Correlation between copy number variation genes (focal events) and selected clinical features
Prostate Adenocarcinoma (Primary solid tumor)
15 July 2014  |  analyses__2014_07_15
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 (2014): Correlation between copy number variation genes (focal events) and selected clinical features. Broad Institute of MIT and Harvard. doi:10.7908/C1Z036XG
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 62 focal events and 13 clinical features across 271 patients, 31 significant findings detected with Q value < 0.25.

  • amp_1q21.3 cnv correlated to 'GLEASON_SCORE_COMBINED',  'GLEASON_SCORE_PRIMARY', and 'GLEASON_SCORE'.

  • amp_3q21.3 cnv correlated to 'GLEASON_SCORE'.

  • amp_8q24.21 cnv correlated to 'GLEASON_SCORE_COMBINED',  'GLEASON_SCORE_PRIMARY', and 'GLEASON_SCORE'.

  • amp_9q34.11 cnv correlated to 'NUMBER.OF.LYMPH.NODES',  'GLEASON_SCORE_COMBINED',  'GLEASON_SCORE_PRIMARY', and 'GLEASON_SCORE'.

  • amp_14q21.1 cnv correlated to 'GLEASON_SCORE'.

  • del_5q11.2 cnv correlated to 'PATHOLOGY.N.STAGE',  'NUMBER.OF.LYMPH.NODES',  'GLEASON_SCORE_COMBINED',  'GLEASON_SCORE_PRIMARY', and 'GLEASON_SCORE'.

  • del_5q13.2 cnv correlated to 'GLEASON_SCORE_COMBINED',  'GLEASON_SCORE_PRIMARY', and 'GLEASON_SCORE'.

  • del_6q14.3 cnv correlated to 'GLEASON_SCORE_COMBINED' and 'PSA_RESULT_PREOP'.

  • del_12p13.1 cnv correlated to 'GLEASON_SCORE_PRIMARY'.

  • 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 'GLEASON_SCORE_COMBINED' and 'GLEASON_SCORE_PRIMARY'.

Results
Overview of the results

Table 1.  Get Full Table Overview of the association between significant copy number variation of 62 focal events and 13 clinical features. Shown in the table are P values (Q values). Thresholded by Q value < 0.25, 31 significant findings detected.

Clinical
Features
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 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
del 5q11 2 38 (14%) 233 0.324
(1.00)
0.00095
(0.719)
2.39e-05
(0.0189)
1
(1.00)
0.649
(1.00)
7.88e-07
(0.000631)
9.74e-07
(0.000777)
3.59e-05
(0.0283)
0.022
(1.00)
7.36e-06
(0.00584)
0.000363
(0.28)
0.355
(1.00)
0.438
(1.00)
amp 9q34 11 25 (9%) 246 0.286
(1.00)
0.00747
(1.00)
0.000887
(0.673)
0.386
(1.00)
0.775
(1.00)
8.76e-05
(0.0686)
4.55e-07
(0.000365)
3.4e-06
(0.0027)
0.0651
(1.00)
1.02e-06
(0.000816)
0.104
(1.00)
0.147
(1.00)
0.555
(1.00)
amp 1q21 3 21 (8%) 250 0.327
(1.00)
0.0107
(1.00)
0.436
(1.00)
0.0497
(1.00)
1
(1.00)
0.401
(1.00)
2.69e-05
(0.0212)
0.000213
(0.166)
0.0514
(1.00)
1.31e-05
(0.0103)
0.146
(1.00)
0.182
(1.00)
1
(1.00)
amp 8q24 21 64 (24%) 207 0.234
(1.00)
0.00506
(1.00)
0.09
(1.00)
1
(1.00)
0.716
(1.00)
0.0859
(1.00)
8.78e-07
(0.000702)
2.88e-06
(0.00229)
0.0528
(1.00)
1.56e-05
(0.0123)
0.13
(1.00)
0.0512
(1.00)
0.813
(1.00)
del 5q13 2 37 (14%) 234 0.859
(1.00)
0.00151
(1.00)
0.00572
(1.00)
1
(1.00)
0.823
(1.00)
0.0024
(1.00)
5.79e-07
(0.000464)
6.31e-05
(0.0494)
0.0106
(1.00)
5.78e-05
(0.0454)
0.0128
(1.00)
0.218
(1.00)
0.293
(1.00)
del 15q21 3 30 (11%) 241 0.983
(1.00)
0.0582
(1.00)
0.00857
(1.00)
0.446
(1.00)
0.491
(1.00)
0.00272
(1.00)
8.7e-08
(7e-05)
2.66e-06
(0.00211)
0.0114
(1.00)
4.01e-07
(0.000322)
0.841
(1.00)
0.279
(1.00)
1
(1.00)
del 16q22 3 93 (34%) 178 0.118
(1.00)
0.0301
(1.00)
0.075
(1.00)
1
(1.00)
0.947
(1.00)
0.0602
(1.00)
0.000184
(0.144)
6.02e-05
(0.0473)
0.317
(1.00)
0.000286
(0.222)
0.139
(1.00)
0.0637
(1.00)
0.719
(1.00)
del 6q14 3 85 (31%) 186 0.0209
(1.00)
0.322
(1.00)
0.0119
(1.00)
0.65
(1.00)
0.0703
(1.00)
0.00773
(1.00)
0.000207
(0.162)
0.000921
(0.698)
0.161
(1.00)
0.000964
(0.729)
0.000213
(0.166)
0.234
(1.00)
0.579
(1.00)
del 16q24 1 105 (39%) 166 0.463
(1.00)
0.00798
(1.00)
0.125
(1.00)
1
(1.00)
0.965
(1.00)
0.0906
(1.00)
0.000215
(0.167)
4.06e-05
(0.0319)
0.419
(1.00)
0.000547
(0.419)
0.0757
(1.00)
0.0982
(1.00)
1
(1.00)
amp 3q21 3 32 (12%) 239 0.0192
(1.00)
0.00797
(1.00)
0.538
(1.00)
1
(1.00)
0.0259
(1.00)
0.603
(1.00)
0.00545
(1.00)
0.00284
(1.00)
0.599
(1.00)
0.000301
(0.233)
0.0138
(1.00)
0.388
(1.00)
0.659
(1.00)
amp 14q21 1 14 (5%) 257 0.0154
(1.00)
0.554
(1.00)
1
(1.00)
0.235
(1.00)
1
(1.00)
0.827
(1.00)
0.00371
(1.00)
0.0806
(1.00)
0.121
(1.00)
0.000257
(0.199)
0.336
(1.00)
0.588
(1.00)
1
(1.00)
del 12p13 1 55 (20%) 216 0.922
(1.00)
0.0123
(1.00)
0.12
(1.00)
0.268
(1.00)
0.614
(1.00)
0.0908
(1.00)
0.00799
(1.00)
0.000203
(0.159)
0.936
(1.00)
0.00214
(1.00)
0.0304
(1.00)
0.219
(1.00)
1
(1.00)
amp 3q26 2 40 (15%) 231 0.089
(1.00)
0.021
(1.00)
0.561
(1.00)
0.553
(1.00)
0.277
(1.00)
0.507
(1.00)
0.0113
(1.00)
0.00323
(1.00)
0.677
(1.00)
0.00166
(1.00)
0.0225
(1.00)
0.326
(1.00)
1
(1.00)
amp 4q13 3 5 (2%) 266 0.172
(1.00)
0.146
(1.00)
0.434
(1.00)
1
(1.00)
0.434
(1.00)
0.544
(1.00)
0.0402
(1.00)
0.0695
(1.00)
0.188
(1.00)
0.0558
(1.00)
0.117
(1.00)
0.45
(1.00)
1
(1.00)
amp 5q33 3 8 (3%) 263 0.0526
(1.00)
0.0304
(1.00)
0.205
(1.00)
0.14
(1.00)
1
(1.00)
0.166
(1.00)
0.0751
(1.00)
0.0277
(1.00)
0.831
(1.00)
0.0035
(1.00)
0.952
(1.00)
0.627
(1.00)
0.215
(1.00)
amp 7p14 3 47 (17%) 224 0.255
(1.00)
0.166
(1.00)
0.578
(1.00)
0.591
(1.00)
0.0747
(1.00)
0.631
(1.00)
0.0754
(1.00)
0.155
(1.00)
0.156
(1.00)
0.0941
(1.00)
0.104
(1.00)
0.802
(1.00)
1
(1.00)
amp 8p11 23 26 (10%) 245 0.087
(1.00)
0.298
(1.00)
0.72
(1.00)
1
(1.00)
0.919
(1.00)
0.706
(1.00)
0.00315
(1.00)
0.00273
(1.00)
0.241
(1.00)
0.00752
(1.00)
0.271
(1.00)
0.526
(1.00)
1
(1.00)
amp 11q13 2 14 (5%) 257 0.0874
(1.00)
0.0023
(1.00)
0.0371
(1.00)
0.235
(1.00)
1
(1.00)
0.0127
(1.00)
0.00359
(1.00)
0.000371
(0.286)
0.91
(1.00)
0.00204
(1.00)
0.174
(1.00)
0.541
(1.00)
0.349
(1.00)
amp 12q23 1 10 (4%) 261 0.975
(1.00)
0.217
(1.00)
0.00884
(1.00)
1
(1.00)
0.789
(1.00)
0.00111
(0.835)
0.00171
(1.00)
0.0095
(1.00)
0.379
(1.00)
0.000659
(0.503)
0.00267
(1.00)
0.578
(1.00)
1
(1.00)
amp 13q12 11 12 (4%) 259 0.00313
(1.00)
0.148
(1.00)
0.289
(1.00)
0.204
(1.00)
0.809
(1.00)
0.312
(1.00)
0.0707
(1.00)
0.00746
(1.00)
0.697
(1.00)
0.243
(1.00)
0.445
(1.00)
0.383
(1.00)
0.304
(1.00)
amp 15q11 2 5 (2%) 266 0.363
(1.00)
0.707
(1.00)
1
(1.00)
1
(1.00)
0.657
(1.00)
0.49
(1.00)
0.992
(1.00)
0.159
(1.00)
0.139
(1.00)
0.404
(1.00)
0.889
(1.00)
0.772
(1.00)
amp 16q11 2 13 (5%) 258 0.0438
(1.00)
0.0204
(1.00)
1
(1.00)
1
(1.00)
0.375
(1.00)
0.827
(1.00)
0.00449
(1.00)
0.00995
(1.00)
0.267
(1.00)
0.00565
(1.00)
0.101
(1.00)
0.106
(1.00)
1
(1.00)
amp 17q23 2 9 (3%) 262 0.3
(1.00)
0.306
(1.00)
1
(1.00)
0.156
(1.00)
0.367
(1.00)
0.937
(1.00)
0.395
(1.00)
0.627
(1.00)
0.641
(1.00)
0.119
(1.00)
0.326
(1.00)
0.463
(1.00)
1
(1.00)
amp 18q21 31 6 (2%) 265 0.0476
(1.00)
0.0515
(1.00)
1
(1.00)
0.107
(1.00)
0.303
(1.00)
0.394
(1.00)
0.00141
(1.00)
0.197
(1.00)
0.00815
(1.00)
0.00263
(1.00)
0.21
(1.00)
0.518
(1.00)
1
(1.00)
amp 19q13 43 5 (2%) 266 0.186
(1.00)
0.0134
(1.00)
1
(1.00)
0.0895
(1.00)
1
(1.00)
0.438
(1.00)
0.0532
(1.00)
0.159
(1.00)
0.188
(1.00)
0.00614
(1.00)
0.214
(1.00)
0.423
(1.00)
1
(1.00)
amp 20q13 2 14 (5%) 257 0.0553
(1.00)
0.00043
(0.33)
0.373
(1.00)
1
(1.00)
0.2
(1.00)
0.183
(1.00)
0.00979
(1.00)
0.00218
(1.00)
0.627
(1.00)
0.0118
(1.00)
0.208
(1.00)
0.268
(1.00)
1
(1.00)
amp xp22 2 8 (3%) 263 0.653
(1.00)
0.126
(1.00)
0.601
(1.00)
0.14
(1.00)
0.736
(1.00)
0.836
(1.00)
0.108
(1.00)
0.0116
(1.00)
0.371
(1.00)
0.16
(1.00)
0.041
(1.00)
0.5
(1.00)
0.166
(1.00)
amp xp22 11 9 (3%) 262 0.852
(1.00)
0.306
(1.00)
1
(1.00)
0.00934
(1.00)
1
(1.00)
0.937
(1.00)
0.159
(1.00)
0.151
(1.00)
0.994
(1.00)
0.229
(1.00)
0.799
(1.00)
0.944
(1.00)
0.262
(1.00)
amp xp22 11 9 (3%) 262 0.389
(1.00)
0.306
(1.00)
1
(1.00)
0.00934
(1.00)
0.762
(1.00)
0.937
(1.00)
0.159
(1.00)
0.0374
(1.00)
0.562
(1.00)
0.487
(1.00)
0.114
(1.00)
0.538
(1.00)
0.216
(1.00)
amp xp21 1 8 (3%) 263 0.183
(1.00)
0.126
(1.00)
0.601
(1.00)
0.00732
(1.00)
0.765
(1.00)
0.913
(1.00)
0.31
(1.00)
0.246
(1.00)
0.899
(1.00)
0.16
(1.00)
0.293
(1.00)
0.196
(1.00)
0.00776
(1.00)
amp xq21 1 7 (3%) 264 0.824
(1.00)
0.518
(1.00)
0.551
(1.00)
1
(1.00)
0.5
(1.00)
0.723
(1.00)
0.564
(1.00)
0.612
(1.00)
0.82
(1.00)
0.531
(1.00)
0.274
(1.00)
0.386
(1.00)
0.344
(1.00)
amp xq21 1 5 (2%) 266 0.435
(1.00)
0.428
(1.00)
0.0894
(1.00)
1
(1.00)
0.657
(1.00)
0.0299
(1.00)
0.331
(1.00)
0.583
(1.00)
0.482
(1.00)
0.404
(1.00)
0.093
(1.00)
0.172
(1.00)
0.0274
(1.00)
amp xq21 31 5 (2%) 266 0.265
(1.00)
1
(1.00)
1
(1.00)
1
(1.00)
0.659
(1.00)
0.438
(1.00)
0.234
(1.00)
0.0235
(1.00)
0.799
(1.00)
0.692
(1.00)
0.661
(1.00)
0.135
(1.00)
0.263
(1.00)
amp xq25 4 (1%) 267 0.1
(1.00)
0.651
(1.00)
1
(1.00)
1
(1.00)
0.633
(1.00)
0.49
(1.00)
0.676
(1.00)
0.287
(1.00)
0.776
(1.00)
0.751
(1.00)
0.995
(1.00)
0.216
(1.00)
amp xq25 6 (2%) 265 0.773
(1.00)
0.719
(1.00)
0.496
(1.00)
1
(1.00)
0.469
(1.00)
0.681
(1.00)
0.339
(1.00)
0.895
(1.00)
0.172
(1.00)
0.541
(1.00)
0.791
(1.00)
0.394
(1.00)
0.0188
(1.00)
amp xq27 1 9 (3%) 262 0.0965
(1.00)
1
(1.00)
1
(1.00)
1
(1.00)
0.766
(1.00)
0.322
(1.00)
0.794
(1.00)
0.627
(1.00)
0.476
(1.00)
0.686
(1.00)
0.627
(1.00)
0.357
(1.00)
0.424
(1.00)
del 1p31 3 33 (12%) 238 0.423
(1.00)
0.153
(1.00)
1
(1.00)
1
(1.00)
0.132
(1.00)
0.938
(1.00)
0.00719
(1.00)
0.0855
(1.00)
0.0323
(1.00)
0.0179
(1.00)
0.561
(1.00)
0.0627
(1.00)
0.199
(1.00)
del 1p22 1 21 (8%) 250 0.742
(1.00)
0.579
(1.00)
0.436
(1.00)
1
(1.00)
0.775
(1.00)
0.413
(1.00)
0.443
(1.00)
0.364
(1.00)
0.749
(1.00)
0.603
(1.00)
0.132
(1.00)
0.343
(1.00)
1
(1.00)
del 1q42 2 22 (8%) 249 0.0267
(1.00)
0.415
(1.00)
0.267
(1.00)
1
(1.00)
0.279
(1.00)
0.253
(1.00)
0.192
(1.00)
0.189
(1.00)
0.853
(1.00)
0.0506
(1.00)
0.045
(1.00)
0.288
(1.00)
0.556
(1.00)
del 2p22 1 17 (6%) 254 0.345
(1.00)
0.201
(1.00)
0.00438
(1.00)
1
(1.00)
0.339
(1.00)
0.000819
(0.622)
0.00664
(1.00)
0.0994
(1.00)
0.0168
(1.00)
0.0136
(1.00)
0.926
(1.00)
0.375
(1.00)
1
(1.00)
del 2q22 1 37 (14%) 234 0.000556
(0.424)
0.807
(1.00)
1
(1.00)
1
(1.00)
0.356
(1.00)
0.701
(1.00)
0.34
(1.00)
0.0115
(1.00)
0.155
(1.00)
0.325
(1.00)
0.583
(1.00)
0.858
(1.00)
0.416
(1.00)
del 2q22 3 34 (13%) 237 0.00413
(1.00)
0.624
(1.00)
1
(1.00)
1
(1.00)
0.494
(1.00)
0.885
(1.00)
0.669
(1.00)
0.614
(1.00)
0.328
(1.00)
0.876
(1.00)
0.723
(1.00)
0.979
(1.00)
1
(1.00)
del 3p13 43 (16%) 228 0.022
(1.00)
0.735
(1.00)
0.774
(1.00)
0.18
(1.00)
0.146
(1.00)
0.644
(1.00)
0.285
(1.00)
0.573
(1.00)
0.512
(1.00)
0.2
(1.00)
0.389
(1.00)
0.779
(1.00)
1
(1.00)
del 3q29 16 (6%) 255 0.177
(1.00)
0.851
(1.00)
0.389
(1.00)
0.264
(1.00)
0.107
(1.00)
0.27
(1.00)
0.477
(1.00)
0.857
(1.00)
0.337
(1.00)
0.615
(1.00)
0.239
(1.00)
0.897
(1.00)
1
(1.00)
del 4q28 1 24 (9%) 247 0.0284
(1.00)
0.0985
(1.00)
0.476
(1.00)
0.373
(1.00)
0.22
(1.00)
0.651
(1.00)
0.0837
(1.00)
0.0595
(1.00)
0.581
(1.00)
0.0583
(1.00)
0.95
(1.00)
0.292
(1.00)
0.299
(1.00)
del 5q21 1 45 (17%) 226 0.113
(1.00)
0.567
(1.00)
0.162
(1.00)
1
(1.00)
1
(1.00)
0.148
(1.00)
0.0697
(1.00)
0.00264
(1.00)
0.52
(1.00)
0.0776
(1.00)
0.207
(1.00)
0.0264
(1.00)
0.733
(1.00)
del 7q31 33 13 (5%) 258 0.437
(1.00)
1
(1.00)
0.332
(1.00)
1
(1.00)
0.551
(1.00)
0.345
(1.00)
0.629
(1.00)
0.205
(1.00)
0.516
(1.00)
0.773
(1.00)
0.968
(1.00)
0.848
(1.00)
1
(1.00)
del 8p21 3 146 (54%) 125 0.401
(1.00)
0.00038
(0.293)
0.0799
(1.00)
1
(1.00)
0.869
(1.00)
0.0568
(1.00)
0.138
(1.00)
0.00259
(1.00)
0.278
(1.00)
0.359
(1.00)
0.00176
(1.00)
0.139
(1.00)
0.728
(1.00)
del 8p11 21 82 (30%) 189 0.433
(1.00)
0.199
(1.00)
1
(1.00)
0.64
(1.00)
0.00597
(1.00)
0.876
(1.00)
0.753
(1.00)
0.233
(1.00)
0.359
(1.00)
0.773
(1.00)
0.0882
(1.00)
0.17
(1.00)
0.191
(1.00)
del 9p23 24 (9%) 247 0.695
(1.00)
0.271
(1.00)
0.0799
(1.00)
1
(1.00)
0.758
(1.00)
0.0745
(1.00)
0.0112
(1.00)
0.022
(1.00)
0.258
(1.00)
0.0428
(1.00)
0.691
(1.00)
0.484
(1.00)
1
(1.00)
del 10q23 31 84 (31%) 187 0.809
(1.00)
0.00707
(1.00)
0.0119
(1.00)
1
(1.00)
0.333
(1.00)
0.012
(1.00)
0.00882
(1.00)
0.0519
(1.00)
0.0871
(1.00)
0.00313
(1.00)
0.615
(1.00)
0.00244
(1.00)
0.236
(1.00)
del 11p11 2 12 (4%) 259 0.714
(1.00)
0.509
(1.00)
0.0994
(1.00)
1
(1.00)
0.117
(1.00)
0.0576
(1.00)
0.448
(1.00)
0.308
(1.00)
0.903
(1.00)
0.302
(1.00)
0.539
(1.00)
0.649
(1.00)
0.0403
(1.00)
del 11q23 2 27 (10%) 244 0.194
(1.00)
0.00164
(1.00)
0.728
(1.00)
0.411
(1.00)
0.398
(1.00)
0.748
(1.00)
0.0331
(1.00)
0.0701
(1.00)
0.218
(1.00)
0.0225
(1.00)
0.224
(1.00)
0.0858
(1.00)
1
(1.00)
del 12q24 31 20 (7%) 251 0.928
(1.00)
0.213
(1.00)
0.436
(1.00)
0.32
(1.00)
1
(1.00)
0.522
(1.00)
0.0341
(1.00)
0.12
(1.00)
0.295
(1.00)
0.0365
(1.00)
0.699
(1.00)
0.367
(1.00)
1
(1.00)
del 13q14 13 116 (43%) 155 0.0514
(1.00)
0.357
(1.00)
0.195
(1.00)
0.0732
(1.00)
0.0269
(1.00)
0.173
(1.00)
0.0256
(1.00)
0.0431
(1.00)
0.345
(1.00)
0.0192
(1.00)
0.43
(1.00)
0.333
(1.00)
0.00389
(1.00)
del 13q22 1 89 (33%) 182 0.0324
(1.00)
0.0689
(1.00)
0.117
(1.00)
0.176
(1.00)
0.273
(1.00)
0.114
(1.00)
0.00393
(1.00)
0.0391
(1.00)
0.0779
(1.00)
0.000387
(0.298)
0.149
(1.00)
0.911
(1.00)
0.00034
(0.263)
del 17p13 1 69 (25%) 202 0.507
(1.00)
0.00644
(1.00)
0.0145
(1.00)
1
(1.00)
0.884
(1.00)
0.0105
(1.00)
0.000411
(0.316)
0.000656
(0.5)
0.177
(1.00)
0.000441
(0.338)
0.593
(1.00)
0.326
(1.00)
0.822
(1.00)
del 17q21 31 53 (20%) 218 0.802
(1.00)
0.811
(1.00)
1
(1.00)
0.587
(1.00)
0.385
(1.00)
0.703
(1.00)
0.867
(1.00)
0.584
(1.00)
0.935
(1.00)
0.888
(1.00)
0.652
(1.00)
0.64
(1.00)
0.763
(1.00)
del 18q22 1 68 (25%) 203 0.743
(1.00)
0.267
(1.00)
0.458
(1.00)
0.602
(1.00)
0.283
(1.00)
0.331
(1.00)
0.0106
(1.00)
0.0377
(1.00)
0.222
(1.00)
0.0121
(1.00)
0.566
(1.00)
0.918
(1.00)
0.136
(1.00)
del 19q13 2 24 (9%) 247 0.094
(1.00)
0.178
(1.00)
0.15
(1.00)
1
(1.00)
0.121
(1.00)
0.106
(1.00)
0.00607
(1.00)
0.00105
(0.793)
0.581
(1.00)
0.00517
(1.00)
0.501
(1.00)
0.328
(1.00)
1
(1.00)
del 21q22 2 26 (10%) 245 0.25
(1.00)
0.129
(1.00)
0.011
(1.00)
0.398
(1.00)
0.73
(1.00)
0.00315
(1.00)
0.8
(1.00)
0.947
(1.00)
0.679
(1.00)
0.965
(1.00)
0.854
(1.00)
0.33
(1.00)
0.0765
(1.00)
del 21q22 3 77 (28%) 194 0.759
(1.00)
0.0281
(1.00)
0.00154
(1.00)
0.625
(1.00)
0.197
(1.00)
0.000773
(0.588)
0.169
(1.00)
0.3
(1.00)
0.346
(1.00)
0.275
(1.00)
0.306
(1.00)
0.16
(1.00)
0.0792
(1.00)
'amp_1q21.3' versus 'GLEASON_SCORE_COMBINED'

P value = 2.69e-05 (Wilcoxon-test), Q value = 0.021

Table S1.  Gene #1: 'amp_1q21.3' versus Clinical Feature #7: 'GLEASON_SCORE_COMBINED'

nPatients Mean (Std.Dev)
ALL 271 7.3 (0.8)
AMP PEAK 1(1Q21.3) MUTATED 21 8.0 (0.9)
AMP PEAK 1(1Q21.3) WILD-TYPE 250 7.2 (0.8)

Figure S1.  Get High-res Image Gene #1: 'amp_1q21.3' versus Clinical Feature #7: 'GLEASON_SCORE_COMBINED'

'amp_1q21.3' versus 'GLEASON_SCORE_PRIMARY'

P value = 0.000213 (Wilcoxon-test), Q value = 0.17

Table S2.  Gene #1: 'amp_1q21.3' versus Clinical Feature #8: 'GLEASON_SCORE_PRIMARY'

nPatients Mean (Std.Dev)
ALL 271 3.5 (0.6)
AMP PEAK 1(1Q21.3) MUTATED 21 3.9 (0.4)
AMP PEAK 1(1Q21.3) WILD-TYPE 250 3.5 (0.6)

Figure S2.  Get High-res Image Gene #1: 'amp_1q21.3' versus Clinical Feature #8: 'GLEASON_SCORE_PRIMARY'

'amp_1q21.3' versus 'GLEASON_SCORE'

P value = 1.31e-05 (Wilcoxon-test), Q value = 0.01

Table S3.  Gene #1: 'amp_1q21.3' versus Clinical Feature #10: 'GLEASON_SCORE'

nPatients Mean (Std.Dev)
ALL 271 7.3 (0.8)
AMP PEAK 1(1Q21.3) MUTATED 21 8.1 (0.9)
AMP PEAK 1(1Q21.3) WILD-TYPE 250 7.3 (0.8)

Figure S3.  Get High-res Image Gene #1: 'amp_1q21.3' versus Clinical Feature #10: 'GLEASON_SCORE'

'amp_3q21.3' versus 'GLEASON_SCORE'

P value = 0.000301 (Wilcoxon-test), Q value = 0.23

Table S4.  Gene #2: 'amp_3q21.3' versus Clinical Feature #10: 'GLEASON_SCORE'

nPatients Mean (Std.Dev)
ALL 271 7.3 (0.8)
AMP PEAK 2(3Q21.3) MUTATED 32 7.8 (1.0)
AMP PEAK 2(3Q21.3) WILD-TYPE 239 7.3 (0.8)

Figure S4.  Get High-res Image Gene #2: 'amp_3q21.3' versus Clinical Feature #10: 'GLEASON_SCORE'

'amp_8q24.21' versus 'GLEASON_SCORE_COMBINED'

P value = 8.78e-07 (Wilcoxon-test), Q value = 7e-04

Table S5.  Gene #8: 'amp_8q24.21' versus Clinical Feature #7: 'GLEASON_SCORE_COMBINED'

nPatients Mean (Std.Dev)
ALL 271 7.3 (0.8)
AMP PEAK 8(8Q24.21) MUTATED 64 7.7 (0.9)
AMP PEAK 8(8Q24.21) WILD-TYPE 207 7.1 (0.7)

Figure S5.  Get High-res Image Gene #8: 'amp_8q24.21' versus Clinical Feature #7: 'GLEASON_SCORE_COMBINED'

'amp_8q24.21' versus 'GLEASON_SCORE_PRIMARY'

P value = 2.88e-06 (Wilcoxon-test), Q value = 0.0023

Table S6.  Gene #8: 'amp_8q24.21' versus Clinical Feature #8: 'GLEASON_SCORE_PRIMARY'

nPatients Mean (Std.Dev)
ALL 271 3.5 (0.6)
AMP PEAK 8(8Q24.21) MUTATED 64 3.8 (0.6)
AMP PEAK 8(8Q24.21) WILD-TYPE 207 3.4 (0.5)

Figure S6.  Get High-res Image Gene #8: 'amp_8q24.21' versus Clinical Feature #8: 'GLEASON_SCORE_PRIMARY'

'amp_8q24.21' versus 'GLEASON_SCORE'

P value = 1.56e-05 (Wilcoxon-test), Q value = 0.012

Table S7.  Gene #8: 'amp_8q24.21' versus Clinical Feature #10: 'GLEASON_SCORE'

nPatients Mean (Std.Dev)
ALL 271 7.3 (0.8)
AMP PEAK 8(8Q24.21) MUTATED 64 7.8 (1.0)
AMP PEAK 8(8Q24.21) WILD-TYPE 207 7.2 (0.7)

Figure S7.  Get High-res Image Gene #8: 'amp_8q24.21' versus Clinical Feature #10: 'GLEASON_SCORE'

'amp_9q34.11' versus 'NUMBER.OF.LYMPH.NODES'

P value = 8.76e-05 (Wilcoxon-test), Q value = 0.069

Table S8.  Gene #9: 'amp_9q34.11' versus Clinical Feature #6: 'NUMBER.OF.LYMPH.NODES'

nPatients Mean (Std.Dev)
ALL 223 0.2 (1.2)
AMP PEAK 9(9Q34.11) MUTATED 23 1.1 (3.1)
AMP PEAK 9(9Q34.11) WILD-TYPE 200 0.1 (0.6)

Figure S8.  Get High-res Image Gene #9: 'amp_9q34.11' versus Clinical Feature #6: 'NUMBER.OF.LYMPH.NODES'

'amp_9q34.11' versus 'GLEASON_SCORE_COMBINED'

P value = 4.55e-07 (Wilcoxon-test), Q value = 0.00037

Table S9.  Gene #9: 'amp_9q34.11' versus Clinical Feature #7: 'GLEASON_SCORE_COMBINED'

nPatients Mean (Std.Dev)
ALL 271 7.3 (0.8)
AMP PEAK 9(9Q34.11) MUTATED 25 8.0 (0.9)
AMP PEAK 9(9Q34.11) WILD-TYPE 246 7.2 (0.8)

Figure S9.  Get High-res Image Gene #9: 'amp_9q34.11' versus Clinical Feature #7: 'GLEASON_SCORE_COMBINED'

'amp_9q34.11' versus 'GLEASON_SCORE_PRIMARY'

P value = 3.4e-06 (Wilcoxon-test), Q value = 0.0027

Table S10.  Gene #9: 'amp_9q34.11' versus Clinical Feature #8: 'GLEASON_SCORE_PRIMARY'

nPatients Mean (Std.Dev)
ALL 271 3.5 (0.6)
AMP PEAK 9(9Q34.11) MUTATED 25 4.0 (0.5)
AMP PEAK 9(9Q34.11) WILD-TYPE 246 3.4 (0.6)

Figure S10.  Get High-res Image Gene #9: 'amp_9q34.11' versus Clinical Feature #8: 'GLEASON_SCORE_PRIMARY'

'amp_9q34.11' versus 'GLEASON_SCORE'

P value = 1.02e-06 (Wilcoxon-test), Q value = 0.00082

Table S11.  Gene #9: 'amp_9q34.11' versus Clinical Feature #10: 'GLEASON_SCORE'

nPatients Mean (Std.Dev)
ALL 271 7.3 (0.8)
AMP PEAK 9(9Q34.11) MUTATED 25 8.0 (0.8)
AMP PEAK 9(9Q34.11) WILD-TYPE 246 7.3 (0.8)

Figure S11.  Get High-res Image Gene #9: 'amp_9q34.11' versus Clinical Feature #10: 'GLEASON_SCORE'

'amp_14q21.1' versus 'GLEASON_SCORE'

P value = 0.000257 (Wilcoxon-test), Q value = 0.2

Table S12.  Gene #13: 'amp_14q21.1' versus Clinical Feature #10: 'GLEASON_SCORE'

nPatients Mean (Std.Dev)
ALL 271 7.3 (0.8)
AMP PEAK 13(14Q21.1) MUTATED 14 8.1 (0.8)
AMP PEAK 13(14Q21.1) WILD-TYPE 257 7.3 (0.8)

Figure S12.  Get High-res Image Gene #13: 'amp_14q21.1' versus Clinical Feature #10: 'GLEASON_SCORE'

'del_5q11.2' versus 'PATHOLOGY.N.STAGE'

P value = 2.39e-05 (Fisher's exact test), Q value = 0.019

Table S13.  Gene #39: 'del_5q11.2' versus Clinical Feature #3: 'PATHOLOGY.N.STAGE'

nPatients 0 1
ALL 201 24
DEL PEAK 10(5Q11.2) MUTATED 23 12
DEL PEAK 10(5Q11.2) WILD-TYPE 178 12

Figure S13.  Get High-res Image Gene #39: 'del_5q11.2' versus Clinical Feature #3: 'PATHOLOGY.N.STAGE'

'del_5q11.2' versus 'NUMBER.OF.LYMPH.NODES'

P value = 7.88e-07 (Wilcoxon-test), Q value = 0.00063

Table S14.  Gene #39: 'del_5q11.2' versus Clinical Feature #6: 'NUMBER.OF.LYMPH.NODES'

nPatients Mean (Std.Dev)
ALL 223 0.2 (1.2)
DEL PEAK 10(5Q11.2) MUTATED 35 0.9 (2.6)
DEL PEAK 10(5Q11.2) WILD-TYPE 188 0.1 (0.6)

Figure S14.  Get High-res Image Gene #39: 'del_5q11.2' versus Clinical Feature #6: 'NUMBER.OF.LYMPH.NODES'

'del_5q11.2' versus 'GLEASON_SCORE_COMBINED'

P value = 9.74e-07 (Wilcoxon-test), Q value = 0.00078

Table S15.  Gene #39: 'del_5q11.2' versus Clinical Feature #7: 'GLEASON_SCORE_COMBINED'

nPatients Mean (Std.Dev)
ALL 271 7.3 (0.8)
DEL PEAK 10(5Q11.2) MUTATED 38 7.9 (1.0)
DEL PEAK 10(5Q11.2) WILD-TYPE 233 7.2 (0.7)

Figure S15.  Get High-res Image Gene #39: 'del_5q11.2' versus Clinical Feature #7: 'GLEASON_SCORE_COMBINED'

'del_5q11.2' versus 'GLEASON_SCORE_PRIMARY'

P value = 3.59e-05 (Wilcoxon-test), Q value = 0.028

Table S16.  Gene #39: 'del_5q11.2' versus Clinical Feature #8: 'GLEASON_SCORE_PRIMARY'

nPatients Mean (Std.Dev)
ALL 271 3.5 (0.6)
DEL PEAK 10(5Q11.2) MUTATED 38 3.8 (0.6)
DEL PEAK 10(5Q11.2) WILD-TYPE 233 3.4 (0.5)

Figure S16.  Get High-res Image Gene #39: 'del_5q11.2' versus Clinical Feature #8: 'GLEASON_SCORE_PRIMARY'

'del_5q11.2' versus 'GLEASON_SCORE'

P value = 7.36e-06 (Wilcoxon-test), Q value = 0.0058

Table S17.  Gene #39: 'del_5q11.2' versus Clinical Feature #10: 'GLEASON_SCORE'

nPatients Mean (Std.Dev)
ALL 271 7.3 (0.8)
DEL PEAK 10(5Q11.2) MUTATED 38 7.9 (1.0)
DEL PEAK 10(5Q11.2) WILD-TYPE 233 7.2 (0.8)

Figure S17.  Get High-res Image Gene #39: 'del_5q11.2' versus Clinical Feature #10: 'GLEASON_SCORE'

'del_5q13.2' versus 'GLEASON_SCORE_COMBINED'

P value = 5.79e-07 (Wilcoxon-test), Q value = 0.00046

Table S18.  Gene #40: 'del_5q13.2' versus Clinical Feature #7: 'GLEASON_SCORE_COMBINED'

nPatients Mean (Std.Dev)
ALL 271 7.3 (0.8)
DEL PEAK 11(5Q13.2) MUTATED 37 7.9 (0.9)
DEL PEAK 11(5Q13.2) WILD-TYPE 234 7.2 (0.7)

Figure S18.  Get High-res Image Gene #40: 'del_5q13.2' versus Clinical Feature #7: 'GLEASON_SCORE_COMBINED'

'del_5q13.2' versus 'GLEASON_SCORE_PRIMARY'

P value = 6.31e-05 (Wilcoxon-test), Q value = 0.049

Table S19.  Gene #40: 'del_5q13.2' versus Clinical Feature #8: 'GLEASON_SCORE_PRIMARY'

nPatients Mean (Std.Dev)
ALL 271 3.5 (0.6)
DEL PEAK 11(5Q13.2) MUTATED 37 3.8 (0.6)
DEL PEAK 11(5Q13.2) WILD-TYPE 234 3.4 (0.5)

Figure S19.  Get High-res Image Gene #40: 'del_5q13.2' versus Clinical Feature #8: 'GLEASON_SCORE_PRIMARY'

'del_5q13.2' versus 'GLEASON_SCORE'

P value = 5.78e-05 (Wilcoxon-test), Q value = 0.045

Table S20.  Gene #40: 'del_5q13.2' versus Clinical Feature #10: 'GLEASON_SCORE'

nPatients Mean (Std.Dev)
ALL 271 7.3 (0.8)
DEL PEAK 11(5Q13.2) MUTATED 37 7.8 (1.0)
DEL PEAK 11(5Q13.2) WILD-TYPE 234 7.2 (0.8)

Figure S20.  Get High-res Image Gene #40: 'del_5q13.2' versus Clinical Feature #10: 'GLEASON_SCORE'

'del_6q14.3' versus 'GLEASON_SCORE_COMBINED'

P value = 0.000207 (Wilcoxon-test), Q value = 0.16

Table S21.  Gene #42: 'del_6q14.3' versus Clinical Feature #7: 'GLEASON_SCORE_COMBINED'

nPatients Mean (Std.Dev)
ALL 271 7.3 (0.8)
DEL PEAK 13(6Q14.3) MUTATED 85 7.5 (0.8)
DEL PEAK 13(6Q14.3) WILD-TYPE 186 7.2 (0.8)

Figure S21.  Get High-res Image Gene #42: 'del_6q14.3' versus Clinical Feature #7: 'GLEASON_SCORE_COMBINED'

'del_6q14.3' versus 'PSA_RESULT_PREOP'

P value = 0.000213 (Wilcoxon-test), Q value = 0.17

Table S22.  Gene #42: 'del_6q14.3' versus Clinical Feature #11: 'PSA_RESULT_PREOP'

nPatients Mean (Std.Dev)
ALL 269 10.4 (11.0)
DEL PEAK 13(6Q14.3) MUTATED 85 13.3 (12.3)
DEL PEAK 13(6Q14.3) WILD-TYPE 184 9.0 (10.1)

Figure S22.  Get High-res Image Gene #42: 'del_6q14.3' versus Clinical Feature #11: 'PSA_RESULT_PREOP'

'del_12p13.1' versus 'GLEASON_SCORE_PRIMARY'

P value = 0.000203 (Wilcoxon-test), Q value = 0.16

Table S23.  Gene #50: 'del_12p13.1' versus Clinical Feature #8: 'GLEASON_SCORE_PRIMARY'

nPatients Mean (Std.Dev)
ALL 271 3.5 (0.6)
DEL PEAK 21(12P13.1) MUTATED 55 3.7 (0.6)
DEL PEAK 21(12P13.1) WILD-TYPE 216 3.4 (0.5)

Figure S23.  Get High-res Image Gene #50: 'del_12p13.1' versus Clinical Feature #8: 'GLEASON_SCORE_PRIMARY'

'del_15q21.3' versus 'GLEASON_SCORE_COMBINED'

P value = 8.7e-08 (Wilcoxon-test), Q value = 7e-05

Table S24.  Gene #54: 'del_15q21.3' versus Clinical Feature #7: 'GLEASON_SCORE_COMBINED'

nPatients Mean (Std.Dev)
ALL 271 7.3 (0.8)
DEL PEAK 25(15Q21.3) MUTATED 30 8.1 (0.9)
DEL PEAK 25(15Q21.3) WILD-TYPE 241 7.2 (0.7)

Figure S24.  Get High-res Image Gene #54: 'del_15q21.3' versus Clinical Feature #7: 'GLEASON_SCORE_COMBINED'

'del_15q21.3' versus 'GLEASON_SCORE_PRIMARY'

P value = 2.66e-06 (Wilcoxon-test), Q value = 0.0021

Table S25.  Gene #54: 'del_15q21.3' versus Clinical Feature #8: 'GLEASON_SCORE_PRIMARY'

nPatients Mean (Std.Dev)
ALL 271 3.5 (0.6)
DEL PEAK 25(15Q21.3) MUTATED 30 4.0 (0.6)
DEL PEAK 25(15Q21.3) WILD-TYPE 241 3.4 (0.5)

Figure S25.  Get High-res Image Gene #54: 'del_15q21.3' versus Clinical Feature #8: 'GLEASON_SCORE_PRIMARY'

'del_15q21.3' versus 'GLEASON_SCORE'

P value = 4.01e-07 (Wilcoxon-test), Q value = 0.00032

Table S26.  Gene #54: 'del_15q21.3' versus Clinical Feature #10: 'GLEASON_SCORE'

nPatients Mean (Std.Dev)
ALL 271 7.3 (0.8)
DEL PEAK 25(15Q21.3) MUTATED 30 8.1 (1.0)
DEL PEAK 25(15Q21.3) WILD-TYPE 241 7.2 (0.8)

Figure S26.  Get High-res Image Gene #54: 'del_15q21.3' versus Clinical Feature #10: 'GLEASON_SCORE'

'del_16q22.3' versus 'GLEASON_SCORE_COMBINED'

P value = 0.000184 (Wilcoxon-test), Q value = 0.14

Table S27.  Gene #55: 'del_16q22.3' versus Clinical Feature #7: 'GLEASON_SCORE_COMBINED'

nPatients Mean (Std.Dev)
ALL 271 7.3 (0.8)
DEL PEAK 26(16Q22.3) MUTATED 93 7.5 (0.9)
DEL PEAK 26(16Q22.3) WILD-TYPE 178 7.2 (0.7)

Figure S27.  Get High-res Image Gene #55: 'del_16q22.3' versus Clinical Feature #7: 'GLEASON_SCORE_COMBINED'

'del_16q22.3' versus 'GLEASON_SCORE_PRIMARY'

P value = 6.02e-05 (Wilcoxon-test), Q value = 0.047

Table S28.  Gene #55: 'del_16q22.3' versus Clinical Feature #8: 'GLEASON_SCORE_PRIMARY'

nPatients Mean (Std.Dev)
ALL 271 3.5 (0.6)
DEL PEAK 26(16Q22.3) MUTATED 93 3.7 (0.6)
DEL PEAK 26(16Q22.3) WILD-TYPE 178 3.4 (0.5)

Figure S28.  Get High-res Image Gene #55: 'del_16q22.3' versus Clinical Feature #8: 'GLEASON_SCORE_PRIMARY'

'del_16q22.3' versus 'GLEASON_SCORE'

P value = 0.000286 (Wilcoxon-test), Q value = 0.22

Table S29.  Gene #55: 'del_16q22.3' versus Clinical Feature #10: 'GLEASON_SCORE'

nPatients Mean (Std.Dev)
ALL 271 7.3 (0.8)
DEL PEAK 26(16Q22.3) MUTATED 93 7.6 (0.9)
DEL PEAK 26(16Q22.3) WILD-TYPE 178 7.2 (0.7)

Figure S29.  Get High-res Image Gene #55: 'del_16q22.3' versus Clinical Feature #10: 'GLEASON_SCORE'

'del_16q24.1' versus 'GLEASON_SCORE_COMBINED'

P value = 0.000215 (Wilcoxon-test), Q value = 0.17

Table S30.  Gene #56: 'del_16q24.1' versus Clinical Feature #7: 'GLEASON_SCORE_COMBINED'

nPatients Mean (Std.Dev)
ALL 271 7.3 (0.8)
DEL PEAK 27(16Q24.1) MUTATED 105 7.5 (0.9)
DEL PEAK 27(16Q24.1) WILD-TYPE 166 7.1 (0.7)

Figure S30.  Get High-res Image Gene #56: 'del_16q24.1' versus Clinical Feature #7: 'GLEASON_SCORE_COMBINED'

'del_16q24.1' versus 'GLEASON_SCORE_PRIMARY'

P value = 4.06e-05 (Wilcoxon-test), Q value = 0.032

Table S31.  Gene #56: 'del_16q24.1' versus Clinical Feature #8: 'GLEASON_SCORE_PRIMARY'

nPatients Mean (Std.Dev)
ALL 271 3.5 (0.6)
DEL PEAK 27(16Q24.1) MUTATED 105 3.7 (0.6)
DEL PEAK 27(16Q24.1) WILD-TYPE 166 3.4 (0.5)

Figure S31.  Get High-res Image Gene #56: 'del_16q24.1' versus Clinical Feature #8: '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 = 271

  • Number of significantly focal cnvs = 62

  • Number of selected clinical features = 13

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

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] 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)
[2] 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)