Correlation between copy number variations of arm-level result and selected clinical features
Ovarian Serous Cystadenocarcinoma (Primary solid tumor)
02 April 2015  |  analyses__2015_04_02
Maintainer Information
Citation Information
doi:10.7908/C1R49PTQ
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/C1R49PTQ
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, 29 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 'Time to Death' and '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'.

  • 10q loss cnv correlated to 'RADIATIONS_RADIATION_REGIMENINDICATION'.

  • 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, 29 significant findings detected.

Clinical
Features 		Time
to
Death 		YEARS
TO
BIRTH 		PRIMARY
SITE
OF
DISEASE 		KARNOFSKY
PERFORMANCE
SCORE 		RADIATIONS
RADIATION
REGIMENINDICATION 		COMPLETENESS
OF
RESECTION 		RACE ETHNICITY
nCNV (%) nWild-Type logrank test Wilcoxon-test Fisher's exact test Wilcoxon-test Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test
12q gain 176 (31%) 397 0.144
(0.824) 		9.49e-08
(2.08e-05) 		0.043
(0.542) 		0.00809
(0.212) 		1
(1.00) 		0.192
(0.877) 		0.103
(0.729) 		0.462
(1.00)
20p gain 287 (50%) 286 0.00904
(0.225) 		1.08e-06
(0.000118) 		0.247
(0.938) 		0.253
(0.942) 		1
(1.00) 		0.499
(1.00) 		0.132
(0.793) 		0.752
(1.00)
1q gain 219 (38%) 354 0.537
(1.00) 		0.000775
(0.0299) 		0.123
(0.786) 		0.0748
(0.654) 		1
(1.00) 		0.678
(1.00) 		0.663
(1.00) 		0.74
(1.00)
2p gain 184 (32%) 389 0.0673
(0.654) 		3.44e-06
(0.000323) 		1
(1.00) 		0.858
(1.00) 		1
(1.00) 		0.708
(1.00) 		0.446
(1.00) 		1
(1.00)
2q gain 153 (27%) 420 0.129
(0.793) 		0.000717
(0.0294) 		0.765
(1.00) 		0.494
(1.00) 		0.175
(0.861) 		1
(1.00) 		0.352
(1.00) 		0.706
(1.00)
3p gain 160 (28%) 413 0.632
(1.00) 		0.00419
(0.12) 		0.404
(1.00) 		0.423
(1.00) 		0.564
(1.00) 		0.329
(1.00) 		0.233
(0.925) 		1
(1.00)
3q gain 272 (47%) 301 0.43
(1.00) 		2.46e-07
(4.04e-05) 		0.421
(1.00) 		0.819
(1.00) 		0.251
(0.939) 		0.649
(1.00) 		0.801
(1.00) 		0.521
(1.00)
5p gain 197 (34%) 376 0.372
(1.00) 		0.00624
(0.171) 		0.0993
(0.709) 		0.483
(1.00) 		1
(1.00) 		0.0669
(0.654) 		0.502
(1.00) 		1
(1.00)
6p gain 168 (29%) 405 0.36
(1.00) 		6.07e-06
(0.000498) 		0.781
(1.00) 		0.0602
(0.648) 		0.559
(1.00) 		1
(1.00) 		0.384
(1.00) 		0.729
(1.00)
6q gain 97 (17%) 476 0.474
(1.00) 		0.000197
(0.0108) 		1
(1.00) 		0.232
(0.925) 		1
(1.00) 		0.789
(1.00) 		0.171
(0.858) 		0.674
(1.00)
7p gain 179 (31%) 394 0.977
(1.00) 		0.000706
(0.0294) 		0.308
(1.00) 		0.162
(0.852) 		0.556
(1.00) 		0.869
(1.00) 		0.088
(0.687) 		0.176
(0.861)
7q gain 199 (35%) 374 0.41
(1.00) 		0.00175
(0.0604) 		1
(1.00) 		0.192
(0.877) 		0.555
(1.00) 		1
(1.00) 		0.109
(0.75) 		1
(1.00)
10p gain 186 (32%) 387 0.34
(1.00) 		1.7e-08
(5.59e-06) 		0.0568
(0.634) 		0.449
(1.00) 		0.247
(0.938) 		0.855
(1.00) 		0.68
(1.00) 		0.507
(1.00)
10q gain 109 (19%) 464 0.557
(1.00) 		0.000641
(0.0294) 		0.0694
(0.654) 		0.915
(1.00) 		1
(1.00) 		0.74
(1.00) 		0.934
(1.00) 		1
(1.00)
12p gain 254 (44%) 319 0.316
(1.00) 		5.96e-10
(3.91e-07) 		0.235
(0.925) 		0.0793
(0.667) 		1
(1.00) 		0.932
(1.00) 		0.35
(1.00) 		0.327
(1.00)
20q gain 326 (57%) 247 0.0336
(0.479) 		3.64e-05
(0.00266) 		0.402
(1.00) 		0.235
(0.925) 		1
(1.00) 		0.598
(1.00) 		0.0294
(0.459) 		0.353
(1.00)
21q gain 109 (19%) 464 0.964
(1.00) 		0.00109
(0.0396) 		0.0412
(0.53) 		0.423
(1.00) 		1
(1.00) 		0.437
(1.00) 		0.657
(1.00) 		0.684
(1.00)
3p loss 94 (16%) 479 0.955
(1.00) 		0.00983
(0.225) 		0.598
(1.00) 		0.525
(1.00) 		0.416
(1.00) 		0.245
(0.938) 		0.342
(1.00) 		1
(1.00)
8q loss 89 (16%) 484 0.111
(0.75) 		0.00345
(0.103) 		1
(1.00) 		0.344
(1.00) 		1
(1.00) 		0.519
(1.00) 		0.71
(1.00) 		0.643
(1.00)
9q loss 286 (50%) 287 0.415
(1.00) 		7.42e-07
(9.73e-05) 		0.434
(1.00) 		0.979
(1.00) 		0.624
(1.00) 		0.741
(1.00) 		0.493
(1.00) 		1
(1.00)
10q loss 124 (22%) 449 0.786
(1.00) 		0.0859
(0.687) 		0.453
(1.00) 		0.956
(1.00) 		0.00994
(0.225) 		1
(1.00) 		0.488
(1.00) 		0.694
(1.00)
11p loss 196 (34%) 377 0.869
(1.00) 		0.00316
(0.0986) 		1
(1.00) 		0.517
(1.00) 		1
(1.00) 		0.782
(1.00) 		0.474
(1.00) 		0.731
(1.00)
14q loss 214 (37%) 359 0.414
(1.00) 		0.000613
(0.0294) 		1
(1.00) 		0.578
(1.00) 		0.297
(1.00) 		0.457
(1.00) 		0.668
(1.00) 		0.188
(0.877)
15q loss 276 (48%) 297 0.64
(1.00) 		0.000192
(0.0108) 		0.421
(1.00) 		0.481
(1.00) 		0.611
(1.00) 		0.678
(1.00) 		0.397
(1.00) 		0.525
(1.00)
16q loss 409 (71%) 164 0.0854
(0.687) 		5.54e-05
(0.00363) 		1
(1.00) 		0.113
(0.75) 		0.561
(1.00) 		0.573
(1.00) 		0.889
(1.00) 		0.159
(0.846)
xp loss 322 (56%) 251 0.872
(1.00) 		0.00978
(0.225) 		0.317
(1.00) 		0.933
(1.00) 		0.26
(0.948) 		0.52
(1.00) 		0.669
(1.00) 		0.759
(1.00)
xq loss 277 (48%) 296 0.664
(1.00) 		0.00223
(0.0731) 		0.625
(1.00) 		0.26
(0.948) 		0.112
(0.75) 		0.653
(1.00) 		0.153
(0.828) 		0.753
(1.00)
1p gain 168 (29%) 405 0.19
(0.877) 		0.0768
(0.663) 		0.778
(1.00) 		0.147
(0.824) 		0.207
(0.89) 		0.432
(1.00) 		0.853
(1.00) 		0.461
(1.00)
4p gain 60 (10%) 513 0.0282
(0.459) 		0.0287
(0.459) 		0.0876
(0.687) 		0.475
(1.00) 		0.283
(0.987) 		0.705
(1.00) 		0.78
(1.00) 		0.255
(0.946)
4q gain 32 (6%) 541 0.0698
(0.654) 		0.0482
(0.596) 		1
(1.00) 		0.168
(0.856) 		0.159
(0.846) 		0.53
(1.00) 		0.462
(1.00)
5q gain 60 (10%) 513 0.931
(1.00) 		0.191
(0.877) 		0.22
(0.89) 		0.148
(0.824) 		1
(1.00) 		0.0991
(0.709) 		0.916
(1.00) 		1
(1.00)
8p gain 118 (21%) 455 0.992
(1.00) 		0.801
(1.00) 		0.439
(1.00) 		0.551
(1.00) 		0.5
(1.00) 		0.656
(1.00) 		0.471
(1.00) 		1
(1.00)
8q gain 240 (42%) 333 0.528
(1.00) 		0.116
(0.761) 		0.304
(1.00) 		0.923
(1.00) 		1
(1.00) 		0.282
(0.987) 		0.132
(0.793) 		0.528
(1.00)
9p gain 89 (16%) 484 0.458
(1.00) 		0.851
(1.00) 		1
(1.00) 		0.682
(1.00) 		0.398
(1.00) 		0.791
(1.00) 		0.694
(1.00) 		0.369
(1.00)
9q gain 43 (8%) 530 0.7
(1.00) 		0.208
(0.89) 		1
(1.00) 		0.542
(1.00) 		0.209
(0.89) 		1
(1.00) 		0.206
(0.89) 		1
(1.00)
11p gain 76 (13%) 497 0.099
(0.709) 		0.7
(1.00) 		1
(1.00) 		0.527
(1.00) 		0.348
(1.00) 		0.447
(1.00) 		0.318
(1.00) 		1
(1.00)
11q gain 112 (20%) 461 0.841
(1.00) 		0.762
(1.00) 		1
(1.00) 		0.727
(1.00) 		1
(1.00) 		0.242
(0.938) 		0.954
(1.00) 		0.218
(0.89)
13q gain 60 (10%) 513 0.745
(1.00) 		0.0159
(0.307) 		1
(1.00) 		0.0566
(0.634) 		0.283
(0.987) 		0.55
(1.00) 		0.845
(1.00) 		0.611
(1.00)
14q gain 58 (10%) 515 0.032
(0.476) 		0.22
(0.89) 		1
(1.00) 		0.766
(1.00) 		0.0283
(0.459) 		0.855
(1.00) 		0.875
(1.00) 		0.608
(1.00)
15q gain 39 (7%) 534 0.258
(0.948) 		0.908
(1.00) 		1
(1.00) 		0.134
(0.793) 		1
(1.00) 		1
(1.00) 		1
(1.00)
16p gain 59 (10%) 514 0.873
(1.00) 		0.191
(0.877) 		1
(1.00) 		0.0528
(0.634) 		1
(1.00) 		0.121
(0.786) 		0.878
(1.00) 		1
(1.00)
16q gain 31 (5%) 542 0.814
(1.00) 		0.948
(1.00) 		1
(1.00) 		0.162
(0.852) 		1
(1.00) 		0.219
(0.89) 		0.726
(1.00) 		1
(1.00)
17p gain 22 (4%) 551 0.171
(0.858) 		0.443
(1.00) 		1
(1.00) 		0.923
(1.00) 		1
(1.00) 		0.422
(1.00) 		1
(1.00)
17q gain 47 (8%) 526 0.552
(1.00) 		0.447
(1.00) 		1
(1.00) 		0.451
(1.00) 		1
(1.00) 		0.0923
(0.709) 		0.392
(1.00) 		1
(1.00)
18p gain 120 (21%) 453 0.152
(0.828) 		0.0356
(0.487) 		1
(1.00) 		0.672
(1.00) 		1
(1.00) 		0.365
(1.00) 		0.971
(1.00) 		1
(1.00)
18q gain 72 (13%) 501 0.279
(0.987) 		0.506
(1.00) 		1
(1.00) 		0.973
(1.00) 		1
(1.00) 		0.857
(1.00) 		0.638
(1.00) 		0.615
(1.00)
19p gain 169 (29%) 404 0.42
(1.00) 		0.0708
(0.654) 		0.78
(1.00) 		0.449
(1.00) 		0.209
(0.89) 		0.359
(1.00) 		0.397
(1.00) 		0.73
(1.00)
19q gain 160 (28%) 413 0.699
(1.00) 		0.0143
(0.302) 		0.0975
(0.709) 		0.752
(1.00) 		0.19
(0.877) 		0.458
(1.00) 		0.0551
(0.634) 		1
(1.00)
22q gain 24 (4%) 549 0.125
(0.789) 		0.691
(1.00) 		0.195
(0.882) 		0.476
(1.00) 		1
(1.00) 		1
(1.00) 		0.577
(1.00) 		1
(1.00)
xp gain 78 (14%) 495 0.588
(1.00) 		0.138
(0.8) 		0.0326
(0.476) 		0.772
(1.00) 		1
(1.00) 		0.132
(0.793) 		0.725
(1.00) 		1
(1.00)
xq gain 108 (19%) 465 0.64
(1.00) 		0.178
(0.861) 		0.0238
(0.421) 		0.692
(1.00) 		1
(1.00) 		1
(1.00) 		0.617
(1.00) 		1
(1.00)
1p loss 64 (11%) 509 0.799
(1.00) 		0.289
(0.991) 		1
(1.00) 		0.148
(0.824) 		0.3
(1.00) 		0.857
(1.00) 		0.594
(1.00) 		0.314
(1.00)
1q loss 43 (8%) 530 0.552
(1.00) 		0.408
(1.00) 		1
(1.00) 		0.181
(0.867) 		0.209
(0.89) 		0.587
(1.00) 		0.375
(1.00) 		0.542
(1.00)
2p loss 53 (9%) 520 0.745
(1.00) 		0.503
(1.00) 		1
(1.00) 		0.166
(0.856) 		1
(1.00) 		0.905
(1.00) 		0.608
(1.00)
2q loss 59 (10%) 514 0.897
(1.00) 		0.0187
(0.351) 		0.219
(0.89) 		0.522
(1.00) 		1
(1.00) 		0.652
(1.00) 		0.797
(1.00) 		0.609
(1.00)
3q loss 43 (8%) 530 0.36
(1.00) 		0.126
(0.79) 		0.329
(1.00) 		0.831
(1.00) 		0.209
(0.89) 		0.766
(1.00) 		0.542
(1.00)
4p loss 313 (55%) 260 0.663
(1.00) 		0.794
(1.00) 		0.409
(1.00) 		0.242
(0.938) 		1
(1.00) 		0.869
(1.00) 		0.554
(1.00) 		1
(1.00)
4q loss 359 (63%) 214 0.641
(1.00) 		0.824
(1.00) 		1
(1.00) 		0.781
(1.00) 		1
(1.00) 		0.833
(1.00) 		0.428
(1.00) 		0.326
(1.00)
5p loss 131 (23%) 442 0.683
(1.00) 		0.0244
(0.421) 		0.732
(1.00) 		0.0388
(0.509) 		1
(1.00) 		0.123
(0.786) 		0.841
(1.00) 		0.705
(1.00)
5q loss 221 (39%) 352 0.538
(1.00) 		0.0152
(0.302) 		1
(1.00) 		0.0537
(0.634) 		1
(1.00) 		0.151
(0.828) 		0.929
(1.00) 		0.527
(1.00)
6p loss 163 (28%) 410 0.287
(0.99) 		0.0693
(0.654) 		1
(1.00) 		0.974
(1.00) 		1
(1.00) 		0.287
(0.99) 		0.426
(1.00) 		0.73
(1.00)
6q loss 238 (42%) 335 0.599
(1.00) 		0.058
(0.634) 		0.502
(1.00) 		0.631
(1.00) 		1
(1.00) 		0.427
(1.00) 		0.0789
(0.667) 		0.524
(1.00)
7p loss 120 (21%) 453 0.828
(1.00) 		0.908
(1.00) 		0.447
(1.00) 		0.0995
(0.709) 		1
(1.00) 		0.539
(1.00) 		0.783
(1.00) 		0.694
(1.00)
7q loss 81 (14%) 492 0.339
(1.00) 		0.211
(0.89) 		0.309
(1.00) 		0.134
(0.793) 		0.368
(1.00) 		0.549
(1.00) 		0.361
(1.00) 		0.371
(1.00)
8p loss 273 (48%) 300 0.137
(0.8) 		0.0309
(0.471) 		0.521
(1.00) 		0.204
(0.89) 		1
(1.00) 		0.303
(1.00) 		0.834
(1.00) 		0.522
(1.00)
9p loss 262 (46%) 311 0.727
(1.00) 		0.013
(0.284) 		0.409
(1.00) 		0.76
(1.00) 		0.595
(1.00) 		0.212
(0.89) 		0.75
(1.00) 		0.526
(1.00)
10p loss 96 (17%) 477 0.581
(1.00) 		0.146
(0.824) 		1
(1.00) 		0.745
(1.00) 		0.424
(1.00) 		0.63
(1.00) 		0.366
(1.00) 		1
(1.00)
11q loss 148 (26%) 425 0.506
(1.00) 		0.0148
(0.302) 		0.545
(1.00) 		0.0738
(0.654) 		1
(1.00) 		0.868
(1.00) 		0.453
(1.00) 		0.708
(1.00)
12p loss 78 (14%) 495 0.927
(1.00) 		0.0725
(0.654) 		1
(1.00) 		0.632
(1.00) 		1
(1.00) 		1
(1.00) 		0.279
(0.987) 		1
(1.00)
12q loss 103 (18%) 470 0.426
(1.00) 		0.331
(1.00) 		1
(1.00) 		0.449
(1.00) 		1
(1.00) 		0.621
(1.00) 		0.856
(1.00) 		1
(1.00)
13q loss 306 (53%) 267 0.527
(1.00) 		0.576
(1.00) 		0.513
(1.00) 		0.987
(1.00) 		0.601
(1.00) 		0.604
(1.00) 		0.707
(1.00) 		0.522
(1.00)
16p loss 331 (58%) 242 0.453
(1.00) 		0.166
(0.856) 		1
(1.00) 		0.991
(1.00) 		0.267
(0.962) 		1
(1.00) 		0.434
(1.00) 		0.0981
(0.709)
17p loss 474 (83%) 99 0.832
(1.00) 		0.32
(1.00) 		0.206
(0.89) 		0.613
(1.00) 		0.435
(1.00) 		0.295
(1.00) 		0.98
(1.00) 		0.385
(1.00)
17q loss 380 (66%) 193 0.822
(1.00) 		0.579
(1.00) 		1
(1.00) 		0.0221
(0.402) 		0.554
(1.00) 		0.372
(1.00) 		0.776
(1.00) 		0.0961
(0.709)
18p loss 231 (40%) 342 0.058
(0.634) 		0.946
(1.00) 		0.498
(1.00) 		0.541
(1.00) 		0.065
(0.654) 		0.346
(1.00) 		0.0364
(0.487) 		1
(1.00)
18q loss 289 (50%) 284 0.0668
(0.654) 		0.326
(1.00) 		0.433
(1.00) 		0.53
(1.00) 		0.249
(0.938) 		0.263
(0.952) 		0.0743
(0.654) 		0.214
(0.89)
19p loss 184 (32%) 389 0.347
(1.00) 		0.0362
(0.487) 		0.324
(1.00) 		0.361
(1.00) 		0.555
(1.00) 		0.276
(0.987) 		0.522
(1.00) 		0.735
(1.00)
19q loss 176 (31%) 397 0.914
(1.00) 		0.518
(1.00) 		0.295
(1.00) 		0.0686
(0.654) 		0.556
(1.00) 		0.11
(0.75) 		0.512
(1.00) 		0.513
(1.00)
20p loss 49 (9%) 524 0.0846
(0.687) 		0.396
(1.00) 		1
(1.00) 		0.421
(1.00) 		0.236
(0.925) 		0.109
(0.75) 		0.77
(1.00) 		0.244
(0.938)
20q loss 32 (6%) 541 0.168
(0.856) 		0.879
(1.00) 		1
(1.00) 		0.476
(1.00) 		1
(1.00) 		1
(1.00) 		0.479
(1.00)
21q loss 195 (34%) 378 0.825
(1.00) 		0.307
(1.00) 		0.797
(1.00) 		0.173
(0.861) 		1
(1.00) 		1
(1.00) 		0.507
(1.00) 		0.752
(1.00)
22q loss 428 (75%) 145 0.179
(0.861) 		0.0876
(0.687) 		0.533
(1.00) 		0.431
(1.00) 		0.575
(1.00) 		0.0645
(0.654) 		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 #4: '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 #4: 'KARNOFSKY_PERFORMANCE_SCORE'

'20p gain' versus 'Time to Death'

P value = 0.00904 (logrank test), Q value = 0.22

Table S16.  Gene #36: '20p gain' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 560 292 0.3 - 180.2 (28.7)
20P GAIN MUTATED 281 163 0.3 - 152.0 (25.0)
20P GAIN WILD-TYPE 279 129 0.3 - 180.2 (29.5)

Figure S16.  Get High-res Image Gene #36: '20p gain' versus Clinical Feature #1: 'Time to Death'

'20p gain' versus 'YEARS_TO_BIRTH'

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

Table S17.  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 S17.  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 S18.  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 S18.  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 S19.  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 S19.  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 = 0.22

Table S20.  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 S20.  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 S21.  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 S21.  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 S22.  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 S22.  Get High-res Image Gene #59: '9q loss' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'10q loss' versus 'RADIATIONS_RADIATION_REGIMENINDICATION'

P value = 0.00994 (Fisher's exact test), Q value = 0.22

Table S23.  Gene #61: '10q loss' versus Clinical Feature #5: 'RADIATIONS_RADIATION_REGIMENINDICATION'

nPatients NO YES
ALL 3 570
10Q LOSS MUTATED 3 121
10Q LOSS WILD-TYPE 0 449

Figure S23.  Get High-res Image Gene #61: '10q loss' versus Clinical Feature #5: 'RADIATIONS_RADIATION_REGIMENINDICATION'

'11p loss' versus 'YEARS_TO_BIRTH'

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

Table S24.  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 S24.  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 S25.  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 S25.  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 S26.  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 S26.  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 S27.  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 S27.  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 = 0.22

Table S28.  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 S28.  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 S29.  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 S29.  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/15096464/transformed.cor.cli.txt

  • Clinical data file = /xchip/cga/gdac-prod/tcga-gdac/jobResults/Append_Data/OV-TP/15085780/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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