Correlation between copy number variation genes (focal events) and selected clinical features
Prostate Adenocarcinoma (Primary solid tumor)
17 October 2014  |  analyses__2014_10_17
Maintainer Information
Citation Information
doi:10.7908/C1G73CMK
Maintained by TCGA GDAC Team (Broad Institute/MD Anderson Cancer Center/Harvard Medical School)
Cite as Broad Institute TCGA Genome Data Analysis Center (2014): Correlation between copy number variation genes (focal events) and selected clinical features. Broad Institute of MIT and Harvard. doi:10.7908/C1G73CMK
Overview
Introduction

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

Summary

Testing the association between copy number variation 65 focal events and 14 clinical features across 363 patients, 68 significant findings detected with Q value < 0.25.

  • amp_3q21.3 cnv correlated to 'GLEASON_SCORE'.

  • amp_3q26.2 cnv correlated to 'GLEASON_SCORE'.

  • amp_5q35.3 cnv correlated to 'AGE'.

  • amp_8p11.23 cnv correlated to 'GLEASON_SCORE_COMBINED',  'GLEASON_SCORE_PRIMARY', and 'GLEASON_SCORE'.

  • amp_8q22.1 cnv correlated to 'PATHOLOGY.T.STAGE',  'GLEASON_SCORE_COMBINED',  'GLEASON_SCORE_PRIMARY', and 'GLEASON_SCORE'.

  • amp_8q24.21 cnv correlated to 'PATHOLOGY.T.STAGE',  'GLEASON_SCORE_COMBINED',  'GLEASON_SCORE_PRIMARY', and 'GLEASON_SCORE'.

  • amp_9q33.3 cnv correlated to 'PATHOLOGY.T.STAGE',  'GLEASON_SCORE_COMBINED',  'GLEASON_SCORE_PRIMARY', and 'GLEASON_SCORE'.

  • amp_11q13.2 cnv correlated to 'GLEASON_SCORE_PRIMARY' and 'GLEASON_SCORE'.

  • amp_12q23.1 cnv correlated to 'GLEASON_SCORE_COMBINED',  'GLEASON_SCORE_PRIMARY', and 'GLEASON_SCORE'.

  • amp_14q21.1 cnv correlated to 'GLEASON_SCORE'.

  • amp_20q13.2 cnv correlated to 'PATHOLOGY.T.STAGE' and 'GLEASON_SCORE'.

  • del_1q42.3 cnv correlated to 'Time to Death'.

  • del_2p21 cnv correlated to 'GLEASON_SCORE_PRIMARY'.

  • del_2q22.1 cnv correlated to 'AGE'.

  • del_5q11.2 cnv correlated to 'PATHOLOGY.T.STAGE',  'GLEASON_SCORE_COMBINED',  'GLEASON_SCORE_PRIMARY', and 'GLEASON_SCORE'.

  • del_5q13.2 cnv correlated to 'PATHOLOGY.T.STAGE',  'GLEASON_SCORE_COMBINED',  'GLEASON_SCORE_PRIMARY', and 'GLEASON_SCORE'.

  • del_5q21.1 cnv correlated to 'GLEASON_SCORE_PRIMARY'.

  • del_6q14.3 cnv correlated to 'GLEASON_SCORE_COMBINED',  'GLEASON_SCORE_PRIMARY', and 'GLEASON_SCORE'.

  • del_8p23.2 cnv correlated to 'PATHOLOGY.T.STAGE' and 'GLEASON_SCORE_PRIMARY'.

  • del_8p21.3 cnv correlated to 'PATHOLOGY.T.STAGE'.

  • del_10q23.31 cnv correlated to 'PATHOLOGY.T.STAGE'.

  • del_11q22.3 cnv correlated to 'GLEASON_SCORE_PRIMARY'.

  • del_12p13.1 cnv correlated to 'PATHOLOGY.T.STAGE' and 'GLEASON_SCORE_PRIMARY'.

  • del_13q22.1 cnv correlated to 'GLEASON_SCORE_COMBINED' and 'GLEASON_SCORE'.

  • del_15q21.3 cnv correlated to 'GLEASON_SCORE_COMBINED',  'GLEASON_SCORE_PRIMARY', and 'GLEASON_SCORE'.

  • del_16q22.3 cnv correlated to 'GLEASON_SCORE_COMBINED',  'GLEASON_SCORE_PRIMARY', and 'GLEASON_SCORE'.

  • del_16q24.1 cnv correlated to 'PATHOLOGY.T.STAGE',  'GLEASON_SCORE_COMBINED',  'GLEASON_SCORE_PRIMARY', and 'GLEASON_SCORE'.

  • del_17p13.1 cnv correlated to 'GLEASON_SCORE_COMBINED',  'GLEASON_SCORE_PRIMARY', and 'GLEASON_SCORE'.

  • del_18q21.31 cnv correlated to 'GLEASON_SCORE_COMBINED' and 'GLEASON_SCORE'.

  • del_18q23 cnv correlated to 'GLEASON_SCORE_COMBINED' and 'GLEASON_SCORE'.

  • del_19q13.2 cnv correlated to 'GLEASON_SCORE_PRIMARY'.

Results
Overview of the results

Table 1.  Get Full Table Overview of the association between significant copy number variation of 65 focal events and 14 clinical features. Shown in the table are P values (Q values). Thresholded by Q value < 0.25, 68 significant findings detected.

Clinical
Features 		Time
to
Death 		AGE PATHOLOGY
T
STAGE 		PATHOLOGY
N
STAGE 		HISTOLOGICAL
TYPE 		COMPLETENESS
OF
RESECTION 		NUMBER
OF
LYMPH
NODES 		GLEASON
SCORE
COMBINED 		GLEASON
SCORE
PRIMARY 		GLEASON
SCORE
SECONDARY 		GLEASON
SCORE 		PSA
RESULT
PREOP 		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 Wilcoxon-test Wilcoxon-test Wilcoxon-test Wilcoxon-test Wilcoxon-test Wilcoxon-test Wilcoxon-test Fisher's exact test
amp 8q22 1 103 (28%) 260 0.365
(1.00) 		0.212
(1.00) 		5e-05
(0.0435) 		0.296
(1.00) 		0.365
(1.00) 		0.0486
(1.00) 		0.22
(1.00) 		1.02e-05
(0.00901) 		1.42e-07
(0.000129) 		0.327
(1.00) 		2.8e-06
(0.00252) 		0.0167
(1.00) 		0.35
(1.00) 		1
(1.00)
amp 8q24 21 98 (27%) 265 0.87
(1.00) 		0.187
(1.00) 		0.00025
(0.211) 		0.213
(1.00) 		1
(1.00) 		0.196
(1.00) 		0.141
(1.00) 		4.16e-06
(0.00372) 		2.09e-07
(0.00019) 		0.167
(1.00) 		2.86e-06
(0.00257) 		0.0225
(1.00) 		0.498
(1.00) 		0.813
(1.00)
amp 9q33 3 38 (10%) 325 0.365
(1.00) 		0.106
(1.00) 		0.00016
(0.136) 		0.00165
(1.00) 		0.0366
(1.00) 		0.304
(1.00) 		0.000423
(0.352) 		1.34e-05
(0.0118) 		2.19e-06
(0.00198) 		0.105
(1.00) 		3.59e-07
(0.000325) 		0.0144
(1.00) 		0.227
(1.00) 		0.553
(1.00)
del 5q11 2 62 (17%) 301 0.83
(1.00) 		0.191
(1.00) 		2e-05
(0.0176) 		0.011
(1.00) 		0.705
(1.00) 		0.689
(1.00) 		0.00305
(1.00) 		1.02e-05
(0.00905) 		5.25e-06
(0.00468) 		0.121
(1.00) 		4.91e-06
(0.00439) 		0.000452
(0.375) 		0.959
(1.00) 		0.44
(1.00)
del 5q13 2 64 (18%) 299 0.861
(1.00) 		0.324
(1.00) 		1e-05
(0.00888) 		0.106
(1.00) 		0.479
(1.00) 		0.792
(1.00) 		0.061
(1.00) 		7.77e-07
(0.000703) 		3.36e-07
(0.000305) 		0.0511
(1.00) 		3.62e-06
(0.00325) 		0.0031
(1.00) 		0.705
(1.00) 		0.294
(1.00)
del 16q24 1 147 (40%) 216 0.631
(1.00) 		0.75
(1.00) 		0.0001
(0.0858) 		0.622
(1.00) 		0.776
(1.00) 		0.874
(1.00) 		0.473
(1.00) 		5.27e-05
(0.0458) 		1.09e-05
(0.00962) 		0.173
(1.00) 		6.5e-05
(0.0562) 		0.00223
(1.00) 		0.0598
(1.00) 		1
(1.00)
amp 8p11 23 41 (11%) 322 0.3
(1.00) 		0.00334
(1.00) 		0.0745
(1.00) 		0.805
(1.00) 		1
(1.00) 		0.193
(1.00) 		0.717
(1.00) 		0.000252
(0.213) 		1.03e-05
(0.00913) 		0.452
(1.00) 		0.000181
(0.154) 		0.0365
(1.00) 		0.414
(1.00) 		1
(1.00)
amp 12q23 1 21 (6%) 342 0.479
(1.00) 		0.394
(1.00) 		0.00401
(1.00) 		0.00214
(1.00) 		0.169
(1.00) 		0.0406
(1.00) 		0.000367
(0.305) 		2.34e-05
(0.0205) 		2.28e-05
(0.02) 		0.0974
(1.00) 		9.76e-07
(0.000882) 		0.00155
(1.00) 		0.23
(1.00) 		1
(1.00)
del 6q14 3 132 (36%) 231 0.591
(1.00) 		0.00147
(1.00) 		0.0391
(1.00) 		0.0072
(1.00) 		1
(1.00) 		0.00054
(0.446) 		0.00381
(1.00) 		9.45e-06
(0.00841) 		9.48e-06
(0.00843) 		0.0984
(1.00) 		4.6e-05
(0.0401) 		0.000581
(0.477) 		0.817
(1.00) 		0.582
(1.00)
del 15q21 3 45 (12%) 318 0.83
(1.00) 		0.817
(1.00) 		0.0032
(1.00) 		0.138
(1.00) 		0.668
(1.00) 		0.403
(1.00) 		0.101
(1.00) 		2.42e-06
(0.00218) 		5.02e-06
(0.00448) 		0.0233
(1.00) 		1.22e-05
(0.0107) 		0.856
(1.00) 		0.383
(1.00) 		1
(1.00)
del 16q22 3 130 (36%) 233 0.765
(1.00) 		0.209
(1.00) 		0.00287
(1.00) 		0.738
(1.00) 		1
(1.00) 		0.699
(1.00) 		0.616
(1.00) 		6.74e-05
(0.0581) 		2.45e-05
(0.0215) 		0.134
(1.00) 		3.72e-05
(0.0325) 		0.00279
(1.00) 		0.0561
(1.00) 		0.719
(1.00)
del 17p13 1 108 (30%) 255 0.866
(1.00) 		0.741
(1.00) 		0.00062
(0.508) 		0.00789
(1.00) 		1
(1.00) 		0.176
(1.00) 		0.00325
(1.00) 		8.37e-06
(0.00746) 		6.11e-05
(0.0529) 		0.0104
(1.00) 		2.96e-06
(0.00265) 		0.921
(1.00) 		0.142
(1.00) 		0.82
(1.00)
amp 11q13 2 25 (7%) 338 0.466
(1.00) 		0.0435
(1.00) 		0.00265
(1.00) 		0.00877
(1.00) 		0.223
(1.00) 		0.201
(1.00) 		0.00179
(1.00) 		0.00032
(0.268) 		5.98e-05
(0.0519) 		0.428
(1.00) 		5.77e-05
(0.0501) 		0.0804
(1.00) 		0.796
(1.00) 		0.348
(1.00)
amp 20q13 2 26 (7%) 337 0.437
(1.00) 		0.0226
(1.00) 		4e-05
(0.0349) 		0.236
(1.00) 		0.237
(1.00) 		0.11
(1.00) 		0.161
(1.00) 		0.00762
(1.00) 		0.000527
(0.435) 		0.661
(1.00) 		8.83e-05
(0.0759) 		0.029
(1.00) 		0.578
(1.00) 		1
(1.00)
del 8p23 2 153 (42%) 210 0.704
(1.00) 		0.415
(1.00) 		4e-05
(0.0349) 		0.138
(1.00) 		0.782
(1.00) 		0.817
(1.00) 		0.0802
(1.00) 		0.0156
(1.00) 		0.000183
(0.156) 		0.731
(1.00) 		0.0662
(1.00) 		0.0911
(1.00) 		0.0656
(1.00) 		0.376
(1.00)
del 12p13 1 82 (23%) 281 0.702
(1.00) 		0.87
(1.00) 		8e-05
(0.069) 		0.041
(1.00) 		0.179
(1.00) 		0.451
(1.00) 		0.0321
(1.00) 		0.000969
(0.787) 		6.23e-05
(0.0539) 		0.286
(1.00) 		0.000341
(0.285) 		0.0729
(1.00) 		0.0154
(1.00) 		1
(1.00)
del 13q22 1 124 (34%) 239 0.0441
(1.00) 		0.00798
(1.00) 		0.03
(1.00) 		0.236
(1.00) 		0.0409
(1.00) 		0.0803
(1.00) 		0.134
(1.00) 		0.000103
(0.088) 		0.0025
(1.00) 		0.00894
(1.00) 		3.21e-06
(0.00288) 		0.0288
(1.00) 		0.924
(1.00) 		0.00046
(0.381)
del 18q21 31 95 (26%) 268 0.934
(1.00) 		0.638
(1.00) 		0.0493
(1.00) 		0.1
(1.00) 		0.527
(1.00) 		0.00488
(1.00) 		0.0551
(1.00) 		9.7e-05
(0.0833) 		0.000853
(0.695) 		0.0169
(1.00) 		8.74e-05
(0.0752) 		0.301
(1.00) 		0.782
(1.00) 		0.396
(1.00)
del 18q23 100 (28%) 263 0.991
(1.00) 		0.249
(1.00) 		0.0537
(1.00) 		0.148
(1.00) 		1
(1.00) 		0.0194
(1.00) 		0.0794
(1.00) 		0.000272
(0.229) 		0.00261
(1.00) 		0.0219
(1.00) 		0.000109
(0.0937) 		0.508
(1.00) 		0.462
(1.00) 		0.443
(1.00)
amp 3q21 3 49 (13%) 314 0.28
(1.00) 		0.0531
(1.00) 		0.00086
(0.7) 		0.0647
(1.00) 		0.397
(1.00) 		0.0166
(1.00) 		0.0263
(1.00) 		0.00495
(1.00) 		0.000558
(0.46) 		0.651
(1.00) 		1.08e-05
(0.00954) 		0.000772
(0.63) 		0.439
(1.00) 		0.657
(1.00)
amp 3q26 2 57 (16%) 306 0.31
(1.00) 		0.181
(1.00) 		0.00286
(1.00) 		0.0295
(1.00) 		0.438
(1.00) 		0.0638
(1.00) 		0.0117
(1.00) 		0.00765
(1.00) 		0.000693
(0.567) 		0.781
(1.00) 		0.000208
(0.176) 		0.00791
(1.00) 		0.412
(1.00) 		1
(1.00)
amp 5q35 3 18 (5%) 345 0.513
(1.00) 		0.000116
(0.0992) 		0.00142
(1.00) 		0.154
(1.00) 		0.49
(1.00) 		0.293
(1.00) 		0.0688
(1.00) 		0.061
(1.00) 		0.0397
(1.00) 		0.614
(1.00) 		0.00172
(1.00) 		0.154
(1.00) 		0.224
(1.00) 		0.261
(1.00)
amp 14q21 1 20 (6%) 343 0.171
(1.00) 		0.0972
(1.00) 		0.331
(1.00) 		0.0786
(1.00) 		0.0288
(1.00) 		0.733
(1.00) 		0.0487
(1.00) 		0.00597
(1.00) 		0.0239
(1.00) 		0.168
(1.00) 		0.00018
(0.153) 		0.974
(1.00) 		0.795
(1.00) 		1
(1.00)
del 1q42 3 32 (9%) 331 1.71e-06
(0.00154) 		0.0617
(1.00) 		0.535
(1.00) 		0.0298
(1.00) 		0.615
(1.00) 		0.0219
(1.00) 		0.0229
(1.00) 		0.0649
(1.00) 		0.0445
(1.00) 		0.75
(1.00) 		0.0567
(1.00) 		0.131
(1.00) 		0.271
(1.00) 		0.555
(1.00)
del 2p21 33 (9%) 330 0.392
(1.00) 		0.398
(1.00) 		0.00789
(1.00) 		0.0344
(1.00) 		0.618
(1.00) 		0.239
(1.00) 		0.0338
(1.00) 		0.000314
(0.263) 		0.000285
(0.24) 		0.0686
(1.00) 		0.000968
(0.787) 		0.449
(1.00) 		0.196
(1.00) 		1
(1.00)
del 2q22 1 64 (18%) 299 0.822
(1.00) 		0.000116
(0.0994) 		0.474
(1.00) 		0.839
(1.00) 		0.479
(1.00) 		0.349
(1.00) 		0.862
(1.00) 		0.0559
(1.00) 		0.000559
(0.46) 		0.406
(1.00) 		0.0652
(1.00) 		0.424
(1.00) 		0.226
(1.00) 		0.414
(1.00)
del 5q21 1 76 (21%) 287 0.756
(1.00) 		0.0233
(1.00) 		0.276
(1.00) 		0.704
(1.00) 		0.316
(1.00) 		0.598
(1.00) 		0.725
(1.00) 		0.00415
(1.00) 		2.32e-05
(0.0204) 		0.612
(1.00) 		0.0473
(1.00) 		0.207
(1.00) 		0.767
(1.00) 		0.733
(1.00)
del 8p21 3 207 (57%) 156 0.698
(1.00) 		0.585
(1.00) 		0.00014
(0.119) 		0.0122
(1.00) 		0.57
(1.00) 		0.813
(1.00) 		0.00849
(1.00) 		0.0369
(1.00) 		0.000301
(0.253) 		0.452
(1.00) 		0.238
(1.00) 		0.00135
(1.00) 		0.194
(1.00) 		0.728
(1.00)
del 10q23 31 109 (30%) 254 0.35
(1.00) 		0.759
(1.00) 		0.0002
(0.17) 		0.0149
(1.00) 		1
(1.00) 		0.236
(1.00) 		0.0143
(1.00) 		0.00285
(1.00) 		0.0499
(1.00) 		0.00961
(1.00) 		0.0012
(0.97) 		0.315
(1.00) 		0.00842
(1.00) 		0.234
(1.00)
del 11q22 3 29 (8%) 334 0.473
(1.00) 		0.0373
(1.00) 		0.00054
(0.446) 		0.761
(1.00) 		0.278
(1.00) 		0.0697
(1.00) 		0.627
(1.00) 		0.000334
(0.28) 		2.68e-05
(0.0235) 		0.364
(1.00) 		0.00219
(1.00) 		0.0207
(1.00) 		0.281
(1.00) 		0.637
(1.00)
del 19q13 2 33 (9%) 330 0.54
(1.00) 		0.0589
(1.00) 		0.134
(1.00) 		0.597
(1.00) 		0.618
(1.00) 		0.275
(1.00) 		0.551
(1.00) 		0.00122
(0.987) 		0.000235
(0.199) 		0.286
(1.00) 		0.00333
(1.00) 		0.439
(1.00) 		0.585
(1.00) 		1
(1.00)
amp 1q22 25 (7%) 338 0.508
(1.00) 		0.0619
(1.00) 		0.00218
(1.00) 		0.348
(1.00) 		0.0522
(1.00) 		0.695
(1.00) 		0.238
(1.00) 		0.00121
(0.981) 		0.0016
(1.00) 		0.173
(1.00) 		0.000433
(0.36) 		0.146
(1.00) 		0.949
(1.00) 		1
(1.00)
amp 4p16 3 14 (4%) 349 0.579
(1.00) 		0.138
(1.00) 		0.00471
(1.00) 		1
(1.00) 		0.0845
(1.00) 		0.213
(1.00) 		0.976
(1.00) 		0.029
(1.00) 		0.0414
(1.00) 		0.387
(1.00) 		0.025
(1.00) 		0.045
(1.00) 		0.567
(1.00) 		1
(1.00)
amp 4q13 3 13 (4%) 350 0.577
(1.00) 		0.121
(1.00) 		0.04
(1.00) 		0.0991
(1.00) 		0.383
(1.00) 		0.17
(1.00) 		0.0553
(1.00) 		0.0058
(1.00) 		0.0162
(1.00) 		0.0941
(1.00) 		0.013
(1.00) 		0.00229
(1.00) 		0.857
(1.00) 		1
(1.00)
amp 7p14 3 70 (19%) 293 0.742
(1.00) 		0.0571
(1.00) 		0.0624
(1.00) 		0.841
(1.00) 		1
(1.00) 		0.011
(1.00) 		0.763
(1.00) 		0.0292
(1.00) 		0.0201
(1.00) 		0.314
(1.00) 		0.00484
(1.00) 		0.0529
(1.00) 		0.376
(1.00) 		1
(1.00)
amp 7q22 1 67 (18%) 296 0.735
(1.00) 		0.0305
(1.00) 		0.208
(1.00) 		0.409
(1.00) 		1
(1.00) 		0.0667
(1.00) 		0.337
(1.00) 		0.0751
(1.00) 		0.0312
(1.00) 		0.593
(1.00) 		0.011
(1.00) 		0.618
(1.00) 		0.628
(1.00) 		1
(1.00)
amp 13q12 11 17 (5%) 346 0.588
(1.00) 		0.00691
(1.00) 		0.0741
(1.00) 		0.459
(1.00) 		0.0183
(1.00) 		0.41
(1.00) 		0.483
(1.00) 		0.188
(1.00) 		0.04
(1.00) 		0.76
(1.00) 		0.171
(1.00) 		0.169
(1.00) 		0.0228
(1.00) 		0.307
(1.00)
amp 15q11 2 10 (3%) 353 0.0527
(1.00) 		0.4
(1.00) 		0.592
(1.00) 		0.00395
(1.00) 		0.309
(1.00) 		0.352
(1.00) 		0.000304
(0.255) 		0.064
(1.00) 		0.00378
(1.00) 		0.817
(1.00) 		0.0133
(1.00) 		0.897
(1.00) 		0.841
(1.00)
amp 16q11 2 18 (5%) 345 0.599
(1.00) 		0.0683
(1.00) 		0.00625
(1.00) 		0.711
(1.00) 		0.131
(1.00) 		0.496
(1.00) 		0.575
(1.00) 		0.0233
(1.00) 		0.0455
(1.00) 		0.328
(1.00) 		0.00566
(1.00) 		0.0529
(1.00) 		0.242
(1.00) 		1
(1.00)
amp 17q23 2 13 (4%) 350 0.697
(1.00) 		0.265
(1.00) 		0.138
(1.00) 		0.409
(1.00) 		0.0739
(1.00) 		0.745
(1.00) 		0.358
(1.00) 		0.222
(1.00) 		0.274
(1.00) 		0.415
(1.00) 		0.0547
(1.00) 		0.29
(1.00) 		0.49
(1.00) 		1
(1.00)
amp 19q13 43 10 (3%) 353 0.594
(1.00) 		0.194
(1.00) 		0.00243
(1.00) 		0.64
(1.00) 		0.309
(1.00) 		0.669
(1.00) 		0.535
(1.00) 		0.107
(1.00) 		0.047
(1.00) 		0.517
(1.00) 		0.00709
(1.00) 		0.0134
(1.00) 		0.47
(1.00) 		1
(1.00)
amp xp22 11 17 (5%) 346 0.659
(1.00) 		0.0455
(1.00) 		0.32
(1.00) 		1
(1.00) 		0.119
(1.00) 		0.176
(1.00) 		0.829
(1.00) 		0.0409
(1.00) 		0.00709
(1.00) 		0.928
(1.00) 		0.0419
(1.00) 		0.841
(1.00) 		0.416
(1.00) 		0.262
(1.00)
amp xp22 11 16 (4%) 347 0.598
(1.00) 		0.246
(1.00) 		0.365
(1.00) 		1
(1.00) 		0.107
(1.00) 		0.176
(1.00) 		0.907
(1.00) 		0.0259
(1.00) 		0.00241
(1.00) 		0.867
(1.00) 		0.0549
(1.00) 		0.162
(1.00) 		0.991
(1.00) 		0.215
(1.00)
amp xp21 1 16 (4%) 347 0.586
(1.00) 		0.00439
(1.00) 		0.124
(1.00) 		0.711
(1.00) 		0.0154
(1.00) 		0.137
(1.00) 		0.575
(1.00) 		0.0168
(1.00) 		0.00453
(1.00) 		0.798
(1.00) 		0.00613
(1.00) 		0.176
(1.00) 		0.816
(1.00) 		0.0073
(1.00)
amp xq21 1 13 (4%) 350 0.569
(1.00) 		0.0535
(1.00) 		0.644
(1.00) 		1
(1.00) 		1
(1.00) 		0.123
(1.00) 		0.937
(1.00) 		0.13
(1.00) 		0.109
(1.00) 		0.67
(1.00) 		0.0181
(1.00) 		0.082
(1.00) 		0.73
(1.00) 		0.347
(1.00)
amp xq21 1 11 (3%) 352 0.594
(1.00) 		0.0126
(1.00) 		0.46
(1.00) 		0.198
(1.00) 		1
(1.00) 		0.121
(1.00) 		0.235
(1.00) 		0.0529
(1.00) 		0.0693
(1.00) 		0.427
(1.00) 		0.00738
(1.00) 		0.0284
(1.00) 		0.618
(1.00) 		0.027
(1.00)
amp xq25 13 (4%) 350 0.54
(1.00) 		0.105
(1.00) 		0.642
(1.00) 		1
(1.00) 		1
(1.00) 		0.125
(1.00) 		0.998
(1.00) 		0.0371
(1.00) 		0.109
(1.00) 		0.199
(1.00) 		0.0299
(1.00) 		0.522
(1.00) 		0.896
(1.00) 		0.0179
(1.00)
amp xq27 1 14 (4%) 349 0.669
(1.00) 		0.00471
(1.00) 		1
(1.00) 		0.701
(1.00) 		1
(1.00) 		0.124
(1.00) 		0.45
(1.00) 		0.691
(1.00) 		0.325
(1.00) 		0.679
(1.00) 		0.295
(1.00) 		0.682
(1.00) 		0.988
(1.00) 		0.427
(1.00)
del 1p31 3 43 (12%) 320 0.877
(1.00) 		0.244
(1.00) 		0.0484
(1.00) 		0.809
(1.00) 		0.379
(1.00) 		0.435
(1.00) 		0.827
(1.00) 		0.00116
(0.942) 		0.0437
(1.00) 		0.005
(1.00) 		0.00389
(1.00) 		0.886
(1.00) 		0.129
(1.00) 		0.2
(1.00)
del 1p22 1 39 (11%) 324 0.395
(1.00) 		0.344
(1.00) 		0.0302
(1.00) 		0.451
(1.00) 		0.376
(1.00) 		0.841
(1.00) 		0.367
(1.00) 		0.0049
(1.00) 		0.00336
(1.00) 		0.316
(1.00) 		0.00737
(1.00) 		0.0119
(1.00) 		0.987
(1.00) 		1
(1.00)
del 1q23 1 19 (5%) 344 0.188
(1.00) 		0.114
(1.00) 		0.855
(1.00) 		1
(1.00) 		1
(1.00) 		0.913
(1.00) 		0.67
(1.00) 		0.149
(1.00) 		0.181
(1.00) 		0.53
(1.00) 		0.987
(1.00) 		0.512
(1.00) 		0.78
(1.00) 		1
(1.00)
del 2q22 3 58 (16%) 305 0.885
(1.00) 		0.00183
(1.00) 		0.859
(1.00) 		1
(1.00) 		0.701
(1.00) 		0.726
(1.00) 		0.856
(1.00) 		0.281
(1.00) 		0.0347
(1.00) 		0.692
(1.00) 		0.135
(1.00) 		0.142
(1.00) 		0.269
(1.00) 		1
(1.00)
del 3p13 59 (16%) 304 0.263
(1.00) 		0.0112
(1.00) 		0.771
(1.00) 		0.386
(1.00) 		0.451
(1.00) 		0.144
(1.00) 		0.359
(1.00) 		0.415
(1.00) 		0.54
(1.00) 		0.641
(1.00) 		0.413
(1.00) 		0.202
(1.00) 		0.714
(1.00) 		1
(1.00)
del 3q29 25 (7%) 338 0.473
(1.00) 		0.279
(1.00) 		0.772
(1.00) 		0.146
(1.00) 		0.223
(1.00) 		0.301
(1.00) 		0.133
(1.00) 		0.113
(1.00) 		0.468
(1.00) 		0.0676
(1.00) 		0.128
(1.00) 		0.134
(1.00) 		0.935
(1.00) 		1
(1.00)
del 4q28 2 37 (10%) 326 0.413
(1.00) 		0.00201
(1.00) 		0.0982
(1.00) 		1
(1.00) 		0.631
(1.00) 		0.62
(1.00) 		0.899
(1.00) 		0.0112
(1.00) 		0.00414
(1.00) 		0.492
(1.00) 		0.0114
(1.00) 		0.544
(1.00) 		0.308
(1.00) 		0.3
(1.00)
del 6p25 1 27 (7%) 336 0.496
(1.00) 		0.341
(1.00) 		0.431
(1.00) 		0.00728
(1.00) 		0.61
(1.00) 		0.34
(1.00) 		0.00398
(1.00) 		0.00186
(1.00) 		0.0341
(1.00) 		0.0269
(1.00) 		0.0046
(1.00) 		0.673
(1.00) 		0.568
(1.00) 		0.00672
(1.00)
del 7q31 33 24 (7%) 339 0.446
(1.00) 		0.369
(1.00) 		0.577
(1.00) 		0.0188
(1.00) 		1
(1.00) 		1
(1.00) 		0.00421
(1.00) 		0.12
(1.00) 		0.0908
(1.00) 		0.649
(1.00) 		0.0776
(1.00) 		0.693
(1.00) 		0.599
(1.00) 		1
(1.00)
del 9p23 32 (9%) 331 0.406
(1.00) 		0.841
(1.00) 		0.144
(1.00) 		0.026
(1.00) 		0.615
(1.00) 		0.34
(1.00) 		0.0124
(1.00) 		0.0068
(1.00) 		0.00412
(1.00) 		0.304
(1.00) 		0.0105
(1.00) 		0.763
(1.00) 		0.167
(1.00) 		1
(1.00)
del 11p11 2 24 (7%) 339 0.438
(1.00) 		0.351
(1.00) 		0.0251
(1.00) 		0.348
(1.00) 		1
(1.00) 		0.123
(1.00) 		0.223
(1.00) 		0.0413
(1.00) 		0.00755
(1.00) 		0.869
(1.00) 		0.0381
(1.00) 		0.24
(1.00) 		0.887
(1.00) 		0.00357
(1.00)
del 11q23 2 35 (10%) 328 0.428
(1.00) 		0.132
(1.00) 		0.0007
(0.572) 		0.783
(1.00) 		0.362
(1.00) 		0.0605
(1.00) 		0.588
(1.00) 		0.000428
(0.356) 		0.000675
(0.553) 		0.103
(1.00) 		0.00198
(1.00) 		0.0486
(1.00) 		0.423
(1.00) 		0.658
(1.00)
del 12q24 32 31 (9%) 332 0.663
(1.00) 		0.725
(1.00) 		0.016
(1.00) 		0.0541
(1.00) 		1
(1.00) 		0.517
(1.00) 		0.0362
(1.00) 		0.0521
(1.00) 		0.0256
(1.00) 		0.534
(1.00) 		0.0314
(1.00) 		0.00858
(1.00) 		0.959
(1.00) 		1
(1.00)
del 13q14 13 168 (46%) 195 0.405
(1.00) 		0.0192
(1.00) 		0.0629
(1.00) 		0.26
(1.00) 		0.0247
(1.00) 		0.0071
(1.00) 		0.25
(1.00) 		0.000344
(0.287) 		0.000561
(0.461) 		0.109
(1.00) 		0.000334
(0.28) 		0.0224
(1.00) 		0.357
(1.00) 		0.0041
(1.00)
del 17q21 31 72 (20%) 291 0.857
(1.00) 		0.411
(1.00) 		0.364
(1.00) 		0.214
(1.00) 		1
(1.00) 		0.898
(1.00) 		0.142
(1.00) 		0.988
(1.00) 		0.639
(1.00) 		0.787
(1.00) 		0.757
(1.00) 		0.384
(1.00) 		0.789
(1.00) 		0.764
(1.00)
del 21q22 2 37 (10%) 326 0.426
(1.00) 		0.178
(1.00) 		0.0185
(1.00) 		0.0623
(1.00) 		0.136
(1.00) 		0.754
(1.00) 		0.0436
(1.00) 		0.424
(1.00) 		0.681
(1.00) 		0.354
(1.00) 		0.209
(1.00) 		0.967
(1.00) 		0.851
(1.00) 		0.0756
(1.00)
del 21q22 3 111 (31%) 252 0.0808
(1.00) 		0.0691
(1.00) 		0.0803
(1.00) 		0.0327
(1.00) 		1
(1.00) 		0.287
(1.00) 		0.017
(1.00) 		0.656
(1.00) 		0.954
(1.00) 		0.286
(1.00) 		0.576
(1.00) 		0.333
(1.00) 		0.849
(1.00) 		0.134
(1.00)
'amp_3q21.3' versus 'GLEASON_SCORE'

P value = 1.08e-05 (Wilcoxon-test), Q value = 0.0095

Table S1.  Gene #2: 'amp_3q21.3' versus Clinical Feature #11: 'GLEASON_SCORE'

nPatients Mean (Std.Dev)
ALL 363 7.5 (1.0)
AMP PEAK 2(3Q21.3) MUTATED 49 8.1 (1.0)
AMP PEAK 2(3Q21.3) WILD-TYPE 314 7.4 (0.9)

Figure S1.  Get High-res Image Gene #2: 'amp_3q21.3' versus Clinical Feature #11: 'GLEASON_SCORE'

'amp_3q26.2' versus 'GLEASON_SCORE'

P value = 0.000208 (Wilcoxon-test), Q value = 0.18

Table S2.  Gene #3: 'amp_3q26.2' versus Clinical Feature #11: 'GLEASON_SCORE'

nPatients Mean (Std.Dev)
ALL 363 7.5 (1.0)
AMP PEAK 3(3Q26.2) MUTATED 57 7.9 (1.0)
AMP PEAK 3(3Q26.2) WILD-TYPE 306 7.4 (0.9)

Figure S2.  Get High-res Image Gene #3: 'amp_3q26.2' versus Clinical Feature #11: 'GLEASON_SCORE'

'amp_5q35.3' versus 'AGE'

P value = 0.000116 (Wilcoxon-test), Q value = 0.099

Table S3.  Gene #6: 'amp_5q35.3' versus Clinical Feature #2: 'AGE'

nPatients Mean (Std.Dev)
ALL 355 60.8 (7.0)
AMP PEAK 6(5Q35.3) MUTATED 18 66.7 (4.1)
AMP PEAK 6(5Q35.3) WILD-TYPE 337 60.5 (6.9)

Figure S3.  Get High-res Image Gene #6: 'amp_5q35.3' versus Clinical Feature #2: 'AGE'

'amp_8p11.23' versus 'GLEASON_SCORE_COMBINED'

P value = 0.000252 (Wilcoxon-test), Q value = 0.21

Table S4.  Gene #9: 'amp_8p11.23' versus Clinical Feature #8: 'GLEASON_SCORE_COMBINED'

nPatients Mean (Std.Dev)
ALL 363 7.4 (0.9)
AMP PEAK 9(8P11.23) MUTATED 41 8.0 (0.9)
AMP PEAK 9(8P11.23) WILD-TYPE 322 7.4 (0.9)

Figure S4.  Get High-res Image Gene #9: 'amp_8p11.23' versus Clinical Feature #8: 'GLEASON_SCORE_COMBINED'

'amp_8p11.23' versus 'GLEASON_SCORE_PRIMARY'

P value = 1.03e-05 (Wilcoxon-test), Q value = 0.0091

Table S5.  Gene #9: 'amp_8p11.23' versus Clinical Feature #9: 'GLEASON_SCORE_PRIMARY'

nPatients Mean (Std.Dev)
ALL 363 3.6 (0.6)
AMP PEAK 9(8P11.23) MUTATED 41 4.0 (0.7)
AMP PEAK 9(8P11.23) WILD-TYPE 322 3.5 (0.6)

Figure S5.  Get High-res Image Gene #9: 'amp_8p11.23' versus Clinical Feature #9: 'GLEASON_SCORE_PRIMARY'

'amp_8p11.23' versus 'GLEASON_SCORE'

P value = 0.000181 (Wilcoxon-test), Q value = 0.15

Table S6.  Gene #9: 'amp_8p11.23' versus Clinical Feature #11: 'GLEASON_SCORE'

nPatients Mean (Std.Dev)
ALL 363 7.5 (1.0)
AMP PEAK 9(8P11.23) MUTATED 41 8.1 (1.0)
AMP PEAK 9(8P11.23) WILD-TYPE 322 7.4 (0.9)

Figure S6.  Get High-res Image Gene #9: 'amp_8p11.23' versus Clinical Feature #11: 'GLEASON_SCORE'

'amp_8q22.1' versus 'PATHOLOGY.T.STAGE'

P value = 5e-05 (Fisher's exact test), Q value = 0.043

Table S7.  Gene #10: 'amp_8q22.1' versus Clinical Feature #3: 'PATHOLOGY.T.STAGE'

nPatients T2 T3 T4
ALL 150 206 5
AMP PEAK 10(8Q22.1) MUTATED 26 74 3
AMP PEAK 10(8Q22.1) WILD-TYPE 124 132 2

Figure S7.  Get High-res Image Gene #10: 'amp_8q22.1' versus Clinical Feature #3: 'PATHOLOGY.T.STAGE'

'amp_8q22.1' versus 'GLEASON_SCORE_COMBINED'

P value = 1.02e-05 (Wilcoxon-test), Q value = 0.009

Table S8.  Gene #10: 'amp_8q22.1' versus Clinical Feature #8: 'GLEASON_SCORE_COMBINED'

nPatients Mean (Std.Dev)
ALL 363 7.4 (0.9)
AMP PEAK 10(8Q22.1) MUTATED 103 7.8 (0.9)
AMP PEAK 10(8Q22.1) WILD-TYPE 260 7.3 (0.9)

Figure S8.  Get High-res Image Gene #10: 'amp_8q22.1' versus Clinical Feature #8: 'GLEASON_SCORE_COMBINED'

'amp_8q22.1' versus 'GLEASON_SCORE_PRIMARY'

P value = 1.42e-07 (Wilcoxon-test), Q value = 0.00013

Table S9.  Gene #10: 'amp_8q22.1' versus Clinical Feature #9: 'GLEASON_SCORE_PRIMARY'

nPatients Mean (Std.Dev)
ALL 363 3.6 (0.6)
AMP PEAK 10(8Q22.1) MUTATED 103 3.9 (0.6)
AMP PEAK 10(8Q22.1) WILD-TYPE 260 3.5 (0.6)

Figure S9.  Get High-res Image Gene #10: 'amp_8q22.1' versus Clinical Feature #9: 'GLEASON_SCORE_PRIMARY'

'amp_8q22.1' versus 'GLEASON_SCORE'

P value = 2.8e-06 (Wilcoxon-test), Q value = 0.0025

Table S10.  Gene #10: 'amp_8q22.1' versus Clinical Feature #11: 'GLEASON_SCORE'

nPatients Mean (Std.Dev)
ALL 363 7.5 (1.0)
AMP PEAK 10(8Q22.1) MUTATED 103 7.9 (1.0)
AMP PEAK 10(8Q22.1) WILD-TYPE 260 7.4 (0.9)

Figure S10.  Get High-res Image Gene #10: 'amp_8q22.1' versus Clinical Feature #11: 'GLEASON_SCORE'

'amp_8q24.21' versus 'PATHOLOGY.T.STAGE'

P value = 0.00025 (Fisher's exact test), Q value = 0.21

Table S11.  Gene #11: 'amp_8q24.21' versus Clinical Feature #3: 'PATHOLOGY.T.STAGE'

nPatients T2 T3 T4
ALL 150 206 5
AMP PEAK 11(8Q24.21) MUTATED 25 71 2
AMP PEAK 11(8Q24.21) WILD-TYPE 125 135 3

Figure S11.  Get High-res Image Gene #11: 'amp_8q24.21' versus Clinical Feature #3: 'PATHOLOGY.T.STAGE'

'amp_8q24.21' versus 'GLEASON_SCORE_COMBINED'

P value = 4.16e-06 (Wilcoxon-test), Q value = 0.0037

Table S12.  Gene #11: 'amp_8q24.21' versus Clinical Feature #8: 'GLEASON_SCORE_COMBINED'

nPatients Mean (Std.Dev)
ALL 363 7.4 (0.9)
AMP PEAK 11(8Q24.21) MUTATED 98 7.8 (0.9)
AMP PEAK 11(8Q24.21) WILD-TYPE 265 7.3 (0.9)

Figure S12.  Get High-res Image Gene #11: 'amp_8q24.21' versus Clinical Feature #8: 'GLEASON_SCORE_COMBINED'

'amp_8q24.21' versus 'GLEASON_SCORE_PRIMARY'

P value = 2.09e-07 (Wilcoxon-test), Q value = 0.00019

Table S13.  Gene #11: 'amp_8q24.21' versus Clinical Feature #9: 'GLEASON_SCORE_PRIMARY'

nPatients Mean (Std.Dev)
ALL 363 3.6 (0.6)
AMP PEAK 11(8Q24.21) MUTATED 98 3.9 (0.6)
AMP PEAK 11(8Q24.21) WILD-TYPE 265 3.5 (0.6)

Figure S13.  Get High-res Image Gene #11: 'amp_8q24.21' versus Clinical Feature #9: 'GLEASON_SCORE_PRIMARY'

'amp_8q24.21' versus 'GLEASON_SCORE'

P value = 2.86e-06 (Wilcoxon-test), Q value = 0.0026

Table S14.  Gene #11: 'amp_8q24.21' versus Clinical Feature #11: 'GLEASON_SCORE'

nPatients Mean (Std.Dev)
ALL 363 7.5 (1.0)
AMP PEAK 11(8Q24.21) MUTATED 98 7.9 (1.0)
AMP PEAK 11(8Q24.21) WILD-TYPE 265 7.4 (0.9)

Figure S14.  Get High-res Image Gene #11: 'amp_8q24.21' versus Clinical Feature #11: 'GLEASON_SCORE'

'amp_9q33.3' versus 'PATHOLOGY.T.STAGE'

P value = 0.00016 (Fisher's exact test), Q value = 0.14

Table S15.  Gene #12: 'amp_9q33.3' versus Clinical Feature #3: 'PATHOLOGY.T.STAGE'

nPatients T2 T3 T4
ALL 150 206 5
AMP PEAK 12(9Q33.3) MUTATED 5 32 1
AMP PEAK 12(9Q33.3) WILD-TYPE 145 174 4

Figure S15.  Get High-res Image Gene #12: 'amp_9q33.3' versus Clinical Feature #3: 'PATHOLOGY.T.STAGE'

'amp_9q33.3' versus 'GLEASON_SCORE_COMBINED'

P value = 1.34e-05 (Wilcoxon-test), Q value = 0.012

Table S16.  Gene #12: 'amp_9q33.3' versus Clinical Feature #8: 'GLEASON_SCORE_COMBINED'

nPatients Mean (Std.Dev)
ALL 363 7.4 (0.9)
AMP PEAK 12(9Q33.3) MUTATED 38 8.1 (1.0)
AMP PEAK 12(9Q33.3) WILD-TYPE 325 7.4 (0.9)

Figure S16.  Get High-res Image Gene #12: 'amp_9q33.3' versus Clinical Feature #8: 'GLEASON_SCORE_COMBINED'

'amp_9q33.3' versus 'GLEASON_SCORE_PRIMARY'

P value = 2.19e-06 (Wilcoxon-test), Q value = 0.002

Table S17.  Gene #12: 'amp_9q33.3' versus Clinical Feature #9: 'GLEASON_SCORE_PRIMARY'

nPatients Mean (Std.Dev)
ALL 363 3.6 (0.6)
AMP PEAK 12(9Q33.3) MUTATED 38 4.1 (0.6)
AMP PEAK 12(9Q33.3) WILD-TYPE 325 3.5 (0.6)

Figure S17.  Get High-res Image Gene #12: 'amp_9q33.3' versus Clinical Feature #9: 'GLEASON_SCORE_PRIMARY'

'amp_9q33.3' versus 'GLEASON_SCORE'

P value = 3.59e-07 (Wilcoxon-test), Q value = 0.00033

Table S18.  Gene #12: 'amp_9q33.3' versus Clinical Feature #11: 'GLEASON_SCORE'

nPatients Mean (Std.Dev)
ALL 363 7.5 (1.0)
AMP PEAK 12(9Q33.3) MUTATED 38 8.2 (0.9)
AMP PEAK 12(9Q33.3) WILD-TYPE 325 7.4 (0.9)

Figure S18.  Get High-res Image Gene #12: 'amp_9q33.3' versus Clinical Feature #11: 'GLEASON_SCORE'

'amp_11q13.2' versus 'GLEASON_SCORE_PRIMARY'

P value = 5.98e-05 (Wilcoxon-test), Q value = 0.052

Table S19.  Gene #13: 'amp_11q13.2' versus Clinical Feature #9: 'GLEASON_SCORE_PRIMARY'

nPatients Mean (Std.Dev)
ALL 363 3.6 (0.6)
AMP PEAK 13(11Q13.2) MUTATED 25 4.1 (0.7)
AMP PEAK 13(11Q13.2) WILD-TYPE 338 3.6 (0.6)

Figure S19.  Get High-res Image Gene #13: 'amp_11q13.2' versus Clinical Feature #9: 'GLEASON_SCORE_PRIMARY'

'amp_11q13.2' versus 'GLEASON_SCORE'

P value = 5.77e-05 (Wilcoxon-test), Q value = 0.05

Table S20.  Gene #13: 'amp_11q13.2' versus Clinical Feature #11: 'GLEASON_SCORE'

nPatients Mean (Std.Dev)
ALL 363 7.5 (1.0)
AMP PEAK 13(11Q13.2) MUTATED 25 8.3 (1.0)
AMP PEAK 13(11Q13.2) WILD-TYPE 338 7.5 (0.9)

Figure S20.  Get High-res Image Gene #13: 'amp_11q13.2' versus Clinical Feature #11: 'GLEASON_SCORE'

'amp_12q23.1' versus 'GLEASON_SCORE_COMBINED'

P value = 2.34e-05 (Wilcoxon-test), Q value = 0.02

Table S21.  Gene #14: 'amp_12q23.1' versus Clinical Feature #8: 'GLEASON_SCORE_COMBINED'

nPatients Mean (Std.Dev)
ALL 363 7.4 (0.9)
AMP PEAK 14(12Q23.1) MUTATED 21 8.3 (0.9)
AMP PEAK 14(12Q23.1) WILD-TYPE 342 7.4 (0.9)

Figure S21.  Get High-res Image Gene #14: 'amp_12q23.1' versus Clinical Feature #8: 'GLEASON_SCORE_COMBINED'

'amp_12q23.1' versus 'GLEASON_SCORE_PRIMARY'

P value = 2.28e-05 (Wilcoxon-test), Q value = 0.02

Table S22.  Gene #14: 'amp_12q23.1' versus Clinical Feature #9: 'GLEASON_SCORE_PRIMARY'

nPatients Mean (Std.Dev)
ALL 363 3.6 (0.6)
AMP PEAK 14(12Q23.1) MUTATED 21 4.2 (0.6)
AMP PEAK 14(12Q23.1) WILD-TYPE 342 3.6 (0.6)

Figure S22.  Get High-res Image Gene #14: 'amp_12q23.1' versus Clinical Feature #9: 'GLEASON_SCORE_PRIMARY'

'amp_12q23.1' versus 'GLEASON_SCORE'

P value = 9.76e-07 (Wilcoxon-test), Q value = 0.00088

Table S23.  Gene #14: 'amp_12q23.1' versus Clinical Feature #11: 'GLEASON_SCORE'

nPatients Mean (Std.Dev)
ALL 363 7.5 (1.0)
AMP PEAK 14(12Q23.1) MUTATED 21 8.5 (0.8)
AMP PEAK 14(12Q23.1) WILD-TYPE 342 7.5 (0.9)

Figure S23.  Get High-res Image Gene #14: 'amp_12q23.1' versus Clinical Feature #11: 'GLEASON_SCORE'

'amp_14q21.1' versus 'GLEASON_SCORE'

P value = 0.00018 (Wilcoxon-test), Q value = 0.15

Table S24.  Gene #16: 'amp_14q21.1' versus Clinical Feature #11: 'GLEASON_SCORE'

nPatients Mean (Std.Dev)
ALL 363 7.5 (1.0)
AMP PEAK 16(14Q21.1) MUTATED 20 8.2 (0.9)
AMP PEAK 16(14Q21.1) WILD-TYPE 343 7.5 (0.9)

Figure S24.  Get High-res Image Gene #16: 'amp_14q21.1' versus Clinical Feature #11: 'GLEASON_SCORE'

'amp_20q13.2' versus 'PATHOLOGY.T.STAGE'

P value = 4e-05 (Fisher's exact test), Q value = 0.035

Table S25.  Gene #21: 'amp_20q13.2' versus Clinical Feature #3: 'PATHOLOGY.T.STAGE'

nPatients T2 T3 T4
ALL 150 206 5
AMP PEAK 21(20Q13.2) MUTATED 2 22 2
AMP PEAK 21(20Q13.2) WILD-TYPE 148 184 3

Figure S25.  Get High-res Image Gene #21: 'amp_20q13.2' versus Clinical Feature #3: 'PATHOLOGY.T.STAGE'

'amp_20q13.2' versus 'GLEASON_SCORE'

P value = 8.83e-05 (Wilcoxon-test), Q value = 0.076

Table S26.  Gene #21: 'amp_20q13.2' versus Clinical Feature #11: 'GLEASON_SCORE'

nPatients Mean (Std.Dev)
ALL 363 7.5 (1.0)
AMP PEAK 21(20Q13.2) MUTATED 26 8.3 (1.0)
AMP PEAK 21(20Q13.2) WILD-TYPE 337 7.5 (0.9)

Figure S26.  Get High-res Image Gene #21: 'amp_20q13.2' versus Clinical Feature #11: 'GLEASON_SCORE'

'del_1q42.3' versus 'Time to Death'

P value = 1.71e-06 (logrank test), Q value = 0.0015

Table S27.  Gene #32: 'del_1q42.3' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 361 6 0.3 - 151.4 (23.9)
DEL PEAK 4(1Q42.3) MUTATED 32 4 0.7 - 94.7 (26.5)
DEL PEAK 4(1Q42.3) WILD-TYPE 329 2 0.3 - 151.4 (23.9)

Figure S27.  Get High-res Image Gene #32: 'del_1q42.3' versus Clinical Feature #1: 'Time to Death'

'del_2p21' versus 'GLEASON_SCORE_PRIMARY'

P value = 0.000285 (Wilcoxon-test), Q value = 0.24

Table S28.  Gene #33: 'del_2p21' versus Clinical Feature #9: 'GLEASON_SCORE_PRIMARY'

nPatients Mean (Std.Dev)
ALL 363 3.6 (0.6)
DEL PEAK 5(2P21) MUTATED 33 4.0 (0.6)
DEL PEAK 5(2P21) WILD-TYPE 330 3.6 (0.6)

Figure S28.  Get High-res Image Gene #33: 'del_2p21' versus Clinical Feature #9: 'GLEASON_SCORE_PRIMARY'

'del_2q22.1' versus 'AGE'

P value = 0.000116 (Wilcoxon-test), Q value = 0.099

Table S29.  Gene #34: 'del_2q22.1' versus Clinical Feature #2: 'AGE'

nPatients Mean (Std.Dev)
ALL 355 60.8 (7.0)
DEL PEAK 6(2Q22.1) MUTATED 63 63.7 (5.7)
DEL PEAK 6(2Q22.1) WILD-TYPE 292 60.1 (7.1)

Figure S29.  Get High-res Image Gene #34: 'del_2q22.1' versus Clinical Feature #2: 'AGE'

'del_5q11.2' versus 'PATHOLOGY.T.STAGE'

P value = 2e-05 (Fisher's exact test), Q value = 0.018

Table S30.  Gene #39: 'del_5q11.2' versus Clinical Feature #3: 'PATHOLOGY.T.STAGE'

nPatients T2 T3 T4
ALL 150 206 5
DEL PEAK 11(5Q11.2) MUTATED 11 50 1
DEL PEAK 11(5Q11.2) WILD-TYPE 139 156 4

Figure S30.  Get High-res Image Gene #39: 'del_5q11.2' versus Clinical Feature #3: 'PATHOLOGY.T.STAGE'

'del_5q11.2' versus 'GLEASON_SCORE_COMBINED'

P value = 1.02e-05 (Wilcoxon-test), Q value = 0.0091

Table S31.  Gene #39: 'del_5q11.2' versus Clinical Feature #8: 'GLEASON_SCORE_COMBINED'

nPatients Mean (Std.Dev)
ALL 363 7.4 (0.9)
DEL PEAK 11(5Q11.2) MUTATED 62 7.9 (0.9)
DEL PEAK 11(5Q11.2) WILD-TYPE 301 7.4 (0.9)

Figure S31.  Get High-res Image Gene #39: 'del_5q11.2' versus Clinical Feature #8: 'GLEASON_SCORE_COMBINED'

'del_5q11.2' versus 'GLEASON_SCORE_PRIMARY'

P value = 5.25e-06 (Wilcoxon-test), Q value = 0.0047

Table S32.  Gene #39: 'del_5q11.2' versus Clinical Feature #9: 'GLEASON_SCORE_PRIMARY'

nPatients Mean (Std.Dev)
ALL 363 3.6 (0.6)
DEL PEAK 11(5Q11.2) MUTATED 62 3.9 (0.6)
DEL PEAK 11(5Q11.2) WILD-TYPE 301 3.5 (0.6)

Figure S32.  Get High-res Image Gene #39: 'del_5q11.2' versus Clinical Feature #9: 'GLEASON_SCORE_PRIMARY'

'del_5q11.2' versus 'GLEASON_SCORE'

P value = 4.91e-06 (Wilcoxon-test), Q value = 0.0044

Table S33.  Gene #39: 'del_5q11.2' versus Clinical Feature #11: 'GLEASON_SCORE'

nPatients Mean (Std.Dev)
ALL 363 7.5 (1.0)
DEL PEAK 11(5Q11.2) MUTATED 62 8.0 (1.0)
DEL PEAK 11(5Q11.2) WILD-TYPE 301 7.4 (0.9)

Figure S33.  Get High-res Image Gene #39: 'del_5q11.2' versus Clinical Feature #11: 'GLEASON_SCORE'

'del_5q13.2' versus 'PATHOLOGY.T.STAGE'

P value = 1e-05 (Fisher's exact test), Q value = 0.0089

Table S34.  Gene #40: 'del_5q13.2' versus Clinical Feature #3: 'PATHOLOGY.T.STAGE'

nPatients T2 T3 T4
ALL 150 206 5
DEL PEAK 12(5Q13.2) MUTATED 9 54 1
DEL PEAK 12(5Q13.2) WILD-TYPE 141 152 4

Figure S34.  Get High-res Image Gene #40: 'del_5q13.2' versus Clinical Feature #3: 'PATHOLOGY.T.STAGE'

'del_5q13.2' versus 'GLEASON_SCORE_COMBINED'

P value = 7.77e-07 (Wilcoxon-test), Q value = 7e-04

Table S35.  Gene #40: 'del_5q13.2' versus Clinical Feature #8: 'GLEASON_SCORE_COMBINED'

nPatients Mean (Std.Dev)
ALL 363 7.4 (0.9)
DEL PEAK 12(5Q13.2) MUTATED 64 7.9 (0.9)
DEL PEAK 12(5Q13.2) WILD-TYPE 299 7.3 (0.9)

Figure S35.  Get High-res Image Gene #40: 'del_5q13.2' versus Clinical Feature #8: 'GLEASON_SCORE_COMBINED'

'del_5q13.2' versus 'GLEASON_SCORE_PRIMARY'

P value = 3.36e-07 (Wilcoxon-test), Q value = 0.00031

Table S36.  Gene #40: 'del_5q13.2' versus Clinical Feature #9: 'GLEASON_SCORE_PRIMARY'

nPatients Mean (Std.Dev)
ALL 363 3.6 (0.6)
DEL PEAK 12(5Q13.2) MUTATED 64 3.9 (0.6)
DEL PEAK 12(5Q13.2) WILD-TYPE 299 3.5 (0.6)

Figure S36.  Get High-res Image Gene #40: 'del_5q13.2' versus Clinical Feature #9: 'GLEASON_SCORE_PRIMARY'

'del_5q13.2' versus 'GLEASON_SCORE'

P value = 3.62e-06 (Wilcoxon-test), Q value = 0.0032

Table S37.  Gene #40: 'del_5q13.2' versus Clinical Feature #11: 'GLEASON_SCORE'

nPatients Mean (Std.Dev)
ALL 363 7.5 (1.0)
DEL PEAK 12(5Q13.2) MUTATED 64 8.0 (1.0)
DEL PEAK 12(5Q13.2) WILD-TYPE 299 7.4 (0.9)

Figure S37.  Get High-res Image Gene #40: 'del_5q13.2' versus Clinical Feature #11: 'GLEASON_SCORE'

'del_5q21.1' versus 'GLEASON_SCORE_PRIMARY'

P value = 2.32e-05 (Wilcoxon-test), Q value = 0.02

Table S38.  Gene #41: 'del_5q21.1' versus Clinical Feature #9: 'GLEASON_SCORE_PRIMARY'

nPatients Mean (Std.Dev)
ALL 363 3.6 (0.6)
DEL PEAK 13(5Q21.1) MUTATED 76 3.9 (0.6)
DEL PEAK 13(5Q21.1) WILD-TYPE 287 3.5 (0.6)

Figure S38.  Get High-res Image Gene #41: 'del_5q21.1' versus Clinical Feature #9: 'GLEASON_SCORE_PRIMARY'

'del_6q14.3' versus 'GLEASON_SCORE_COMBINED'

P value = 9.45e-06 (Wilcoxon-test), Q value = 0.0084

Table S39.  Gene #43: 'del_6q14.3' versus Clinical Feature #8: 'GLEASON_SCORE_COMBINED'

nPatients Mean (Std.Dev)
ALL 363 7.4 (0.9)
DEL PEAK 15(6Q14.3) MUTATED 132 7.7 (0.9)
DEL PEAK 15(6Q14.3) WILD-TYPE 231 7.3 (0.9)

Figure S39.  Get High-res Image Gene #43: 'del_6q14.3' versus Clinical Feature #8: 'GLEASON_SCORE_COMBINED'

'del_6q14.3' versus 'GLEASON_SCORE_PRIMARY'

P value = 9.48e-06 (Wilcoxon-test), Q value = 0.0084

Table S40.  Gene #43: 'del_6q14.3' versus Clinical Feature #9: 'GLEASON_SCORE_PRIMARY'

nPatients Mean (Std.Dev)
ALL 363 3.6 (0.6)
DEL PEAK 15(6Q14.3) MUTATED 132 3.8 (0.6)
DEL PEAK 15(6Q14.3) WILD-TYPE 231 3.5 (0.6)

Figure S40.  Get High-res Image Gene #43: 'del_6q14.3' versus Clinical Feature #9: 'GLEASON_SCORE_PRIMARY'

'del_6q14.3' versus 'GLEASON_SCORE'

P value = 4.6e-05 (Wilcoxon-test), Q value = 0.04

Table S41.  Gene #43: 'del_6q14.3' versus Clinical Feature #11: 'GLEASON_SCORE'

nPatients Mean (Std.Dev)
ALL 363 7.5 (1.0)
DEL PEAK 15(6Q14.3) MUTATED 132 7.8 (1.0)
DEL PEAK 15(6Q14.3) WILD-TYPE 231 7.4 (0.9)

Figure S41.  Get High-res Image Gene #43: 'del_6q14.3' versus Clinical Feature #11: 'GLEASON_SCORE'

'del_8p23.2' versus 'PATHOLOGY.T.STAGE'

P value = 4e-05 (Fisher's exact test), Q value = 0.035

Table S42.  Gene #45: 'del_8p23.2' versus Clinical Feature #3: 'PATHOLOGY.T.STAGE'

nPatients T2 T3 T4
ALL 150 206 5
DEL PEAK 17(8P23.2) MUTATED 44 105 4
DEL PEAK 17(8P23.2) WILD-TYPE 106 101 1

Figure S42.  Get High-res Image Gene #45: 'del_8p23.2' versus Clinical Feature #3: 'PATHOLOGY.T.STAGE'

'del_8p23.2' versus 'GLEASON_SCORE_PRIMARY'

P value = 0.000183 (Wilcoxon-test), Q value = 0.16

Table S43.  Gene #45: 'del_8p23.2' versus Clinical Feature #9: 'GLEASON_SCORE_PRIMARY'

nPatients Mean (Std.Dev)
ALL 363 3.6 (0.6)
DEL PEAK 17(8P23.2) MUTATED 153 3.7 (0.6)
DEL PEAK 17(8P23.2) WILD-TYPE 210 3.5 (0.6)

Figure S43.  Get High-res Image Gene #45: 'del_8p23.2' versus Clinical Feature #9: 'GLEASON_SCORE_PRIMARY'

'del_8p21.3' versus 'PATHOLOGY.T.STAGE'

P value = 0.00014 (Fisher's exact test), Q value = 0.12

Table S44.  Gene #46: 'del_8p21.3' versus Clinical Feature #3: 'PATHOLOGY.T.STAGE'

nPatients T2 T3 T4
ALL 150 206 5
DEL PEAK 18(8P21.3) MUTATED 67 136 4
DEL PEAK 18(8P21.3) WILD-TYPE 83 70 1

Figure S44.  Get High-res Image Gene #46: 'del_8p21.3' versus Clinical Feature #3: 'PATHOLOGY.T.STAGE'

'del_10q23.31' versus 'PATHOLOGY.T.STAGE'

P value = 2e-04 (Fisher's exact test), Q value = 0.17

Table S45.  Gene #48: 'del_10q23.31' versus Clinical Feature #3: 'PATHOLOGY.T.STAGE'

nPatients T2 T3 T4
ALL 150 206 5
DEL PEAK 20(10Q23.31) MUTATED 29 77 3
DEL PEAK 20(10Q23.31) WILD-TYPE 121 129 2

Figure S45.  Get High-res Image Gene #48: 'del_10q23.31' versus Clinical Feature #3: 'PATHOLOGY.T.STAGE'

'del_11q22.3' versus 'GLEASON_SCORE_PRIMARY'

P value = 2.68e-05 (Wilcoxon-test), Q value = 0.023

Table S46.  Gene #50: 'del_11q22.3' versus Clinical Feature #9: 'GLEASON_SCORE_PRIMARY'

nPatients Mean (Std.Dev)
ALL 363 3.6 (0.6)
DEL PEAK 22(11Q22.3) MUTATED 29 4.1 (0.7)
DEL PEAK 22(11Q22.3) WILD-TYPE 334 3.6 (0.6)

Figure S46.  Get High-res Image Gene #50: 'del_11q22.3' versus Clinical Feature #9: 'GLEASON_SCORE_PRIMARY'

'del_12p13.1' versus 'PATHOLOGY.T.STAGE'

P value = 8e-05 (Fisher's exact test), Q value = 0.069

Table S47.  Gene #52: 'del_12p13.1' versus Clinical Feature #3: 'PATHOLOGY.T.STAGE'

nPatients T2 T3 T4
ALL 150 206 5
DEL PEAK 24(12P13.1) MUTATED 18 62 2
DEL PEAK 24(12P13.1) WILD-TYPE 132 144 3

Figure S47.  Get High-res Image Gene #52: 'del_12p13.1' versus Clinical Feature #3: 'PATHOLOGY.T.STAGE'

'del_12p13.1' versus 'GLEASON_SCORE_PRIMARY'

P value = 6.23e-05 (Wilcoxon-test), Q value = 0.054

Table S48.  Gene #52: 'del_12p13.1' versus Clinical Feature #9: 'GLEASON_SCORE_PRIMARY'

nPatients Mean (Std.Dev)
ALL 363 3.6 (0.6)
DEL PEAK 24(12P13.1) MUTATED 82 3.8 (0.6)
DEL PEAK 24(12P13.1) WILD-TYPE 281 3.5 (0.6)

Figure S48.  Get High-res Image Gene #52: 'del_12p13.1' versus Clinical Feature #9: 'GLEASON_SCORE_PRIMARY'

'del_13q22.1' versus 'GLEASON_SCORE_COMBINED'

P value = 0.000103 (Wilcoxon-test), Q value = 0.088

Table S49.  Gene #55: 'del_13q22.1' versus Clinical Feature #8: 'GLEASON_SCORE_COMBINED'

nPatients Mean (Std.Dev)
ALL 363 7.4 (0.9)
DEL PEAK 27(13Q22.1) MUTATED 124 7.7 (1.0)
DEL PEAK 27(13Q22.1) WILD-TYPE 239 7.3 (0.9)

Figure S49.  Get High-res Image Gene #55: 'del_13q22.1' versus Clinical Feature #8: 'GLEASON_SCORE_COMBINED'

'del_13q22.1' versus 'GLEASON_SCORE'

P value = 3.21e-06 (Wilcoxon-test), Q value = 0.0029

Table S50.  Gene #55: 'del_13q22.1' versus Clinical Feature #11: 'GLEASON_SCORE'

nPatients Mean (Std.Dev)
ALL 363 7.5 (1.0)
DEL PEAK 27(13Q22.1) MUTATED 124 7.8 (1.0)
DEL PEAK 27(13Q22.1) WILD-TYPE 239 7.3 (0.9)

Figure S50.  Get High-res Image Gene #55: 'del_13q22.1' versus Clinical Feature #11: 'GLEASON_SCORE'

'del_15q21.3' versus 'GLEASON_SCORE_COMBINED'

P value = 2.42e-06 (Wilcoxon-test), Q value = 0.0022

Table S51.  Gene #56: 'del_15q21.3' versus Clinical Feature #8: 'GLEASON_SCORE_COMBINED'

nPatients Mean (Std.Dev)
ALL 363 7.4 (0.9)
DEL PEAK 28(15Q21.3) MUTATED 45 8.1 (1.0)
DEL PEAK 28(15Q21.3) WILD-TYPE 318 7.4 (0.9)

Figure S51.  Get High-res Image Gene #56: 'del_15q21.3' versus Clinical Feature #8: 'GLEASON_SCORE_COMBINED'

'del_15q21.3' versus 'GLEASON_SCORE_PRIMARY'

P value = 5.02e-06 (Wilcoxon-test), Q value = 0.0045

Table S52.  Gene #56: 'del_15q21.3' versus Clinical Feature #9: 'GLEASON_SCORE_PRIMARY'

nPatients Mean (Std.Dev)
ALL 363 3.6 (0.6)
DEL PEAK 28(15Q21.3) MUTATED 45 4.0 (0.6)
DEL PEAK 28(15Q21.3) WILD-TYPE 318 3.5 (0.6)

Figure S52.  Get High-res Image Gene #56: 'del_15q21.3' versus Clinical Feature #9: 'GLEASON_SCORE_PRIMARY'

'del_15q21.3' versus 'GLEASON_SCORE'

P value = 1.22e-05 (Wilcoxon-test), Q value = 0.011

Table S53.  Gene #56: 'del_15q21.3' versus Clinical Feature #11: 'GLEASON_SCORE'

nPatients Mean (Std.Dev)
ALL 363 7.5 (1.0)
DEL PEAK 28(15Q21.3) MUTATED 45 8.1 (1.0)
DEL PEAK 28(15Q21.3) WILD-TYPE 318 7.4 (0.9)

Figure S53.  Get High-res Image Gene #56: 'del_15q21.3' versus Clinical Feature #11: 'GLEASON_SCORE'

'del_16q22.3' versus 'GLEASON_SCORE_COMBINED'

P value = 6.74e-05 (Wilcoxon-test), Q value = 0.058

Table S54.  Gene #57: 'del_16q22.3' versus Clinical Feature #8: 'GLEASON_SCORE_COMBINED'

nPatients Mean (Std.Dev)
ALL 363 7.4 (0.9)
DEL PEAK 29(16Q22.3) MUTATED 130 7.7 (0.9)
DEL PEAK 29(16Q22.3) WILD-TYPE 233 7.3 (0.9)

Figure S54.  Get High-res Image Gene #57: 'del_16q22.3' versus Clinical Feature #8: 'GLEASON_SCORE_COMBINED'

'del_16q22.3' versus 'GLEASON_SCORE_PRIMARY'

P value = 2.45e-05 (Wilcoxon-test), Q value = 0.021

Table S55.  Gene #57: 'del_16q22.3' versus Clinical Feature #9: 'GLEASON_SCORE_PRIMARY'

nPatients Mean (Std.Dev)
ALL 363 3.6 (0.6)
DEL PEAK 29(16Q22.3) MUTATED 130 3.8 (0.6)
DEL PEAK 29(16Q22.3) WILD-TYPE 233 3.5 (0.6)

Figure S55.  Get High-res Image Gene #57: 'del_16q22.3' versus Clinical Feature #9: 'GLEASON_SCORE_PRIMARY'

'del_16q22.3' versus 'GLEASON_SCORE'

P value = 3.72e-05 (Wilcoxon-test), Q value = 0.033

Table S56.  Gene #57: 'del_16q22.3' versus Clinical Feature #11: 'GLEASON_SCORE'

nPatients Mean (Std.Dev)
ALL 363 7.5 (1.0)
DEL PEAK 29(16Q22.3) MUTATED 130 7.8 (1.0)
DEL PEAK 29(16Q22.3) WILD-TYPE 233 7.4 (0.9)

Figure S56.  Get High-res Image Gene #57: 'del_16q22.3' versus Clinical Feature #11: 'GLEASON_SCORE'

'del_16q24.1' versus 'PATHOLOGY.T.STAGE'

P value = 1e-04 (Fisher's exact test), Q value = 0.086

Table S57.  Gene #58: 'del_16q24.1' versus Clinical Feature #3: 'PATHOLOGY.T.STAGE'

nPatients T2 T3 T4
ALL 150 206 5
DEL PEAK 30(16Q24.1) MUTATED 43 103 1
DEL PEAK 30(16Q24.1) WILD-TYPE 107 103 4

Figure S57.  Get High-res Image Gene #58: 'del_16q24.1' versus Clinical Feature #3: 'PATHOLOGY.T.STAGE'

'del_16q24.1' versus 'GLEASON_SCORE_COMBINED'

P value = 5.27e-05 (Wilcoxon-test), Q value = 0.046

Table S58.  Gene #58: 'del_16q24.1' versus Clinical Feature #8: 'GLEASON_SCORE_COMBINED'

nPatients Mean (Std.Dev)
ALL 363 7.4 (0.9)
DEL PEAK 30(16Q24.1) MUTATED 147 7.7 (0.9)
DEL PEAK 30(16Q24.1) WILD-TYPE 216 7.3 (0.9)

Figure S58.  Get High-res Image Gene #58: 'del_16q24.1' versus Clinical Feature #8: 'GLEASON_SCORE_COMBINED'

'del_16q24.1' versus 'GLEASON_SCORE_PRIMARY'

P value = 1.09e-05 (Wilcoxon-test), Q value = 0.0096

Table S59.  Gene #58: 'del_16q24.1' versus Clinical Feature #9: 'GLEASON_SCORE_PRIMARY'

nPatients Mean (Std.Dev)
ALL 363 3.6 (0.6)
DEL PEAK 30(16Q24.1) MUTATED 147 3.8 (0.6)
DEL PEAK 30(16Q24.1) WILD-TYPE 216 3.5 (0.6)

Figure S59.  Get High-res Image Gene #58: 'del_16q24.1' versus Clinical Feature #9: 'GLEASON_SCORE_PRIMARY'

'del_16q24.1' versus 'GLEASON_SCORE'

P value = 6.5e-05 (Wilcoxon-test), Q value = 0.056

Table S60.  Gene #58: 'del_16q24.1' versus Clinical Feature #11: 'GLEASON_SCORE'

nPatients Mean (Std.Dev)
ALL 363 7.5 (1.0)
DEL PEAK 30(16Q24.1) MUTATED 147 7.8 (1.0)
DEL PEAK 30(16Q24.1) WILD-TYPE 216 7.3 (0.9)

Figure S60.  Get High-res Image Gene #58: 'del_16q24.1' versus Clinical Feature #11: 'GLEASON_SCORE'

'del_17p13.1' versus 'GLEASON_SCORE_COMBINED'

P value = 8.37e-06 (Wilcoxon-test), Q value = 0.0075

Table S61.  Gene #59: 'del_17p13.1' versus Clinical Feature #8: 'GLEASON_SCORE_COMBINED'

nPatients Mean (Std.Dev)
ALL 363 7.4 (0.9)
DEL PEAK 31(17P13.1) MUTATED 108 7.8 (1.0)
DEL PEAK 31(17P13.1) WILD-TYPE 255 7.3 (0.8)

Figure S61.  Get High-res Image Gene #59: 'del_17p13.1' versus Clinical Feature #8: 'GLEASON_SCORE_COMBINED'

'del_17p13.1' versus 'GLEASON_SCORE_PRIMARY'

P value = 6.11e-05 (Wilcoxon-test), Q value = 0.053

Table S62.  Gene #59: 'del_17p13.1' versus Clinical Feature #9: 'GLEASON_SCORE_PRIMARY'

nPatients Mean (Std.Dev)
ALL 363 3.6 (0.6)
DEL PEAK 31(17P13.1) MUTATED 108 3.8 (0.6)
DEL PEAK 31(17P13.1) WILD-TYPE 255 3.5 (0.6)

Figure S62.  Get High-res Image Gene #59: 'del_17p13.1' versus Clinical Feature #9: 'GLEASON_SCORE_PRIMARY'

'del_17p13.1' versus 'GLEASON_SCORE'

P value = 2.96e-06 (Wilcoxon-test), Q value = 0.0027

Table S63.  Gene #59: 'del_17p13.1' versus Clinical Feature #11: 'GLEASON_SCORE'

nPatients Mean (Std.Dev)
ALL 363 7.5 (1.0)
DEL PEAK 31(17P13.1) MUTATED 108 7.9 (1.0)
DEL PEAK 31(17P13.1) WILD-TYPE 255 7.4 (0.9)

Figure S63.  Get High-res Image Gene #59: 'del_17p13.1' versus Clinical Feature #11: 'GLEASON_SCORE'

'del_18q21.31' versus 'GLEASON_SCORE_COMBINED'

P value = 9.7e-05 (Wilcoxon-test), Q value = 0.083

Table S64.  Gene #61: 'del_18q21.31' versus Clinical Feature #8: 'GLEASON_SCORE_COMBINED'

nPatients Mean (Std.Dev)
ALL 363 7.4 (0.9)
DEL PEAK 33(18Q21.31) MUTATED 95 7.8 (1.0)
DEL PEAK 33(18Q21.31) WILD-TYPE 268 7.3 (0.9)

Figure S64.  Get High-res Image Gene #61: 'del_18q21.31' versus Clinical Feature #8: 'GLEASON_SCORE_COMBINED'

'del_18q21.31' versus 'GLEASON_SCORE'

P value = 8.74e-05 (Wilcoxon-test), Q value = 0.075

Table S65.  Gene #61: 'del_18q21.31' versus Clinical Feature #11: 'GLEASON_SCORE'

nPatients Mean (Std.Dev)
ALL 363 7.5 (1.0)
DEL PEAK 33(18Q21.31) MUTATED 95 7.9 (1.0)
DEL PEAK 33(18Q21.31) WILD-TYPE 268 7.4 (0.9)

Figure S65.  Get High-res Image Gene #61: 'del_18q21.31' versus Clinical Feature #11: 'GLEASON_SCORE'

'del_18q23' versus 'GLEASON_SCORE_COMBINED'

P value = 0.000272 (Wilcoxon-test), Q value = 0.23

Table S66.  Gene #62: 'del_18q23' versus Clinical Feature #8: 'GLEASON_SCORE_COMBINED'

nPatients Mean (Std.Dev)
ALL 363 7.4 (0.9)
DEL PEAK 34(18Q23) MUTATED 100 7.7 (1.0)
DEL PEAK 34(18Q23) WILD-TYPE 263 7.3 (0.9)

Figure S66.  Get High-res Image Gene #62: 'del_18q23' versus Clinical Feature #8: 'GLEASON_SCORE_COMBINED'

'del_18q23' versus 'GLEASON_SCORE'

P value = 0.000109 (Wilcoxon-test), Q value = 0.094

Table S67.  Gene #62: 'del_18q23' versus Clinical Feature #11: 'GLEASON_SCORE'

nPatients Mean (Std.Dev)
ALL 363 7.5 (1.0)
DEL PEAK 34(18Q23) MUTATED 100 7.8 (1.0)
DEL PEAK 34(18Q23) WILD-TYPE 263 7.4 (0.9)

Figure S67.  Get High-res Image Gene #62: 'del_18q23' versus Clinical Feature #11: 'GLEASON_SCORE'

'del_19q13.2' versus 'GLEASON_SCORE_PRIMARY'

P value = 0.000235 (Wilcoxon-test), Q value = 0.2

Table S68.  Gene #63: 'del_19q13.2' versus Clinical Feature #9: 'GLEASON_SCORE_PRIMARY'

nPatients Mean (Std.Dev)
ALL 363 3.6 (0.6)
DEL PEAK 35(19Q13.2) MUTATED 33 4.0 (0.7)
DEL PEAK 35(19Q13.2) WILD-TYPE 330 3.6 (0.6)

Figure S68.  Get High-res Image Gene #63: 'del_19q13.2' versus Clinical Feature #9: 'GLEASON_SCORE_PRIMARY'

Methods & Data
Input

  • Copy number data file = transformed.cor.cli.txt

  • Clinical data file = PRAD-TP.merged_data.txt

  • Number of patients = 363

  • Number of significantly focal cnvs = 65

  • Number of selected clinical features = 14

  • Exclude genes that fewer than K tumors have mutations, K = 3

Survival analysis

For survival clinical features, the Kaplan-Meier survival curves of tumors with and without gene mutations were plotted and the statistical significance P values were estimated by logrank test (Bland and Altman 2004) using the 'survdiff' function in R

Fisher's exact test

For binary or multi-class clinical features (nominal or ordinal), two-tailed Fisher's exact tests (Fisher 1922) were used to estimate the P values using the 'fisher.test' function in R

Q value calculation

For multiple hypothesis correction, Q value is the False Discovery Rate (FDR) analogue of the P value (Benjamini and Hochberg 1995), defined as the minimum FDR at which the test may be called significant. We used the 'Benjamini and Hochberg' method of 'p.adjust' function in R to convert P values into Q values.

Download Results

In addition to the links below, the full results of the analysis summarized in this report can also be downloaded programmatically using firehose_get, or interactively from either the Broad GDAC website or TCGA Data Coordination Center Portal.

References
[1] Bland and Altman, Statistics notes: The logrank test, BMJ 328(7447):1073 (2004)
[2] Fisher, R.A., On the interpretation of chi-square from contingency tables, and the calculation of P, Journal of the Royal Statistical Society 85(1):87-94 (1922)
[3] Benjamini and Hochberg, Controlling the false discovery rate: a practical and powerful approach to multiple testing, Journal of the Royal Statistical Society Series B 59:289-300 (1995)
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