Correlation between copy number variations of arm-level result and selected clinical features
Ovarian Serous Cystadenocarcinoma (Primary solid tumor)
17 October 2014  |  analyses__2014_10_17
Maintainer Information
Citation Information
doi:10.7908/C13J3BV0
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/C13J3BV0
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 80 arm-level events and 8 clinical features across 571 patients, 12 significant findings detected with Q value < 0.25.

  • 2p gain cnv correlated to 'AGE'.

  • 3q gain cnv correlated to 'AGE'.

  • 6p gain cnv correlated to 'AGE'.

  • 6q gain cnv correlated to 'AGE'.

  • 10p gain cnv correlated to 'AGE'.

  • 12p gain cnv correlated to 'AGE'.

  • 12q gain cnv correlated to 'AGE'.

  • 20p gain cnv correlated to 'AGE'.

  • 20q gain cnv correlated to 'AGE'.

  • 9q loss cnv correlated to 'AGE'.

  • 15q loss cnv correlated to 'AGE'.

  • 16q loss cnv correlated to 'AGE'.

Results
Overview of the results

Table 1.  Get Full Table Overview of the association between significant copy number variation of 80 arm-level events and 8 clinical features. Shown in the table are P values (Q values). Thresholded by Q value < 0.25, 12 significant findings detected.

Clinical
Features 		Time
to
Death 		AGE 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
2p gain 183 (32%) 388 0.111
(1.00) 		3.39e-06
(0.00213) 		1
(1.00) 		0.6
(1.00) 		1
(1.00) 		0.829
(1.00) 		0.677
(1.00) 		1
(1.00)
3q gain 271 (47%) 300 0.516
(1.00) 		2.29e-07
(0.000144) 		0.178
(1.00) 		0.978
(1.00) 		0.251
(1.00) 		0.508
(1.00) 		0.708
(1.00) 		0.521
(1.00)
6p gain 166 (29%) 405 0.262
(1.00) 		7.09e-06
(0.00444) 		0.749
(1.00) 		0.113
(1.00) 		0.56
(1.00) 		1
(1.00) 		0.185
(1.00) 		0.729
(1.00)
6q gain 97 (17%) 474 0.418
(1.00) 		0.000187
(0.116) 		1
(1.00) 		0.196
(1.00) 		1
(1.00) 		0.708
(1.00) 		0.201
(1.00) 		0.676
(1.00)
10p gain 185 (32%) 386 0.465
(1.00) 		1.92e-08
(1.21e-05) 		0.106
(1.00) 		0.381
(1.00) 		0.246
(1.00) 		0.885
(1.00) 		0.487
(1.00) 		0.507
(1.00)
12p gain 253 (44%) 318 0.384
(1.00) 		5.59e-10
(3.54e-07) 		0.348
(1.00) 		0.12
(1.00) 		1
(1.00) 		0.961
(1.00) 		0.501
(1.00) 		0.327
(1.00)
12q gain 175 (31%) 396 0.177
(1.00) 		9.32e-08
(5.89e-05) 		0.0838
(1.00) 		0.018
(1.00) 		1
(1.00) 		0.207
(1.00) 		0.155
(1.00) 		0.462
(1.00)
20p gain 286 (50%) 285 0.00921
(1.00) 		1.02e-06
(0.000639) 		0.75
(1.00) 		0.343
(1.00) 		1
(1.00) 		0.443
(1.00) 		0.228
(1.00) 		0.752
(1.00)
20q gain 324 (57%) 247 0.0428
(1.00) 		4.14e-05
(0.0259) 		0.76
(1.00) 		0.309
(1.00) 		1
(1.00) 		0.508
(1.00) 		0.0164
(1.00) 		0.355
(1.00)
9q loss 285 (50%) 286 0.429
(1.00) 		6.97e-07
(0.000439) 		0.493
(1.00) 		0.865
(1.00) 		0.624
(1.00) 		0.837
(1.00) 		0.577
(1.00) 		1
(1.00)
15q loss 276 (48%) 295 0.51
(1.00) 		0.000167
(0.104) 		0.486
(1.00) 		0.586
(1.00) 		0.612
(1.00) 		0.757
(1.00) 		0.553
(1.00) 		0.524
(1.00)
16q loss 408 (71%) 163 0.12
(1.00) 		4.81e-05
(0.0301) 		0.748
(1.00) 		0.0859
(1.00) 		0.562
(1.00) 		0.532
(1.00) 		0.901
(1.00) 		0.157
(1.00)
1p gain 167 (29%) 404 0.183
(1.00) 		0.0765
(1.00) 		0.333
(1.00) 		0.244
(1.00) 		0.206
(1.00) 		0.273
(1.00) 		0.847
(1.00) 		0.461
(1.00)
1q gain 218 (38%) 353 0.537
(1.00) 		0.000758
(0.47) 		0.262
(1.00) 		0.121
(1.00) 		1
(1.00) 		0.756
(1.00) 		0.572
(1.00) 		0.741
(1.00)
2q gain 152 (27%) 419 0.126
(1.00) 		0.000717
(0.445) 		1
(1.00) 		0.721
(1.00) 		0.174
(1.00) 		1
(1.00) 		0.446
(1.00) 		0.707
(1.00)
3p gain 160 (28%) 411 0.711
(1.00) 		0.00398
(1.00) 		0.731
(1.00) 		0.368
(1.00) 		0.563
(1.00) 		0.467
(1.00) 		0.311
(1.00) 		1
(1.00)
4p gain 59 (10%) 512 0.0411
(1.00) 		0.0291
(1.00) 		0.354
(1.00) 		0.195
(1.00) 		0.279
(1.00) 		0.361
(1.00) 		0.453
(1.00) 		0.257
(1.00)
4q gain 32 (6%) 539 0.0645
(1.00) 		0.047
(1.00) 		1
(1.00) 		0.18
(1.00) 		0.159
(1.00) 		0.519
(1.00) 		0.464
(1.00)
5p gain 195 (34%) 376 0.446
(1.00) 		0.00701
(1.00) 		0.114
(1.00) 		0.322
(1.00) 		1
(1.00) 		0.0379
(1.00) 		0.441
(1.00) 		1
(1.00)
5q gain 59 (10%) 512 0.923
(1.00) 		0.21
(1.00) 		0.348
(1.00) 		0.16
(1.00) 		1
(1.00) 		0.137
(1.00) 		0.91
(1.00) 		1
(1.00)
7p gain 178 (31%) 393 0.939
(1.00) 		0.000763
(0.471) 		0.775
(1.00) 		0.119
(1.00) 		0.556
(1.00) 		0.803
(1.00) 		0.0333
(1.00) 		0.177
(1.00)
7q gain 198 (35%) 373 0.476
(1.00) 		0.00187
(1.00) 		0.797
(1.00) 		0.137
(1.00) 		0.555
(1.00) 		0.961
(1.00) 		0.0411
(1.00) 		1
(1.00)
8p gain 117 (20%) 454 0.921
(1.00) 		0.809
(1.00) 		0.607
(1.00) 		0.804
(1.00) 		0.498
(1.00) 		0.493
(1.00) 		0.506
(1.00) 		1
(1.00)
8q gain 239 (42%) 332 0.394
(1.00) 		0.113
(1.00) 		0.323
(1.00) 		0.729
(1.00) 		1
(1.00) 		0.122
(1.00) 		0.173
(1.00) 		0.527
(1.00)
9p gain 88 (15%) 483 0.471
(1.00) 		0.861
(1.00) 		1
(1.00) 		0.264
(1.00) 		0.395
(1.00) 		1
(1.00) 		0.709
(1.00) 		0.369
(1.00)
9q gain 43 (8%) 528 0.705
(1.00) 		0.212
(1.00) 		1
(1.00) 		0.508
(1.00) 		0.21
(1.00) 		1
(1.00) 		0.189
(1.00) 		1
(1.00)
10q gain 108 (19%) 463 0.76
(1.00) 		0.000719
(0.446) 		0.167
(1.00) 		0.852
(1.00) 		1
(1.00) 		0.739
(1.00) 		0.697
(1.00) 		1
(1.00)
11p gain 76 (13%) 495 0.0956
(1.00) 		0.692
(1.00) 		1
(1.00) 		0.47
(1.00) 		0.349
(1.00) 		0.448
(1.00) 		0.335
(1.00) 		1
(1.00)
11q gain 112 (20%) 459 0.897
(1.00) 		0.776
(1.00) 		1
(1.00) 		0.651
(1.00) 		1
(1.00) 		0.317
(1.00) 		1
(1.00) 		0.219
(1.00)
13q gain 59 (10%) 512 0.676
(1.00) 		0.016
(1.00) 		1
(1.00) 		0.178
(1.00) 		0.279
(1.00) 		0.813
(1.00) 		0.62
(1.00) 		0.611
(1.00)
14q gain 58 (10%) 513 0.0667
(1.00) 		0.215
(1.00) 		1
(1.00) 		0.813
(1.00) 		0.0285
(1.00) 		0.864
(1.00) 		0.909
(1.00) 		0.608
(1.00)
15q gain 39 (7%) 532 0.162
(1.00) 		0.915
(1.00) 		1
(1.00) 		0.114
(1.00) 		1
(1.00) 		1
(1.00) 		1
(1.00)
16p gain 59 (10%) 512 0.865
(1.00) 		0.188
(1.00) 		1
(1.00) 		0.0439
(1.00) 		1
(1.00) 		0.118
(1.00) 		0.912
(1.00) 		1
(1.00)
16q gain 31 (5%) 540 0.771
(1.00) 		0.955
(1.00) 		1
(1.00) 		0.147
(1.00) 		1
(1.00) 		0.18
(1.00) 		0.801
(1.00) 		1
(1.00)
17p gain 22 (4%) 549 0.168
(1.00) 		0.447
(1.00) 		1
(1.00) 		0.961
(1.00) 		1
(1.00) 		0.37
(1.00) 		1
(1.00)
17q gain 47 (8%) 524 0.633
(1.00) 		0.443
(1.00) 		1
(1.00) 		0.487
(1.00) 		1
(1.00) 		0.0901
(1.00) 		0.386
(1.00) 		1
(1.00)
18p gain 119 (21%) 452 0.135
(1.00) 		0.0357
(1.00) 		1
(1.00) 		0.916
(1.00) 		1
(1.00) 		0.629
(1.00) 		0.955
(1.00) 		1
(1.00)
18q gain 72 (13%) 499 0.31
(1.00) 		0.497
(1.00) 		1
(1.00) 		0.967
(1.00) 		1
(1.00) 		0.861
(1.00) 		0.72
(1.00) 		0.615
(1.00)
19p gain 168 (29%) 403 0.355
(1.00) 		0.0706
(1.00) 		0.752
(1.00) 		0.66
(1.00) 		0.208
(1.00) 		0.424
(1.00) 		0.253
(1.00) 		0.729
(1.00)
19q gain 160 (28%) 411 0.793
(1.00) 		0.0137
(1.00) 		0.152
(1.00) 		0.837
(1.00) 		0.191
(1.00) 		0.425
(1.00) 		0.0296
(1.00) 		0.734
(1.00)
21q gain 109 (19%) 462 0.987
(1.00) 		0.00105
(0.65) 		0.0718
(1.00) 		0.368
(1.00) 		1
(1.00) 		0.524
(1.00) 		0.722
(1.00) 		0.686
(1.00)
22q gain 24 (4%) 547 0.156
(1.00) 		0.684
(1.00) 		0.163
(1.00) 		0.439
(1.00) 		1
(1.00) 		1
(1.00) 		0.648
(1.00) 		1
(1.00)
xq gain 105 (18%) 466 0.579
(1.00) 		0.15
(1.00) 		0.0678
(1.00) 		0.506
(1.00) 		1
(1.00) 		0.74
(1.00) 		0.858
(1.00) 		1
(1.00)
1p loss 64 (11%) 507 0.912
(1.00) 		0.285
(1.00) 		1
(1.00) 		0.126
(1.00) 		0.3
(1.00) 		0.864
(1.00) 		0.486
(1.00) 		0.304
(1.00)
1q loss 43 (8%) 528 0.681
(1.00) 		0.403
(1.00) 		1
(1.00) 		0.161
(1.00) 		0.21
(1.00) 		0.737
(1.00) 		0.292
(1.00) 		0.529
(1.00)
2p loss 53 (9%) 518 0.798
(1.00) 		0.497
(1.00) 		1
(1.00) 		0.145
(1.00) 		1
(1.00) 		0.948
(1.00) 		0.608
(1.00)
2q loss 59 (10%) 512 0.843
(1.00) 		0.0185
(1.00) 		0.353
(1.00) 		0.481
(1.00) 		1
(1.00) 		0.661
(1.00) 		0.907
(1.00) 		0.609
(1.00)
3p loss 93 (16%) 478 0.999
(1.00) 		0.0109
(1.00) 		0.516
(1.00) 		0.473
(1.00) 		0.414
(1.00) 		0.242
(1.00) 		0.364
(1.00) 		1
(1.00)
3q loss 43 (8%) 528 0.306
(1.00) 		0.125
(1.00) 		0.275
(1.00) 		0.784
(1.00) 		0.21
(1.00) 		0.759
(1.00) 		0.545
(1.00)
4p loss 312 (55%) 259 0.641
(1.00) 		0.8
(1.00) 		0.169
(1.00) 		0.317
(1.00) 		1
(1.00) 		0.757
(1.00) 		0.609
(1.00) 		1
(1.00)
4q loss 358 (63%) 213 0.504
(1.00) 		0.839
(1.00) 		0.78
(1.00) 		0.906
(1.00) 		1
(1.00) 		0.799
(1.00) 		0.549
(1.00) 		0.326
(1.00)
5p loss 131 (23%) 440 0.778
(1.00) 		0.0236
(1.00) 		0.652
(1.00) 		0.0267
(1.00) 		1
(1.00) 		0.103
(1.00) 		0.844
(1.00) 		0.705
(1.00)
5q loss 221 (39%) 350 0.508
(1.00) 		0.0143
(1.00) 		1
(1.00) 		0.0339
(1.00) 		1
(1.00) 		0.162
(1.00) 		0.937
(1.00) 		0.526
(1.00)
6p loss 163 (29%) 408 0.314
(1.00) 		0.0732
(1.00) 		0.738
(1.00) 		0.913
(1.00) 		1
(1.00) 		0.309
(1.00) 		0.549
(1.00) 		0.729
(1.00)
6q loss 238 (42%) 333 0.593
(1.00) 		0.062
(1.00) 		0.148
(1.00) 		0.753
(1.00) 		1
(1.00) 		0.408
(1.00) 		0.103
(1.00) 		0.524
(1.00)
7p loss 120 (21%) 451 0.917
(1.00) 		0.897
(1.00) 		0.614
(1.00) 		0.0798
(1.00) 		1
(1.00) 		0.393
(1.00) 		0.758
(1.00) 		0.694
(1.00)
7q loss 81 (14%) 490 0.297
(1.00) 		0.216
(1.00) 		0.468
(1.00) 		0.114
(1.00) 		0.369
(1.00) 		0.548
(1.00) 		0.343
(1.00) 		0.371
(1.00)
8p loss 273 (48%) 298 0.121
(1.00) 		0.0284
(1.00) 		0.174
(1.00) 		0.142
(1.00) 		1
(1.00) 		0.393
(1.00) 		0.782
(1.00) 		0.522
(1.00)
8q loss 89 (16%) 482 0.147
(1.00) 		0.00338
(1.00) 		1
(1.00) 		0.295
(1.00) 		1
(1.00) 		0.435
(1.00) 		0.675
(1.00) 		0.645
(1.00)
9p loss 262 (46%) 309 0.756
(1.00) 		0.012
(1.00) 		0.456
(1.00) 		0.64
(1.00) 		0.596
(1.00) 		0.169
(1.00) 		0.671
(1.00) 		0.526
(1.00)
10p loss 96 (17%) 475 0.62
(1.00) 		0.143
(1.00) 		1
(1.00) 		0.678
(1.00) 		0.425
(1.00) 		0.543
(1.00) 		0.383
(1.00) 		1
(1.00)
10q loss 124 (22%) 447 0.771
(1.00) 		0.0828
(1.00) 		0.621
(1.00) 		0.983
(1.00) 		0.01
(1.00) 		0.892
(1.00) 		0.501
(1.00) 		0.693
(1.00)
11p loss 196 (34%) 375 0.842
(1.00) 		0.00292
(1.00) 		1
(1.00) 		0.603
(1.00) 		1
(1.00) 		0.756
(1.00) 		0.36
(1.00) 		0.73
(1.00)
11q loss 148 (26%) 423 0.55
(1.00) 		0.0141
(1.00) 		0.277
(1.00) 		0.0905
(1.00) 		1
(1.00) 		0.825
(1.00) 		0.483
(1.00) 		0.707
(1.00)
12p loss 78 (14%) 493 0.912
(1.00) 		0.0756
(1.00) 		1
(1.00) 		0.698
(1.00) 		1
(1.00) 		1
(1.00) 		0.24
(1.00) 		1
(1.00)
12q loss 103 (18%) 468 0.418
(1.00) 		0.342
(1.00) 		1
(1.00) 		0.376
(1.00) 		1
(1.00) 		0.625
(1.00) 		0.795
(1.00) 		1
(1.00)
13q loss 305 (53%) 266 0.537
(1.00) 		0.582
(1.00) 		0.749
(1.00) 		0.813
(1.00) 		0.6
(1.00) 		0.724
(1.00) 		0.5
(1.00) 		0.523
(1.00)
14q loss 212 (37%) 359 0.485
(1.00) 		0.000696
(0.433) 		0.78
(1.00) 		0.752
(1.00) 		0.298
(1.00) 		0.538
(1.00) 		0.437
(1.00) 		0.186
(1.00)
16p loss 330 (58%) 241 0.492
(1.00) 		0.161
(1.00) 		0.76
(1.00) 		0.908
(1.00) 		0.267
(1.00) 		0.901
(1.00) 		0.483
(1.00) 		0.0979
(1.00)
17p loss 473 (83%) 98 0.89
(1.00) 		0.327
(1.00) 		0.531
(1.00) 		0.896
(1.00) 		0.432
(1.00) 		0.392
(1.00) 		0.762
(1.00) 		0.383
(1.00)
17q loss 379 (66%) 192 0.851
(1.00) 		0.58
(1.00) 		0.8
(1.00) 		0.00916
(1.00) 		0.554
(1.00) 		0.468
(1.00) 		0.717
(1.00) 		0.0953
(1.00)
18p loss 231 (40%) 340 0.0751
(1.00) 		0.968
(1.00) 		0.763
(1.00) 		0.44
(1.00) 		0.0657
(1.00) 		0.364
(1.00) 		0.0346
(1.00) 		1
(1.00)
18q loss 289 (51%) 282 0.128
(1.00) 		0.311
(1.00) 		0.491
(1.00) 		0.416
(1.00) 		0.249
(1.00) 		0.264
(1.00) 		0.104
(1.00) 		0.214
(1.00)
19p loss 184 (32%) 387 0.268
(1.00) 		0.0344
(1.00) 		0.196
(1.00) 		0.296
(1.00) 		0.555
(1.00) 		0.307
(1.00) 		0.571
(1.00) 		0.734
(1.00)
19q loss 176 (31%) 395 0.994
(1.00) 		0.503
(1.00) 		0.18
(1.00) 		0.0518
(1.00) 		0.556
(1.00) 		0.16
(1.00) 		0.547
(1.00) 		0.511
(1.00)
20p loss 49 (9%) 522 0.0554
(1.00) 		0.402
(1.00) 		1
(1.00) 		0.383
(1.00) 		0.236
(1.00) 		0.0821
(1.00) 		0.762
(1.00) 		0.246
(1.00)
20q loss 32 (6%) 539 0.137
(1.00) 		0.872
(1.00) 		1
(1.00) 		0.439
(1.00) 		1
(1.00) 		1
(1.00) 		0.481
(1.00)
21q loss 194 (34%) 377 0.809
(1.00) 		0.315
(1.00) 		0.405
(1.00) 		0.127
(1.00) 		1
(1.00) 		1
(1.00) 		0.302
(1.00) 		0.752
(1.00)
22q loss 427 (75%) 144 0.234
(1.00) 		0.081
(1.00) 		0.266
(1.00) 		0.371
(1.00) 		0.576
(1.00) 		0.0394
(1.00) 		1
(1.00) 		1
(1.00)
xq loss 274 (48%) 297 0.807
(1.00) 		0.00184
(1.00) 		0.75
(1.00) 		0.273
(1.00) 		0.11
(1.00) 		0.557
(1.00) 		0.115
(1.00) 		0.757
(1.00)
'2p gain' versus 'AGE'

P value = 3.39e-06 (Wilcoxon-test), Q value = 0.0021

Table S1.  Gene #3: '2p gain' versus Clinical Feature #2: 'AGE'

nPatients Mean (Std.Dev)
ALL 550 59.8 (11.6)
2P GAIN MUTATED 174 63.3 (11.3)
2P GAIN WILD-TYPE 376 58.2 (11.4)

Figure S1.  Get High-res Image Gene #3: '2p gain' versus Clinical Feature #2: 'AGE'

'3q gain' versus 'AGE'

P value = 2.29e-07 (Wilcoxon-test), Q value = 0.00014

Table S2.  Gene #6: '3q gain' versus Clinical Feature #2: 'AGE'

nPatients Mean (Std.Dev)
ALL 550 59.8 (11.6)
3Q GAIN MUTATED 264 62.5 (11.1)
3Q GAIN WILD-TYPE 286 57.4 (11.5)

Figure S2.  Get High-res Image Gene #6: '3q gain' versus Clinical Feature #2: 'AGE'

'6p gain' versus 'AGE'

P value = 7.09e-06 (Wilcoxon-test), Q value = 0.0044

Table S3.  Gene #11: '6p gain' versus Clinical Feature #2: 'AGE'

nPatients Mean (Std.Dev)
ALL 550 59.8 (11.6)
6P GAIN MUTATED 162 63.2 (11.0)
6P GAIN WILD-TYPE 388 58.4 (11.6)

Figure S3.  Get High-res Image Gene #11: '6p gain' versus Clinical Feature #2: 'AGE'

'6q gain' versus 'AGE'

P value = 0.000187 (Wilcoxon-test), Q value = 0.12

Table S4.  Gene #12: '6q gain' versus Clinical Feature #2: 'AGE'

nPatients Mean (Std.Dev)
ALL 550 59.8 (11.6)
6Q GAIN MUTATED 93 63.8 (10.6)
6Q GAIN WILD-TYPE 457 59.0 (11.6)

Figure S4.  Get High-res Image Gene #12: '6q gain' versus Clinical Feature #2: 'AGE'

'10p gain' versus 'AGE'

P value = 1.92e-08 (Wilcoxon-test), Q value = 1.2e-05

Table S5.  Gene #19: '10p gain' versus Clinical Feature #2: 'AGE'

nPatients Mean (Std.Dev)
ALL 550 59.8 (11.6)
10P GAIN MUTATED 179 63.7 (10.9)
10P GAIN WILD-TYPE 371 57.9 (11.5)

Figure S5.  Get High-res Image Gene #19: '10p gain' versus Clinical Feature #2: 'AGE'

'12p gain' versus 'AGE'

P value = 5.59e-10 (Wilcoxon-test), Q value = 3.5e-07

Table S6.  Gene #23: '12p gain' versus Clinical Feature #2: 'AGE'

nPatients Mean (Std.Dev)
ALL 550 59.8 (11.6)
12P GAIN MUTATED 240 63.3 (11.1)
12P GAIN WILD-TYPE 310 57.1 (11.2)

Figure S6.  Get High-res Image Gene #23: '12p gain' versus Clinical Feature #2: 'AGE'

'12q gain' versus 'AGE'

P value = 9.32e-08 (Wilcoxon-test), Q value = 5.9e-05

Table S7.  Gene #24: '12q gain' versus Clinical Feature #2: 'AGE'

nPatients Mean (Std.Dev)
ALL 550 59.8 (11.6)
12Q GAIN MUTATED 165 63.8 (10.4)
12Q GAIN WILD-TYPE 385 58.1 (11.7)

Figure S7.  Get High-res Image Gene #24: '12q gain' versus Clinical Feature #2: 'AGE'

'20p gain' versus 'AGE'

P value = 1.02e-06 (Wilcoxon-test), Q value = 0.00064

Table S8.  Gene #36: '20p gain' versus Clinical Feature #2: 'AGE'

nPatients Mean (Std.Dev)
ALL 550 59.8 (11.6)
20P GAIN MUTATED 277 62.2 (11.6)
20P GAIN WILD-TYPE 273 57.4 (11.1)

Figure S8.  Get High-res Image Gene #36: '20p gain' versus Clinical Feature #2: 'AGE'

'20q gain' versus 'AGE'

P value = 4.14e-05 (Wilcoxon-test), Q value = 0.026

Table S9.  Gene #37: '20q gain' versus Clinical Feature #2: 'AGE'

nPatients Mean (Std.Dev)
ALL 550 59.8 (11.6)
20Q GAIN MUTATED 313 61.6 (11.8)
20Q GAIN WILD-TYPE 237 57.4 (10.9)

Figure S9.  Get High-res Image Gene #37: '20q gain' versus Clinical Feature #2: 'AGE'

'9q loss' versus 'AGE'

P value = 6.97e-07 (Wilcoxon-test), Q value = 0.00044

Table S10.  Gene #58: '9q loss' versus Clinical Feature #2: 'AGE'

nPatients Mean (Std.Dev)
ALL 550 59.8 (11.6)
9Q LOSS MUTATED 271 62.4 (11.3)
9Q LOSS WILD-TYPE 279 57.4 (11.3)

Figure S10.  Get High-res Image Gene #58: '9q loss' versus Clinical Feature #2: 'AGE'

'15q loss' versus 'AGE'

P value = 0.000167 (Wilcoxon-test), Q value = 0.1

Table S11.  Gene #67: '15q loss' versus Clinical Feature #2: 'AGE'

nPatients Mean (Std.Dev)
ALL 550 59.8 (11.6)
15Q LOSS MUTATED 268 61.7 (11.3)
15Q LOSS WILD-TYPE 282 58.0 (11.6)

Figure S11.  Get High-res Image Gene #67: '15q loss' versus Clinical Feature #2: 'AGE'

'16q loss' versus 'AGE'

P value = 4.81e-05 (Wilcoxon-test), Q value = 0.03

Table S12.  Gene #69: '16q loss' versus Clinical Feature #2: 'AGE'

nPatients Mean (Std.Dev)
ALL 550 59.8 (11.6)
16Q LOSS MUTATED 393 61.2 (11.4)
16Q LOSS WILD-TYPE 157 56.5 (11.5)

Figure S12.  Get High-res Image Gene #69: '16q loss' versus Clinical Feature #2: 'AGE'

Methods & Data
Input

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

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

  • Number of patients = 571

  • Number of significantly arm-level cnvs = 80

  • 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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