Correlation between copy number variations of arm-level result and selected clinical features
Prostate Adenocarcinoma (Primary solid tumor)
28 January 2016  |  analyses__2016_01_28
Maintainer Information
Citation Information
Maintained by TCGA GDAC Team (Broad Institute/MD Anderson Cancer Center/Harvard Medical School)
Cite as Broad Institute TCGA Genome Data Analysis Center (2016): Correlation between copy number variations of arm-level result and selected clinical features. Broad Institute of MIT and Harvard. doi:10.7908/C10Z72R2
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 492 patients, 321 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 'GLEASON_SCORE' and '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'.

  • 4q gain cnv correlated to 'PATHOLOGY_N_STAGE'.

  • 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',  'RESIDUAL_TUMOR', and 'GLEASON_SCORE'.

  • 8p gain cnv correlated to 'YEARS_TO_BIRTH',  'PATHOLOGY_T_STAGE',  'RESIDUAL_TUMOR',  'GLEASON_SCORE', and 'PSA_VALUE'.

  • 8q gain cnv correlated to 'YEARS_TO_BIRTH',  '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 'NUMBER_OF_LYMPH_NODES' and 'GLEASON_SCORE'.

  • 10q gain cnv correlated to 'NUMBER_OF_LYMPH_NODES' and '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',  'GLEASON_SCORE', and 'PSA_VALUE'.

  • 16q gain cnv correlated to 'YEARS_TO_BIRTH'.

  • 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',  'NUMBER_OF_LYMPH_NODES', and 'GLEASON_SCORE'.

  • 18q gain cnv correlated to 'Time to Death' and 'PATHOLOGY_T_STAGE'.

  • 19p gain cnv correlated to 'PATHOLOGY_T_STAGE',  'PATHOLOGY_N_STAGE',  'RESIDUAL_TUMOR',  'NUMBER_OF_LYMPH_NODES', and 'GLEASON_SCORE'.

  • 19q gain cnv correlated to 'PATHOLOGY_T_STAGE',  'PATHOLOGY_N_STAGE',  'RESIDUAL_TUMOR',  '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',  'RESIDUAL_TUMOR',  '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' and 'PATHOLOGY_T_STAGE'.

  • 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 'PATHOLOGY_T_STAGE',  'PATHOLOGY_N_STAGE',  'RADIATION_THERAPY',  'RESIDUAL_TUMOR',  'NUMBER_OF_LYMPH_NODES', and 'GLEASON_SCORE'.

  • 4q loss cnv correlated to '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',  'RESIDUAL_TUMOR',  '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 'PATHOLOGY_N_STAGE',  'NUMBER_OF_LYMPH_NODES', and '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'.

  • 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',  '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 'GLEASON_SCORE'.

  • 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, 321 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%) 454 0.0422
(0.139)
0.0852
(0.238)
0.00413
(0.0256)
0.0111
(0.0522)
0.0336
(0.117)
0.295
(0.551)
0.159
(0.376)
0.000414
(0.00485)
3.01e-07
(2.21e-05)
0.0221
(0.0832)
0.388
(0.661)
xq loss 38 (8%) 454 0.0422
(0.139)
0.0852
(0.238)
0.0041
(0.0256)
0.0111
(0.0522)
0.0336
(0.117)
0.295
(0.551)
0.156
(0.37)
0.000414
(0.00485)
3.01e-07
(2.21e-05)
0.0221
(0.0832)
0.391
(0.665)
3q gain 54 (11%) 438 0.0932
(0.254)
0.00347
(0.0226)
2e-05
(0.000476)
0.0203
(0.0794)
0.102
(0.272)
0.191
(0.426)
0.0102
(0.0498)
0.00104
(0.00915)
2.53e-09
(1.11e-06)
0.0426
(0.14)
0.636
(0.889)
5p gain 23 (5%) 469 0.403
(0.678)
0.00182
(0.0141)
0.00015
(0.0024)
0.00242
(0.0175)
0.0274
(0.1)
0.493
(0.765)
0.018
(0.0741)
5.9e-05
(0.00112)
1.92e-06
(8.46e-05)
0.359
(0.625)
12p gain 15 (3%) 477 0.552
(0.814)
0.00652
(0.0344)
0.00171
(0.0133)
0.0499
(0.156)
0.0772
(0.218)
1
(1.00)
0.0029
(0.0199)
0.00846
(0.0428)
3.13e-06
(0.00011)
0.509
(0.781)
12q gain 18 (4%) 474 0.55
(0.814)
0.0399
(0.134)
0.00392
(0.0247)
0.039
(0.132)
0.0111
(0.0522)
1
(1.00)
9e-05
(0.00155)
0.00502
(0.0292)
1.9e-06
(8.46e-05)
0.856
(1.00)
20q gain 29 (6%) 463 0.463
(0.739)
0.00341
(0.0225)
0.00023
(0.00326)
0.0665
(0.2)
0.0765
(0.218)
1
(1.00)
0.0434
(0.142)
0.0132
(0.0574)
0.000329
(0.0042)
0.21
(0.449)
1
(1.00)
22q loss 47 (10%) 445 0.227
(0.468)
0.481
(0.757)
2e-05
(0.000476)
0.000716
(0.00692)
0.0128
(0.0571)
0.634
(0.888)
0.0101
(0.0494)
0.000565
(0.00578)
3.76e-08
(4.36e-06)
0.0709
(0.208)
0.492
(0.765)
3p gain 40 (8%) 452 0.263
(0.504)
0.00152
(0.0123)
0.00156
(0.0125)
0.0484
(0.154)
0.177
(0.404)
0.0967
(0.261)
0.039
(0.132)
0.00316
(0.0212)
2.34e-08
(3.8e-06)
0.363
(0.629)
0.525
(0.794)
5q gain 12 (2%) 480 0.674
(0.918)
0.000167
(0.00258)
0.00871
(0.0435)
0.00675
(0.0351)
1
(1.00)
1
(1.00)
0.0221
(0.0832)
0.000307
(0.00404)
0.00198
(0.0151)
0.182
(0.411)
9p gain 34 (7%) 458 0.827
(1.00)
0.00442
(0.0272)
9e-05
(0.00155)
0.000466
(0.00537)
0.177
(0.404)
0.251
(0.492)
0.0131
(0.0574)
8.33e-05
(0.0015)
1.04e-06
(5.73e-05)
0.543
(0.81)
0.347
(0.617)
9q gain 48 (10%) 444 0.977
(1.00)
0.0124
(0.0552)
1e-05
(0.000293)
1.46e-05
(0.00039)
0.171
(0.395)
0.148
(0.354)
0.0109
(0.0522)
5.43e-07
(3.67e-05)
2.59e-08
(3.8e-06)
0.948
(1.00)
0.46
(0.739)
11p gain 27 (5%) 465 0.552
(0.814)
0.0288
(0.104)
0.00163
(0.0128)
0.00293
(0.02)
0.133
(0.328)
1
(1.00)
0.00861
(0.0433)
0.00107
(0.00931)
1.4e-05
(0.000386)
0.324
(0.592)
0.259
(0.5)
11q gain 30 (6%) 462 0.514
(0.785)
0.033
(0.117)
0.00274
(0.0191)
0.00232
(0.0172)
0.25
(0.491)
1
(1.00)
0.0122
(0.055)
0.000622
(0.0063)
2.11e-06
(8.83e-05)
0.665
(0.913)
0.262
(0.503)
4p loss 23 (5%) 469 0.55
(0.814)
0.117
(0.303)
0.0497
(0.156)
0.000159
(0.0025)
0.0442
(0.144)
0.493
(0.765)
0.0188
(0.0768)
1.13e-05
(0.00032)
1.51e-06
(7.83e-05)
0.849
(1.00)
1
(1.00)
6q loss 41 (8%) 451 0.0475
(0.152)
0.381
(0.653)
0.00159
(0.0126)
0.00746
(0.0384)
0.0209
(0.0809)
0.619
(0.87)
0.121
(0.306)
0.00086
(0.00814)
9.51e-09
(2.79e-06)
0.483
(0.757)
0.125
(0.313)
8q loss 21 (4%) 471 0.000979
(0.0087)
0.845
(1.00)
0.00112
(0.00957)
0.00446
(0.0272)
0.0585
(0.179)
1
(1.00)
0.436
(0.717)
0.000221
(0.00326)
0.0419
(0.139)
0.333
(0.604)
1
(1.00)
13q loss 78 (16%) 414 0.705
(0.931)
0.0673
(0.202)
0.00067
(0.0067)
0.0121
(0.0546)
0.569
(0.834)
0.708
(0.931)
0.0262
(0.0968)
0.0048
(0.0287)
1.65e-11
(1.45e-08)
0.143
(0.347)
0.437
(0.718)
17p loss 76 (15%) 416 0.86
(1.00)
0.347
(0.617)
0.00093
(0.00835)
0.011
(0.0522)
0.179
(0.408)
0.706
(0.931)
0.0404
(0.135)
0.000816
(0.0078)
2.91e-06
(0.000109)
0.0418
(0.139)
0.703
(0.931)
18q loss 100 (20%) 392 0.726
(0.943)
0.303
(0.562)
0.0013
(0.0109)
0.000362
(0.00455)
0.0368
(0.126)
1
(1.00)
3e-05
(0.00066)
4.61e-05
(0.000954)
2.12e-08
(3.8e-06)
0.274
(0.522)
0.747
(0.956)
8p gain 68 (14%) 424 0.706
(0.931)
0.00624
(0.0335)
0.00811
(0.0413)
0.731
(0.946)
0.318
(0.584)
0.235
(0.476)
0.0113
(0.0527)
0.856
(1.00)
2.45e-07
(2.16e-05)
0.0883
(0.246)
0.658
(0.906)
8q gain 126 (26%) 366 0.694
(0.931)
0.0701
(0.208)
0.00024
(0.00335)
0.205
(0.444)
0.202
(0.444)
0.535
(0.803)
0.00092
(0.00835)
0.134
(0.329)
4.66e-08
(4.55e-06)
0.0764
(0.218)
0.739
(0.954)
16p gain 32 (7%) 460 0.24
(0.48)
0.202
(0.444)
0.00071
(0.00692)
0.00232
(0.0172)
0.25
(0.491)
1
(1.00)
0.191
(0.426)
0.00141
(0.0115)
2.98e-06
(0.000109)
0.0717
(0.209)
1
(1.00)
17p gain 8 (2%) 484 0.745
(0.956)
0.359
(0.625)
0.0168
(0.0712)
0.00652
(0.0344)
0.0745
(0.215)
1
(1.00)
0.796
(0.992)
0.00128
(0.0109)
0.0553
(0.171)
0.976
(1.00)
18p gain 19 (4%) 473 0.22
(0.461)
0.00995
(0.0492)
0.00236
(0.0173)
0.00535
(0.0306)
1
(1.00)
1
(1.00)
0.594
(0.849)
0.00558
(0.0313)
0.0765
(0.218)
0.455
(0.735)
1
(1.00)
19p gain 12 (2%) 480 0.644
(0.896)
0.261
(0.502)
0.00053
(0.00555)
0.0115
(0.0531)
0.663
(0.912)
1
(1.00)
0.0613
(0.187)
0.000926
(0.00835)
0.000226
(0.00326)
0.933
(1.00)
19q gain 12 (2%) 480 0.622
(0.873)
0.205
(0.444)
0.00052
(0.00553)
0.0115
(0.0531)
1
(1.00)
1
(1.00)
0.0622
(0.188)
0.000926
(0.00835)
0.000226
(0.00326)
0.955
(1.00)
1
(1.00)
20p gain 26 (5%) 466 0.319
(0.584)
0.0474
(0.152)
0.00624
(0.0335)
0.0495
(0.156)
0.111
(0.288)
1
(1.00)
0.259
(0.5)
0.0116
(0.0533)
0.000516
(0.00553)
0.203
(0.444)
21q gain 21 (4%) 471 0.382
(0.653)
0.00541
(0.0307)
0.0158
(0.0674)
0.0362
(0.125)
1
(1.00)
0.462
(0.739)
0.0932
(0.254)
0.00448
(0.0272)
5.71e-05
(0.00112)
0.707
(0.931)
1
(1.00)
4q loss 16 (3%) 476 0.653
(0.904)
0.248
(0.49)
0.108
(0.284)
0.015
(0.065)
0.0111
(0.0522)
0.374
(0.645)
0.0361
(0.125)
0.000556
(0.00576)
5.89e-06
(0.000199)
0.593
(0.848)
5q loss 23 (5%) 469 0.585
(0.843)
0.706
(0.931)
3e-05
(0.00066)
0.00051
(0.00553)
0.00925
(0.046)
1
(1.00)
0.139
(0.341)
6.25e-05
(0.00115)
1.92e-06
(8.46e-05)
0.986
(1.00)
1
(1.00)
6p loss 26 (5%) 466 0.272
(0.519)
0.762
(0.964)
0.00201
(0.0151)
0.00364
(0.0233)
0.226
(0.468)
1
(1.00)
0.0897
(0.249)
0.00254
(0.0181)
9.2e-06
(0.000289)
0.164
(0.387)
0.307
(0.568)
10p loss 41 (8%) 451 0.741
(0.955)
0.132
(0.326)
2e-05
(0.000476)
0.000292
(0.00389)
0.223
(0.465)
1
(1.00)
0.0175
(0.0725)
2.63e-05
(0.000609)
2.96e-06
(0.000109)
0.396
(0.67)
1
(1.00)
10q loss 43 (9%) 449 0.784
(0.983)
0.277
(0.524)
0.0002
(0.00303)
0.000381
(0.00472)
0.244
(0.483)
1
(1.00)
0.00633
(0.0338)
4.66e-05
(0.000954)
3.96e-08
(4.36e-06)
0.56
(0.822)
0.583
(0.843)
14q loss 25 (5%) 467 0.354
(0.625)
0.101
(0.271)
0.00051
(0.00553)
0.0296
(0.106)
1
(1.00)
0.523
(0.793)
0.0175
(0.0725)
0.0336
(0.117)
0.0004
(0.00482)
0.128
(0.319)
1
(1.00)
15q loss 35 (7%) 457 0.849
(1.00)
0.0174
(0.0725)
1e-05
(0.000293)
0.00298
(0.0202)
0.177
(0.404)
1
(1.00)
0.143
(0.346)
0.000925
(0.00835)
7.26e-06
(0.000237)
0.239
(0.48)
1
(1.00)
16q loss 107 (22%) 385 0.356
(0.625)
0.223
(0.465)
0.00068
(0.00672)
0.0727
(0.211)
0.499
(0.772)
1
(1.00)
0.0153
(0.066)
0.0278
(0.102)
9.76e-07
(5.73e-05)
0.319
(0.584)
1
(1.00)
6p gain 10 (2%) 482 0.0397
(0.134)
0.331
(0.603)
0.18
(0.408)
0.0216
(0.0832)
0.102
(0.271)
1
(1.00)
0.217
(0.458)
0.0162
(0.0687)
0.031
(0.11)
0.333
(0.604)
6q gain 6 (1%) 486 0.72
(0.941)
0.0716
(0.209)
0.484
(0.757)
0.0781
(0.219)
0.131
(0.323)
1
(1.00)
0.236
(0.476)
0.046
(0.148)
0.0909
(0.249)
0.769
(0.967)
7p gain 101 (21%) 391 0.116
(0.3)
0.012
(0.0542)
0.0382
(0.13)
0.438
(0.718)
0.483
(0.757)
0.745
(0.956)
0.00201
(0.0151)
0.233
(0.476)
3.88e-05
(0.000832)
0.697
(0.931)
0.724
(0.943)
14q gain 10 (2%) 482 0.391
(0.665)
0.0293
(0.105)
0.797
(0.992)
0.217
(0.458)
0.00277
(0.0192)
0.253
(0.492)
0.0452
(0.146)
0.213
(0.455)
0.00366
(0.0233)
0.432
(0.716)
17q gain 11 (2%) 481 0.719
(0.941)
0.219
(0.461)
0.00451
(0.0272)
0.00675
(0.0351)
0.165
(0.387)
1
(1.00)
0.843
(1.00)
0.00258
(0.0183)
0.0706
(0.208)
0.538
(0.805)
5p loss 12 (2%) 480 0.727
(0.943)
0.839
(1.00)
0.00047
(0.00537)
0.123
(0.31)
0.00498
(0.0292)
1
(1.00)
0.0619
(0.188)
0.149
(0.355)
5.56e-05
(0.00111)
0.206
(0.444)
1
(1.00)
9p loss 21 (4%) 471 0.41
(0.687)
0.348
(0.617)
0.0204
(0.0794)
0.0696
(0.207)
0.49
(0.765)
1
(1.00)
0.919
(1.00)
0.0217
(0.0832)
0.00595
(0.0327)
0.528
(0.798)
1
(1.00)
12p loss 47 (10%) 445 0.36
(0.627)
0.582
(0.842)
0.00565
(0.0315)
0.000521
(0.00553)
0.482
(0.757)
0.381
(0.653)
0.254
(0.493)
0.000399
(0.00482)
0.000505
(0.00553)
0.145
(0.35)
1
(1.00)
17q loss 20 (4%) 472 0.0771
(0.218)
0.548
(0.813)
0.0199
(0.0793)
0.364
(0.629)
0.727
(0.943)
1
(1.00)
0.0346
(0.12)
0.337
(0.606)
0.00332
(0.0221)
0.581
(0.842)
1
(1.00)
18p loss 67 (14%) 425 0.928
(1.00)
0.224
(0.465)
0.00611
(0.0332)
0.11
(0.288)
0.101
(0.271)
0.42
(0.699)
0.00787
(0.0403)
0.0456
(0.147)
7.39e-07
(4.65e-05)
0.756
(0.961)
0.698
(0.931)
20p loss 19 (4%) 473 0.227
(0.468)
0.806
(1.00)
0.0523
(0.163)
0.0218
(0.0832)
0.073
(0.211)
1
(1.00)
0.909
(1.00)
0.00523
(0.0301)
0.376
(0.646)
0.875
(1.00)
0.349
(0.618)
21q loss 24 (5%) 468 0.586
(0.843)
0.737
(0.953)
0.0024
(0.0175)
0.00364
(0.0233)
0.525
(0.794)
0.508
(0.781)
0.341
(0.612)
0.00138
(0.0114)
0.000329
(0.0042)
0.207
(0.445)
1
(1.00)
1p gain 15 (3%) 477 0.634
(0.888)
0.17
(0.395)
0.00025
(0.00344)
0.299
(0.558)
0.0259
(0.0963)
1
(1.00)
0.202
(0.444)
0.454
(0.735)
0.000261
(0.00353)
0.498
(0.772)
1
(1.00)
1q gain 26 (5%) 466 0.51
(0.781)
0.202
(0.444)
6e-05
(0.00112)
0.104
(0.274)
0.0334
(0.117)
0.537
(0.805)
0.127
(0.315)
0.102
(0.271)
9.82e-05
(0.00166)
0.646
(0.898)
1
(1.00)
7q gain 94 (19%) 398 0.131
(0.323)
0.0202
(0.0793)
0.0936
(0.254)
0.874
(1.00)
0.472
(0.753)
1
(1.00)
0.00112
(0.00957)
0.992
(1.00)
0.000118
(0.00196)
0.873
(1.00)
0.708
(0.931)
xp gain 7 (1%) 485 0.763
(0.964)
0.204
(0.444)
0.0195
(0.0786)
0.119
(0.303)
0.573
(0.834)
1
(1.00)
0.00602
(0.0329)
0.182
(0.411)
0.00501
(0.0292)
0.795
(0.992)
xq gain 7 (1%) 485 0.763
(0.964)
0.204
(0.444)
0.0192
(0.0782)
0.119
(0.303)
0.573
(0.834)
1
(1.00)
0.00557
(0.0313)
0.182
(0.411)
0.00501
(0.0292)
0.795
(0.992)
1p loss 22 (4%) 470 0.533
(0.803)
0.542
(0.81)
0.0246
(0.0921)
0.244
(0.483)
0.0442
(0.144)
1
(1.00)
0.435
(0.717)
0.173
(0.399)
1.91e-05
(0.000476)
0.283
(0.534)
1
(1.00)
1q loss 6 (1%) 486 0.751
(0.958)
0.67
(0.917)
0.196
(0.436)
0.228
(0.471)
0.507
(0.78)
1
(1.00)
0.0553
(0.171)
0.0768
(0.218)
0.0909
(0.249)
0.363
(0.629)
2q loss 18 (4%) 474 0.604
(0.859)
0.0197
(0.0789)
0.0194
(0.0786)
0.749
(0.957)
0.707
(0.931)
1
(1.00)
0.118
(0.303)
0.519
(0.789)
0.0202
(0.0793)
0.673
(0.918)
9q loss 11 (2%) 481 0.682
(0.925)
1
(1.00)
0.126
(0.315)
0.0909
(0.249)
1
(1.00)
1
(1.00)
0.685
(0.927)
0.071
(0.208)
0.013
(0.0573)
0.343
(0.613)
1
(1.00)
11p loss 8 (2%) 484 0.00506
(0.0293)
0.308
(0.568)
0.0749
(0.215)
1
(1.00)
1
(1.00)
1
(1.00)
0.145
(0.35)
0.721
(0.941)
0.0196
(0.0786)
0.995
(1.00)
12q loss 20 (4%) 472 0.546
(0.811)
0.936
(1.00)
0.122
(0.308)
0.0171
(0.0721)
1
(1.00)
1
(1.00)
0.237
(0.476)
0.0158
(0.0674)
0.00135
(0.0112)
0.462
(0.739)
1
(1.00)
2p gain 11 (2%) 481 0.694
(0.931)
0.615
(0.869)
1
(1.00)
1
(1.00)
1
(1.00)
1
(1.00)
0.216
(0.458)
0.488
(0.763)
0.0578
(0.178)
0.0498
(0.156)
10p gain 15 (3%) 477 0.45
(0.733)
0.17
(0.395)
0.303
(0.562)
0.149
(0.355)
0.705
(0.931)
0.356
(0.625)
0.153
(0.364)
0.0288
(0.104)
0.00263
(0.0185)
0.459
(0.738)
1
(1.00)
10q gain 14 (3%) 478 0.442
(0.723)
0.724
(0.943)
0.455
(0.735)
0.269
(0.515)
0.233
(0.476)
0.336
(0.606)
0.171
(0.395)
0.0677
(0.202)
0.0259
(0.0963)
0.231
(0.474)
1
(1.00)
18q gain 10 (2%) 482 0.0657
(0.198)
0.112
(0.289)
0.0283
(0.103)
0.4
(0.676)
1
(1.00)
1
(1.00)
0.686
(0.927)
0.515
(0.785)
0.243
(0.483)
0.589
(0.845)
1
(1.00)
2p loss 14 (3%) 478 0.535
(0.803)
0.00694
(0.0359)
0.0132
(0.0574)
1
(1.00)
1
(1.00)
1
(1.00)
0.199
(0.443)
0.763
(0.964)
0.166
(0.387)
0.241
(0.481)
8p loss 171 (35%) 321 0.405
(0.679)
0.475
(0.756)
0.00012
(0.00196)
0.146
(0.352)
0.771
(0.967)
1
(1.00)
0.455
(0.735)
0.0528
(0.164)
0.653
(0.904)
0.256
(0.496)
0.161
(0.381)
11q loss 5 (1%) 487 0.898
(1.00)
0.337
(0.606)
0.0274
(0.1)
0.333
(0.604)
1
(1.00)
1
(1.00)
0.103
(0.274)
0.0341
(0.119)
0.697
(0.931)
19p loss 19 (4%) 473 0.575
(0.836)
0.0103
(0.0498)
0.215
(0.457)
1
(1.00)
0.718
(0.941)
1
(1.00)
0.425
(0.706)
0.746
(0.956)
0.01
(0.0493)
0.944
(1.00)
1
(1.00)
19q loss 18 (4%) 474 0.585
(0.843)
0.0174
(0.0725)
0.118
(0.303)
1
(1.00)
0.478
(0.757)
1
(1.00)
0.369
(0.636)
0.832
(1.00)
0.0202
(0.0793)
0.77
(0.967)
1
(1.00)
2q gain 7 (1%) 485 0.795
(0.992)
0.414
(0.692)
0.747
(0.956)
1
(1.00)
0.507
(0.78)
1
(1.00)
0.237
(0.476)
0.827
(1.00)
0.281
(0.531)
0.00569
(0.0315)
4q gain 10 (2%) 482 0.67
(0.917)
0.204
(0.444)
0.183
(0.411)
0.0909
(0.249)
0.336
(0.606)
0.253
(0.492)
0.544
(0.81)
0.121
(0.306)
0.582
(0.842)
0.234
(0.476)
16q gain 7 (1%) 485 0.838
(1.00)
0.0118
(0.0537)
0.356
(0.625)
1
(1.00)
0.573
(0.834)
1
(1.00)
1
(1.00)
0.955
(1.00)
0.18
(0.409)
0.614
(0.869)
1
(1.00)
22q gain 4 (1%) 488 0.799
(0.993)
0.433
(0.716)
0.676
(0.919)
0.557
(0.819)
0.432
(0.716)
1
(1.00)
0.658
(0.906)
0.616
(0.869)
0.0221
(0.0832)
0.237
(0.476)
3p loss 9 (2%) 483 0.656
(0.906)
0.769
(0.967)
0.251
(0.492)
0.166
(0.387)
0.284
(0.534)
1
(1.00)
0.217
(0.458)
0.142
(0.346)
0.00342
(0.0225)
0.122
(0.307)
3q loss 5 (1%) 487 0.693
(0.931)
0.29
(0.545)
0.688
(0.929)
0.59
(0.845)
0.507
(0.78)
1
(1.00)
0.343
(0.613)
0.274
(0.522)
0.00393
(0.0247)
0.207
(0.445)
20q loss 8 (2%) 484 0.76
(0.964)
0.358
(0.625)
0.286
(0.538)
0.617
(0.869)
0.231
(0.474)
1
(1.00)
0.607
(0.862)
0.517
(0.788)
0.0605
(0.185)
0.601
(0.858)
1
(1.00)
4p gain 9 (2%) 483 0.675
(0.918)
0.105
(0.277)
0.252
(0.492)
0.672
(0.918)
1
(1.00)
1
(1.00)
0.642
(0.896)
0.395
(0.67)
0.435
(0.717)
0.418
(0.698)
1
(1.00)
13q gain 8 (2%) 484 0.48
(0.757)
0.458
(0.738)
0.21
(0.449)
0.617
(0.869)
0.605
(0.859)
0.208
(0.445)
0.483
(0.757)
0.649
(0.901)
0.705
(0.931)
0.234
(0.476)
15q gain 6 (1%) 486 0.755
(0.961)
0.925
(1.00)
1
(1.00)
0.303
(0.562)
0.573
(0.834)
1
(1.00)
1
(1.00)
0.401
(0.676)
0.11
(0.288)
0.355
(0.625)
16p loss 31 (6%) 461 0.477
(0.757)
0.878
(1.00)
0.718
(0.941)
0.443
(0.723)
1
(1.00)
1
(1.00)
0.444
(0.724)
0.312
(0.574)
0.0961
(0.26)
0.869
(1.00)
1
(1.00)
'1p gain' versus 'PATHOLOGY_T_STAGE'

P value = 0.00025 (Fisher's exact test), Q value = 0.0034

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

nPatients T2 T3 T4
ALL 187 288 10
1P GAIN MUTATED 0 13 2
1P GAIN WILD-TYPE 187 275 8

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

'1p gain' versus 'RADIATION_THERAPY'

P value = 0.0259 (Fisher's exact test), Q value = 0.096

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

nPatients NO YES
ALL 390 59
1P GAIN MUTATED 9 5
1P GAIN WILD-TYPE 381 54

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

'1p gain' versus 'GLEASON_SCORE'

P value = 0.000261 (Wilcoxon-test), Q value = 0.0035

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

nPatients Mean (Std.Dev)
ALL 492 7.6 (1.0)
1P GAIN MUTATED 15 8.6 (0.9)
1P GAIN WILD-TYPE 477 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 = 6e-05 (Fisher's exact test), Q value = 0.0011

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

nPatients T2 T3 T4
ALL 187 288 10
1Q GAIN MUTATED 2 21 3
1Q GAIN WILD-TYPE 185 267 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 = 0.0334 (Fisher's exact test), Q value = 0.12

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

nPatients NO YES
ALL 390 59
1Q GAIN MUTATED 18 7
1Q GAIN WILD-TYPE 372 52

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

'1q gain' versus 'GLEASON_SCORE'

P value = 9.82e-05 (Wilcoxon-test), Q value = 0.0017

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

nPatients Mean (Std.Dev)
ALL 492 7.6 (1.0)
1Q GAIN MUTATED 26 8.4 (0.9)
1Q GAIN WILD-TYPE 466 7.6 (1.0)

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

'2p gain' versus 'GLEASON_SCORE'

P value = 0.0578 (Wilcoxon-test), Q value = 0.18

Table S7.  Gene #3: '2p gain' versus Clinical Feature #9: 'GLEASON_SCORE'

nPatients Mean (Std.Dev)
ALL 492 7.6 (1.0)
2P GAIN MUTATED 11 8.2 (1.1)
2P GAIN WILD-TYPE 481 7.6 (1.0)

Figure S7.  Get High-res Image Gene #3: '2p gain' versus Clinical Feature #9: 'GLEASON_SCORE'

'2p gain' versus 'PSA_VALUE'

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

Table S8.  Gene #3: '2p gain' versus Clinical Feature #10: 'PSA_VALUE'

nPatients Mean (Std.Dev)
ALL 435 1.8 (15.9)
2P GAIN MUTATED 8 1.8 (2.5)
2P GAIN WILD-TYPE 427 1.8 (16.1)

Figure S8.  Get High-res Image Gene #3: '2p gain' versus Clinical Feature #10: 'PSA_VALUE'

'2q gain' versus 'PSA_VALUE'

P value = 0.00569 (Wilcoxon-test), Q value = 0.032

Table S9.  Gene #4: '2q gain' versus Clinical Feature #10: 'PSA_VALUE'

nPatients Mean (Std.Dev)
ALL 435 1.8 (15.9)
2Q GAIN MUTATED 5 2.6 (3.0)
2Q GAIN WILD-TYPE 430 1.7 (16.0)

Figure S9.  Get High-res Image Gene #4: '2q gain' versus Clinical Feature #10: 'PSA_VALUE'

'3p gain' versus 'YEARS_TO_BIRTH'

P value = 0.00152 (Wilcoxon-test), Q value = 0.012

Table S10.  Gene #5: '3p gain' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 481 61.0 (6.8)
3P GAIN MUTATED 38 64.4 (5.5)
3P GAIN WILD-TYPE 443 60.7 (6.8)

Figure S10.  Get High-res Image Gene #5: '3p gain' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'3p gain' versus 'PATHOLOGY_T_STAGE'

P value = 0.00156 (Fisher's exact test), Q value = 0.012

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

nPatients T2 T3 T4
ALL 187 288 10
3P GAIN MUTATED 7 30 3
3P GAIN WILD-TYPE 180 258 7

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

'3p gain' versus 'PATHOLOGY_N_STAGE'

P value = 0.0484 (Fisher's exact test), Q value = 0.15

Table S12.  Gene #5: '3p gain' versus Clinical Feature #4: 'PATHOLOGY_N_STAGE'

nPatients 0 1
ALL 343 77
3P GAIN MUTATED 27 12
3P GAIN WILD-TYPE 316 65

Figure S12.  Get High-res Image Gene #5: '3p gain' versus Clinical Feature #4: 'PATHOLOGY_N_STAGE'

'3p gain' versus 'RESIDUAL_TUMOR'

P value = 0.039 (Fisher's exact test), Q value = 0.13

Table S13.  Gene #5: '3p gain' versus Clinical Feature #7: 'RESIDUAL_TUMOR'

nPatients R0 R1 R2 RX
ALL 313 144 5 15
3P GAIN MUTATED 18 18 1 1
3P GAIN WILD-TYPE 295 126 4 14

Figure S13.  Get High-res Image Gene #5: '3p gain' versus Clinical Feature #7: 'RESIDUAL_TUMOR'

'3p gain' versus 'NUMBER_OF_LYMPH_NODES'

P value = 0.00316 (Wilcoxon-test), Q value = 0.021

Table S14.  Gene #5: '3p gain' versus Clinical Feature #8: 'NUMBER_OF_LYMPH_NODES'

nPatients Mean (Std.Dev)
ALL 402 0.4 (1.4)
3P GAIN MUTATED 35 1.1 (2.0)
3P GAIN WILD-TYPE 367 0.4 (1.3)

Figure S14.  Get High-res Image Gene #5: '3p gain' versus Clinical Feature #8: 'NUMBER_OF_LYMPH_NODES'

'3p gain' versus 'GLEASON_SCORE'

P value = 2.34e-08 (Wilcoxon-test), Q value = 3.8e-06

Table S15.  Gene #5: '3p gain' versus Clinical Feature #9: 'GLEASON_SCORE'

nPatients Mean (Std.Dev)
ALL 492 7.6 (1.0)
3P GAIN MUTATED 40 8.5 (0.9)
3P GAIN WILD-TYPE 452 7.5 (1.0)

Figure S15.  Get High-res Image Gene #5: '3p gain' versus Clinical Feature #9: 'GLEASON_SCORE'

'3q gain' versus 'YEARS_TO_BIRTH'

P value = 0.00347 (Wilcoxon-test), Q value = 0.023

Table S16.  Gene #6: '3q gain' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 481 61.0 (6.8)
3Q GAIN MUTATED 52 63.6 (5.9)
3Q GAIN WILD-TYPE 429 60.7 (6.8)

Figure S16.  Get High-res Image Gene #6: '3q gain' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'3q gain' versus 'PATHOLOGY_T_STAGE'

P value = 2e-05 (Fisher's exact test), Q value = 0.00048

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

nPatients T2 T3 T4
ALL 187 288 10
3Q GAIN MUTATED 7 43 4
3Q GAIN WILD-TYPE 180 245 6

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

'3q gain' versus 'PATHOLOGY_N_STAGE'

P value = 0.0203 (Fisher's exact test), Q value = 0.079

Table S18.  Gene #6: '3q gain' versus Clinical Feature #4: 'PATHOLOGY_N_STAGE'

nPatients 0 1
ALL 343 77
3Q GAIN MUTATED 36 16
3Q GAIN WILD-TYPE 307 61

Figure S18.  Get High-res Image Gene #6: '3q gain' versus Clinical Feature #4: 'PATHOLOGY_N_STAGE'

'3q gain' versus 'RESIDUAL_TUMOR'

P value = 0.0102 (Fisher's exact test), Q value = 0.05

Table S19.  Gene #6: '3q gain' versus Clinical Feature #7: 'RESIDUAL_TUMOR'

nPatients R0 R1 R2 RX
ALL 313 144 5 15
3Q GAIN MUTATED 24 25 1 2
3Q GAIN WILD-TYPE 289 119 4 13

Figure S19.  Get High-res Image Gene #6: '3q gain' versus Clinical Feature #7: 'RESIDUAL_TUMOR'

'3q gain' versus 'NUMBER_OF_LYMPH_NODES'

P value = 0.00104 (Wilcoxon-test), Q value = 0.0091

Table S20.  Gene #6: '3q gain' versus Clinical Feature #8: 'NUMBER_OF_LYMPH_NODES'

nPatients Mean (Std.Dev)
ALL 402 0.4 (1.4)
3Q GAIN MUTATED 47 1.0 (2.0)
3Q GAIN WILD-TYPE 355 0.4 (1.2)

Figure S20.  Get High-res Image Gene #6: '3q gain' versus Clinical Feature #8: 'NUMBER_OF_LYMPH_NODES'

'3q gain' versus 'GLEASON_SCORE'

P value = 2.53e-09 (Wilcoxon-test), Q value = 1.1e-06

Table S21.  Gene #6: '3q gain' versus Clinical Feature #9: 'GLEASON_SCORE'

nPatients Mean (Std.Dev)
ALL 492 7.6 (1.0)
3Q GAIN MUTATED 54 8.4 (0.9)
3Q GAIN WILD-TYPE 438 7.5 (1.0)

Figure S21.  Get High-res Image Gene #6: '3q gain' versus Clinical Feature #9: 'GLEASON_SCORE'

'3q gain' versus 'PSA_VALUE'

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

Table S22.  Gene #6: '3q gain' versus Clinical Feature #10: 'PSA_VALUE'

nPatients Mean (Std.Dev)
ALL 435 1.8 (15.9)
3Q GAIN MUTATED 45 2.3 (7.6)
3Q GAIN WILD-TYPE 390 1.7 (16.7)

Figure S22.  Get High-res Image Gene #6: '3q gain' versus Clinical Feature #10: 'PSA_VALUE'

'4q gain' versus 'PATHOLOGY_N_STAGE'

P value = 0.0909 (Fisher's exact test), Q value = 0.25

Table S23.  Gene #8: '4q gain' versus Clinical Feature #4: 'PATHOLOGY_N_STAGE'

nPatients 0 1
ALL 343 77
4Q GAIN MUTATED 6 4
4Q GAIN WILD-TYPE 337 73

Figure S23.  Get High-res Image Gene #8: '4q gain' versus Clinical Feature #4: 'PATHOLOGY_N_STAGE'

'5p gain' versus 'YEARS_TO_BIRTH'

P value = 0.00182 (Wilcoxon-test), Q value = 0.014

Table S24.  Gene #9: '5p gain' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 481 61.0 (6.8)
5P GAIN MUTATED 23 65.3 (5.5)
5P GAIN WILD-TYPE 458 60.8 (6.8)

Figure S24.  Get High-res Image Gene #9: '5p gain' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'5p gain' versus 'PATHOLOGY_T_STAGE'

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

Table S25.  Gene #9: '5p gain' versus Clinical Feature #3: 'PATHOLOGY_T_STAGE'

nPatients T2 T3 T4
ALL 187 288 10
5P GAIN MUTATED 1 20 2
5P GAIN WILD-TYPE 186 268 8

Figure S25.  Get High-res Image Gene #9: '5p gain' versus Clinical Feature #3: 'PATHOLOGY_T_STAGE'

'5p gain' versus 'PATHOLOGY_N_STAGE'

P value = 0.00242 (Fisher's exact test), Q value = 0.017

Table S26.  Gene #9: '5p gain' versus Clinical Feature #4: 'PATHOLOGY_N_STAGE'

nPatients 0 1
ALL 343 77
5P GAIN MUTATED 12 10
5P GAIN WILD-TYPE 331 67

Figure S26.  Get High-res Image Gene #9: '5p gain' versus Clinical Feature #4: 'PATHOLOGY_N_STAGE'

'5p gain' versus 'RADIATION_THERAPY'

P value = 0.0274 (Fisher's exact test), Q value = 0.1

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

nPatients NO YES
ALL 390 59
5P GAIN MUTATED 13 6
5P GAIN WILD-TYPE 377 53

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

'5p gain' versus 'RESIDUAL_TUMOR'

P value = 0.018 (Fisher's exact test), Q value = 0.074

Table S28.  Gene #9: '5p gain' versus Clinical Feature #7: 'RESIDUAL_TUMOR'

nPatients R0 R1 R2 RX
ALL 313 144 5 15
5P GAIN MUTATED 9 12 1 1
5P GAIN WILD-TYPE 304 132 4 14

Figure S28.  Get High-res Image Gene #9: '5p gain' versus Clinical Feature #7: 'RESIDUAL_TUMOR'

'5p gain' versus 'NUMBER_OF_LYMPH_NODES'

P value = 5.9e-05 (Wilcoxon-test), Q value = 0.0011

Table S29.  Gene #9: '5p gain' versus Clinical Feature #8: 'NUMBER_OF_LYMPH_NODES'

nPatients Mean (Std.Dev)
ALL 402 0.4 (1.4)
5P GAIN MUTATED 19 1.7 (2.6)
5P GAIN WILD-TYPE 383 0.4 (1.2)

Figure S29.  Get High-res Image Gene #9: '5p gain' versus Clinical Feature #8: 'NUMBER_OF_LYMPH_NODES'

'5p gain' versus 'GLEASON_SCORE'

P value = 1.92e-06 (Wilcoxon-test), Q value = 8.5e-05

Table S30.  Gene #9: '5p gain' versus Clinical Feature #9: 'GLEASON_SCORE'

nPatients Mean (Std.Dev)
ALL 492 7.6 (1.0)
5P GAIN MUTATED 23 8.6 (0.8)
5P GAIN WILD-TYPE 469 7.6 (1.0)

Figure S30.  Get High-res Image Gene #9: '5p gain' versus Clinical Feature #9: 'GLEASON_SCORE'

'5q gain' versus 'YEARS_TO_BIRTH'

P value = 0.000167 (Wilcoxon-test), Q value = 0.0026

Table S31.  Gene #10: '5q gain' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 481 61.0 (6.8)
5Q GAIN MUTATED 12 68.1 (3.8)
5Q GAIN WILD-TYPE 469 60.8 (6.8)

Figure S31.  Get High-res Image Gene #10: '5q gain' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'5q gain' versus 'PATHOLOGY_T_STAGE'

P value = 0.00871 (Fisher's exact test), Q value = 0.044

Table S32.  Gene #10: '5q gain' versus Clinical Feature #3: 'PATHOLOGY_T_STAGE'

nPatients T2 T3 T4
ALL 187 288 10
5Q GAIN MUTATED 0 12 0
5Q GAIN WILD-TYPE 187 276 10

Figure S32.  Get High-res Image Gene #10: '5q gain' versus Clinical Feature #3: 'PATHOLOGY_T_STAGE'

'5q gain' versus 'PATHOLOGY_N_STAGE'

P value = 0.00675 (Fisher's exact test), Q value = 0.035

Table S33.  Gene #10: '5q gain' versus Clinical Feature #4: 'PATHOLOGY_N_STAGE'

nPatients 0 1
ALL 343 77
5Q GAIN MUTATED 5 6
5Q GAIN WILD-TYPE 338 71

Figure S33.  Get High-res Image Gene #10: '5q gain' versus Clinical Feature #4: 'PATHOLOGY_N_STAGE'

'5q gain' versus 'RESIDUAL_TUMOR'

P value = 0.0221 (Fisher's exact test), Q value = 0.083

Table S34.  Gene #10: '5q gain' versus Clinical Feature #7: 'RESIDUAL_TUMOR'

nPatients R0 R1 R2 RX
ALL 313 144 5 15
5Q GAIN MUTATED 4 6 1 1
5Q GAIN WILD-TYPE 309 138 4 14

Figure S34.  Get High-res Image Gene #10: '5q gain' versus Clinical Feature #7: 'RESIDUAL_TUMOR'

'5q gain' versus 'NUMBER_OF_LYMPH_NODES'

P value = 0.000307 (Wilcoxon-test), Q value = 0.004

Table S35.  Gene #10: '5q gain' versus Clinical Feature #8: 'NUMBER_OF_LYMPH_NODES'

nPatients Mean (Std.Dev)
ALL 402 0.4 (1.4)
5Q GAIN MUTATED 10 2.3 (3.0)
5Q GAIN WILD-TYPE 392 0.4 (1.3)

Figure S35.  Get High-res Image Gene #10: '5q gain' versus Clinical Feature #8: 'NUMBER_OF_LYMPH_NODES'

'5q gain' versus 'GLEASON_SCORE'

P value = 0.00198 (Wilcoxon-test), Q value = 0.015

Table S36.  Gene #10: '5q gain' versus Clinical Feature #9: 'GLEASON_SCORE'

nPatients Mean (Std.Dev)
ALL 492 7.6 (1.0)
5Q GAIN MUTATED 12 8.5 (0.8)
5Q GAIN WILD-TYPE 480 7.6 (1.0)

Figure S36.  Get High-res Image Gene #10: '5q gain' versus Clinical Feature #9: 'GLEASON_SCORE'

'6p gain' versus 'Time to Death'

P value = 0.0397 (logrank test), Q value = 0.13

Table S37.  Gene #11: '6p gain' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 492 9 0.8 - 165.2 (30.6)
6P GAIN MUTATED 10 1 4.3 - 109.2 (37.4)
6P GAIN WILD-TYPE 482 8 0.8 - 165.2 (30.5)

Figure S37.  Get High-res Image Gene #11: '6p gain' versus Clinical Feature #1: 'Time to Death'

'6p gain' versus 'PATHOLOGY_N_STAGE'

P value = 0.0216 (Fisher's exact test), Q value = 0.083

Table S38.  Gene #11: '6p gain' versus Clinical Feature #4: 'PATHOLOGY_N_STAGE'

nPatients 0 1
ALL 343 77
6P GAIN MUTATED 5 5
6P GAIN WILD-TYPE 338 72

Figure S38.  Get High-res Image Gene #11: '6p gain' versus Clinical Feature #4: 'PATHOLOGY_N_STAGE'

'6p gain' versus 'NUMBER_OF_LYMPH_NODES'

P value = 0.0162 (Wilcoxon-test), Q value = 0.069

Table S39.  Gene #11: '6p gain' versus Clinical Feature #8: 'NUMBER_OF_LYMPH_NODES'

nPatients Mean (Std.Dev)
ALL 402 0.4 (1.4)
6P GAIN MUTATED 10 0.8 (1.0)
6P GAIN WILD-TYPE 392 0.4 (1.4)

Figure S39.  Get High-res Image Gene #11: '6p gain' versus Clinical Feature #8: 'NUMBER_OF_LYMPH_NODES'

'6p gain' versus 'GLEASON_SCORE'

P value = 0.031 (Wilcoxon-test), Q value = 0.11

Table S40.  Gene #11: '6p gain' versus Clinical Feature #9: 'GLEASON_SCORE'

nPatients Mean (Std.Dev)
ALL 492 7.6 (1.0)
6P GAIN MUTATED 10 8.3 (0.9)
6P GAIN WILD-TYPE 482 7.6 (1.0)

Figure S40.  Get High-res Image Gene #11: '6p gain' versus Clinical Feature #9: 'GLEASON_SCORE'

'6q gain' versus 'YEARS_TO_BIRTH'

P value = 0.0716 (Wilcoxon-test), Q value = 0.21

Table S41.  Gene #12: '6q gain' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 481 61.0 (6.8)
6Q GAIN MUTATED 5 66.6 (5.0)
6Q GAIN WILD-TYPE 476 60.9 (6.8)

Figure S41.  Get High-res Image Gene #12: '6q gain' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'6q gain' versus 'PATHOLOGY_N_STAGE'

P value = 0.0781 (Fisher's exact test), Q value = 0.22

Table S42.  Gene #12: '6q gain' versus Clinical Feature #4: 'PATHOLOGY_N_STAGE'

nPatients 0 1
ALL 343 77
6Q GAIN MUTATED 3 3
6Q GAIN WILD-TYPE 340 74

Figure S42.  Get High-res Image Gene #12: '6q gain' versus Clinical Feature #4: 'PATHOLOGY_N_STAGE'

'6q gain' versus 'NUMBER_OF_LYMPH_NODES'

P value = 0.046 (Wilcoxon-test), Q value = 0.15

Table S43.  Gene #12: '6q gain' versus Clinical Feature #8: 'NUMBER_OF_LYMPH_NODES'

nPatients Mean (Std.Dev)
ALL 402 0.4 (1.4)
6Q GAIN MUTATED 6 1.0 (1.3)
6Q GAIN WILD-TYPE 396 0.4 (1.4)

Figure S43.  Get High-res Image Gene #12: '6q gain' versus Clinical Feature #8: 'NUMBER_OF_LYMPH_NODES'

'6q gain' versus 'GLEASON_SCORE'

P value = 0.0909 (Wilcoxon-test), Q value = 0.25

Table S44.  Gene #12: '6q gain' versus Clinical Feature #9: 'GLEASON_SCORE'

nPatients Mean (Std.Dev)
ALL 492 7.6 (1.0)
6Q GAIN MUTATED 6 8.3 (1.0)
6Q GAIN WILD-TYPE 486 7.6 (1.0)

Figure S44.  Get High-res Image Gene #12: '6q gain' versus Clinical Feature #9: 'GLEASON_SCORE'

'7p gain' versus 'YEARS_TO_BIRTH'

P value = 0.012 (Wilcoxon-test), Q value = 0.054

Table S45.  Gene #13: '7p gain' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 481 61.0 (6.8)
7P GAIN MUTATED 99 62.3 (6.6)
7P GAIN WILD-TYPE 382 60.6 (6.8)

Figure S45.  Get High-res Image Gene #13: '7p gain' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'7p gain' versus 'PATHOLOGY_T_STAGE'

P value = 0.0382 (Fisher's exact test), Q value = 0.13

Table S46.  Gene #13: '7p gain' versus Clinical Feature #3: 'PATHOLOGY_T_STAGE'

nPatients T2 T3 T4
ALL 187 288 10
7P GAIN MUTATED 29 71 1
7P GAIN WILD-TYPE 158 217 9

Figure S46.  Get High-res Image Gene #13: '7p gain' versus Clinical Feature #3: 'PATHOLOGY_T_STAGE'

'7p gain' versus 'RESIDUAL_TUMOR'

P value = 0.00201 (Fisher's exact test), Q value = 0.015

Table S47.  Gene #13: '7p gain' versus Clinical Feature #7: 'RESIDUAL_TUMOR'

nPatients R0 R1 R2 RX
ALL 313 144 5 15
7P GAIN MUTATED 49 44 1 4
7P GAIN WILD-TYPE 264 100 4 11

Figure S47.  Get High-res Image Gene #13: '7p gain' versus Clinical Feature #7: 'RESIDUAL_TUMOR'

'7p gain' versus 'GLEASON_SCORE'

P value = 3.88e-05 (Wilcoxon-test), Q value = 0.00083

Table S48.  Gene #13: '7p gain' versus Clinical Feature #9: 'GLEASON_SCORE'

nPatients Mean (Std.Dev)
ALL 492 7.6 (1.0)
7P GAIN MUTATED 101 8.0 (1.1)
7P GAIN WILD-TYPE 391 7.5 (1.0)

Figure S48.  Get High-res Image Gene #13: '7p gain' versus Clinical Feature #9: 'GLEASON_SCORE'

'7q gain' versus 'YEARS_TO_BIRTH'

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

Table S49.  Gene #14: '7q gain' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 481 61.0 (6.8)
7Q GAIN MUTATED 92 62.3 (6.8)
7Q GAIN WILD-TYPE 389 60.7 (6.8)

Figure S49.  Get High-res Image Gene #14: '7q gain' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'7q gain' versus 'RESIDUAL_TUMOR'

P value = 0.00112 (Fisher's exact test), Q value = 0.0096

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

nPatients R0 R1 R2 RX
ALL 313 144 5 15
7Q GAIN MUTATED 44 42 1 4
7Q GAIN WILD-TYPE 269 102 4 11

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

'7q gain' versus 'GLEASON_SCORE'

P value = 0.000118 (Wilcoxon-test), Q value = 0.002

Table S51.  Gene #14: '7q gain' versus Clinical Feature #9: 'GLEASON_SCORE'

nPatients Mean (Std.Dev)
ALL 492 7.6 (1.0)
7Q GAIN MUTATED 94 8.0 (1.1)
7Q GAIN WILD-TYPE 398 7.5 (1.0)

Figure S51.  Get High-res Image Gene #14: '7q gain' versus Clinical Feature #9: 'GLEASON_SCORE'

'8p gain' versus 'YEARS_TO_BIRTH'

P value = 0.00624 (Wilcoxon-test), Q value = 0.034

Table S52.  Gene #15: '8p gain' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 481 61.0 (6.8)
8P GAIN MUTATED 68 62.9 (6.3)
8P GAIN WILD-TYPE 413 60.7 (6.8)

Figure S52.  Get High-res Image Gene #15: '8p gain' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'8p gain' versus 'PATHOLOGY_T_STAGE'

P value = 0.00811 (Fisher's exact test), Q value = 0.041

Table S53.  Gene #15: '8p gain' versus Clinical Feature #3: 'PATHOLOGY_T_STAGE'

nPatients T2 T3 T4
ALL 187 288 10
8P GAIN MUTATED 16 49 3
8P GAIN WILD-TYPE 171 239 7

Figure S53.  Get High-res Image Gene #15: '8p gain' versus Clinical Feature #3: 'PATHOLOGY_T_STAGE'

'8p gain' versus 'RESIDUAL_TUMOR'

P value = 0.0113 (Fisher's exact test), Q value = 0.053

Table S54.  Gene #15: '8p gain' versus Clinical Feature #7: 'RESIDUAL_TUMOR'

nPatients R0 R1 R2 RX
ALL 313 144 5 15
8P GAIN MUTATED 33 31 1 1
8P GAIN WILD-TYPE 280 113 4 14

Figure S54.  Get High-res Image Gene #15: '8p gain' versus Clinical Feature #7: 'RESIDUAL_TUMOR'

'8p gain' versus 'GLEASON_SCORE'

P value = 2.45e-07 (Wilcoxon-test), Q value = 2.2e-05

Table S55.  Gene #15: '8p gain' versus Clinical Feature #9: 'GLEASON_SCORE'

nPatients Mean (Std.Dev)
ALL 492 7.6 (1.0)
8P GAIN MUTATED 68 8.2 (1.0)
8P GAIN WILD-TYPE 424 7.5 (1.0)

Figure S55.  Get High-res Image Gene #15: '8p gain' versus Clinical Feature #9: 'GLEASON_SCORE'

'8p gain' versus 'PSA_VALUE'

P value = 0.0883 (Wilcoxon-test), Q value = 0.25

Table S56.  Gene #15: '8p gain' versus Clinical Feature #10: 'PSA_VALUE'

nPatients Mean (Std.Dev)
ALL 435 1.8 (15.9)
8P GAIN MUTATED 58 1.4 (4.3)
8P GAIN WILD-TYPE 377 1.8 (17.1)

Figure S56.  Get High-res Image Gene #15: '8p gain' versus Clinical Feature #10: 'PSA_VALUE'

'8q gain' versus 'YEARS_TO_BIRTH'

P value = 0.0701 (Wilcoxon-test), Q value = 0.21

Table S57.  Gene #16: '8q gain' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 481 61.0 (6.8)
8Q GAIN MUTATED 123 61.9 (6.4)
8Q GAIN WILD-TYPE 358 60.7 (6.9)

Figure S57.  Get High-res Image Gene #16: '8q gain' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'8q gain' versus 'PATHOLOGY_T_STAGE'

P value = 0.00024 (Fisher's exact test), Q value = 0.0034

Table S58.  Gene #16: '8q gain' versus Clinical Feature #3: 'PATHOLOGY_T_STAGE'

nPatients T2 T3 T4
ALL 187 288 10
8Q GAIN MUTATED 30 91 4
8Q GAIN WILD-TYPE 157 197 6

Figure S58.  Get High-res Image Gene #16: '8q gain' versus Clinical Feature #3: 'PATHOLOGY_T_STAGE'

'8q gain' versus 'RESIDUAL_TUMOR'

P value = 0.00092 (Fisher's exact test), Q value = 0.0084

Table S59.  Gene #16: '8q gain' versus Clinical Feature #7: 'RESIDUAL_TUMOR'

nPatients R0 R1 R2 RX
ALL 313 144 5 15
8Q GAIN MUTATED 62 53 1 5
8Q GAIN WILD-TYPE 251 91 4 10

Figure S59.  Get High-res Image Gene #16: '8q gain' versus Clinical Feature #7: 'RESIDUAL_TUMOR'

'8q gain' versus 'GLEASON_SCORE'

P value = 4.66e-08 (Wilcoxon-test), Q value = 4.6e-06

Table S60.  Gene #16: '8q gain' versus Clinical Feature #9: 'GLEASON_SCORE'

nPatients Mean (Std.Dev)
ALL 492 7.6 (1.0)
8Q GAIN MUTATED 126 8.0 (1.1)
8Q GAIN WILD-TYPE 366 7.5 (0.9)

Figure S60.  Get High-res Image Gene #16: '8q gain' versus Clinical Feature #9: 'GLEASON_SCORE'

'8q gain' versus 'PSA_VALUE'

P value = 0.0764 (Wilcoxon-test), Q value = 0.22

Table S61.  Gene #16: '8q gain' versus Clinical Feature #10: 'PSA_VALUE'

nPatients Mean (Std.Dev)
ALL 435 1.8 (15.9)
8Q GAIN MUTATED 109 4.2 (31.1)
8Q GAIN WILD-TYPE 326 0.9 (4.0)

Figure S61.  Get High-res Image Gene #16: '8q gain' versus Clinical Feature #10: 'PSA_VALUE'

'9p gain' versus 'YEARS_TO_BIRTH'

P value = 0.00442 (Wilcoxon-test), Q value = 0.027

Table S62.  Gene #17: '9p gain' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 481 61.0 (6.8)
9P GAIN MUTATED 34 64.3 (5.9)
9P GAIN WILD-TYPE 447 60.7 (6.8)

Figure S62.  Get High-res Image Gene #17: '9p gain' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'9p gain' versus 'PATHOLOGY_T_STAGE'

P value = 9e-05 (Fisher's exact test), Q value = 0.0016

Table S63.  Gene #17: '9p gain' versus Clinical Feature #3: 'PATHOLOGY_T_STAGE'

nPatients T2 T3 T4
ALL 187 288 10
9P GAIN MUTATED 2 30 1
9P GAIN WILD-TYPE 185 258 9

Figure S63.  Get High-res Image Gene #17: '9p gain' versus Clinical Feature #3: 'PATHOLOGY_T_STAGE'

'9p gain' versus 'PATHOLOGY_N_STAGE'

P value = 0.000466 (Fisher's exact test), Q value = 0.0054

Table S64.  Gene #17: '9p gain' versus Clinical Feature #4: 'PATHOLOGY_N_STAGE'

nPatients 0 1
ALL 343 77
9P GAIN MUTATED 18 14
9P GAIN WILD-TYPE 325 63

Figure S64.  Get High-res Image Gene #17: '9p gain' versus Clinical Feature #4: 'PATHOLOGY_N_STAGE'

'9p gain' versus 'RESIDUAL_TUMOR'

P value = 0.0131 (Fisher's exact test), Q value = 0.057

Table S65.  Gene #17: '9p gain' versus Clinical Feature #7: 'RESIDUAL_TUMOR'

nPatients R0 R1 R2 RX
ALL 313 144 5 15
9P GAIN MUTATED 14 17 1 0
9P GAIN WILD-TYPE 299 127 4 15

Figure S65.  Get High-res Image Gene #17: '9p gain' versus Clinical Feature #7: 'RESIDUAL_TUMOR'

'9p gain' versus 'NUMBER_OF_LYMPH_NODES'

P value = 8.33e-05 (Wilcoxon-test), Q value = 0.0015

Table S66.  Gene #17: '9p gain' versus Clinical Feature #8: 'NUMBER_OF_LYMPH_NODES'

nPatients Mean (Std.Dev)
ALL 402 0.4 (1.4)
9P GAIN MUTATED 32 0.8 (1.4)
9P GAIN WILD-TYPE 370 0.4 (1.4)

Figure S66.  Get High-res Image Gene #17: '9p gain' versus Clinical Feature #8: 'NUMBER_OF_LYMPH_NODES'

'9p gain' versus 'GLEASON_SCORE'

P value = 1.04e-06 (Wilcoxon-test), Q value = 5.7e-05

Table S67.  Gene #17: '9p gain' versus Clinical Feature #9: 'GLEASON_SCORE'

nPatients Mean (Std.Dev)
ALL 492 7.6 (1.0)
9P GAIN MUTATED 34 8.4 (0.9)
9P GAIN WILD-TYPE 458 7.5 (1.0)

Figure S67.  Get High-res Image Gene #17: '9p gain' versus Clinical Feature #9: 'GLEASON_SCORE'

'9q gain' versus 'YEARS_TO_BIRTH'

P value = 0.0124 (Wilcoxon-test), Q value = 0.055

Table S68.  Gene #18: '9q gain' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 481 61.0 (6.8)
9Q GAIN MUTATED 48 63.5 (5.7)
9Q GAIN WILD-TYPE 433 60.7 (6.9)

Figure S68.  Get High-res Image Gene #18: '9q gain' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'9q gain' versus 'PATHOLOGY_T_STAGE'

P value = 1e-05 (Fisher's exact test), Q value = 0.00029

Table S69.  Gene #18: '9q gain' versus Clinical Feature #3: 'PATHOLOGY_T_STAGE'

nPatients T2 T3 T4
ALL 187 288 10
9Q GAIN MUTATED 3 42 2
9Q GAIN WILD-TYPE 184 246 8

Figure S69.  Get High-res Image Gene #18: '9q gain' versus Clinical Feature #3: 'PATHOLOGY_T_STAGE'

'9q gain' versus 'PATHOLOGY_N_STAGE'

P value = 1.46e-05 (Fisher's exact test), Q value = 0.00039

Table S70.  Gene #18: '9q gain' versus Clinical Feature #4: 'PATHOLOGY_N_STAGE'

nPatients 0 1
ALL 343 77
9Q GAIN MUTATED 25 20
9Q GAIN WILD-TYPE 318 57

Figure S70.  Get High-res Image Gene #18: '9q gain' versus Clinical Feature #4: 'PATHOLOGY_N_STAGE'

'9q gain' versus 'RESIDUAL_TUMOR'

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

Table S71.  Gene #18: '9q gain' versus Clinical Feature #7: 'RESIDUAL_TUMOR'

nPatients R0 R1 R2 RX
ALL 313 144 5 15
9Q GAIN MUTATED 21 23 1 1
9Q GAIN WILD-TYPE 292 121 4 14

Figure S71.  Get High-res Image Gene #18: '9q gain' versus Clinical Feature #7: 'RESIDUAL_TUMOR'

'9q gain' versus 'NUMBER_OF_LYMPH_NODES'

P value = 5.43e-07 (Wilcoxon-test), Q value = 3.7e-05

Table S72.  Gene #18: '9q gain' versus Clinical Feature #8: 'NUMBER_OF_LYMPH_NODES'

nPatients Mean (Std.Dev)
ALL 402 0.4 (1.4)
9Q GAIN MUTATED 45 1.3 (2.6)
9Q GAIN WILD-TYPE 357 0.3 (1.1)

Figure S72.  Get High-res Image Gene #18: '9q gain' versus Clinical Feature #8: 'NUMBER_OF_LYMPH_NODES'

'9q gain' versus 'GLEASON_SCORE'

P value = 2.59e-08 (Wilcoxon-test), Q value = 3.8e-06

Table S73.  Gene #18: '9q gain' versus Clinical Feature #9: 'GLEASON_SCORE'

nPatients Mean (Std.Dev)
ALL 492 7.6 (1.0)
9Q GAIN MUTATED 48 8.4 (0.9)
9Q GAIN WILD-TYPE 444 7.5 (1.0)

Figure S73.  Get High-res Image Gene #18: '9q gain' versus Clinical Feature #9: 'GLEASON_SCORE'

'10p gain' versus 'NUMBER_OF_LYMPH_NODES'

P value = 0.0288 (Wilcoxon-test), Q value = 0.1

Table S74.  Gene #19: '10p gain' versus Clinical Feature #8: 'NUMBER_OF_LYMPH_NODES'

nPatients Mean (Std.Dev)
ALL 402 0.4 (1.4)
10P GAIN MUTATED 14 1.2 (2.9)
10P GAIN WILD-TYPE 388 0.4 (1.3)

Figure S74.  Get High-res Image Gene #19: '10p gain' versus Clinical Feature #8: 'NUMBER_OF_LYMPH_NODES'

'10p gain' versus 'GLEASON_SCORE'

P value = 0.00263 (Wilcoxon-test), Q value = 0.019

Table S75.  Gene #19: '10p gain' versus Clinical Feature #9: 'GLEASON_SCORE'

nPatients Mean (Std.Dev)
ALL 492 7.6 (1.0)
10P GAIN MUTATED 15 8.4 (0.9)
10P GAIN WILD-TYPE 477 7.6 (1.0)

Figure S75.  Get High-res Image Gene #19: '10p gain' versus Clinical Feature #9: 'GLEASON_SCORE'

'10q gain' versus 'NUMBER_OF_LYMPH_NODES'

P value = 0.0677 (Wilcoxon-test), Q value = 0.2

Table S76.  Gene #20: '10q gain' versus Clinical Feature #8: 'NUMBER_OF_LYMPH_NODES'

nPatients Mean (Std.Dev)
ALL 402 0.4 (1.4)
10Q GAIN MUTATED 13 1.5 (3.3)
10Q GAIN WILD-TYPE 389 0.4 (1.2)

Figure S76.  Get High-res Image Gene #20: '10q gain' versus Clinical Feature #8: 'NUMBER_OF_LYMPH_NODES'

'10q gain' versus 'GLEASON_SCORE'

P value = 0.0259 (Wilcoxon-test), Q value = 0.096

Table S77.  Gene #20: '10q gain' versus Clinical Feature #9: 'GLEASON_SCORE'

nPatients Mean (Std.Dev)
ALL 492 7.6 (1.0)
10Q GAIN MUTATED 14 8.2 (1.0)
10Q GAIN WILD-TYPE 478 7.6 (1.0)

Figure S77.  Get High-res Image Gene #20: '10q gain' versus Clinical Feature #9: 'GLEASON_SCORE'

'11p gain' versus 'YEARS_TO_BIRTH'

P value = 0.0288 (Wilcoxon-test), Q value = 0.1

Table S78.  Gene #21: '11p gain' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 481 61.0 (6.8)
11P GAIN MUTATED 27 63.4 (6.1)
11P GAIN WILD-TYPE 454 60.8 (6.8)

Figure S78.  Get High-res Image Gene #21: '11p gain' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'11p gain' versus 'PATHOLOGY_T_STAGE'

P value = 0.00163 (Fisher's exact test), Q value = 0.013

Table S79.  Gene #21: '11p gain' versus Clinical Feature #3: 'PATHOLOGY_T_STAGE'

nPatients T2 T3 T4
ALL 187 288 10
11P GAIN MUTATED 3 22 2
11P GAIN WILD-TYPE 184 266 8

Figure S79.  Get High-res Image Gene #21: '11p gain' versus Clinical Feature #3: 'PATHOLOGY_T_STAGE'

'11p gain' versus 'PATHOLOGY_N_STAGE'

P value = 0.00293 (Fisher's exact test), Q value = 0.02

Table S80.  Gene #21: '11p gain' versus Clinical Feature #4: 'PATHOLOGY_N_STAGE'

nPatients 0 1
ALL 343 77
11P GAIN MUTATED 15 11
11P GAIN WILD-TYPE 328 66

Figure S80.  Get High-res Image Gene #21: '11p gain' versus Clinical Feature #4: 'PATHOLOGY_N_STAGE'

'11p gain' versus 'RESIDUAL_TUMOR'

P value = 0.00861 (Fisher's exact test), Q value = 0.043

Table S81.  Gene #21: '11p gain' versus Clinical Feature #7: 'RESIDUAL_TUMOR'

nPatients R0 R1 R2 RX
ALL 313 144 5 15
11P GAIN MUTATED 10 15 0 2
11P GAIN WILD-TYPE 303 129 5 13

Figure S81.  Get High-res Image Gene #21: '11p gain' versus Clinical Feature #7: 'RESIDUAL_TUMOR'

'11p gain' versus 'NUMBER_OF_LYMPH_NODES'

P value = 0.00107 (Wilcoxon-test), Q value = 0.0093

Table S82.  Gene #21: '11p gain' versus Clinical Feature #8: 'NUMBER_OF_LYMPH_NODES'

nPatients Mean (Std.Dev)
ALL 402 0.4 (1.4)
11P GAIN MUTATED 26 0.8 (1.5)
11P GAIN WILD-TYPE 376 0.4 (1.4)

Figure S82.  Get High-res Image Gene #21: '11p gain' versus Clinical Feature #8: 'NUMBER_OF_LYMPH_NODES'

'11p gain' versus 'GLEASON_SCORE'

P value = 1.4e-05 (Wilcoxon-test), Q value = 0.00039

Table S83.  Gene #21: '11p gain' versus Clinical Feature #9: 'GLEASON_SCORE'

nPatients Mean (Std.Dev)
ALL 492 7.6 (1.0)
11P GAIN MUTATED 27 8.5 (1.0)
11P GAIN WILD-TYPE 465 7.6 (1.0)

Figure S83.  Get High-res Image Gene #21: '11p gain' versus Clinical Feature #9: 'GLEASON_SCORE'

'11q gain' versus 'YEARS_TO_BIRTH'

P value = 0.033 (Wilcoxon-test), Q value = 0.12

Table S84.  Gene #22: '11q gain' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 481 61.0 (6.8)
11Q GAIN MUTATED 30 63.3 (6.2)
11Q GAIN WILD-TYPE 451 60.8 (6.8)

Figure S84.  Get High-res Image Gene #22: '11q gain' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'11q gain' versus 'PATHOLOGY_T_STAGE'

P value = 0.00274 (Fisher's exact test), Q value = 0.019

Table S85.  Gene #22: '11q gain' versus Clinical Feature #3: 'PATHOLOGY_T_STAGE'

nPatients T2 T3 T4
ALL 187 288 10
11Q GAIN MUTATED 4 24 2
11Q GAIN WILD-TYPE 183 264 8

Figure S85.  Get High-res Image Gene #22: '11q gain' versus Clinical Feature #3: 'PATHOLOGY_T_STAGE'

'11q gain' versus 'PATHOLOGY_N_STAGE'

P value = 0.00232 (Fisher's exact test), Q value = 0.017

Table S86.  Gene #22: '11q gain' versus Clinical Feature #4: 'PATHOLOGY_N_STAGE'

nPatients 0 1
ALL 343 77
11Q GAIN MUTATED 17 12
11Q GAIN WILD-TYPE 326 65

Figure S86.  Get High-res Image Gene #22: '11q gain' versus Clinical Feature #4: 'PATHOLOGY_N_STAGE'

'11q gain' versus 'RESIDUAL_TUMOR'

P value = 0.0122 (Fisher's exact test), Q value = 0.055

Table S87.  Gene #22: '11q gain' versus Clinical Feature #7: 'RESIDUAL_TUMOR'

nPatients R0 R1 R2 RX
ALL 313 144 5 15
11Q GAIN MUTATED 12 16 0 2
11Q GAIN WILD-TYPE 301 128 5 13

Figure S87.  Get High-res Image Gene #22: '11q gain' versus Clinical Feature #7: 'RESIDUAL_TUMOR'

'11q gain' versus 'NUMBER_OF_LYMPH_NODES'

P value = 0.000622 (Wilcoxon-test), Q value = 0.0063

Table S88.  Gene #22: '11q gain' versus Clinical Feature #8: 'NUMBER_OF_LYMPH_NODES'

nPatients Mean (Std.Dev)
ALL 402 0.4 (1.4)
11Q GAIN MUTATED 28 0.8 (1.4)
11Q GAIN WILD-TYPE 374 0.4 (1.4)

Figure S88.  Get High-res Image Gene #22: '11q gain' versus Clinical Feature #8: 'NUMBER_OF_LYMPH_NODES'

'11q gain' versus 'GLEASON_SCORE'

P value = 2.11e-06 (Wilcoxon-test), Q value = 8.8e-05

Table S89.  Gene #22: '11q gain' versus Clinical Feature #9: 'GLEASON_SCORE'

nPatients Mean (Std.Dev)
ALL 492 7.6 (1.0)
11Q GAIN MUTATED 30 8.5 (0.9)
11Q GAIN WILD-TYPE 462 7.6 (1.0)

Figure S89.  Get High-res Image Gene #22: '11q gain' versus Clinical Feature #9: 'GLEASON_SCORE'

'12p gain' versus 'YEARS_TO_BIRTH'

P value = 0.00652 (Wilcoxon-test), Q value = 0.034

Table S90.  Gene #23: '12p gain' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 481 61.0 (6.8)
12P GAIN MUTATED 15 65.7 (5.4)
12P GAIN WILD-TYPE 466 60.8 (6.8)

Figure S90.  Get High-res Image Gene #23: '12p gain' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'12p gain' versus 'PATHOLOGY_T_STAGE'

P value = 0.00171 (Fisher's exact test), Q value = 0.013

Table S91.  Gene #23: '12p gain' versus Clinical Feature #3: 'PATHOLOGY_T_STAGE'

nPatients T2 T3 T4
ALL 187 288 10
12P GAIN MUTATED 0 15 0
12P GAIN WILD-TYPE 187 273 10

Figure S91.  Get High-res Image Gene #23: '12p gain' versus Clinical Feature #3: 'PATHOLOGY_T_STAGE'

'12p gain' versus 'PATHOLOGY_N_STAGE'

P value = 0.0499 (Fisher's exact test), Q value = 0.16

Table S92.  Gene #23: '12p gain' versus Clinical Feature #4: 'PATHOLOGY_N_STAGE'

nPatients 0 1
ALL 343 77
12P GAIN MUTATED 7 5
12P GAIN WILD-TYPE 336 72

Figure S92.  Get High-res Image Gene #23: '12p gain' versus Clinical Feature #4: 'PATHOLOGY_N_STAGE'

'12p gain' versus 'RADIATION_THERAPY'

P value = 0.0772 (Fisher's exact test), Q value = 0.22

Table S93.  Gene #23: '12p gain' versus Clinical Feature #5: 'RADIATION_THERAPY'

nPatients NO YES
ALL 390 59
12P GAIN MUTATED 9 4
12P GAIN WILD-TYPE 381 55

Figure S93.  Get High-res Image Gene #23: '12p gain' versus Clinical Feature #5: 'RADIATION_THERAPY'

'12p gain' versus 'RESIDUAL_TUMOR'

P value = 0.0029 (Fisher's exact test), Q value = 0.02

Table S94.  Gene #23: '12p gain' versus Clinical Feature #7: 'RESIDUAL_TUMOR'

nPatients R0 R1 R2 RX
ALL 313 144 5 15
12P GAIN MUTATED 4 10 1 0
12P GAIN WILD-TYPE 309 134 4 15

Figure S94.  Get High-res Image Gene #23: '12p gain' versus Clinical Feature #7: 'RESIDUAL_TUMOR'

'12p gain' versus 'NUMBER_OF_LYMPH_NODES'

P value = 0.00846 (Wilcoxon-test), Q value = 0.043

Table S95.  Gene #23: '12p gain' versus Clinical Feature #8: 'NUMBER_OF_LYMPH_NODES'

nPatients Mean (Std.Dev)
ALL 402 0.4 (1.4)
12P GAIN MUTATED 12 1.1 (2.0)
12P GAIN WILD-TYPE 390 0.4 (1.3)

Figure S95.  Get High-res Image Gene #23: '12p gain' versus Clinical Feature #8: 'NUMBER_OF_LYMPH_NODES'

'12p gain' versus 'GLEASON_SCORE'

P value = 3.13e-06 (Wilcoxon-test), Q value = 0.00011

Table S96.  Gene #23: '12p gain' versus Clinical Feature #9: 'GLEASON_SCORE'

nPatients Mean (Std.Dev)
ALL 492 7.6 (1.0)
12P GAIN MUTATED 15 8.9 (0.6)
12P GAIN WILD-TYPE 477 7.6 (1.0)

Figure S96.  Get High-res Image Gene #23: '12p gain' versus Clinical Feature #9: 'GLEASON_SCORE'

'12q gain' versus 'YEARS_TO_BIRTH'

P value = 0.0399 (Wilcoxon-test), Q value = 0.13

Table S97.  Gene #24: '12q gain' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 481 61.0 (6.8)
12Q GAIN MUTATED 18 64.4 (5.8)
12Q GAIN WILD-TYPE 463 60.8 (6.8)

Figure S97.  Get High-res Image Gene #24: '12q gain' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'12q gain' versus 'PATHOLOGY_T_STAGE'

P value = 0.00392 (Fisher's exact test), Q value = 0.025

Table S98.  Gene #24: '12q gain' versus Clinical Feature #3: 'PATHOLOGY_T_STAGE'

nPatients T2 T3 T4
ALL 187 288 10
12Q GAIN MUTATED 1 16 1
12Q GAIN WILD-TYPE 186 272 9

Figure S98.  Get High-res Image Gene #24: '12q gain' versus Clinical Feature #3: 'PATHOLOGY_T_STAGE'

'12q gain' versus 'PATHOLOGY_N_STAGE'

P value = 0.039 (Fisher's exact test), Q value = 0.13

Table S99.  Gene #24: '12q gain' versus Clinical Feature #4: 'PATHOLOGY_N_STAGE'

nPatients 0 1
ALL 343 77
12Q GAIN MUTATED 9 6
12Q GAIN WILD-TYPE 334 71

Figure S99.  Get High-res Image Gene #24: '12q gain' versus Clinical Feature #4: 'PATHOLOGY_N_STAGE'

'12q gain' versus 'RADIATION_THERAPY'

P value = 0.0111 (Fisher's exact test), Q value = 0.052

Table S100.  Gene #24: '12q gain' versus Clinical Feature #5: 'RADIATION_THERAPY'

nPatients NO YES
ALL 390 59
12Q GAIN MUTATED 10 6
12Q GAIN WILD-TYPE 380 53

Figure S100.  Get High-res Image Gene #24: '12q gain' versus Clinical Feature #5: 'RADIATION_THERAPY'

'12q gain' versus 'RESIDUAL_TUMOR'

P value = 9e-05 (Fisher's exact test), Q value = 0.0016

Table S101.  Gene #24: '12q gain' versus Clinical Feature #7: 'RESIDUAL_TUMOR'

nPatients R0 R1 R2 RX
ALL 313 144 5 15
12Q GAIN MUTATED 3 14 1 0
12Q GAIN WILD-TYPE 310 130 4 15

Figure S101.  Get High-res Image Gene #24: '12q gain' versus Clinical Feature #7: 'RESIDUAL_TUMOR'

'12q gain' versus 'NUMBER_OF_LYMPH_NODES'

P value = 0.00502 (Wilcoxon-test), Q value = 0.029

Table S102.  Gene #24: '12q gain' versus Clinical Feature #8: 'NUMBER_OF_LYMPH_NODES'

nPatients Mean (Std.Dev)
ALL 402 0.4 (1.4)
12Q GAIN MUTATED 14 1.0 (1.8)
12Q GAIN WILD-TYPE 388 0.4 (1.3)

Figure S102.  Get High-res Image Gene #24: '12q gain' versus Clinical Feature #8: 'NUMBER_OF_LYMPH_NODES'

'12q gain' versus 'GLEASON_SCORE'

P value = 1.9e-06 (Wilcoxon-test), Q value = 8.5e-05

Table S103.  Gene #24: '12q gain' versus Clinical Feature #9: 'GLEASON_SCORE'

nPatients Mean (Std.Dev)
ALL 492 7.6 (1.0)
12Q GAIN MUTATED 18 8.8 (0.7)
12Q GAIN WILD-TYPE 474 7.6 (1.0)

Figure S103.  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 S104.  Gene #26: '14q gain' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 481 61.0 (6.8)
14Q GAIN MUTATED 10 65.2 (5.4)
14Q GAIN WILD-TYPE 471 60.9 (6.8)

Figure S104.  Get High-res Image Gene #26: '14q gain' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'14q gain' versus 'RADIATION_THERAPY'

P value = 0.00277 (Fisher's exact test), Q value = 0.019

Table S105.  Gene #26: '14q gain' versus Clinical Feature #5: 'RADIATION_THERAPY'

nPatients NO YES
ALL 390 59
14Q GAIN MUTATED 4 5
14Q GAIN WILD-TYPE 386 54

Figure S105.  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 S106.  Gene #26: '14q gain' versus Clinical Feature #7: 'RESIDUAL_TUMOR'

nPatients R0 R1 R2 RX
ALL 313 144 5 15
14Q GAIN MUTATED 3 6 0 1
14Q GAIN WILD-TYPE 310 138 5 14

Figure S106.  Get High-res Image Gene #26: '14q gain' versus Clinical Feature #7: 'RESIDUAL_TUMOR'

'14q gain' versus 'GLEASON_SCORE'

P value = 0.00366 (Wilcoxon-test), Q value = 0.023

Table S107.  Gene #26: '14q gain' versus Clinical Feature #9: 'GLEASON_SCORE'

nPatients Mean (Std.Dev)
ALL 492 7.6 (1.0)
14Q GAIN MUTATED 10 8.5 (0.7)
14Q GAIN WILD-TYPE 482 7.6 (1.0)

Figure S107.  Get High-res Image Gene #26: '14q gain' versus Clinical Feature #9: 'GLEASON_SCORE'

'16p gain' versus 'PATHOLOGY_T_STAGE'

P value = 0.00071 (Fisher's exact test), Q value = 0.0069

Table S108.  Gene #28: '16p gain' versus Clinical Feature #3: 'PATHOLOGY_T_STAGE'

nPatients T2 T3 T4
ALL 187 288 10
16P GAIN MUTATED 3 28 1
16P GAIN WILD-TYPE 184 260 9

Figure S108.  Get High-res Image Gene #28: '16p gain' versus Clinical Feature #3: 'PATHOLOGY_T_STAGE'

'16p gain' versus 'PATHOLOGY_N_STAGE'

P value = 0.00232 (Fisher's exact test), Q value = 0.017

Table S109.  Gene #28: '16p gain' versus Clinical Feature #4: 'PATHOLOGY_N_STAGE'

nPatients 0 1
ALL 343 77
16P GAIN MUTATED 17 12
16P GAIN WILD-TYPE 326 65

Figure S109.  Get High-res Image Gene #28: '16p gain' versus Clinical Feature #4: 'PATHOLOGY_N_STAGE'

'16p gain' versus 'NUMBER_OF_LYMPH_NODES'

P value = 0.00141 (Wilcoxon-test), Q value = 0.011

Table S110.  Gene #28: '16p gain' versus Clinical Feature #8: 'NUMBER_OF_LYMPH_NODES'

nPatients Mean (Std.Dev)
ALL 402 0.4 (1.4)
16P GAIN MUTATED 27 0.8 (1.6)
16P GAIN WILD-TYPE 375 0.4 (1.3)

Figure S110.  Get High-res Image Gene #28: '16p gain' versus Clinical Feature #8: 'NUMBER_OF_LYMPH_NODES'

'16p gain' versus 'GLEASON_SCORE'

P value = 2.98e-06 (Wilcoxon-test), Q value = 0.00011

Table S111.  Gene #28: '16p gain' versus Clinical Feature #9: 'GLEASON_SCORE'

nPatients Mean (Std.Dev)
ALL 492 7.6 (1.0)
16P GAIN MUTATED 32 8.5 (1.0)
16P GAIN WILD-TYPE 460 7.5 (1.0)

Figure S111.  Get High-res Image Gene #28: '16p gain' versus Clinical Feature #9: 'GLEASON_SCORE'

'16p gain' versus 'PSA_VALUE'

P value = 0.0717 (Wilcoxon-test), Q value = 0.21

Table S112.  Gene #28: '16p gain' versus Clinical Feature #10: 'PSA_VALUE'

nPatients Mean (Std.Dev)
ALL 435 1.8 (15.9)
16P GAIN MUTATED 28 1.1 (2.4)
16P GAIN WILD-TYPE 407 1.8 (16.5)

Figure S112.  Get High-res Image Gene #28: '16p gain' versus Clinical Feature #10: 'PSA_VALUE'

'16q gain' versus 'YEARS_TO_BIRTH'

P value = 0.0118 (Wilcoxon-test), Q value = 0.054

Table S113.  Gene #29: '16q gain' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 481 61.0 (6.8)
16Q GAIN MUTATED 7 67.0 (3.9)
16Q GAIN WILD-TYPE 474 60.9 (6.8)

Figure S113.  Get High-res Image Gene #29: '16q gain' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'17p gain' versus 'PATHOLOGY_T_STAGE'

P value = 0.0168 (Fisher's exact test), Q value = 0.071

Table S114.  Gene #30: '17p gain' versus Clinical Feature #3: 'PATHOLOGY_T_STAGE'

nPatients T2 T3 T4
ALL 187 288 10
17P GAIN MUTATED 0 7 1
17P GAIN WILD-TYPE 187 281 9

Figure S114.  Get High-res Image Gene #30: '17p gain' versus Clinical Feature #3: 'PATHOLOGY_T_STAGE'

'17p gain' versus 'PATHOLOGY_N_STAGE'

P value = 0.00652 (Fisher's exact test), Q value = 0.034

Table S115.  Gene #30: '17p gain' versus Clinical Feature #4: 'PATHOLOGY_N_STAGE'

nPatients 0 1
ALL 343 77
17P GAIN MUTATED 3 5
17P GAIN WILD-TYPE 340 72

Figure S115.  Get High-res Image Gene #30: '17p gain' versus Clinical Feature #4: 'PATHOLOGY_N_STAGE'

'17p gain' versus 'RADIATION_THERAPY'

P value = 0.0745 (Fisher's exact test), Q value = 0.21

Table S116.  Gene #30: '17p gain' versus Clinical Feature #5: 'RADIATION_THERAPY'

nPatients NO YES
ALL 390 59
17P GAIN MUTATED 5 3
17P GAIN WILD-TYPE 385 56

Figure S116.  Get High-res Image Gene #30: '17p gain' versus Clinical Feature #5: 'RADIATION_THERAPY'

'17p gain' versus 'NUMBER_OF_LYMPH_NODES'

P value = 0.00128 (Wilcoxon-test), Q value = 0.011

Table S117.  Gene #30: '17p gain' versus Clinical Feature #8: 'NUMBER_OF_LYMPH_NODES'

nPatients Mean (Std.Dev)
ALL 402 0.4 (1.4)
17P GAIN MUTATED 8 2.1 (3.7)
17P GAIN WILD-TYPE 394 0.4 (1.3)

Figure S117.  Get High-res Image Gene #30: '17p gain' versus Clinical Feature #8: 'NUMBER_OF_LYMPH_NODES'

'17p gain' versus 'GLEASON_SCORE'

P value = 0.0553 (Wilcoxon-test), Q value = 0.17

Table S118.  Gene #30: '17p gain' versus Clinical Feature #9: 'GLEASON_SCORE'

nPatients Mean (Std.Dev)
ALL 492 7.6 (1.0)
17P GAIN MUTATED 8 8.4 (1.2)
17P GAIN WILD-TYPE 484 7.6 (1.0)

Figure S118.  Get High-res Image Gene #30: '17p gain' versus Clinical Feature #9: 'GLEASON_SCORE'

'17q gain' versus 'PATHOLOGY_T_STAGE'

P value = 0.00451 (Fisher's exact test), Q value = 0.027

Table S119.  Gene #31: '17q gain' versus Clinical Feature #3: 'PATHOLOGY_T_STAGE'

nPatients T2 T3 T4
ALL 187 288 10
17Q GAIN MUTATED 0 10 1
17Q GAIN WILD-TYPE 187 278 9

Figure S119.  Get High-res Image Gene #31: '17q gain' versus Clinical Feature #3: 'PATHOLOGY_T_STAGE'

'17q gain' versus 'PATHOLOGY_N_STAGE'

P value = 0.00675 (Fisher's exact test), Q value = 0.035

Table S120.  Gene #31: '17q gain' versus Clinical Feature #4: 'PATHOLOGY_N_STAGE'

nPatients 0 1
ALL 343 77
17Q GAIN MUTATED 5 6
17Q GAIN WILD-TYPE 338 71

Figure S120.  Get High-res Image Gene #31: '17q gain' versus Clinical Feature #4: 'PATHOLOGY_N_STAGE'

'17q gain' versus 'NUMBER_OF_LYMPH_NODES'

P value = 0.00258 (Wilcoxon-test), Q value = 0.018

Table S121.  Gene #31: '17q gain' versus Clinical Feature #8: 'NUMBER_OF_LYMPH_NODES'

nPatients Mean (Std.Dev)
ALL 402 0.4 (1.4)
17Q GAIN MUTATED 11 1.6 (3.2)
17Q GAIN WILD-TYPE 391 0.4 (1.3)

Figure S121.  Get High-res Image Gene #31: '17q gain' versus Clinical Feature #8: 'NUMBER_OF_LYMPH_NODES'

'17q gain' versus 'GLEASON_SCORE'

P value = 0.0706 (Wilcoxon-test), Q value = 0.21

Table S122.  Gene #31: '17q gain' versus Clinical Feature #9: 'GLEASON_SCORE'

nPatients Mean (Std.Dev)
ALL 492 7.6 (1.0)
17Q GAIN MUTATED 11 8.2 (1.1)
17Q GAIN WILD-TYPE 481 7.6 (1.0)

Figure S122.  Get High-res Image Gene #31: '17q gain' versus Clinical Feature #9: 'GLEASON_SCORE'

'18p gain' versus 'YEARS_TO_BIRTH'

P value = 0.00995 (Wilcoxon-test), Q value = 0.049

Table S123.  Gene #32: '18p gain' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 481 61.0 (6.8)
18P GAIN MUTATED 19 64.9 (6.2)
18P GAIN WILD-TYPE 462 60.8 (6.8)

Figure S123.  Get High-res Image Gene #32: '18p gain' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'18p gain' versus 'PATHOLOGY_T_STAGE'

P value = 0.00236 (Fisher's exact test), Q value = 0.017

Table S124.  Gene #32: '18p gain' versus Clinical Feature #3: 'PATHOLOGY_T_STAGE'

nPatients T2 T3 T4
ALL 187 288 10
18P GAIN MUTATED 1 17 1
18P GAIN WILD-TYPE 186 271 9

Figure S124.  Get High-res Image Gene #32: '18p gain' versus Clinical Feature #3: 'PATHOLOGY_T_STAGE'

'18p gain' versus 'PATHOLOGY_N_STAGE'

P value = 0.00535 (Fisher's exact test), Q value = 0.031

Table S125.  Gene #32: '18p gain' versus Clinical Feature #4: 'PATHOLOGY_N_STAGE'

nPatients 0 1
ALL 343 77
18P GAIN MUTATED 9 8
18P GAIN WILD-TYPE 334 69

Figure S125.  Get High-res Image Gene #32: '18p gain' versus Clinical Feature #4: 'PATHOLOGY_N_STAGE'

'18p gain' versus 'NUMBER_OF_LYMPH_NODES'

P value = 0.00558 (Wilcoxon-test), Q value = 0.031

Table S126.  Gene #32: '18p gain' versus Clinical Feature #8: 'NUMBER_OF_LYMPH_NODES'

nPatients Mean (Std.Dev)
ALL 402 0.4 (1.4)
18P GAIN MUTATED 17 1.1 (2.6)
18P GAIN WILD-TYPE 385 0.4 (1.3)

Figure S126.  Get High-res Image Gene #32: '18p gain' versus Clinical Feature #8: 'NUMBER_OF_LYMPH_NODES'

'18p gain' versus 'GLEASON_SCORE'

P value = 0.0765 (Wilcoxon-test), Q value = 0.22

Table S127.  Gene #32: '18p gain' versus Clinical Feature #9: 'GLEASON_SCORE'

nPatients Mean (Std.Dev)
ALL 492 7.6 (1.0)
18P GAIN MUTATED 19 8.0 (0.9)
18P GAIN WILD-TYPE 473 7.6 (1.0)

Figure S127.  Get High-res Image Gene #32: '18p gain' versus Clinical Feature #9: 'GLEASON_SCORE'

'18q gain' versus 'Time to Death'

P value = 0.0657 (logrank test), Q value = 0.2

Table S128.  Gene #33: '18q gain' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 492 9 0.8 - 165.2 (30.6)
18Q GAIN MUTATED 10 1 10.6 - 75.9 (47.2)
18Q GAIN WILD-TYPE 482 8 0.8 - 165.2 (30.4)

Figure S128.  Get High-res Image Gene #33: '18q gain' versus Clinical Feature #1: 'Time to Death'

'18q gain' versus 'PATHOLOGY_T_STAGE'

P value = 0.0283 (Fisher's exact test), Q value = 0.1

Table S129.  Gene #33: '18q gain' versus Clinical Feature #3: 'PATHOLOGY_T_STAGE'

nPatients T2 T3 T4
ALL 187 288 10
18Q GAIN MUTATED 0 10 0
18Q GAIN WILD-TYPE 187 278 10

Figure S129.  Get High-res Image Gene #33: '18q gain' versus Clinical Feature #3: 'PATHOLOGY_T_STAGE'

'19p gain' versus 'PATHOLOGY_T_STAGE'

P value = 0.00053 (Fisher's exact test), Q value = 0.0056

Table S130.  Gene #34: '19p gain' versus Clinical Feature #3: 'PATHOLOGY_T_STAGE'

nPatients T2 T3 T4
ALL 187 288 10
19P GAIN MUTATED 0 10 2
19P GAIN WILD-TYPE 187 278 8

Figure S130.  Get High-res Image Gene #34: '19p gain' versus Clinical Feature #3: 'PATHOLOGY_T_STAGE'

'19p gain' versus 'PATHOLOGY_N_STAGE'

P value = 0.0115 (Fisher's exact test), Q value = 0.053

Table S131.  Gene #34: '19p gain' versus Clinical Feature #4: 'PATHOLOGY_N_STAGE'

nPatients 0 1
ALL 343 77
19P GAIN MUTATED 6 6
19P GAIN WILD-TYPE 337 71

Figure S131.  Get High-res Image Gene #34: '19p gain' versus Clinical Feature #4: 'PATHOLOGY_N_STAGE'

'19p gain' versus 'RESIDUAL_TUMOR'

P value = 0.0613 (Fisher's exact test), Q value = 0.19

Table S132.  Gene #34: '19p gain' versus Clinical Feature #7: 'RESIDUAL_TUMOR'

nPatients R0 R1 R2 RX
ALL 313 144 5 15
19P GAIN MUTATED 4 8 0 0
19P GAIN WILD-TYPE 309 136 5 15

Figure S132.  Get High-res Image Gene #34: '19p gain' versus Clinical Feature #7: 'RESIDUAL_TUMOR'

'19p gain' versus 'NUMBER_OF_LYMPH_NODES'

P value = 0.000926 (Wilcoxon-test), Q value = 0.0084

Table S133.  Gene #34: '19p gain' versus Clinical Feature #8: 'NUMBER_OF_LYMPH_NODES'

nPatients Mean (Std.Dev)
ALL 402 0.4 (1.4)
19P GAIN MUTATED 12 1.2 (2.2)
19P GAIN WILD-TYPE 390 0.4 (1.3)

Figure S133.  Get High-res Image Gene #34: '19p gain' versus Clinical Feature #8: 'NUMBER_OF_LYMPH_NODES'

'19p gain' versus 'GLEASON_SCORE'

P value = 0.000226 (Wilcoxon-test), Q value = 0.0033

Table S134.  Gene #34: '19p gain' versus Clinical Feature #9: 'GLEASON_SCORE'

nPatients Mean (Std.Dev)
ALL 492 7.6 (1.0)
19P GAIN MUTATED 12 8.8 (0.9)
19P GAIN WILD-TYPE 480 7.6 (1.0)

Figure S134.  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 = 0.0055

Table S135.  Gene #35: '19q gain' versus Clinical Feature #3: 'PATHOLOGY_T_STAGE'

nPatients T2 T3 T4
ALL 187 288 10
19Q GAIN MUTATED 0 10 2
19Q GAIN WILD-TYPE 187 278 8

Figure S135.  Get High-res Image Gene #35: '19q gain' versus Clinical Feature #3: 'PATHOLOGY_T_STAGE'

'19q gain' versus 'PATHOLOGY_N_STAGE'

P value = 0.0115 (Fisher's exact test), Q value = 0.053

Table S136.  Gene #35: '19q gain' versus Clinical Feature #4: 'PATHOLOGY_N_STAGE'

nPatients 0 1
ALL 343 77
19Q GAIN MUTATED 6 6
19Q GAIN WILD-TYPE 337 71

Figure S136.  Get High-res Image Gene #35: '19q gain' versus Clinical Feature #4: 'PATHOLOGY_N_STAGE'

'19q gain' versus 'RESIDUAL_TUMOR'

P value = 0.0622 (Fisher's exact test), Q value = 0.19

Table S137.  Gene #35: '19q gain' versus Clinical Feature #7: 'RESIDUAL_TUMOR'

nPatients R0 R1 R2 RX
ALL 313 144 5 15
19Q GAIN MUTATED 4 8 0 0
19Q GAIN WILD-TYPE 309 136 5 15

Figure S137.  Get High-res Image Gene #35: '19q gain' versus Clinical Feature #7: 'RESIDUAL_TUMOR'

'19q gain' versus 'NUMBER_OF_LYMPH_NODES'

P value = 0.000926 (Wilcoxon-test), Q value = 0.0084

Table S138.  Gene #35: '19q gain' versus Clinical Feature #8: 'NUMBER_OF_LYMPH_NODES'

nPatients Mean (Std.Dev)
ALL 402 0.4 (1.4)
19Q GAIN MUTATED 12 1.2 (2.2)
19Q GAIN WILD-TYPE 390 0.4 (1.3)

Figure S138.  Get High-res Image Gene #35: '19q gain' versus Clinical Feature #8: 'NUMBER_OF_LYMPH_NODES'

'19q gain' versus 'GLEASON_SCORE'

P value = 0.000226 (Wilcoxon-test), Q value = 0.0033

Table S139.  Gene #35: '19q gain' versus Clinical Feature #9: 'GLEASON_SCORE'

nPatients Mean (Std.Dev)
ALL 492 7.6 (1.0)
19Q GAIN MUTATED 12 8.8 (0.9)
19Q GAIN WILD-TYPE 480 7.6 (1.0)

Figure S139.  Get High-res Image Gene #35: '19q gain' versus Clinical Feature #9: 'GLEASON_SCORE'

'20p gain' versus 'YEARS_TO_BIRTH'

P value = 0.0474 (Wilcoxon-test), Q value = 0.15

Table S140.  Gene #36: '20p gain' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 481 61.0 (6.8)
20P GAIN MUTATED 25 63.4 (4.6)
20P GAIN WILD-TYPE 456 60.8 (6.9)

Figure S140.  Get High-res Image Gene #36: '20p gain' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'20p gain' versus 'PATHOLOGY_T_STAGE'

P value = 0.00624 (Fisher's exact test), Q value = 0.034

Table S141.  Gene #36: '20p gain' versus Clinical Feature #3: 'PATHOLOGY_T_STAGE'

nPatients T2 T3 T4
ALL 187 288 10
20P GAIN MUTATED 3 21 1
20P GAIN WILD-TYPE 184 267 9

Figure S141.  Get High-res Image Gene #36: '20p gain' versus Clinical Feature #3: 'PATHOLOGY_T_STAGE'

'20p gain' versus 'PATHOLOGY_N_STAGE'

P value = 0.0495 (Fisher's exact test), Q value = 0.16

Table S142.  Gene #36: '20p gain' versus Clinical Feature #4: 'PATHOLOGY_N_STAGE'

nPatients 0 1
ALL 343 77
20P GAIN MUTATED 15 8
20P GAIN WILD-TYPE 328 69

Figure S142.  Get High-res Image Gene #36: '20p gain' versus Clinical Feature #4: 'PATHOLOGY_N_STAGE'

'20p gain' versus 'NUMBER_OF_LYMPH_NODES'

P value = 0.0116 (Wilcoxon-test), Q value = 0.053

Table S143.  Gene #36: '20p gain' versus Clinical Feature #8: 'NUMBER_OF_LYMPH_NODES'

nPatients Mean (Std.Dev)
ALL 402 0.4 (1.4)
20P GAIN MUTATED 22 0.8 (1.4)
20P GAIN WILD-TYPE 380 0.4 (1.4)

Figure S143.  Get High-res Image Gene #36: '20p gain' versus Clinical Feature #8: 'NUMBER_OF_LYMPH_NODES'

'20p gain' versus 'GLEASON_SCORE'

P value = 0.000516 (Wilcoxon-test), Q value = 0.0055

Table S144.  Gene #36: '20p gain' versus Clinical Feature #9: 'GLEASON_SCORE'

nPatients Mean (Std.Dev)
ALL 492 7.6 (1.0)
20P GAIN MUTATED 26 8.3 (1.2)
20P GAIN WILD-TYPE 466 7.6 (1.0)

Figure S144.  Get High-res Image Gene #36: '20p gain' versus Clinical Feature #9: 'GLEASON_SCORE'

'20q gain' versus 'YEARS_TO_BIRTH'

P value = 0.00341 (Wilcoxon-test), Q value = 0.022

Table S145.  Gene #37: '20q gain' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 481 61.0 (6.8)
20Q GAIN MUTATED 28 64.4 (4.4)
20Q GAIN WILD-TYPE 453 60.8 (6.9)

Figure S145.  Get High-res Image Gene #37: '20q gain' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'20q gain' versus 'PATHOLOGY_T_STAGE'

P value = 0.00023 (Fisher's exact test), Q value = 0.0033

Table S146.  Gene #37: '20q gain' versus Clinical Feature #3: 'PATHOLOGY_T_STAGE'

nPatients T2 T3 T4
ALL 187 288 10
20Q GAIN MUTATED 3 23 3
20Q GAIN WILD-TYPE 184 265 7

Figure S146.  Get High-res Image Gene #37: '20q gain' versus Clinical Feature #3: 'PATHOLOGY_T_STAGE'

'20q gain' versus 'PATHOLOGY_N_STAGE'

P value = 0.0665 (Fisher's exact test), Q value = 0.2

Table S147.  Gene #37: '20q gain' versus Clinical Feature #4: 'PATHOLOGY_N_STAGE'

nPatients 0 1
ALL 343 77
20Q GAIN MUTATED 18 9
20Q GAIN WILD-TYPE 325 68

Figure S147.  Get High-res Image Gene #37: '20q gain' versus Clinical Feature #4: 'PATHOLOGY_N_STAGE'

'20q gain' versus 'RADIATION_THERAPY'

P value = 0.0765 (Fisher's exact test), Q value = 0.22

Table S148.  Gene #37: '20q gain' versus Clinical Feature #5: 'RADIATION_THERAPY'

nPatients NO YES
ALL 390 59
20Q GAIN MUTATED 21 7
20Q GAIN WILD-TYPE 369 52

Figure S148.  Get High-res Image Gene #37: '20q gain' versus Clinical Feature #5: 'RADIATION_THERAPY'

'20q gain' versus 'RESIDUAL_TUMOR'

P value = 0.0434 (Fisher's exact test), Q value = 0.14

Table S149.  Gene #37: '20q gain' versus Clinical Feature #7: 'RESIDUAL_TUMOR'

nPatients R0 R1 R2 RX
ALL 313 144 5 15
20Q GAIN MUTATED 12 15 0 1
20Q GAIN WILD-TYPE 301 129 5 14

Figure S149.  Get High-res Image Gene #37: '20q gain' versus Clinical Feature #7: 'RESIDUAL_TUMOR'

'20q gain' versus 'NUMBER_OF_LYMPH_NODES'

P value = 0.0132 (Wilcoxon-test), Q value = 0.057

Table S150.  Gene #37: '20q gain' versus Clinical Feature #8: 'NUMBER_OF_LYMPH_NODES'

nPatients Mean (Std.Dev)
ALL 402 0.4 (1.4)
20Q GAIN MUTATED 26 0.7 (1.3)
20Q GAIN WILD-TYPE 376 0.4 (1.4)

Figure S150.  Get High-res Image Gene #37: '20q gain' versus Clinical Feature #8: 'NUMBER_OF_LYMPH_NODES'

'20q gain' versus 'GLEASON_SCORE'

P value = 0.000329 (Wilcoxon-test), Q value = 0.0042

Table S151.  Gene #37: '20q gain' versus Clinical Feature #9: 'GLEASON_SCORE'

nPatients Mean (Std.Dev)
ALL 492 7.6 (1.0)
20Q GAIN MUTATED 29 8.3 (1.1)
20Q GAIN WILD-TYPE 463 7.6 (1.0)

Figure S151.  Get High-res Image Gene #37: '20q gain' versus Clinical Feature #9: 'GLEASON_SCORE'

'21q gain' versus 'YEARS_TO_BIRTH'

P value = 0.00541 (Wilcoxon-test), Q value = 0.031

Table S152.  Gene #38: '21q gain' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 481 61.0 (6.8)
21Q GAIN MUTATED 21 64.9 (5.4)
21Q GAIN WILD-TYPE 460 60.8 (6.8)

Figure S152.  Get High-res Image Gene #38: '21q gain' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'21q gain' versus 'PATHOLOGY_T_STAGE'

P value = 0.0158 (Fisher's exact test), Q value = 0.067

Table S153.  Gene #38: '21q gain' versus Clinical Feature #3: 'PATHOLOGY_T_STAGE'

nPatients T2 T3 T4
ALL 187 288 10
21Q GAIN MUTATED 2 19 0
21Q GAIN WILD-TYPE 185 269 10

Figure S153.  Get High-res Image Gene #38: '21q gain' versus Clinical Feature #3: 'PATHOLOGY_T_STAGE'

'21q gain' versus 'PATHOLOGY_N_STAGE'

P value = 0.0362 (Fisher's exact test), Q value = 0.12

Table S154.  Gene #38: '21q gain' versus Clinical Feature #4: 'PATHOLOGY_N_STAGE'

nPatients 0 1
ALL 343 77
21Q GAIN MUTATED 13 8
21Q GAIN WILD-TYPE 330 69

Figure S154.  Get High-res Image Gene #38: '21q gain' versus Clinical Feature #4: 'PATHOLOGY_N_STAGE'

'21q gain' versus 'NUMBER_OF_LYMPH_NODES'

P value = 0.00448 (Wilcoxon-test), Q value = 0.027

Table S155.  Gene #38: '21q gain' versus Clinical Feature #8: 'NUMBER_OF_LYMPH_NODES'

nPatients Mean (Std.Dev)
ALL 402 0.4 (1.4)
21Q GAIN MUTATED 21 1.2 (2.2)
21Q GAIN WILD-TYPE 381 0.4 (1.3)

Figure S155.  Get High-res Image Gene #38: '21q gain' versus Clinical Feature #8: 'NUMBER_OF_LYMPH_NODES'

'21q gain' versus 'GLEASON_SCORE'

P value = 5.71e-05 (Wilcoxon-test), Q value = 0.0011

Table S156.  Gene #38: '21q gain' versus Clinical Feature #9: 'GLEASON_SCORE'

nPatients Mean (Std.Dev)
ALL 492 7.6 (1.0)
21Q GAIN MUTATED 21 8.5 (0.9)
21Q GAIN WILD-TYPE 471 7.6 (1.0)

Figure S156.  Get High-res Image Gene #38: '21q gain' versus Clinical Feature #9: 'GLEASON_SCORE'

'22q gain' versus 'GLEASON_SCORE'

P value = 0.0221 (Wilcoxon-test), Q value = 0.083

Table S157.  Gene #39: '22q gain' versus Clinical Feature #9: 'GLEASON_SCORE'

nPatients Mean (Std.Dev)
ALL 492 7.6 (1.0)
22Q GAIN MUTATED 4 8.8 (0.5)
22Q GAIN WILD-TYPE 488 7.6 (1.0)

Figure S157.  Get High-res Image Gene #39: '22q gain' versus Clinical Feature #9: 'GLEASON_SCORE'

'xp gain' versus 'PATHOLOGY_T_STAGE'

P value = 0.0195 (Fisher's exact test), Q value = 0.079

Table S158.  Gene #40: 'xp gain' versus Clinical Feature #3: 'PATHOLOGY_T_STAGE'

nPatients T2 T3 T4
ALL 187 288 10
XP GAIN MUTATED 0 6 1
XP GAIN WILD-TYPE 187 282 9

Figure S158.  Get High-res Image Gene #40: 'xp gain' versus Clinical Feature #3: 'PATHOLOGY_T_STAGE'

'xp gain' versus 'RESIDUAL_TUMOR'

P value = 0.00602 (Fisher's exact test), Q value = 0.033

Table S159.  Gene #40: 'xp gain' versus Clinical Feature #7: 'RESIDUAL_TUMOR'

nPatients R0 R1 R2 RX
ALL 313 144 5 15
XP GAIN MUTATED 1 5 1 0
XP GAIN WILD-TYPE 312 139 4 15

Figure S159.  Get High-res Image Gene #40: 'xp gain' versus Clinical Feature #7: 'RESIDUAL_TUMOR'

'xp gain' versus 'GLEASON_SCORE'

P value = 0.00501 (Wilcoxon-test), Q value = 0.029

Table S160.  Gene #40: 'xp gain' versus Clinical Feature #9: 'GLEASON_SCORE'

nPatients Mean (Std.Dev)
ALL 492 7.6 (1.0)
XP GAIN MUTATED 7 8.7 (0.8)
XP GAIN WILD-TYPE 485 7.6 (1.0)

Figure S160.  Get High-res Image Gene #40: 'xp gain' versus Clinical Feature #9: 'GLEASON_SCORE'

'xq gain' versus 'PATHOLOGY_T_STAGE'

P value = 0.0192 (Fisher's exact test), Q value = 0.078

Table S161.  Gene #41: 'xq gain' versus Clinical Feature #3: 'PATHOLOGY_T_STAGE'

nPatients T2 T3 T4
ALL 187 288 10
XQ GAIN MUTATED 0 6 1
XQ GAIN WILD-TYPE 187 282 9

Figure S161.  Get High-res Image Gene #41: 'xq gain' versus Clinical Feature #3: 'PATHOLOGY_T_STAGE'

'xq gain' versus 'RESIDUAL_TUMOR'

P value = 0.00557 (Fisher's exact test), Q value = 0.031

Table S162.  Gene #41: 'xq gain' versus Clinical Feature #7: 'RESIDUAL_TUMOR'

nPatients R0 R1 R2 RX
ALL 313 144 5 15
XQ GAIN MUTATED 1 5 1 0
XQ GAIN WILD-TYPE 312 139 4 15

Figure S162.  Get High-res Image Gene #41: 'xq gain' versus Clinical Feature #7: 'RESIDUAL_TUMOR'

'xq gain' versus 'GLEASON_SCORE'

P value = 0.00501 (Wilcoxon-test), Q value = 0.029

Table S163.  Gene #41: 'xq gain' versus Clinical Feature #9: 'GLEASON_SCORE'

nPatients Mean (Std.Dev)
ALL 492 7.6 (1.0)
XQ GAIN MUTATED 7 8.7 (0.8)
XQ GAIN WILD-TYPE 485 7.6 (1.0)

Figure S163.  Get High-res Image Gene #41: 'xq gain' versus Clinical Feature #9: 'GLEASON_SCORE'

'1p loss' versus 'PATHOLOGY_T_STAGE'

P value = 0.0246 (Fisher's exact test), Q value = 0.092

Table S164.  Gene #42: '1p loss' versus Clinical Feature #3: 'PATHOLOGY_T_STAGE'

nPatients T2 T3 T4
ALL 187 288 10
1P LOSS MUTATED 3 18 1
1P LOSS WILD-TYPE 184 270 9

Figure S164.  Get High-res Image Gene #42: '1p loss' versus Clinical Feature #3: 'PATHOLOGY_T_STAGE'

'1p loss' versus 'RADIATION_THERAPY'

P value = 0.0442 (Fisher's exact test), Q value = 0.14

Table S165.  Gene #42: '1p loss' versus Clinical Feature #5: 'RADIATION_THERAPY'

nPatients NO YES
ALL 390 59
1P LOSS MUTATED 15 6
1P LOSS WILD-TYPE 375 53

Figure S165.  Get High-res Image Gene #42: '1p loss' versus Clinical Feature #5: 'RADIATION_THERAPY'

'1p loss' versus 'GLEASON_SCORE'

P value = 1.91e-05 (Wilcoxon-test), Q value = 0.00048

Table S166.  Gene #42: '1p loss' versus Clinical Feature #9: 'GLEASON_SCORE'

nPatients Mean (Std.Dev)
ALL 492 7.6 (1.0)
1P LOSS MUTATED 22 8.5 (0.9)
1P LOSS WILD-TYPE 470 7.6 (1.0)

Figure S166.  Get High-res Image Gene #42: '1p loss' versus Clinical Feature #9: 'GLEASON_SCORE'

'1q loss' versus 'RESIDUAL_TUMOR'

P value = 0.0553 (Fisher's exact test), Q value = 0.17

Table S167.  Gene #43: '1q loss' versus Clinical Feature #7: 'RESIDUAL_TUMOR'

nPatients R0 R1 R2 RX
ALL 313 144 5 15
1Q LOSS MUTATED 1 5 0 0
1Q LOSS WILD-TYPE 312 139 5 15

Figure S167.  Get High-res Image Gene #43: '1q loss' versus Clinical Feature #7: 'RESIDUAL_TUMOR'

'1q loss' versus 'NUMBER_OF_LYMPH_NODES'

P value = 0.0768 (Wilcoxon-test), Q value = 0.22

Table S168.  Gene #43: '1q loss' versus Clinical Feature #8: 'NUMBER_OF_LYMPH_NODES'

nPatients Mean (Std.Dev)
ALL 402 0.4 (1.4)
1Q LOSS MUTATED 4 1.2 (1.5)
1Q LOSS WILD-TYPE 398 0.4 (1.4)

Figure S168.  Get High-res Image Gene #43: '1q loss' versus Clinical Feature #8: 'NUMBER_OF_LYMPH_NODES'

'1q loss' versus 'GLEASON_SCORE'

P value = 0.0909 (Wilcoxon-test), Q value = 0.25

Table S169.  Gene #43: '1q loss' versus Clinical Feature #9: 'GLEASON_SCORE'

nPatients Mean (Std.Dev)
ALL 492 7.6 (1.0)
1Q LOSS MUTATED 6 8.3 (1.0)
1Q LOSS WILD-TYPE 486 7.6 (1.0)

Figure S169.  Get High-res Image Gene #43: '1q loss' versus Clinical Feature #9: 'GLEASON_SCORE'

'2p loss' versus 'YEARS_TO_BIRTH'

P value = 0.00694 (Wilcoxon-test), Q value = 0.036

Table S170.  Gene #44: '2p loss' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 481 61.0 (6.8)
2P LOSS MUTATED 14 65.8 (6.0)
2P LOSS WILD-TYPE 467 60.8 (6.8)

Figure S170.  Get High-res Image Gene #44: '2p loss' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'2p loss' versus 'PATHOLOGY_T_STAGE'

P value = 0.0132 (Fisher's exact test), Q value = 0.057

Table S171.  Gene #44: '2p loss' versus Clinical Feature #3: 'PATHOLOGY_T_STAGE'

nPatients T2 T3 T4
ALL 187 288 10
2P LOSS MUTATED 1 12 1
2P LOSS WILD-TYPE 186 276 9

Figure S171.  Get High-res Image Gene #44: '2p loss' versus Clinical Feature #3: 'PATHOLOGY_T_STAGE'

'2q loss' versus 'YEARS_TO_BIRTH'

P value = 0.0197 (Wilcoxon-test), Q value = 0.079

Table S172.  Gene #45: '2q loss' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 481 61.0 (6.8)
2Q LOSS MUTATED 18 64.8 (6.5)
2Q LOSS WILD-TYPE 463 60.8 (6.8)

Figure S172.  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 = 0.079

Table S173.  Gene #45: '2q loss' versus Clinical Feature #3: 'PATHOLOGY_T_STAGE'

nPatients T2 T3 T4
ALL 187 288 10
2Q LOSS MUTATED 2 15 1
2Q LOSS WILD-TYPE 185 273 9

Figure S173.  Get High-res Image Gene #45: '2q loss' versus Clinical Feature #3: 'PATHOLOGY_T_STAGE'

'2q loss' versus 'GLEASON_SCORE'

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

Table S174.  Gene #45: '2q loss' versus Clinical Feature #9: 'GLEASON_SCORE'

nPatients Mean (Std.Dev)
ALL 492 7.6 (1.0)
2Q LOSS MUTATED 18 8.2 (1.0)
2Q LOSS WILD-TYPE 474 7.6 (1.0)

Figure S174.  Get High-res Image Gene #45: '2q loss' versus Clinical Feature #9: 'GLEASON_SCORE'

'3p loss' versus 'GLEASON_SCORE'

P value = 0.00342 (Wilcoxon-test), Q value = 0.022

Table S175.  Gene #46: '3p loss' versus Clinical Feature #9: 'GLEASON_SCORE'

nPatients Mean (Std.Dev)
ALL 492 7.6 (1.0)
3P LOSS MUTATED 9 8.7 (1.1)
3P LOSS WILD-TYPE 483 7.6 (1.0)

Figure S175.  Get High-res Image Gene #46: '3p loss' versus Clinical Feature #9: 'GLEASON_SCORE'

'3q loss' versus 'GLEASON_SCORE'

P value = 0.00393 (Wilcoxon-test), Q value = 0.025

Table S176.  Gene #47: '3q loss' versus Clinical Feature #9: 'GLEASON_SCORE'

nPatients Mean (Std.Dev)
ALL 492 7.6 (1.0)
3Q LOSS MUTATED 5 9.0 (0.7)
3Q LOSS WILD-TYPE 487 7.6 (1.0)

Figure S176.  Get High-res Image Gene #47: '3q loss' versus Clinical Feature #9: 'GLEASON_SCORE'

'4p loss' versus 'PATHOLOGY_T_STAGE'

P value = 0.0497 (Fisher's exact test), Q value = 0.16

Table S177.  Gene #48: '4p loss' versus Clinical Feature #3: 'PATHOLOGY_T_STAGE'

nPatients T2 T3 T4
ALL 187 288 10
4P LOSS MUTATED 4 18 1
4P LOSS WILD-TYPE 183 270 9

Figure S177.  Get High-res Image Gene #48: '4p loss' versus Clinical Feature #3: 'PATHOLOGY_T_STAGE'

'4p loss' versus 'PATHOLOGY_N_STAGE'

P value = 0.000159 (Fisher's exact test), Q value = 0.0025

Table S178.  Gene #48: '4p loss' versus Clinical Feature #4: 'PATHOLOGY_N_STAGE'

nPatients 0 1
ALL 343 77
4P LOSS MUTATED 11 12
4P LOSS WILD-TYPE 332 65

Figure S178.  Get High-res Image Gene #48: '4p loss' versus Clinical Feature #4: 'PATHOLOGY_N_STAGE'

'4p loss' versus 'RADIATION_THERAPY'

P value = 0.0442 (Fisher's exact test), Q value = 0.14

Table S179.  Gene #48: '4p loss' versus Clinical Feature #5: 'RADIATION_THERAPY'

nPatients NO YES
ALL 390 59
4P LOSS MUTATED 15 6
4P LOSS WILD-TYPE 375 53

Figure S179.  Get High-res Image Gene #48: '4p loss' versus Clinical Feature #5: 'RADIATION_THERAPY'

'4p loss' versus 'RESIDUAL_TUMOR'

P value = 0.0188 (Fisher's exact test), Q value = 0.077

Table S180.  Gene #48: '4p loss' versus Clinical Feature #7: 'RESIDUAL_TUMOR'

nPatients R0 R1 R2 RX
ALL 313 144 5 15
4P LOSS MUTATED 8 13 0 1
4P LOSS WILD-TYPE 305 131 5 14

Figure S180.  Get High-res Image Gene #48: '4p loss' versus Clinical Feature #7: 'RESIDUAL_TUMOR'

'4p loss' versus 'NUMBER_OF_LYMPH_NODES'

P value = 1.13e-05 (Wilcoxon-test), Q value = 0.00032

Table S181.  Gene #48: '4p loss' versus Clinical Feature #8: 'NUMBER_OF_LYMPH_NODES'

nPatients Mean (Std.Dev)
ALL 402 0.4 (1.4)
4P LOSS MUTATED 22 1.3 (1.7)
4P LOSS WILD-TYPE 380 0.4 (1.3)

Figure S181.  Get High-res Image Gene #48: '4p loss' versus Clinical Feature #8: 'NUMBER_OF_LYMPH_NODES'

'4p loss' versus 'GLEASON_SCORE'

P value = 1.51e-06 (Wilcoxon-test), Q value = 7.8e-05

Table S182.  Gene #48: '4p loss' versus Clinical Feature #9: 'GLEASON_SCORE'

nPatients Mean (Std.Dev)
ALL 492 7.6 (1.0)
4P LOSS MUTATED 23 8.6 (0.7)
4P LOSS WILD-TYPE 469 7.6 (1.0)

Figure S182.  Get High-res Image Gene #48: '4p loss' versus Clinical Feature #9: 'GLEASON_SCORE'

'4q loss' versus 'PATHOLOGY_N_STAGE'

P value = 0.015 (Fisher's exact test), Q value = 0.065

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

nPatients 0 1
ALL 343 77
4Q LOSS MUTATED 9 7
4Q LOSS WILD-TYPE 334 70

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

'4q loss' versus 'RADIATION_THERAPY'

P value = 0.0111 (Fisher's exact test), Q value = 0.052

Table S184.  Gene #49: '4q loss' versus Clinical Feature #5: 'RADIATION_THERAPY'

nPatients NO YES
ALL 390 59
4Q LOSS MUTATED 10 6
4Q LOSS WILD-TYPE 380 53

Figure S184.  Get High-res Image Gene #49: '4q loss' versus Clinical Feature #5: 'RADIATION_THERAPY'

'4q loss' versus 'RESIDUAL_TUMOR'

P value = 0.0361 (Fisher's exact test), Q value = 0.12

Table S185.  Gene #49: '4q loss' versus Clinical Feature #7: 'RESIDUAL_TUMOR'

nPatients R0 R1 R2 RX
ALL 313 144 5 15
4Q LOSS MUTATED 5 10 0 0
4Q LOSS WILD-TYPE 308 134 5 15

Figure S185.  Get High-res Image Gene #49: '4q loss' versus Clinical Feature #7: 'RESIDUAL_TUMOR'

'4q loss' versus 'NUMBER_OF_LYMPH_NODES'

P value = 0.000556 (Wilcoxon-test), Q value = 0.0058

Table S186.  Gene #49: '4q loss' versus Clinical Feature #8: 'NUMBER_OF_LYMPH_NODES'

nPatients Mean (Std.Dev)
ALL 402 0.4 (1.4)
4Q LOSS MUTATED 15 1.2 (1.7)
4Q LOSS WILD-TYPE 387 0.4 (1.3)

Figure S186.  Get High-res Image Gene #49: '4q loss' versus Clinical Feature #8: 'NUMBER_OF_LYMPH_NODES'

'4q loss' versus 'GLEASON_SCORE'

P value = 5.89e-06 (Wilcoxon-test), Q value = 2e-04

Table S187.  Gene #49: '4q loss' versus Clinical Feature #9: 'GLEASON_SCORE'

nPatients Mean (Std.Dev)
ALL 492 7.6 (1.0)
4Q LOSS MUTATED 16 8.8 (0.6)
4Q LOSS WILD-TYPE 476 7.6 (1.0)

Figure S187.  Get High-res Image Gene #49: '4q loss' versus Clinical Feature #9: 'GLEASON_SCORE'

'5p loss' versus 'PATHOLOGY_T_STAGE'

P value = 0.00047 (Fisher's exact test), Q value = 0.0054

Table S188.  Gene #50: '5p loss' versus Clinical Feature #3: 'PATHOLOGY_T_STAGE'

nPatients T2 T3 T4
ALL 187 288 10
5P LOSS MUTATED 0 10 2
5P LOSS WILD-TYPE 187 278 8

Figure S188.  Get High-res Image Gene #50: '5p loss' versus Clinical Feature #3: 'PATHOLOGY_T_STAGE'

'5p loss' versus 'RADIATION_THERAPY'

P value = 0.00498 (Fisher's exact test), Q value = 0.029

Table S189.  Gene #50: '5p loss' versus Clinical Feature #5: 'RADIATION_THERAPY'

nPatients NO YES
ALL 390 59
5P LOSS MUTATED 5 5
5P LOSS WILD-TYPE 385 54

Figure S189.  Get High-res Image Gene #50: '5p loss' versus Clinical Feature #5: 'RADIATION_THERAPY'

'5p loss' versus 'RESIDUAL_TUMOR'

P value = 0.0619 (Fisher's exact test), Q value = 0.19

Table S190.  Gene #50: '5p loss' versus Clinical Feature #7: 'RESIDUAL_TUMOR'

nPatients R0 R1 R2 RX
ALL 313 144 5 15
5P LOSS MUTATED 4 8 0 0
5P LOSS WILD-TYPE 309 136 5 15

Figure S190.  Get High-res Image Gene #50: '5p loss' versus Clinical Feature #7: 'RESIDUAL_TUMOR'

'5p loss' versus 'GLEASON_SCORE'

P value = 5.56e-05 (Wilcoxon-test), Q value = 0.0011

Table S191.  Gene #50: '5p loss' versus Clinical Feature #9: 'GLEASON_SCORE'

nPatients Mean (Std.Dev)
ALL 492 7.6 (1.0)
5P LOSS MUTATED 12 8.8 (0.7)
5P LOSS WILD-TYPE 480 7.6 (1.0)

Figure S191.  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 = 0.00066

Table S192.  Gene #51: '5q loss' versus Clinical Feature #3: 'PATHOLOGY_T_STAGE'

nPatients T2 T3 T4
ALL 187 288 10
5Q LOSS MUTATED 2 17 4
5Q LOSS WILD-TYPE 185 271 6

Figure S192.  Get High-res Image Gene #51: '5q loss' versus Clinical Feature #3: 'PATHOLOGY_T_STAGE'

'5q loss' versus 'PATHOLOGY_N_STAGE'

P value = 0.00051 (Fisher's exact test), Q value = 0.0055

Table S193.  Gene #51: '5q loss' versus Clinical Feature #4: 'PATHOLOGY_N_STAGE'

nPatients 0 1
ALL 343 77
5Q LOSS MUTATED 11 11
5Q LOSS WILD-TYPE 332 66

Figure S193.  Get High-res Image Gene #51: '5q loss' versus Clinical Feature #4: 'PATHOLOGY_N_STAGE'

'5q loss' versus 'RADIATION_THERAPY'

P value = 0.00925 (Fisher's exact test), Q value = 0.046

Table S194.  Gene #51: '5q loss' versus Clinical Feature #5: 'RADIATION_THERAPY'

nPatients NO YES
ALL 390 59
5Q LOSS MUTATED 13 7
5Q LOSS WILD-TYPE 377 52

Figure S194.  Get High-res Image Gene #51: '5q loss' versus Clinical Feature #5: 'RADIATION_THERAPY'

'5q loss' versus 'NUMBER_OF_LYMPH_NODES'

P value = 6.25e-05 (Wilcoxon-test), Q value = 0.0011

Table S195.  Gene #51: '5q loss' versus Clinical Feature #8: 'NUMBER_OF_LYMPH_NODES'

nPatients Mean (Std.Dev)
ALL 402 0.4 (1.4)
5Q LOSS MUTATED 20 1.0 (1.5)
5Q LOSS WILD-TYPE 382 0.4 (1.4)

Figure S195.  Get High-res Image Gene #51: '5q loss' versus Clinical Feature #8: 'NUMBER_OF_LYMPH_NODES'

'5q loss' versus 'GLEASON_SCORE'

P value = 1.92e-06 (Wilcoxon-test), Q value = 8.5e-05

Table S196.  Gene #51: '5q loss' versus Clinical Feature #9: 'GLEASON_SCORE'

nPatients Mean (Std.Dev)
ALL 492 7.6 (1.0)
5Q LOSS MUTATED 23 8.6 (0.8)
5Q LOSS WILD-TYPE 469 7.6 (1.0)

Figure S196.  Get High-res Image Gene #51: '5q loss' versus Clinical Feature #9: 'GLEASON_SCORE'

'6p loss' versus 'PATHOLOGY_T_STAGE'

P value = 0.00201 (Fisher's exact test), Q value = 0.015

Table S197.  Gene #52: '6p loss' versus Clinical Feature #3: 'PATHOLOGY_T_STAGE'

nPatients T2 T3 T4
ALL 187 288 10
6P LOSS MUTATED 4 18 3
6P LOSS WILD-TYPE 183 270 7

Figure S197.  Get High-res Image Gene #52: '6p loss' versus Clinical Feature #3: 'PATHOLOGY_T_STAGE'

'6p loss' versus 'PATHOLOGY_N_STAGE'

P value = 0.00364 (Fisher's exact test), Q value = 0.023

Table S198.  Gene #52: '6p loss' versus Clinical Feature #4: 'PATHOLOGY_N_STAGE'

nPatients 0 1
ALL 343 77
6P LOSS MUTATED 13 10
6P LOSS WILD-TYPE 330 67

Figure S198.  Get High-res Image Gene #52: '6p loss' versus Clinical Feature #4: 'PATHOLOGY_N_STAGE'

'6p loss' versus 'RESIDUAL_TUMOR'

P value = 0.0897 (Fisher's exact test), Q value = 0.25

Table S199.  Gene #52: '6p loss' versus Clinical Feature #7: 'RESIDUAL_TUMOR'

nPatients R0 R1 R2 RX
ALL 313 144 5 15
6P LOSS MUTATED 11 13 0 0
6P LOSS WILD-TYPE 302 131 5 15

Figure S199.  Get High-res Image Gene #52: '6p loss' versus Clinical Feature #7: 'RESIDUAL_TUMOR'

'6p loss' versus 'NUMBER_OF_LYMPH_NODES'

P value = 0.00254 (Wilcoxon-test), Q value = 0.018

Table S200.  Gene #52: '6p loss' versus Clinical Feature #8: 'NUMBER_OF_LYMPH_NODES'

nPatients Mean (Std.Dev)
ALL 402 0.4 (1.4)
6P LOSS MUTATED 22 0.6 (0.8)
6P LOSS WILD-TYPE 380 0.4 (1.4)

Figure S200.  Get High-res Image Gene #52: '6p loss' versus Clinical Feature #8: 'NUMBER_OF_LYMPH_NODES'

'6p loss' versus 'GLEASON_SCORE'

P value = 9.2e-06 (Wilcoxon-test), Q value = 0.00029

Table S201.  Gene #52: '6p loss' versus Clinical Feature #9: 'GLEASON_SCORE'

nPatients Mean (Std.Dev)
ALL 492 7.6 (1.0)
6P LOSS MUTATED 26 8.5 (0.9)
6P LOSS WILD-TYPE 466 7.6 (1.0)

Figure S201.  Get High-res Image Gene #52: '6p loss' versus Clinical Feature #9: 'GLEASON_SCORE'

'6q loss' versus 'Time to Death'

P value = 0.0475 (logrank test), Q value = 0.15

Table S202.  Gene #53: '6q loss' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 492 9 0.8 - 165.2 (30.6)
6Q LOSS MUTATED 41 2 1.0 - 75.8 (29.9)
6Q LOSS WILD-TYPE 451 7 0.8 - 165.2 (30.7)

Figure S202.  Get High-res Image Gene #53: '6q loss' versus Clinical Feature #1: 'Time to Death'

'6q loss' versus 'PATHOLOGY_T_STAGE'

P value = 0.00159 (Fisher's exact test), Q value = 0.013

Table S203.  Gene #53: '6q loss' versus Clinical Feature #3: 'PATHOLOGY_T_STAGE'

nPatients T2 T3 T4
ALL 187 288 10
6Q LOSS MUTATED 7 30 3
6Q LOSS WILD-TYPE 180 258 7

Figure S203.  Get High-res Image Gene #53: '6q loss' versus Clinical Feature #3: 'PATHOLOGY_T_STAGE'

'6q loss' versus 'PATHOLOGY_N_STAGE'

P value = 0.00746 (Fisher's exact test), Q value = 0.038

Table S204.  Gene #53: '6q loss' versus Clinical Feature #4: 'PATHOLOGY_N_STAGE'

nPatients 0 1
ALL 343 77
6Q LOSS MUTATED 25 14
6Q LOSS WILD-TYPE 318 63

Figure S204.  Get High-res Image Gene #53: '6q loss' versus Clinical Feature #4: 'PATHOLOGY_N_STAGE'

'6q loss' versus 'RADIATION_THERAPY'

P value = 0.0209 (Fisher's exact test), Q value = 0.081

Table S205.  Gene #53: '6q loss' versus Clinical Feature #5: 'RADIATION_THERAPY'

nPatients NO YES
ALL 390 59
6Q LOSS MUTATED 28 10
6Q LOSS WILD-TYPE 362 49

Figure S205.  Get High-res Image Gene #53: '6q loss' versus Clinical Feature #5: 'RADIATION_THERAPY'

'6q loss' versus 'NUMBER_OF_LYMPH_NODES'

P value = 0.00086 (Wilcoxon-test), Q value = 0.0081

Table S206.  Gene #53: '6q loss' versus Clinical Feature #8: 'NUMBER_OF_LYMPH_NODES'

nPatients Mean (Std.Dev)
ALL 402 0.4 (1.4)
6Q LOSS MUTATED 38 0.8 (1.3)
6Q LOSS WILD-TYPE 364 0.4 (1.4)

Figure S206.  Get High-res Image Gene #53: '6q loss' versus Clinical Feature #8: 'NUMBER_OF_LYMPH_NODES'

'6q loss' versus 'GLEASON_SCORE'

P value = 9.51e-09 (Wilcoxon-test), Q value = 2.8e-06

Table S207.  Gene #53: '6q loss' versus Clinical Feature #9: 'GLEASON_SCORE'

nPatients Mean (Std.Dev)
ALL 492 7.6 (1.0)
6Q LOSS MUTATED 41 8.5 (0.9)
6Q LOSS WILD-TYPE 451 7.5 (1.0)

Figure S207.  Get High-res Image Gene #53: '6q loss' versus Clinical Feature #9: 'GLEASON_SCORE'

'8p loss' versus 'PATHOLOGY_T_STAGE'

P value = 0.00012 (Fisher's exact test), Q value = 0.002

Table S208.  Gene #54: '8p loss' versus Clinical Feature #3: 'PATHOLOGY_T_STAGE'

nPatients T2 T3 T4
ALL 187 288 10
8P LOSS MUTATED 45 121 3
8P LOSS WILD-TYPE 142 167 7

Figure S208.  Get High-res Image Gene #54: '8p loss' versus Clinical Feature #3: 'PATHOLOGY_T_STAGE'

'8p loss' versus 'NUMBER_OF_LYMPH_NODES'

P value = 0.0528 (Wilcoxon-test), Q value = 0.16

Table S209.  Gene #54: '8p loss' versus Clinical Feature #8: 'NUMBER_OF_LYMPH_NODES'

nPatients Mean (Std.Dev)
ALL 402 0.4 (1.4)
8P LOSS MUTATED 141 0.6 (1.8)
8P LOSS WILD-TYPE 261 0.3 (1.0)

Figure S209.  Get High-res Image Gene #54: '8p loss' versus Clinical Feature #8: 'NUMBER_OF_LYMPH_NODES'

'8q loss' versus 'Time to Death'

P value = 0.000979 (logrank test), Q value = 0.0087

Table S210.  Gene #55: '8q loss' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 492 9 0.8 - 165.2 (30.6)
8Q LOSS MUTATED 21 2 1.0 - 109.2 (26.4)
8Q LOSS WILD-TYPE 471 7 0.8 - 165.2 (30.7)

Figure S210.  Get High-res Image Gene #55: '8q loss' versus Clinical Feature #1: 'Time to Death'

'8q loss' versus 'PATHOLOGY_T_STAGE'

P value = 0.00112 (Fisher's exact test), Q value = 0.0096

Table S211.  Gene #55: '8q loss' versus Clinical Feature #3: 'PATHOLOGY_T_STAGE'

nPatients T2 T3 T4
ALL 187 288 10
8Q LOSS MUTATED 1 19 1
8Q LOSS WILD-TYPE 186 269 9

Figure S211.  Get High-res Image Gene #55: '8q loss' versus Clinical Feature #3: 'PATHOLOGY_T_STAGE'

'8q loss' versus 'PATHOLOGY_N_STAGE'

P value = 0.00446 (Fisher's exact test), Q value = 0.027

Table S212.  Gene #55: '8q loss' versus Clinical Feature #4: 'PATHOLOGY_N_STAGE'

nPatients 0 1
ALL 343 77
8Q LOSS MUTATED 11 9
8Q LOSS WILD-TYPE 332 68

Figure S212.  Get High-res Image Gene #55: '8q loss' versus Clinical Feature #4: 'PATHOLOGY_N_STAGE'

'8q loss' versus 'RADIATION_THERAPY'

P value = 0.0585 (Fisher's exact test), Q value = 0.18

Table S213.  Gene #55: '8q loss' versus Clinical Feature #5: 'RADIATION_THERAPY'

nPatients NO YES
ALL 390 59
8Q LOSS MUTATED 12 5
8Q LOSS WILD-TYPE 378 54

Figure S213.  Get High-res Image Gene #55: '8q loss' versus Clinical Feature #5: 'RADIATION_THERAPY'

'8q loss' versus 'NUMBER_OF_LYMPH_NODES'

P value = 0.000221 (Wilcoxon-test), Q value = 0.0033

Table S214.  Gene #55: '8q loss' versus Clinical Feature #8: 'NUMBER_OF_LYMPH_NODES'

nPatients Mean (Std.Dev)
ALL 402 0.4 (1.4)
8Q LOSS MUTATED 18 1.5 (2.2)
8Q LOSS WILD-TYPE 384 0.4 (1.3)

Figure S214.  Get High-res Image Gene #55: '8q loss' versus Clinical Feature #8: 'NUMBER_OF_LYMPH_NODES'

'8q loss' versus 'GLEASON_SCORE'

P value = 0.0419 (Wilcoxon-test), Q value = 0.14

Table S215.  Gene #55: '8q loss' versus Clinical Feature #9: 'GLEASON_SCORE'

nPatients Mean (Std.Dev)
ALL 492 7.6 (1.0)
8Q LOSS MUTATED 21 8.0 (1.0)
8Q LOSS WILD-TYPE 471 7.6 (1.0)

Figure S215.  Get High-res Image Gene #55: '8q loss' versus Clinical Feature #9: 'GLEASON_SCORE'

'9p loss' versus 'PATHOLOGY_T_STAGE'

P value = 0.0204 (Fisher's exact test), Q value = 0.079

Table S216.  Gene #56: '9p loss' versus Clinical Feature #3: 'PATHOLOGY_T_STAGE'

nPatients T2 T3 T4
ALL 187 288 10
9P LOSS MUTATED 4 15 2
9P LOSS WILD-TYPE 183 273 8

Figure S216.  Get High-res Image Gene #56: '9p loss' versus Clinical Feature #3: 'PATHOLOGY_T_STAGE'

'9p loss' versus 'PATHOLOGY_N_STAGE'

P value = 0.0696 (Fisher's exact test), Q value = 0.21

Table S217.  Gene #56: '9p loss' versus Clinical Feature #4: 'PATHOLOGY_N_STAGE'

nPatients 0 1
ALL 343 77
9P LOSS MUTATED 13 7
9P LOSS WILD-TYPE 330 70

Figure S217.  Get High-res Image Gene #56: '9p loss' versus Clinical Feature #4: 'PATHOLOGY_N_STAGE'

'9p loss' versus 'NUMBER_OF_LYMPH_NODES'

P value = 0.0217 (Wilcoxon-test), Q value = 0.083

Table S218.  Gene #56: '9p loss' versus Clinical Feature #8: 'NUMBER_OF_LYMPH_NODES'

nPatients Mean (Std.Dev)
ALL 402 0.4 (1.4)
9P LOSS MUTATED 18 1.4 (2.9)
9P LOSS WILD-TYPE 384 0.4 (1.2)

Figure S218.  Get High-res Image Gene #56: '9p loss' versus Clinical Feature #8: 'NUMBER_OF_LYMPH_NODES'

'9p loss' versus 'GLEASON_SCORE'

P value = 0.00595 (Wilcoxon-test), Q value = 0.033

Table S219.  Gene #56: '9p loss' versus Clinical Feature #9: 'GLEASON_SCORE'

nPatients Mean (Std.Dev)
ALL 492 7.6 (1.0)
9P LOSS MUTATED 21 8.2 (1.1)
9P LOSS WILD-TYPE 471 7.6 (1.0)

Figure S219.  Get High-res Image Gene #56: '9p loss' versus Clinical Feature #9: 'GLEASON_SCORE'

'9q loss' versus 'PATHOLOGY_N_STAGE'

P value = 0.0909 (Fisher's exact test), Q value = 0.25

Table S220.  Gene #57: '9q loss' versus Clinical Feature #4: 'PATHOLOGY_N_STAGE'

nPatients 0 1
ALL 343 77
9Q LOSS MUTATED 6 4
9Q LOSS WILD-TYPE 337 73

Figure S220.  Get High-res Image Gene #57: '9q loss' versus Clinical Feature #4: 'PATHOLOGY_N_STAGE'

'9q loss' versus 'NUMBER_OF_LYMPH_NODES'

P value = 0.071 (Wilcoxon-test), Q value = 0.21

Table S221.  Gene #57: '9q loss' versus Clinical Feature #8: 'NUMBER_OF_LYMPH_NODES'

nPatients Mean (Std.Dev)
ALL 402 0.4 (1.4)
9Q LOSS MUTATED 10 1.9 (3.7)
9Q LOSS WILD-TYPE 392 0.4 (1.2)

Figure S221.  Get High-res Image Gene #57: '9q loss' versus Clinical Feature #8: 'NUMBER_OF_LYMPH_NODES'

'9q loss' versus 'GLEASON_SCORE'

P value = 0.013 (Wilcoxon-test), Q value = 0.057

Table S222.  Gene #57: '9q loss' versus Clinical Feature #9: 'GLEASON_SCORE'

nPatients Mean (Std.Dev)
ALL 492 7.6 (1.0)
9Q LOSS MUTATED 11 8.4 (1.0)
9Q LOSS WILD-TYPE 481 7.6 (1.0)

Figure S222.  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 = 0.00048

Table S223.  Gene #58: '10p loss' versus Clinical Feature #3: 'PATHOLOGY_T_STAGE'

nPatients T2 T3 T4
ALL 187 288 10
10P LOSS MUTATED 7 28 6
10P LOSS WILD-TYPE 180 260 4

Figure S223.  Get High-res Image Gene #58: '10p loss' versus Clinical Feature #3: 'PATHOLOGY_T_STAGE'

'10p loss' versus 'PATHOLOGY_N_STAGE'

P value = 0.000292 (Fisher's exact test), Q value = 0.0039

Table S224.  Gene #58: '10p loss' versus Clinical Feature #4: 'PATHOLOGY_N_STAGE'

nPatients 0 1
ALL 343 77
10P LOSS MUTATED 22 16
10P LOSS WILD-TYPE 321 61

Figure S224.  Get High-res Image Gene #58: '10p loss' versus Clinical Feature #4: 'PATHOLOGY_N_STAGE'

'10p loss' versus 'RESIDUAL_TUMOR'

P value = 0.0175 (Fisher's exact test), Q value = 0.072

Table S225.  Gene #58: '10p loss' versus Clinical Feature #7: 'RESIDUAL_TUMOR'

nPatients R0 R1 R2 RX
ALL 313 144 5 15
10P LOSS MUTATED 19 20 1 0
10P LOSS WILD-TYPE 294 124 4 15

Figure S225.  Get High-res Image Gene #58: '10p loss' versus Clinical Feature #7: 'RESIDUAL_TUMOR'

'10p loss' versus 'NUMBER_OF_LYMPH_NODES'

P value = 2.63e-05 (Wilcoxon-test), Q value = 0.00061

Table S226.  Gene #58: '10p loss' versus Clinical Feature #8: 'NUMBER_OF_LYMPH_NODES'

nPatients Mean (Std.Dev)
ALL 402 0.4 (1.4)
10P LOSS MUTATED 37 1.3 (2.2)
10P LOSS WILD-TYPE 365 0.3 (1.2)

Figure S226.  Get High-res Image Gene #58: '10p loss' versus Clinical Feature #8: 'NUMBER_OF_LYMPH_NODES'

'10p loss' versus 'GLEASON_SCORE'

P value = 2.96e-06 (Wilcoxon-test), Q value = 0.00011

Table S227.  Gene #58: '10p loss' versus Clinical Feature #9: 'GLEASON_SCORE'

nPatients Mean (Std.Dev)
ALL 492 7.6 (1.0)
10P LOSS MUTATED 41 8.3 (1.0)
10P LOSS WILD-TYPE 451 7.5 (1.0)

Figure S227.  Get High-res Image Gene #58: '10p loss' versus Clinical Feature #9: 'GLEASON_SCORE'

'10q loss' versus 'PATHOLOGY_T_STAGE'

P value = 2e-04 (Fisher's exact test), Q value = 0.003

Table S228.  Gene #59: '10q loss' versus Clinical Feature #3: 'PATHOLOGY_T_STAGE'

nPatients T2 T3 T4
ALL 187 288 10
10Q LOSS MUTATED 9 29 5
10Q LOSS WILD-TYPE 178 259 5

Figure S228.  Get High-res Image Gene #59: '10q loss' versus Clinical Feature #3: 'PATHOLOGY_T_STAGE'

'10q loss' versus 'PATHOLOGY_N_STAGE'

P value = 0.000381 (Fisher's exact test), Q value = 0.0047

Table S229.  Gene #59: '10q loss' versus Clinical Feature #4: 'PATHOLOGY_N_STAGE'

nPatients 0 1
ALL 343 77
10Q LOSS MUTATED 24 17
10Q LOSS WILD-TYPE 319 60

Figure S229.  Get High-res Image Gene #59: '10q loss' versus Clinical Feature #4: 'PATHOLOGY_N_STAGE'

'10q loss' versus 'RESIDUAL_TUMOR'

P value = 0.00633 (Fisher's exact test), Q value = 0.034

Table S230.  Gene #59: '10q loss' versus Clinical Feature #7: 'RESIDUAL_TUMOR'

nPatients R0 R1 R2 RX
ALL 313 144 5 15
10Q LOSS MUTATED 19 23 0 0
10Q LOSS WILD-TYPE 294 121 5 15

Figure S230.  Get High-res Image Gene #59: '10q loss' versus Clinical Feature #7: 'RESIDUAL_TUMOR'

'10q loss' versus 'NUMBER_OF_LYMPH_NODES'

P value = 4.66e-05 (Wilcoxon-test), Q value = 0.00095

Table S231.  Gene #59: '10q loss' versus Clinical Feature #8: 'NUMBER_OF_LYMPH_NODES'

nPatients Mean (Std.Dev)
ALL 402 0.4 (1.4)
10Q LOSS MUTATED 40 1.1 (1.9)
10Q LOSS WILD-TYPE 362 0.4 (1.3)

Figure S231.  Get High-res Image Gene #59: '10q loss' versus Clinical Feature #8: 'NUMBER_OF_LYMPH_NODES'

'10q loss' versus 'GLEASON_SCORE'

P value = 3.96e-08 (Wilcoxon-test), Q value = 4.4e-06

Table S232.  Gene #59: '10q loss' versus Clinical Feature #9: 'GLEASON_SCORE'

nPatients Mean (Std.Dev)
ALL 492 7.6 (1.0)
10Q LOSS MUTATED 43 8.4 (0.9)
10Q LOSS WILD-TYPE 449 7.5 (1.0)

Figure S232.  Get High-res Image Gene #59: '10q loss' versus Clinical Feature #9: 'GLEASON_SCORE'

'11p loss' versus 'Time to Death'

P value = 0.00506 (logrank test), Q value = 0.029

Table S233.  Gene #60: '11p loss' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 492 9 0.8 - 165.2 (30.6)
11P LOSS MUTATED 8 1 4.3 - 67.5 (26.5)
11P LOSS WILD-TYPE 484 8 0.8 - 165.2 (30.8)

Figure S233.  Get High-res Image Gene #60: '11p loss' versus Clinical Feature #1: 'Time to Death'

'11p loss' versus 'PATHOLOGY_T_STAGE'

P value = 0.0749 (Fisher's exact test), Q value = 0.22

Table S234.  Gene #60: '11p loss' versus Clinical Feature #3: 'PATHOLOGY_T_STAGE'

nPatients T2 T3 T4
ALL 187 288 10
11P LOSS MUTATED 1 5 1
11P LOSS WILD-TYPE 186 283 9

Figure S234.  Get High-res Image Gene #60: '11p loss' versus Clinical Feature #3: 'PATHOLOGY_T_STAGE'

'11p loss' versus 'GLEASON_SCORE'

P value = 0.0196 (Wilcoxon-test), Q value = 0.079

Table S235.  Gene #60: '11p loss' versus Clinical Feature #9: 'GLEASON_SCORE'

nPatients Mean (Std.Dev)
ALL 492 7.6 (1.0)
11P LOSS MUTATED 8 8.5 (1.1)
11P LOSS WILD-TYPE 484 7.6 (1.0)

Figure S235.  Get High-res Image Gene #60: '11p loss' versus Clinical Feature #9: 'GLEASON_SCORE'

'11q loss' versus 'PATHOLOGY_T_STAGE'

P value = 0.0274 (Fisher's exact test), Q value = 0.1

Table S236.  Gene #61: '11q loss' versus Clinical Feature #3: 'PATHOLOGY_T_STAGE'

nPatients T2 T3 T4
ALL 187 288 10
11Q LOSS MUTATED 0 4 1
11Q LOSS WILD-TYPE 187 284 9

Figure S236.  Get High-res Image Gene #61: '11q loss' versus Clinical Feature #3: 'PATHOLOGY_T_STAGE'

'11q loss' versus 'GLEASON_SCORE'

P value = 0.0341 (Wilcoxon-test), Q value = 0.12

Table S237.  Gene #61: '11q loss' versus Clinical Feature #9: 'GLEASON_SCORE'

nPatients Mean (Std.Dev)
ALL 492 7.6 (1.0)
11Q LOSS MUTATED 5 8.6 (0.9)
11Q LOSS WILD-TYPE 487 7.6 (1.0)

Figure S237.  Get High-res Image Gene #61: '11q loss' versus Clinical Feature #9: 'GLEASON_SCORE'

'12p loss' versus 'PATHOLOGY_T_STAGE'

P value = 0.00565 (Fisher's exact test), Q value = 0.031

Table S238.  Gene #62: '12p loss' versus Clinical Feature #3: 'PATHOLOGY_T_STAGE'

nPatients T2 T3 T4
ALL 187 288 10
12P LOSS MUTATED 10 34 3
12P LOSS WILD-TYPE 177 254 7

Figure S238.  Get High-res Image Gene #62: '12p loss' versus Clinical Feature #3: 'PATHOLOGY_T_STAGE'

'12p loss' versus 'PATHOLOGY_N_STAGE'

P value = 0.000521 (Fisher's exact test), Q value = 0.0055

Table S239.  Gene #62: '12p loss' versus Clinical Feature #4: 'PATHOLOGY_N_STAGE'

nPatients 0 1
ALL 343 77
12P LOSS MUTATED 29 18
12P LOSS WILD-TYPE 314 59

Figure S239.  Get High-res Image Gene #62: '12p loss' versus Clinical Feature #4: 'PATHOLOGY_N_STAGE'

'12p loss' versus 'NUMBER_OF_LYMPH_NODES'

P value = 0.000399 (Wilcoxon-test), Q value = 0.0048

Table S240.  Gene #62: '12p loss' versus Clinical Feature #8: 'NUMBER_OF_LYMPH_NODES'

nPatients Mean (Std.Dev)
ALL 402 0.4 (1.4)
12P LOSS MUTATED 45 0.7 (1.1)
12P LOSS WILD-TYPE 357 0.4 (1.4)

Figure S240.  Get High-res Image Gene #62: '12p loss' versus Clinical Feature #8: 'NUMBER_OF_LYMPH_NODES'

'12p loss' versus 'GLEASON_SCORE'

P value = 0.000505 (Wilcoxon-test), Q value = 0.0055

Table S241.  Gene #62: '12p loss' versus Clinical Feature #9: 'GLEASON_SCORE'

nPatients Mean (Std.Dev)
ALL 492 7.6 (1.0)
12P LOSS MUTATED 47 8.1 (1.0)
12P LOSS WILD-TYPE 445 7.6 (1.0)

Figure S241.  Get High-res Image Gene #62: '12p loss' versus Clinical Feature #9: 'GLEASON_SCORE'

'12q loss' versus 'PATHOLOGY_N_STAGE'

P value = 0.0171 (Fisher's exact test), Q value = 0.072

Table S242.  Gene #63: '12q loss' versus Clinical Feature #4: 'PATHOLOGY_N_STAGE'

nPatients 0 1
ALL 343 77
12Q LOSS MUTATED 12 8
12Q LOSS WILD-TYPE 331 69

Figure S242.  Get High-res Image Gene #63: '12q loss' versus Clinical Feature #4: 'PATHOLOGY_N_STAGE'

'12q loss' versus 'NUMBER_OF_LYMPH_NODES'

P value = 0.0158 (Wilcoxon-test), Q value = 0.067

Table S243.  Gene #63: '12q loss' versus Clinical Feature #8: 'NUMBER_OF_LYMPH_NODES'

nPatients Mean (Std.Dev)
ALL 402 0.4 (1.4)
12Q LOSS MUTATED 19 0.7 (1.3)
12Q LOSS WILD-TYPE 383 0.4 (1.4)

Figure S243.  Get High-res Image Gene #63: '12q loss' versus Clinical Feature #8: 'NUMBER_OF_LYMPH_NODES'

'12q loss' versus 'GLEASON_SCORE'

P value = 0.00135 (Wilcoxon-test), Q value = 0.011

Table S244.  Gene #63: '12q loss' versus Clinical Feature #9: 'GLEASON_SCORE'

nPatients Mean (Std.Dev)
ALL 492 7.6 (1.0)
12Q LOSS MUTATED 20 8.3 (1.0)
12Q LOSS WILD-TYPE 472 7.6 (1.0)

Figure S244.  Get High-res Image Gene #63: '12q loss' versus Clinical Feature #9: 'GLEASON_SCORE'

'13q loss' versus 'YEARS_TO_BIRTH'

P value = 0.0673 (Wilcoxon-test), Q value = 0.2

Table S245.  Gene #64: '13q loss' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 481 61.0 (6.8)
13Q LOSS MUTATED 76 62.2 (6.7)
13Q LOSS WILD-TYPE 405 60.7 (6.8)

Figure S245.  Get High-res Image Gene #64: '13q loss' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'13q loss' versus 'PATHOLOGY_T_STAGE'

P value = 0.00067 (Fisher's exact test), Q value = 0.0067

Table S246.  Gene #64: '13q loss' versus Clinical Feature #3: 'PATHOLOGY_T_STAGE'

nPatients T2 T3 T4
ALL 187 288 10
13Q LOSS MUTATED 16 58 3
13Q LOSS WILD-TYPE 171 230 7

Figure S246.  Get High-res Image Gene #64: '13q loss' versus Clinical Feature #3: 'PATHOLOGY_T_STAGE'

'13q loss' versus 'PATHOLOGY_N_STAGE'

P value = 0.0121 (Fisher's exact test), Q value = 0.055

Table S247.  Gene #64: '13q loss' versus Clinical Feature #4: 'PATHOLOGY_N_STAGE'

nPatients 0 1
ALL 343 77
13Q LOSS MUTATED 51 21
13Q LOSS WILD-TYPE 292 56

Figure S247.  Get High-res Image Gene #64: '13q loss' versus Clinical Feature #4: 'PATHOLOGY_N_STAGE'

'13q loss' versus 'RESIDUAL_TUMOR'

P value = 0.0262 (Fisher's exact test), Q value = 0.097

Table S248.  Gene #64: '13q loss' versus Clinical Feature #7: 'RESIDUAL_TUMOR'

nPatients R0 R1 R2 RX
ALL 313 144 5 15
13Q LOSS MUTATED 39 33 0 3
13Q LOSS WILD-TYPE 274 111 5 12

Figure S248.  Get High-res Image Gene #64: '13q loss' versus Clinical Feature #7: 'RESIDUAL_TUMOR'

'13q loss' versus 'NUMBER_OF_LYMPH_NODES'

P value = 0.0048 (Wilcoxon-test), Q value = 0.029

Table S249.  Gene #64: '13q loss' versus Clinical Feature #8: 'NUMBER_OF_LYMPH_NODES'

nPatients Mean (Std.Dev)
ALL 402 0.4 (1.4)
13Q LOSS MUTATED 69 0.8 (1.7)
13Q LOSS WILD-TYPE 333 0.4 (1.3)

Figure S249.  Get High-res Image Gene #64: '13q loss' versus Clinical Feature #8: 'NUMBER_OF_LYMPH_NODES'

'13q loss' versus 'GLEASON_SCORE'

P value = 1.65e-11 (Wilcoxon-test), Q value = 1.4e-08

Table S250.  Gene #64: '13q loss' versus Clinical Feature #9: 'GLEASON_SCORE'

nPatients Mean (Std.Dev)
ALL 492 7.6 (1.0)
13Q LOSS MUTATED 78 8.3 (0.9)
13Q LOSS WILD-TYPE 414 7.5 (1.0)

Figure S250.  Get High-res Image Gene #64: '13q loss' versus Clinical Feature #9: 'GLEASON_SCORE'

'14q loss' versus 'PATHOLOGY_T_STAGE'

P value = 0.00051 (Fisher's exact test), Q value = 0.0055

Table S251.  Gene #65: '14q loss' versus Clinical Feature #3: 'PATHOLOGY_T_STAGE'

nPatients T2 T3 T4
ALL 187 288 10
14Q LOSS MUTATED 2 21 2
14Q LOSS WILD-TYPE 185 267 8

Figure S251.  Get High-res Image Gene #65: '14q loss' versus Clinical Feature #3: 'PATHOLOGY_T_STAGE'

'14q loss' versus 'PATHOLOGY_N_STAGE'

P value = 0.0296 (Fisher's exact test), Q value = 0.11

Table S252.  Gene #65: '14q loss' versus Clinical Feature #4: 'PATHOLOGY_N_STAGE'

nPatients 0 1
ALL 343 77
14Q LOSS MUTATED 16 9
14Q LOSS WILD-TYPE 327 68

Figure S252.  Get High-res Image Gene #65: '14q loss' versus Clinical Feature #4: 'PATHOLOGY_N_STAGE'

'14q loss' versus 'RESIDUAL_TUMOR'

P value = 0.0175 (Fisher's exact test), Q value = 0.072

Table S253.  Gene #65: '14q loss' versus Clinical Feature #7: 'RESIDUAL_TUMOR'

nPatients R0 R1 R2 RX
ALL 313 144 5 15
14Q LOSS MUTATED 9 14 0 1
14Q LOSS WILD-TYPE 304 130 5 14

Figure S253.  Get High-res Image Gene #65: '14q loss' versus Clinical Feature #7: 'RESIDUAL_TUMOR'

'14q loss' versus 'NUMBER_OF_LYMPH_NODES'

P value = 0.0336 (Wilcoxon-test), Q value = 0.12

Table S254.  Gene #65: '14q loss' versus Clinical Feature #8: 'NUMBER_OF_LYMPH_NODES'

nPatients Mean (Std.Dev)
ALL 402 0.4 (1.4)
14Q LOSS MUTATED 25 0.6 (1.0)
14Q LOSS WILD-TYPE 377 0.4 (1.4)

Figure S254.  Get High-res Image Gene #65: '14q loss' versus Clinical Feature #8: 'NUMBER_OF_LYMPH_NODES'

'14q loss' versus 'GLEASON_SCORE'

P value = 4e-04 (Wilcoxon-test), Q value = 0.0048

Table S255.  Gene #65: '14q loss' versus Clinical Feature #9: 'GLEASON_SCORE'

nPatients Mean (Std.Dev)
ALL 492 7.6 (1.0)
14Q LOSS MUTATED 25 8.3 (0.9)
14Q LOSS WILD-TYPE 467 7.6 (1.0)

Figure S255.  Get High-res Image Gene #65: '14q loss' versus Clinical Feature #9: 'GLEASON_SCORE'

'15q loss' versus 'YEARS_TO_BIRTH'

P value = 0.0174 (Wilcoxon-test), Q value = 0.072

Table S256.  Gene #66: '15q loss' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 481 61.0 (6.8)
15Q LOSS MUTATED 35 63.7 (6.3)
15Q LOSS WILD-TYPE 446 60.8 (6.8)

Figure S256.  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 = 0.00029

Table S257.  Gene #66: '15q loss' versus Clinical Feature #3: 'PATHOLOGY_T_STAGE'

nPatients T2 T3 T4
ALL 187 288 10
15Q LOSS MUTATED 1 31 3
15Q LOSS WILD-TYPE 186 257 7

Figure S257.  Get High-res Image Gene #66: '15q loss' versus Clinical Feature #3: 'PATHOLOGY_T_STAGE'

'15q loss' versus 'PATHOLOGY_N_STAGE'

P value = 0.00298 (Fisher's exact test), Q value = 0.02

Table S258.  Gene #66: '15q loss' versus Clinical Feature #4: 'PATHOLOGY_N_STAGE'

nPatients 0 1
ALL 343 77
15Q LOSS MUTATED 19 13
15Q LOSS WILD-TYPE 324 64

Figure S258.  Get High-res Image Gene #66: '15q loss' versus Clinical Feature #4: 'PATHOLOGY_N_STAGE'

'15q loss' versus 'NUMBER_OF_LYMPH_NODES'

P value = 0.000925 (Wilcoxon-test), Q value = 0.0084

Table S259.  Gene #66: '15q loss' versus Clinical Feature #8: 'NUMBER_OF_LYMPH_NODES'

nPatients Mean (Std.Dev)
ALL 402 0.4 (1.4)
15Q LOSS MUTATED 32 0.9 (1.5)
15Q LOSS WILD-TYPE 370 0.4 (1.3)

Figure S259.  Get High-res Image Gene #66: '15q loss' versus Clinical Feature #8: 'NUMBER_OF_LYMPH_NODES'

'15q loss' versus 'GLEASON_SCORE'

P value = 7.26e-06 (Wilcoxon-test), Q value = 0.00024

Table S260.  Gene #66: '15q loss' versus Clinical Feature #9: 'GLEASON_SCORE'

nPatients Mean (Std.Dev)
ALL 492 7.6 (1.0)
15Q LOSS MUTATED 35 8.4 (1.0)
15Q LOSS WILD-TYPE 457 7.6 (1.0)

Figure S260.  Get High-res Image Gene #66: '15q loss' versus Clinical Feature #9: 'GLEASON_SCORE'

'16q loss' versus 'PATHOLOGY_T_STAGE'

P value = 0.00068 (Fisher's exact test), Q value = 0.0067

Table S261.  Gene #68: '16q loss' versus Clinical Feature #3: 'PATHOLOGY_T_STAGE'

nPatients T2 T3 T4
ALL 187 288 10
16Q LOSS MUTATED 25 78 3
16Q LOSS WILD-TYPE 162 210 7

Figure S261.  Get High-res Image Gene #68: '16q loss' versus Clinical Feature #3: 'PATHOLOGY_T_STAGE'

'16q loss' versus 'PATHOLOGY_N_STAGE'

P value = 0.0727 (Fisher's exact test), Q value = 0.21

Table S262.  Gene #68: '16q loss' versus Clinical Feature #4: 'PATHOLOGY_N_STAGE'

nPatients 0 1
ALL 343 77
16Q LOSS MUTATED 73 24
16Q LOSS WILD-TYPE 270 53

Figure S262.  Get High-res Image Gene #68: '16q loss' versus Clinical Feature #4: 'PATHOLOGY_N_STAGE'

'16q loss' versus 'RESIDUAL_TUMOR'

P value = 0.0153 (Fisher's exact test), Q value = 0.066

Table S263.  Gene #68: '16q loss' versus Clinical Feature #7: 'RESIDUAL_TUMOR'

nPatients R0 R1 R2 RX
ALL 313 144 5 15
16Q LOSS MUTATED 57 44 0 2
16Q LOSS WILD-TYPE 256 100 5 13

Figure S263.  Get High-res Image Gene #68: '16q loss' versus Clinical Feature #7: 'RESIDUAL_TUMOR'

'16q loss' versus 'NUMBER_OF_LYMPH_NODES'

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

Table S264.  Gene #68: '16q loss' versus Clinical Feature #8: 'NUMBER_OF_LYMPH_NODES'

nPatients Mean (Std.Dev)
ALL 402 0.4 (1.4)
16Q LOSS MUTATED 92 0.6 (1.4)
16Q LOSS WILD-TYPE 310 0.4 (1.4)

Figure S264.  Get High-res Image Gene #68: '16q loss' versus Clinical Feature #8: 'NUMBER_OF_LYMPH_NODES'

'16q loss' versus 'GLEASON_SCORE'

P value = 9.76e-07 (Wilcoxon-test), Q value = 5.7e-05

Table S265.  Gene #68: '16q loss' versus Clinical Feature #9: 'GLEASON_SCORE'

nPatients Mean (Std.Dev)
ALL 492 7.6 (1.0)
16Q LOSS MUTATED 107 8.0 (1.0)
16Q LOSS WILD-TYPE 385 7.5 (1.0)

Figure S265.  Get High-res Image Gene #68: '16q loss' versus Clinical Feature #9: 'GLEASON_SCORE'

'17p loss' versus 'PATHOLOGY_T_STAGE'

P value = 0.00093 (Fisher's exact test), Q value = 0.0084

Table S266.  Gene #69: '17p loss' versus Clinical Feature #3: 'PATHOLOGY_T_STAGE'

nPatients T2 T3 T4
ALL 187 288 10
17P LOSS MUTATED 15 58 1
17P LOSS WILD-TYPE 172 230 9

Figure S266.  Get High-res Image Gene #69: '17p loss' versus Clinical Feature #3: 'PATHOLOGY_T_STAGE'

'17p loss' versus 'PATHOLOGY_N_STAGE'

P value = 0.011 (Fisher's exact test), Q value = 0.052

Table S267.  Gene #69: '17p loss' versus Clinical Feature #4: 'PATHOLOGY_N_STAGE'

nPatients 0 1
ALL 343 77
17P LOSS MUTATED 50 21
17P LOSS WILD-TYPE 293 56

Figure S267.  Get High-res Image Gene #69: '17p loss' versus Clinical Feature #4: 'PATHOLOGY_N_STAGE'

'17p loss' versus 'RESIDUAL_TUMOR'

P value = 0.0404 (Fisher's exact test), Q value = 0.14

Table S268.  Gene #69: '17p loss' versus Clinical Feature #7: 'RESIDUAL_TUMOR'

nPatients R0 R1 R2 RX
ALL 313 144 5 15
17P LOSS MUTATED 40 33 0 2
17P LOSS WILD-TYPE 273 111 5 13

Figure S268.  Get High-res Image Gene #69: '17p loss' versus Clinical Feature #7: 'RESIDUAL_TUMOR'

'17p loss' versus 'NUMBER_OF_LYMPH_NODES'

P value = 0.000816 (Wilcoxon-test), Q value = 0.0078

Table S269.  Gene #69: '17p loss' versus Clinical Feature #8: 'NUMBER_OF_LYMPH_NODES'

nPatients Mean (Std.Dev)
ALL 402 0.4 (1.4)
17P LOSS MUTATED 67 0.9 (1.7)
17P LOSS WILD-TYPE 335 0.3 (1.3)

Figure S269.  Get High-res Image Gene #69: '17p loss' versus Clinical Feature #8: 'NUMBER_OF_LYMPH_NODES'

'17p loss' versus 'GLEASON_SCORE'

P value = 2.91e-06 (Wilcoxon-test), Q value = 0.00011

Table S270.  Gene #69: '17p loss' versus Clinical Feature #9: 'GLEASON_SCORE'

nPatients Mean (Std.Dev)
ALL 492 7.6 (1.0)
17P LOSS MUTATED 76 8.1 (1.0)
17P LOSS WILD-TYPE 416 7.5 (1.0)

Figure S270.  Get High-res Image Gene #69: '17p loss' versus Clinical Feature #9: 'GLEASON_SCORE'

'17p loss' versus 'PSA_VALUE'

P value = 0.0418 (Wilcoxon-test), Q value = 0.14

Table S271.  Gene #69: '17p loss' versus Clinical Feature #10: 'PSA_VALUE'

nPatients Mean (Std.Dev)
ALL 435 1.8 (15.9)
17P LOSS MUTATED 67 6.8 (39.7)
17P LOSS WILD-TYPE 368 0.8 (3.4)

Figure S271.  Get High-res Image Gene #69: '17p loss' versus Clinical Feature #10: 'PSA_VALUE'

'17q loss' versus 'Time to Death'

P value = 0.0771 (logrank test), Q value = 0.22

Table S272.  Gene #70: '17q loss' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 492 9 0.8 - 165.2 (30.6)
17Q LOSS MUTATED 20 2 4.8 - 115.1 (38.3)
17Q LOSS WILD-TYPE 472 7 0.8 - 165.2 (30.4)

Figure S272.  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 S273.  Gene #70: '17q loss' versus Clinical Feature #3: 'PATHOLOGY_T_STAGE'

nPatients T2 T3 T4
ALL 187 288 10
17Q LOSS MUTATED 2 17 0
17Q LOSS WILD-TYPE 185 271 10

Figure S273.  Get High-res Image Gene #70: '17q loss' versus Clinical Feature #3: 'PATHOLOGY_T_STAGE'

'17q loss' versus 'RESIDUAL_TUMOR'

P value = 0.0346 (Fisher's exact test), Q value = 0.12

Table S274.  Gene #70: '17q loss' versus Clinical Feature #7: 'RESIDUAL_TUMOR'

nPatients R0 R1 R2 RX
ALL 313 144 5 15
17Q LOSS MUTATED 7 11 0 1
17Q LOSS WILD-TYPE 306 133 5 14

Figure S274.  Get High-res Image Gene #70: '17q loss' versus Clinical Feature #7: 'RESIDUAL_TUMOR'

'17q loss' versus 'GLEASON_SCORE'

P value = 0.00332 (Wilcoxon-test), Q value = 0.022

Table S275.  Gene #70: '17q loss' versus Clinical Feature #9: 'GLEASON_SCORE'

nPatients Mean (Std.Dev)
ALL 492 7.6 (1.0)
17Q LOSS MUTATED 20 8.3 (1.0)
17Q LOSS WILD-TYPE 472 7.6 (1.0)

Figure S275.  Get High-res Image Gene #70: '17q loss' versus Clinical Feature #9: 'GLEASON_SCORE'

'18p loss' versus 'PATHOLOGY_T_STAGE'

P value = 0.00611 (Fisher's exact test), Q value = 0.033

Table S276.  Gene #71: '18p loss' versus Clinical Feature #3: 'PATHOLOGY_T_STAGE'

nPatients T2 T3 T4
ALL 187 288 10
18P LOSS MUTATED 17 46 4
18P LOSS WILD-TYPE 170 242 6

Figure S276.  Get High-res Image Gene #71: '18p loss' versus Clinical Feature #3: 'PATHOLOGY_T_STAGE'

'18p loss' versus 'RESIDUAL_TUMOR'

P value = 0.00787 (Fisher's exact test), Q value = 0.04

Table S277.  Gene #71: '18p loss' versus Clinical Feature #7: 'RESIDUAL_TUMOR'

nPatients R0 R1 R2 RX
ALL 313 144 5 15
18P LOSS MUTATED 34 31 0 0
18P LOSS WILD-TYPE 279 113 5 15

Figure S277.  Get High-res Image Gene #71: '18p loss' versus Clinical Feature #7: 'RESIDUAL_TUMOR'

'18p loss' versus 'NUMBER_OF_LYMPH_NODES'

P value = 0.0456 (Wilcoxon-test), Q value = 0.15

Table S278.  Gene #71: '18p loss' versus Clinical Feature #8: 'NUMBER_OF_LYMPH_NODES'

nPatients Mean (Std.Dev)
ALL 402 0.4 (1.4)
18P LOSS MUTATED 60 0.7 (1.5)
18P LOSS WILD-TYPE 342 0.4 (1.3)

Figure S278.  Get High-res Image Gene #71: '18p loss' versus Clinical Feature #8: 'NUMBER_OF_LYMPH_NODES'

'18p loss' versus 'GLEASON_SCORE'

P value = 7.39e-07 (Wilcoxon-test), Q value = 4.6e-05

Table S279.  Gene #71: '18p loss' versus Clinical Feature #9: 'GLEASON_SCORE'

nPatients Mean (Std.Dev)
ALL 492 7.6 (1.0)
18P LOSS MUTATED 67 8.2 (1.0)
18P LOSS WILD-TYPE 425 7.5 (1.0)

Figure S279.  Get High-res Image Gene #71: '18p loss' versus Clinical Feature #9: 'GLEASON_SCORE'

'18q loss' versus 'PATHOLOGY_T_STAGE'

P value = 0.0013 (Fisher's exact test), Q value = 0.011

Table S280.  Gene #72: '18q loss' versus Clinical Feature #3: 'PATHOLOGY_T_STAGE'

nPatients T2 T3 T4
ALL 187 288 10
18Q LOSS MUTATED 24 71 4
18Q LOSS WILD-TYPE 163 217 6

Figure S280.  Get High-res Image Gene #72: '18q loss' versus Clinical Feature #3: 'PATHOLOGY_T_STAGE'

'18q loss' versus 'PATHOLOGY_N_STAGE'

P value = 0.000362 (Fisher's exact test), Q value = 0.0046

Table S281.  Gene #72: '18q loss' versus Clinical Feature #4: 'PATHOLOGY_N_STAGE'

nPatients 0 1
ALL 343 77
18Q LOSS MUTATED 62 29
18Q LOSS WILD-TYPE 281 48

Figure S281.  Get High-res Image Gene #72: '18q loss' versus Clinical Feature #4: 'PATHOLOGY_N_STAGE'

'18q loss' versus 'RADIATION_THERAPY'

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

Table S282.  Gene #72: '18q loss' versus Clinical Feature #5: 'RADIATION_THERAPY'

nPatients NO YES
ALL 390 59
18Q LOSS MUTATED 72 18
18Q LOSS WILD-TYPE 318 41

Figure S282.  Get High-res Image Gene #72: '18q loss' versus Clinical Feature #5: 'RADIATION_THERAPY'

'18q loss' versus 'RESIDUAL_TUMOR'

P value = 3e-05 (Fisher's exact test), Q value = 0.00066

Table S283.  Gene #72: '18q loss' versus Clinical Feature #7: 'RESIDUAL_TUMOR'

nPatients R0 R1 R2 RX
ALL 313 144 5 15
18Q LOSS MUTATED 47 49 0 2
18Q LOSS WILD-TYPE 266 95 5 13

Figure S283.  Get High-res Image Gene #72: '18q loss' versus Clinical Feature #7: 'RESIDUAL_TUMOR'

'18q loss' versus 'NUMBER_OF_LYMPH_NODES'

P value = 4.61e-05 (Wilcoxon-test), Q value = 0.00095

Table S284.  Gene #72: '18q loss' versus Clinical Feature #8: 'NUMBER_OF_LYMPH_NODES'

nPatients Mean (Std.Dev)
ALL 402 0.4 (1.4)
18Q LOSS MUTATED 87 0.9 (2.3)
18Q LOSS WILD-TYPE 315 0.3 (0.9)

Figure S284.  Get High-res Image Gene #72: '18q loss' versus Clinical Feature #8: 'NUMBER_OF_LYMPH_NODES'

'18q loss' versus 'GLEASON_SCORE'

P value = 2.12e-08 (Wilcoxon-test), Q value = 3.8e-06

Table S285.  Gene #72: '18q loss' versus Clinical Feature #9: 'GLEASON_SCORE'

nPatients Mean (Std.Dev)
ALL 492 7.6 (1.0)
18Q LOSS MUTATED 100 8.1 (1.0)
18Q LOSS WILD-TYPE 392 7.5 (1.0)

Figure S285.  Get High-res Image Gene #72: '18q loss' versus Clinical Feature #9: 'GLEASON_SCORE'

'19p loss' versus 'YEARS_TO_BIRTH'

P value = 0.0103 (Wilcoxon-test), Q value = 0.05

Table S286.  Gene #73: '19p loss' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 481 61.0 (6.8)
19P LOSS MUTATED 19 64.6 (5.8)
19P LOSS WILD-TYPE 462 60.8 (6.8)

Figure S286.  Get High-res Image Gene #73: '19p loss' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'19p loss' versus 'GLEASON_SCORE'

P value = 0.01 (Wilcoxon-test), Q value = 0.049

Table S287.  Gene #73: '19p loss' versus Clinical Feature #9: 'GLEASON_SCORE'

nPatients Mean (Std.Dev)
ALL 492 7.6 (1.0)
19P LOSS MUTATED 19 8.2 (1.0)
19P LOSS WILD-TYPE 473 7.6 (1.0)

Figure S287.  Get High-res Image Gene #73: '19p loss' versus Clinical Feature #9: 'GLEASON_SCORE'

'19q loss' versus 'YEARS_TO_BIRTH'

P value = 0.0174 (Wilcoxon-test), Q value = 0.072

Table S288.  Gene #74: '19q loss' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 481 61.0 (6.8)
19Q LOSS MUTATED 18 64.4 (6.0)
19Q LOSS WILD-TYPE 463 60.8 (6.8)

Figure S288.  Get High-res Image Gene #74: '19q loss' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'19q loss' versus 'GLEASON_SCORE'

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

Table S289.  Gene #74: '19q loss' versus Clinical Feature #9: 'GLEASON_SCORE'

nPatients Mean (Std.Dev)
ALL 492 7.6 (1.0)
19Q LOSS MUTATED 18 8.2 (1.0)
19Q LOSS WILD-TYPE 474 7.6 (1.0)

Figure S289.  Get High-res Image Gene #74: '19q loss' versus Clinical Feature #9: 'GLEASON_SCORE'

'20p loss' versus 'PATHOLOGY_T_STAGE'

P value = 0.0523 (Fisher's exact test), Q value = 0.16

Table S290.  Gene #75: '20p loss' versus Clinical Feature #3: 'PATHOLOGY_T_STAGE'

nPatients T2 T3 T4
ALL 187 288 10
20P LOSS MUTATED 3 15 1
20P LOSS WILD-TYPE 184 273 9

Figure S290.  Get High-res Image Gene #75: '20p loss' versus Clinical Feature #3: 'PATHOLOGY_T_STAGE'

'20p loss' versus 'PATHOLOGY_N_STAGE'

P value = 0.0218 (Fisher's exact test), Q value = 0.083

Table S291.  Gene #75: '20p loss' versus Clinical Feature #4: 'PATHOLOGY_N_STAGE'

nPatients 0 1
ALL 343 77
20P LOSS MUTATED 10 7
20P LOSS WILD-TYPE 333 70

Figure S291.  Get High-res Image Gene #75: '20p loss' versus Clinical Feature #4: 'PATHOLOGY_N_STAGE'

'20p loss' versus 'RADIATION_THERAPY'

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

Table S292.  Gene #75: '20p loss' versus Clinical Feature #5: 'RADIATION_THERAPY'

nPatients NO YES
ALL 390 59
20P LOSS MUTATED 13 5
20P LOSS WILD-TYPE 377 54

Figure S292.  Get High-res Image Gene #75: '20p loss' versus Clinical Feature #5: 'RADIATION_THERAPY'

'20p loss' versus 'NUMBER_OF_LYMPH_NODES'

P value = 0.00523 (Wilcoxon-test), Q value = 0.03

Table S293.  Gene #75: '20p loss' versus Clinical Feature #8: 'NUMBER_OF_LYMPH_NODES'

nPatients Mean (Std.Dev)
ALL 402 0.4 (1.4)
20P LOSS MUTATED 16 1.4 (2.1)
20P LOSS WILD-TYPE 386 0.4 (1.3)

Figure S293.  Get High-res Image Gene #75: '20p loss' versus Clinical Feature #8: 'NUMBER_OF_LYMPH_NODES'

'20q loss' versus 'GLEASON_SCORE'

P value = 0.0605 (Wilcoxon-test), Q value = 0.18

Table S294.  Gene #76: '20q loss' versus Clinical Feature #9: 'GLEASON_SCORE'

nPatients Mean (Std.Dev)
ALL 492 7.6 (1.0)
20Q LOSS MUTATED 8 8.2 (0.9)
20Q LOSS WILD-TYPE 484 7.6 (1.0)

Figure S294.  Get High-res Image Gene #76: '20q loss' versus Clinical Feature #9: 'GLEASON_SCORE'

'21q loss' versus 'PATHOLOGY_T_STAGE'

P value = 0.0024 (Fisher's exact test), Q value = 0.017

Table S295.  Gene #77: '21q loss' versus Clinical Feature #3: 'PATHOLOGY_T_STAGE'

nPatients T2 T3 T4
ALL 187 288 10
21Q LOSS MUTATED 4 17 3
21Q LOSS WILD-TYPE 183 271 7

Figure S295.  Get High-res Image Gene #77: '21q loss' versus Clinical Feature #3: 'PATHOLOGY_T_STAGE'

'21q loss' versus 'PATHOLOGY_N_STAGE'

P value = 0.00364 (Fisher's exact test), Q value = 0.023

Table S296.  Gene #77: '21q loss' versus Clinical Feature #4: 'PATHOLOGY_N_STAGE'

nPatients 0 1
ALL 343 77
21Q LOSS MUTATED 13 10
21Q LOSS WILD-TYPE 330 67

Figure S296.  Get High-res Image Gene #77: '21q loss' versus Clinical Feature #4: 'PATHOLOGY_N_STAGE'

'21q loss' versus 'NUMBER_OF_LYMPH_NODES'

P value = 0.00138 (Wilcoxon-test), Q value = 0.011

Table S297.  Gene #77: '21q loss' versus Clinical Feature #8: 'NUMBER_OF_LYMPH_NODES'

nPatients Mean (Std.Dev)
ALL 402 0.4 (1.4)
21Q LOSS MUTATED 22 1.1 (2.4)
21Q LOSS WILD-TYPE 380 0.4 (1.3)

Figure S297.  Get High-res Image Gene #77: '21q loss' versus Clinical Feature #8: 'NUMBER_OF_LYMPH_NODES'

'21q loss' versus 'GLEASON_SCORE'

P value = 0.000329 (Wilcoxon-test), Q value = 0.0042

Table S298.  Gene #77: '21q loss' versus Clinical Feature #9: 'GLEASON_SCORE'

nPatients Mean (Std.Dev)
ALL 492 7.6 (1.0)
21Q LOSS MUTATED 24 8.3 (1.0)
21Q LOSS WILD-TYPE 468 7.6 (1.0)

Figure S298.  Get High-res Image Gene #77: '21q loss' versus Clinical Feature #9: 'GLEASON_SCORE'

'22q loss' versus 'PATHOLOGY_T_STAGE'

P value = 2e-05 (Fisher's exact test), Q value = 0.00048

Table S299.  Gene #78: '22q loss' versus Clinical Feature #3: 'PATHOLOGY_T_STAGE'

nPatients T2 T3 T4
ALL 187 288 10
22Q LOSS MUTATED 5 39 2
22Q LOSS WILD-TYPE 182 249 8

Figure S299.  Get High-res Image Gene #78: '22q loss' versus Clinical Feature #3: 'PATHOLOGY_T_STAGE'

'22q loss' versus 'PATHOLOGY_N_STAGE'

P value = 0.000716 (Fisher's exact test), Q value = 0.0069

Table S300.  Gene #78: '22q loss' versus Clinical Feature #4: 'PATHOLOGY_N_STAGE'

nPatients 0 1
ALL 343 77
22Q LOSS MUTATED 27 17
22Q LOSS WILD-TYPE 316 60

Figure S300.  Get High-res Image Gene #78: '22q loss' versus Clinical Feature #4: 'PATHOLOGY_N_STAGE'

'22q loss' versus 'RADIATION_THERAPY'

P value = 0.0128 (Fisher's exact test), Q value = 0.057

Table S301.  Gene #78: '22q loss' versus Clinical Feature #5: 'RADIATION_THERAPY'

nPatients NO YES
ALL 390 59
22Q LOSS MUTATED 30 11
22Q LOSS WILD-TYPE 360 48

Figure S301.  Get High-res Image Gene #78: '22q loss' versus Clinical Feature #5: 'RADIATION_THERAPY'

'22q loss' versus 'RESIDUAL_TUMOR'

P value = 0.0101 (Fisher's exact test), Q value = 0.049

Table S302.  Gene #78: '22q loss' versus Clinical Feature #7: 'RESIDUAL_TUMOR'

nPatients R0 R1 R2 RX
ALL 313 144 5 15
22Q LOSS MUTATED 22 24 0 0
22Q LOSS WILD-TYPE 291 120 5 15

Figure S302.  Get High-res Image Gene #78: '22q loss' versus Clinical Feature #7: 'RESIDUAL_TUMOR'

'22q loss' versus 'NUMBER_OF_LYMPH_NODES'

P value = 0.000565 (Wilcoxon-test), Q value = 0.0058

Table S303.  Gene #78: '22q loss' versus Clinical Feature #8: 'NUMBER_OF_LYMPH_NODES'

nPatients Mean (Std.Dev)
ALL 402 0.4 (1.4)
22Q LOSS MUTATED 43 0.9 (2.4)
22Q LOSS WILD-TYPE 359 0.4 (1.2)

Figure S303.  Get High-res Image Gene #78: '22q loss' versus Clinical Feature #8: 'NUMBER_OF_LYMPH_NODES'

'22q loss' versus 'GLEASON_SCORE'

P value = 3.76e-08 (Wilcoxon-test), Q value = 4.4e-06

Table S304.  Gene #78: '22q loss' versus Clinical Feature #9: 'GLEASON_SCORE'

nPatients Mean (Std.Dev)
ALL 492 7.6 (1.0)
22Q LOSS MUTATED 47 8.4 (0.9)
22Q LOSS WILD-TYPE 445 7.5 (1.0)

Figure S304.  Get High-res Image Gene #78: '22q loss' versus Clinical Feature #9: 'GLEASON_SCORE'

'22q loss' versus 'PSA_VALUE'

P value = 0.0709 (Wilcoxon-test), Q value = 0.21

Table S305.  Gene #78: '22q loss' versus Clinical Feature #10: 'PSA_VALUE'

nPatients Mean (Std.Dev)
ALL 435 1.8 (15.9)
22Q LOSS MUTATED 41 10.5 (50.4)
22Q LOSS WILD-TYPE 394 0.8 (3.7)

Figure S305.  Get High-res Image Gene #78: '22q loss' versus Clinical Feature #10: 'PSA_VALUE'

'xp loss' versus 'Time to Death'

P value = 0.0422 (logrank test), Q value = 0.14

Table S306.  Gene #79: 'xp loss' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 492 9 0.8 - 165.2 (30.6)
XP LOSS MUTATED 38 2 1.0 - 94.4 (36.2)
XP LOSS WILD-TYPE 454 7 0.8 - 165.2 (30.4)

Figure S306.  Get High-res Image Gene #79: 'xp loss' versus Clinical Feature #1: 'Time to Death'

'xp loss' versus 'YEARS_TO_BIRTH'

P value = 0.0852 (Wilcoxon-test), Q value = 0.24

Table S307.  Gene #79: 'xp loss' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 481 61.0 (6.8)
XP LOSS MUTATED 38 62.8 (6.8)
XP LOSS WILD-TYPE 443 60.8 (6.8)

Figure S307.  Get High-res Image Gene #79: 'xp loss' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'xp loss' versus 'PATHOLOGY_T_STAGE'

P value = 0.00413 (Fisher's exact test), Q value = 0.026

Table S308.  Gene #79: 'xp loss' versus Clinical Feature #3: 'PATHOLOGY_T_STAGE'

nPatients T2 T3 T4
ALL 187 288 10
XP LOSS MUTATED 6 29 2
XP LOSS WILD-TYPE 181 259 8

Figure S308.  Get High-res Image Gene #79: 'xp loss' versus Clinical Feature #3: 'PATHOLOGY_T_STAGE'

'xp loss' versus 'PATHOLOGY_N_STAGE'

P value = 0.0111 (Fisher's exact test), Q value = 0.052

Table S309.  Gene #79: 'xp loss' versus Clinical Feature #4: 'PATHOLOGY_N_STAGE'

nPatients 0 1
ALL 343 77
XP LOSS MUTATED 23 13
XP LOSS WILD-TYPE 320 64

Figure S309.  Get High-res Image Gene #79: 'xp loss' versus Clinical Feature #4: 'PATHOLOGY_N_STAGE'

'xp loss' versus 'RADIATION_THERAPY'

P value = 0.0336 (Fisher's exact test), Q value = 0.12

Table S310.  Gene #79: 'xp loss' versus Clinical Feature #5: 'RADIATION_THERAPY'

nPatients NO YES
ALL 390 59
XP LOSS MUTATED 26 9
XP LOSS WILD-TYPE 364 50

Figure S310.  Get High-res Image Gene #79: 'xp loss' versus Clinical Feature #5: 'RADIATION_THERAPY'

'xp loss' versus 'NUMBER_OF_LYMPH_NODES'

P value = 0.000414 (Wilcoxon-test), Q value = 0.0049

Table S311.  Gene #79: 'xp loss' versus Clinical Feature #8: 'NUMBER_OF_LYMPH_NODES'

nPatients Mean (Std.Dev)
ALL 402 0.4 (1.4)
XP LOSS MUTATED 35 1.0 (1.6)
XP LOSS WILD-TYPE 367 0.4 (1.3)

Figure S311.  Get High-res Image Gene #79: 'xp loss' versus Clinical Feature #8: 'NUMBER_OF_LYMPH_NODES'

'xp loss' versus 'GLEASON_SCORE'

P value = 3.01e-07 (Wilcoxon-test), Q value = 2.2e-05

Table S312.  Gene #79: 'xp loss' versus Clinical Feature #9: 'GLEASON_SCORE'

nPatients Mean (Std.Dev)
ALL 492 7.6 (1.0)
XP LOSS MUTATED 38 8.4 (0.9)
XP LOSS WILD-TYPE 454 7.5 (1.0)

Figure S312.  Get High-res Image Gene #79: 'xp loss' versus Clinical Feature #9: 'GLEASON_SCORE'

'xp loss' versus 'PSA_VALUE'

P value = 0.0221 (Wilcoxon-test), Q value = 0.083

Table S313.  Gene #79: 'xp loss' versus Clinical Feature #10: 'PSA_VALUE'

nPatients Mean (Std.Dev)
ALL 435 1.8 (15.9)
XP LOSS MUTATED 34 10.7 (55.2)
XP LOSS WILD-TYPE 401 1.0 (4.1)

Figure S313.  Get High-res Image Gene #79: 'xp loss' versus Clinical Feature #10: 'PSA_VALUE'

'xq loss' versus 'Time to Death'

P value = 0.0422 (logrank test), Q value = 0.14

Table S314.  Gene #80: 'xq loss' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 492 9 0.8 - 165.2 (30.6)
XQ LOSS MUTATED 38 2 1.0 - 94.4 (36.2)
XQ LOSS WILD-TYPE 454 7 0.8 - 165.2 (30.4)

Figure S314.  Get High-res Image Gene #80: 'xq loss' versus Clinical Feature #1: 'Time to Death'

'xq loss' versus 'YEARS_TO_BIRTH'

P value = 0.0852 (Wilcoxon-test), Q value = 0.24

Table S315.  Gene #80: 'xq loss' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 481 61.0 (6.8)
XQ LOSS MUTATED 38 62.8 (6.8)
XQ LOSS WILD-TYPE 443 60.8 (6.8)

Figure S315.  Get High-res Image Gene #80: 'xq loss' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'xq loss' versus 'PATHOLOGY_T_STAGE'

P value = 0.0041 (Fisher's exact test), Q value = 0.026

Table S316.  Gene #80: 'xq loss' versus Clinical Feature #3: 'PATHOLOGY_T_STAGE'

nPatients T2 T3 T4
ALL 187 288 10
XQ LOSS MUTATED 6 29 2
XQ LOSS WILD-TYPE 181 259 8

Figure S316.  Get High-res Image Gene #80: 'xq loss' versus Clinical Feature #3: 'PATHOLOGY_T_STAGE'

'xq loss' versus 'PATHOLOGY_N_STAGE'

P value = 0.0111 (Fisher's exact test), Q value = 0.052

Table S317.  Gene #80: 'xq loss' versus Clinical Feature #4: 'PATHOLOGY_N_STAGE'

nPatients 0 1
ALL 343 77
XQ LOSS MUTATED 23 13
XQ LOSS WILD-TYPE 320 64

Figure S317.  Get High-res Image Gene #80: 'xq loss' versus Clinical Feature #4: 'PATHOLOGY_N_STAGE'

'xq loss' versus 'RADIATION_THERAPY'

P value = 0.0336 (Fisher's exact test), Q value = 0.12

Table S318.  Gene #80: 'xq loss' versus Clinical Feature #5: 'RADIATION_THERAPY'

nPatients NO YES
ALL 390 59
XQ LOSS MUTATED 26 9
XQ LOSS WILD-TYPE 364 50

Figure S318.  Get High-res Image Gene #80: 'xq loss' versus Clinical Feature #5: 'RADIATION_THERAPY'

'xq loss' versus 'NUMBER_OF_LYMPH_NODES'

P value = 0.000414 (Wilcoxon-test), Q value = 0.0049

Table S319.  Gene #80: 'xq loss' versus Clinical Feature #8: 'NUMBER_OF_LYMPH_NODES'

nPatients Mean (Std.Dev)
ALL 402 0.4 (1.4)
XQ LOSS MUTATED 35 1.0 (1.6)
XQ LOSS WILD-TYPE 367 0.4 (1.3)

Figure S319.  Get High-res Image Gene #80: 'xq loss' versus Clinical Feature #8: 'NUMBER_OF_LYMPH_NODES'

'xq loss' versus 'GLEASON_SCORE'

P value = 3.01e-07 (Wilcoxon-test), Q value = 2.2e-05

Table S320.  Gene #80: 'xq loss' versus Clinical Feature #9: 'GLEASON_SCORE'

nPatients Mean (Std.Dev)
ALL 492 7.6 (1.0)
XQ LOSS MUTATED 38 8.4 (0.9)
XQ LOSS WILD-TYPE 454 7.5 (1.0)

Figure S320.  Get High-res Image Gene #80: 'xq loss' versus Clinical Feature #9: 'GLEASON_SCORE'

'xq loss' versus 'PSA_VALUE'

P value = 0.0221 (Wilcoxon-test), Q value = 0.083

Table S321.  Gene #80: 'xq loss' versus Clinical Feature #10: 'PSA_VALUE'

nPatients Mean (Std.Dev)
ALL 435 1.8 (15.9)
XQ LOSS MUTATED 34 10.7 (55.2)
XQ LOSS WILD-TYPE 401 1.0 (4.1)

Figure S321.  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/22533740/transformed.cor.cli.txt

  • Clinical data file = /xchip/cga/gdac-prod/tcga-gdac/jobResults/Append_Data/PRAD-TP/22506989/PRAD-TP.merged_data.txt

  • Number of patients = 492

  • 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)