Correlation between copy number variation genes (focal events) and selected clinical features
Glioblastoma Multiforme (Primary solid tumor)
02 April 2015  |  analyses__2015_04_02
Maintainer Information
Citation Information
doi:10.7908/C1XK8DKX
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 variation genes (focal events) and selected clinical features. Broad Institute of MIT and Harvard. doi:10.7908/C1XK8DKX
Overview
Introduction

This pipeline computes the correlation between significant copy number variation (cnv focal) genes and selected clinical features.

Summary

Testing the association between copy number variation 71 focal events and 8 clinical features across 570 patients, 27 significant findings detected with Q value < 0.25.

  • amp_3q26.33 cnv correlated to 'HISTOLOGICAL_TYPE'.

  • amp_7p11.2 cnv correlated to 'Time to Death' and 'YEARS_TO_BIRTH'.

  • amp_7q11.21 cnv correlated to 'Time to Death' and 'YEARS_TO_BIRTH'.

  • amp_7q21.2 cnv correlated to 'Time to Death' and 'YEARS_TO_BIRTH'.

  • amp_7q31.2 cnv correlated to 'Time to Death' and 'YEARS_TO_BIRTH'.

  • amp_14q32.33 cnv correlated to 'YEARS_TO_BIRTH'.

  • amp_17q25.1 cnv correlated to 'YEARS_TO_BIRTH'.

  • amp_21q21.1 cnv correlated to 'YEARS_TO_BIRTH'.

  • del_1p36.23 cnv correlated to 'GENDER'.

  • del_9p21.3 cnv correlated to 'YEARS_TO_BIRTH'.

  • del_10p15.3 cnv correlated to 'Time to Death' and 'YEARS_TO_BIRTH'.

  • del_10p13 cnv correlated to 'Time to Death',  'YEARS_TO_BIRTH', and 'HISTOLOGICAL_TYPE'.

  • del_10p11.23 cnv correlated to 'Time to Death',  'YEARS_TO_BIRTH', and 'HISTOLOGICAL_TYPE'.

  • del_10q23.31 cnv correlated to 'Time to Death' and 'YEARS_TO_BIRTH'.

  • del_10q26.3 cnv correlated to 'Time to Death' and 'YEARS_TO_BIRTH'.

  • del_11p15.5 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 71 focal events and 8 clinical features. Shown in the table are P values (Q values). Thresholded by Q value < 0.25, 27 significant findings detected.

Clinical
Features 		Time
to
Death 		YEARS
TO
BIRTH 		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
del 10p13 464 (81%) 106 2.25e-05
(0.00107) 		2.33e-08
(3.31e-06) 		0.0471
(0.51) 		0.718
(0.996) 		0.00824
(0.191) 		0.82
(1.00) 		0.119
(0.745) 		0.27
(0.892)
del 10p11 23 469 (82%) 101 1.95e-06
(0.000138) 		7.72e-11
(2.19e-08) 		0.116
(0.745) 		0.0919
(0.646) 		0.00305
(0.0855) 		0.816
(1.00) 		0.169
(0.823) 		0.252
(0.879)
amp 7p11 2 500 (88%) 70 1.01e-06
(8.17e-05) 		9.64e-13
(5.48e-10) 		0.243
(0.877) 		0.0444
(0.51) 		0.0465
(0.51) 		0.105
(0.701) 		0.463
(0.946) 		0.0606
(0.583)
amp 7q11 21 458 (80%) 112 2.08e-05
(0.00107) 		1.04e-07
(1.18e-05) 		0.198
(0.828) 		0.409
(0.937) 		0.0131
(0.265) 		0.145
(0.802) 		0.262
(0.892) 		0.14
(0.802)
amp 7q21 2 473 (83%) 97 0.000132
(0.00467) 		3.89e-06
(0.000245) 		0.425
(0.937) 		0.313
(0.912) 		0.108
(0.714) 		0.192
(0.826) 		0.0375
(0.495) 		0.0444
(0.51)
amp 7q31 2 466 (82%) 104 0.00226
(0.0675) 		0.00097
(0.0306) 		0.268
(0.892) 		0.869
(1.00) 		0.256
(0.883) 		0.0647
(0.608) 		0.0485
(0.51) 		0.0554
(0.552)
del 10p15 3 463 (81%) 107 3.44e-05
(0.0015) 		1.11e-08
(2.11e-06) 		0.153
(0.813) 		0.414
(0.937) 		0.024
(0.378) 		0.649
(0.987) 		0.182
(0.823) 		0.274
(0.894)
del 10q23 31 507 (89%) 63 5.62e-05
(0.00228) 		2.29e-07
(2.16e-05) 		0.785
(1.00) 		0.0867
(0.646) 		0.023
(0.373) 		0.888
(1.00) 		0.358
(0.92) 		0.635
(0.978)
del 10q26 3 508 (89%) 62 0.00316
(0.0855) 		9.13e-06
(0.000519) 		0.681
(0.994) 		0.0879
(0.646) 		0.089
(0.646) 		1
(1.00) 		0.0839
(0.646) 		0.632
(0.976)
amp 3q26 33 108 (19%) 462 0.19
(0.823) 		0.0316
(0.473) 		0.662
(0.992) 		0.698
(0.994) 		0.00068
(0.0227) 		0.91
(1.00) 		0.188
(0.823) 		0.701
(0.994)
amp 14q32 33 36 (6%) 534 0.404
(0.937) 		0.00533
(0.138) 		0.486
(0.948) 		0.307
(0.912) 		0.463
(0.946) 		0.856
(1.00) 		0.812
(1.00) 		1
(1.00)
amp 17q25 1 83 (15%) 487 0.0373
(0.495) 		0.00839
(0.191) 		0.183
(0.823) 		0.442
(0.937) 		0.783
(1.00) 		0.529
(0.948) 		0.159
(0.823) 		0.692
(0.994)
amp 21q21 1 69 (12%) 501 0.847
(1.00) 		0.00977
(0.213) 		1
(1.00) 		0.386
(0.925) 		0.201
(0.828) 		0.413
(0.937) 		0.0903
(0.646) 		0.378
(0.925)
del 1p36 23 132 (23%) 438 0.786
(1.00) 		0.126
(0.764) 		0.0109
(0.229) 		0.0667
(0.608) 		0.536
(0.948) 		0.526
(0.948) 		0.175
(0.823) 		0.311
(0.912)
del 9p21 3 417 (73%) 153 0.0183
(0.315) 		6.51e-05
(0.00247) 		0.44
(0.937) 		0.166
(0.823) 		0.664
(0.992) 		0.315
(0.912) 		0.546
(0.954) 		0.745
(1.00)
del 11p15 5 129 (23%) 441 0.0404
(0.51) 		0.00596
(0.147) 		0.219
(0.846) 		0.16
(0.823) 		0.528
(0.948) 		0.831
(1.00) 		1
(1.00) 		1
(1.00)
amp 1p36 21 91 (16%) 479 0.0752
(0.637) 		0.27
(0.892) 		0.483
(0.948) 		0.184
(0.823) 		0.0161
(0.295) 		0.715
(0.996) 		0.0893
(0.646) 		0.4
(0.937)
amp 1q32 1 158 (28%) 412 0.269
(0.892) 		0.178
(0.823) 		1
(1.00) 		0.359
(0.92) 		1
(1.00) 		0.843
(1.00) 		0.879
(1.00) 		0.526
(0.948)
amp 1q44 98 (17%) 472 0.559
(0.954) 		0.947
(1.00) 		0.214
(0.846) 		0.514
(0.948) 		0.144
(0.802) 		0.48
(0.948) 		0.908
(1.00) 		0.424
(0.937)
amp 2p24 3 49 (9%) 521 0.212
(0.846) 		0.277
(0.896) 		0.445
(0.937) 		0.916
(1.00) 		1
(1.00) 		0.754
(1.00) 		0.6
(0.967) 		0.612
(0.97)
amp 4p16 3 48 (8%) 522 0.609
(0.97) 		0.849
(1.00) 		0.356
(0.92) 		0.382
(0.925) 		0.904
(1.00) 		0.632
(0.976) 		0.776
(1.00) 		1
(1.00)
amp 4q12 107 (19%) 463 0.22
(0.846) 		0.147
(0.802) 		0.442
(0.937) 		0.842
(1.00) 		0.505
(0.948) 		0.305
(0.912) 		0.682
(0.994) 		1
(1.00)
amp 8q24 21 70 (12%) 500 0.0709
(0.622) 		0.441
(0.937) 		0.517
(0.948) 		0.926
(1.00) 		0.875
(1.00) 		0.788
(1.00) 		0.227
(0.846) 		1
(1.00)
amp 11p13 30 (5%) 540 0.785
(1.00) 		0.28
(0.896) 		1
(1.00) 		0.597
(0.966) 		0.737
(1.00) 		1
(1.00) 		0.769
(1.00) 		0.515
(0.948)
amp 12p13 32 84 (15%) 486 0.993
(1.00) 		0.173
(0.823) 		1
(1.00) 		0.845
(1.00) 		0.943
(1.00) 		0.532
(0.948) 		0.558
(0.954) 		0.688
(0.994)
amp 12q14 1 134 (24%) 436 0.286
(0.896) 		0.703
(0.994) 		0.419
(0.937) 		0.961
(1.00) 		0.719
(0.996) 		0.834
(1.00) 		0.722
(0.996) 		0.31
(0.912)
amp 12q15 92 (16%) 478 0.56
(0.954) 		0.579
(0.954) 		0.353
(0.92) 		0.98
(1.00) 		0.758
(1.00) 		0.546
(0.954) 		0.552
(0.954) 		0.229
(0.846)
amp 13q34 32 (6%) 538 0.827
(1.00) 		0.691
(0.994) 		0.36
(0.92) 		0.534
(0.948) 		0.477
(0.948) 		0.699
(0.994) 		1
(1.00) 		1
(1.00)
amp 13q34 30 (5%) 540 0.692
(0.994) 		0.415
(0.937) 		0.568
(0.954) 		0.39
(0.93) 		0.733
(1.00) 		0.843
(1.00) 		0.486
(0.948) 		1
(1.00)
amp 17p13 2 51 (9%) 519 0.704
(0.994) 		0.496
(0.948) 		0.293
(0.899) 		0.957
(1.00) 		0.521
(0.948) 		0.533
(0.948) 		0.711
(0.996) 		1
(1.00)
amp 19p13 3 240 (42%) 330 0.142
(0.802) 		0.673
(0.994) 		0.931
(1.00) 		0.17
(0.823) 		0.527
(0.948) 		0.857
(1.00) 		0.411
(0.937) 		0.571
(0.954)
amp 19p13 2 245 (43%) 325 0.244
(0.877) 		0.983
(1.00) 		1
(1.00) 		0.56
(0.954) 		0.47
(0.948) 		1
(1.00) 		0.724
(0.996) 		0.77
(1.00)
amp 19q12 213 (37%) 357 0.566
(0.954) 		0.503
(0.948) 		0.595
(0.966) 		0.893
(1.00) 		0.581
(0.954) 		0.854
(1.00) 		0.753
(1.00) 		0.385
(0.925)
del 1p36 32 96 (17%) 474 0.489
(0.948) 		0.618
(0.971) 		0.0293
(0.45) 		0.667
(0.994) 		0.119
(0.745) 		0.723
(0.996) 		0.0919
(0.646) 		0.7
(0.994)
del 1p32 3 60 (11%) 510 0.583
(0.955) 		0.0554
(0.552) 		0.126
(0.764) 		0.642
(0.985) 		0.577
(0.954) 		0.147
(0.802) 		0.266
(0.892) 		1
(1.00)
del 1p22 1 47 (8%) 523 0.497
(0.948) 		0.359
(0.92) 		1
(1.00) 		0.366
(0.921) 		0.073
(0.628) 		0.518
(0.948) 		1
(1.00) 		1
(1.00)
del 1q42 11 49 (9%) 521 0.142
(0.802) 		0.288
(0.896) 		1
(1.00) 		0.0434
(0.51) 		0.83
(1.00) 		0.152
(0.813) 		0.358
(0.92) 		0.251
(0.879)
del 1q44 34 (6%) 536 0.428
(0.937) 		0.32
(0.92) 		1
(1.00) 		0.299
(0.906) 		0.873
(1.00) 		0.851
(1.00) 		0.88
(1.00) 		0.475
(0.948)
del 2q22 1 46 (8%) 524 0.289
(0.896) 		0.094
(0.647) 		0.431
(0.937) 		0.578
(0.954) 		0.252
(0.879) 		0.0712
(0.622) 		0.41
(0.937) 		0.612
(0.97)
del 2q37 1 54 (9%) 516 0.878
(1.00) 		0.75
(1.00) 		0.188
(0.823) 		0.652
(0.987) 		1
(1.00) 		0.362
(0.921) 		0.466
(0.946) 		1
(1.00)
del 3p21 1 53 (9%) 517 0.0478
(0.51) 		0.0148
(0.28) 		0.769
(1.00) 		0.608
(0.97) 		0.334
(0.92) 		0.0474
(0.51) 		0.491
(0.948) 		0.338
(0.92)
del 3q13 31 56 (10%) 514 0.908
(1.00) 		0.397
(0.937) 		0.568
(0.954) 		0.252
(0.879) 		0.775
(1.00) 		0.231
(0.846) 		0.523
(0.948) 		0.347
(0.92)
del 3q22 1 58 (10%) 512 0.98
(1.00) 		0.385
(0.925) 		1
(1.00) 		0.458
(0.946) 		0.778
(1.00) 		0.56
(0.954) 		0.29
(0.896) 		0.366
(0.921)
del 3q29 65 (11%) 505 0.179
(0.823) 		0.571
(0.954) 		1
(1.00) 		0.342
(0.92) 		1
(1.00) 		0.262
(0.892) 		1
(1.00) 		1
(1.00)
del 4p16 3 76 (13%) 494 0.0788
(0.646) 		0.0921
(0.646) 		0.257
(0.883) 		0.376
(0.925) 		0.251
(0.879) 		0.0675
(0.608) 		0.444
(0.937) 		0.658
(0.988)
del 4q34 3 91 (16%) 479 0.0601
(0.583) 		0.115
(0.745) 		0.0464
(0.51) 		0.688
(0.994) 		0.948
(1.00) 		0.181
(0.823) 		0.225
(0.846) 		1
(1.00)
del 5q34 68 (12%) 502 0.0355
(0.492) 		0.273
(0.894) 		0.186
(0.823) 		0.574
(0.954) 		0.451
(0.945) 		0.784
(1.00) 		0.0665
(0.608) 		0.164
(0.823)
del 6q22 31 157 (28%) 413 0.0223
(0.372) 		0.219
(0.846) 		0.0841
(0.646) 		0.58
(0.954) 		0.421
(0.937) 		0.921
(1.00) 		0.513
(0.948) 		0.193
(0.826)
del 6q26 178 (31%) 392 0.0877
(0.646) 		0.886
(1.00) 		0.197
(0.828) 		0.975
(1.00) 		0.201
(0.828) 		0.632
(0.976) 		0.97
(1.00) 		0.355
(0.92)
del 8p23 2 66 (12%) 504 0.344
(0.92) 		0.0409
(0.51) 		0.286
(0.896) 		0.327
(0.92) 		0.866
(1.00) 		0.678
(0.994) 		0.0179
(0.315) 		0.376
(0.925)
del 9q34 2 79 (14%) 491 0.941
(1.00) 		0.961
(1.00) 		0.901
(1.00) 		0.724
(0.996) 		0.0508
(0.525) 		0.442
(0.937) 		0.225
(0.846) 		0.229
(0.846)
del 11p11 2 105 (18%) 465 0.141
(0.802) 		0.676
(0.994) 		0.224
(0.846) 		0.518
(0.948) 		0.234
(0.851) 		0.818
(1.00) 		0.709
(0.996) 		1
(1.00)
del 11q14 1 96 (17%) 474 0.947
(1.00) 		0.533
(0.948) 		0.36
(0.92) 		0.757
(1.00) 		0.287
(0.896) 		0.153
(0.813) 		0.953
(1.00) 		0.7
(0.994)
del 12p13 1 71 (12%) 499 0.168
(0.823) 		0.982
(1.00) 		0.438
(0.937) 		0.423
(0.937) 		0.308
(0.912) 		0.281
(0.896) 		0.123
(0.759) 		1
(1.00)
del 12q12 76 (13%) 494 0.653
(0.987) 		0.653
(0.987) 		0.615
(0.97) 		0.835
(1.00) 		1
(1.00) 		0.435
(0.937) 		0.453
(0.945) 		0.658
(0.988)
del 12q15 78 (14%) 492 0.678
(0.994) 		0.644
(0.987) 		0.454
(0.945) 		0.402
(0.937) 		0.827
(1.00) 		0.3
(0.906) 		0.379
(0.925) 		0.21
(0.846)
del 13q14 2 238 (42%) 332 0.851
(1.00) 		0.744
(1.00) 		0.544
(0.954) 		0.731
(1.00) 		0.33
(0.92) 		0.653
(0.987) 		0.324
(0.92) 		1
(1.00)
del 13q22 1 226 (40%) 344 0.797
(1.00) 		0.954
(1.00) 		0.93
(1.00) 		0.227
(0.846) 		0.338
(0.92) 		0.466
(0.946) 		0.719
(0.996) 		0.379
(0.925)
del 14q13 1 175 (31%) 395 0.488
(0.948) 		0.565
(0.954) 		0.0945
(0.647) 		0.459
(0.946) 		0.351
(0.92) 		0.5
(0.948) 		0.333
(0.92) 		0.119
(0.745)
del 14q24 2 171 (30%) 399 0.884
(1.00) 		0.514
(0.948) 		0.224
(0.846) 		0.745
(1.00) 		0.296
(0.905) 		0.437
(0.937) 		0.688
(0.994) 		1
(1.00)
del 15q14 151 (26%) 419 0.325
(0.92) 		0.0334
(0.483) 		0.698
(0.994) 		0.919
(1.00) 		0.963
(1.00) 		0.313
(0.912) 		0.382
(0.925) 		0.327
(0.92)
del 16p12 2 92 (16%) 478 0.137
(0.802) 		0.206
(0.843) 		0.353
(0.92) 		0.549
(0.954) 		0.435
(0.937) 		0.546
(0.954) 		0.904
(1.00) 		1
(1.00)
del 16q23 1 99 (17%) 471 0.17
(0.823) 		0.754
(1.00) 		0.822
(1.00) 		0.142
(0.802) 		0.626
(0.976) 		0.034
(0.483) 		0.608
(0.97) 		0.703
(0.994)
del 17p13 2 85 (15%) 485 0.854
(1.00) 		0.573
(0.954) 		0.28
(0.896) 		0.328
(0.92) 		1
(1.00) 		0.619
(0.971) 		0.775
(1.00) 		1
(1.00)
del 17p13 1 95 (17%) 475 0.627
(0.976) 		0.102
(0.691) 		0.0849
(0.646) 		0.977
(1.00) 		0.808
(1.00) 		0.189
(0.823) 		0.953
(1.00) 		1
(1.00)
del 17q11 2 70 (12%) 500 0.59
(0.962) 		0.532
(0.948) 		0.794
(1.00) 		0.373
(0.925) 		1
(1.00) 		0.077
(0.643) 		0.733
(1.00) 		1
(1.00)
del 18q22 3 82 (14%) 488 0.992
(1.00) 		0.507
(0.948) 		0.808
(1.00) 		0.161
(0.823) 		0.782
(1.00) 		0.614
(0.97) 		0.357
(0.92) 		0.4
(0.937)
del 19q13 41 99 (17%) 471 0.0144
(0.28) 		0.477
(0.948) 		0.822
(1.00) 		0.601
(0.967) 		0.592
(0.963) 		1
(1.00) 		0.548
(0.954) 		1
(1.00)
del 21q21 1 56 (10%) 514 0.514
(0.948) 		0.41
(0.937) 		0.775
(1.00) 		0.417
(0.937) 		0.847
(1.00) 		0.181
(0.823) 		0.927
(1.00) 		0.366
(0.921)
del 22q13 32 212 (37%) 358 0.407
(0.937) 		0.155
(0.813) 		0.929
(1.00) 		0.505
(0.948) 		0.969
(1.00) 		0.713
(0.996) 		0.225
(0.846) 		1
(1.00)
del xp22 2 117 (21%) 453 0.2
(0.828) 		0.492
(0.948) 		1
(1.00) 		0.463
(0.946) 		0.956
(1.00) 		1
(1.00) 		0.621
(0.972) 		0.474
(0.948)
'amp_3q26.33' versus 'HISTOLOGICAL_TYPE'

P value = 0.00068 (Fisher's exact test), Q value = 0.023

Table S1.  Gene #5: 'amp_3q26.33' versus Clinical Feature #5: 'HISTOLOGICAL_TYPE'

nPatients GLIOBLASTOMA MULTIFORME (GBM) TREATED PRIMARY GBM UNTREATED PRIMARY (DE NOVO) GBM
ALL 27 18 525
AMP PEAK 5(3Q26.33) MUTATED 0 0 108
AMP PEAK 5(3Q26.33) WILD-TYPE 27 18 417

Figure S1.  Get High-res Image Gene #5: 'amp_3q26.33' versus Clinical Feature #5: 'HISTOLOGICAL_TYPE'

'amp_7p11.2' versus 'Time to Death'

P value = 1.01e-06 (logrank test), Q value = 8.2e-05

Table S2.  Gene #8: 'amp_7p11.2' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 569 465 0.1 - 127.6 (11.8)
AMP PEAK 8(7P11.2) MUTATED 499 417 0.1 - 127.6 (11.5)
AMP PEAK 8(7P11.2) WILD-TYPE 70 48 0.2 - 115.9 (16.4)

Figure S2.  Get High-res Image Gene #8: 'amp_7p11.2' versus Clinical Feature #1: 'Time to Death'

'amp_7p11.2' versus 'YEARS_TO_BIRTH'

P value = 9.64e-13 (Wilcoxon-test), Q value = 5.5e-10

Table S3.  Gene #8: 'amp_7p11.2' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 570 57.7 (14.5)
AMP PEAK 8(7P11.2) MUTATED 500 59.8 (12.5)
AMP PEAK 8(7P11.2) WILD-TYPE 70 43.1 (18.8)

Figure S3.  Get High-res Image Gene #8: 'amp_7p11.2' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'amp_7q11.21' versus 'Time to Death'

P value = 2.08e-05 (logrank test), Q value = 0.0011

Table S4.  Gene #9: 'amp_7q11.21' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 569 465 0.1 - 127.6 (11.8)
AMP PEAK 9(7Q11.21) MUTATED 457 379 0.1 - 127.6 (11.3)
AMP PEAK 9(7Q11.21) WILD-TYPE 112 86 0.2 - 120.6 (14.8)

Figure S4.  Get High-res Image Gene #9: 'amp_7q11.21' versus Clinical Feature #1: 'Time to Death'

'amp_7q11.21' versus 'YEARS_TO_BIRTH'

P value = 1.04e-07 (Wilcoxon-test), Q value = 1.2e-05

Table S5.  Gene #9: 'amp_7q11.21' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 570 57.7 (14.5)
AMP PEAK 9(7Q11.21) MUTATED 458 59.8 (12.4)
AMP PEAK 9(7Q11.21) WILD-TYPE 112 49.1 (18.7)

Figure S5.  Get High-res Image Gene #9: 'amp_7q11.21' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'amp_7q21.2' versus 'Time to Death'

P value = 0.000132 (logrank test), Q value = 0.0047

Table S6.  Gene #10: 'amp_7q21.2' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 569 465 0.1 - 127.6 (11.8)
AMP PEAK 10(7Q21.2) MUTATED 472 393 0.1 - 127.6 (11.7)
AMP PEAK 10(7Q21.2) WILD-TYPE 97 72 0.1 - 120.6 (14.7)

Figure S6.  Get High-res Image Gene #10: 'amp_7q21.2' versus Clinical Feature #1: 'Time to Death'

'amp_7q21.2' versus 'YEARS_TO_BIRTH'

P value = 3.89e-06 (Wilcoxon-test), Q value = 0.00025

Table S7.  Gene #10: 'amp_7q21.2' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 570 57.7 (14.5)
AMP PEAK 10(7Q21.2) MUTATED 473 59.5 (12.5)
AMP PEAK 10(7Q21.2) WILD-TYPE 97 49.2 (19.9)

Figure S7.  Get High-res Image Gene #10: 'amp_7q21.2' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'amp_7q31.2' versus 'Time to Death'

P value = 0.00226 (logrank test), Q value = 0.068

Table S8.  Gene #11: 'amp_7q31.2' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 569 465 0.1 - 127.6 (11.8)
AMP PEAK 11(7Q31.2) MUTATED 465 384 0.1 - 127.6 (11.7)
AMP PEAK 11(7Q31.2) WILD-TYPE 104 81 0.1 - 120.6 (14.2)

Figure S8.  Get High-res Image Gene #11: 'amp_7q31.2' versus Clinical Feature #1: 'Time to Death'

'amp_7q31.2' versus 'YEARS_TO_BIRTH'

P value = 0.00097 (Wilcoxon-test), Q value = 0.031

Table S9.  Gene #11: 'amp_7q31.2' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 570 57.7 (14.5)
AMP PEAK 11(7Q31.2) MUTATED 466 59.2 (12.7)
AMP PEAK 11(7Q31.2) WILD-TYPE 104 51.4 (19.7)

Figure S9.  Get High-res Image Gene #11: 'amp_7q31.2' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'amp_14q32.33' versus 'YEARS_TO_BIRTH'

P value = 0.00533 (Wilcoxon-test), Q value = 0.14

Table S10.  Gene #19: 'amp_14q32.33' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 570 57.7 (14.5)
AMP PEAK 19(14Q32.33) MUTATED 36 63.4 (14.4)
AMP PEAK 19(14Q32.33) WILD-TYPE 534 57.4 (14.4)

Figure S10.  Get High-res Image Gene #19: 'amp_14q32.33' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'amp_17q25.1' versus 'YEARS_TO_BIRTH'

P value = 0.00839 (Wilcoxon-test), Q value = 0.19

Table S11.  Gene #21: 'amp_17q25.1' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 570 57.7 (14.5)
AMP PEAK 21(17Q25.1) MUTATED 83 61.2 (13.6)
AMP PEAK 21(17Q25.1) WILD-TYPE 487 57.1 (14.6)

Figure S11.  Get High-res Image Gene #21: 'amp_17q25.1' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'amp_21q21.1' versus 'YEARS_TO_BIRTH'

P value = 0.00977 (Wilcoxon-test), Q value = 0.21

Table S12.  Gene #25: 'amp_21q21.1' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 570 57.7 (14.5)
AMP PEAK 25(21Q21.1) MUTATED 69 62.0 (13.3)
AMP PEAK 25(21Q21.1) WILD-TYPE 501 57.1 (14.6)

Figure S12.  Get High-res Image Gene #25: 'amp_21q21.1' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'del_1p36.23' versus 'GENDER'

P value = 0.0109 (Fisher's exact test), Q value = 0.23

Table S13.  Gene #27: 'del_1p36.23' versus Clinical Feature #3: 'GENDER'

nPatients FEMALE MALE
ALL 224 346
DEL PEAK 2(1P36.23) MUTATED 39 93
DEL PEAK 2(1P36.23) WILD-TYPE 185 253

Figure S13.  Get High-res Image Gene #27: 'del_1p36.23' versus Clinical Feature #3: 'GENDER'

'del_9p21.3' versus 'YEARS_TO_BIRTH'

P value = 6.51e-05 (Wilcoxon-test), Q value = 0.0025

Table S14.  Gene #44: 'del_9p21.3' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 570 57.7 (14.5)
DEL PEAK 19(9P21.3) MUTATED 417 59.1 (13.8)
DEL PEAK 19(9P21.3) WILD-TYPE 153 53.9 (15.7)

Figure S14.  Get High-res Image Gene #44: 'del_9p21.3' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'del_10p15.3' versus 'Time to Death'

P value = 3.44e-05 (logrank test), Q value = 0.0015

Table S15.  Gene #46: 'del_10p15.3' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 569 465 0.1 - 127.6 (11.8)
DEL PEAK 21(10P15.3) MUTATED 462 386 0.1 - 120.6 (11.8)
DEL PEAK 21(10P15.3) WILD-TYPE 107 79 0.1 - 127.6 (12.9)

Figure S15.  Get High-res Image Gene #46: 'del_10p15.3' versus Clinical Feature #1: 'Time to Death'

'del_10p15.3' versus 'YEARS_TO_BIRTH'

P value = 1.11e-08 (Wilcoxon-test), Q value = 2.1e-06

Table S16.  Gene #46: 'del_10p15.3' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 570 57.7 (14.5)
DEL PEAK 21(10P15.3) MUTATED 463 59.8 (12.6)
DEL PEAK 21(10P15.3) WILD-TYPE 107 48.8 (18.5)

Figure S16.  Get High-res Image Gene #46: 'del_10p15.3' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'del_10p13' versus 'Time to Death'

P value = 2.25e-05 (logrank test), Q value = 0.0011

Table S17.  Gene #47: 'del_10p13' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 569 465 0.1 - 127.6 (11.8)
DEL PEAK 22(10P13) MUTATED 463 387 0.1 - 120.6 (11.8)
DEL PEAK 22(10P13) WILD-TYPE 106 78 0.1 - 127.6 (12.5)

Figure S17.  Get High-res Image Gene #47: 'del_10p13' versus Clinical Feature #1: 'Time to Death'

'del_10p13' versus 'YEARS_TO_BIRTH'

P value = 2.33e-08 (Wilcoxon-test), Q value = 3.3e-06

Table S18.  Gene #47: 'del_10p13' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 570 57.7 (14.5)
DEL PEAK 22(10P13) MUTATED 464 59.8 (12.4)
DEL PEAK 22(10P13) WILD-TYPE 106 48.8 (19.1)

Figure S18.  Get High-res Image Gene #47: 'del_10p13' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'del_10p13' versus 'HISTOLOGICAL_TYPE'

P value = 0.00824 (Fisher's exact test), Q value = 0.19

Table S19.  Gene #47: 'del_10p13' versus Clinical Feature #5: 'HISTOLOGICAL_TYPE'

nPatients GLIOBLASTOMA MULTIFORME (GBM) TREATED PRIMARY GBM UNTREATED PRIMARY (DE NOVO) GBM
ALL 27 18 525
DEL PEAK 22(10P13) MUTATED 18 11 435
DEL PEAK 22(10P13) WILD-TYPE 9 7 90

Figure S19.  Get High-res Image Gene #47: 'del_10p13' versus Clinical Feature #5: 'HISTOLOGICAL_TYPE'

'del_10p11.23' versus 'Time to Death'

P value = 1.95e-06 (logrank test), Q value = 0.00014

Table S20.  Gene #48: 'del_10p11.23' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 569 465 0.1 - 127.6 (11.8)
DEL PEAK 23(10P11.23) MUTATED 468 391 0.1 - 120.6 (11.8)
DEL PEAK 23(10P11.23) WILD-TYPE 101 74 0.1 - 127.6 (14.5)

Figure S20.  Get High-res Image Gene #48: 'del_10p11.23' versus Clinical Feature #1: 'Time to Death'

'del_10p11.23' versus 'YEARS_TO_BIRTH'

P value = 7.72e-11 (Wilcoxon-test), Q value = 2.2e-08

Table S21.  Gene #48: 'del_10p11.23' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 570 57.7 (14.5)
DEL PEAK 23(10P11.23) MUTATED 469 60.0 (12.3)
DEL PEAK 23(10P11.23) WILD-TYPE 101 47.3 (18.8)

Figure S21.  Get High-res Image Gene #48: 'del_10p11.23' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'del_10p11.23' versus 'HISTOLOGICAL_TYPE'

P value = 0.00305 (Fisher's exact test), Q value = 0.086

Table S22.  Gene #48: 'del_10p11.23' versus Clinical Feature #5: 'HISTOLOGICAL_TYPE'

nPatients GLIOBLASTOMA MULTIFORME (GBM) TREATED PRIMARY GBM UNTREATED PRIMARY (DE NOVO) GBM
ALL 27 18 525
DEL PEAK 23(10P11.23) MUTATED 19 10 440
DEL PEAK 23(10P11.23) WILD-TYPE 8 8 85

Figure S22.  Get High-res Image Gene #48: 'del_10p11.23' versus Clinical Feature #5: 'HISTOLOGICAL_TYPE'

'del_10q23.31' versus 'Time to Death'

P value = 5.62e-05 (logrank test), Q value = 0.0023

Table S23.  Gene #49: 'del_10q23.31' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 569 465 0.1 - 127.6 (11.8)
DEL PEAK 24(10Q23.31) MUTATED 506 419 0.1 - 127.6 (11.8)
DEL PEAK 24(10Q23.31) WILD-TYPE 63 46 0.4 - 115.9 (14.1)

Figure S23.  Get High-res Image Gene #49: 'del_10q23.31' versus Clinical Feature #1: 'Time to Death'

'del_10q23.31' versus 'YEARS_TO_BIRTH'

P value = 2.29e-07 (Wilcoxon-test), Q value = 2.2e-05

Table S24.  Gene #49: 'del_10q23.31' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 570 57.7 (14.5)
DEL PEAK 24(10Q23.31) MUTATED 507 59.0 (13.4)
DEL PEAK 24(10Q23.31) WILD-TYPE 63 47.2 (18.6)

Figure S24.  Get High-res Image Gene #49: 'del_10q23.31' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'del_10q26.3' versus 'Time to Death'

P value = 0.00316 (logrank test), Q value = 0.086

Table S25.  Gene #50: 'del_10q26.3' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 569 465 0.1 - 127.6 (11.8)
DEL PEAK 25(10Q26.3) MUTATED 507 418 0.1 - 127.6 (11.8)
DEL PEAK 25(10Q26.3) WILD-TYPE 62 47 0.4 - 100.0 (12.8)

Figure S25.  Get High-res Image Gene #50: 'del_10q26.3' versus Clinical Feature #1: 'Time to Death'

'del_10q26.3' versus 'YEARS_TO_BIRTH'

P value = 9.13e-06 (Wilcoxon-test), Q value = 0.00052

Table S26.  Gene #50: 'del_10q26.3' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 570 57.7 (14.5)
DEL PEAK 25(10Q26.3) MUTATED 508 58.9 (13.5)
DEL PEAK 25(10Q26.3) WILD-TYPE 62 48.3 (18.7)

Figure S26.  Get High-res Image Gene #50: 'del_10q26.3' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'del_11p15.5' versus 'YEARS_TO_BIRTH'

P value = 0.00596 (Wilcoxon-test), Q value = 0.15

Table S27.  Gene #51: 'del_11p15.5' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 570 57.7 (14.5)
DEL PEAK 26(11P15.5) MUTATED 129 53.9 (16.4)
DEL PEAK 26(11P15.5) WILD-TYPE 441 58.8 (13.7)

Figure S27.  Get High-res Image Gene #51: 'del_11p15.5' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

Methods & Data
Input

  • Copy number data file = all_lesions.txt from GISTIC pipeline

  • Processed Copy number data file = /xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_Correlate_Genomic_Events_Preprocess/GBM-TP/15096471/transformed.cor.cli.txt

  • Clinical data file = /xchip/cga/gdac-prod/tcga-gdac/jobResults/Append_Data/GBM-TP/15078636/GBM-TP.merged_data.txt

  • Number of patients = 570

  • Number of significantly focal cnvs = 71

  • Number of selected clinical features = 8

  • Exclude genes 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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