Correlation between copy number variations of arm-level result and selected clinical features
Ovarian Serous Cystadenocarcinoma (Primary solid tumor)
28 January 2016  |  analyses__2016_01_28
Maintainer Information
Citation Information
doi:10.7908/C1JH3KK0
Maintained by TCGA GDAC Team (Broad Institute/MD Anderson Cancer Center/Harvard Medical School)
Cite as Broad Institute TCGA Genome Data Analysis Center (2016): Correlation between copy number variations of arm-level result and selected clinical features. Broad Institute of MIT and Harvard. doi:10.7908/C1JH3KK0
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 7 clinical features across 573 patients, 28 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'.

  • 13q gain cnv correlated to 'YEARS_TO_BIRTH'.

  • 19q gain cnv correlated to 'YEARS_TO_BIRTH'.

  • 20p gain cnv correlated to 'YEARS_TO_BIRTH'.

  • 20q gain cnv correlated to 'YEARS_TO_BIRTH'.

  • 21q gain 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 7 clinical features. Shown in the table are P values (Q values). Thresholded by Q value < 0.25, 28 significant findings detected.

Clinical
Features 		Time
to
Death 		YEARS
TO
BIRTH 		TUMOR
TISSUE
SITE 		RADIATION
THERAPY 		KARNOFSKY
PERFORMANCE
SCORE 		RESIDUAL
TUMOR 		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
12q gain 177 (31%) 396 0.227
(0.895) 		3.04e-07
(3.49e-05) 		0.0459
(0.598) 		0.165
(0.84) 		0.00903
(0.193) 		0.252
(0.895) 		0.462
(1.00)
1q gain 221 (39%) 352 0.375
(1.00) 		0.000323
(0.0143) 		0.128
(0.785) 		0.162
(0.84) 		0.042
(0.588) 		0.678
(1.00) 		0.74
(1.00)
2p gain 186 (32%) 387 0.0583
(0.629) 		5.5e-06
(0.000395) 		1
(1.00) 		0.182
(0.853) 		0.858
(1.00) 		0.874
(1.00) 		1
(1.00)
2q gain 153 (27%) 420 0.252
(0.895) 		0.00314
(0.09) 		0.767
(1.00) 		1
(1.00) 		0.494
(1.00) 		1
(1.00) 		0.706
(1.00)
3p gain 162 (28%) 411 0.33
(0.948) 		0.00429
(0.112) 		0.408
(1.00) 		1
(1.00) 		0.423
(1.00) 		0.326
(0.941) 		1
(1.00)
3q gain 275 (48%) 298 0.0857
(0.698) 		1.03e-07
(1.97e-05) 		0.425
(1.00) 		0.374
(1.00) 		0.819
(1.00) 		0.649
(1.00) 		0.521
(1.00)
5p gain 197 (34%) 376 0.957
(1.00) 		0.00886
(0.193) 		0.0982
(0.705) 		0.663
(1.00) 		0.483
(1.00) 		0.0712
(0.681) 		1
(1.00)
6p gain 171 (30%) 402 0.202
(0.872) 		8.9e-07
(7.3e-05) 		0.782
(1.00) 		1
(1.00) 		0.0527
(0.619) 		1
(1.00) 		0.729
(1.00)
6q gain 100 (17%) 473 0.469
(1.00) 		1.85e-05
(0.00118) 		1
(1.00) 		0.593
(1.00) 		0.232
(0.895) 		0.827
(1.00) 		0.674
(1.00)
7p gain 176 (31%) 397 0.266
(0.918) 		0.000536
(0.022) 		0.299
(0.938) 		0.641
(1.00) 		0.185
(0.853) 		1
(1.00) 		0.179
(0.853)
7q gain 200 (35%) 373 0.12
(0.785) 		0.0011
(0.0394) 		1
(1.00) 		0.665
(1.00) 		0.192
(0.869) 		0.959
(1.00) 		1
(1.00)
10p gain 187 (33%) 386 0.31
(0.941) 		4.09e-08
(1.17e-05) 		0.0576
(0.629) 		0.665
(1.00) 		0.404
(1.00) 		0.855
(1.00) 		0.506
(1.00)
10q gain 108 (19%) 465 0.391
(1.00) 		0.00508
(0.127) 		0.0696
(0.678) 		0.589
(1.00) 		0.915
(1.00) 		0.742
(1.00) 		0.694
(1.00)
12p gain 256 (45%) 317 0.231
(0.895) 		1.14e-09
(6.54e-07) 		0.235
(0.895) 		0.659
(1.00) 		0.0679
(0.672) 		0.93
(1.00) 		0.326
(0.941)
13q gain 61 (11%) 512 0.319
(0.941) 		0.0091
(0.193) 		1
(1.00) 		1
(1.00) 		0.202
(0.872) 		0.546
(1.00) 		0.612
(1.00)
19q gain 162 (28%) 411 0.0573
(0.629) 		0.00392
(0.107) 		0.101
(0.705) 		0.137
(0.785) 		1
(1.00) 		0.578
(1.00) 		0.733
(1.00)
20p gain 286 (50%) 287 0.0466
(0.598) 		2.88e-07
(3.49e-05) 		0.248
(0.895) 		0.373
(1.00) 		0.253
(0.895) 		0.499
(1.00) 		0.751
(1.00)
20q gain 325 (57%) 248 0.208
(0.872) 		3.05e-05
(0.00175) 		0.4
(1.00) 		0.657
(1.00) 		0.235
(0.895) 		0.598
(1.00) 		0.353
(0.978)
21q gain 107 (19%) 466 0.632
(1.00) 		0.00148
(0.0499) 		0.0404
(0.58) 		0.59
(1.00) 		0.423
(1.00) 		0.625
(1.00) 		0.679
(1.00)
8q loss 90 (16%) 483 0.726
(1.00) 		0.00857
(0.193) 		1
(1.00) 		0.568
(1.00) 		0.431
(1.00) 		0.522
(1.00) 		1
(1.00)
9q loss 287 (50%) 286 0.609
(1.00) 		4.07e-07
(3.89e-05) 		0.435
(1.00) 		1
(1.00) 		0.979
(1.00) 		0.739
(1.00) 		1
(1.00)
11p loss 198 (35%) 375 0.647
(1.00) 		0.00162
(0.0516) 		0.152
(0.821) 		0.348
(0.975) 		0.957
(1.00) 		0.78
(1.00) 		0.731
(1.00)
14q loss 216 (38%) 357 0.237
(0.895) 		0.000709
(0.0271) 		1
(1.00) 		1
(1.00) 		0.578
(1.00) 		0.458
(1.00) 		0.193
(0.869)
15q loss 277 (48%) 296 0.27
(0.923) 		0.000136
(0.0065) 		0.423
(1.00) 		1
(1.00) 		0.481
(1.00) 		0.676
(1.00) 		0.525
(1.00)
16q loss 409 (71%) 164 0.0771
(0.681) 		5.44e-05
(0.00284) 		1
(1.00) 		1
(1.00) 		0.129
(0.785) 		0.575
(1.00) 		0.159
(0.84)
xp loss 324 (57%) 249 0.965
(1.00) 		0.0106
(0.217) 		0.315
(0.941) 		0.397
(1.00) 		0.933
(1.00) 		0.52
(1.00) 		0.759
(1.00)
xq loss 281 (49%) 292 0.35
(0.975) 		0.002
(0.0604) 		0.626
(1.00) 		0.21
(0.872) 		0.397
(1.00) 		0.655
(1.00) 		0.752
(1.00)
1p gain 173 (30%) 400 0.0899
(0.698) 		0.051
(0.619) 		0.781
(1.00) 		0.638
(1.00) 		0.0834
(0.698) 		0.435
(1.00) 		0.462
(1.00)
4p gain 61 (11%) 512 0.0592
(0.629) 		0.0395
(0.58) 		0.0894
(0.698) 		0.0927
(0.7) 		0.765
(1.00) 		0.706
(1.00) 		1
(1.00)
4q gain 32 (6%) 541 0.138
(0.785) 		0.0624
(0.638) 		1
(1.00) 		0.254
(0.895) 		0.168
(0.84) 		0.445
(1.00)
5q gain 59 (10%) 514 0.716
(1.00) 		0.172
(0.849) 		0.217
(0.872) 		1
(1.00) 		0.148
(0.818) 		0.167
(0.84) 		1
(1.00)
8p gain 125 (22%) 448 0.764
(1.00) 		0.756
(1.00) 		0.467
(1.00) 		0.592
(1.00) 		0.789
(1.00) 		0.74
(1.00) 		0.701
(1.00)
8q gain 248 (43%) 325 0.25
(0.895) 		0.0977
(0.705) 		0.314
(0.941) 		0.393
(1.00) 		0.72
(1.00) 		0.279
(0.932) 		1
(1.00)
9p gain 89 (16%) 484 0.386
(1.00) 		0.815
(1.00) 		1
(1.00) 		0.572
(1.00) 		0.682
(1.00) 		0.79
(1.00) 		0.37
(1.00)
9q gain 43 (8%) 530 0.645
(1.00) 		0.182
(0.853) 		1
(1.00) 		0.324
(0.941) 		0.542
(1.00) 		1
(1.00) 		1
(1.00)
11p gain 73 (13%) 500 0.0588
(0.629) 		0.682
(1.00) 		1
(1.00) 		1
(1.00) 		0.527
(1.00) 		1
(1.00)
11q gain 112 (20%) 461 0.867
(1.00) 		0.999
(1.00) 		1
(1.00) 		0.589
(1.00) 		0.727
(1.00) 		0.0758
(0.681) 		0.218
(0.872)
14q gain 57 (10%) 516 0.0889
(0.698) 		0.249
(0.895) 		1
(1.00) 		0.413
(1.00) 		0.766
(1.00) 		0.856
(1.00) 		0.609
(1.00)
15q gain 38 (7%) 535 0.117
(0.782) 		0.769
(1.00) 		1
(1.00) 		1
(1.00) 		0.134
(0.785) 		1
(1.00)
16p gain 59 (10%) 514 0.728
(1.00) 		0.204
(0.872) 		1
(1.00) 		1
(1.00) 		0.0528
(0.619) 		0.121
(0.785) 		1
(1.00)
16q gain 32 (6%) 541 0.731
(1.00) 		0.95
(1.00) 		1
(1.00) 		1
(1.00) 		0.162
(0.84) 		0.219
(0.872) 		1
(1.00)
17p gain 21 (4%) 552 0.105
(0.726) 		0.241
(0.895) 		1
(1.00) 		1
(1.00) 		0.923
(1.00) 		1
(1.00)
17q gain 41 (7%) 532 0.921
(1.00) 		0.495
(1.00) 		1
(1.00) 		1
(1.00) 		0.347
(0.975) 		0.0915
(0.7) 		1
(1.00)
18p gain 119 (21%) 454 0.125
(0.785) 		0.0255
(0.407) 		1
(1.00) 		0.589
(1.00) 		0.449
(1.00) 		0.363
(0.997) 		1
(1.00)
18q gain 67 (12%) 506 0.178
(0.853) 		0.549
(1.00) 		1
(1.00) 		1
(1.00) 		0.745
(1.00) 		0.858
(1.00) 		0.612
(1.00)
19p gain 169 (29%) 404 0.65
(1.00) 		0.0496
(0.619) 		0.783
(1.00) 		0.153
(0.821) 		0.449
(1.00) 		0.275
(0.932) 		0.731
(1.00)
22q gain 23 (4%) 550 0.183
(0.853) 		0.851
(1.00) 		0.186
(0.853) 		1
(1.00) 		0.476
(1.00) 		1
(1.00) 		1
(1.00)
xp gain 78 (14%) 495 0.775
(1.00) 		0.138
(0.785) 		0.0328
(0.509) 		0.524
(1.00) 		0.772
(1.00) 		0.131
(0.785) 		1
(1.00)
xq gain 108 (19%) 465 0.859
(1.00) 		0.15
(0.818) 		0.0237
(0.389) 		0.589
(1.00) 		0.692
(1.00) 		1
(1.00) 		1
(1.00)
1p loss 60 (10%) 513 0.844
(1.00) 		0.402
(1.00) 		1
(1.00) 		0.419
(1.00) 		0.148
(0.818) 		0.859
(1.00) 		0.302
(0.938)
1q loss 40 (7%) 533 0.49
(1.00) 		0.721
(1.00) 		1
(1.00) 		0.283
(0.938) 		0.181
(0.853) 		0.588
(1.00) 		0.527
(1.00)
2p loss 52 (9%) 521 0.956
(1.00) 		0.654
(1.00) 		1
(1.00) 		1
(1.00) 		0.166
(0.84) 		1
(1.00)
2q loss 62 (11%) 511 0.638
(1.00) 		0.0374
(0.564) 		0.231
(0.895) 		1
(1.00) 		0.522
(1.00) 		0.655
(1.00) 		1
(1.00)
3p loss 96 (17%) 477 0.363
(0.997) 		0.0139
(0.266) 		0.608
(1.00) 		1
(1.00) 		0.424
(1.00) 		0.242
(0.895) 		1
(1.00)
3q loss 42 (7%) 531 0.471
(1.00) 		0.24
(0.895) 		0.317
(0.941) 		0.317
(0.941) 		0.739
(1.00) 		0.557
(1.00)
4p loss 312 (54%) 261 0.499
(1.00) 		0.775
(1.00) 		0.412
(1.00) 		1
(1.00) 		0.126
(0.785) 		0.736
(1.00) 		1
(1.00)
4q loss 360 (63%) 213 0.96
(1.00) 		0.614
(1.00) 		1
(1.00) 		0.656
(1.00) 		0.781
(1.00) 		0.668
(1.00) 		0.326
(0.941)
5p loss 132 (23%) 441 0.997
(1.00) 		0.0157
(0.291) 		0.735
(1.00) 		0.593
(1.00) 		0.117
(0.782) 		0.124
(0.785) 		0.706
(1.00)
5q loss 226 (39%) 347 0.291
(0.938) 		0.0214
(0.372) 		1
(1.00) 		1
(1.00) 		0.135
(0.785) 		0.194
(0.869) 		0.532
(1.00)
6p loss 159 (28%) 414 0.399
(1.00) 		0.061
(0.636) 		1
(1.00) 		0.616
(1.00) 		0.91
(1.00) 		0.279
(0.932) 		0.73
(1.00)
6q loss 236 (41%) 337 0.695
(1.00) 		0.0856
(0.698) 		0.5
(1.00) 		1
(1.00) 		0.631
(1.00) 		0.429
(1.00) 		0.526
(1.00)
7p loss 121 (21%) 452 0.722
(1.00) 		0.679
(1.00) 		0.45
(1.00) 		0.59
(1.00) 		0.0995
(0.705) 		0.543
(1.00) 		0.694
(1.00)
7q loss 79 (14%) 494 0.919
(1.00) 		0.289
(0.938) 		0.3
(0.938) 		0.534
(1.00) 		0.134
(0.785) 		0.549
(1.00) 		0.617
(1.00)
8p loss 268 (47%) 305 0.304
(0.938) 		0.0468
(0.598) 		0.513
(1.00) 		1
(1.00) 		0.264
(0.918) 		0.277
(0.932) 		0.754
(1.00)
9p loss 264 (46%) 309 0.799
(1.00) 		0.021
(0.372) 		0.413
(1.00) 		1
(1.00) 		0.76
(1.00) 		0.209
(0.872) 		0.526
(1.00)
10p loss 98 (17%) 475 0.969
(1.00) 		0.212
(0.872) 		1
(1.00) 		0.595
(1.00) 		0.745
(1.00) 		0.629
(1.00) 		0.652
(1.00)
10q loss 127 (22%) 446 0.613
(1.00) 		0.0947
(0.705) 		0.464
(1.00) 		0.303
(0.938) 		0.956
(1.00) 		1
(1.00) 		1
(1.00)
11q loss 147 (26%) 426 0.287
(0.938) 		0.0135
(0.266) 		0.0804
(0.698) 		0.607
(1.00) 		0.29
(0.938) 		0.867
(1.00) 		0.708
(1.00)
12p loss 78 (14%) 495 0.828
(1.00) 		0.0751
(0.681) 		1
(1.00) 		1
(1.00) 		0.632
(1.00) 		1
(1.00) 		1
(1.00)
12q loss 105 (18%) 468 0.678
(1.00) 		0.381
(1.00) 		1
(1.00) 		0.59
(1.00) 		0.405
(1.00) 		0.675
(1.00) 		1
(1.00)
13q loss 304 (53%) 269 0.206
(0.872) 		0.598
(1.00) 		0.517
(1.00) 		0.673
(1.00) 		0.888
(1.00) 		0.609
(1.00) 		0.524
(1.00)
16p loss 332 (58%) 241 0.421
(1.00) 		0.168
(0.84) 		1
(1.00) 		0.077
(0.681) 		0.926
(1.00) 		1
(1.00) 		0.0973
(0.705)
17p loss 474 (83%) 99 0.645
(1.00) 		0.377
(1.00) 		0.207
(0.872) 		1
(1.00) 		0.613
(1.00) 		0.294
(0.938) 		0.385
(1.00)
17q loss 384 (67%) 189 0.621
(1.00) 		0.608
(1.00) 		0.801
(1.00) 		1
(1.00) 		0.0221
(0.373) 		0.573
(1.00) 		0.0889
(0.698)
18p loss 229 (40%) 344 0.0446
(0.598) 		0.987
(1.00) 		0.496
(1.00) 		0.0855
(0.698) 		0.749
(1.00) 		0.348
(0.975) 		1
(1.00)
18q loss 285 (50%) 288 0.246
(0.895) 		0.4
(1.00) 		0.528
(1.00) 		0.209
(0.872) 		0.73
(1.00) 		0.266
(0.918) 		0.207
(0.872)
19p loss 182 (32%) 391 0.916
(1.00) 		0.074
(0.681) 		1
(1.00) 		1
(1.00) 		0.323
(0.941) 		0.219
(0.872) 		0.737
(1.00)
19q loss 173 (30%) 400 0.3
(0.938) 		1
(1.00) 		0.288
(0.938) 		1
(1.00) 		0.129
(0.785) 		0.216
(0.872) 		0.513
(1.00)
20p loss 50 (9%) 523 0.296
(0.938) 		0.324
(0.941) 		1
(1.00) 		0.376
(1.00) 		0.421
(1.00) 		0.106
(0.727) 		0.244
(0.895)
20q loss 33 (6%) 540 0.349
(0.975) 		0.897
(1.00) 		1
(1.00) 		1
(1.00) 		0.476
(1.00) 		0.496
(1.00)
21q loss 198 (35%) 375 0.316
(0.941) 		0.267
(0.918) 		0.797
(1.00) 		0.663
(1.00) 		0.173
(0.85) 		0.957
(1.00) 		0.75
(1.00)
22q loss 429 (75%) 144 0.484
(1.00) 		0.141
(0.795) 		0.529
(1.00) 		0.34
(0.971) 		0.387
(1.00) 		0.0634
(0.638) 		1
(1.00)
'1q gain' versus 'YEARS_TO_BIRTH'

P value = 0.000323 (Wilcoxon-test), Q value = 0.014

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 211 62.0 (10.7)
1Q GAIN WILD-TYPE 341 58.5 (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 = 5.5e-06 (Wilcoxon-test), Q value = 0.00039

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 177 63.2 (11.2)
2P GAIN WILD-TYPE 375 58.3 (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 = 0.00314 (Wilcoxon-test), Q value = 0.09

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 62.2 (10.8)
2Q GAIN WILD-TYPE 406 59.0 (11.7)

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 = 0.00429 (Wilcoxon-test), Q value = 0.11

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 156 62.1 (11.3)
3P GAIN WILD-TYPE 396 58.9 (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 = 1.03e-07 (Wilcoxon-test), Q value = 2e-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 268 62.5 (11.1)
3Q GAIN WILD-TYPE 284 57.3 (11.4)

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 = 0.00886 (Wilcoxon-test), Q value = 0.19

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 61.6 (11.7)
5P GAIN WILD-TYPE 360 58.9 (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 = 8.9e-07 (Wilcoxon-test), Q value = 7.3e-05

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 167 63.4 (10.9)
6P GAIN WILD-TYPE 385 58.3 (11.5)

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 = 1.85e-05 (Wilcoxon-test), Q value = 0.0012

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 96 64.3 (10.6)
6Q GAIN WILD-TYPE 456 58.9 (11.5)

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 = 0.000536 (Wilcoxon-test), Q value = 0.022

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 169 62.4 (10.9)
7P GAIN WILD-TYPE 383 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 = 0.0011 (Wilcoxon-test), Q value = 0.039

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 192 62.0 (11.1)
7Q GAIN WILD-TYPE 360 58.7 (11.7)

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 = 4.09e-08 (Wilcoxon-test), Q value = 1.2e-05

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 181 63.6 (11.0)
10P GAIN WILD-TYPE 371 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 = 0.00508 (Wilcoxon-test), Q value = 0.13

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 104 62.6 (11.2)
10Q GAIN WILD-TYPE 448 59.2 (11.6)

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 = 1.14e-09 (Wilcoxon-test), Q value = 6.5e-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 243 63.3 (11.1)
12P GAIN WILD-TYPE 309 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 = 3.04e-07 (Wilcoxon-test), Q value = 3.5e-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 167 63.6 (10.4)
12Q GAIN WILD-TYPE 385 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 = 0.00903 (Wilcoxon-test), Q value = 0.19

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 16 83.8 (10.9)
12Q GAIN WILD-TYPE 66 73.8 (13.9)

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

'13q gain' versus 'YEARS_TO_BIRTH'

P value = 0.0091 (Wilcoxon-test), Q value = 0.19

Table S16.  Gene #25: '13q gain' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 552 59.8 (11.6)
13Q GAIN MUTATED 58 63.3 (9.6)
13Q GAIN WILD-TYPE 494 59.4 (11.7)

Figure S16.  Get High-res Image Gene #25: '13q gain' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'19q gain' versus 'YEARS_TO_BIRTH'

P value = 0.00392 (Wilcoxon-test), Q value = 0.11

Table S17.  Gene #35: '19q gain' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 552 59.8 (11.6)
19Q GAIN MUTATED 156 62.3 (11.5)
19Q GAIN WILD-TYPE 396 58.9 (11.5)

Figure S17.  Get High-res Image Gene #35: '19q gain' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'20p gain' versus 'YEARS_TO_BIRTH'

P value = 2.88e-07 (Wilcoxon-test), Q value = 3.5e-05

Table S18.  Gene #36: '20p gain' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 552 59.8 (11.6)
20P GAIN MUTATED 277 62.3 (11.5)
20P GAIN WILD-TYPE 275 57.3 (11.1)

Figure S18.  Get High-res Image Gene #36: '20p gain' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'20q gain' versus 'YEARS_TO_BIRTH'

P value = 3.05e-05 (Wilcoxon-test), Q value = 0.0018

Table S19.  Gene #37: '20q gain' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 552 59.8 (11.6)
20Q GAIN MUTATED 314 61.7 (11.8)
20Q GAIN WILD-TYPE 238 57.4 (10.8)

Figure S19.  Get High-res Image Gene #37: '20q gain' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'21q gain' versus 'YEARS_TO_BIRTH'

P value = 0.00148 (Wilcoxon-test), Q value = 0.05

Table S20.  Gene #38: '21q gain' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 552 59.8 (11.6)
21Q GAIN MUTATED 104 63.1 (10.6)
21Q GAIN WILD-TYPE 448 59.1 (11.7)

Figure S20.  Get High-res Image Gene #38: '21q gain' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'8q loss' versus 'YEARS_TO_BIRTH'

P value = 0.00857 (Wilcoxon-test), Q value = 0.19

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 62.9 (11.9)
8Q LOSS WILD-TYPE 467 59.3 (11.4)

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 = 4.07e-07 (Wilcoxon-test), Q value = 3.9e-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 273 62.4 (11.3)
9Q LOSS WILD-TYPE 279 57.3 (11.3)

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

'11p loss' versus 'YEARS_TO_BIRTH'

P value = 0.00162 (Wilcoxon-test), Q value = 0.052

Table S23.  Gene #62: '11p loss' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 552 59.8 (11.6)
11P LOSS MUTATED 191 62.0 (11.5)
11P LOSS WILD-TYPE 361 58.7 (11.4)

Figure S23.  Get High-res Image Gene #62: '11p loss' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'14q loss' versus 'YEARS_TO_BIRTH'

P value = 0.000709 (Wilcoxon-test), Q value = 0.027

Table S24.  Gene #67: '14q loss' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 552 59.8 (11.6)
14Q LOSS MUTATED 210 61.9 (11.3)
14Q LOSS WILD-TYPE 342 58.6 (11.6)

Figure S24.  Get High-res Image Gene #67: '14q loss' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'15q loss' versus 'YEARS_TO_BIRTH'

P value = 0.000136 (Wilcoxon-test), Q value = 0.0065

Table S25.  Gene #68: '15q loss' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 552 59.8 (11.6)
15Q LOSS MUTATED 269 61.8 (11.3)
15Q LOSS WILD-TYPE 283 58.0 (11.5)

Figure S25.  Get High-res Image Gene #68: '15q loss' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'16q loss' versus 'YEARS_TO_BIRTH'

P value = 5.44e-05 (Wilcoxon-test), Q value = 0.0028

Table S26.  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 (11.4)
16Q LOSS WILD-TYPE 158 56.6 (11.4)

Figure S26.  Get High-res Image Gene #70: '16q loss' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'xp loss' versus 'YEARS_TO_BIRTH'

P value = 0.0106 (Wilcoxon-test), Q value = 0.22

Table S27.  Gene #81: 'xp loss' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 552 59.8 (11.6)
XP LOSS MUTATED 312 58.8 (11.5)
XP LOSS WILD-TYPE 240 61.2 (11.6)

Figure S27.  Get High-res Image Gene #81: 'xp loss' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'xq loss' versus 'YEARS_TO_BIRTH'

P value = 0.002 (Wilcoxon-test), Q value = 0.06

Table S28.  Gene #82: 'xq loss' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 552 59.8 (11.6)
XQ LOSS MUTATED 269 58.3 (11.3)
XQ LOSS WILD-TYPE 283 61.3 (11.6)

Figure S28.  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/22534547/transformed.cor.cli.txt

  • Clinical data file = /xchip/cga/gdac-prod/tcga-gdac/jobResults/Append_Data/OV-TP/22507289/OV-TP.merged_data.txt

  • Number of patients = 573

  • Number of significantly arm-level cnvs = 82

  • Number of selected clinical features = 7

  • 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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