Correlation between copy number variations of arm-level result and selected clinical features
Prostate Adenocarcinoma (Primary solid tumor)
17 October 2014  |  analyses__2014_10_17
Maintainer Information
Citation Information
doi:10.7908/C1KW5F0K
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 variations of arm-level result and selected clinical features. Broad Institute of MIT and Harvard. doi:10.7908/C1KW5F0K
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 75 arm-level events and 14 clinical features across 363 patients, 42 significant findings detected with Q value < 0.25.

  • 3p gain cnv correlated to 'GLEASON_SCORE'.

  • 3q gain cnv correlated to 'GLEASON_SCORE'.

  • 8p gain cnv correlated to 'GLEASON_SCORE_COMBINED' and 'GLEASON_SCORE'.

  • 8q gain cnv correlated to 'GLEASON_SCORE_PRIMARY'.

  • 9q gain cnv correlated to 'GLEASON_SCORE_PRIMARY' and 'GLEASON_SCORE'.

  • 4p loss cnv correlated to 'PATHOLOGY.N.STAGE',  'NUMBER.OF.LYMPH.NODES',  'GLEASON_SCORE_COMBINED',  'GLEASON_SCORE_PRIMARY', and 'GLEASON_SCORE'.

  • 4q loss cnv correlated to 'GLEASON_SCORE_COMBINED' and 'GLEASON_SCORE'.

  • 5p loss cnv correlated to 'GLEASON_SCORE_PRIMARY'.

  • 5q loss cnv correlated to 'GLEASON_SCORE_COMBINED',  'GLEASON_SCORE_PRIMARY', and 'GLEASON_SCORE'.

  • 6p loss cnv correlated to 'GLEASON_SCORE_PRIMARY' and 'GLEASON_SCORE'.

  • 6q loss cnv correlated to 'GLEASON_SCORE_COMBINED',  'GLEASON_SCORE_PRIMARY', and 'GLEASON_SCORE'.

  • 10p loss cnv correlated to 'GLEASON_SCORE_COMBINED' and 'GLEASON_SCORE'.

  • 10q loss cnv correlated to 'GLEASON_SCORE_COMBINED',  'GLEASON_SCORE_SECONDARY', and 'GLEASON_SCORE'.

  • 13q loss cnv correlated to 'GLEASON_SCORE_COMBINED' and 'GLEASON_SCORE'.

  • 15q loss cnv correlated to 'GLEASON_SCORE_PRIMARY'.

  • 16q loss cnv correlated to 'GLEASON_SCORE_PRIMARY'.

  • 17p loss cnv correlated to 'GLEASON_SCORE'.

  • 18p loss cnv correlated to 'GLEASON_SCORE'.

  • 18q loss cnv correlated to 'GLEASON_SCORE_COMBINED' and 'GLEASON_SCORE'.

  • 22q loss cnv correlated to 'GLEASON_SCORE_COMBINED',  'GLEASON_SCORE_PRIMARY', and 'GLEASON_SCORE'.

  • xq loss cnv correlated to 'GLEASON_SCORE_COMBINED',  'GLEASON_SCORE_PRIMARY', and 'GLEASON_SCORE'.

Results
Overview of the results

Table 1.  Get Full Table Overview of the association between significant copy number variation of 75 arm-level events and 14 clinical features. Shown in the table are P values (Q values). Thresholded by Q value < 0.25, 42 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
4p loss 14 (4%) 349 0.599
(1.00) 		0.333
(1.00) 		0.0347
(1.00) 		0.000151
(0.149) 		0.406
(1.00) 		0.00237
(1.00) 		2.31e-06
(0.00235) 		2.14e-06
(0.00218) 		0.000147
(0.145) 		0.00106
(1.00) 		2.2e-05
(0.0222) 		0.205
(1.00) 		0.536
(1.00) 		1
(1.00)
5q loss 12 (3%) 351 0.698
(1.00) 		0.989
(1.00) 		0.0156
(1.00) 		0.0569
(1.00) 		1
(1.00) 		0.615
(1.00) 		0.0282
(1.00) 		6.02e-05
(0.06) 		5.46e-06
(0.00553) 		0.397
(1.00) 		4.18e-05
(0.042) 		0.403
(1.00) 		0.841
(1.00) 		1
(1.00)
6q loss 29 (8%) 334 0.406
(1.00) 		0.439
(1.00) 		0.00985
(1.00) 		0.00335
(1.00) 		1
(1.00) 		0.0962
(1.00) 		0.000893
(0.857) 		2.98e-07
(0.000305) 		6.91e-06
(0.007) 		0.00273
(1.00) 		4.88e-08
(5.01e-05) 		0.634
(1.00) 		0.708
(1.00) 		0.125
(1.00)
10q loss 32 (9%) 331 0.753
(1.00) 		0.249
(1.00) 		0.0168
(1.00) 		0.0232
(1.00) 		1
(1.00) 		0.0375
(1.00) 		0.0128
(1.00) 		1.45e-06
(0.00148) 		0.000688
(0.667) 		0.000121
(0.12) 		2.03e-06
(0.00207) 		0.264
(1.00) 		0.814
(1.00) 		0.583
(1.00)
22q loss 32 (9%) 331 0.534
(1.00) 		0.503
(1.00) 		0.00068
(0.66) 		0.026
(1.00) 		0.0969
(1.00) 		0.12
(1.00) 		0.018
(1.00) 		1.09e-05
(0.011) 		2.11e-05
(0.0213) 		0.0312
(1.00) 		3.01e-06
(0.00306) 		0.672
(1.00) 		0.207
(1.00) 		0.493
(1.00)
xq loss 29 (8%) 334 0.428
(1.00) 		0.0944
(1.00) 		0.118
(1.00) 		0.157
(1.00) 		0.278
(1.00) 		0.518
(1.00) 		0.0747
(1.00) 		3.12e-06
(0.00316) 		1.26e-06
(0.00129) 		0.0689
(1.00) 		1.45e-05
(0.0146) 		0.0904
(1.00) 		0.376
(1.00) 		0.386
(1.00)
8p gain 48 (13%) 315 0.976
(1.00) 		0.0169
(1.00) 		0.107
(1.00) 		1
(1.00) 		0.231
(1.00) 		0.102
(1.00) 		0.743
(1.00) 		7.1e-05
(0.0707) 		0.000667
(0.647) 		0.0555
(1.00) 		8.1e-05
(0.0806) 		0.016
(1.00) 		0.874
(1.00) 		0.658
(1.00)
9q gain 32 (9%) 331 0.397
(1.00) 		0.0431
(1.00) 		0.00088
(0.845) 		0.0232
(1.00) 		0.0969
(1.00) 		0.237
(1.00) 		0.0088
(1.00) 		0.00127
(1.00) 		4.87e-05
(0.0487) 		0.505
(1.00) 		3.76e-05
(0.0379) 		0.0138
(1.00) 		0.722
(1.00) 		0.461
(1.00)
4q loss 10 (3%) 353 0.669
(1.00) 		0.343
(1.00) 		0.0637
(1.00) 		0.0404
(1.00) 		0.309
(1.00) 		0.0691
(1.00) 		0.0257
(1.00) 		0.000144
(0.143) 		0.00168
(1.00) 		0.00939
(1.00) 		0.000174
(0.171) 		0.336
(1.00) 		0.107
(1.00) 		1
(1.00)
6p loss 15 (4%) 348 0.617
(1.00) 		0.629
(1.00) 		0.028
(1.00) 		0.0114
(1.00) 		1
(1.00) 		0.25
(1.00) 		0.00591
(1.00) 		0.00177
(1.00) 		0.000106
(0.105) 		0.635
(1.00) 		0.000118
(0.117) 		0.84
(1.00) 		0.149
(1.00) 		0.306
(1.00)
10p loss 30 (8%) 333 0.746
(1.00) 		0.0887
(1.00) 		0.00077
(0.742) 		0.0418
(1.00) 		1
(1.00) 		0.0452
(1.00) 		0.0247
(1.00) 		4e-05
(0.0402) 		0.000394
(0.385) 		0.00718
(1.00) 		4.46e-05
(0.0446) 		0.459
(1.00) 		0.612
(1.00) 		1
(1.00)
13q loss 53 (15%) 310 0.222
(1.00) 		0.116
(1.00) 		0.0404
(1.00) 		0.0404
(1.00) 		0.701
(1.00) 		0.171
(1.00) 		0.0172
(1.00) 		1.05e-06
(0.00107) 		0.000305
(0.3) 		0.000421
(0.411) 		6.29e-08
(6.45e-05) 		0.0464
(1.00) 		0.456
(1.00) 		0.439
(1.00)
18q loss 71 (20%) 292 0.635
(1.00) 		0.397
(1.00) 		0.0608
(1.00) 		0.00813
(1.00) 		1
(1.00) 		0.00037
(0.362) 		0.003
(1.00) 		5e-06
(0.00507) 		0.00164
(1.00) 		0.000358
(0.351) 		4.57e-07
(0.000468) 		0.212
(1.00) 		0.534
(1.00) 		0.753
(1.00)
3p gain 26 (7%) 337 0.445
(1.00) 		0.00721
(1.00) 		0.0118
(1.00) 		0.377
(1.00) 		1
(1.00) 		0.304
(1.00) 		0.313
(1.00) 		0.0278
(1.00) 		0.00628
(1.00) 		0.618
(1.00) 		3.82e-05
(0.0384) 		0.596
(1.00) 		0.304
(1.00) 		0.527
(1.00)
3q gain 35 (10%) 328 0.142
(1.00) 		0.0254
(1.00) 		0.00062
(0.603) 		0.289
(1.00) 		1
(1.00) 		0.24
(1.00) 		0.171
(1.00) 		0.0181
(1.00) 		0.000485
(0.472) 		0.968
(1.00) 		8.7e-05
(0.0865) 		0.0665
(1.00) 		0.157
(1.00) 		0.635
(1.00)
8q gain 78 (21%) 285 0.667
(1.00) 		0.279
(1.00) 		0.0346
(1.00) 		0.703
(1.00) 		0.314
(1.00) 		0.489
(1.00) 		0.529
(1.00) 		0.00116
(1.00) 		2.75e-05
(0.0277) 		0.813
(1.00) 		0.00267
(1.00) 		0.065
(1.00) 		0.647
(1.00) 		0.731
(1.00)
5p loss 7 (2%) 356 0.754
(1.00) 		0.807
(1.00) 		0.00877
(1.00) 		0.264
(1.00) 		1
(1.00) 		0.564
(1.00) 		0.352
(1.00) 		0.000492
(0.478) 		5.36e-05
(0.0535) 		0.236
(1.00) 		0.000929
(0.889) 		0.497
(1.00) 		0.867
(1.00) 		1
(1.00)
15q loss 22 (6%) 341 0.485
(1.00) 		0.276
(1.00) 		0.00135
(1.00) 		0.2
(1.00) 		0.563
(1.00) 		0.86
(1.00) 		0.198
(1.00) 		0.000939
(0.897) 		4.37e-05
(0.0438) 		0.516
(1.00) 		0.00216
(1.00) 		0.493
(1.00) 		0.39
(1.00) 		1
(1.00)
16q loss 69 (19%) 294 0.768
(1.00) 		0.569
(1.00) 		0.102
(1.00) 		0.842
(1.00) 		1
(1.00) 		0.646
(1.00) 		0.826
(1.00) 		0.00332
(1.00) 		0.000216
(0.213) 		0.519
(1.00) 		0.00565
(1.00) 		0.0543
(1.00) 		0.303
(1.00) 		1
(1.00)
17p loss 53 (15%) 310 0.248
(1.00) 		0.509
(1.00) 		0.00584
(1.00) 		0.015
(1.00) 		0.701
(1.00) 		0.166
(1.00) 		0.00745
(1.00) 		0.000311
(0.305) 		0.000355
(0.349) 		0.176
(1.00) 		0.000205
(0.202) 		0.211
(1.00) 		0.211
(1.00) 		0.7
(1.00)
18p loss 48 (13%) 315 0.325
(1.00) 		0.497
(1.00) 		0.0978
(1.00) 		0.484
(1.00) 		0.685
(1.00) 		0.0512
(1.00) 		0.35
(1.00) 		0.00078
(0.751) 		0.00507
(1.00) 		0.0192
(1.00) 		4.6e-05
(0.046) 		0.411
(1.00) 		0.903
(1.00) 		0.702
(1.00)
1p gain 11 (3%) 352 0.71
(1.00) 		0.177
(1.00) 		0.00147
(1.00) 		0.64
(1.00) 		1
(1.00) 		0.669
(1.00) 		0.627
(1.00) 		0.025
(1.00) 		0.0329
(1.00) 		0.259
(1.00) 		0.00253
(1.00) 		0.0102
(1.00) 		0.829
(1.00) 		1
(1.00)
1q gain 17 (5%) 346 0.59
(1.00) 		0.498
(1.00) 		0.00862
(1.00) 		0.711
(1.00) 		0.47
(1.00) 		0.717
(1.00) 		0.559
(1.00) 		0.0219
(1.00) 		0.00393
(1.00) 		0.655
(1.00) 		0.00501
(1.00) 		0.0261
(1.00) 		0.604
(1.00) 		1
(1.00)
2p gain 7 (2%) 356 0.703
(1.00) 		0.354
(1.00) 		1
(1.00) 		1
(1.00) 		1
(1.00) 		0.511
(1.00) 		0.412
(1.00) 		0.188
(1.00) 		0.139
(1.00) 		0.98
(1.00) 		0.368
(1.00) 		0.411
(1.00) 		0.025
(1.00)
2q gain 5 (1%) 358 0.777
(1.00) 		0.267
(1.00) 		1
(1.00) 		1
(1.00) 		1
(1.00) 		0.419
(1.00) 		0.479
(1.00) 		0.173
(1.00) 		0.063
(1.00) 		0.821
(1.00) 		0.521
(1.00) 		0.59
(1.00) 		0.082
(1.00)
4p gain 6 (2%) 357 0.707
(1.00) 		0.0924
(1.00) 		0.453
(1.00) 		0.599
(1.00) 		1
(1.00) 		0.745
(1.00) 		0.312
(1.00) 		0.832
(1.00) 		0.753
(1.00) 		0.553
(1.00) 		0.743
(1.00) 		0.274
(1.00) 		0.38
(1.00) 		1
(1.00)
4q gain 5 (1%) 358 0.72
(1.00) 		0.0456
(1.00) 		0.442
(1.00) 		1
(1.00) 		1
(1.00) 		0.697
(1.00) 		0.357
(1.00) 		0.647
(1.00) 		0.489
(1.00) 		0.923
(1.00) 		0.232
(1.00) 		0.203
(1.00) 		0.185
(1.00)
5p gain 15 (4%) 348 0.627
(1.00) 		0.0105
(1.00) 		0.00126
(1.00) 		0.0356
(1.00) 		0.428
(1.00) 		0.15
(1.00) 		0.00748
(1.00) 		0.0469
(1.00) 		0.00646
(1.00) 		0.972
(1.00) 		0.00031
(0.305) 		0.085
(1.00) 		0.0633
(1.00)
5q gain 8 (2%) 355 0.722
(1.00) 		0.00214
(1.00) 		0.0394
(1.00) 		0.0917
(1.00) 		1
(1.00) 		0.0982
(1.00) 		0.0351
(1.00) 		0.289
(1.00) 		0.357
(1.00) 		0.536
(1.00) 		0.0231
(1.00) 		0.118
(1.00) 		0.00213
(1.00)
6p gain 5 (1%) 358 0.0893
(1.00) 		0.601
(1.00) 		0.443
(1.00) 		0.151
(1.00) 		0.168
(1.00) 		0.311
(1.00) 		0.108
(1.00) 		0.0469
(1.00) 		0.0274
(1.00) 		0.604
(1.00) 		0.234
(1.00) 		0.505
(1.00) 		0.426
(1.00)
6q gain 4 (1%) 359 0.686
(1.00) 		0.121
(1.00) 		0.661
(1.00) 		0.463
(1.00) 		0.136
(1.00) 		0.417
(1.00) 		0.508
(1.00) 		0.078
(1.00) 		0.0382
(1.00) 		0.665
(1.00) 		0.35
(1.00) 		0.906
(1.00) 		0.902
(1.00)
7p gain 68 (19%) 295 0.183
(1.00) 		0.0225
(1.00) 		0.166
(1.00) 		1
(1.00) 		0.476
(1.00) 		0.0148
(1.00) 		0.9
(1.00) 		0.0171
(1.00) 		0.0247
(1.00) 		0.125
(1.00) 		0.00229
(1.00) 		0.184
(1.00) 		0.519
(1.00) 		1
(1.00)
7q gain 62 (17%) 301 0.2
(1.00) 		0.036
(1.00) 		0.366
(1.00) 		0.136
(1.00) 		0.705
(1.00) 		0.0122
(1.00) 		0.114
(1.00) 		0.0611
(1.00) 		0.0737
(1.00) 		0.231
(1.00) 		0.0114
(1.00) 		0.201
(1.00) 		0.237
(1.00) 		1
(1.00)
9p gain 19 (5%) 344 0.496
(1.00) 		0.0219
(1.00) 		0.0112
(1.00) 		0.154
(1.00) 		0.143
(1.00) 		0.186
(1.00) 		0.0923
(1.00) 		0.0721
(1.00) 		0.0207
(1.00) 		0.813
(1.00) 		0.00146
(1.00) 		0.00721
(1.00) 		0.908
(1.00) 		0.346
(1.00)
10p gain 9 (2%) 354 0.649
(1.00) 		0.505
(1.00) 		0.393
(1.00) 		0.322
(1.00) 		0.282
(1.00) 		0.425
(1.00) 		0.357
(1.00) 		0.682
(1.00) 		0.732
(1.00) 		0.436
(1.00) 		0.0282
(1.00) 		0.878
(1.00) 		0.929
(1.00) 		1
(1.00)
10q gain 10 (3%) 353 0.613
(1.00) 		0.665
(1.00) 		0.306
(1.00) 		0.622
(1.00) 		0.309
(1.00) 		0.467
(1.00) 		0.362
(1.00) 		0.661
(1.00) 		0.56
(1.00) 		0.889
(1.00) 		0.0556
(1.00) 		0.433
(1.00) 		0.0786
(1.00) 		1
(1.00)
11p gain 13 (4%) 350 0.55
(1.00) 		0.39
(1.00) 		0.0658
(1.00) 		0.0765
(1.00) 		1
(1.00) 		0.102
(1.00) 		0.0934
(1.00) 		0.0136
(1.00) 		0.007
(1.00) 		0.229
(1.00) 		0.00152
(1.00) 		0.795
(1.00) 		0.469
(1.00) 		0.263
(1.00)
11q gain 15 (4%) 348 0.528
(1.00) 		0.358
(1.00) 		0.0678
(1.00) 		0.124
(1.00) 		1
(1.00) 		0.102
(1.00) 		0.182
(1.00) 		0.00317
(1.00) 		0.00138
(1.00) 		0.202
(1.00) 		0.000381
(0.373) 		0.425
(1.00) 		0.963
(1.00) 		0.262
(1.00)
12p gain 8 (2%) 355 0.675
(1.00) 		0.0384
(1.00) 		0.0393
(1.00) 		0.0403
(1.00) 		1
(1.00) 		0.0117
(1.00) 		0.0166
(1.00) 		0.00836
(1.00) 		0.00746
(1.00) 		0.267
(1.00) 		0.000719
(0.695) 		0.115
(1.00) 		0.222
(1.00)
12q gain 8 (2%) 355 0.659
(1.00) 		0.104
(1.00) 		0.0388
(1.00) 		0.0403
(1.00) 		1
(1.00) 		0.00124
(1.00) 		0.0166
(1.00) 		0.00836
(1.00) 		0.000899
(0.861) 		0.607
(1.00) 		0.000719
(0.695) 		0.0976
(1.00) 		0.222
(1.00)
13q gain 5 (1%) 358 0.63
(1.00) 		0.73
(1.00) 		1
(1.00) 		1
(1.00) 		0.168
(1.00) 		0.695
(1.00) 		0.412
(1.00) 		0.11
(1.00) 		0.908
(1.00) 		0.019
(1.00) 		0.802
(1.00) 		0.904
(1.00) 		0.317
(1.00)
14q gain 8 (2%) 355 0.0682
(1.00) 		0.11
(1.00) 		1
(1.00) 		0.264
(1.00) 		0.255
(1.00) 		0.0825
(1.00) 		0.192
(1.00) 		0.0399
(1.00) 		0.0211
(1.00) 		0.607
(1.00) 		0.0061
(1.00) 		0.406
(1.00) 		0.588
(1.00)
15q gain 5 (1%) 358 0.765
(1.00) 		0.443
(1.00) 		1
(1.00) 		0.541
(1.00) 		1
(1.00) 		0.695
(1.00) 		0.683
(1.00) 		0.541
(1.00) 		0.561
(1.00) 		0.604
(1.00) 		0.166
(1.00) 		0.698
(1.00) 		0.615
(1.00)
16p gain 20 (6%) 343 0.506
(1.00) 		0.281
(1.00) 		0.0042
(1.00) 		0.0786
(1.00) 		0.527
(1.00) 		0.731
(1.00) 		0.0714
(1.00) 		0.0119
(1.00) 		0.000879
(0.845) 		0.54
(1.00) 		0.00177
(1.00) 		0.785
(1.00) 		0.181
(1.00) 		1
(1.00)
16q gain 7 (2%) 356 0.81
(1.00) 		0.0254
(1.00) 		0.319
(1.00) 		0.541
(1.00) 		1
(1.00) 		0.772
(1.00) 		0.788
(1.00) 		0.188
(1.00) 		0.0765
(1.00) 		0.98
(1.00) 		0.104
(1.00) 		0.5
(1.00) 		0.717
(1.00) 		1
(1.00)
17p gain 5 (1%) 358 0.791
(1.00) 		0.652
(1.00) 		0.138
(1.00) 		0.151
(1.00) 		1
(1.00) 		0.697
(1.00) 		0.0638
(1.00) 		0.369
(1.00) 		0.063
(1.00) 		0.821
(1.00) 		0.428
(1.00) 		0.997
(1.00) 		0.212
(1.00)
17q gain 6 (2%) 357 0.759
(1.00) 		0.888
(1.00) 		0.119
(1.00) 		0.0403
(1.00) 		1
(1.00) 		0.745
(1.00) 		0.00875
(1.00) 		0.232
(1.00) 		0.0436
(1.00) 		0.93
(1.00) 		0.295
(1.00) 		0.529
(1.00) 		0.372
(1.00)
18p gain 12 (3%) 351 0.655
(1.00) 		0.0626
(1.00) 		0.0321
(1.00) 		0.16
(1.00) 		1
(1.00) 		1
(1.00) 		0.156
(1.00) 		0.191
(1.00) 		0.494
(1.00) 		0.397
(1.00) 		0.298
(1.00) 		0.254
(1.00) 		0.908
(1.00) 		1
(1.00)
18q gain 5 (1%) 358 0.775
(1.00) 		0.124
(1.00) 		0.141
(1.00) 		1
(1.00) 		1
(1.00) 		1
(1.00) 		0.357
(1.00) 		0.462
(1.00) 		0.908
(1.00) 		0.255
(1.00) 		0.55
(1.00) 		0.712
(1.00) 		0.746
(1.00)
19p gain 6 (2%) 357 0.697
(1.00) 		0.443
(1.00) 		0.0133
(1.00) 		1
(1.00) 		1
(1.00) 		0.512
(1.00) 		0.939
(1.00) 		0.022
(1.00) 		0.0145
(1.00) 		0.246
(1.00) 		0.0317
(1.00) 		0.0089
(1.00) 		0.966
(1.00)
19q gain 6 (2%) 357 0.649
(1.00) 		0.337
(1.00) 		0.013
(1.00) 		1
(1.00) 		1
(1.00) 		0.511
(1.00) 		0.939
(1.00) 		0.022
(1.00) 		0.0436
(1.00) 		0.0844
(1.00) 		0.0317
(1.00) 		0.0156
(1.00) 		0.834
(1.00) 		1
(1.00)
20p gain 13 (4%) 350 0.582
(1.00) 		0.207
(1.00) 		0.139
(1.00) 		0.0991
(1.00) 		1
(1.00) 		0.545
(1.00) 		0.0585
(1.00) 		0.018
(1.00) 		0.0346
(1.00) 		0.111
(1.00) 		0.00377
(1.00) 		0.858
(1.00) 		0.928
(1.00)
20q gain 16 (4%) 347 0.51
(1.00) 		0.0623
(1.00) 		0.0146
(1.00) 		0.261
(1.00) 		1
(1.00) 		0.302
(1.00) 		0.169
(1.00) 		0.0334
(1.00) 		0.0122
(1.00) 		0.417
(1.00) 		0.00122
(1.00) 		0.152
(1.00) 		0.843
(1.00) 		1
(1.00)
21q gain 13 (4%) 350 0.496
(1.00) 		0.00894
(1.00) 		0.141
(1.00) 		0.409
(1.00) 		0.383
(1.00) 		0.184
(1.00) 		0.405
(1.00) 		0.151
(1.00) 		0.0346
(1.00) 		0.792
(1.00) 		0.0023
(1.00) 		0.277
(1.00) 		0.253
(1.00) 		1
(1.00)
xq gain 4 (1%) 359 0.761
(1.00) 		0.264
(1.00) 		0.188
(1.00) 		1
(1.00) 		1
(1.00) 		0.0259
(1.00) 		0.412
(1.00) 		0.149
(1.00) 		0.0382
(1.00) 		0.8
(1.00) 		0.0527
(1.00) 		0.473
(1.00) 		0.776
(1.00)
1p loss 13 (4%) 350 0.532
(1.00) 		0.542
(1.00) 		0.139
(1.00) 		0.701
(1.00) 		1
(1.00) 		0.65
(1.00) 		0.45
(1.00) 		0.00139
(1.00) 		0.00134
(1.00) 		0.111
(1.00) 		0.00182
(1.00) 		0.505
(1.00) 		0.053
(1.00) 		1
(1.00)
2p loss 9 (2%) 354 0.575
(1.00) 		0.0528
(1.00) 		0.193
(1.00) 		0.368
(1.00) 		1
(1.00) 		0.809
(1.00) 		0.213
(1.00) 		0.293
(1.00) 		0.258
(1.00) 		0.559
(1.00) 		0.687
(1.00) 		0.352
(1.00) 		0.561
(1.00)
2q loss 10 (3%) 353 0.575
(1.00) 		0.127
(1.00) 		0.112
(1.00) 		0.367
(1.00) 		1
(1.00) 		0.672
(1.00) 		0.188
(1.00) 		0.197
(1.00) 		0.186
(1.00) 		0.517
(1.00) 		0.526
(1.00) 		0.54
(1.00) 		0.561
(1.00)
3p loss 6 (2%) 357 0.616
(1.00) 		0.602
(1.00) 		0.457
(1.00) 		0.207
(1.00) 		1
(1.00) 		0.224
(1.00) 		0.12
(1.00) 		0.00178
(1.00) 		0.0436
(1.00) 		0.0029
(1.00) 		0.000447
(0.435) 		0.279
(1.00) 		0.265
(1.00)
3q loss 4 (1%) 359 0.644
(1.00) 		0.297
(1.00) 		0.66
(1.00) 		1
(1.00) 		1
(1.00) 		0.416
(1.00) 		0.412
(1.00) 		0.0236
(1.00) 		0.0916
(1.00) 		0.0497
(1.00) 		0.00486
(1.00) 		0.259
(1.00) 		0.65
(1.00)
8p loss 121 (33%) 242 0.986
(1.00) 		0.856
(1.00) 		0.00134
(1.00) 		0.233
(1.00) 		1
(1.00) 		0.882
(1.00) 		0.163
(1.00) 		0.736
(1.00) 		0.0167
(1.00) 		0.0534
(1.00) 		0.887
(1.00) 		0.611
(1.00) 		0.103
(1.00) 		0.162
(1.00)
8q loss 19 (5%) 344 0.0021
(1.00) 		0.944
(1.00) 		0.00503
(1.00) 		0.00726
(1.00) 		1
(1.00) 		0.0964
(1.00) 		0.000703
(0.681) 		0.0285
(1.00) 		0.015
(1.00) 		0.376
(1.00) 		0.029
(1.00) 		0.661
(1.00) 		0.405
(1.00) 		1
(1.00)
9p loss 15 (4%) 348 0.592
(1.00) 		0.504
(1.00) 		0.0694
(1.00) 		0.0478
(1.00) 		1
(1.00) 		0.765
(1.00) 		0.0159
(1.00) 		0.0128
(1.00) 		0.0294
(1.00) 		0.101
(1.00) 		0.00199
(1.00) 		0.922
(1.00) 		0.83
(1.00) 		1
(1.00)
9q loss 6 (2%) 357 0.741
(1.00) 		0.466
(1.00) 		1
(1.00) 		1
(1.00) 		1
(1.00) 		0.698
(1.00) 		0.761
(1.00) 		0.0322
(1.00) 		0.395
(1.00) 		0.0159
(1.00) 		0.00525
(1.00) 		0.671
(1.00) 		0.452
(1.00) 		1
(1.00)
11p loss 3 (1%) 360 0.0871
(1.00) 		0.297
(1.00) 		1
(1.00) 		1
(1.00) 		0.286
(1.00) 		0.479
(1.00) 		0.255
(1.00) 		0.0521
(1.00) 		0.646
(1.00) 		0.321
(1.00) 		0.472
(1.00) 		0.489
(1.00)
12p loss 31 (9%) 332 0.376
(1.00) 		0.843
(1.00) 		0.17
(1.00) 		0.0623
(1.00) 		0.613
(1.00) 		0.29
(1.00) 		0.0732
(1.00) 		0.00176
(1.00) 		0.00116
(1.00) 		0.132
(1.00) 		0.00304
(1.00) 		0.449
(1.00) 		0.0467
(1.00) 		1
(1.00)
12q loss 13 (4%) 350 0.607
(1.00) 		0.789
(1.00) 		0.201
(1.00) 		0.0991
(1.00) 		1
(1.00) 		0.571
(1.00) 		0.101
(1.00) 		0.0312
(1.00) 		0.007
(1.00) 		0.463
(1.00) 		0.0219
(1.00) 		0.757
(1.00) 		0.69
(1.00) 		1
(1.00)
14q loss 18 (5%) 345 0.373
(1.00) 		0.774
(1.00) 		0.0157
(1.00) 		0.304
(1.00) 		0.49
(1.00) 		0.283
(1.00) 		0.336
(1.00) 		0.00359
(1.00) 		0.00408
(1.00) 		0.168
(1.00) 		0.00349
(1.00) 		0.032
(1.00) 		0.283
(1.00) 		1
(1.00)
16p loss 21 (6%) 342 0.464
(1.00) 		0.948
(1.00) 		1
(1.00) 		0.33
(1.00) 		1
(1.00) 		0.695
(1.00) 		0.224
(1.00) 		0.397
(1.00) 		0.116
(1.00) 		0.794
(1.00) 		0.24
(1.00) 		0.703
(1.00) 		0.731
(1.00) 		1
(1.00)
17q loss 12 (3%) 351 0.596
(1.00) 		0.741
(1.00) 		0.222
(1.00) 		1
(1.00) 		1
(1.00) 		0.0937
(1.00) 		0.506
(1.00) 		0.0368
(1.00) 		0.0231
(1.00) 		0.446
(1.00) 		0.15
(1.00) 		0.978
(1.00) 		0.344
(1.00) 		1
(1.00)
19p loss 13 (4%) 350 0.569
(1.00) 		0.0552
(1.00) 		0.375
(1.00) 		1
(1.00) 		1
(1.00) 		0.65
(1.00) 		0.912
(1.00) 		0.0235
(1.00) 		0.0162
(1.00) 		0.415
(1.00) 		0.072
(1.00) 		0.261
(1.00) 		0.186
(1.00) 		1
(1.00)
19q loss 13 (4%) 350 0.569
(1.00) 		0.0552
(1.00) 		0.376
(1.00) 		1
(1.00) 		1
(1.00) 		0.649
(1.00) 		0.912
(1.00) 		0.0235
(1.00) 		0.0162
(1.00) 		0.415
(1.00) 		0.072
(1.00) 		0.261
(1.00) 		0.186
(1.00) 		1
(1.00)
20p loss 13 (4%) 350 0.0861
(1.00) 		0.518
(1.00) 		0.0387
(1.00) 		0.198
(1.00) 		1
(1.00) 		1
(1.00) 		0.151
(1.00) 		0.992
(1.00) 		0.109
(1.00) 		0.0657
(1.00) 		0.807
(1.00) 		0.132
(1.00) 		0.642
(1.00) 		0.346
(1.00)
20q loss 7 (2%) 356 0.752
(1.00) 		0.0504
(1.00) 		0.0431
(1.00) 		1
(1.00) 		1
(1.00) 		1
(1.00) 		0.803
(1.00) 		0.188
(1.00) 		0.0139
(1.00) 		0.473
(1.00) 		0.269
(1.00) 		0.152
(1.00) 		0.726
(1.00) 		1
(1.00)
21q loss 14 (4%) 349 0.616
(1.00) 		0.718
(1.00) 		0.0339
(1.00) 		0.0256
(1.00) 		0.406
(1.00) 		0.651
(1.00) 		0.00896
(1.00) 		0.000704
(0.681) 		0.00153
(1.00) 		0.0762
(1.00) 		0.00079
(0.76) 		0.0893
(1.00) 		0.394
(1.00) 		1
(1.00)
'3p gain' versus 'GLEASON_SCORE'

P value = 3.82e-05 (Wilcoxon-test), Q value = 0.038

Table S1.  Gene #5: '3p gain' versus Clinical Feature #11: 'GLEASON_SCORE'

nPatients Mean (Std.Dev)
ALL 363 7.5 (1.0)
3P GAIN MUTATED 26 8.3 (1.0)
3P GAIN WILD-TYPE 337 7.5 (0.9)

Figure S1.  Get High-res Image Gene #5: '3p gain' versus Clinical Feature #11: 'GLEASON_SCORE'

'3q gain' versus 'GLEASON_SCORE'

P value = 8.7e-05 (Wilcoxon-test), Q value = 0.086

Table S2.  Gene #6: '3q gain' versus Clinical Feature #11: 'GLEASON_SCORE'

nPatients Mean (Std.Dev)
ALL 363 7.5 (1.0)
3Q GAIN MUTATED 35 8.1 (1.0)
3Q GAIN WILD-TYPE 328 7.4 (0.9)

Figure S2.  Get High-res Image Gene #6: '3q gain' versus Clinical Feature #11: 'GLEASON_SCORE'

'8p gain' versus 'GLEASON_SCORE_COMBINED'

P value = 7.1e-05 (Wilcoxon-test), Q value = 0.071

Table S3.  Gene #15: '8p gain' versus Clinical Feature #8: 'GLEASON_SCORE_COMBINED'

nPatients Mean (Std.Dev)
ALL 363 7.4 (0.9)
8P GAIN MUTATED 48 7.9 (0.9)
8P GAIN WILD-TYPE 315 7.4 (0.9)

Figure S3.  Get High-res Image Gene #15: '8p gain' versus Clinical Feature #8: 'GLEASON_SCORE_COMBINED'

'8p gain' versus 'GLEASON_SCORE'

P value = 8.1e-05 (Wilcoxon-test), Q value = 0.081

Table S4.  Gene #15: '8p gain' versus Clinical Feature #11: 'GLEASON_SCORE'

nPatients Mean (Std.Dev)
ALL 363 7.5 (1.0)
8P GAIN MUTATED 48 8.0 (1.0)
8P GAIN WILD-TYPE 315 7.4 (0.9)

Figure S4.  Get High-res Image Gene #15: '8p gain' versus Clinical Feature #11: 'GLEASON_SCORE'

'8q gain' versus 'GLEASON_SCORE_PRIMARY'

P value = 2.75e-05 (Wilcoxon-test), Q value = 0.028

Table S5.  Gene #16: '8q gain' versus Clinical Feature #9: 'GLEASON_SCORE_PRIMARY'

nPatients Mean (Std.Dev)
ALL 363 3.6 (0.6)
8Q GAIN MUTATED 78 3.9 (0.6)
8Q GAIN WILD-TYPE 285 3.5 (0.6)

Figure S5.  Get High-res Image Gene #16: '8q gain' versus Clinical Feature #9: 'GLEASON_SCORE_PRIMARY'

'9q gain' versus 'GLEASON_SCORE_PRIMARY'

P value = 4.87e-05 (Wilcoxon-test), Q value = 0.049

Table S6.  Gene #18: '9q gain' versus Clinical Feature #9: 'GLEASON_SCORE_PRIMARY'

nPatients Mean (Std.Dev)
ALL 363 3.6 (0.6)
9Q GAIN MUTATED 32 4.0 (0.6)
9Q GAIN WILD-TYPE 331 3.6 (0.6)

Figure S6.  Get High-res Image Gene #18: '9q gain' versus Clinical Feature #9: 'GLEASON_SCORE_PRIMARY'

'9q gain' versus 'GLEASON_SCORE'

P value = 3.76e-05 (Wilcoxon-test), Q value = 0.038

Table S7.  Gene #18: '9q gain' versus Clinical Feature #11: 'GLEASON_SCORE'

nPatients Mean (Std.Dev)
ALL 363 7.5 (1.0)
9Q GAIN MUTATED 32 8.2 (0.9)
9Q GAIN WILD-TYPE 331 7.5 (0.9)

Figure S7.  Get High-res Image Gene #18: '9q gain' versus Clinical Feature #11: 'GLEASON_SCORE'

'4p loss' versus 'PATHOLOGY.N.STAGE'

P value = 0.000151 (Fisher's exact test), Q value = 0.15

Table S8.  Gene #45: '4p loss' versus Clinical Feature #4: 'PATHOLOGY.N.STAGE'

nPatients 0 1
ALL 263 44
4P LOSS MUTATED 6 8
4P LOSS WILD-TYPE 257 36

Figure S8.  Get High-res Image Gene #45: '4p loss' versus Clinical Feature #4: 'PATHOLOGY.N.STAGE'

'4p loss' versus 'NUMBER.OF.LYMPH.NODES'

P value = 2.31e-06 (Wilcoxon-test), Q value = 0.0023

Table S9.  Gene #45: '4p loss' versus Clinical Feature #7: 'NUMBER.OF.LYMPH.NODES'

nPatients Mean (Std.Dev)
ALL 303 0.3 (1.3)
4P LOSS MUTATED 14 1.3 (1.6)
4P LOSS WILD-TYPE 289 0.3 (1.3)

Figure S9.  Get High-res Image Gene #45: '4p loss' versus Clinical Feature #7: 'NUMBER.OF.LYMPH.NODES'

'4p loss' versus 'GLEASON_SCORE_COMBINED'

P value = 2.14e-06 (Wilcoxon-test), Q value = 0.0022

Table S10.  Gene #45: '4p loss' versus Clinical Feature #8: 'GLEASON_SCORE_COMBINED'

nPatients Mean (Std.Dev)
ALL 363 7.4 (0.9)
4P LOSS MUTATED 14 8.6 (0.7)
4P LOSS WILD-TYPE 349 7.4 (0.9)

Figure S10.  Get High-res Image Gene #45: '4p loss' versus Clinical Feature #8: 'GLEASON_SCORE_COMBINED'

'4p loss' versus 'GLEASON_SCORE_PRIMARY'

P value = 0.000147 (Wilcoxon-test), Q value = 0.15

Table S11.  Gene #45: '4p loss' versus Clinical Feature #9: 'GLEASON_SCORE_PRIMARY'

nPatients Mean (Std.Dev)
ALL 363 3.6 (0.6)
4P LOSS MUTATED 14 4.2 (0.4)
4P LOSS WILD-TYPE 349 3.6 (0.6)

Figure S11.  Get High-res Image Gene #45: '4p loss' versus Clinical Feature #9: 'GLEASON_SCORE_PRIMARY'

'4p loss' versus 'GLEASON_SCORE'

P value = 2.2e-05 (Wilcoxon-test), Q value = 0.022

Table S12.  Gene #45: '4p loss' versus Clinical Feature #11: 'GLEASON_SCORE'

nPatients Mean (Std.Dev)
ALL 363 7.5 (1.0)
4P LOSS MUTATED 14 8.6 (0.8)
4P LOSS WILD-TYPE 349 7.5 (0.9)

Figure S12.  Get High-res Image Gene #45: '4p loss' versus Clinical Feature #11: 'GLEASON_SCORE'

'4q loss' versus 'GLEASON_SCORE_COMBINED'

P value = 0.000144 (Wilcoxon-test), Q value = 0.14

Table S13.  Gene #46: '4q loss' versus Clinical Feature #8: 'GLEASON_SCORE_COMBINED'

nPatients Mean (Std.Dev)
ALL 363 7.4 (0.9)
4Q LOSS MUTATED 10 8.6 (0.8)
4Q LOSS WILD-TYPE 353 7.4 (0.9)

Figure S13.  Get High-res Image Gene #46: '4q loss' versus Clinical Feature #8: 'GLEASON_SCORE_COMBINED'

'4q loss' versus 'GLEASON_SCORE'

P value = 0.000174 (Wilcoxon-test), Q value = 0.17

Table S14.  Gene #46: '4q loss' versus Clinical Feature #11: 'GLEASON_SCORE'

nPatients Mean (Std.Dev)
ALL 363 7.5 (1.0)
4Q LOSS MUTATED 10 8.7 (0.8)
4Q LOSS WILD-TYPE 353 7.5 (0.9)

Figure S14.  Get High-res Image Gene #46: '4q loss' versus Clinical Feature #11: 'GLEASON_SCORE'

'5p loss' versus 'GLEASON_SCORE_PRIMARY'

P value = 5.36e-05 (Wilcoxon-test), Q value = 0.053

Table S15.  Gene #47: '5p loss' versus Clinical Feature #9: 'GLEASON_SCORE_PRIMARY'

nPatients Mean (Std.Dev)
ALL 363 3.6 (0.6)
5P LOSS MUTATED 7 4.7 (0.5)
5P LOSS WILD-TYPE 356 3.6 (0.6)

Figure S15.  Get High-res Image Gene #47: '5p loss' versus Clinical Feature #9: 'GLEASON_SCORE_PRIMARY'

'5q loss' versus 'GLEASON_SCORE_COMBINED'

P value = 6.02e-05 (Wilcoxon-test), Q value = 0.06

Table S16.  Gene #48: '5q loss' versus Clinical Feature #8: 'GLEASON_SCORE_COMBINED'

nPatients Mean (Std.Dev)
ALL 363 7.4 (0.9)
5Q LOSS MUTATED 12 8.5 (0.8)
5Q LOSS WILD-TYPE 351 7.4 (0.9)

Figure S16.  Get High-res Image Gene #48: '5q loss' versus Clinical Feature #8: 'GLEASON_SCORE_COMBINED'

'5q loss' versus 'GLEASON_SCORE_PRIMARY'

P value = 5.46e-06 (Wilcoxon-test), Q value = 0.0055

Table S17.  Gene #48: '5q loss' versus Clinical Feature #9: 'GLEASON_SCORE_PRIMARY'

nPatients Mean (Std.Dev)
ALL 363 3.6 (0.6)
5Q LOSS MUTATED 12 4.5 (0.5)
5Q LOSS WILD-TYPE 351 3.6 (0.6)

Figure S17.  Get High-res Image Gene #48: '5q loss' versus Clinical Feature #9: 'GLEASON_SCORE_PRIMARY'

'5q loss' versus 'GLEASON_SCORE'

P value = 4.18e-05 (Wilcoxon-test), Q value = 0.042

Table S18.  Gene #48: '5q loss' versus Clinical Feature #11: 'GLEASON_SCORE'

nPatients Mean (Std.Dev)
ALL 363 7.5 (1.0)
5Q LOSS MUTATED 12 8.7 (0.8)
5Q LOSS WILD-TYPE 351 7.5 (0.9)

Figure S18.  Get High-res Image Gene #48: '5q loss' versus Clinical Feature #11: 'GLEASON_SCORE'

'6p loss' versus 'GLEASON_SCORE_PRIMARY'

P value = 0.000106 (Wilcoxon-test), Q value = 0.11

Table S19.  Gene #49: '6p loss' versus Clinical Feature #9: 'GLEASON_SCORE_PRIMARY'

nPatients Mean (Std.Dev)
ALL 363 3.6 (0.6)
6P LOSS MUTATED 15 4.2 (0.4)
6P LOSS WILD-TYPE 348 3.6 (0.6)

Figure S19.  Get High-res Image Gene #49: '6p loss' versus Clinical Feature #9: 'GLEASON_SCORE_PRIMARY'

'6p loss' versus 'GLEASON_SCORE'

P value = 0.000118 (Wilcoxon-test), Q value = 0.12

Table S20.  Gene #49: '6p loss' versus Clinical Feature #11: 'GLEASON_SCORE'

nPatients Mean (Std.Dev)
ALL 363 7.5 (1.0)
6P LOSS MUTATED 15 8.5 (0.8)
6P LOSS WILD-TYPE 348 7.5 (0.9)

Figure S20.  Get High-res Image Gene #49: '6p loss' versus Clinical Feature #11: 'GLEASON_SCORE'

'6q loss' versus 'GLEASON_SCORE_COMBINED'

P value = 2.98e-07 (Wilcoxon-test), Q value = 3e-04

Table S21.  Gene #50: '6q loss' versus Clinical Feature #8: 'GLEASON_SCORE_COMBINED'

nPatients Mean (Std.Dev)
ALL 363 7.4 (0.9)
6Q LOSS MUTATED 29 8.3 (0.9)
6Q LOSS WILD-TYPE 334 7.4 (0.9)

Figure S21.  Get High-res Image Gene #50: '6q loss' versus Clinical Feature #8: 'GLEASON_SCORE_COMBINED'

'6q loss' versus 'GLEASON_SCORE_PRIMARY'

P value = 6.91e-06 (Wilcoxon-test), Q value = 0.007

Table S22.  Gene #50: '6q loss' versus Clinical Feature #9: 'GLEASON_SCORE_PRIMARY'

nPatients Mean (Std.Dev)
ALL 363 3.6 (0.6)
6Q LOSS MUTATED 29 4.1 (0.6)
6Q LOSS WILD-TYPE 334 3.6 (0.6)

Figure S22.  Get High-res Image Gene #50: '6q loss' versus Clinical Feature #9: 'GLEASON_SCORE_PRIMARY'

'6q loss' versus 'GLEASON_SCORE'

P value = 4.88e-08 (Wilcoxon-test), Q value = 5e-05

Table S23.  Gene #50: '6q loss' versus Clinical Feature #11: 'GLEASON_SCORE'

nPatients Mean (Std.Dev)
ALL 363 7.5 (1.0)
6Q LOSS MUTATED 29 8.5 (0.9)
6Q LOSS WILD-TYPE 334 7.4 (0.9)

Figure S23.  Get High-res Image Gene #50: '6q loss' versus Clinical Feature #11: 'GLEASON_SCORE'

'10p loss' versus 'GLEASON_SCORE_COMBINED'

P value = 4e-05 (Wilcoxon-test), Q value = 0.04

Table S24.  Gene #55: '10p loss' versus Clinical Feature #8: 'GLEASON_SCORE_COMBINED'

nPatients Mean (Std.Dev)
ALL 363 7.4 (0.9)
10P LOSS MUTATED 30 8.2 (1.0)
10P LOSS WILD-TYPE 333 7.4 (0.9)

Figure S24.  Get High-res Image Gene #55: '10p loss' versus Clinical Feature #8: 'GLEASON_SCORE_COMBINED'

'10p loss' versus 'GLEASON_SCORE'

P value = 4.46e-05 (Wilcoxon-test), Q value = 0.045

Table S25.  Gene #55: '10p loss' versus Clinical Feature #11: 'GLEASON_SCORE'

nPatients Mean (Std.Dev)
ALL 363 7.5 (1.0)
10P LOSS MUTATED 30 8.2 (1.0)
10P LOSS WILD-TYPE 333 7.4 (0.9)

Figure S25.  Get High-res Image Gene #55: '10p loss' versus Clinical Feature #11: 'GLEASON_SCORE'

'10q loss' versus 'GLEASON_SCORE_COMBINED'

P value = 1.45e-06 (Wilcoxon-test), Q value = 0.0015

Table S26.  Gene #56: '10q loss' versus Clinical Feature #8: 'GLEASON_SCORE_COMBINED'

nPatients Mean (Std.Dev)
ALL 363 7.4 (0.9)
10Q LOSS MUTATED 32 8.2 (1.0)
10Q LOSS WILD-TYPE 331 7.4 (0.9)

Figure S26.  Get High-res Image Gene #56: '10q loss' versus Clinical Feature #8: 'GLEASON_SCORE_COMBINED'

'10q loss' versus 'GLEASON_SCORE_SECONDARY'

P value = 0.000121 (Wilcoxon-test), Q value = 0.12

Table S27.  Gene #56: '10q loss' versus Clinical Feature #10: 'GLEASON_SCORE_SECONDARY'

nPatients Mean (Std.Dev)
ALL 363 3.9 (0.6)
10Q LOSS MUTATED 32 4.3 (0.6)
10Q LOSS WILD-TYPE 331 3.8 (0.6)

Figure S27.  Get High-res Image Gene #56: '10q loss' versus Clinical Feature #10: 'GLEASON_SCORE_SECONDARY'

'10q loss' versus 'GLEASON_SCORE'

P value = 2.03e-06 (Wilcoxon-test), Q value = 0.0021

Table S28.  Gene #56: '10q loss' versus Clinical Feature #11: 'GLEASON_SCORE'

nPatients Mean (Std.Dev)
ALL 363 7.5 (1.0)
10Q LOSS MUTATED 32 8.3 (1.0)
10Q LOSS WILD-TYPE 331 7.4 (0.9)

Figure S28.  Get High-res Image Gene #56: '10q loss' versus Clinical Feature #11: 'GLEASON_SCORE'

'13q loss' versus 'GLEASON_SCORE_COMBINED'

P value = 1.05e-06 (Wilcoxon-test), Q value = 0.0011

Table S29.  Gene #60: '13q loss' versus Clinical Feature #8: 'GLEASON_SCORE_COMBINED'

nPatients Mean (Std.Dev)
ALL 363 7.4 (0.9)
13Q LOSS MUTATED 53 8.1 (1.0)
13Q LOSS WILD-TYPE 310 7.3 (0.9)

Figure S29.  Get High-res Image Gene #60: '13q loss' versus Clinical Feature #8: 'GLEASON_SCORE_COMBINED'

'13q loss' versus 'GLEASON_SCORE'

P value = 6.29e-08 (Wilcoxon-test), Q value = 6.4e-05

Table S30.  Gene #60: '13q loss' versus Clinical Feature #11: 'GLEASON_SCORE'

nPatients Mean (Std.Dev)
ALL 363 7.5 (1.0)
13Q LOSS MUTATED 53 8.2 (1.0)
13Q LOSS WILD-TYPE 310 7.4 (0.9)

Figure S30.  Get High-res Image Gene #60: '13q loss' versus Clinical Feature #11: 'GLEASON_SCORE'

'15q loss' versus 'GLEASON_SCORE_PRIMARY'

P value = 4.37e-05 (Wilcoxon-test), Q value = 0.044

Table S31.  Gene #62: '15q loss' versus Clinical Feature #9: 'GLEASON_SCORE_PRIMARY'

nPatients Mean (Std.Dev)
ALL 363 3.6 (0.6)
15Q LOSS MUTATED 22 4.1 (0.6)
15Q LOSS WILD-TYPE 341 3.6 (0.6)

Figure S31.  Get High-res Image Gene #62: '15q loss' versus Clinical Feature #9: 'GLEASON_SCORE_PRIMARY'

'16q loss' versus 'GLEASON_SCORE_PRIMARY'

P value = 0.000216 (Wilcoxon-test), Q value = 0.21

Table S32.  Gene #64: '16q loss' versus Clinical Feature #9: 'GLEASON_SCORE_PRIMARY'

nPatients Mean (Std.Dev)
ALL 363 3.6 (0.6)
16Q LOSS MUTATED 69 3.9 (0.6)
16Q LOSS WILD-TYPE 294 3.5 (0.6)

Figure S32.  Get High-res Image Gene #64: '16q loss' versus Clinical Feature #9: 'GLEASON_SCORE_PRIMARY'

'17p loss' versus 'GLEASON_SCORE'

P value = 0.000205 (Wilcoxon-test), Q value = 0.2

Table S33.  Gene #65: '17p loss' versus Clinical Feature #11: 'GLEASON_SCORE'

nPatients Mean (Std.Dev)
ALL 363 7.5 (1.0)
17P LOSS MUTATED 53 7.9 (0.9)
17P LOSS WILD-TYPE 310 7.4 (0.9)

Figure S33.  Get High-res Image Gene #65: '17p loss' versus Clinical Feature #11: 'GLEASON_SCORE'

'18p loss' versus 'GLEASON_SCORE'

P value = 4.6e-05 (Wilcoxon-test), Q value = 0.046

Table S34.  Gene #67: '18p loss' versus Clinical Feature #11: 'GLEASON_SCORE'

nPatients Mean (Std.Dev)
ALL 363 7.5 (1.0)
18P LOSS MUTATED 48 8.1 (1.0)
18P LOSS WILD-TYPE 315 7.4 (0.9)

Figure S34.  Get High-res Image Gene #67: '18p loss' versus Clinical Feature #11: 'GLEASON_SCORE'

'18q loss' versus 'GLEASON_SCORE_COMBINED'

P value = 5e-06 (Wilcoxon-test), Q value = 0.0051

Table S35.  Gene #68: '18q loss' versus Clinical Feature #8: 'GLEASON_SCORE_COMBINED'

nPatients Mean (Std.Dev)
ALL 363 7.4 (0.9)
18Q LOSS MUTATED 71 7.9 (1.0)
18Q LOSS WILD-TYPE 292 7.3 (0.9)

Figure S35.  Get High-res Image Gene #68: '18q loss' versus Clinical Feature #8: 'GLEASON_SCORE_COMBINED'

'18q loss' versus 'GLEASON_SCORE'

P value = 4.57e-07 (Wilcoxon-test), Q value = 0.00047

Table S36.  Gene #68: '18q loss' versus Clinical Feature #11: 'GLEASON_SCORE'

nPatients Mean (Std.Dev)
ALL 363 7.5 (1.0)
18Q LOSS MUTATED 71 8.1 (1.0)
18Q LOSS WILD-TYPE 292 7.4 (0.9)

Figure S36.  Get High-res Image Gene #68: '18q loss' versus Clinical Feature #11: 'GLEASON_SCORE'

'22q loss' versus 'GLEASON_SCORE_COMBINED'

P value = 1.09e-05 (Wilcoxon-test), Q value = 0.011

Table S37.  Gene #74: '22q loss' versus Clinical Feature #8: 'GLEASON_SCORE_COMBINED'

nPatients Mean (Std.Dev)
ALL 363 7.4 (0.9)
22Q LOSS MUTATED 32 8.2 (1.0)
22Q LOSS WILD-TYPE 331 7.4 (0.9)

Figure S37.  Get High-res Image Gene #74: '22q loss' versus Clinical Feature #8: 'GLEASON_SCORE_COMBINED'

'22q loss' versus 'GLEASON_SCORE_PRIMARY'

P value = 2.11e-05 (Wilcoxon-test), Q value = 0.021

Table S38.  Gene #74: '22q loss' versus Clinical Feature #9: 'GLEASON_SCORE_PRIMARY'

nPatients Mean (Std.Dev)
ALL 363 3.6 (0.6)
22Q LOSS MUTATED 32 4.1 (0.6)
22Q LOSS WILD-TYPE 331 3.6 (0.6)

Figure S38.  Get High-res Image Gene #74: '22q loss' versus Clinical Feature #9: 'GLEASON_SCORE_PRIMARY'

'22q loss' versus 'GLEASON_SCORE'

P value = 3.01e-06 (Wilcoxon-test), Q value = 0.0031

Table S39.  Gene #74: '22q loss' versus Clinical Feature #11: 'GLEASON_SCORE'

nPatients Mean (Std.Dev)
ALL 363 7.5 (1.0)
22Q LOSS MUTATED 32 8.3 (0.9)
22Q LOSS WILD-TYPE 331 7.4 (0.9)

Figure S39.  Get High-res Image Gene #74: '22q loss' versus Clinical Feature #11: 'GLEASON_SCORE'

'xq loss' versus 'GLEASON_SCORE_COMBINED'

P value = 3.12e-06 (Wilcoxon-test), Q value = 0.0032

Table S40.  Gene #75: 'xq loss' versus Clinical Feature #8: 'GLEASON_SCORE_COMBINED'

nPatients Mean (Std.Dev)
ALL 363 7.4 (0.9)
XQ LOSS MUTATED 29 8.2 (0.9)
XQ LOSS WILD-TYPE 334 7.4 (0.9)

Figure S40.  Get High-res Image Gene #75: 'xq loss' versus Clinical Feature #8: 'GLEASON_SCORE_COMBINED'

'xq loss' versus 'GLEASON_SCORE_PRIMARY'

P value = 1.26e-06 (Wilcoxon-test), Q value = 0.0013

Table S41.  Gene #75: 'xq loss' versus Clinical Feature #9: 'GLEASON_SCORE_PRIMARY'

nPatients Mean (Std.Dev)
ALL 363 3.6 (0.6)
XQ LOSS MUTATED 29 4.1 (0.5)
XQ LOSS WILD-TYPE 334 3.6 (0.6)

Figure S41.  Get High-res Image Gene #75: 'xq loss' versus Clinical Feature #9: 'GLEASON_SCORE_PRIMARY'

'xq loss' versus 'GLEASON_SCORE'

P value = 1.45e-05 (Wilcoxon-test), Q value = 0.015

Table S42.  Gene #75: 'xq loss' versus Clinical Feature #11: 'GLEASON_SCORE'

nPatients Mean (Std.Dev)
ALL 363 7.5 (1.0)
XQ LOSS MUTATED 29 8.2 (0.9)
XQ LOSS WILD-TYPE 334 7.4 (0.9)

Figure S42.  Get High-res Image Gene #75: 'xq loss' versus Clinical Feature #11: 'GLEASON_SCORE'

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 arm-level cnvs = 75

  • Number of selected clinical features = 14

  • 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)
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