Correlation between copy number variations of arm-level result and selected clinical features
Glioblastoma Multiforme (Primary solid tumor)
15 July 2014  |  analyses__2014_07_15
Maintainer Information
Citation Information
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/C11C1VKH
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 560 patients, 10 significant findings detected with Q value < 0.25.

  • 7p gain cnv correlated to 'Time to Death' and 'AGE'.

  • 7q gain cnv correlated to 'Time to Death' and 'AGE'.

  • 10p gain cnv correlated to 'AGE'.

  • 20p gain cnv correlated to 'AGE'.

  • 10p loss cnv correlated to 'Time to Death' and 'AGE'.

  • 10q loss cnv correlated to 'Time to Death' and '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, 10 significant findings detected.

Clinical
Features
Time
to
Death
AGE GENDER KARNOFSKY
PERFORMANCE
SCORE
HISTOLOGICAL
TYPE
RADIATIONS
RADIATION
REGIMENINDICATION
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
7p gain 454 (81%) 106 9.22e-05
(0.0583)
6.74e-06
(0.00429)
1
(1.00)
0.714
(1.00)
0.0153
(1.00)
0.133
(1.00)
0.0468
(1.00)
0.27
(1.00)
7q gain 459 (82%) 101 0.000243
(0.153)
2.32e-05
(0.0147)
0.368
(1.00)
0.899
(1.00)
0.0265
(1.00)
0.0995
(1.00)
0.0304
(1.00)
0.249
(1.00)
10p loss 466 (83%) 94 1.95e-05
(0.0124)
4.66e-09
(2.98e-06)
0.249
(1.00)
0.166
(1.00)
0.00266
(1.00)
0.716
(1.00)
0.127
(1.00)
0.237
(1.00)
10q loss 478 (85%) 82 6.1e-05
(0.0387)
3.5e-08
(2.23e-05)
0.541
(1.00)
0.0146
(1.00)
0.0125
(1.00)
0.61
(1.00)
0.0749
(1.00)
0.0931
(1.00)
10p gain 12 (2%) 548 0.00399
(1.00)
0.000192
(0.121)
0.0706
(1.00)
0.64
(1.00)
0.542
(1.00)
1
(1.00)
0.0226
(1.00)
0.268
(1.00)
20p gain 216 (39%) 344 0.543
(1.00)
9.16e-05
(0.058)
0.287
(1.00)
0.492
(1.00)
0.494
(1.00)
0.515
(1.00)
0.0361
(1.00)
1
(1.00)
1p gain 81 (14%) 479 0.243
(1.00)
0.511
(1.00)
0.624
(1.00)
0.234
(1.00)
0.146
(1.00)
0.368
(1.00)
0.837
(1.00)
0.67
(1.00)
1q gain 87 (16%) 473 0.588
(1.00)
0.529
(1.00)
0.403
(1.00)
0.243
(1.00)
0.202
(1.00)
0.383
(1.00)
0.567
(1.00)
0.689
(1.00)
2p gain 36 (6%) 524 0.7
(1.00)
0.845
(1.00)
0.111
(1.00)
0.509
(1.00)
1
(1.00)
0.854
(1.00)
0.135
(1.00)
1
(1.00)
2q gain 35 (6%) 525 0.584
(1.00)
0.345
(1.00)
0.284
(1.00)
0.353
(1.00)
1
(1.00)
1
(1.00)
0.124
(1.00)
1
(1.00)
3p gain 56 (10%) 504 0.947
(1.00)
0.0286
(1.00)
0.391
(1.00)
0.899
(1.00)
0.496
(1.00)
1
(1.00)
1
(1.00)
1
(1.00)
3q gain 61 (11%) 499 0.917
(1.00)
0.0477
(1.00)
0.581
(1.00)
0.837
(1.00)
0.418
(1.00)
0.772
(1.00)
0.457
(1.00)
1
(1.00)
4p gain 36 (6%) 524 0.928
(1.00)
0.466
(1.00)
0.86
(1.00)
0.0761
(1.00)
1
(1.00)
0.712
(1.00)
0.406
(1.00)
0.584
(1.00)
4q gain 33 (6%) 527 0.94
(1.00)
0.536
(1.00)
0.467
(1.00)
0.0726
(1.00)
1
(1.00)
0.441
(1.00)
0.369
(1.00)
1
(1.00)
5p gain 49 (9%) 511 0.854
(1.00)
0.646
(1.00)
0.168
(1.00)
0.21
(1.00)
0.0383
(1.00)
0.633
(1.00)
0.912
(1.00)
0.308
(1.00)
5q gain 41 (7%) 519 0.684
(1.00)
0.56
(1.00)
0.134
(1.00)
0.743
(1.00)
0.052
(1.00)
0.49
(1.00)
0.643
(1.00)
0.612
(1.00)
6p gain 23 (4%) 537 0.424
(1.00)
0.707
(1.00)
0.514
(1.00)
0.513
(1.00)
1
(1.00)
0.171
(1.00)
0.264
(1.00)
1
(1.00)
6q gain 22 (4%) 538 0.371
(1.00)
0.396
(1.00)
0.828
(1.00)
0.475
(1.00)
1
(1.00)
0.485
(1.00)
0.527
(1.00)
1
(1.00)
8p gain 52 (9%) 508 0.86
(1.00)
0.769
(1.00)
0.657
(1.00)
0.589
(1.00)
0.894
(1.00)
0.642
(1.00)
0.114
(1.00)
1
(1.00)
8q gain 59 (11%) 501 0.451
(1.00)
0.34
(1.00)
0.481
(1.00)
0.691
(1.00)
0.911
(1.00)
1
(1.00)
0.337
(1.00)
1
(1.00)
9p gain 47 (8%) 513 0.658
(1.00)
0.681
(1.00)
0.163
(1.00)
0.884
(1.00)
0.315
(1.00)
0.745
(1.00)
0.462
(1.00)
0.249
(1.00)
9q gain 71 (13%) 489 0.733
(1.00)
0.875
(1.00)
0.195
(1.00)
0.649
(1.00)
0.601
(1.00)
1
(1.00)
0.63
(1.00)
0.652
(1.00)
10q gain 3 (1%) 557 0.481
(1.00)
0.664
(1.00)
0.564
(1.00)
1
(1.00)
0.238
(1.00)
1
(1.00)
0.0742
(1.00)
11p gain 17 (3%) 543 0.584
(1.00)
0.936
(1.00)
0.806
(1.00)
0.377
(1.00)
1
(1.00)
0.601
(1.00)
0.756
(1.00)
0.341
(1.00)
11q gain 14 (2%) 546 0.142
(1.00)
0.111
(1.00)
0.267
(1.00)
0.165
(1.00)
0.601
(1.00)
0.244
(1.00)
1
(1.00)
0.305
(1.00)
12p gain 58 (10%) 502 0.6
(1.00)
0.386
(1.00)
0.571
(1.00)
0.795
(1.00)
0.91
(1.00)
0.552
(1.00)
0.921
(1.00)
1
(1.00)
12q gain 47 (8%) 513 0.983
(1.00)
0.748
(1.00)
0.278
(1.00)
0.944
(1.00)
0.549
(1.00)
0.624
(1.00)
0.133
(1.00)
0.612
(1.00)
13q gain 10 (2%) 550 0.551
(1.00)
0.0115
(1.00)
0.202
(1.00)
0.0712
(1.00)
0.297
(1.00)
0.0811
(1.00)
0.644
(1.00)
1
(1.00)
14q gain 22 (4%) 538 0.269
(1.00)
0.0627
(1.00)
0.513
(1.00)
0.465
(1.00)
0.0536
(1.00)
0.645
(1.00)
1
(1.00)
1
(1.00)
15q gain 24 (4%) 536 0.513
(1.00)
0.909
(1.00)
0.527
(1.00)
0.09
(1.00)
0.45
(1.00)
0.177
(1.00)
1
(1.00)
1
(1.00)
16p gain 38 (7%) 522 0.0298
(1.00)
0.817
(1.00)
0.306
(1.00)
0.95
(1.00)
1
(1.00)
0.0726
(1.00)
0.254
(1.00)
1
(1.00)
16q gain 37 (7%) 523 0.114
(1.00)
0.84
(1.00)
0.606
(1.00)
0.84
(1.00)
1
(1.00)
0.0999
(1.00)
0.214
(1.00)
1
(1.00)
17p gain 47 (8%) 513 0.244
(1.00)
0.042
(1.00)
0.212
(1.00)
0.382
(1.00)
0.276
(1.00)
0.329
(1.00)
0.367
(1.00)
1
(1.00)
17q gain 58 (10%) 502 0.0412
(1.00)
0.0231
(1.00)
0.479
(1.00)
0.467
(1.00)
0.5
(1.00)
0.299
(1.00)
0.49
(1.00)
0.377
(1.00)
18p gain 57 (10%) 503 0.793
(1.00)
0.422
(1.00)
0.669
(1.00)
0.232
(1.00)
0.174
(1.00)
0.881
(1.00)
0.358
(1.00)
0.357
(1.00)
18q gain 57 (10%) 503 0.946
(1.00)
0.25
(1.00)
0.2
(1.00)
0.235
(1.00)
0.174
(1.00)
0.653
(1.00)
0.569
(1.00)
1
(1.00)
19p gain 218 (39%) 342 0.42
(1.00)
0.831
(1.00)
0.859
(1.00)
0.909
(1.00)
0.337
(1.00)
0.71
(1.00)
0.595
(1.00)
0.551
(1.00)
19q gain 193 (34%) 367 0.447
(1.00)
0.655
(1.00)
0.716
(1.00)
0.945
(1.00)
0.923
(1.00)
0.634
(1.00)
0.333
(1.00)
0.357
(1.00)
20q gain 214 (38%) 346 0.734
(1.00)
0.000431
(0.271)
0.247
(1.00)
0.669
(1.00)
0.476
(1.00)
0.513
(1.00)
0.0499
(1.00)
1
(1.00)
21q gain 62 (11%) 498 0.564
(1.00)
0.119
(1.00)
1
(1.00)
0.128
(1.00)
0.0515
(1.00)
1
(1.00)
0.0967
(1.00)
0.376
(1.00)
22q gain 34 (6%) 526 0.44
(1.00)
0.601
(1.00)
1
(1.00)
0.318
(1.00)
0.599
(1.00)
1
(1.00)
0.59
(1.00)
0.154
(1.00)
xq gain 16 (3%) 544 0.867
(1.00)
0.541
(1.00)
1
(1.00)
0.621
(1.00)
0.262
(1.00)
0.17
(1.00)
0.726
(1.00)
0.248
(1.00)
1p loss 15 (3%) 545 0.272
(1.00)
0.0548
(1.00)
0.424
(1.00)
0.817
(1.00)
0.626
(1.00)
0.575
(1.00)
0.73
(1.00)
1
(1.00)
1q loss 14 (2%) 546 0.537
(1.00)
0.0281
(1.00)
1
(1.00)
0.17
(1.00)
1
(1.00)
0.39
(1.00)
1
(1.00)
1
(1.00)
2p loss 32 (6%) 528 0.756
(1.00)
0.0863
(1.00)
0.135
(1.00)
0.865
(1.00)
1
(1.00)
0.17
(1.00)
0.671
(1.00)
1
(1.00)
2q loss 32 (6%) 528 0.932
(1.00)
0.115
(1.00)
0.263
(1.00)
0.596
(1.00)
0.313
(1.00)
0.0771
(1.00)
0.671
(1.00)
1
(1.00)
3p loss 40 (7%) 520 0.273
(1.00)
0.0617
(1.00)
1
(1.00)
0.987
(1.00)
0.287
(1.00)
0.113
(1.00)
0.566
(1.00)
0.21
(1.00)
3q loss 34 (6%) 526 0.739
(1.00)
0.621
(1.00)
0.589
(1.00)
0.643
(1.00)
0.415
(1.00)
0.572
(1.00)
0.686
(1.00)
0.523
(1.00)
4p loss 53 (9%) 507 0.718
(1.00)
0.694
(1.00)
0.184
(1.00)
0.252
(1.00)
0.526
(1.00)
0.643
(1.00)
0.609
(1.00)
0.308
(1.00)
4q loss 53 (9%) 507 0.211
(1.00)
0.17
(1.00)
0.659
(1.00)
0.208
(1.00)
1
(1.00)
0.643
(1.00)
0.565
(1.00)
0.278
(1.00)
5p loss 42 (8%) 518 0.0515
(1.00)
0.49
(1.00)
1
(1.00)
0.561
(1.00)
0.772
(1.00)
0.0373
(1.00)
0.0851
(1.00)
0.21
(1.00)
5q loss 43 (8%) 517 0.1
(1.00)
0.54
(1.00)
1
(1.00)
0.751
(1.00)
0.325
(1.00)
0.127
(1.00)
0.268
(1.00)
0.0512
(1.00)
6p loss 86 (15%) 474 0.00594
(1.00)
0.428
(1.00)
0.811
(1.00)
0.503
(1.00)
0.571
(1.00)
0.53
(1.00)
0.207
(1.00)
0.701
(1.00)
6q loss 123 (22%) 437 0.354
(1.00)
0.795
(1.00)
0.348
(1.00)
0.618
(1.00)
0.764
(1.00)
1
(1.00)
0.172
(1.00)
0.478
(1.00)
7p loss 8 (1%) 552 0.346
(1.00)
0.0509
(1.00)
1
(1.00)
0.744
(1.00)
1
(1.00)
0.446
(1.00)
0.557
(1.00)
1
(1.00)
7q loss 6 (1%) 554 0.518
(1.00)
0.023
(1.00)
1
(1.00)
0.304
(1.00)
1
(1.00)
0.67
(1.00)
0.458
(1.00)
1
(1.00)
8p loss 58 (10%) 502 0.637
(1.00)
0.193
(1.00)
0.156
(1.00)
0.395
(1.00)
0.91
(1.00)
0.552
(1.00)
0.00787
(1.00)
0.621
(1.00)
8q loss 42 (8%) 518 0.217
(1.00)
0.23
(1.00)
0.416
(1.00)
0.248
(1.00)
1
(1.00)
1
(1.00)
0.364
(1.00)
1
(1.00)
9p loss 195 (35%) 365 0.605
(1.00)
0.558
(1.00)
0.717
(1.00)
0.631
(1.00)
0.547
(1.00)
0.775
(1.00)
0.358
(1.00)
0.064
(1.00)
9q loss 90 (16%) 470 0.551
(1.00)
0.554
(1.00)
0.29
(1.00)
0.594
(1.00)
0.0953
(1.00)
1
(1.00)
0.103
(1.00)
0.233
(1.00)
11p loss 97 (17%) 463 0.174
(1.00)
0.845
(1.00)
0.0861
(1.00)
0.675
(1.00)
0.379
(1.00)
0.632
(1.00)
0.663
(1.00)
0.7
(1.00)
11q loss 92 (16%) 468 0.883
(1.00)
0.432
(1.00)
0.414
(1.00)
0.685
(1.00)
1
(1.00)
0.271
(1.00)
1
(1.00)
0.229
(1.00)
12p loss 59 (11%) 501 0.978
(1.00)
0.521
(1.00)
0.401
(1.00)
0.792
(1.00)
1
(1.00)
0.66
(1.00)
0.372
(1.00)
1
(1.00)
12q loss 58 (10%) 502 0.982
(1.00)
0.562
(1.00)
0.479
(1.00)
0.624
(1.00)
0.654
(1.00)
0.882
(1.00)
0.366
(1.00)
0.347
(1.00)
13q loss 181 (32%) 379 0.785
(1.00)
0.683
(1.00)
0.926
(1.00)
0.819
(1.00)
0.551
(1.00)
0.629
(1.00)
0.378
(1.00)
0.759
(1.00)
14q loss 145 (26%) 415 0.989
(1.00)
0.688
(1.00)
0.431
(1.00)
0.886
(1.00)
0.718
(1.00)
0.837
(1.00)
0.0906
(1.00)
0.312
(1.00)
15q loss 101 (18%) 459 0.732
(1.00)
0.0701
(1.00)
0.5
(1.00)
0.889
(1.00)
0.688
(1.00)
0.0763
(1.00)
0.47
(1.00)
0.249
(1.00)
16p loss 63 (11%) 497 0.0481
(1.00)
0.34
(1.00)
0.683
(1.00)
0.87
(1.00)
0.324
(1.00)
0.061
(1.00)
0.929
(1.00)
1
(1.00)
16q loss 82 (15%) 478 0.0178
(1.00)
0.775
(1.00)
1
(1.00)
0.591
(1.00)
0.641
(1.00)
0.0286
(1.00)
0.272
(1.00)
0.702
(1.00)
17p loss 61 (11%) 499 0.746
(1.00)
0.492
(1.00)
0.27
(1.00)
0.937
(1.00)
0.749
(1.00)
0.191
(1.00)
0.863
(1.00)
1
(1.00)
17q loss 40 (7%) 520 0.991
(1.00)
0.5
(1.00)
0.502
(1.00)
0.698
(1.00)
1
(1.00)
0.0339
(1.00)
0.73
(1.00)
0.595
(1.00)
18p loss 68 (12%) 492 0.125
(1.00)
0.849
(1.00)
0.51
(1.00)
0.463
(1.00)
0.772
(1.00)
1
(1.00)
0.356
(1.00)
0.645
(1.00)
18q loss 60 (11%) 500 0.295
(1.00)
0.811
(1.00)
0.78
(1.00)
0.186
(1.00)
0.745
(1.00)
0.245
(1.00)
0.231
(1.00)
0.14
(1.00)
19p loss 25 (4%) 535 0.432
(1.00)
0.662
(1.00)
0.677
(1.00)
0.938
(1.00)
0.633
(1.00)
1
(1.00)
0.833
(1.00)
1
(1.00)
19q loss 33 (6%) 527 0.512
(1.00)
0.662
(1.00)
0.716
(1.00)
0.516
(1.00)
0.188
(1.00)
0.849
(1.00)
0.877
(1.00)
1
(1.00)
20p loss 18 (3%) 542 0.837
(1.00)
0.367
(1.00)
0.219
(1.00)
0.926
(1.00)
1
(1.00)
1
(1.00)
0.266
(1.00)
0.341
(1.00)
20q loss 16 (3%) 544 0.746
(1.00)
0.694
(1.00)
0.196
(1.00)
0.984
(1.00)
1
(1.00)
0.596
(1.00)
0.556
(1.00)
1
(1.00)
21q loss 40 (7%) 520 0.974
(1.00)
0.971
(1.00)
0.502
(1.00)
0.325
(1.00)
0.86
(1.00)
0.481
(1.00)
1
(1.00)
0.229
(1.00)
22q loss 178 (32%) 382 0.503
(1.00)
0.0935
(1.00)
1
(1.00)
0.458
(1.00)
0.343
(1.00)
0.697
(1.00)
0.934
(1.00)
1
(1.00)
xq loss 104 (19%) 456 0.301
(1.00)
0.792
(1.00)
0.505
(1.00)
0.312
(1.00)
0.837
(1.00)
0.726
(1.00)
0.226
(1.00)
0.473
(1.00)
'7p gain' versus 'Time to Death'

P value = 9.22e-05 (logrank test), Q value = 0.058

Table S1.  Gene #13: '7p gain' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 560 462 0.1 - 127.6 (10.1)
7P GAIN MUTATED 454 382 0.1 - 127.6 (9.7)
7P GAIN WILD-TYPE 106 80 0.2 - 108.8 (13.0)

Figure S1.  Get High-res Image Gene #13: '7p gain' versus Clinical Feature #1: 'Time to Death'

'7p gain' versus 'AGE'

P value = 6.74e-06 (Wilcoxon-test), Q value = 0.0043

Table S2.  Gene #13: '7p gain' versus Clinical Feature #2: 'AGE'

nPatients Mean (Std.Dev)
ALL 560 57.9 (14.5)
7P GAIN MUTATED 454 59.7 (12.4)
7P GAIN WILD-TYPE 106 50.1 (19.3)

Figure S2.  Get High-res Image Gene #13: '7p gain' versus Clinical Feature #2: 'AGE'

'7q gain' versus 'Time to Death'

P value = 0.000243 (logrank test), Q value = 0.15

Table S3.  Gene #14: '7q gain' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 560 462 0.1 - 127.6 (10.1)
7Q GAIN MUTATED 459 383 0.1 - 127.6 (9.6)
7Q GAIN WILD-TYPE 101 79 0.2 - 108.8 (14.0)

Figure S3.  Get High-res Image Gene #14: '7q gain' versus Clinical Feature #1: 'Time to Death'

'7q gain' versus 'AGE'

P value = 2.32e-05 (Wilcoxon-test), Q value = 0.015

Table S4.  Gene #14: '7q gain' versus Clinical Feature #2: 'AGE'

nPatients Mean (Std.Dev)
ALL 560 57.9 (14.5)
7Q GAIN MUTATED 459 59.6 (12.3)
7Q GAIN WILD-TYPE 101 49.9 (20.0)

Figure S4.  Get High-res Image Gene #14: '7q gain' versus Clinical Feature #2: 'AGE'

'10p gain' versus 'AGE'

P value = 0.000192 (Wilcoxon-test), Q value = 0.12

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

nPatients Mean (Std.Dev)
ALL 560 57.9 (14.5)
10P GAIN MUTATED 12 38.1 (18.1)
10P GAIN WILD-TYPE 548 58.3 (14.1)

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

'20p gain' versus 'AGE'

P value = 9.16e-05 (Wilcoxon-test), Q value = 0.058

Table S6.  Gene #36: '20p gain' versus Clinical Feature #2: 'AGE'

nPatients Mean (Std.Dev)
ALL 560 57.9 (14.5)
20P GAIN MUTATED 216 60.9 (13.1)
20P GAIN WILD-TYPE 344 56.0 (15.0)

Figure S6.  Get High-res Image Gene #36: '20p gain' versus Clinical Feature #2: 'AGE'

'10p loss' versus 'Time to Death'

P value = 1.95e-05 (logrank test), Q value = 0.012

Table S7.  Gene #59: '10p loss' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 560 462 0.1 - 127.6 (10.1)
10P LOSS MUTATED 466 391 0.1 - 127.6 (9.9)
10P LOSS WILD-TYPE 94 71 0.2 - 108.8 (12.5)

Figure S7.  Get High-res Image Gene #59: '10p loss' versus Clinical Feature #1: 'Time to Death'

'10p loss' versus 'AGE'

P value = 4.66e-09 (Wilcoxon-test), Q value = 3e-06

Table S8.  Gene #59: '10p loss' versus Clinical Feature #2: 'AGE'

nPatients Mean (Std.Dev)
ALL 560 57.9 (14.5)
10P LOSS MUTATED 466 59.8 (12.6)
10P LOSS WILD-TYPE 94 48.2 (18.7)

Figure S8.  Get High-res Image Gene #59: '10p loss' versus Clinical Feature #2: 'AGE'

'10q loss' versus 'Time to Death'

P value = 6.1e-05 (logrank test), Q value = 0.039

Table S9.  Gene #60: '10q loss' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 560 462 0.1 - 127.6 (10.1)
10Q LOSS MUTATED 478 400 0.1 - 127.6 (9.9)
10Q LOSS WILD-TYPE 82 62 0.2 - 108.8 (12.2)

Figure S9.  Get High-res Image Gene #60: '10q loss' versus Clinical Feature #1: 'Time to Death'

'10q loss' versus 'AGE'

P value = 3.5e-08 (Wilcoxon-test), Q value = 2.2e-05

Table S10.  Gene #60: '10q loss' versus Clinical Feature #2: 'AGE'

nPatients Mean (Std.Dev)
ALL 560 57.9 (14.5)
10Q LOSS MUTATED 478 59.5 (12.9)
10Q LOSS WILD-TYPE 82 48.1 (18.5)

Figure S10.  Get High-res Image Gene #60: '10q loss' versus Clinical Feature #2: 'AGE'

Methods & Data
Input
  • Copy number data file = transformed.cor.cli.txt

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

  • Number of patients = 560

  • 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)