6 (1.0)

Figure S159. Get High-res Image Gene #42: '1p loss' versus Clinical Feature #9: 'GLEASON_SCORE'

'1q loss' versus 'RESIDUAL_TUMOR'

P value = 0.0565 (Fisher's exact test), Q value = 0.18

Table S160. Gene #43: '1q loss' versus Clinical Feature #7: 'RESIDUAL_TUMOR'

nPatients	R0	R1	R2	RX
ALL	312	143	5	15
1Q LOSS MUTATED	1	5	0	0
1Q LOSS WILD-TYPE	311	138	5	15

Figure S160. Get High-res Image Gene #43: '1q loss' versus Clinical Feature #7: 'RESIDUAL_TUMOR'

'1q loss' versus 'NUMBER_OF_LYMPH_NODES'

P value = 0.0749 (Wilcoxon-test), Q value = 0.22

Table S161. Gene #43: '1q loss' versus Clinical Feature #8: 'NUMBER_OF_LYMPH_NODES'

	nPatients	Mean (Std.Dev)
ALL	401	0.4 (1.4)
1Q LOSS MUTATED	4	1.2 (1.5)
1Q LOSS WILD-TYPE	397	0.4 (1.4)

Figure S161. Get High-res Image Gene #43: '1q loss' versus Clinical Feature #8: 'NUMBER_OF_LYMPH_NODES'

'1q loss' versus 'GLEASON_SCORE'

P value = 0.0895 (Wilcoxon-test), Q value = 0.25

Table S162. Gene #43: '1q loss' versus Clinical Feature #9: 'GLEASON_SCORE'

	nPatients	Mean (Std.Dev)
ALL	491	7.6 (1.0)
1Q LOSS MUTATED	6	8.3 (1.0)
1Q LOSS WILD-TYPE	485	7.6 (1.0)

Figure S162. Get High-res Image Gene #43: '1q loss' versus Clinical Feature #9: 'GLEASON_SCORE'

'2p loss' versus 'YEARS_TO_BIRTH'

P value = 0.00247 (Wilcoxon-test), Q value = 0.019

Table S163. Gene #44: '2p loss' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

	nPatients	Mean (Std.Dev)
ALL	480	61.0 (6.8)
2P LOSS MUTATED	15	66.2 (6.0)
2P LOSS WILD-TYPE	465	60.8 (6.8)

Figure S163. Get High-res Image Gene #44: '2p loss' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'2p loss' versus 'PATHOLOGY_T_STAGE'

P value = 0.00983 (Fisher's exact test), Q value = 0.048

Table S164. Gene #44: '2p loss' versus Clinical Feature #3: 'PATHOLOGY_T_STAGE'

nPatients	T2	T3	T4
ALL	188	287	10
2P LOSS MUTATED	1	13	1
2P LOSS WILD-TYPE	187	274	9

Figure S164. Get High-res Image Gene #44: '2p loss' versus Clinical Feature #3: 'PATHOLOGY_T_STAGE'

'2p loss' versus 'GLEASON_SCORE'

P value = 0.089 (Wilcoxon-test), Q value = 0.25

Table S165. Gene #44: '2p loss' versus Clinical Feature #9: 'GLEASON_SCORE'

	nPatients	Mean (Std.Dev)
ALL	491	7.6 (1.0)
2P LOSS MUTATED	15	8.1 (1.0)
2P LOSS WILD-TYPE	476	7.6 (1.0)

Figure S165. Get High-res Image Gene #44: '2p loss' versus Clinical Feature #9: 'GLEASON_SCORE'

'2q loss' versus 'YEARS_TO_BIRTH'

P value = 0.0196 (Wilcoxon-test), Q value = 0.078

Table S166. Gene #45: '2q loss' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

	nPatients	Mean (Std.Dev)
ALL	480	61.0 (6.8)
2Q LOSS MUTATED	18	64.8 (6.5)
2Q LOSS WILD-TYPE	462	60.8 (6.8)

Figure S166. Get High-res Image Gene #45: '2q loss' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'2q loss' versus 'PATHOLOGY_T_STAGE'

P value = 0.0194 (Fisher's exact test), Q value = 0.078

Table S167. Gene #45: '2q loss' versus Clinical Feature #3: 'PATHOLOGY_T_STAGE'

nPatients	T2	T3	T4
ALL	188	287	10
2Q LOSS MUTATED	2	15	1
2Q LOSS WILD-TYPE	186	272	9

Figure S167. Get High-res Image Gene #45: '2q loss' versus Clinical Feature #3: 'PATHOLOGY_T_STAGE'

'2q loss' versus 'GLEASON_SCORE'

P value = 0.0195 (Wilcoxon-test), Q value = 0.078

Table S168. Gene #45: '2q loss' versus Clinical Feature #9: 'GLEASON_SCORE'

	nPatients	Mean (Std.Dev)
ALL	491	7.6 (1.0)
2Q LOSS MUTATED	18	8.2 (1.0)
2Q LOSS WILD-TYPE	473	7.6 (1.0)

Figure S168. Get High-res Image Gene #45: '2q loss' versus Clinical Feature #9: 'GLEASON_SCORE'

'3p loss' versus 'GLEASON_SCORE'

P value = 0.00333 (Wilcoxon-test), Q value = 0.024

Table S169. Gene #46: '3p loss' versus Clinical Feature #9: 'GLEASON_SCORE'

	nPatients	Mean (Std.Dev)
ALL	491	7.6 (1.0)
3P LOSS MUTATED	9	8.7 (1.1)
3P LOSS WILD-TYPE	482	7.6 (1.0)

Figure S169. Get High-res Image Gene #46: '3p loss' versus Clinical Feature #9: 'GLEASON_SCORE'

'3q loss' versus 'GLEASON_SCORE'

P value = 0.00384 (Wilcoxon-test), Q value = 0.026

Table S170. Gene #47: '3q loss' versus Clinical Feature #9: 'GLEASON_SCORE'

	nPatients	Mean (Std.Dev)
ALL	491	7.6 (1.0)
3Q LOSS MUTATED	5	9.0 (0.7)
3Q LOSS WILD-TYPE	486	7.6 (1.0)

Figure S170. Get High-res Image Gene #47: '3q loss' versus Clinical Feature #9: 'GLEASON_SCORE'

'4p loss' versus 'YEARS_TO_BIRTH'

P value = 0.0735 (Wilcoxon-test), Q value = 0.22

Table S171. Gene #48: '4p loss' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

	nPatients	Mean (Std.Dev)
ALL	480	61.0 (6.8)
4P LOSS MUTATED	24	63.3 (7.5)
4P LOSS WILD-TYPE	456	60.9 (6.8)

Figure S171. Get High-res Image Gene #48: '4p loss' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'4p loss' versus 'PATHOLOGY_T_STAGE'

P value = 0.0119 (Fisher's exact test), Q value = 0.055

Table S172. Gene #48: '4p loss' versus Clinical Feature #3: 'PATHOLOGY_T_STAGE'

nPatients	T2	T3	T4
ALL	188	287	10
4P LOSS MUTATED	4	18	2
4P LOSS WILD-TYPE	184	269	8

Figure S172. Get High-res Image Gene #48: '4p loss' versus Clinical Feature #3: 'PATHOLOGY_T_STAGE'

'4p loss' versus 'PATHOLOGY_N_STAGE'

P value = 4.87e-05 (Fisher's exact test), Q value = 0.001

Table S173. Gene #48: '4p loss' versus Clinical Feature #4: 'PATHOLOGY_N_STAGE'

nPatients	0	1
ALL	342	77
4P LOSS MUTATED	11	13
4P LOSS WILD-TYPE	331	64

Figure S173. Get High-res Image Gene #48: '4p loss' versus Clinical Feature #4: 'PATHOLOGY_N_STAGE'

'4p loss' versus 'RADIATION_THERAPY'

P value = 0.0539 (Fisher's exact test), Q value = 0.17

Table S174. Gene #48: '4p loss' versus Clinical Feature #5: 'RADIATION_THERAPY'

nPatients	NO	YES
ALL	378	57
4P LOSS MUTATED	16	6
4P LOSS WILD-TYPE	362	51

Figure S174. Get High-res Image Gene #48: '4p loss' versus Clinical Feature #5: 'RADIATION_THERAPY'

'4p loss' versus 'RESIDUAL_TUMOR'

P value = 0.00919 (Fisher's exact test), Q value = 0.045

Table S175. Gene #48: '4p loss' versus Clinical Feature #7: 'RESIDUAL_TUMOR'

nPatients	R0	R1	R2	RX
ALL	312	143	5	15
4P LOSS MUTATED	8	14	0	1
4P LOSS WILD-TYPE	304	129	5	14

Figure S175. Get High-res Image Gene #48: '4p loss' versus Clinical Feature #7: 'RESIDUAL_TUMOR'

'4p loss' versus 'NUMBER_OF_LYMPH_NODES'

P value = 2.28e-06 (Wilcoxon-test), Q value = 0.00011

Table S176. Gene #48: '4p loss' versus Clinical Feature #8: 'NUMBER_OF_LYMPH_NODES'

	nPatients	Mean (Std.Dev)
ALL	401	0.4 (1.4)
4P LOSS MUTATED	23	1.3 (1.7)
4P LOSS WILD-TYPE	378	0.4 (1.3)

Figure S176. Get High-res Image Gene #48: '4p loss' versus Clinical Feature #8: 'NUMBER_OF_LYMPH_NODES'

'4p loss' versus 'GLEASON_SCORE'

P value = 3.09e-07 (Wilcoxon-test), Q value = 2.5e-05

Table S177. Gene #48: '4p loss' versus Clinical Feature #9: 'GLEASON_SCORE'

	nPatients	Mean (Std.Dev)
ALL	491	7.6 (1.0)
4P LOSS MUTATED	24	8.7 (0.8)
4P LOSS WILD-TYPE	467	7.6 (1.0)

Figure S177. Get High-res Image Gene #48: '4p loss' versus Clinical Feature #9: 'GLEASON_SCORE'

'4q loss' versus 'PATHOLOGY_T_STAGE'

P value = 0.018 (Fisher's exact test), Q value = 0.076

Table S178. Gene #49: '4q loss' versus Clinical Feature #3: 'PATHOLOGY_T_STAGE'

nPatients	T2	T3	T4
ALL	188	287	10
4Q LOSS MUTATED	3	11	2
4Q LOSS WILD-TYPE	185	276	8

Figure S178. Get High-res Image Gene #49: '4q loss' versus Clinical Feature #3: 'PATHOLOGY_T_STAGE'

'4q loss' versus 'PATHOLOGY_N_STAGE'

P value = 0.00338 (Fisher's exact test), Q value = 0.024

Table S179. Gene #49: '4q loss' versus Clinical Feature #4: 'PATHOLOGY_N_STAGE'

nPatients	0	1
ALL	342	77
4Q LOSS MUTATED	8	8
4Q LOSS WILD-TYPE	334	69

Figure S179. Get High-res Image Gene #49: '4q loss' versus Clinical Feature #4: 'PATHOLOGY_N_STAGE'

'4q loss' versus 'RADIATION_THERAPY'

P value = 0.0109 (Fisher's exact test), Q value = 0.052

Table S180. Gene #49: '4q loss' versus Clinical Feature #5: 'RADIATION_THERAPY'

nPatients	NO	YES
ALL	378	57
4Q LOSS MUTATED	10	6
4Q LOSS WILD-TYPE	368	51

Figure S180. Get High-res Image Gene #49: '4q loss' versus Clinical Feature #5: 'RADIATION_THERAPY'

'4q loss' versus 'RESIDUAL_TUMOR'

P value = 0.0347 (Fisher's exact test), Q value = 0.12

Table S181. Gene #49: '4q loss' versus Clinical Feature #7: 'RESIDUAL_TUMOR'

nPatients	R0	R1	R2	RX
ALL	312	143	5	15
4Q LOSS MUTATED	5	10	0	0
4Q LOSS WILD-TYPE	307	133	5	15

Figure S181. Get High-res Image Gene #49: '4q loss' versus Clinical Feature #7: 'RESIDUAL_TUMOR'

'4q loss' versus 'NUMBER_OF_LYMPH_NODES'

P value = 0.000502 (Wilcoxon-test), Q value = 0.006

Table S182. Gene #49: '4q loss' versus Clinical Feature #8: 'NUMBER_OF_LYMPH_NODES'

	nPatients	Mean (Std.Dev)
ALL	401	0.4 (1.4)
4Q LOSS MUTATED	15	1.2 (1.7)
4Q LOSS WILD-TYPE	386	0.4 (1.3)

Figure S182. Get High-res Image Gene #49: '4q loss' versus Clinical Feature #8: 'NUMBER_OF_LYMPH_NODES'

'4q loss' versus 'GLEASON_SCORE'

P value = 2.9e-06 (Wilcoxon-test), Q value = 0.00012

Table S183. Gene #49: '4q loss' versus Clinical Feature #9: 'GLEASON_SCORE'

	nPatients	Mean (Std.Dev)
ALL	491	7.6 (1.0)
4Q LOSS MUTATED	16	8.8 (0.7)
4Q LOSS WILD-TYPE	475	7.6 (1.0)

Figure S183. Get High-res Image Gene #49: '4q loss' versus Clinical Feature #9: 'GLEASON_SCORE'

'5p loss' versus 'PATHOLOGY_T_STAGE'

P value = 0.00046 (Fisher's exact test), Q value = 0.0057

Table S184. Gene #50: '5p loss' versus Clinical Feature #3: 'PATHOLOGY_T_STAGE'

nPatients	T2	T3	T4
ALL	188	287	10
5P LOSS MUTATED	0	10	2
5P LOSS WILD-TYPE	188	277	8

Figure S184. Get High-res Image Gene #50: '5p loss' versus Clinical Feature #3: 'PATHOLOGY_T_STAGE'

'5p loss' versus 'RADIATION_THERAPY'

P value = 0.0049 (Fisher's exact test), Q value = 0.03

Table S185. Gene #50: '5p loss' versus Clinical Feature #5: 'RADIATION_THERAPY'

nPatients	NO	YES
ALL	378	57
5P LOSS MUTATED	5	5
5P LOSS WILD-TYPE	373	52

Figure S185. Get High-res Image Gene #50: '5p loss' versus Clinical Feature #5: 'RADIATION_THERAPY'

'5p loss' versus 'RESIDUAL_TUMOR'

P value = 0.0626 (Fisher's exact test), Q value = 0.19

Table S186. Gene #50: '5p loss' versus Clinical Feature #7: 'RESIDUAL_TUMOR'

nPatients	R0	R1	R2	RX
ALL	312	143	5	15
5P LOSS MUTATED	4	8	0	0
5P LOSS WILD-TYPE	308	135	5	15

Figure S186. Get High-res Image Gene #50: '5p loss' versus Clinical Feature #7: 'RESIDUAL_TUMOR'

'5p loss' versus 'GLEASON_SCORE'

P value = 5.31e-05 (Wilcoxon-test), Q value = 0.001

Table S187. Gene #50: '5p loss' versus Clinical Feature #9: 'GLEASON_SCORE'

	nPatients	Mean (Std.Dev)
ALL	491	7.6 (1.0)
5P LOSS MUTATED	12	8.8 (0.7)
5P LOSS WILD-TYPE	479	7.6 (1.0)

Figure S187. Get High-res Image Gene #50: '5p loss' versus Clinical Feature #9: 'GLEASON_SCORE'

'5q loss' versus 'PATHOLOGY_T_STAGE'

P value = 3e-05 (Fisher's exact test), Q value = 0.00069

Table S188. Gene #51: '5q loss' versus Clinical Feature #3: 'PATHOLOGY_T_STAGE'

nPatients	T2	T3	T4
ALL	188	287	10
5Q LOSS MUTATED	2	16	4
5Q LOSS WILD-TYPE	186	271	6

Figure S188. Get High-res Image Gene #51: '5q loss' versus Clinical Feature #3: 'PATHOLOGY_T_STAGE'

'5q loss' versus 'PATHOLOGY_N_STAGE'

P value = 0.00158 (Fisher's exact test), Q value = 0.014

Table S189. Gene #51: '5q loss' versus Clinical Feature #4: 'PATHOLOGY_N_STAGE'

nPatients	0	1
ALL	342	77
5Q LOSS MUTATED	11	10
5Q LOSS WILD-TYPE	331	67

Figure S189. Get High-res Image Gene #51: '5q loss' versus Clinical Feature #4: 'PATHOLOGY_N_STAGE'

'5q loss' versus 'RADIATION_THERAPY'

P value = 0.00655 (Fisher's exact test), Q value = 0.036

Table S190. Gene #51: '5q loss' versus Clinical Feature #5: 'RADIATION_THERAPY'

nPatients	NO	YES
ALL	378	57
5Q LOSS MUTATED	12	7
5Q LOSS WILD-TYPE	366	50

Figure S190. Get High-res Image Gene #51: '5q loss' versus Clinical Feature #5: 'RADIATION_THERAPY'

'5q loss' versus 'NUMBER_OF_LYMPH_NODES'

P value = 0.00021 (Wilcoxon-test), Q value = 0.0032

Table S191. Gene #51: '5q loss' versus Clinical Feature #8: 'NUMBER_OF_LYMPH_NODES'

	nPatients	Mean (Std.Dev)
ALL	401	0.4 (1.4)
5Q LOSS MUTATED	19	1.0 (1.5)
5Q LOSS WILD-TYPE	382	0.4 (1.4)

Figure S191. Get High-res Image Gene #51: '5q loss' versus Clinical Feature #8: 'NUMBER_OF_LYMPH_NODES'

'5q loss' versus 'GLEASON_SCORE'

P value = 5.46e-07 (Wilcoxon-test), Q value = 4e-05

Table S192. Gene #51: '5q loss' versus Clinical Feature #9: 'GLEASON_SCORE'

	nPatients	Mean (Std.Dev)
ALL	491	7.6 (1.0)
5Q LOSS MUTATED	22	8.7 (0.7)
5Q LOSS WILD-TYPE	469	7.6 (1.0)

Figure S192. Get High-res Image Gene #51: '5q loss' versus Clinical Feature #9: 'GLEASON_SCORE'

'6p loss' versus 'PATHOLOGY_T_STAGE'

P value = 0.00067 (Fisher's exact test), Q value = 0.0074

Table S193. Gene #52: '6p loss' versus Clinical Feature #3: 'PATHOLOGY_T_STAGE'

nPatients	T2	T3	T4
ALL	188	287	10
6P LOSS MUTATED	3	18	3
6P LOSS WILD-TYPE	185	269	7

Figure S193. Get High-res Image Gene #52: '6p loss' versus Clinical Feature #3: 'PATHOLOGY_T_STAGE'

'6p loss' versus 'PATHOLOGY_N_STAGE'

P value = 0.00247 (Fisher's exact test), Q value = 0.019

Table S194. Gene #52: '6p loss' versus Clinical Feature #4: 'PATHOLOGY_N_STAGE'

nPatients	0	1
ALL	342	77
6P LOSS MUTATED	12	10
6P LOSS WILD-TYPE	330	67

Figure S194. Get High-res Image Gene #52: '6p loss' versus Clinical Feature #4: 'PATHOLOGY_N_STAGE'

'6p loss' versus 'NUMBER_OF_LYMPH_NODES'

P value = 0.00125 (Wilcoxon-test), Q value = 0.012

Table S195. Gene #52: '6p loss' versus Clinical Feature #8: 'NUMBER_OF_LYMPH_NODES'

	nPatients	Mean (Std.Dev)
ALL	401	0.4 (1.4)
6P LOSS MUTATED	21	0.7 (0.8)
6P LOSS WILD-TYPE	380	0.4 (1.4)

Figure S195. Get High-res Image Gene #52: '6p loss' versus Clinical Feature #8: 'NUMBER_OF_LYMPH_NODES'

'6p loss' versus 'GLEASON_SCORE'

P value = 3.22e-06 (Wilcoxon-test), Q value = 0.00013

Table S196. Gene #52: '6p loss' versus Clinical Feature #9: 'GLEASON_SCORE'

	nPatients	Mean (Std.Dev)
ALL	491	7.6 (1.0)
6P LOSS MUTATED	25	8.6 (0.9)
6P LOSS WILD-TYPE	466	7.6 (1.0)

Figure S196. Get High-res Image Gene #52: '6p loss' versus Clinical Feature #9: 'GLEASON_SCORE'

'6q loss' versus 'Time to Death'

P value = 0.0514 (logrank test), Q value = 0.16

Table S197. Gene #53: '6q loss' versus Clinical Feature #1: 'Time to Death'

	nPatients	nDeath	Duration Range (Median), Month
ALL	489	9	0.7 - 165.2 (28.8)
6Q LOSS MUTATED	39	2	1.0 - 75.8 (31.4)
6Q LOSS WILD-TYPE	450	7	0.7 - 165.2 (28.8)

Figure S197. Get High-res Image Gene #53: '6q loss' versus Clinical Feature #1: 'Time to Death'

'6q loss' versus 'PATHOLOGY_T_STAGE'

P value = 0.00108 (Fisher's exact test), Q value = 0.011

Table S198. Gene #53: '6q loss' versus Clinical Feature #3: 'PATHOLOGY_T_STAGE'

nPatients	T2	T3	T4
ALL	188	287	10
6Q LOSS MUTATED	6	29	3
6Q LOSS WILD-TYPE	182	258	7

Figure S198. Get High-res Image Gene #53: '6q loss' versus Clinical Feature #3: 'PATHOLOGY_T_STAGE'

'6q loss' versus 'PATHOLOGY_N_STAGE'

P value = 0.00314 (Fisher's exact test), Q value = 0.023

Table S199. Gene #53: '6q loss' versus Clinical Feature #4: 'PATHOLOGY_N_STAGE'

nPatients	0	1
ALL	342	77
6Q LOSS MUTATED	23	14
6Q LOSS WILD-TYPE	319	63

Figure S199. Get High-res Image Gene #53: '6q loss' versus Clinical Feature #4: 'PATHOLOGY_N_STAGE'

'6q loss' versus 'RADIATION_THERAPY'

P value = 0.0149 (Fisher's exact test), Q value = 0.067

Table S200. Gene #53: '6q loss' versus Clinical Feature #5: 'RADIATION_THERAPY'

nPatients	NO	YES
ALL	378	57
6Q LOSS MUTATED	25	10
6Q LOSS WILD-TYPE	353	47

Figure S200. Get High-res Image Gene #53: '6q loss' versus Clinical Feature #5: 'RADIATION_THERAPY'

'6q loss' versus 'NUMBER_OF_LYMPH_NODES'

P value = 0.00129 (Wilcoxon-test), Q value = 0.012

Table S201. Gene #53: '6q loss' versus Clinical Feature #8: 'NUMBER_OF_LYMPH_NODES'

	nPatients	Mean (Std.Dev)
ALL	401	0.4 (1.4)
6Q LOSS MUTATED	36	0.8 (1.3)
6Q LOSS WILD-TYPE	365	0.4 (1.4)

Figure S201. Get High-res Image Gene #53: '6q loss' versus Clinical Feature #8: 'NUMBER_OF_LYMPH_NODES'

'6q loss' versus 'GLEASON_SCORE'

P value = 7.94e-09 (Wilcoxon-test), Q value = 2.9e-06

Table S202. Gene #53: '6q loss' versus Clinical Feature #9: 'GLEASON_SCORE'

	nPatients	Mean (Std.Dev)
ALL	491	7.6 (1.0)
6Q LOSS MUTATED	39	8.5 (0.9)
6Q LOSS WILD-TYPE	452	7.5 (1.0)

Figure S202. Get High-res Image Gene #53: '6q loss' versus Clinical Feature #9: 'GLEASON_SCORE'

'8p loss' versus 'PATHOLOGY_T_STAGE'

P value = 0.00022 (Fisher's exact test), Q value = 0.0033

Table S203. Gene #54: '8p loss' versus Clinical Feature #3: 'PATHOLOGY_T_STAGE'

nPatients	T2	T3	T4
ALL	188	287	10
8P LOSS MUTATED	44	118	3
8P LOSS WILD-TYPE	144	169	7

Figure S203. Get High-res Image Gene #54: '8p loss' versus Clinical Feature #3: 'PATHOLOGY_T_STAGE'

'8p loss' versus 'NUMBER_OF_LYMPH_NODES'

P value = 0.0819 (Wilcoxon-test), Q value = 0.24

Table S204. Gene #54: '8p loss' versus Clinical Feature #8: 'NUMBER_OF_LYMPH_NODES'

	nPatients	Mean (Std.Dev)
ALL	401	0.4 (1.4)
8P LOSS MUTATED	137	0.6 (1.8)
8P LOSS WILD-TYPE	264	0.3 (1.0)

Figure S204. Get High-res Image Gene #54: '8p loss' versus Clinical Feature #8: 'NUMBER_OF_LYMPH_NODES'

'8q loss' versus 'Time to Death'

P value = 0.00438 (logrank test), Q value = 0.028

Table S205. Gene #55: '8q loss' versus Clinical Feature #1: 'Time to Death'

	nPatients	nDeath	Duration Range (Median), Month
ALL	489	9	0.7 - 165.2 (28.8)
8Q LOSS MUTATED	24	2	1.0 - 109.2 (29.6)
8Q LOSS WILD-TYPE	465	7	0.7 - 165.2 (28.8)

Figure S205. Get High-res Image Gene #55: '8q loss' versus Clinical Feature #1: 'Time to Death'

'8q loss' versus 'PATHOLOGY_T_STAGE'

P value = 0.00074 (Fisher's exact test), Q value = 0.0078

Table S206. Gene #55: '8q loss' versus Clinical Feature #3: 'PATHOLOGY_T_STAGE'

nPatients	T2	T3	T4
ALL	188	287	10
8Q LOSS MUTATED	2	20	2
8Q LOSS WILD-TYPE	186	267	8

Figure S206. Get High-res Image Gene #55: '8q loss' versus Clinical Feature #3: 'PATHOLOGY_T_STAGE'

'8q loss' versus 'PATHOLOGY_N_STAGE'

P value = 0.0421 (Fisher's exact test), Q value = 0.14

Table S207. Gene #55: '8q loss' versus Clinical Feature #4: 'PATHOLOGY_N_STAGE'

nPatients	0	1
ALL	342	77
8Q LOSS MUTATED	14	8
8Q LOSS WILD-TYPE	328	69

Figure S207. Get High-res Image Gene #55: '8q loss' versus Clinical Feature #4: 'PATHOLOGY_N_STAGE'

'8q loss' versus 'RADIATION_THERAPY'

P value = 0.0883 (Fisher's exact test), Q value = 0.25

Table S208. Gene #55: '8q loss' versus Clinical Feature #5: 'RADIATION_THERAPY'

nPatients	NO	YES
ALL	378	57
8Q LOSS MUTATED	14	5
8Q LOSS WILD-TYPE	364	52

Figure S208. Get High-res Image Gene #55: '8q loss' versus Clinical Feature #5: 'RADIATION_THERAPY'

'8q loss' versus 'NUMBER_OF_LYMPH_NODES'

P value = 0.0084 (Wilcoxon-test), Q value = 0.042

Table S209. Gene #55: '8q loss' versus Clinical Feature #8: 'NUMBER_OF_LYMPH_NODES'

	nPatients	Mean (Std.Dev)
ALL	401	0.4 (1.4)
8Q LOSS MUTATED	20	0.9 (1.4)
8Q LOSS WILD-TYPE	381	0.4 (1.4)

Figure S209. Get High-res Image Gene #55: '8q loss' versus Clinical Feature #8: 'NUMBER_OF_LYMPH_NODES'

'8q loss' versus 'GLEASON_SCORE'

P value = 0.0853 (Wilcoxon-test), Q value = 0.24

Table S210. Gene #55: '8q loss' versus Clinical Feature #9: 'GLEASON_SCORE'

	nPatients	Mean (Std.Dev)
ALL	491	7.6 (1.0)
8Q LOSS MUTATED	24	8.0 (1.1)
8Q LOSS WILD-TYPE	467	7.6 (1.0)

Figure S210. Get High-res Image Gene #55: '8q loss' versus Clinical Feature #9: 'GLEASON_SCORE'

'9p loss' versus 'PATHOLOGY_T_STAGE'

P value = 0.0184 (Fisher's exact test), Q value = 0.076

Table S211. Gene #56: '9p loss' versus Clinical Feature #3: 'PATHOLOGY_T_STAGE'

nPatients	T2	T3	T4
ALL	188	287	10
9P LOSS MUTATED	4	15	2
9P LOSS WILD-TYPE	184	272	8

Figure S211. Get High-res Image Gene #56: '9p loss' versus Clinical Feature #3: 'PATHOLOGY_T_STAGE'

'9p loss' versus 'PATHOLOGY_N_STAGE'

P value = 0.0701 (Fisher's exact test), Q value = 0.21

Table S212. Gene #56: '9p loss' versus Clinical Feature #4: 'PATHOLOGY_N_STAGE'

nPatients	0	1
ALL	342	77
9P LOSS MUTATED	13	7
9P LOSS WILD-TYPE	329	70

Figure S212. Get High-res Image Gene #56: '9p loss' versus Clinical Feature #4: 'PATHOLOGY_N_STAGE'

'9p loss' versus 'NUMBER_OF_LYMPH_NODES'

P value = 0.0202 (Wilcoxon-test), Q value = 0.079

Table S213. Gene #56: '9p loss' versus Clinical Feature #8: 'NUMBER_OF_LYMPH_NODES'

	nPatients	Mean (Std.Dev)
ALL	401	0.4 (1.4)
9P LOSS MUTATED	18	1.4 (2.9)
9P LOSS WILD-TYPE	383	0.4 (1.2)

Figure S213. Get High-res Image Gene #56: '9p loss' versus Clinical Feature #8: 'NUMBER_OF_LYMPH_NODES'

'9p loss' versus 'GLEASON_SCORE'

P value = 0.00571 (Wilcoxon-test), Q value = 0.033

Table S214. Gene #56: '9p loss' versus Clinical Feature #9: 'GLEASON_SCORE'

	nPatients	Mean (Std.Dev)
ALL	491	7.6 (1.0)
9P LOSS MUTATED	21	8.2 (1.1)
9P LOSS WILD-TYPE	470	7.6 (1.0)

Figure S214. Get High-res Image Gene #56: '9p loss' versus Clinical Feature #9: 'GLEASON_SCORE'

'9q loss' versus 'GLEASON_SCORE'

P value = 0.0151 (Wilcoxon-test), Q value = 0.068

Table S215. Gene #57: '9q loss' versus Clinical Feature #9: 'GLEASON_SCORE'

	nPatients	Mean (Std.Dev)
ALL	491	7.6 (1.0)
9Q LOSS MUTATED	10	8.4 (1.1)
9Q LOSS WILD-TYPE	481	7.6 (1.0)

Figure S215. Get High-res Image Gene #57: '9q loss' versus Clinical Feature #9: 'GLEASON_SCORE'

'10p loss' versus 'PATHOLOGY_T_STAGE'

P value = 2e-05 (Fisher's exact test), Q value = 0.00051

Table S216. Gene #58: '10p loss' versus Clinical Feature #3: 'PATHOLOGY_T_STAGE'

nPatients	T2	T3	T4
ALL	188	287	10
10P LOSS MUTATED	7	28	6
10P LOSS WILD-TYPE	181	259	4

Figure S216. Get High-res Image Gene #58: '10p loss' versus Clinical Feature #3: 'PATHOLOGY_T_STAGE'

'10p loss' versus 'PATHOLOGY_N_STAGE'

P value = 3e-04 (Fisher's exact test), Q value = 0.0041

Table S217. Gene #58: '10p loss' versus Clinical Feature #4: 'PATHOLOGY_N_STAGE'

nPatients	0	1
ALL	342	77
10P LOSS MUTATED	22	16
10P LOSS WILD-TYPE	320	61

Figure S217. Get High-res Image Gene #58: '10p loss' versus Clinical Feature #4: 'PATHOLOGY_N_STAGE'

'10p loss' versus 'RESIDUAL_TUMOR'

P value = 0.0177 (Fisher's exact test), Q value = 0.075

Table S218. Gene #58: '10p loss' versus Clinical Feature #7: 'RESIDUAL_TUMOR'

nPatients	R0	R1	R2	RX
ALL	312	143	5	15
10P LOSS MUTATED	19	20	1	0
10P LOSS WILD-TYPE	293	123	4	15

Figure S218. Get High-res Image Gene #58: '10p loss' versus Clinical Feature #7: 'RESIDUAL_TUMOR'

'10p loss' versus 'NUMBER_OF_LYMPH_NODES'

P value = 2.21e-05 (Wilcoxon-test), Q value = 0.00054

Table S219. Gene #58: '10p loss' versus Clinical Feature #8: 'NUMBER_OF_LYMPH_NODES'

	nPatients	Mean (Std.Dev)
ALL	401	0.4 (1.4)
10P LOSS MUTATED	37	1.3 (2.2)
10P LOSS WILD-TYPE	364	0.3 (1.2)

Figure S219. Get High-res Image Gene #58: '10p loss' versus Clinical Feature #8: 'NUMBER_OF_LYMPH_NODES'

'10p loss' versus 'GLEASON_SCORE'

P value = 2.68e-06 (Wilcoxon-test), Q value = 0.00012

Table S220. Gene #58: '10p loss' versus Clinical Feature #9: 'GLEASON_SCORE'

	nPatients	Mean (Std.Dev)
ALL	491	7.6 (1.0)
10P LOSS MUTATED	41	8.3 (1.0)
10P LOSS WILD-TYPE	450	7.5 (1.0)

Figure S220. Get High-res Image Gene #58: '10p loss' versus Clinical Feature #9: 'GLEASON_SCORE'

'10q loss' versus 'PATHOLOGY_T_STAGE'

P value = 0.00019 (Fisher's exact test), Q value = 0.0029

Table S221. Gene #59: '10q loss' versus Clinical Feature #3: 'PATHOLOGY_T_STAGE'

nPatients	T2	T3	T4
ALL	188	287	10
10Q LOSS MUTATED	9	29	5
10Q LOSS WILD-TYPE	179	258	5

Figure S221. Get High-res Image Gene #59: '10q loss' versus Clinical Feature #3: 'PATHOLOGY_T_STAGE'

'10q loss' versus 'PATHOLOGY_N_STAGE'

P value = 0.000384 (Fisher's exact test), Q value = 0.0048

Table S222. Gene #59: '10q loss' versus Clinical Feature #4: 'PATHOLOGY_N_STAGE'

nPatients	0	1
ALL	342	77
10Q LOSS MUTATED	24	17
10Q LOSS WILD-TYPE	318	60

Figure S222. Get High-res Image Gene #59: '10q loss' versus Clinical Feature #4: 'PATHOLOGY_N_STAGE'

'10q loss' versus 'RESIDUAL_TUMOR'

P value = 0.00611 (Fisher's exact test), Q value = 0.034

Table S223. Gene #59: '10q loss' versus Clinical Feature #7: 'RESIDUAL_TUMOR'

nPatients	R0	R1	R2	RX
ALL	312	143	5	15
10Q LOSS MUTATED	19	23	0	0
10Q LOSS WILD-TYPE	293	120	5	15

Figure S223. Get High-res Image Gene #59: '10q loss' versus Clinical Feature #7: 'RESIDUAL_TUMOR'

'10q loss' versus 'NUMBER_OF_LYMPH_NODES'

P value = 3.91e-05 (Wilcoxon-test), Q value = 0.00088

Table S224. Gene #59: '10q loss' versus Clinical Feature #8: 'NUMBER_OF_LYMPH_NODES'

	nPatients	Mean (Std.Dev)
ALL	401	0.4 (1.4)
10Q LOSS MUTATED	40	1.1 (1.9)
10Q LOSS WILD-TYPE	361	0.4 (1.3)

Figure S224. Get High-res Image Gene #59: '10q loss' versus Clinical Feature #8: 'NUMBER_OF_LYMPH_NODES'

'10q loss' versus 'GLEASON_SCORE'

P value = 3.5e-08 (Wilcoxon-test), Q value = 4.4e-06

Table S225. Gene #59: '10q loss' versus Clinical Feature #9: 'GLEASON_SCORE'

	nPatients	Mean (Std.Dev)
ALL	491	7.6 (1.0)
10Q LOSS MUTATED	43	8.4 (0.9)
10Q LOSS WILD-TYPE	448	7.5 (1.0)

Figure S225. Get High-res Image Gene #59: '10q loss' versus Clinical Feature #9: 'GLEASON_SCORE'

'11p loss' versus 'Time to Death'

P value = 0.00635 (logrank test), Q value = 0.035

Table S226. Gene #60: '11p loss' versus Clinical Feature #1: 'Time to Death'

	nPatients	nDeath	Duration Range (Median), Month
ALL	489	9	0.7 - 165.2 (28.8)
11P LOSS MUTATED	8	1	4.3 - 67.5 (26.5)
11P LOSS WILD-TYPE	481	8	0.7 - 165.2 (29.0)

Figure S226. Get High-res Image Gene #60: '11p loss' versus Clinical Feature #1: 'Time to Death'

'11p loss' versus 'PATHOLOGY_T_STAGE'

P value = 0.0753 (Fisher's exact test), Q value = 0.22

Table S227. Gene #60: '11p loss' versus Clinical Feature #3: 'PATHOLOGY_T_STAGE'

nPatients	T2	T3	T4
ALL	188	287	10
11P LOSS MUTATED	1	5	1
11P LOSS WILD-TYPE	187	282	9

Figure S227. Get High-res Image Gene #60: '11p loss' versus Clinical Feature #3: 'PATHOLOGY_T_STAGE'

'11p loss' versus 'GLEASON_SCORE'

P value = 0.0191 (Wilcoxon-test), Q value = 0.078

Table S228. Gene #60: '11p loss' versus Clinical Feature #9: 'GLEASON_SCORE'

	nPatients	Mean (Std.Dev)
ALL	491	7.6 (1.0)
11P LOSS MUTATED	8	8.5 (1.1)
11P LOSS WILD-TYPE	483	7.6 (1.0)

Figure S228. Get High-res Image Gene #60: '11p loss' versus Clinical Feature #9: 'GLEASON_SCORE'

'11q loss' versus 'PATHOLOGY_T_STAGE'

P value = 0.0273 (Fisher's exact test), Q value = 0.1

Table S229. Gene #61: '11q loss' versus Clinical Feature #3: 'PATHOLOGY_T_STAGE'

nPatients	T2	T3	T4
ALL	188	287	10
11Q LOSS MUTATED	0	4	1
11Q LOSS WILD-TYPE	188	283	9

Figure S229. Get High-res Image Gene #61: '11q loss' versus Clinical Feature #3: 'PATHOLOGY_T_STAGE'

'11q loss' versus 'GLEASON_SCORE'

P value = 0.0335 (Wilcoxon-test), Q value = 0.12

Table S230. Gene #61: '11q loss' versus Clinical Feature #9: 'GLEASON_SCORE'

	nPatients	Mean (Std.Dev)
ALL	491	7.6 (1.0)
11Q LOSS MUTATED	5	8.6 (0.9)
11Q LOSS WILD-TYPE	486	7.6 (1.0)

Figure S230. Get High-res Image Gene #61: '11q loss' versus Clinical Feature #9: 'GLEASON_SCORE'

'12p loss' versus 'PATHOLOGY_T_STAGE'

P value = 0.0049 (Fisher's exact test), Q value = 0.03

Table S231. Gene #62: '12p loss' versus Clinical Feature #3: 'PATHOLOGY_T_STAGE'

nPatients	T2	T3	T4
ALL	188	287	10
12P LOSS MUTATED	10	35	3
12P LOSS WILD-TYPE	178	252	7

Figure S231. Get High-res Image Gene #62: '12p loss' versus Clinical Feature #3: 'PATHOLOGY_T_STAGE'

'12p loss' versus 'PATHOLOGY_N_STAGE'

P value = 0.00109 (Fisher's exact test), Q value = 0.011

Table S232. Gene #62: '12p loss' versus Clinical Feature #4: 'PATHOLOGY_N_STAGE'

nPatients	0	1
ALL	342	77
12P LOSS MUTATED	30	18
12P LOSS WILD-TYPE	312	59

Figure S232. Get High-res Image Gene #62: '12p loss' versus Clinical Feature #4: 'PATHOLOGY_N_STAGE'

'12p loss' versus 'NUMBER_OF_LYMPH_NODES'

P value = 0.00051 (Wilcoxon-test), Q value = 0.0061

Table S233. Gene #62: '12p loss' versus Clinical Feature #8: 'NUMBER_OF_LYMPH_NODES'

	nPatients	Mean (Std.Dev)
ALL	401	0.4 (1.4)
12P LOSS MUTATED	46	0.7 (1.1)
12P LOSS WILD-TYPE	355	0.4 (1.4)

Figure S233. Get High-res Image Gene #62: '12p loss' versus Clinical Feature #8: 'NUMBER_OF_LYMPH_NODES'

'12p loss' versus 'GLEASON_SCORE'

P value = 0.000243 (Wilcoxon-test), Q value = 0.0035

Table S234. Gene #62: '12p loss' versus Clinical Feature #9: 'GLEASON_SCORE'

	nPatients	Mean (Std.Dev)
ALL	491	7.6 (1.0)
12P LOSS MUTATED	48	8.1 (1.0)
12P LOSS WILD-TYPE	443	7.6 (1.0)

Figure S234. Get High-res Image Gene #62: '12p loss' versus Clinical Feature #9: 'GLEASON_SCORE'

'12q loss' versus 'PATHOLOGY_N_STAGE'

P value = 0.0174 (Fisher's exact test), Q value = 0.074

Table S235. Gene #63: '12q loss' versus Clinical Feature #4: 'PATHOLOGY_N_STAGE'

nPatients	0	1
ALL	342	77
12Q LOSS MUTATED	12	8
12Q LOSS WILD-TYPE	330	69

Figure S235. Get High-res Image Gene #63: '12q loss' versus Clinical Feature #4: 'PATHOLOGY_N_STAGE'

'12q loss' versus 'NUMBER_OF_LYMPH_NODES'

P value = 0.0146 (Wilcoxon-test), Q value = 0.066

Table S236. Gene #63: '12q loss' versus Clinical Feature #8: 'NUMBER_OF_LYMPH_NODES'

	nPatients	Mean (Std.Dev)
ALL	401	0.4 (1.4)
12Q LOSS MUTATED	19	0.7 (1.3)
12Q LOSS WILD-TYPE	382	0.4 (1.4)

Figure S236. Get High-res Image Gene #63: '12q loss' versus Clinical Feature #8: 'NUMBER_OF_LYMPH_NODES'

'12q loss' versus 'GLEASON_SCORE'

P value = 0.00129 (Wilcoxon-test), Q value = 0.012

Table S237. Gene #63: '12q loss' versus Clinical Feature #9: 'GLEASON_SCORE'

	nPatients	Mean (Std.Dev)
ALL	491	7.6 (1.0)
12Q LOSS MUTATED	20	8.3 (1.0)
12Q LOSS WILD-TYPE	471	7.6 (1.0)

Figure S237. Get High-res Image Gene #63: '12q loss' versus Clinical Feature #9: 'GLEASON_SCORE'

'13q loss' versus 'YEARS_TO_BIRTH'

P value = 0.082 (Wilcoxon-test), Q value = 0.24

Table S238. Gene #64: '13q loss' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

	nPatients	Mean (Std.Dev)
ALL	480	61.0 (6.8)
13Q LOSS MUTATED	75	62.2 (6.8)
13Q LOSS WILD-TYPE	405	60.8 (6.8)

Figure S238. Get High-res Image Gene #64: '13q loss' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'13q loss' versus 'PATHOLOGY_T_STAGE'

P value = 8e-04 (Fisher's exact test), Q value = 0.0084

Table S239. Gene #64: '13q loss' versus Clinical Feature #3: 'PATHOLOGY_T_STAGE'

nPatients	T2	T3	T4
ALL	188	287	10
13Q LOSS MUTATED	16	57	3
13Q LOSS WILD-TYPE	172	230	7

Figure S239. Get High-res Image Gene #64: '13q loss' versus Clinical Feature #3: 'PATHOLOGY_T_STAGE'

'13q loss' versus 'PATHOLOGY_N_STAGE'

P value = 0.0112 (Fisher's exact test), Q value = 0.053

Table S240. Gene #64: '13q loss' versus Clinical Feature #4: 'PATHOLOGY_N_STAGE'

nPatients	0	1
ALL	342	77
13Q LOSS MUTATED	50	21
13Q LOSS WILD-TYPE	292	56

Figure S240. Get High-res Image Gene #64: '13q loss' versus Clinical Feature #4: 'PATHOLOGY_N_STAGE'

'13q loss' versus 'RESIDUAL_TUMOR'

P value = 0.0361 (Fisher's exact test), Q value = 0.12

Table S241. Gene #64: '13q loss' versus Clinical Feature #7: 'RESIDUAL_TUMOR'

nPatients	R0	R1	R2	RX
ALL	312	143	5	15
13Q LOSS MUTATED	39	32	0	3
13Q LOSS WILD-TYPE	273	111	5	12

Figure S241. Get High-res Image Gene #64: '13q loss' versus Clinical Feature #7: 'RESIDUAL_TUMOR'

'13q loss' versus 'NUMBER_OF_LYMPH_NODES'

P value = 0.00318 (Wilcoxon-test), Q value = 0.023

Table S242. Gene #64: '13q loss' versus Clinical Feature #8: 'NUMBER_OF_LYMPH_NODES'

	nPatients	Mean (Std.Dev)
ALL	401	0.4 (1.4)
13Q LOSS MUTATED	68	0.8 (1.7)
13Q LOSS WILD-TYPE	333	0.3 (1.3)

Figure S242. Get High-res Image Gene #64: '13q loss' versus Clinical Feature #8: 'NUMBER_OF_LYMPH_NODES'

'13q loss' versus 'GLEASON_SCORE'

P value = 3.23e-11 (Wilcoxon-test), Q value = 2.8e-08

Table S243. Gene #64: '13q loss' versus Clinical Feature #9: 'GLEASON_SCORE'

	nPatients	Mean (Std.Dev)
ALL	491	7.6 (1.0)
13Q LOSS MUTATED	77	8.3 (0.9)
13Q LOSS WILD-TYPE	414	7.5 (1.0)

Figure S243. Get High-res Image Gene #64: '13q loss' versus Clinical Feature #9: 'GLEASON_SCORE'

'14q loss' versus 'PATHOLOGY_T_STAGE'

P value = 0.00054 (Fisher's exact test), Q value = 0.0063

Table S244. Gene #65: '14q loss' versus Clinical Feature #3: 'PATHOLOGY_T_STAGE'

nPatients	T2	T3	T4
ALL	188	287	10
14Q LOSS MUTATED	2	21	2
14Q LOSS WILD-TYPE	186	266	8

Figure S244. Get High-res Image Gene #65: '14q loss' versus Clinical Feature #3: 'PATHOLOGY_T_STAGE'

'14q loss' versus 'PATHOLOGY_N_STAGE'

P value = 0.0299 (Fisher's exact test), Q value = 0.11

Table S245. Gene #65: '14q loss' versus Clinical Feature #4: 'PATHOLOGY_N_STAGE'

nPatients	0	1
ALL	342	77
14Q LOSS MUTATED	16	9
14Q LOSS WILD-TYPE	326	68

Figure S245. Get High-res Image Gene #65: '14q loss' versus Clinical Feature #4: 'PATHOLOGY_N_STAGE'

'14q loss' versus 'RESIDUAL_TUMOR'

P value = 0.0165 (Fisher's exact test), Q value = 0.072

Table S246. Gene #65: '14q loss' versus Clinical Feature #7: 'RESIDUAL_TUMOR'

nPatients	R0	R1	R2	RX
ALL	312	143	5	15
14Q LOSS MUTATED	9	14	0	1
14Q LOSS WILD-TYPE	303	129	5	14

Figure S246. Get High-res Image Gene #65: '14q loss' versus Clinical Feature #7: 'RESIDUAL_TUMOR'

'14q loss' versus 'NUMBER_OF_LYMPH_NODES'

P value = 0.0312 (Wilcoxon-test), Q value = 0.11

Table S247. Gene #65: '14q loss' versus Clinical Feature #8: 'NUMBER_OF_LYMPH_NODES'

	nPatients	Mean (Std.Dev)
ALL	401	0.4 (1.4)
14Q LOSS MUTATED	25	0.6 (1.0)
14Q LOSS WILD-TYPE	376	0.4 (1.4)

Figure S247. Get High-res Image Gene #65: '14q loss' versus Clinical Feature #8: 'NUMBER_OF_LYMPH_NODES'

'14q loss' versus 'GLEASON_SCORE'

P value = 0.000376 (Wilcoxon-test), Q value = 0.0048

Table S248. Gene #65: '14q loss' versus Clinical Feature #9: 'GLEASON_SCORE'

	nPatients	Mean (Std.Dev)
ALL	491	7.6 (1.0)
14Q LOSS MUTATED	25	8.3 (0.9)
14Q LOSS WILD-TYPE	466	7.6 (1.0)

Figure S248. Get High-res Image Gene #65: '14q loss' versus Clinical Feature #9: 'GLEASON_SCORE'

'15q loss' versus 'YEARS_TO_BIRTH'

P value = 0.0192 (Wilcoxon-test), Q value = 0.078

Table S249. Gene #66: '15q loss' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

	nPatients	Mean (Std.Dev)
ALL	480	61.0 (6.8)
15Q LOSS MUTATED	36	63.7 (6.3)
15Q LOSS WILD-TYPE	444	60.8 (6.8)

Figure S249. Get High-res Image Gene #66: '15q loss' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'15q loss' versus 'PATHOLOGY_T_STAGE'

P value = 1e-05 (Fisher's exact test), Q value = 0.00033

Table S250. Gene #66: '15q loss' versus Clinical Feature #3: 'PATHOLOGY_T_STAGE'

nPatients	T2	T3	T4
ALL	188	287	10
15Q LOSS MUTATED	2	31	3
15Q LOSS WILD-TYPE	186	256	7

Figure S250. Get High-res Image Gene #66: '15q loss' versus Clinical Feature #3: 'PATHOLOGY_T_STAGE'

'15q loss' versus 'PATHOLOGY_N_STAGE'

P value = 0.00352 (Fisher's exact test), Q value = 0.024

Table S251. Gene #66: '15q loss' versus Clinical Feature #4: 'PATHOLOGY_N_STAGE'

nPatients	0	1
ALL	342	77
15Q LOSS MUTATED	20	13
15Q LOSS WILD-TYPE	322	64

Figure S251. Get High-res Image Gene #66: '15q loss' versus Clinical Feature #4: 'PATHOLOGY_N_STAGE'

'15q loss' versus 'NUMBER_OF_LYMPH_NODES'

P value = 0.00132 (Wilcoxon-test), Q value = 0.012

Table S252. Gene #66: '15q loss' versus Clinical Feature #8: 'NUMBER_OF_LYMPH_NODES'

	nPatients	Mean (Std.Dev)
ALL	401	0.4 (1.4)
15Q LOSS MUTATED	33	0.9 (1.5)
15Q LOSS WILD-TYPE	368	0.4 (1.3)

Figure S252. Get High-res Image Gene #66: '15q loss' versus Clinical Feature #8: 'NUMBER_OF_LYMPH_NODES'

'15q loss' versus 'GLEASON_SCORE'

P value = 1.4e-05 (Wilcoxon-test), Q value = 0.00041

Table S253. Gene #66: '15q loss' versus Clinical Feature #9: 'GLEASON_SCORE'

	nPatients	Mean (Std.Dev)
ALL	491	7.6 (1.0)
15Q LOSS MUTATED	36	8.3 (1.0)
15Q LOSS WILD-TYPE	455	7.5 (1.0)

Figure S253. Get High-res Image Gene #66: '15q loss' versus Clinical Feature #9: 'GLEASON_SCORE'

'16p loss' versus 'GLEASON_SCORE'

P value = 0.0577 (Wilcoxon-test), Q value = 0.18

Table S254. Gene #67: '16p loss' versus Clinical Feature #9: 'GLEASON_SCORE'

	nPatients	Mean (Std.Dev)
ALL	491	7.6 (1.0)
16P LOSS MUTATED	32	8.0 (1.1)
16P LOSS WILD-TYPE	459	7.6 (1.0)

Figure S254. Get High-res Image Gene #67: '16p loss' versus Clinical Feature #9: 'GLEASON_SCORE'

'16q loss' versus 'PATHOLOGY_T_STAGE'

P value = 0.00246 (Fisher's exact test), Q value = 0.019

Table S255. Gene #68: '16q loss' versus Clinical Feature #3: 'PATHOLOGY_T_STAGE'

nPatients	T2	T3	T4
ALL	188	287	10
16Q LOSS MUTATED	26	76	3
16Q LOSS WILD-TYPE	162	211	7

Figure S255. Get High-res Image Gene #68: '16q loss' versus Clinical Feature #3: 'PATHOLOGY_T_STAGE'

'16q loss' versus 'PATHOLOGY_N_STAGE'

P value = 0.071 (Fisher's exact test), Q value = 0.21

Table S256. Gene #68: '16q loss' versus Clinical Feature #4: 'PATHOLOGY_N_STAGE'

nPatients	0	1
ALL	342	77
16Q LOSS MUTATED	72	24
16Q LOSS WILD-TYPE	270	53

Figure S256. Get High-res Image Gene #68: '16q loss' versus Clinical Feature #4: 'PATHOLOGY_N_STAGE'

'16q loss' versus 'RESIDUAL_TUMOR'

P value = 0.0177 (Fisher's exact test), Q value = 0.075

Table S257. Gene #68: '16q loss' versus Clinical Feature #7: 'RESIDUAL_TUMOR'

nPatients	R0	R1	R2	RX
ALL	312	143	5	15
16Q LOSS MUTATED	56	43	0	2
16Q LOSS WILD-TYPE	256	100	5	13

Figure S257. Get High-res Image Gene #68: '16q loss' versus Clinical Feature #7: 'RESIDUAL_TUMOR'

'16q loss' versus 'NUMBER_OF_LYMPH_NODES'

P value = 0.0406 (Wilcoxon-test), Q value = 0.14

Table S258. Gene #68: '16q loss' versus Clinical Feature #8: 'NUMBER_OF_LYMPH_NODES'

	nPatients	Mean (Std.Dev)
ALL	401	0.4 (1.4)
16Q LOSS MUTATED	91	0.6 (1.4)
16Q LOSS WILD-TYPE	310	0.4 (1.4)

Figure S258. Get High-res Image Gene #68: '16q loss' versus Clinical Feature #8: 'NUMBER_OF_LYMPH_NODES'

'16q loss' versus 'GLEASON_SCORE'

P value = 4.42e-06 (Wilcoxon-test), Q value = 0.00017

Table S259. Gene #68: '16q loss' versus Clinical Feature #9: 'GLEASON_SCORE'

	nPatients	Mean (Std.Dev)
ALL	491	7.6 (1.0)
16Q LOSS MUTATED	106	8.0 (1.0)
16Q LOSS WILD-TYPE	385	7.5 (1.0)

Figure S259. Get High-res Image Gene #68: '16q loss' versus Clinical Feature #9: 'GLEASON_SCORE'

'17p loss' versus 'PATHOLOGY_T_STAGE'

P value = 0.00106 (Fisher's exact test), Q value = 0.011

Table S260. Gene #69: '17p loss' versus Clinical Feature #3: 'PATHOLOGY_T_STAGE'

nPatients	T2	T3	T4
ALL	188	287	10
17P LOSS MUTATED	15	57	1
17P LOSS WILD-TYPE	173	230	9

Figure S260. Get High-res Image Gene #69: '17p loss' versus Clinical Feature #3: 'PATHOLOGY_T_STAGE'

'17p loss' versus 'PATHOLOGY_N_STAGE'

P value = 0.0104 (Fisher's exact test), Q value = 0.05

Table S261. Gene #69: '17p loss' versus Clinical Feature #4: 'PATHOLOGY_N_STAGE'

nPatients	0	1
ALL	342	77
17P LOSS MUTATED	49	21
17P LOSS WILD-TYPE	293	56

Figure S261. Get High-res Image Gene #69: '17p loss' versus Clinical Feature #4: 'PATHOLOGY_N_STAGE'

'17p loss' versus 'RESIDUAL_TUMOR'

P value = 0.0567 (Fisher's exact test), Q value = 0.18

Table S262. Gene #69: '17p loss' versus Clinical Feature #7: 'RESIDUAL_TUMOR'

nPatients	R0	R1	R2	RX
ALL	312	143	5	15
17P LOSS MUTATED	40	32	0	2
17P LOSS WILD-TYPE	272	111	5	13

Figure S262. Get High-res Image Gene #69: '17p loss' versus Clinical Feature #7: 'RESIDUAL_TUMOR'

'17p loss' versus 'NUMBER_OF_LYMPH_NODES'

P value = 0.00152 (Wilcoxon-test), Q value = 0.013

Table S263. Gene #69: '17p loss' versus Clinical Feature #8: 'NUMBER_OF_LYMPH_NODES'

	nPatients	Mean (Std.Dev)
ALL	401	0.4 (1.4)
17P LOSS MUTATED	66	0.9 (1.7)
17P LOSS WILD-TYPE	335	0.3 (1.3)

Figure S263. Get High-res Image Gene #69: '17p loss' versus Clinical Feature #8: 'NUMBER_OF_LYMPH_NODES'

'17p loss' versus 'GLEASON_SCORE'

P value = 4.98e-06 (Wilcoxon-test), Q value = 0.00018

Table S264. Gene #69: '17p loss' versus Clinical Feature #9: 'GLEASON_SCORE'

	nPatients	Mean (Std.Dev)
ALL	491	7.6 (1.0)
17P LOSS MUTATED	75	8.1 (1.0)
17P LOSS WILD-TYPE	416	7.5 (1.0)

Figure S264. Get High-res Image Gene #69: '17p loss' versus Clinical Feature #9: 'GLEASON_SCORE'

'17p loss' versus 'PSA_VALUE'

P value = 0.0413 (Wilcoxon-test), Q value = 0.14

Table S265. Gene #69: '17p loss' versus Clinical Feature #10: 'PSA_VALUE'

	nPatients	Mean (Std.Dev)
ALL	434	1.8 (16.0)
17P LOSS MUTATED	65	7.0 (40.3)
17P LOSS WILD-TYPE	369	0.9 (3.5)

Figure S265. Get High-res Image Gene #69: '17p loss' versus Clinical Feature #10: 'PSA_VALUE'

'17q loss' versus 'Time to Death'

P value = 0.0683 (logrank test), Q value = 0.21

Table S266. Gene #70: '17q loss' versus Clinical Feature #1: 'Time to Death'

	nPatients	nDeath	Duration Range (Median), Month
ALL	489	9	0.7 - 165.2 (28.8)
17Q LOSS MUTATED	20	2	1.7 - 115.1 (33.5)
17Q LOSS WILD-TYPE	469	7	0.7 - 165.2 (28.8)

Figure S266. Get High-res Image Gene #70: '17q loss' versus Clinical Feature #1: 'Time to Death'

'17q loss' versus 'PATHOLOGY_T_STAGE'

P value = 0.0199 (Fisher's exact test), Q value = 0.079

Table S267. Gene #70: '17q loss' versus Clinical Feature #3: 'PATHOLOGY_T_STAGE'

nPatients	T2	T3	T4
ALL	188	287	10
17Q LOSS MUTATED	2	17	0
17Q LOSS WILD-TYPE	186	270	10

Figure S267. Get High-res Image Gene #70: '17q loss' versus Clinical Feature #3: 'PATHOLOGY_T_STAGE'

'17q loss' versus 'RESIDUAL_TUMOR'

P value = 0.0338 (Fisher's exact test), Q value = 0.12

Table S268. Gene #70: '17q loss' versus Clinical Feature #7: 'RESIDUAL_TUMOR'

nPatients	R0	R1	R2	RX
ALL	312	143	5	15
17Q LOSS MUTATED	7	11	0	1
17Q LOSS WILD-TYPE	305	132	5	14

Figure S268. Get High-res Image Gene #70: '17q loss' versus Clinical Feature #7: 'RESIDUAL_TUMOR'

'17q loss' versus 'GLEASON_SCORE'

P value = 0.00318 (Wilcoxon-test), Q value = 0.023

Table S269. Gene #70: '17q loss' versus Clinical Feature #9: 'GLEASON_SCORE'

	nPatients	Mean (Std.Dev)
ALL	491	7.6 (1.0)
17Q LOSS MUTATED	20	8.3 (1.0)
17Q LOSS WILD-TYPE	471	7.6 (1.0)

Figure S269. Get High-res Image Gene #70: '17q loss' versus Clinical Feature #9: 'GLEASON_SCORE'

'18p loss' versus 'PATHOLOGY_T_STAGE'

P value = 0.00622 (Fisher's exact test), Q value = 0.035

Table S270. Gene #71: '18p loss' versus Clinical Feature #3: 'PATHOLOGY_T_STAGE'

nPatients	T2	T3	T4
ALL	188	287	10
18P LOSS MUTATED	17	46	4
18P LOSS WILD-TYPE	171	241	6

Figure S270. Get High-res Image Gene #71: '18p loss' versus Clinical Feature #3: 'PATHOLOGY_T_STAGE'

'18p loss' versus 'RADIATION_THERAPY'

P value = 0.0887 (Fisher's exact test), Q value = 0.25

Table S271. Gene #71: '18p loss' versus Clinical Feature #5: 'RADIATION_THERAPY'

nPatients	NO	YES
ALL	378	57
18P LOSS MUTATED	45	12
18P LOSS WILD-TYPE	333	45

Figure S271. Get High-res Image Gene #71: '18p loss' versus Clinical Feature #5: 'RADIATION_THERAPY'

'18p loss' versus 'RESIDUAL_TUMOR'

P value = 0.00493 (Fisher's exact test), Q value = 0.03

Table S272. Gene #71: '18p loss' versus Clinical Feature #7: 'RESIDUAL_TUMOR'

nPatients	R0	R1	R2	RX
ALL	312	143	5	15
18P LOSS MUTATED	33	31	0	0
18P LOSS WILD-TYPE	279	112	5	15

Figure S272. Get High-res Image Gene #71: '18p loss' versus Clinical Feature #7: 'RESIDUAL_TUMOR'

'18p loss' versus 'NUMBER_OF_LYMPH_NODES'

P value = 0.0857 (Wilcoxon-test), Q value = 0.24

Table S273. Gene #71: '18p loss' versus Clinical Feature #8: 'NUMBER_OF_LYMPH_NODES'

	nPatients	Mean (Std.Dev)
ALL	401	0.4 (1.4)
18P LOSS MUTATED	60	0.7 (1.5)
18P LOSS WILD-TYPE	341	0.4 (1.3)

Figure S273. Get High-res Image Gene #71: '18p loss' versus Clinical Feature #8: 'NUMBER_OF_LYMPH_NODES'

'18p loss' versus 'GLEASON_SCORE'

P value = 6.43e-07 (Wilcoxon-test), Q value = 4.3e-05

Table S274. Gene #71: '18p loss' versus Clinical Feature #9: 'GLEASON_SCORE'

	nPatients	Mean (Std.Dev)
ALL	491	7.6 (1.0)
18P LOSS MUTATED	67	8.2 (1.0)
18P LOSS WILD-TYPE	424	7.5 (1.0)

Figure S274. Get High-res Image Gene #71: '18p loss' versus Clinical Feature #9: 'GLEASON_SCORE'

'18q loss' versus 'PATHOLOGY_T_STAGE'

P value = 0.00111 (Fisher's exact test), Q value = 0.011

Table S275. Gene #72: '18q loss' versus Clinical Feature #3: 'PATHOLOGY_T_STAGE'

nPatients	T2	T3	T4
ALL	188	287	10
18Q LOSS MUTATED	24	71	4
18Q LOSS WILD-TYPE	164	216	6

Figure S275. Get High-res Image Gene #72: '18q loss' versus Clinical Feature #3: 'PATHOLOGY_T_STAGE'

'18q loss' versus 'PATHOLOGY_N_STAGE'

P value = 0.000371 (Fisher's exact test), Q value = 0.0048

Table S276. Gene #72: '18q loss' versus Clinical Feature #4: 'PATHOLOGY_N_STAGE'

nPatients	0	1
ALL	342	77
18Q LOSS MUTATED	62	29
18Q LOSS WILD-TYPE	280	48

Figure S276. Get High-res Image Gene #72: '18q loss' versus Clinical Feature #4: 'PATHOLOGY_N_STAGE'

'18q loss' versus 'RADIATION_THERAPY'

P value = 0.0206 (Fisher's exact test), Q value = 0.08

Table S277. Gene #72: '18q loss' versus Clinical Feature #5: 'RADIATION_THERAPY'

nPatients	NO	YES
ALL	378	57
18Q LOSS MUTATED	68	18
18Q LOSS WILD-TYPE	310	39

Figure S277. Get High-res Image Gene #72: '18q loss' versus Clinical Feature #5: 'RADIATION_THERAPY'

'18q loss' versus 'RESIDUAL_TUMOR'

P value = 5e-05 (Fisher's exact test), Q value = 0.001

Table S278. Gene #72: '18q loss' versus Clinical Feature #7: 'RESIDUAL_TUMOR'

nPatients	R0	R1	R2	RX
ALL	312	143	5	15
18Q LOSS MUTATED	47	49	0	2
18Q LOSS WILD-TYPE	265	94	5	13

Figure S278. Get High-res Image Gene #72: '18q loss' versus Clinical Feature #7: 'RESIDUAL_TUMOR'

'18q loss' versus 'NUMBER_OF_LYMPH_NODES'

P value = 0.000116 (Wilcoxon-test), Q value = 0.002

Table S279. Gene #72: '18q loss' versus Clinical Feature #8: 'NUMBER_OF_LYMPH_NODES'

	nPatients	Mean (Std.Dev)
ALL	401	0.4 (1.4)
18Q LOSS MUTATED	87	0.9 (2.3)
18Q LOSS WILD-TYPE	314	0.3 (0.9)

Figure S279. Get High-res Image Gene #72: '18q loss' versus Clinical Feature #8: 'NUMBER_OF_LYMPH_NODES'

'18q loss' versus 'GLEASON_SCORE'

P value = 1.74e-08 (Wilcoxon-test), Q value = 3.2e-06

Table S280. Gene #72: '18q loss' versus Clinical Feature #9: 'GLEASON_SCORE'

	nPatients	Mean (Std.Dev)
ALL	491	7.6 (1.0)
18Q LOSS MUTATED	100	8.1 (1.0)
18Q LOSS WILD-TYPE	391	7.5 (1.0)

Figure S280. Get High-res Image Gene #72: '18q loss' versus Clinical Feature #9: 'GLEASON_SCORE'

'19p loss' versus 'YEARS_TO_BIRTH'

P value = 0.0123 (Wilcoxon-test), Q value = 0.056

Table S281. Gene #73: '19p loss' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

	nPatients	Mean (Std.Dev)
ALL	480	61.0 (6.8)
19P LOSS MUTATED	17	64.7 (6.1)
19P LOSS WILD-TYPE	463	60.8 (6.8)

Figure S281. Get High-res Image Gene #73: '19p loss' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'19p loss' versus 'GLEASON_SCORE'

P value = 0.0382 (Wilcoxon-test), Q value = 0.13

Table S282. Gene #73: '19p loss' versus Clinical Feature #9: 'GLEASON_SCORE'

	nPatients	Mean (Std.Dev)
ALL	491	7.6 (1.0)
19P LOSS MUTATED	17	8.1 (1.0)
19P LOSS WILD-TYPE	474	7.6 (1.0)

Figure S282. Get High-res Image Gene #73: '19p loss' versus Clinical Feature #9: 'GLEASON_SCORE'

'19q loss' versus 'YEARS_TO_BIRTH'

P value = 0.0123 (Wilcoxon-test), Q value = 0.056

Table S283. Gene #74: '19q loss' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

	nPatients	Mean (Std.Dev)
ALL	480	61.0 (6.8)
19Q LOSS MUTATED	17	64.7 (6.1)
19Q LOSS WILD-TYPE	463	60.8 (6.8)

Figure S283. Get High-res Image Gene #74: '19q loss' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'19q loss' versus 'GLEASON_SCORE'

P value = 0.0382 (Wilcoxon-test), Q value = 0.13

Table S284. Gene #74: '19q loss' versus Clinical Feature #9: 'GLEASON_SCORE'

	nPatients	Mean (Std.Dev)
ALL	491	7.6 (1.0)
19Q LOSS MUTATED	17	8.1 (1.0)
19Q LOSS WILD-TYPE	474	7.6 (1.0)

Figure S284. Get High-res Image Gene #74: '19q loss' versus Clinical Feature #9: 'GLEASON_SCORE'

'20p loss' versus 'PATHOLOGY_T_STAGE'

P value = 0.0447 (Fisher's exact test), Q value = 0.15

Table S285. Gene #75: '20p loss' versus Clinical Feature #3: 'PATHOLOGY_T_STAGE'

nPatients	T2	T3	T4
ALL	188	287	10
20P LOSS MUTATED	3	15	1
20P LOSS WILD-TYPE	185	272	9

Figure S285. Get High-res Image Gene #75: '20p loss' versus Clinical Feature #3: 'PATHOLOGY_T_STAGE'

'20p loss' versus 'PATHOLOGY_N_STAGE'

P value = 0.022 (Fisher's exact test), Q value = 0.084

Table S286. Gene #75: '20p loss' versus Clinical Feature #4: 'PATHOLOGY_N_STAGE'

nPatients	0	1
ALL	342	77
20P LOSS MUTATED	10	7
20P LOSS WILD-TYPE	332	70

Figure S286. Get High-res Image Gene #75: '20p loss' versus Clinical Feature #4: 'PATHOLOGY_N_STAGE'

'20p loss' versus 'RADIATION_THERAPY'

P value = 0.0578 (Fisher's exact test), Q value = 0.18

Table S287. Gene #75: '20p loss' versus Clinical Feature #5: 'RADIATION_THERAPY'

nPatients	NO	YES
ALL	378	57
20P LOSS MUTATED	12	5
20P LOSS WILD-TYPE	366	52

Figure S287. Get High-res Image Gene #75: '20p loss' versus Clinical Feature #5: 'RADIATION_THERAPY'

'20p loss' versus 'NUMBER_OF_LYMPH_NODES'

P value = 0.00484 (Wilcoxon-test), Q value = 0.03

Table S288. Gene #75: '20p loss' versus Clinical Feature #8: 'NUMBER_OF_LYMPH_NODES'

	nPatients	Mean (Std.Dev)
ALL	401	0.4 (1.4)
20P LOSS MUTATED	16	1.4 (2.1)
20P LOSS WILD-TYPE	385	0.4 (1.3)

Figure S288. Get High-res Image Gene #75: '20p loss' versus Clinical Feature #8: 'NUMBER_OF_LYMPH_NODES'

'20q loss' versus 'PATHOLOGY_T_STAGE'

P value = 0.048 (Fisher's exact test), Q value = 0.15

Table S289. Gene #76: '20q loss' versus Clinical Feature #3: 'PATHOLOGY_T_STAGE'

nPatients	T2	T3	T4
ALL	188	287	10
20Q LOSS MUTATED	1	7	1
20Q LOSS WILD-TYPE	187	280	9

Figure S289. Get High-res Image Gene #76: '20q loss' versus Clinical Feature #3: 'PATHOLOGY_T_STAGE'

'21q loss' versus 'PATHOLOGY_T_STAGE'

P value = 0.00211 (Fisher's exact test), Q value = 0.017

Table S290. Gene #77: '21q loss' versus Clinical Feature #3: 'PATHOLOGY_T_STAGE'

nPatients	T2	T3	T4
ALL	188	287	10
21Q LOSS MUTATED	4	17	3
21Q LOSS WILD-TYPE	184	270	7

Figure S290. Get High-res Image Gene #77: '21q loss' versus Clinical Feature #3: 'PATHOLOGY_T_STAGE'

'21q loss' versus 'PATHOLOGY_N_STAGE'

P value = 0.00371 (Fisher's exact test), Q value = 0.025

Table S291. Gene #77: '21q loss' versus Clinical Feature #4: 'PATHOLOGY_N_STAGE'

nPatients	0	1
ALL	342	77
21Q LOSS MUTATED	13	10
21Q LOSS WILD-TYPE	329	67

Figure S291. Get High-res Image Gene #77: '21q loss' versus Clinical Feature #4: 'PATHOLOGY_N_STAGE'

'21q loss' versus 'NUMBER_OF_LYMPH_NODES'

P value = 0.00124 (Wilcoxon-test), Q value = 0.012

Table S292. Gene #77: '21q loss' versus Clinical Feature #8: 'NUMBER_OF_LYMPH_NODES'

	nPatients	Mean (Std.Dev)
ALL	401	0.4 (1.4)
21Q LOSS MUTATED	22	1.1 (2.4)
21Q LOSS WILD-TYPE	379	0.4 (1.3)

Figure S292. Get High-res Image Gene #77: '21q loss' versus Clinical Feature #8: 'NUMBER_OF_LYMPH_NODES'

'21q loss' versus 'GLEASON_SCORE'

P value = 0.000309 (Wilcoxon-test), Q value = 0.0042

Table S293. Gene #77: '21q loss' versus Clinical Feature #9: 'GLEASON_SCORE'

	nPatients	Mean (Std.Dev)
ALL	491	7.6 (1.0)
21Q LOSS MUTATED	24	8.3 (1.0)
21Q LOSS WILD-TYPE	467	7.6 (1.0)

Figure S293. Get High-res Image Gene #77: '21q loss' versus Clinical Feature #9: 'GLEASON_SCORE'

'22q loss' versus 'PATHOLOGY_T_STAGE'

P value = 3e-05 (Fisher's exact test), Q value = 0.00069

Table S294. Gene #78: '22q loss' versus Clinical Feature #3: 'PATHOLOGY_T_STAGE'

nPatients	T2	T3	T4
ALL	188	287	10
22Q LOSS MUTATED	5	39	2
22Q LOSS WILD-TYPE	183	248	8

Figure S294. Get High-res Image Gene #78: '22q loss' versus Clinical Feature #3: 'PATHOLOGY_T_STAGE'

'22q loss' versus 'PATHOLOGY_N_STAGE'

P value = 0.000733 (Fisher's exact test), Q value = 0.0078

Table S295. Gene #78: '22q loss' versus Clinical Feature #4: 'PATHOLOGY_N_STAGE'

nPatients	0	1
ALL	342	77
22Q LOSS MUTATED	27	17
22Q LOSS WILD-TYPE	315	60

Figure S295. Get High-res Image Gene #78: '22q loss' versus Clinical Feature #4: 'PATHOLOGY_N_STAGE'

'22q loss' versus 'RADIATION_THERAPY'

P value = 0.011 (Fisher's exact test), Q value = 0.052

Table S296. Gene #78: '22q loss' versus Clinical Feature #5: 'RADIATION_THERAPY'

nPatients	NO	YES
ALL	378	57
22Q LOSS MUTATED	29	11
22Q LOSS WILD-TYPE	349	46

Figure S296. Get High-res Image Gene #78: '22q loss' versus Clinical Feature #5: 'RADIATION_THERAPY'

'22q loss' versus 'RESIDUAL_TUMOR'

P value = 0.00893 (Fisher's exact test), Q value = 0.045

Table S297. Gene #78: '22q loss' versus Clinical Feature #7: 'RESIDUAL_TUMOR'

nPatients	R0	R1	R2	RX
ALL	312	143	5	15
22Q LOSS MUTATED	22	24	0	0
22Q LOSS WILD-TYPE	290	119	5	15

Figure S297. Get High-res Image Gene #78: '22q loss' versus Clinical Feature #7: 'RESIDUAL_TUMOR'

'22q loss' versus 'NUMBER_OF_LYMPH_NODES'

P value = 0.000482 (Wilcoxon-test), Q value = 0.0059

Table S298. Gene #78: '22q loss' versus Clinical Feature #8: 'NUMBER_OF_LYMPH_NODES'

	nPatients	Mean (Std.Dev)
ALL	401	0.4 (1.4)
22Q LOSS MUTATED	43	0.9 (2.4)
22Q LOSS WILD-TYPE	358	0.4 (1.2)

Figure S298. Get High-res Image Gene #78: '22q loss' versus Clinical Feature #8: 'NUMBER_OF_LYMPH_NODES'

'22q loss' versus 'GLEASON_SCORE'

P value = 3.31e-08 (Wilcoxon-test), Q value = 4.4e-06

Table S299. Gene #78: '22q loss' versus Clinical Feature #9: 'GLEASON_SCORE'

	nPatients	Mean (Std.Dev)
ALL	491	7.6 (1.0)
22Q LOSS MUTATED	47	8.4 (0.9)
22Q LOSS WILD-TYPE	444	7.5 (1.0)

Figure S299. Get High-res Image Gene #78: '22q loss' versus Clinical Feature #9: 'GLEASON_SCORE'

'22q loss' versus 'PSA_VALUE'

P value = 0.0752 (Wilcoxon-test), Q value = 0.22

Table S300. Gene #78: '22q loss' versus Clinical Feature #10: 'PSA_VALUE'

	nPatients	Mean (Std.Dev)
ALL	434	1.8 (16.0)
22Q LOSS MUTATED	41	10.5 (50.4)
22Q LOSS WILD-TYPE	393	0.9 (3.8)

Figure S300. Get High-res Image Gene #78: '22q loss' versus Clinical Feature #10: 'PSA_VALUE'

'xp loss' versus 'Time to Death'

P value = 0.0575 (logrank test), Q value = 0.18

Table S301. Gene #79: 'xp loss' versus Clinical Feature #1: 'Time to Death'

	nPatients	nDeath	Duration Range (Median), Month
ALL	489	9	0.7 - 165.2 (28.8)
XP LOSS MUTATED	38	2	1.0 - 113.3 (38.1)
XP LOSS WILD-TYPE	451	7	0.7 - 165.2 (28.7)

Figure S301. Get High-res Image Gene #79: 'xp loss' versus Clinical Feature #1: 'Time to Death'

'xp loss' versus 'YEARS_TO_BIRTH'

P value = 0.0733 (Wilcoxon-test), Q value = 0.22

Table S302. Gene #79: 'xp loss' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

	nPatients	Mean (Std.Dev)
ALL	480	61.0 (6.8)
XP LOSS MUTATED	38	62.8 (6.8)
XP LOSS WILD-TYPE	442	60.8 (6.8)

Figure S302. Get High-res Image Gene #79: 'xp loss' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'xp loss' versus 'PATHOLOGY_T_STAGE'

P value = 0.0112 (Fisher's exact test), Q value = 0.053

Table S303. Gene #79: 'xp loss' versus Clinical Feature #3: 'PATHOLOGY_T_STAGE'

nPatients	T2	T3	T4
ALL	188	287	10
XP LOSS MUTATED	7	28	2
XP LOSS WILD-TYPE	181	259	8

Figure S303. Get High-res Image Gene #79: 'xp loss' versus Clinical Feature #3: 'PATHOLOGY_T_STAGE'

'xp loss' versus 'PATHOLOGY_N_STAGE'

P value = 0.023 (Fisher's exact test), Q value = 0.087

Table S304. Gene #79: 'xp loss' versus Clinical Feature #4: 'PATHOLOGY_N_STAGE'

nPatients	0	1
ALL	342	77
XP LOSS MUTATED	24	12
XP LOSS WILD-TYPE	318	65

Figure S304. Get High-res Image Gene #79: 'xp loss' versus Clinical Feature #4: 'PATHOLOGY_N_STAGE'

'xp loss' versus 'RADIATION_THERAPY'

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

Table S305. Gene #79: 'xp loss' versus Clinical Feature #5: 'RADIATION_THERAPY'

nPatients	NO	YES
ALL	378	57
XP LOSS MUTATED	26	9
XP LOSS WILD-TYPE	352	48

Figure S305. Get High-res Image Gene #79: 'xp loss' versus Clinical Feature #5: 'RADIATION_THERAPY'

'xp loss' versus 'NUMBER_OF_LYMPH_NODES'

P value = 0.00782 (Wilcoxon-test), Q value = 0.04

Table S306. Gene #79: 'xp loss' versus Clinical Feature #8: 'NUMBER_OF_LYMPH_NODES'

	nPatients	Mean (Std.Dev)
ALL	401	0.4 (1.4)
XP LOSS MUTATED	35	0.9 (1.6)
XP LOSS WILD-TYPE	366	0.4 (1.3)

Figure S306. Get High-res Image Gene #79: 'xp loss' versus Clinical Feature #8: 'NUMBER_OF_LYMPH_NODES'

'xp loss' versus 'GLEASON_SCORE'

P value = 1.45e-06 (Wilcoxon-test), Q value = 8e-05

Table S307. Gene #79: 'xp loss' versus Clinical Feature #9: 'GLEASON_SCORE'

	nPatients	Mean (Std.Dev)
ALL	491	7.6 (1.0)
XP LOSS MUTATED	38	8.4 (0.9)
XP LOSS WILD-TYPE	453	7.5 (1.0)

Figure S307. Get High-res Image Gene #79: 'xp loss' versus Clinical Feature #9: 'GLEASON_SCORE'

'xp loss' versus 'PSA_VALUE'

P value = 0.0172 (Wilcoxon-test), Q value = 0.074

Table S308. Gene #79: 'xp loss' versus Clinical Feature #10: 'PSA_VALUE'

	nPatients	Mean (Std.Dev)
ALL	434	1.8 (16.0)
XP LOSS MUTATED	34	10.7 (55.2)
XP LOSS WILD-TYPE	400	1.0 (4.2)

Figure S308. Get High-res Image Gene #79: 'xp loss' versus Clinical Feature #10: 'PSA_VALUE'

'xq loss' versus 'Time to Death'

P value = 0.0575 (logrank test), Q value = 0.18

Table S309. Gene #80: 'xq loss' versus Clinical Feature #1: 'Time to Death'

	nPatients	nDeath	Duration Range (Median), Month
ALL	489	9	0.7 - 165.2 (28.8)
XQ LOSS MUTATED	38	2	1.0 - 113.3 (38.1)
XQ LOSS WILD-TYPE	451	7	0.7 - 165.2 (28.7)

Figure S309. Get High-res Image Gene #80: 'xq loss' versus Clinical Feature #1: 'Time to Death'

'xq loss' versus 'YEARS_TO_BIRTH'

P value = 0.0733 (Wilcoxon-test), Q value = 0.22

Table S310. Gene #80: 'xq loss' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

	nPatients	Mean (Std.Dev)
ALL	480	61.0 (6.8)
XQ LOSS MUTATED	38	62.8 (6.8)
XQ LOSS WILD-TYPE	442	60.8 (6.8)

Figure S310. Get High-res Image Gene #80: 'xq loss' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'xq loss' versus 'PATHOLOGY_T_STAGE'

P value = 0.0117 (Fisher's exact test), Q value = 0.055

Table S311. Gene #80: 'xq loss' versus Clinical Feature #3: 'PATHOLOGY_T_STAGE'

nPatients	T2	T3	T4
ALL	188	287	10
XQ LOSS MUTATED	7	28	2
XQ LOSS WILD-TYPE	181	259	8

Figure S311. Get High-res Image Gene #80: 'xq loss' versus Clinical Feature #3: 'PATHOLOGY_T_STAGE'

'xq loss' versus 'PATHOLOGY_N_STAGE'

P value = 0.023 (Fisher's exact test), Q value = 0.087

Table S312. Gene #80: 'xq loss' versus Clinical Feature #4: 'PATHOLOGY_N_STAGE'

nPatients	0	1
ALL	342	77
XQ LOSS MUTATED	24	12
XQ LOSS WILD-TYPE	318	65

Figure S312. Get High-res Image Gene #80: 'xq loss' versus Clinical Feature #4: 'PATHOLOGY_N_STAGE'

'xq loss' versus 'RADIATION_THERAPY'

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

Table S313. Gene #80: 'xq loss' versus Clinical Feature #5: 'RADIATION_THERAPY'

nPatients	NO	YES
ALL	378	57
XQ LOSS MUTATED	26	9
XQ LOSS WILD-TYPE	352	48

Figure S313. Get High-res Image Gene #80: 'xq loss' versus Clinical Feature #5: 'RADIATION_THERAPY'

'xq loss' versus 'NUMBER_OF_LYMPH_NODES'

P value = 0.00782 (Wilcoxon-test), Q value = 0.04

Table S314. Gene #80: 'xq loss' versus Clinical Feature #8: 'NUMBER_OF_LYMPH_NODES'

	nPatients	Mean (Std.Dev)
ALL	401	0.4 (1.4)
XQ LOSS MUTATED	35	0.9 (1.6)
XQ LOSS WILD-TYPE	366	0.4 (1.3)

Figure S314. Get High-res Image Gene #80: 'xq loss' versus Clinical Feature #8: 'NUMBER_OF_LYMPH_NODES'

'xq loss' versus 'GLEASON_SCORE'

P value = 1.45e-06 (Wilcoxon-test), Q value = 8e-05

Table S315. Gene #80: 'xq loss' versus Clinical Feature #9: 'GLEASON_SCORE'

	nPatients	Mean (Std.Dev)
ALL	491	7.6 (1.0)
XQ LOSS MUTATED	38	8.4 (0.9)
XQ LOSS WILD-TYPE	453	7.5 (1.0)

Figure S315. Get High-res Image Gene #80: 'xq loss' versus Clinical Feature #9: 'GLEASON_SCORE'

'xq loss' versus 'PSA_VALUE'

P value = 0.0172 (Wilcoxon-test), Q value = 0.074

Table S316. Gene #80: 'xq loss' versus Clinical Feature #10: 'PSA_VALUE'

	nPatients	Mean (Std.Dev)
ALL	434	1.8 (16.0)
XQ LOSS MUTATED	34	10.7 (55.2)
XQ LOSS WILD-TYPE	400	1.0 (4.2)

Figure S316. Get High-res Image Gene #80: 'xq loss' versus Clinical Feature #10: 'PSA_VALUE'

Methods & Data

Input

Copy number data file = broad_values_by_arm.txt from GISTIC pipeline
Processed Copy number data file = /xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_Correlate_Genomic_Events_Preprocess/PRAD-TP/19782427/transformed.cor.cli.txt
Clinical data file = /xchip/cga/gdac-prod/tcga-gdac/jobResults/Append_Data/PRAD-TP/19775467/PRAD-TP.merged_data.txt
Number of patients = 491
Number of significantly arm-level cnvs = 80
Number of selected clinical features = 11
Exclude regions that fewer than K tumors have mutations, K = 3

Survival analysis

For survival clinical features, the Kaplan-Meier survival curves of tumors with and without gene mutations were plotted and the statistical significance P values were estimated by logrank test (Bland and Altman 2004) using the 'survdiff' function in R

Fisher's exact test

For binary or multi-class clinical features (nominal or ordinal), two-tailed Fisher's exact tests (Fisher 1922) were used to estimate the P values using the 'fisher.test' function in R

Q value calculation

For multiple hypothesis correction, Q value is the False Discovery Rate (FDR) analogue of the P value (Benjamini and Hochberg 1995), defined as the minimum FDR at which the test may be called significant. We used the 'Benjamini and Hochberg' method of 'p.adjust' function in R to convert P values into Q values.

Download Results

In addition to the links below, the full results of the analysis summarized in this report can also be downloaded programmatically using firehose_get, or interactively from either the Broad GDAC website or TCGA Data Coordination Center Portal.

References

[1] Bland and Altman, Statistics notes: The logrank test, BMJ 328(7447):1073 (2004)

[2] Fisher, R.A., On the interpretation of chi-square from contingency tables, and the calculation of P, Journal of the Royal Statistical Society 85(1):87-94 (1922)

[3] Benjamini and Hochberg, Controlling the false discovery rate: a practical and powerful approach to multiple testing, Journal of the Royal Statistical Society Series B 59:289-300 (1995)

Made with Nozzle