Correlation between copy number variations of arm-level result and selected clinical features
Ovarian Serous Cystadenocarcinoma (Primary solid tumor)
21 August 2015  |  analyses__2015_08_21
Maintainer Information
Citation Information
doi:10.7908/C1JH3KDR
Maintained by TCGA GDAC Team (Broad Institute/MD Anderson Cancer Center/Harvard Medical School)
Cite as Broad Institute TCGA Genome Data Analysis Center (2015): Correlation between copy number variations of arm-level result and selected clinical features. Broad Institute of MIT and Harvard. doi:10.7908/C1JH3KDR
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 82 arm-level events and 8 clinical features across 573 patients, 27 significant findings detected with Q value < 0.25.

  • 1q gain cnv correlated to 'YEARS_TO_BIRTH'.

  • 2p gain cnv correlated to 'YEARS_TO_BIRTH'.

  • 2q gain cnv correlated to 'YEARS_TO_BIRTH'.

  • 3p gain cnv correlated to 'YEARS_TO_BIRTH'.

  • 3q gain cnv correlated to 'YEARS_TO_BIRTH'.

  • 5p gain cnv correlated to 'YEARS_TO_BIRTH'.

  • 6p gain cnv correlated to 'YEARS_TO_BIRTH'.

  • 6q gain cnv correlated to 'YEARS_TO_BIRTH'.

  • 7p gain cnv correlated to 'YEARS_TO_BIRTH'.

  • 7q gain cnv correlated to 'YEARS_TO_BIRTH'.

  • 10p gain cnv correlated to 'YEARS_TO_BIRTH'.

  • 10q gain cnv correlated to 'YEARS_TO_BIRTH'.

  • 12p gain cnv correlated to 'YEARS_TO_BIRTH'.

  • 12q gain cnv correlated to 'YEARS_TO_BIRTH' and 'KARNOFSKY_PERFORMANCE_SCORE'.

  • 20p gain cnv correlated to 'YEARS_TO_BIRTH'.

  • 20q gain cnv correlated to 'YEARS_TO_BIRTH'.

  • 21q gain cnv correlated to 'YEARS_TO_BIRTH'.

  • 3p loss cnv correlated to 'YEARS_TO_BIRTH'.

  • 8q loss cnv correlated to 'YEARS_TO_BIRTH'.

  • 9q loss cnv correlated to 'YEARS_TO_BIRTH'.

  • 11p loss cnv correlated to 'YEARS_TO_BIRTH'.

  • 14q loss cnv correlated to 'YEARS_TO_BIRTH'.

  • 15q loss cnv correlated to 'YEARS_TO_BIRTH'.

  • 16q loss cnv correlated to 'YEARS_TO_BIRTH'.

  • xp loss cnv correlated to 'YEARS_TO_BIRTH'.

  • xq loss cnv correlated to 'YEARS_TO_BIRTH'.

Results
Overview of the results

Table 1.  Get Full Table Overview of the association between significant copy number variation of 82 arm-level events and 8 clinical features. Shown in the table are P values (Q values). Thresholded by Q value < 0.25, 27 significant findings detected.

Clinical
Features 		Time
to
Death 		YEARS
TO
BIRTH 		TUMOR
TISSUE
SITE 		RADIATION
THERAPY 		KARNOFSKY
PERFORMANCE
SCORE 		RESIDUAL
TUMOR 		RACE ETHNICITY
nCNV (%) nWild-Type logrank test Wilcoxon-test Fisher's exact test Fisher's exact test Wilcoxon-test Fisher's exact test Fisher's exact test Fisher's exact test
12q gain 176 (31%) 397 0.339
(1.00) 		9.49e-08
(2.08e-05) 		0.0444
(0.595) 		0.177
(0.867) 		0.00809
(0.212) 		0.191
(0.886) 		0.103
(0.728) 		0.462
(1.00)
1q gain 219 (38%) 354 0.574
(1.00) 		0.000775
(0.0299) 		0.126
(0.797) 		0.162
(0.852) 		0.0748
(0.681) 		0.678
(1.00) 		0.663
(1.00) 		0.74
(1.00)
2p gain 184 (32%) 389 0.0983
(0.723) 		3.44e-06
(0.000323) 		1
(1.00) 		0.332
(1.00) 		0.858
(1.00) 		0.708
(1.00) 		0.444
(1.00) 		1
(1.00)
2q gain 153 (27%) 420 0.199
(0.902) 		0.000717
(0.0294) 		0.77
(1.00) 		1
(1.00) 		0.494
(1.00) 		1
(1.00) 		0.352
(1.00) 		0.706
(1.00)
3p gain 160 (28%) 413 0.549
(1.00) 		0.00419
(0.12) 		0.403
(1.00) 		1
(1.00) 		0.423
(1.00) 		0.325
(1.00) 		0.232
(0.952) 		1
(1.00)
3q gain 272 (47%) 301 0.388
(1.00) 		2.46e-07
(4.04e-05) 		0.42
(1.00) 		0.373
(1.00) 		0.819
(1.00) 		0.649
(1.00) 		0.804
(1.00) 		0.521
(1.00)
5p gain 197 (34%) 376 0.519
(1.00) 		0.00624
(0.171) 		0.101
(0.723) 		0.666
(1.00) 		0.483
(1.00) 		0.0683
(0.681) 		0.502
(1.00) 		1
(1.00)
6p gain 168 (29%) 405 0.199
(0.902) 		6.07e-06
(0.000498) 		0.781
(1.00) 		1
(1.00) 		0.0602
(0.659) 		1
(1.00) 		0.386
(1.00) 		0.729
(1.00)
6q gain 97 (17%) 476 0.492
(1.00) 		0.000197
(0.0108) 		1
(1.00) 		0.594
(1.00) 		0.232
(0.952) 		0.789
(1.00) 		0.175
(0.867) 		0.674
(1.00)
7p gain 179 (31%) 394 0.972
(1.00) 		0.000706
(0.0294) 		0.308
(1.00) 		0.645
(1.00) 		0.162
(0.852) 		0.87
(1.00) 		0.089
(0.721) 		0.176
(0.867)
7q gain 199 (35%) 374 0.475
(1.00) 		0.00175
(0.0604) 		1
(1.00) 		0.665
(1.00) 		0.192
(0.886) 		1
(1.00) 		0.108
(0.73) 		1
(1.00)
10p gain 186 (32%) 387 0.473
(1.00) 		1.7e-08
(5.59e-06) 		0.0568
(0.656) 		0.666
(1.00) 		0.449
(1.00) 		0.854
(1.00) 		0.682
(1.00) 		0.507
(1.00)
10q gain 109 (19%) 464 0.798
(1.00) 		0.000641
(0.0294) 		0.0703
(0.681) 		0.588
(1.00) 		0.915
(1.00) 		0.742
(1.00) 		0.934
(1.00) 		1
(1.00)
12p gain 254 (44%) 319 0.695
(1.00) 		5.96e-10
(3.91e-07) 		0.235
(0.953) 		0.661
(1.00) 		0.0793
(0.69) 		0.93
(1.00) 		0.347
(1.00) 		0.327
(1.00)
20p gain 287 (50%) 286 0.0175
(0.349) 		1.08e-06
(0.000118) 		0.248
(0.967) 		0.681
(1.00) 		0.253
(0.981) 		0.497
(1.00) 		0.13
(0.799) 		0.752
(1.00)
20q gain 326 (57%) 247 0.0752
(0.681) 		3.64e-05
(0.00266) 		0.397
(1.00) 		1
(1.00) 		0.235
(0.953) 		0.597
(1.00) 		0.0299
(0.491) 		0.353
(1.00)
21q gain 109 (19%) 464 0.984
(1.00) 		0.00109
(0.0396) 		0.042
(0.574) 		0.589
(1.00) 		0.423
(1.00) 		0.438
(1.00) 		0.657
(1.00) 		0.684
(1.00)
3p loss 94 (16%) 479 0.569
(1.00) 		0.00983
(0.239) 		0.601
(1.00) 		1
(1.00) 		0.525
(1.00) 		0.244
(0.961) 		0.341
(1.00) 		1
(1.00)
8q loss 89 (16%) 484 0.332
(1.00) 		0.00345
(0.103) 		1
(1.00) 		0.574
(1.00) 		0.344
(1.00) 		0.518
(1.00) 		0.711
(1.00) 		0.643
(1.00)
9q loss 286 (50%) 287 0.706
(1.00) 		7.42e-07
(9.73e-05) 		0.432
(1.00) 		1
(1.00) 		0.979
(1.00) 		0.74
(1.00) 		0.491
(1.00) 		1
(1.00)
11p loss 196 (34%) 377 0.99
(1.00) 		0.00316
(0.0986) 		1
(1.00) 		1
(1.00) 		0.517
(1.00) 		0.779
(1.00) 		0.472
(1.00) 		0.731
(1.00)
14q loss 214 (37%) 359 0.463
(1.00) 		0.000613
(0.0294) 		1
(1.00) 		1
(1.00) 		0.578
(1.00) 		0.455
(1.00) 		0.665
(1.00) 		0.188
(0.886)
15q loss 276 (48%) 297 0.704
(1.00) 		0.000192
(0.0108) 		0.422
(1.00) 		1
(1.00) 		0.481
(1.00) 		0.678
(1.00) 		0.399
(1.00) 		0.525
(1.00)
16q loss 409 (71%) 164 0.0944
(0.723) 		5.54e-05
(0.00363) 		1
(1.00) 		1
(1.00) 		0.113
(0.75) 		0.573
(1.00) 		0.889
(1.00) 		0.159
(0.852)
xp loss 322 (56%) 251 0.77
(1.00) 		0.00978
(0.239) 		0.317
(1.00) 		0.396
(1.00) 		0.933
(1.00) 		0.521
(1.00) 		0.67
(1.00) 		0.759
(1.00)
xq loss 277 (48%) 296 0.631
(1.00) 		0.00223
(0.0731) 		0.624
(1.00) 		0.204
(0.908) 		0.26
(0.998) 		0.653
(1.00) 		0.155
(0.85) 		0.753
(1.00)
1p gain 168 (29%) 405 0.179
(0.867) 		0.0768
(0.681) 		0.775
(1.00) 		0.635
(1.00) 		0.147
(0.824) 		0.433
(1.00) 		0.853
(1.00) 		0.461
(1.00)
4p gain 60 (10%) 513 0.0417
(0.574) 		0.0287
(0.491) 		0.0885
(0.721) 		0.097
(0.723) 		0.475
(1.00) 		0.707
(1.00) 		0.784
(1.00) 		0.255
(0.985)
4q gain 32 (6%) 541 0.135
(0.799) 		0.0482
(0.62) 		1
(1.00) 		0.265
(1.00) 		0.168
(0.856) 		0.53
(1.00) 		0.462
(1.00)
5q gain 60 (10%) 513 0.802
(1.00) 		0.191
(0.886) 		0.218
(0.912) 		1
(1.00) 		0.148
(0.824) 		0.1
(0.723) 		0.916
(1.00) 		1
(1.00)
8p gain 118 (21%) 455 0.948
(1.00) 		0.801
(1.00) 		0.442
(1.00) 		0.589
(1.00) 		0.551
(1.00) 		0.655
(1.00) 		0.471
(1.00) 		1
(1.00)
8q gain 240 (42%) 333 0.423
(1.00) 		0.116
(0.761) 		0.303
(1.00) 		0.403
(1.00) 		0.923
(1.00) 		0.283
(1.00) 		0.131
(0.799) 		0.528
(1.00)
9p gain 89 (16%) 484 0.508
(1.00) 		0.851
(1.00) 		1
(1.00) 		0.579
(1.00) 		0.682
(1.00) 		0.79
(1.00) 		0.695
(1.00) 		0.369
(1.00)
9q gain 43 (8%) 530 0.678
(1.00) 		0.208
(0.911) 		1
(1.00) 		0.339
(1.00) 		0.542
(1.00) 		1
(1.00) 		0.205
(0.908) 		1
(1.00)
11p gain 76 (13%) 497 0.148
(0.824) 		0.7
(1.00) 		1
(1.00) 		0.511
(1.00) 		0.527
(1.00) 		0.447
(1.00) 		0.315
(1.00) 		1
(1.00)
11q gain 112 (20%) 461 0.965
(1.00) 		0.762
(1.00) 		1
(1.00) 		0.589
(1.00) 		0.727
(1.00) 		0.241
(0.961) 		0.952
(1.00) 		0.218
(0.912)
13q gain 60 (10%) 513 0.572
(1.00) 		0.0159
(0.326) 		1
(1.00) 		1
(1.00) 		0.0566
(0.656) 		0.547
(1.00) 		0.844
(1.00) 		0.611
(1.00)
14q gain 58 (10%) 515 0.181
(0.867) 		0.22
(0.912) 		1
(1.00) 		0.427
(1.00) 		0.766
(1.00) 		0.859
(1.00) 		0.875
(1.00) 		0.608
(1.00)
15q gain 39 (7%) 534 0.0901
(0.721) 		0.908
(1.00) 		1
(1.00) 		1
(1.00) 		0.134
(0.799) 		1
(1.00) 		1
(1.00)
16p gain 59 (10%) 514 0.841
(1.00) 		0.191
(0.886) 		1
(1.00) 		1
(1.00) 		0.0528
(0.656) 		0.12
(0.78) 		0.879
(1.00) 		1
(1.00)
16q gain 31 (5%) 542 0.686
(1.00) 		0.948
(1.00) 		1
(1.00) 		1
(1.00) 		0.162
(0.852) 		0.22
(0.912) 		0.727
(1.00) 		1
(1.00)
17p gain 22 (4%) 551 0.0478
(0.62) 		0.443
(1.00) 		1
(1.00) 		1
(1.00) 		0.923
(1.00) 		0.423
(1.00) 		1
(1.00)
17q gain 47 (8%) 526 0.361
(1.00) 		0.447
(1.00) 		1
(1.00) 		1
(1.00) 		0.451
(1.00) 		0.0933
(0.723) 		0.392
(1.00) 		1
(1.00)
18p gain 120 (21%) 453 0.0293
(0.491) 		0.0356
(0.54) 		1
(1.00) 		0.589
(1.00) 		0.672
(1.00) 		0.363
(1.00) 		0.971
(1.00) 		1
(1.00)
18q gain 72 (13%) 501 0.0573
(0.656) 		0.506
(1.00) 		1
(1.00) 		1
(1.00) 		0.973
(1.00) 		0.859
(1.00) 		0.635
(1.00) 		0.615
(1.00)
19p gain 169 (29%) 404 0.844
(1.00) 		0.0708
(0.681) 		0.781
(1.00) 		0.161
(0.852) 		0.449
(1.00) 		0.36
(1.00) 		0.395
(1.00) 		0.73
(1.00)
19q gain 160 (28%) 413 0.27
(1.00) 		0.0143
(0.321) 		0.0996
(0.723) 		0.133
(0.799) 		0.752
(1.00) 		0.458
(1.00) 		0.0547
(0.656) 		1
(1.00)
22q gain 24 (4%) 549 0.081
(0.69) 		0.691
(1.00) 		0.195
(0.893) 		1
(1.00) 		0.476
(1.00) 		1
(1.00) 		0.577
(1.00) 		1
(1.00)
xp gain 78 (14%) 495 0.82
(1.00) 		0.138
(0.801) 		0.0339
(0.529) 		0.516
(1.00) 		0.772
(1.00) 		0.132
(0.799) 		0.723
(1.00) 		1
(1.00)
xq gain 108 (19%) 465 0.756
(1.00) 		0.178
(0.867) 		0.0242
(0.433) 		0.589
(1.00) 		0.692
(1.00) 		1
(1.00) 		0.618
(1.00) 		1
(1.00)
1p loss 64 (11%) 509 0.942
(1.00) 		0.289
(1.00) 		1
(1.00) 		0.452
(1.00) 		0.148
(0.824) 		0.857
(1.00) 		0.592
(1.00) 		0.314
(1.00)
1q loss 43 (8%) 530 0.497
(1.00) 		0.408
(1.00) 		1
(1.00) 		0.31
(1.00) 		0.181
(0.867) 		0.586
(1.00) 		0.376
(1.00) 		0.542
(1.00)
2p loss 53 (9%) 520 0.801
(1.00) 		0.503
(1.00) 		1
(1.00) 		1
(1.00) 		0.166
(0.853) 		0.904
(1.00) 		0.608
(1.00)
2q loss 59 (10%) 514 0.863
(1.00) 		0.0187
(0.362) 		0.219
(0.912) 		1
(1.00) 		0.522
(1.00) 		0.657
(1.00) 		0.794
(1.00) 		0.609
(1.00)
3q loss 43 (8%) 530 0.683
(1.00) 		0.126
(0.797) 		0.33
(1.00) 		0.31
(1.00) 		0.831
(1.00) 		0.765
(1.00) 		0.542
(1.00)
4p loss 313 (55%) 260 0.935
(1.00) 		0.794
(1.00) 		0.41
(1.00) 		1
(1.00) 		0.242
(0.961) 		0.869
(1.00) 		0.554
(1.00) 		1
(1.00)
4q loss 359 (63%) 214 0.869
(1.00) 		0.824
(1.00) 		1
(1.00) 		0.655
(1.00) 		0.781
(1.00) 		0.836
(1.00) 		0.428
(1.00) 		0.326
(1.00)
5p loss 131 (23%) 442 0.983
(1.00) 		0.0244
(0.433) 		0.731
(1.00) 		0.594
(1.00) 		0.0388
(0.553) 		0.123
(0.794) 		0.841
(1.00) 		0.705
(1.00)
5q loss 221 (39%) 352 0.375
(1.00) 		0.0152
(0.321) 		1
(1.00) 		1
(1.00) 		0.0537
(0.656) 		0.15
(0.829) 		0.928
(1.00) 		0.527
(1.00)
6p loss 163 (28%) 410 0.245
(0.961) 		0.0693
(0.681) 		1
(1.00) 		0.62
(1.00) 		0.974
(1.00) 		0.281
(1.00) 		0.425
(1.00) 		0.73
(1.00)
6q loss 238 (42%) 335 0.734
(1.00) 		0.058
(0.656) 		0.501
(1.00) 		1
(1.00) 		0.631
(1.00) 		0.429
(1.00) 		0.0799
(0.69) 		0.524
(1.00)
7p loss 120 (21%) 453 0.912
(1.00) 		0.908
(1.00) 		0.447
(1.00) 		0.59
(1.00) 		0.0995
(0.723) 		0.541
(1.00) 		0.782
(1.00) 		0.694
(1.00)
7q loss 81 (14%) 492 0.707
(1.00) 		0.211
(0.911) 		0.309
(1.00) 		0.554
(1.00) 		0.134
(0.799) 		0.55
(1.00) 		0.362
(1.00) 		0.371
(1.00)
8p loss 273 (48%) 300 0.322
(1.00) 		0.0309
(0.494) 		0.517
(1.00) 		1
(1.00) 		0.204
(0.908) 		0.299
(1.00) 		0.836
(1.00) 		0.522
(1.00)
9p loss 262 (46%) 311 0.86
(1.00) 		0.013
(0.304) 		0.41
(1.00) 		1
(1.00) 		0.76
(1.00) 		0.211
(0.911) 		0.752
(1.00) 		0.526
(1.00)
10p loss 96 (17%) 477 0.514
(1.00) 		0.146
(0.824) 		1
(1.00) 		0.596
(1.00) 		0.745
(1.00) 		0.631
(1.00) 		0.369
(1.00) 		1
(1.00)
10q loss 124 (22%) 449 0.863
(1.00) 		0.0859
(0.721) 		0.453
(1.00) 		0.287
(1.00) 		0.956
(1.00) 		1
(1.00) 		0.487
(1.00) 		0.694
(1.00)
11q loss 148 (26%) 425 0.759
(1.00) 		0.0148
(0.321) 		0.543
(1.00) 		0.608
(1.00) 		0.0738
(0.681) 		0.867
(1.00) 		0.453
(1.00) 		0.708
(1.00)
12p loss 78 (14%) 495 0.72
(1.00) 		0.0725
(0.681) 		1
(1.00) 		1
(1.00) 		0.632
(1.00) 		1
(1.00) 		0.281
(1.00) 		1
(1.00)
12q loss 103 (18%) 470 0.272
(1.00) 		0.331
(1.00) 		1
(1.00) 		0.59
(1.00) 		0.449
(1.00) 		0.621
(1.00) 		0.855
(1.00) 		1
(1.00)
13q loss 306 (53%) 267 0.485
(1.00) 		0.576
(1.00) 		0.514
(1.00) 		0.672
(1.00) 		0.987
(1.00) 		0.598
(1.00) 		0.705
(1.00) 		0.522
(1.00)
16p loss 331 (58%) 242 0.453
(1.00) 		0.166
(0.853) 		1
(1.00) 		0.0737
(0.681) 		0.991
(1.00) 		1
(1.00) 		0.431
(1.00) 		0.0981
(0.723)
17p loss 474 (83%) 99 0.651
(1.00) 		0.32
(1.00) 		0.206
(0.908) 		1
(1.00) 		0.613
(1.00) 		0.295
(1.00) 		0.98
(1.00) 		0.385
(1.00)
17q loss 380 (66%) 193 0.764
(1.00) 		0.579
(1.00) 		1
(1.00) 		0.668
(1.00) 		0.0221
(0.414) 		0.37
(1.00) 		0.778
(1.00) 		0.0961
(0.723)
18p loss 231 (40%) 342 0.0603
(0.659) 		0.946
(1.00) 		0.496
(1.00) 		0.165
(0.853) 		0.541
(1.00) 		0.346
(1.00) 		0.0373
(0.544) 		1
(1.00)
18q loss 289 (50%) 284 0.0768
(0.681) 		0.326
(1.00) 		0.434
(1.00) 		0.373
(1.00) 		0.53
(1.00) 		0.265
(1.00) 		0.0748
(0.681) 		0.214
(0.912)
19p loss 184 (32%) 389 0.666
(1.00) 		0.0362
(0.54) 		0.323
(1.00) 		1
(1.00) 		0.361
(1.00) 		0.276
(1.00) 		0.522
(1.00) 		0.735
(1.00)
19q loss 176 (31%) 397 0.566
(1.00) 		0.518
(1.00) 		0.294
(1.00) 		1
(1.00) 		0.0686
(0.681) 		0.109
(0.73) 		0.513
(1.00) 		0.513
(1.00)
20p loss 49 (9%) 524 0.109
(0.73) 		0.396
(1.00) 		1
(1.00) 		0.381
(1.00) 		0.421
(1.00) 		0.107
(0.73) 		0.77
(1.00) 		0.244
(0.961)
20q loss 32 (6%) 541 0.138
(0.801) 		0.879
(1.00) 		1
(1.00) 		1
(1.00) 		0.476
(1.00) 		1
(1.00) 		0.479
(1.00)
21q loss 195 (34%) 378 0.737
(1.00) 		0.307
(1.00) 		0.798
(1.00) 		0.662
(1.00) 		0.173
(0.867) 		1
(1.00) 		0.507
(1.00) 		0.752
(1.00)
22q loss 428 (75%) 145 0.108
(0.73) 		0.0876
(0.721) 		0.536
(1.00) 		0.336
(1.00) 		0.431
(1.00) 		0.0656
(0.681) 		1
(1.00) 		1
(1.00)
'1q gain' versus 'YEARS_TO_BIRTH'

P value = 0.000775 (Wilcoxon-test), Q value = 0.03

Table S1.  Gene #2: '1q gain' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 552 59.8 (11.6)
1Q GAIN MUTATED 209 61.9 (10.7)
1Q GAIN WILD-TYPE 343 58.6 (11.9)

Figure S1.  Get High-res Image Gene #2: '1q gain' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'2p gain' versus 'YEARS_TO_BIRTH'

P value = 3.44e-06 (Wilcoxon-test), Q value = 0.00032

Table S2.  Gene #3: '2p gain' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 552 59.8 (11.6)
2P GAIN MUTATED 175 63.3 (11.2)
2P GAIN WILD-TYPE 377 58.2 (11.4)

Figure S2.  Get High-res Image Gene #3: '2p gain' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'2q gain' versus 'YEARS_TO_BIRTH'

P value = 0.000717 (Wilcoxon-test), Q value = 0.029

Table S3.  Gene #4: '2q gain' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 552 59.8 (11.6)
2Q GAIN MUTATED 146 62.6 (11.1)
2Q GAIN WILD-TYPE 406 58.8 (11.6)

Figure S3.  Get High-res Image Gene #4: '2q gain' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'3p gain' versus 'YEARS_TO_BIRTH'

P value = 0.00419 (Wilcoxon-test), Q value = 0.12

Table S4.  Gene #5: '3p gain' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 552 59.8 (11.6)
3P GAIN MUTATED 154 62.1 (11.3)
3P GAIN WILD-TYPE 398 59.0 (11.5)

Figure S4.  Get High-res Image Gene #5: '3p gain' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'3q gain' versus 'YEARS_TO_BIRTH'

P value = 2.46e-07 (Wilcoxon-test), Q value = 4e-05

Table S5.  Gene #6: '3q gain' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 552 59.8 (11.6)
3Q GAIN MUTATED 265 62.5 (11.1)
3Q GAIN WILD-TYPE 287 57.4 (11.5)

Figure S5.  Get High-res Image Gene #6: '3q gain' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'5p gain' versus 'YEARS_TO_BIRTH'

P value = 0.00624 (Wilcoxon-test), Q value = 0.17

Table S6.  Gene #9: '5p gain' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 552 59.8 (11.6)
5P GAIN MUTATED 192 61.7 (11.7)
5P GAIN WILD-TYPE 360 58.8 (11.4)

Figure S6.  Get High-res Image Gene #9: '5p gain' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'6p gain' versus 'YEARS_TO_BIRTH'

P value = 6.07e-06 (Wilcoxon-test), Q value = 5e-04

Table S7.  Gene #11: '6p gain' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 552 59.8 (11.6)
6P GAIN MUTATED 164 63.2 (10.9)
6P GAIN WILD-TYPE 388 58.4 (11.6)

Figure S7.  Get High-res Image Gene #11: '6p gain' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'6q gain' versus 'YEARS_TO_BIRTH'

P value = 0.000197 (Wilcoxon-test), Q value = 0.011

Table S8.  Gene #12: '6q gain' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 552 59.8 (11.6)
6Q GAIN MUTATED 93 63.8 (10.6)
6Q GAIN WILD-TYPE 459 59.0 (11.6)

Figure S8.  Get High-res Image Gene #12: '6q gain' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'7p gain' versus 'YEARS_TO_BIRTH'

P value = 0.000706 (Wilcoxon-test), Q value = 0.029

Table S9.  Gene #13: '7p gain' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 552 59.8 (11.6)
7P GAIN MUTATED 171 62.3 (10.8)
7P GAIN WILD-TYPE 381 58.7 (11.7)

Figure S9.  Get High-res Image Gene #13: '7p gain' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'7q gain' versus 'YEARS_TO_BIRTH'

P value = 0.00175 (Wilcoxon-test), Q value = 0.06

Table S10.  Gene #14: '7q gain' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 552 59.8 (11.6)
7Q GAIN MUTATED 190 62.0 (11.2)
7Q GAIN WILD-TYPE 362 58.7 (11.6)

Figure S10.  Get High-res Image Gene #14: '7q gain' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'10p gain' versus 'YEARS_TO_BIRTH'

P value = 1.7e-08 (Wilcoxon-test), Q value = 5.6e-06

Table S11.  Gene #19: '10p gain' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 552 59.8 (11.6)
10P GAIN MUTATED 180 63.7 (10.9)
10P GAIN WILD-TYPE 372 58.0 (11.4)

Figure S11.  Get High-res Image Gene #19: '10p gain' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'10q gain' versus 'YEARS_TO_BIRTH'

P value = 0.000641 (Wilcoxon-test), Q value = 0.029

Table S12.  Gene #20: '10q gain' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 552 59.8 (11.6)
10Q GAIN MUTATED 105 63.2 (11.1)
10Q GAIN WILD-TYPE 447 59.0 (11.5)

Figure S12.  Get High-res Image Gene #20: '10q gain' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'12p gain' versus 'YEARS_TO_BIRTH'

P value = 5.96e-10 (Wilcoxon-test), Q value = 3.9e-07

Table S13.  Gene #23: '12p gain' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 552 59.8 (11.6)
12P GAIN MUTATED 241 63.3 (11.1)
12P GAIN WILD-TYPE 311 57.1 (11.2)

Figure S13.  Get High-res Image Gene #23: '12p gain' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'12q gain' versus 'YEARS_TO_BIRTH'

P value = 9.49e-08 (Wilcoxon-test), Q value = 2.1e-05

Table S14.  Gene #24: '12q gain' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 552 59.8 (11.6)
12Q GAIN MUTATED 166 63.7 (10.3)
12Q GAIN WILD-TYPE 386 58.2 (11.7)

Figure S14.  Get High-res Image Gene #24: '12q gain' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'12q gain' versus 'KARNOFSKY_PERFORMANCE_SCORE'

P value = 0.00809 (Wilcoxon-test), Q value = 0.21

Table S15.  Gene #24: '12q gain' versus Clinical Feature #5: 'KARNOFSKY_PERFORMANCE_SCORE'

nPatients Mean (Std.Dev)
ALL 82 75.7 (13.9)
12Q GAIN MUTATED 17 83.5 (10.6)
12Q GAIN WILD-TYPE 65 73.7 (14.0)

Figure S15.  Get High-res Image Gene #24: '12q gain' versus Clinical Feature #5: 'KARNOFSKY_PERFORMANCE_SCORE'

'20p gain' versus 'YEARS_TO_BIRTH'

P value = 1.08e-06 (Wilcoxon-test), Q value = 0.00012

Table S16.  Gene #36: '20p gain' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 552 59.8 (11.6)
20P GAIN MUTATED 278 62.2 (11.5)
20P GAIN WILD-TYPE 274 57.4 (11.1)

Figure S16.  Get High-res Image Gene #36: '20p gain' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'20q gain' versus 'YEARS_TO_BIRTH'

P value = 3.64e-05 (Wilcoxon-test), Q value = 0.0027

Table S17.  Gene #37: '20q gain' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 552 59.8 (11.6)
20Q GAIN MUTATED 315 61.6 (11.8)
20Q GAIN WILD-TYPE 237 57.4 (10.9)

Figure S17.  Get High-res Image Gene #37: '20q gain' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'21q gain' versus 'YEARS_TO_BIRTH'

P value = 0.00109 (Wilcoxon-test), Q value = 0.04

Table S18.  Gene #38: '21q gain' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 552 59.8 (11.6)
21Q GAIN MUTATED 106 63.1 (10.5)
21Q GAIN WILD-TYPE 446 59.1 (11.7)

Figure S18.  Get High-res Image Gene #38: '21q gain' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'3p loss' versus 'YEARS_TO_BIRTH'

P value = 0.00983 (Wilcoxon-test), Q value = 0.24

Table S19.  Gene #46: '3p loss' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 552 59.8 (11.6)
3P LOSS MUTATED 92 62.8 (11.6)
3P LOSS WILD-TYPE 460 59.2 (11.5)

Figure S19.  Get High-res Image Gene #46: '3p loss' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'8q loss' versus 'YEARS_TO_BIRTH'

P value = 0.00345 (Wilcoxon-test), Q value = 0.1

Table S20.  Gene #57: '8q loss' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 552 59.8 (11.6)
8Q LOSS MUTATED 85 63.1 (11.5)
8Q LOSS WILD-TYPE 467 59.2 (11.5)

Figure S20.  Get High-res Image Gene #57: '8q loss' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'9q loss' versus 'YEARS_TO_BIRTH'

P value = 7.42e-07 (Wilcoxon-test), Q value = 9.7e-05

Table S21.  Gene #59: '9q loss' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 552 59.8 (11.6)
9Q LOSS MUTATED 272 62.3 (11.3)
9Q LOSS WILD-TYPE 280 57.4 (11.3)

Figure S21.  Get High-res Image Gene #59: '9q loss' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'11p loss' versus 'YEARS_TO_BIRTH'

P value = 0.00316 (Wilcoxon-test), Q value = 0.099

Table S22.  Gene #62: '11p loss' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 552 59.8 (11.6)
11P LOSS MUTATED 189 61.9 (11.5)
11P LOSS WILD-TYPE 363 58.8 (11.5)

Figure S22.  Get High-res Image Gene #62: '11p loss' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'14q loss' versus 'YEARS_TO_BIRTH'

P value = 0.000613 (Wilcoxon-test), Q value = 0.029

Table S23.  Gene #67: '14q loss' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 552 59.8 (11.6)
14Q LOSS MUTATED 208 62.0 (11.5)
14Q LOSS WILD-TYPE 344 58.5 (11.5)

Figure S23.  Get High-res Image Gene #67: '14q loss' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'15q loss' versus 'YEARS_TO_BIRTH'

P value = 0.000192 (Wilcoxon-test), Q value = 0.011

Table S24.  Gene #68: '15q loss' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 552 59.8 (11.6)
15Q LOSS MUTATED 268 61.7 (11.3)
15Q LOSS WILD-TYPE 284 58.1 (11.5)

Figure S24.  Get High-res Image Gene #68: '15q loss' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'16q loss' versus 'YEARS_TO_BIRTH'

P value = 5.54e-05 (Wilcoxon-test), Q value = 0.0036

Table S25.  Gene #70: '16q loss' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 552 59.8 (11.6)
16Q LOSS MUTATED 394 61.1 (11.3)
16Q LOSS WILD-TYPE 158 56.6 (11.5)

Figure S25.  Get High-res Image Gene #70: '16q loss' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'xp loss' versus 'YEARS_TO_BIRTH'

P value = 0.00978 (Wilcoxon-test), Q value = 0.24

Table S26.  Gene #81: 'xp loss' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 552 59.8 (11.6)
XP LOSS MUTATED 310 58.8 (11.5)
XP LOSS WILD-TYPE 242 61.2 (11.5)

Figure S26.  Get High-res Image Gene #81: 'xp loss' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'xq loss' versus 'YEARS_TO_BIRTH'

P value = 0.00223 (Wilcoxon-test), Q value = 0.073

Table S27.  Gene #82: 'xq loss' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 552 59.8 (11.6)
XQ LOSS MUTATED 266 58.3 (11.5)
XQ LOSS WILD-TYPE 286 61.2 (11.5)

Figure S27.  Get High-res Image Gene #82: 'xq loss' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

Methods & Data
Input

  • Copy number data file = broad_values_by_arm.txt from GISTIC pipeline

  • Processed Copy number data file = /xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_Correlate_Genomic_Events_Preprocess/OV-TP/19783384/transformed.cor.cli.txt

  • Clinical data file = /xchip/cga/gdac-prod/tcga-gdac/jobResults/Append_Data/OV-TP/19775421/OV-TP.merged_data.txt

  • Number of patients = 573

  • Number of significantly arm-level cnvs = 82

  • Number of selected clinical features = 8

  • 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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