Correlation between copy number variation genes (focal events) and selected clinical features
Glioblastoma Multiforme (Primary solid tumor)
28 January 2016  |  analyses__2016_01_28
Maintainer Information
Citation Information
doi:10.7908/C180521Q
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 variation genes (focal events) and selected clinical features. Broad Institute of MIT and Harvard. doi:10.7908/C180521Q
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 68 focal events and 8 clinical features across 573 patients, 39 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',  'YEARS_TO_BIRTH', and 'KARNOFSKY_PERFORMANCE_SCORE'.

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

  • 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_1q42.11 cnv correlated to 'KARNOFSKY_PERFORMANCE_SCORE'.

  • del_3p21.1 cnv correlated to 'YEARS_TO_BIRTH'.

  • del_6q22.1 cnv correlated to 'Time to Death'.

  • del_8p23.2 cnv correlated to 'RACE'.

  • 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_10q11.23 cnv correlated to 'Time to Death',  'YEARS_TO_BIRTH',  'KARNOFSKY_PERFORMANCE_SCORE',  'HISTOLOGICAL_TYPE', and 'RACE'.

  • 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'.

  • del_19q13.41 cnv correlated to 'Time to Death'.

Results
Overview of the results

Table 1.  Get Full Table Overview of the association between significant copy number variation of 68 focal events and 8 clinical features. Shown in the table are P values (Q values). Thresholded by Q value < 0.25, 39 significant findings detected.

Clinical
Features 		Time
to
Death 		YEARS
TO
BIRTH 		GENDER RADIATION
THERAPY 		KARNOFSKY
PERFORMANCE
SCORE 		HISTOLOGICAL
TYPE 		RACE 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 Fisher's exact test
del 10q11 23 485 (85%) 88 6.35e-07
(3.47e-05) 		4.21e-10
(7.64e-08) 		0.343
(0.836) 		0.3
(0.798) 		0.00335
(0.0794) 		0.0161
(0.227) 		0.0133
(0.213) 		0.422
(0.871)
amp 7p11 2 503 (88%) 70 6.38e-07
(3.47e-05) 		8.46e-13
(4.6e-10) 		0.243
(0.76) 		0.179
(0.722) 		0.0162
(0.227) 		0.076
(0.574) 		0.436
(0.875) 		0.0594
(0.492)
amp 7q11 21 461 (80%) 112 1.6e-05
(0.000622) 		8.45e-08
(7.66e-06) 		0.197
(0.736) 		0.276
(0.777) 		0.407
(0.871) 		0.0162
(0.227) 		0.256
(0.771) 		0.0802
(0.586)
del 10p13 467 (82%) 106 6.1e-06
(0.000277) 		1.92e-08
(2.09e-06) 		0.0471
(0.45) 		1
(1.00) 		0.424
(0.871) 		0.0163
(0.227) 		0.125
(0.638) 		0.268
(0.777)
del 10p11 23 472 (82%) 101 4.7e-07
(3.19e-05) 		6.31e-11
(1.72e-08) 		0.116
(0.638) 		0.87
(1.00) 		0.0379
(0.42) 		0.00468
(0.0943) 		0.171
(0.722) 		0.25
(0.76)
amp 7q21 2 476 (83%) 97 7.44e-05
(0.00238) 		3.33e-06
(0.000165) 		0.425
(0.871) 		0.505
(0.916) 		0.324
(0.822) 		0.139
(0.672) 		0.0331
(0.4) 		0.0434
(0.443)
amp 7q31 2 469 (82%) 104 0.00141
(0.0384) 		0.000849
(0.0243) 		0.268
(0.777) 		0.194
(0.735) 		0.854
(1.00) 		0.312
(0.798) 		0.0431
(0.443) 		0.0541
(0.476)
del 10p15 3 466 (81%) 107 2.4e-05
(0.000871) 		9.02e-09
(1.23e-06) 		0.153
(0.701) 		0.633
(0.955) 		0.213
(0.76) 		0.0377
(0.42) 		0.187
(0.722) 		0.272
(0.777)
del 10q23 31 510 (89%) 63 6.84e-05
(0.00232) 		2.03e-07
(1.58e-05) 		0.785
(0.993) 		0.842
(1.00) 		0.073
(0.56) 		0.0343
(0.406) 		0.332
(0.833) 		0.634
(0.955)
del 10q26 3 511 (89%) 62 0.0037
(0.0838) 		8.19e-06
(0.000343) 		0.681
(0.955) 		0.313
(0.798) 		0.0512
(0.464) 		0.117
(0.638) 		0.083
(0.586) 		0.632
(0.955)
amp 3q26 33 109 (19%) 464 0.125
(0.638) 		0.0268
(0.331) 		0.587
(0.955) 		0.0814
(0.586) 		0.472
(0.895) 		0.00272
(0.0705) 		0.16
(0.711) 		0.701
(0.955)
amp 14q32 33 36 (6%) 537 0.378
(0.858) 		0.00573
(0.108) 		0.486
(0.905) 		1
(1.00) 		0.269
(0.777) 		0.474
(0.895) 		0.728
(0.975) 		1
(1.00)
amp 17q25 1 84 (15%) 489 0.0207
(0.275) 		0.00652
(0.118) 		0.183
(0.722) 		0.155
(0.702) 		0.407
(0.871) 		0.672
(0.955) 		0.184
(0.722) 		0.694
(0.955)
amp 21q21 1 70 (12%) 503 0.993
(1.00) 		0.00761
(0.134) 		0.897
(1.00) 		0.7
(0.955) 		0.981
(1.00) 		0.151
(0.697) 		0.0897
(0.6) 		0.378
(0.858)
del 1p36 23 132 (23%) 441 0.961
(1.00) 		0.114
(0.638) 		0.0109
(0.18) 		0.883
(1.00) 		0.209
(0.76) 		0.669
(0.955) 		0.417
(0.871) 		0.312
(0.798)
del 1q42 11 50 (9%) 523 0.0938
(0.6) 		0.233
(0.76) 		0.881
(1.00) 		0.375
(0.858) 		0.00336
(0.0794) 		0.638
(0.955) 		0.412
(0.871) 		0.258
(0.771)
del 3p21 1 54 (9%) 519 0.0461
(0.448) 		0.00938
(0.16) 		0.884
(1.00) 		0.284
(0.785) 		0.414
(0.871) 		0.473
(0.895) 		0.542
(0.941) 		0.344
(0.836)
del 6q22 1 155 (27%) 418 0.0041
(0.0892) 		0.141
(0.672) 		0.249
(0.76) 		0.121
(0.638) 		0.784
(0.993) 		0.487
(0.905) 		0.465
(0.895) 		0.195
(0.735)
del 8p23 2 66 (12%) 507 0.349
(0.844) 		0.0447
(0.443) 		0.286
(0.786) 		0.696
(0.955) 		0.305
(0.798) 		0.871
(1.00) 		0.0156
(0.227) 		0.376
(0.858)
del 9p21 3 419 (73%) 154 0.0363
(0.42) 		8.2e-05
(0.00248) 		0.563
(0.941) 		0.205
(0.752) 		0.0443
(0.443) 		0.677
(0.955) 		0.493
(0.906) 		0.745
(0.982)
del 11p15 5 132 (23%) 441 0.0543
(0.476) 		0.00568
(0.108) 		0.224
(0.76) 		1
(1.00) 		0.0554
(0.478) 		0.554
(0.941) 		0.964
(1.00) 		1
(1.00)
del 19q13 41 100 (17%) 473 0.00464
(0.0943) 		0.335
(0.833) 		0.91
(1.00) 		0.137
(0.672) 		0.613
(0.955) 		0.526
(0.931) 		0.608
(0.955) 		1
(1.00)
amp 1p36 21 92 (16%) 481 0.0501
(0.462) 		0.24
(0.76) 		0.415
(0.871) 		0.0924
(0.6) 		0.0946
(0.6) 		0.0593
(0.492) 		0.0729
(0.56) 		0.402
(0.871)
amp 1q32 1 159 (28%) 414 0.307
(0.798) 		0.168
(0.722) 		0.924
(1.00) 		0.127
(0.638) 		0.249
(0.76) 		1
(1.00) 		0.877
(1.00) 		0.526
(0.931)
amp 1q44 99 (17%) 474 0.571
(0.942) 		0.888
(1.00) 		0.176
(0.722) 		0.186
(0.722) 		0.363
(0.848) 		0.301
(0.798) 		0.954
(1.00) 		0.426
(0.871)
amp 2p24 3 49 (9%) 524 0.187
(0.722) 		0.265
(0.777) 		0.445
(0.881) 		1
(1.00) 		0.75
(0.982) 		1
(1.00) 		0.605
(0.955) 		0.612
(0.955)
amp 4p16 3 48 (8%) 525 0.532
(0.932) 		0.827
(1.00) 		0.356
(0.846) 		0.821
(1.00) 		0.149
(0.691) 		0.752
(0.982) 		0.777
(0.991) 		1
(1.00)
amp 4q12 108 (19%) 465 0.233
(0.76) 		0.156
(0.702) 		0.382
(0.858) 		0.0778
(0.58) 		0.881
(1.00) 		0.629
(0.955) 		0.552
(0.941) 		1
(1.00)
amp 8q24 21 69 (12%) 504 0.0704
(0.555) 		0.335
(0.833) 		0.694
(0.955) 		0.553
(0.941) 		0.866
(1.00) 		0.767
(0.991) 		0.49
(0.906) 		1
(1.00)
amp 11p13 30 (5%) 543 0.672
(0.955) 		0.273
(0.777) 		1
(1.00) 		0.406
(0.871) 		0.598
(0.955) 		0.749
(0.982) 		0.767
(0.991) 		0.513
(0.926)
amp 12p13 32 84 (15%) 489 0.948
(1.00) 		0.161
(0.711) 		1
(1.00) 		0.217
(0.76) 		0.876
(1.00) 		0.846
(1.00) 		0.555
(0.941) 		0.686
(0.955)
amp 12q14 1 134 (23%) 439 0.284
(0.785) 		0.662
(0.955) 		0.419
(0.871) 		0.303
(0.798) 		0.472
(0.895) 		0.622
(0.955) 		0.719
(0.967) 		0.31
(0.798)
amp 12q15 93 (16%) 480 0.464
(0.895) 		0.644
(0.955) 		0.353
(0.846) 		1
(1.00) 		0.916
(1.00) 		0.855
(1.00) 		0.527
(0.931) 		0.23
(0.76)
amp 13q34 32 (6%) 541 0.792
(0.995) 		0.674
(0.955) 		0.457
(0.89) 		0.593
(0.955) 		0.611
(0.955) 		0.497
(0.909) 		1
(1.00) 		1
(1.00)
amp 13q34 30 (5%) 543 0.655
(0.955) 		0.403
(0.871) 		0.568
(0.941) 		1
(1.00) 		0.462
(0.894) 		0.75
(0.982) 		0.492
(0.906) 		1
(1.00)
amp 17p13 2 51 (9%) 522 0.608
(0.955) 		0.514
(0.926) 		0.293
(0.797) 		0.184
(0.722) 		0.892
(1.00) 		0.641
(0.955) 		0.714
(0.964) 		1
(1.00)
amp 19p13 3 244 (43%) 329 0.0954
(0.6) 		0.663
(0.955) 		0.931
(1.00) 		0.312
(0.798) 		0.24
(0.76) 		0.532
(0.932) 		0.426
(0.871) 		0.769
(0.991)
amp 19q12 215 (38%) 358 0.671
(0.955) 		0.482
(0.905) 		0.66
(0.955) 		0.12
(0.638) 		0.747
(0.982) 		0.442
(0.878) 		0.72
(0.967) 		0.388
(0.868)
del 1p36 32 97 (17%) 476 0.661
(0.955) 		0.561
(0.941) 		0.0226
(0.286) 		0.619
(0.955) 		0.752
(0.982) 		0.234
(0.76) 		0.0841
(0.586) 		0.7
(0.955)
del 1p32 3 61 (11%) 512 0.422
(0.871) 		0.0429
(0.443) 		0.127
(0.638) 		0.42
(0.871) 		0.576
(0.945) 		0.862
(1.00) 		0.275
(0.777) 		1
(1.00)
del 1p22 1 48 (8%) 525 0.628
(0.955) 		0.292
(0.797) 		0.878
(1.00) 		1
(1.00) 		0.69
(0.955) 		0.103
(0.611) 		1
(1.00) 		1
(1.00)
del 1q44 35 (6%) 538 0.303
(0.798) 		0.243
(0.76) 		0.86
(1.00) 		0.428
(0.871) 		0.0947
(0.6) 		0.597
(0.955) 		1
(1.00) 		0.486
(0.905)
del 2q22 1 47 (8%) 526 0.28
(0.781) 		0.0959
(0.6) 		0.439
(0.875) 		0.106
(0.615) 		0.66
(0.955) 		0.139
(0.672) 		0.227
(0.76) 		0.611
(0.955)
del 2q37 1 55 (10%) 518 0.949
(1.00) 		0.756
(0.984) 		0.245
(0.76) 		0.202
(0.749) 		0.811
(1.00) 		1
(1.00) 		0.695
(0.955) 		1
(1.00)
del 3q13 31 56 (10%) 517 0.956
(1.00) 		0.381
(0.858) 		0.567
(0.941) 		0.832
(1.00) 		0.218
(0.76) 		0.854
(1.00) 		0.487
(0.905) 		0.344
(0.836)
del 3q29 65 (11%) 508 0.228
(0.76) 		0.548
(0.941) 		1
(1.00) 		1
(1.00) 		0.596
(0.955) 		1
(1.00) 		1
(1.00) 		1
(1.00)
del 4p16 3 78 (14%) 495 0.109
(0.622) 		0.122
(0.638) 		0.264
(0.777) 		0.855
(1.00) 		0.37
(0.856) 		0.657
(0.955) 		0.535
(0.933) 		0.663
(0.955)
del 4q34 3 93 (16%) 480 0.0615
(0.5) 		0.143
(0.678) 		0.0494
(0.462) 		0.177
(0.722) 		0.665
(0.955) 		0.771
(0.991) 		0.185
(0.722) 		1
(1.00)
del 5q34 69 (12%) 504 0.0185
(0.252) 		0.277
(0.777) 		0.237
(0.76) 		0.568
(0.941) 		0.43
(0.871) 		0.342
(0.836) 		0.0416
(0.443) 		0.168
(0.722)
del 6q26 179 (31%) 394 0.0597
(0.492) 		0.861
(1.00) 		0.231
(0.76) 		0.59
(0.955) 		0.802
(0.998) 		0.217
(0.76) 		0.97
(1.00) 		0.355
(0.846)
del 9q34 2 79 (14%) 494 0.798
(0.996) 		0.994
(1.00) 		0.901
(1.00) 		0.584
(0.954) 		0.778
(0.991) 		0.0841
(0.586) 		0.25
(0.76) 		0.23
(0.76)
del 11p11 2 105 (18%) 468 0.181
(0.722) 		0.643
(0.955) 		0.224
(0.76) 		1
(1.00) 		0.297
(0.798) 		0.272
(0.777) 		0.775
(0.991) 		1
(1.00)
del 11q14 1 96 (17%) 477 0.831
(1.00) 		0.563
(0.941) 		0.36
(0.848) 		0.619
(0.955) 		0.734
(0.979) 		0.249
(0.76) 		0.909
(1.00) 		0.7
(0.955)
del 12p13 1 72 (13%) 501 0.145
(0.682) 		0.903
(1.00) 		0.367
(0.853) 		0.569
(0.941) 		0.639
(0.955) 		0.519
(0.931) 		0.102
(0.611) 		1
(1.00)
del 12q12 77 (13%) 496 0.654
(0.955) 		0.577
(0.945) 		0.707
(0.957) 		0.196
(0.736) 		0.668
(0.955) 		1
(1.00) 		0.431
(0.871) 		0.66
(0.955)
del 12q15 79 (14%) 494 0.782
(0.993) 		0.569
(0.941) 		0.46
(0.893) 		0.14
(0.672) 		0.566
(0.941) 		0.701
(0.955) 		0.34
(0.836) 		0.214
(0.76)
del 13q14 2 240 (42%) 333 0.707
(0.957) 		0.763
(0.991) 		0.603
(0.955) 		0.0995
(0.608) 		0.847
(1.00) 		0.5
(0.911) 		0.435
(0.875) 		1
(1.00)
del 13q22 1 228 (40%) 345 0.622
(0.955) 		0.974
(1.00) 		0.931
(1.00) 		0.127
(0.638) 		0.296
(0.798) 		0.455
(0.89) 		0.806
(1.00) 		0.378
(0.858)
del 14q13 1 176 (31%) 397 0.567
(0.941) 		0.599
(0.955) 		0.115
(0.638) 		0.501
(0.911) 		0.732
(0.978) 		0.438
(0.875) 		0.261
(0.775) 		0.119
(0.638)
del 14q24 2 171 (30%) 402 0.827
(1.00) 		0.474
(0.895) 		0.224
(0.76) 		0.103
(0.611) 		0.792
(0.995) 		0.179
(0.722) 		0.689
(0.955) 		1
(1.00)
del 15q14 154 (27%) 419 0.236
(0.76) 		0.0223
(0.286) 		0.7
(0.955) 		0.257
(0.771) 		0.857
(1.00) 		0.628
(0.955) 		0.447
(0.881) 		0.332
(0.833)
del 16p12 2 92 (16%) 481 0.0986
(0.608) 		0.221
(0.76) 		0.354
(0.846) 		0.17
(0.722) 		0.186
(0.722) 		0.402
(0.871) 		0.907
(1.00) 		1
(1.00)
del 16q23 1 100 (17%) 473 0.106
(0.615) 		0.818
(1.00) 		0.91
(1.00) 		0.0939
(0.6) 		0.525
(0.931) 		0.745
(0.982) 		0.67
(0.955) 		0.703
(0.956)
del 17p13 1 98 (17%) 475 0.629
(0.955) 		0.065
(0.52) 		0.0899
(0.6) 		0.868
(1.00) 		0.744
(0.982) 		0.864
(1.00) 		0.91
(1.00) 		1
(1.00)
del 17q11 2 72 (13%) 501 0.397
(0.871) 		0.39
(0.87) 		0.797
(0.996) 		0.453
(0.889) 		0.423
(0.871) 		0.681
(0.955) 		0.79
(0.995) 		1
(1.00)
del 18q22 3 82 (14%) 491 0.861
(1.00) 		0.533
(0.932) 		0.808
(1.00) 		0.213
(0.76) 		0.129
(0.644) 		0.892
(1.00) 		0.361
(0.848) 		0.399
(0.871)
del 21q21 1 56 (10%) 517 0.523
(0.931) 		0.393
(0.871) 		0.775
(0.991) 		1
(1.00) 		0.331
(0.833) 		1
(1.00) 		0.927
(1.00) 		0.363
(0.848)
del 22q13 32 212 (37%) 361 0.555
(0.941) 		0.179
(0.722) 		0.929
(1.00) 		0.796
(0.996) 		0.618
(0.955) 		0.861
(1.00) 		0.193
(0.735) 		1
(1.00)
'amp_3q26.33' versus 'HISTOLOGICAL_TYPE'

P value = 0.00272 (Fisher's exact test), Q value = 0.07

Table S1.  Gene #5: 'amp_3q26.33' versus Clinical Feature #6: 'HISTOLOGICAL_TYPE'

nPatients GLIOBLASTOMA MULTIFORME (GBM) TREATED PRIMARY GBM UNTREATED PRIMARY (DE NOVO) GBM
ALL 30 18 525
AMP PEAK 5(3Q26.33) MUTATED 1 0 108
AMP PEAK 5(3Q26.33) WILD-TYPE 29 18 417

Figure S1.  Get High-res Image Gene #5: 'amp_3q26.33' versus Clinical Feature #6: 'HISTOLOGICAL_TYPE'

'amp_7p11.2' versus 'Time to Death'

P value = 6.38e-07 (logrank test), Q value = 3.5e-05

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

nPatients nDeath Duration Range (Median), Month
ALL 570 473 0.1 - 127.6 (12.2)
AMP PEAK 8(7P11.2) MUTATED 500 424 0.1 - 127.6 (11.8)
AMP PEAK 8(7P11.2) WILD-TYPE 70 49 0.2 - 115.9 (17.2)

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 = 8.46e-13 (Wilcoxon-test), Q value = 4.6e-10

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

nPatients Mean (Std.Dev)
ALL 573 57.8 (14.5)
AMP PEAK 8(7P11.2) MUTATED 503 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_7p11.2' versus 'KARNOFSKY_PERFORMANCE_SCORE'

P value = 0.0162 (Wilcoxon-test), Q value = 0.23

Table S4.  Gene #8: 'amp_7p11.2' versus Clinical Feature #5: 'KARNOFSKY_PERFORMANCE_SCORE'

nPatients Mean (Std.Dev)
ALL 426 77.1 (15.8)
AMP PEAK 8(7P11.2) MUTATED 374 76.4 (16.2)
AMP PEAK 8(7P11.2) WILD-TYPE 52 81.9 (11.7)

Figure S4.  Get High-res Image Gene #8: 'amp_7p11.2' versus Clinical Feature #5: 'KARNOFSKY_PERFORMANCE_SCORE'

'amp_7q11.21' versus 'Time to Death'

P value = 1.6e-05 (logrank test), Q value = 0.00062

Table S5.  Gene #9: 'amp_7q11.21' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 570 473 0.1 - 127.6 (12.2)
AMP PEAK 9(7Q11.21) MUTATED 458 386 0.1 - 127.6 (11.8)
AMP PEAK 9(7Q11.21) WILD-TYPE 112 87 0.2 - 120.6 (15.7)

Figure S5.  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 = 8.45e-08 (Wilcoxon-test), Q value = 7.7e-06

Table S6.  Gene #9: 'amp_7q11.21' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 573 57.8 (14.5)
AMP PEAK 9(7Q11.21) MUTATED 461 59.9 (12.4)
AMP PEAK 9(7Q11.21) WILD-TYPE 112 49.1 (18.7)

Figure S6.  Get High-res Image Gene #9: 'amp_7q11.21' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'amp_7q11.21' versus 'HISTOLOGICAL_TYPE'

P value = 0.0162 (Fisher's exact test), Q value = 0.23

Table S7.  Gene #9: 'amp_7q11.21' versus Clinical Feature #6: 'HISTOLOGICAL_TYPE'

nPatients GLIOBLASTOMA MULTIFORME (GBM) TREATED PRIMARY GBM UNTREATED PRIMARY (DE NOVO) GBM
ALL 30 18 525
AMP PEAK 9(7Q11.21) MUTATED 22 10 429
AMP PEAK 9(7Q11.21) WILD-TYPE 8 8 96

Figure S7.  Get High-res Image Gene #9: 'amp_7q11.21' versus Clinical Feature #6: 'HISTOLOGICAL_TYPE'

'amp_7q21.2' versus 'Time to Death'

P value = 7.44e-05 (logrank test), Q value = 0.0024

Table S8.  Gene #10: 'amp_7q21.2' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 570 473 0.1 - 127.6 (12.2)
AMP PEAK 10(7Q21.2) MUTATED 473 401 0.1 - 127.6 (11.9)
AMP PEAK 10(7Q21.2) WILD-TYPE 97 72 0.1 - 120.6 (15.1)

Figure S8.  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 = 3.33e-06 (Wilcoxon-test), Q value = 0.00016

Table S9.  Gene #10: 'amp_7q21.2' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 573 57.8 (14.5)
AMP PEAK 10(7Q21.2) MUTATED 476 59.5 (12.5)
AMP PEAK 10(7Q21.2) WILD-TYPE 97 49.2 (19.9)

Figure S9.  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 = 0.00141 (logrank test), Q value = 0.038

Table S10.  Gene #11: 'amp_7q31.2' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 570 473 0.1 - 127.6 (12.2)
AMP PEAK 11(7Q31.2) MUTATED 466 392 0.1 - 127.6 (12.0)
AMP PEAK 11(7Q31.2) WILD-TYPE 104 81 0.1 - 120.6 (14.8)

Figure S10.  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 = 0.000849 (Wilcoxon-test), Q value = 0.024

Table S11.  Gene #11: 'amp_7q31.2' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 573 57.8 (14.5)
AMP PEAK 11(7Q31.2) MUTATED 469 59.2 (12.7)
AMP PEAK 11(7Q31.2) WILD-TYPE 104 51.4 (19.7)

Figure S11.  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 = 0.00573 (Wilcoxon-test), Q value = 0.11

Table S12.  Gene #19: 'amp_14q32.33' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 573 57.8 (14.5)
AMP PEAK 19(14Q32.33) MUTATED 36 63.4 (14.4)
AMP PEAK 19(14Q32.33) WILD-TYPE 537 57.4 (14.4)

Figure S12.  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 = 0.00652 (Wilcoxon-test), Q value = 0.12

Table S13.  Gene #21: 'amp_17q25.1' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 573 57.8 (14.5)
AMP PEAK 21(17Q25.1) MUTATED 84 61.3 (13.6)
AMP PEAK 21(17Q25.1) WILD-TYPE 489 57.2 (14.6)

Figure S13.  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 = 0.00761 (Wilcoxon-test), Q value = 0.13

Table S14.  Gene #24: 'amp_21q21.1' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 573 57.8 (14.5)
AMP PEAK 24(21Q21.1) MUTATED 70 62.1 (13.3)
AMP PEAK 24(21Q21.1) WILD-TYPE 503 57.2 (14.6)

Figure S14.  Get High-res Image Gene #24: '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 = 0.18

Table S15.  Gene #26: 'del_1p36.23' versus Clinical Feature #3: 'GENDER'

nPatients FEMALE MALE
ALL 225 348
DEL PEAK 2(1P36.23) MUTATED 39 93
DEL PEAK 2(1P36.23) WILD-TYPE 186 255

Figure S15.  Get High-res Image Gene #26: 'del_1p36.23' versus Clinical Feature #3: 'GENDER'

'del_1q42.11' versus 'KARNOFSKY_PERFORMANCE_SCORE'

P value = 0.00336 (Wilcoxon-test), Q value = 0.079

Table S16.  Gene #29: 'del_1q42.11' versus Clinical Feature #5: 'KARNOFSKY_PERFORMANCE_SCORE'

nPatients Mean (Std.Dev)
ALL 426 77.1 (15.8)
DEL PEAK 5(1Q42.11) MUTATED 40 68.0 (21.4)
DEL PEAK 5(1Q42.11) WILD-TYPE 386 78.0 (14.8)

Figure S16.  Get High-res Image Gene #29: 'del_1q42.11' versus Clinical Feature #5: 'KARNOFSKY_PERFORMANCE_SCORE'

'del_3p21.1' versus 'YEARS_TO_BIRTH'

P value = 0.00938 (Wilcoxon-test), Q value = 0.16

Table S17.  Gene #33: 'del_3p21.1' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 573 57.8 (14.5)
DEL PEAK 9(3P21.1) MUTATED 54 51.7 (16.6)
DEL PEAK 9(3P21.1) WILD-TYPE 519 58.4 (14.1)

Figure S17.  Get High-res Image Gene #33: 'del_3p21.1' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'del_6q22.1' versus 'Time to Death'

P value = 0.0041 (logrank test), Q value = 0.089

Table S18.  Gene #39: 'del_6q22.1' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 570 473 0.1 - 127.6 (12.2)
DEL PEAK 15(6Q22.1) MUTATED 154 135 0.2 - 94.8 (10.5)
DEL PEAK 15(6Q22.1) WILD-TYPE 416 338 0.1 - 127.6 (12.6)

Figure S18.  Get High-res Image Gene #39: 'del_6q22.1' versus Clinical Feature #1: 'Time to Death'

'del_8p23.2' versus 'RACE'

P value = 0.0156 (Fisher's exact test), Q value = 0.23

Table S19.  Gene #41: 'del_8p23.2' versus Clinical Feature #7: 'RACE'

nPatients ASIAN BLACK OR AFRICAN AMERICAN WHITE
ALL 13 50 487
DEL PEAK 17(8P23.2) MUTATED 5 4 53
DEL PEAK 17(8P23.2) WILD-TYPE 8 46 434

Figure S19.  Get High-res Image Gene #41: 'del_8p23.2' versus Clinical Feature #7: 'RACE'

'del_9p21.3' versus 'YEARS_TO_BIRTH'

P value = 8.2e-05 (Wilcoxon-test), Q value = 0.0025

Table S20.  Gene #42: 'del_9p21.3' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 573 57.8 (14.5)
DEL PEAK 18(9P21.3) MUTATED 419 59.2 (13.8)
DEL PEAK 18(9P21.3) WILD-TYPE 154 54.0 (15.7)

Figure S20.  Get High-res Image Gene #42: 'del_9p21.3' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'del_10p15.3' versus 'Time to Death'

P value = 2.4e-05 (logrank test), Q value = 0.00087

Table S21.  Gene #44: 'del_10p15.3' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 570 473 0.1 - 127.6 (12.2)
DEL PEAK 20(10P15.3) MUTATED 464 393 0.1 - 120.6 (12.1)
DEL PEAK 20(10P15.3) WILD-TYPE 106 80 0.1 - 127.6 (14.6)

Figure S21.  Get High-res Image Gene #44: 'del_10p15.3' versus Clinical Feature #1: 'Time to Death'

'del_10p15.3' versus 'YEARS_TO_BIRTH'

P value = 9.02e-09 (Wilcoxon-test), Q value = 1.2e-06

Table S22.  Gene #44: 'del_10p15.3' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 573 57.8 (14.5)
DEL PEAK 20(10P15.3) MUTATED 466 59.8 (12.6)
DEL PEAK 20(10P15.3) WILD-TYPE 107 48.8 (18.5)

Figure S22.  Get High-res Image Gene #44: 'del_10p15.3' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'del_10p13' versus 'Time to Death'

P value = 6.1e-06 (logrank test), Q value = 0.00028

Table S23.  Gene #45: 'del_10p13' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 570 473 0.1 - 127.6 (12.2)
DEL PEAK 21(10P13) MUTATED 465 395 0.1 - 120.6 (12.2)
DEL PEAK 21(10P13) WILD-TYPE 105 78 0.1 - 127.6 (14.5)

Figure S23.  Get High-res Image Gene #45: 'del_10p13' versus Clinical Feature #1: 'Time to Death'

'del_10p13' versus 'YEARS_TO_BIRTH'

P value = 1.92e-08 (Wilcoxon-test), Q value = 2.1e-06

Table S24.  Gene #45: 'del_10p13' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 573 57.8 (14.5)
DEL PEAK 21(10P13) MUTATED 467 59.8 (12.4)
DEL PEAK 21(10P13) WILD-TYPE 106 48.8 (19.1)

Figure S24.  Get High-res Image Gene #45: 'del_10p13' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'del_10p13' versus 'HISTOLOGICAL_TYPE'

P value = 0.0163 (Fisher's exact test), Q value = 0.23

Table S25.  Gene #45: 'del_10p13' versus Clinical Feature #6: 'HISTOLOGICAL_TYPE'

nPatients GLIOBLASTOMA MULTIFORME (GBM) TREATED PRIMARY GBM UNTREATED PRIMARY (DE NOVO) GBM
ALL 30 18 525
DEL PEAK 21(10P13) MUTATED 21 11 435
DEL PEAK 21(10P13) WILD-TYPE 9 7 90

Figure S25.  Get High-res Image Gene #45: 'del_10p13' versus Clinical Feature #6: 'HISTOLOGICAL_TYPE'

'del_10p11.23' versus 'Time to Death'

P value = 4.7e-07 (logrank test), Q value = 3.2e-05

Table S26.  Gene #46: 'del_10p11.23' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 570 473 0.1 - 127.6 (12.2)
DEL PEAK 22(10P11.23) MUTATED 470 399 0.1 - 120.6 (12.0)
DEL PEAK 22(10P11.23) WILD-TYPE 100 74 0.1 - 127.6 (16.2)

Figure S26.  Get High-res Image Gene #46: 'del_10p11.23' versus Clinical Feature #1: 'Time to Death'

'del_10p11.23' versus 'YEARS_TO_BIRTH'

P value = 6.31e-11 (Wilcoxon-test), Q value = 1.7e-08

Table S27.  Gene #46: 'del_10p11.23' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 573 57.8 (14.5)
DEL PEAK 22(10P11.23) MUTATED 472 60.0 (12.3)
DEL PEAK 22(10P11.23) WILD-TYPE 101 47.3 (18.8)

Figure S27.  Get High-res Image Gene #46: 'del_10p11.23' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'del_10p11.23' versus 'HISTOLOGICAL_TYPE'

P value = 0.00468 (Fisher's exact test), Q value = 0.094

Table S28.  Gene #46: 'del_10p11.23' versus Clinical Feature #6: 'HISTOLOGICAL_TYPE'

nPatients GLIOBLASTOMA MULTIFORME (GBM) TREATED PRIMARY GBM UNTREATED PRIMARY (DE NOVO) GBM
ALL 30 18 525
DEL PEAK 22(10P11.23) MUTATED 22 10 440
DEL PEAK 22(10P11.23) WILD-TYPE 8 8 85

Figure S28.  Get High-res Image Gene #46: 'del_10p11.23' versus Clinical Feature #6: 'HISTOLOGICAL_TYPE'

'del_10q11.23' versus 'Time to Death'

P value = 6.35e-07 (logrank test), Q value = 3.5e-05

Table S29.  Gene #47: 'del_10q11.23' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 570 473 0.1 - 127.6 (12.2)
DEL PEAK 23(10Q11.23) MUTATED 483 409 0.1 - 120.6 (12.1)
DEL PEAK 23(10Q11.23) WILD-TYPE 87 64 0.4 - 127.6 (14.7)

Figure S29.  Get High-res Image Gene #47: 'del_10q11.23' versus Clinical Feature #1: 'Time to Death'

'del_10q11.23' versus 'YEARS_TO_BIRTH'

P value = 4.21e-10 (Wilcoxon-test), Q value = 7.6e-08

Table S30.  Gene #47: 'del_10q11.23' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 573 57.8 (14.5)
DEL PEAK 23(10Q11.23) MUTATED 485 59.8 (12.6)
DEL PEAK 23(10Q11.23) WILD-TYPE 88 46.6 (18.8)

Figure S30.  Get High-res Image Gene #47: 'del_10q11.23' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'del_10q11.23' versus 'KARNOFSKY_PERFORMANCE_SCORE'

P value = 0.00335 (Wilcoxon-test), Q value = 0.079

Table S31.  Gene #47: 'del_10q11.23' versus Clinical Feature #5: 'KARNOFSKY_PERFORMANCE_SCORE'

nPatients Mean (Std.Dev)
ALL 426 77.1 (15.8)
DEL PEAK 23(10Q11.23) MUTATED 365 76.2 (16.3)
DEL PEAK 23(10Q11.23) WILD-TYPE 61 82.3 (11.2)

Figure S31.  Get High-res Image Gene #47: 'del_10q11.23' versus Clinical Feature #5: 'KARNOFSKY_PERFORMANCE_SCORE'

'del_10q11.23' versus 'HISTOLOGICAL_TYPE'

P value = 0.0161 (Fisher's exact test), Q value = 0.23

Table S32.  Gene #47: 'del_10q11.23' versus Clinical Feature #6: 'HISTOLOGICAL_TYPE'

nPatients GLIOBLASTOMA MULTIFORME (GBM) TREATED PRIMARY GBM UNTREATED PRIMARY (DE NOVO) GBM
ALL 30 18 525
DEL PEAK 23(10Q11.23) MUTATED 22 12 451
DEL PEAK 23(10Q11.23) WILD-TYPE 8 6 74

Figure S32.  Get High-res Image Gene #47: 'del_10q11.23' versus Clinical Feature #6: 'HISTOLOGICAL_TYPE'

'del_10q11.23' versus 'RACE'

P value = 0.0133 (Fisher's exact test), Q value = 0.21

Table S33.  Gene #47: 'del_10q11.23' versus Clinical Feature #7: 'RACE'

nPatients ASIAN BLACK OR AFRICAN AMERICAN WHITE
ALL 13 50 487
DEL PEAK 23(10Q11.23) MUTATED 7 41 416
DEL PEAK 23(10Q11.23) WILD-TYPE 6 9 71

Figure S33.  Get High-res Image Gene #47: 'del_10q11.23' versus Clinical Feature #7: 'RACE'

'del_10q23.31' versus 'Time to Death'

P value = 6.84e-05 (logrank test), Q value = 0.0023

Table S34.  Gene #48: 'del_10q23.31' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 570 473 0.1 - 127.6 (12.2)
DEL PEAK 24(10Q23.31) MUTATED 507 427 0.1 - 127.6 (12.2)
DEL PEAK 24(10Q23.31) WILD-TYPE 63 46 0.4 - 115.9 (14.1)

Figure S34.  Get High-res Image Gene #48: 'del_10q23.31' versus Clinical Feature #1: 'Time to Death'

'del_10q23.31' versus 'YEARS_TO_BIRTH'

P value = 2.03e-07 (Wilcoxon-test), Q value = 1.6e-05

Table S35.  Gene #48: 'del_10q23.31' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 573 57.8 (14.5)
DEL PEAK 24(10Q23.31) MUTATED 510 59.1 (13.4)
DEL PEAK 24(10Q23.31) WILD-TYPE 63 47.2 (18.6)

Figure S35.  Get High-res Image Gene #48: 'del_10q23.31' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'del_10q26.3' versus 'Time to Death'

P value = 0.0037 (logrank test), Q value = 0.084

Table S36.  Gene #49: 'del_10q26.3' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 570 473 0.1 - 127.6 (12.2)
DEL PEAK 25(10Q26.3) MUTATED 508 426 0.1 - 127.6 (12.2)
DEL PEAK 25(10Q26.3) WILD-TYPE 62 47 0.4 - 100.0 (12.8)

Figure S36.  Get High-res Image Gene #49: 'del_10q26.3' versus Clinical Feature #1: 'Time to Death'

'del_10q26.3' versus 'YEARS_TO_BIRTH'

P value = 8.19e-06 (Wilcoxon-test), Q value = 0.00034

Table S37.  Gene #49: 'del_10q26.3' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 573 57.8 (14.5)
DEL PEAK 25(10Q26.3) MUTATED 511 58.9 (13.5)
DEL PEAK 25(10Q26.3) WILD-TYPE 62 48.3 (18.7)

Figure S37.  Get High-res Image Gene #49: 'del_10q26.3' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'del_11p15.5' versus 'YEARS_TO_BIRTH'

P value = 0.00568 (Wilcoxon-test), Q value = 0.11

Table S38.  Gene #50: 'del_11p15.5' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 573 57.8 (14.5)
DEL PEAK 26(11P15.5) MUTATED 132 54.0 (16.4)
DEL PEAK 26(11P15.5) WILD-TYPE 441 58.9 (13.7)

Figure S38.  Get High-res Image Gene #50: 'del_11p15.5' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'del_19q13.41' versus 'Time to Death'

P value = 0.00464 (logrank test), Q value = 0.094

Table S39.  Gene #66: 'del_19q13.41' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 570 473 0.1 - 127.6 (12.2)
DEL PEAK 42(19Q13.41) MUTATED 99 84 0.2 - 127.6 (14.5)
DEL PEAK 42(19Q13.41) WILD-TYPE 471 389 0.1 - 92.7 (11.8)

Figure S39.  Get High-res Image Gene #66: 'del_19q13.41' versus Clinical Feature #1: 'Time to Death'

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/22538153/transformed.cor.cli.txt

  • Clinical data file = /xchip/cga/gdac-prod/tcga-gdac/jobResults/Append_Data/GBM-TP/22506586/GBM-TP.merged_data.txt

  • Number of patients = 573

  • Number of significantly focal cnvs = 68

  • 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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