Correlation between copy number variations of arm-level result and selected clinical features
Ovarian Serous Cystadenocarcinoma (Primary solid tumor)
15 July 2014  |  analyses__2014_07_15
Maintainer Information
Citation Information
doi:10.7908/C1RX99W0
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/C1RX99W0
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 562 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 176 (31%) 386 0.117
(1.00) 		9.38e-06
(0.00587) 		1
(1.00) 		0.524
(1.00) 		1
(1.00) 		0.837
(1.00) 		0.769
(1.00) 		1
(1.00)
3q gain 265 (47%) 297 0.557
(1.00) 		3.7e-08
(2.33e-05) 		0.175
(1.00) 		0.729
(1.00) 		0.251
(1.00) 		0.76
(1.00) 		0.485
(1.00) 		0.522
(1.00)
6p gain 163 (29%) 399 0.299
(1.00) 		2.07e-05
(0.0129) 		0.747
(1.00) 		0.103
(1.00) 		0.56
(1.00) 		1
(1.00) 		0.197
(1.00) 		0.729
(1.00)
6q gain 96 (17%) 466 0.432
(1.00) 		0.000256
(0.159) 		1
(1.00) 		0.187
(1.00) 		1
(1.00) 		0.74
(1.00) 		0.196
(1.00) 		0.676
(1.00)
10p gain 181 (32%) 381 0.365
(1.00) 		3.57e-08
(2.25e-05) 		0.103
(1.00) 		0.389
(1.00) 		0.244
(1.00) 		0.663
(1.00) 		0.368
(1.00) 		0.509
(1.00)
12p gain 249 (44%) 313 0.298
(1.00) 		8.2e-10
(5.17e-07) 		0.349
(1.00) 		0.042
(1.00) 		1
(1.00) 		0.574
(1.00) 		0.511
(1.00) 		0.326
(1.00)
12q gain 173 (31%) 389 0.156
(1.00) 		6.64e-08
(4.17e-05) 		0.0857
(1.00) 		0.0137
(1.00) 		1
(1.00) 		0.663
(1.00) 		0.0195
(1.00) 		0.462
(1.00)
20p gain 280 (50%) 282 0.0185
(1.00) 		1.29e-06
(0.000808) 		0.746
(1.00) 		0.141
(1.00) 		0.623
(1.00) 		0.869
(1.00) 		0.25
(1.00) 		0.752
(1.00)
20q gain 317 (56%) 245 0.0591
(1.00) 		2.42e-05
(0.0151) 		0.757
(1.00) 		0.309
(1.00) 		1
(1.00) 		1
(1.00) 		0.019
(1.00) 		0.521
(1.00)
9q loss 280 (50%) 282 0.403
(1.00) 		8.06e-07
(0.000506) 		0.493
(1.00) 		0.928
(1.00) 		0.623
(1.00) 		0.868
(1.00) 		0.504
(1.00) 		1
(1.00)
15q loss 272 (48%) 290 0.406
(1.00) 		0.000214
(0.133) 		0.48
(1.00) 		0.777
(1.00) 		0.613
(1.00) 		0.752
(1.00) 		0.561
(1.00) 		0.525
(1.00)
16q loss 400 (71%) 162 0.153
(1.00) 		1.86e-05
(0.0116) 		0.748
(1.00) 		0.187
(1.00) 		0.561
(1.00) 		0.664
(1.00) 		0.862
(1.00) 		0.159
(1.00)
1p gain 166 (30%) 396 0.261
(1.00) 		0.0476
(1.00) 		0.339
(1.00) 		0.0778
(1.00) 		0.21
(1.00) 		0.297
(1.00) 		0.849
(1.00) 		0.462
(1.00)
1q gain 216 (38%) 346 0.646
(1.00) 		0.000413
(0.256) 		0.265
(1.00) 		0.033
(1.00) 		1
(1.00) 		1
(1.00) 		0.671
(1.00) 		0.744
(1.00)
2q gain 148 (26%) 414 0.115
(1.00) 		0.000947
(0.582) 		1
(1.00) 		0.871
(1.00) 		0.171
(1.00) 		1
(1.00) 		0.515
(1.00) 		0.704
(1.00)
3p gain 154 (27%) 408 0.57
(1.00) 		0.000767
(0.473) 		0.723
(1.00) 		0.707
(1.00) 		0.565
(1.00) 		0.218
(1.00) 		0.239
(1.00) 		0.461
(1.00)
4p gain 57 (10%) 505 0.0536
(1.00) 		0.0335
(1.00) 		0.348
(1.00) 		0.433
(1.00) 		0.275
(1.00) 		0.41
(1.00) 		0.293
(1.00) 		0.264
(1.00)
4q gain 32 (6%) 530 0.243
(1.00) 		0.0721
(1.00) 		1
(1.00) 		0.481
(1.00) 		0.162
(1.00) 		0.584
(1.00) 		0.471
(1.00)
5p gain 193 (34%) 369 0.432
(1.00) 		0.00242
(1.00) 		0.115
(1.00) 		0.243
(1.00) 		1
(1.00) 		0.0537
(1.00) 		0.418
(1.00) 		1
(1.00)
5q gain 59 (10%) 503 0.909
(1.00) 		0.141
(1.00) 		0.355
(1.00) 		0.362
(1.00) 		1
(1.00) 		0.122
(1.00) 		0.899
(1.00) 		1
(1.00)
7p gain 178 (32%) 384 0.955
(1.00) 		0.000493
(0.305) 		0.379
(1.00) 		0.0383
(1.00) 		0.555
(1.00) 		1
(1.00) 		0.0554
(1.00) 		0.175
(1.00)
7q gain 193 (34%) 369 0.445
(1.00) 		0.00286
(1.00) 		0.798
(1.00) 		0.0479
(1.00) 		0.555
(1.00) 		0.573
(1.00) 		0.0145
(1.00) 		1
(1.00)
8p gain 116 (21%) 446 0.778
(1.00) 		0.945
(1.00) 		0.608
(1.00) 		0.845
(1.00) 		0.501
(1.00) 		0.666
(1.00) 		0.507
(1.00) 		1
(1.00)
8q gain 236 (42%) 326 0.36
(1.00) 		0.118
(1.00) 		0.329
(1.00) 		0.644
(1.00) 		1
(1.00) 		0.0732
(1.00) 		0.164
(1.00) 		0.527
(1.00)
9p gain 88 (16%) 474 0.464
(1.00) 		0.835
(1.00) 		1
(1.00) 		0.22
(1.00) 		0.401
(1.00) 		1
(1.00) 		0.605
(1.00) 		0.37
(1.00)
9q gain 43 (8%) 519 0.698
(1.00) 		0.221
(1.00) 		1
(1.00) 		0.496
(1.00) 		0.213
(1.00) 		1
(1.00) 		0.176
(1.00) 		1
(1.00)
10q gain 105 (19%) 457 0.685
(1.00) 		0.00202
(1.00) 		0.163
(1.00) 		0.884
(1.00) 		1
(1.00) 		1
(1.00) 		0.548
(1.00) 		0.696
(1.00)
11p gain 75 (13%) 487 0.116
(1.00) 		0.567
(1.00) 		1
(1.00) 		0.472
(1.00) 		0.35
(1.00) 		0.224
(1.00) 		1
(1.00)
11q gain 111 (20%) 451 0.945
(1.00) 		0.953
(1.00) 		1
(1.00) 		0.317
(1.00) 		1
(1.00) 		0.578
(1.00) 		0.981
(1.00) 		0.219
(1.00)
13q gain 60 (11%) 502 0.68
(1.00) 		0.00856
(1.00) 		1
(1.00) 		0.482
(1.00) 		0.288
(1.00) 		0.673
(1.00) 		0.64
(1.00) 		0.614
(1.00)
14q gain 57 (10%) 505 0.0609
(1.00) 		0.266
(1.00) 		1
(1.00) 		0.771
(1.00) 		0.0284
(1.00) 		0.72
(1.00) 		0.897
(1.00) 		0.608
(1.00)
15q gain 38 (7%) 524 0.169
(1.00) 		0.779
(1.00) 		1
(1.00) 		0.1
(1.00) 		1
(1.00) 		1
(1.00) 		1
(1.00)
16p gain 58 (10%) 504 0.903
(1.00) 		0.256
(1.00) 		1
(1.00) 		0.0358
(1.00) 		1
(1.00) 		0.277
(1.00) 		0.9
(1.00) 		1
(1.00)
16q gain 30 (5%) 532 0.817
(1.00) 		0.738
(1.00) 		1
(1.00) 		0.13
(1.00) 		1
(1.00) 		0.378
(1.00) 		1
(1.00) 		1
(1.00)
17p gain 22 (4%) 540 0.17
(1.00) 		0.459
(1.00) 		1
(1.00) 		0.936
(1.00) 		1
(1.00) 		0.323
(1.00) 		1
(1.00)
17q gain 49 (9%) 513 0.818
(1.00) 		0.457
(1.00) 		1
(1.00) 		0.433
(1.00) 		1
(1.00) 		0.00688
(1.00) 		0.294
(1.00) 		1
(1.00)
18p gain 117 (21%) 445 0.147
(1.00) 		0.0425
(1.00) 		1
(1.00) 		0.692
(1.00) 		1
(1.00) 		0.813
(1.00) 		0.983
(1.00) 		1
(1.00)
18q gain 71 (13%) 491 0.326
(1.00) 		0.479
(1.00) 		1
(1.00) 		0.704
(1.00) 		1
(1.00) 		0.723
(1.00) 		0.832
(1.00) 		0.617
(1.00)
19p gain 165 (29%) 397 0.49
(1.00) 		0.0759
(1.00) 		0.75
(1.00) 		0.692
(1.00) 		1
(1.00) 		1
(1.00) 		0.378
(1.00) 		0.73
(1.00)
19q gain 159 (28%) 403 0.65
(1.00) 		0.0125
(1.00) 		0.155
(1.00) 		0.762
(1.00) 		0.194
(1.00) 		0.857
(1.00) 		0.0465
(1.00) 		0.734
(1.00)
21q gain 109 (19%) 453 0.999
(1.00) 		0.000941
(0.58) 		0.0721
(1.00) 		0.368
(1.00) 		1
(1.00) 		0.574
(1.00) 		0.903
(1.00) 		0.691
(1.00)
22q gain 25 (4%) 537 0.0506
(1.00) 		0.646
(1.00) 		0.169
(1.00) 		0.426
(1.00) 		1
(1.00) 		1
(1.00) 		0.74
(1.00) 		1
(1.00)
xq gain 104 (19%) 458 0.663
(1.00) 		0.128
(1.00) 		0.0695
(1.00) 		0.784
(1.00) 		1
(1.00) 		1
(1.00) 		0.738
(1.00) 		1
(1.00)
1p loss 60 (11%) 502 0.912
(1.00) 		0.347
(1.00) 		1
(1.00) 		0.314
(1.00) 		0.288
(1.00) 		1
(1.00) 		0.695
(1.00) 		0.276
(1.00)
1q loss 39 (7%) 523 0.885
(1.00) 		0.504
(1.00) 		1
(1.00) 		0.459
(1.00) 		0.194
(1.00) 		0.479
(1.00) 		0.488
(1.00)
2p loss 53 (9%) 509 0.928
(1.00) 		0.406
(1.00) 		1
(1.00) 		0.131
(1.00) 		1
(1.00) 		1
(1.00) 		0.607
(1.00)
2q loss 59 (10%) 503 0.988
(1.00) 		0.0143
(1.00) 		0.36
(1.00) 		0.131
(1.00) 		1
(1.00) 		1
(1.00) 		0.768
(1.00) 		0.608
(1.00)
3p loss 93 (17%) 469 0.995
(1.00) 		0.0152
(1.00) 		0.523
(1.00) 		0.485
(1.00) 		0.419
(1.00) 		0.0383
(1.00) 		0.555
(1.00) 		1
(1.00)
3q loss 41 (7%) 521 0.378
(1.00) 		0.189
(1.00) 		0.264
(1.00) 		0.803
(1.00) 		0.204
(1.00) 		0.728
(1.00) 		0.536
(1.00)
4p loss 308 (55%) 254 0.491
(1.00) 		0.967
(1.00) 		0.167
(1.00) 		0.155
(1.00) 		1
(1.00) 		0.66
(1.00) 		0.618
(1.00) 		1
(1.00)
4q loss 352 (63%) 210 0.429
(1.00) 		0.741
(1.00) 		0.778
(1.00) 		0.842
(1.00) 		1
(1.00) 		0.644
(1.00) 		0.516
(1.00) 		0.326
(1.00)
5p loss 127 (23%) 435 0.808
(1.00) 		0.0511
(1.00) 		0.645
(1.00) 		0.062
(1.00) 		1
(1.00) 		0.742
(1.00) 		0.64
(1.00) 		0.702
(1.00)
5q loss 216 (38%) 346 0.433
(1.00) 		0.0251
(1.00) 		1
(1.00) 		0.172
(1.00) 		1
(1.00) 		0.778
(1.00) 		0.863
(1.00) 		0.522
(1.00)
6p loss 162 (29%) 400 0.214
(1.00) 		0.0939
(1.00) 		0.745
(1.00) 		0.97
(1.00) 		1
(1.00) 		0.494
(1.00) 		0.51
(1.00) 		0.729
(1.00)
6q loss 235 (42%) 327 0.667
(1.00) 		0.092
(1.00) 		0.149
(1.00) 		0.668
(1.00) 		1
(1.00) 		1
(1.00) 		0.0722
(1.00) 		0.523
(1.00)
7p loss 117 (21%) 445 0.825
(1.00) 		0.907
(1.00) 		0.608
(1.00) 		0.0694
(1.00) 		1
(1.00) 		0.357
(1.00) 		0.708
(1.00) 		0.694
(1.00)
7q loss 81 (14%) 481 0.29
(1.00) 		0.226
(1.00) 		0.47
(1.00) 		0.1
(1.00) 		0.374
(1.00) 		0.474
(1.00) 		0.319
(1.00) 		0.369
(1.00)
8p loss 267 (48%) 295 0.159
(1.00) 		0.0262
(1.00) 		0.174
(1.00) 		0.0813
(1.00) 		1
(1.00) 		0.341
(1.00) 		0.919
(1.00) 		0.521
(1.00)
8q loss 87 (15%) 475 0.0951
(1.00) 		0.00564
(1.00) 		1
(1.00) 		0.179
(1.00) 		1
(1.00) 		0.74
(1.00) 		0.747
(1.00) 		0.644
(1.00)
9p loss 255 (45%) 307 0.809
(1.00) 		0.0133
(1.00) 		0.455
(1.00) 		0.281
(1.00) 		0.593
(1.00) 		0.381
(1.00) 		0.892
(1.00) 		0.523
(1.00)
10p loss 93 (17%) 469 0.399
(1.00) 		0.149
(1.00) 		1
(1.00) 		0.886
(1.00) 		0.419
(1.00) 		0.621
(1.00) 		0.371
(1.00) 		1
(1.00)
10q loss 122 (22%) 440 0.878
(1.00) 		0.0778
(1.00) 		0.62
(1.00) 		0.981
(1.00) 		0.01
(1.00) 		1
(1.00) 		0.511
(1.00) 		0.693
(1.00)
11p loss 191 (34%) 371 0.976
(1.00) 		0.00386
(1.00) 		1
(1.00) 		0.837
(1.00) 		1
(1.00) 		0.655
(1.00) 		0.689
(1.00) 		0.729
(1.00)
11q loss 144 (26%) 418 0.662
(1.00) 		0.0334
(1.00) 		0.274
(1.00) 		0.148
(1.00) 		1
(1.00) 		0.601
(1.00) 		0.568
(1.00) 		0.704
(1.00)
12p loss 77 (14%) 485 0.807
(1.00) 		0.0915
(1.00) 		1
(1.00) 		0.322
(1.00) 		1
(1.00) 		1
(1.00) 		0.14
(1.00) 		1
(1.00)
12q loss 102 (18%) 460 0.346
(1.00) 		0.34
(1.00) 		1
(1.00) 		0.989
(1.00) 		1
(1.00) 		1
(1.00) 		0.831
(1.00) 		1
(1.00)
13q loss 298 (53%) 264 0.504
(1.00) 		0.694
(1.00) 		0.75
(1.00) 		0.952
(1.00) 		0.603
(1.00) 		0.645
(1.00) 		0.462
(1.00) 		0.524
(1.00)
14q loss 206 (37%) 356 0.596
(1.00) 		0.00103
(0.631) 		0.783
(1.00) 		0.787
(1.00) 		0.302
(1.00) 		0.631
(1.00) 		0.36
(1.00) 		0.182
(1.00)
16p loss 322 (57%) 240 0.402
(1.00) 		0.0765
(1.00) 		0.758
(1.00) 		0.877
(1.00) 		0.265
(1.00) 		0.871
(1.00) 		0.398
(1.00) 		0.1
(1.00)
17p loss 466 (83%) 96 0.812
(1.00) 		0.346
(1.00) 		0.526
(1.00) 		0.94
(1.00) 		0.431
(1.00) 		0.0955
(1.00) 		0.907
(1.00) 		0.383
(1.00)
17q loss 372 (66%) 190 0.544
(1.00) 		0.573
(1.00) 		0.798
(1.00) 		0.00647
(1.00) 		0.554
(1.00) 		0.0615
(1.00) 		0.788
(1.00) 		0.098
(1.00)
18p loss 230 (41%) 332 0.083
(1.00) 		0.998
(1.00) 		0.765
(1.00) 		0.995
(1.00) 		0.068
(1.00) 		0.872
(1.00) 		0.0936
(1.00) 		1
(1.00)
18q loss 286 (51%) 276 0.125
(1.00) 		0.266
(1.00) 		0.496
(1.00) 		0.981
(1.00) 		0.249
(1.00) 		1
(1.00) 		0.159
(1.00) 		0.213
(1.00)
19p loss 180 (32%) 382 0.171
(1.00) 		0.0165
(1.00) 		0.193
(1.00) 		0.893
(1.00) 		1
(1.00) 		0.307
(1.00) 		0.632
(1.00) 		0.734
(1.00)
19q loss 170 (30%) 392 0.774
(1.00) 		0.38
(1.00) 		0.172
(1.00) 		0.281
(1.00) 		0.557
(1.00) 		0.165
(1.00) 		0.576
(1.00) 		0.503
(1.00)
20p loss 48 (9%) 514 0.0917
(1.00) 		0.339
(1.00) 		1
(1.00) 		0.369
(1.00) 		0.235
(1.00) 		0.732
(1.00) 		0.229
(1.00)
20q loss 31 (6%) 531 0.142
(1.00) 		0.978
(1.00) 		1
(1.00) 		0.426
(1.00) 		1
(1.00) 		1
(1.00) 		0.471
(1.00)
21q loss 190 (34%) 372 0.789
(1.00) 		0.324
(1.00) 		0.405
(1.00) 		0.48
(1.00) 		1
(1.00) 		1
(1.00) 		0.303
(1.00) 		1
(1.00)
22q loss 419 (75%) 143 0.155
(1.00) 		0.116
(1.00) 		0.272
(1.00) 		0.677
(1.00) 		0.574
(1.00) 		0.0625
(1.00) 		0.902
(1.00) 		1
(1.00)
xq loss 270 (48%) 292 0.774
(1.00) 		0.00235
(1.00) 		0.749
(1.00) 		0.805
(1.00) 		0.11
(1.00) 		0.868
(1.00) 		0.156
(1.00) 		0.757
(1.00)
'2p gain' versus 'AGE'

P value = 9.38e-06 (Wilcoxon-test), Q value = 0.0059

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

nPatients Mean (Std.Dev)
ALL 541 59.8 (11.6)
2P GAIN MUTATED 167 63.1 (11.2)
2P GAIN WILD-TYPE 374 58.3 (11.5)

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

'3q gain' versus 'AGE'

P value = 3.7e-08 (Wilcoxon-test), Q value = 2.3e-05

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

nPatients Mean (Std.Dev)
ALL 541 59.8 (11.6)
3Q GAIN MUTATED 258 62.7 (11.2)
3Q GAIN WILD-TYPE 283 57.2 (11.4)

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

'6p gain' versus 'AGE'

P value = 2.07e-05 (Wilcoxon-test), Q value = 0.013

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

nPatients Mean (Std.Dev)
ALL 541 59.8 (11.6)
6P GAIN MUTATED 159 63.0 (11.0)
6P GAIN WILD-TYPE 382 58.5 (11.6)

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

'6q gain' versus 'AGE'

P value = 0.000256 (Wilcoxon-test), Q value = 0.16

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

nPatients Mean (Std.Dev)
ALL 541 59.8 (11.6)
6Q GAIN MUTATED 92 63.7 (10.6)
6Q GAIN WILD-TYPE 449 59.0 (11.7)

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

'10p gain' versus 'AGE'

P value = 3.57e-08 (Wilcoxon-test), Q value = 2.2e-05

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

nPatients Mean (Std.Dev)
ALL 541 59.8 (11.6)
10P GAIN MUTATED 175 63.7 (10.9)
10P GAIN WILD-TYPE 366 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 = 8.2e-10 (Wilcoxon-test), Q value = 5.2e-07

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

nPatients Mean (Std.Dev)
ALL 541 59.8 (11.6)
12P GAIN MUTATED 236 63.3 (11.1)
12P GAIN WILD-TYPE 305 57.1 (11.3)

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

'12q gain' versus 'AGE'

P value = 6.64e-08 (Wilcoxon-test), Q value = 4.2e-05

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

nPatients Mean (Std.Dev)
ALL 541 59.8 (11.6)
12Q GAIN MUTATED 163 63.8 (10.4)
12Q GAIN WILD-TYPE 378 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 = 1.29e-06 (Wilcoxon-test), Q value = 0.00081

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

nPatients Mean (Std.Dev)
ALL 541 59.8 (11.6)
20P GAIN MUTATED 271 62.2 (11.7)
20P GAIN WILD-TYPE 270 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 = 2.42e-05 (Wilcoxon-test), Q value = 0.015

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

nPatients Mean (Std.Dev)
ALL 541 59.8 (11.6)
20Q GAIN MUTATED 306 61.7 (11.8)
20Q GAIN WILD-TYPE 235 57.3 (10.9)

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

'9q loss' versus 'AGE'

P value = 8.06e-07 (Wilcoxon-test), Q value = 0.00051

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

nPatients Mean (Std.Dev)
ALL 541 59.8 (11.6)
9Q LOSS MUTATED 266 62.3 (11.3)
9Q LOSS WILD-TYPE 275 57.3 (11.4)

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

'15q loss' versus 'AGE'

P value = 0.000214 (Wilcoxon-test), Q value = 0.13

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

nPatients Mean (Std.Dev)
ALL 541 59.8 (11.6)
15Q LOSS MUTATED 264 61.7 (11.3)
15Q LOSS WILD-TYPE 277 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 = 1.86e-05 (Wilcoxon-test), Q value = 0.012

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

nPatients Mean (Std.Dev)
ALL 541 59.8 (11.6)
16Q LOSS MUTATED 385 61.2 (11.4)
16Q LOSS WILD-TYPE 156 56.3 (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 = 562

  • 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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