Correlation between copy number variation genes (focal events) and selected clinical features
Glioblastoma Multiforme (Primary solid tumor)
21 August 2015  |  analyses__2015_08_21
Maintainer Information
Citation Information
doi:10.7908/C1M61JG0
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/C1M61JG0
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 571 patients, 31 significant findings detected with Q value < 0.25.

  • amp_1p36.21 cnv correlated to 'HISTOLOGICAL_TYPE'.

  • 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',  '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_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'.

  • 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 71 focal events and 8 clinical features. Shown in the table are P values (Q values). Thresholded by Q value < 0.25, 31 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
amp 7q11 21 459 (80%) 112 1.89e-05
(0.000865) 		1.02e-07
(1.16e-05) 		0.197
(0.787) 		0.276
(0.821) 		0.458
(0.938) 		0.0133
(0.243) 		0.254
(0.807) 		0.14
(0.719)
del 10p13 465 (81%) 106 6.55e-06
(0.000372) 		2.25e-08
(3.2e-06) 		0.0469
(0.503) 		1
(1.00) 		0.472
(0.94) 		0.0117
(0.229) 		0.127
(0.689) 		0.27
(0.82)
del 10p11 23 470 (82%) 101 5.07e-07
(3.6e-05) 		7.43e-11
(2.11e-08) 		0.116
(0.689) 		0.87
(1.00) 		0.0447
(0.488) 		0.00431
(0.117) 		0.158
(0.772) 		0.251
(0.807)
amp 7p11 2 501 (88%) 70 5.03e-07
(3.6e-05) 		9.44e-13
(5.36e-10) 		0.242
(0.807) 		0.179
(0.787) 		0.0187
(0.312) 		0.0652
(0.607) 		0.462
(0.94) 		0.0602
(0.57)
amp 7q21 2 474 (83%) 97 8.47e-05
(0.00301) 		3.81e-06
(0.00024) 		0.424
(0.931) 		0.505
(0.947) 		0.363
(0.897) 		0.133
(0.709) 		0.0349
(0.441) 		0.0441
(0.488)
amp 7q31 2 467 (82%) 104 0.00115
(0.0343) 		0.000958
(0.0302) 		0.268
(0.82) 		0.194
(0.787) 		0.924
(1.00) 		0.29
(0.827) 		0.0481
(0.506) 		0.0549
(0.553)
del 10p15 3 464 (81%) 107 1.98e-05
(0.000865) 		1.07e-08
(2.02e-06) 		0.126
(0.689) 		0.633
(0.977) 		0.244
(0.807) 		0.0294
(0.422) 		0.196
(0.787) 		0.273
(0.821)
del 10q23 31 508 (89%) 63 7.48e-05
(0.00283) 		2.24e-07
(2.12e-05) 		0.785
(1.00) 		0.842
(1.00) 		0.0821
(0.644) 		0.0248
(0.38) 		0.334
(0.881) 		0.635
(0.977)
del 10q26 3 509 (89%) 62 0.00396
(0.113) 		8.97e-06
(0.000463) 		0.68
(0.997) 		0.312
(0.851) 		0.0575
(0.558) 		0.0915
(0.675) 		0.0821
(0.644) 		0.632
(0.977)
amp 1p36 21 91 (16%) 480 0.058
(0.558) 		0.271
(0.82) 		0.483
(0.94) 		0.125
(0.689) 		0.134
(0.709) 		0.0128
(0.242) 		0.0794
(0.644) 		0.399
(0.915)
amp 3q26 33 108 (19%) 463 0.19
(0.787) 		0.032
(0.435) 		0.662
(0.992) 		0.0818
(0.644) 		0.558
(0.95) 		0.00059
(0.0197) 		0.166
(0.785) 		0.701
(0.997)
amp 14q32 33 36 (6%) 535 0.366
(0.897) 		0.00533
(0.138) 		0.487
(0.94) 		1
(1.00) 		0.246
(0.807) 		0.467
(0.94) 		0.729
(1.00) 		1
(1.00)
amp 17q25 1 83 (15%) 488 0.0297
(0.422) 		0.00843
(0.184) 		0.184
(0.787) 		0.156
(0.772) 		0.519
(0.947) 		0.789
(1.00) 		0.181
(0.787) 		0.691
(0.997)
amp 21q21 1 69 (12%) 502 0.931
(1.00) 		0.00982
(0.207) 		1
(1.00) 		0.701
(0.997) 		0.821
(1.00) 		0.209
(0.787) 		0.0854
(0.647) 		0.378
(0.897)
del 1p36 23 132 (23%) 439 0.871
(1.00) 		0.127
(0.689) 		0.0109
(0.221) 		0.883
(1.00) 		0.203
(0.787) 		0.479
(0.94) 		0.164
(0.784) 		0.312
(0.851)
del 1q42 11 49 (9%) 522 0.122
(0.689) 		0.29
(0.827) 		1
(1.00) 		0.376
(0.897) 		0.00641
(0.152) 		0.907
(1.00) 		0.363
(0.897) 		0.25
(0.807)
del 9p21 3 418 (73%) 153 0.0335
(0.435) 		6.29e-05
(0.00255) 		0.498
(0.94) 		0.205
(0.787) 		0.0337
(0.435) 		0.689
(0.997) 		0.49
(0.94) 		0.744
(1.00)
del 11p15 5 129 (23%) 442 0.0533
(0.55) 		0.00591
(0.146) 		0.219
(0.79) 		1
(1.00) 		0.0697
(0.61) 		0.496
(0.94) 		1
(1.00) 		1
(1.00)
del 19q13 41 99 (17%) 472 0.00747
(0.17) 		0.475
(0.94) 		0.821
(1.00) 		0.25
(0.807) 		0.682
(0.997) 		0.567
(0.95) 		0.609
(0.975) 		1
(1.00)
amp 1q32 1 158 (28%) 413 0.376
(0.897) 		0.18
(0.787) 		1
(1.00) 		0.127
(0.689) 		0.288
(0.827) 		0.966
(1.00) 		0.879
(1.00) 		0.526
(0.947)
amp 1q44 98 (17%) 473 0.613
(0.975) 		0.95
(1.00) 		0.213
(0.787) 		0.186
(0.787) 		0.455
(0.938) 		0.137
(0.715) 		0.954
(1.00) 		0.424
(0.931)
amp 2p24 3 49 (9%) 522 0.24
(0.806) 		0.275
(0.821) 		0.445
(0.932) 		1
(1.00) 		0.708
(1) 		1
(1.00) 		0.599
(0.972) 		0.612
(0.975)
amp 4p16 3 48 (8%) 523 0.566
(0.95) 		0.85
(1.00) 		0.356
(0.897) 		0.821
(1.00) 		0.163
(0.783) 		0.751
(1.00) 		0.779
(1.00) 		1
(1.00)
amp 4q12 108 (19%) 463 0.218
(0.79) 		0.142
(0.719) 		0.382
(0.897) 		0.078
(0.644) 		0.813
(1.00) 		0.682
(0.997) 		0.552
(0.95) 		1
(1.00)
amp 8q24 21 70 (12%) 501 0.0838
(0.644) 		0.441
(0.932) 		0.516
(0.947) 		0.329
(0.881) 		0.918
(1.00) 		0.82
(1.00) 		0.23
(0.79) 		1
(1.00)
amp 11p13 30 (5%) 541 0.727
(1.00) 		0.279
(0.825) 		1
(1.00) 		0.406
(0.926) 		0.627
(0.977) 		0.739
(1.00) 		0.769
(1.00) 		0.514
(0.947)
amp 12p13 32 84 (15%) 487 0.944
(1.00) 		0.173
(0.787) 		1
(1.00) 		0.216
(0.79) 		0.936
(1.00) 		0.891
(1.00) 		0.556
(0.95) 		0.687
(0.997)
amp 12q14 1 134 (23%) 437 0.201
(0.787) 		0.699
(0.997) 		0.419
(0.931) 		0.304
(0.85) 		0.531
(0.947) 		0.692
(0.997) 		0.72
(1) 		0.31
(0.851)
amp 12q15 92 (16%) 479 0.449
(0.937) 		0.576
(0.957) 		0.354
(0.897) 		1
(1.00) 		0.791
(1.00) 		0.763
(1.00) 		0.526
(0.947) 		0.229
(0.79)
amp 13q34 32 (6%) 539 0.777
(1.00) 		0.689
(0.997) 		0.456
(0.938) 		0.593
(0.972) 		0.579
(0.959) 		0.481
(0.94) 		1
(1.00) 		1
(1.00)
amp 13q34 30 (5%) 541 0.641
(0.978) 		0.414
(0.931) 		0.568
(0.95) 		1
(1.00) 		0.432
(0.932) 		0.74
(1.00) 		0.493
(0.94) 		1
(1.00)
amp 17p13 2 51 (9%) 520 0.642
(0.978) 		0.496
(0.94) 		0.293
(0.827) 		0.185
(0.787) 		0.936
(1.00) 		0.527
(0.947) 		0.713
(1) 		1
(1.00)
amp 19p13 3 241 (42%) 330 0.157
(0.772) 		0.68
(0.997) 		1
(1.00) 		0.313
(0.851) 		0.226
(0.79) 		0.52
(0.947) 		0.428
(0.931) 		0.769
(1.00)
amp 19p13 2 246 (43%) 325 0.265
(0.82) 		0.976
(1.00) 		1
(1.00) 		0.378
(0.897) 		0.55
(0.95) 		0.555
(0.95) 		0.748
(1.00) 		0.77
(1.00)
amp 19q12 214 (37%) 357 0.726
(1.00) 		0.496
(0.94) 		0.596
(0.972) 		0.12
(0.689) 		0.789
(1.00) 		0.473
(0.94) 		0.718
(1) 		0.387
(0.897)
del 1p36 32 96 (17%) 475 0.556
(0.95) 		0.619
(0.975) 		0.0294
(0.422) 		0.619
(0.975) 		0.863
(1.00) 		0.104
(0.689) 		0.0837
(0.644) 		0.7
(0.997)
del 1p32 3 60 (11%) 511 0.615
(0.975) 		0.0555
(0.553) 		0.127
(0.689) 		0.42
(0.931) 		0.735
(1.00) 		0.535
(0.947) 		0.27
(0.82) 		1
(1.00)
del 1p22 1 47 (8%) 524 0.55
(0.95) 		0.36
(0.897) 		1
(1.00) 		1
(1.00) 		0.894
(1.00) 		0.0673
(0.61) 		1
(1.00) 		1
(1.00)
del 1q44 34 (6%) 537 0.386
(0.897) 		0.321
(0.868) 		1
(1.00) 		0.429
(0.931) 		0.161
(0.783) 		0.878
(1.00) 		0.883
(1.00) 		0.474
(0.94)
del 2q22 1 47 (8%) 524 0.27
(0.82) 		0.0904
(0.675) 		0.439
(0.932) 		0.106
(0.689) 		0.622
(0.976) 		0.113
(0.689) 		0.229
(0.79) 		0.611
(0.975)
del 2q37 1 55 (10%) 516 0.91
(1.00) 		0.777
(1.00) 		0.245
(0.807) 		0.203
(0.787) 		0.855
(1.00) 		0.92
(1.00) 		0.602
(0.972) 		1
(1.00)
del 3p21 1 53 (9%) 518 0.0444
(0.488) 		0.0147
(0.26) 		0.768
(1.00) 		0.283
(0.827) 		0.569
(0.95) 		0.341
(0.884) 		0.495
(0.94) 		0.337
(0.881)
del 3q13 31 56 (10%) 515 0.877
(1.00) 		0.398
(0.915) 		0.567
(0.95) 		0.832
(1.00) 		0.239
(0.806) 		0.777
(1.00) 		0.528
(0.947) 		0.346
(0.894)
del 3q22 1 58 (10%) 513 0.949
(1.00) 		0.385
(0.897) 		1
(1.00) 		0.832
(1.00) 		0.43
(0.931) 		0.784
(1.00) 		0.311
(0.851) 		0.365
(0.897)
del 3q29 65 (11%) 506 0.174
(0.787) 		0.57
(0.95) 		1
(1.00) 		1
(1.00) 		0.643
(0.978) 		1
(1.00) 		1
(1.00) 		1
(1.00)
del 4p16 3 77 (13%) 494 0.0948
(0.682) 		0.0984
(0.689) 		0.211
(0.787) 		0.855
(1.00) 		0.269
(0.82) 		0.497
(0.94) 		0.53
(0.947) 		0.661
(0.992)
del 4q34 3 92 (16%) 479 0.0428
(0.488) 		0.121
(0.689) 		0.0361
(0.446) 		0.178
(0.787) 		0.784
(1.00) 		0.852
(1.00) 		0.178
(0.787) 		1
(1.00)
del 5q34 69 (12%) 502 0.0217
(0.342) 		0.289
(0.827) 		0.236
(0.806) 		0.567
(0.95) 		0.467
(0.94) 		0.208
(0.787) 		0.0407
(0.485) 		0.17
(0.785)
del 6q22 31 157 (27%) 414 0.0206
(0.334) 		0.221
(0.79) 		0.0839
(0.644) 		0.0699
(0.61) 		0.682
(0.997) 		0.412
(0.931) 		0.534
(0.947) 		0.193
(0.787)
del 6q26 178 (31%) 393 0.0767
(0.644) 		0.891
(1.00) 		0.196
(0.787) 		0.59
(0.972) 		0.745
(1.00) 		0.19
(0.787) 		0.97
(1.00) 		0.355
(0.897)
del 8p23 2 66 (12%) 505 0.372
(0.897) 		0.041
(0.485) 		0.285
(0.827) 		0.696
(0.997) 		0.334
(0.881) 		0.93
(1.00) 		0.0163
(0.281) 		0.376
(0.897)
del 9q34 2 79 (14%) 492 0.923
(1.00) 		0.963
(1.00) 		0.901
(1.00) 		0.584
(0.964) 		0.829
(1.00) 		0.0698
(0.61) 		0.252
(0.807) 		0.229
(0.79)
del 11p11 2 105 (18%) 466 0.169
(0.785) 		0.675
(0.997) 		0.224
(0.79) 		1
(1.00) 		0.337
(0.881) 		0.239
(0.806) 		0.773
(1.00) 		1
(1.00)
del 11q14 1 96 (17%) 475 0.847
(1.00) 		0.533
(0.947) 		0.359
(0.897) 		0.619
(0.975) 		0.67
(0.997) 		0.293
(0.827) 		0.91
(1.00) 		0.7
(0.997)
del 12p13 1 71 (12%) 500 0.121
(0.689) 		0.984
(1.00) 		0.437
(0.932) 		0.569
(0.95) 		0.491
(0.94) 		0.295
(0.829) 		0.117
(0.689) 		1
(1.00)
del 12q12 76 (13%) 495 0.596
(0.972) 		0.655
(0.99) 		0.615
(0.975) 		0.197
(0.787) 		0.518
(0.947) 		1
(1.00) 		0.427
(0.931) 		0.657
(0.99)
del 12q15 78 (14%) 493 0.719
(1) 		0.646
(0.978) 		0.454
(0.938) 		0.141
(0.719) 		0.704
(0.997) 		0.83
(1.00) 		0.333
(0.881) 		0.209
(0.787)
del 13q14 2 239 (42%) 332 0.746
(1.00) 		0.753
(1.00) 		0.544
(0.95) 		0.0998
(0.689) 		0.869
(1.00) 		0.445
(0.932) 		0.435
(0.932) 		1
(1.00)
del 13q22 1 227 (40%) 344 0.718
(1) 		0.963
(1.00) 		0.861
(1.00) 		0.127
(0.689) 		0.31
(0.851) 		0.415
(0.931) 		0.804
(1.00) 		0.378
(0.897)
del 14q13 1 176 (31%) 395 0.602
(0.972) 		0.555
(0.95) 		0.114
(0.689) 		0.422
(0.931) 		0.827
(1.00) 		0.538
(0.949) 		0.259
(0.814) 		0.119
(0.689)
del 14q24 2 171 (30%) 400 0.867
(1.00) 		0.511
(0.947) 		0.224
(0.79) 		0.103
(0.689) 		0.887
(1.00) 		0.254
(0.807) 		0.711
(1) 		1
(1.00)
del 15q14 152 (27%) 419 0.291
(0.827) 		0.0327
(0.435) 		0.629
(0.977) 		0.258
(0.813) 		0.886
(1.00) 		0.896
(1.00) 		0.462
(0.94) 		0.328
(0.881)
del 16p12 2 92 (16%) 479 0.108
(0.689) 		0.208
(0.787) 		0.354
(0.897) 		0.17
(0.785) 		0.211
(0.787) 		0.442
(0.932) 		0.907
(1.00) 		1
(1.00)
del 16q23 1 99 (17%) 472 0.136
(0.715) 		0.75
(1.00) 		0.821
(1.00) 		0.0941
(0.682) 		0.629
(0.977) 		0.63
(0.977) 		0.64
(0.978) 		0.702
(0.997)
del 17p13 2 86 (15%) 485 0.722
(1.00) 		0.558
(0.95) 		0.338
(0.881) 		0.49
(0.94) 		0.382
(0.897) 		0.847
(1.00) 		0.603
(0.972) 		1
(1.00)
del 17p13 1 96 (17%) 475 0.754
(1.00) 		0.0989
(0.689) 		0.108
(0.689) 		0.868
(1.00) 		0.932
(1.00) 		1
(1.00) 		0.871
(1.00) 		1
(1.00)
del 17q11 2 70 (12%) 501 0.521
(0.947) 		0.533
(0.947) 		0.794
(1.00) 		0.454
(0.938) 		0.739
(1.00) 		1
(1.00) 		0.737
(1.00) 		1
(1.00)
del 18q22 3 82 (14%) 489 0.886
(1.00) 		0.509
(0.947) 		0.808
(1.00) 		0.213
(0.787) 		0.109
(0.689) 		0.789
(1.00) 		0.382
(0.897) 		0.399
(0.915)
del 21q21 1 56 (10%) 515 0.492
(0.94) 		0.409
(0.928) 		0.775
(1.00) 		1
(1.00) 		0.357
(0.897) 		0.924
(1.00) 		0.929
(1.00) 		0.365
(0.897)
del 22q13 32 212 (37%) 359 0.566
(0.95) 		0.157
(0.772) 		0.929
(1.00) 		0.7
(0.997) 		0.717
(1) 		0.97
(1.00) 		0.195
(0.787) 		1
(1.00)
del xp22 2 118 (21%) 453 0.123
(0.689) 		0.507
(0.947) 		1
(1.00) 		0.645
(0.978) 		0.437
(0.932) 		0.918
(1.00) 		0.672
(0.997) 		0.474
(0.94)
'amp_1p36.21' versus 'HISTOLOGICAL_TYPE'

P value = 0.0128 (Fisher's exact test), Q value = 0.24

Table S1.  Gene #1: 'amp_1p36.21' versus Clinical Feature #6: 'HISTOLOGICAL_TYPE'

nPatients GLIOBLASTOMA MULTIFORME (GBM) TREATED PRIMARY GBM UNTREATED PRIMARY (DE NOVO) GBM
ALL 28 18 525
AMP PEAK 1(1P36.21) MUTATED 0 1 90
AMP PEAK 1(1P36.21) WILD-TYPE 28 17 435

Figure S1.  Get High-res Image Gene #1: 'amp_1p36.21' versus Clinical Feature #6: 'HISTOLOGICAL_TYPE'

'amp_3q26.33' versus 'HISTOLOGICAL_TYPE'

P value = 0.00059 (Fisher's exact test), Q value = 0.02

Table S2.  Gene #5: 'amp_3q26.33' versus Clinical Feature #6: 'HISTOLOGICAL_TYPE'

nPatients GLIOBLASTOMA MULTIFORME (GBM) TREATED PRIMARY GBM UNTREATED PRIMARY (DE NOVO) GBM
ALL 28 18 525
AMP PEAK 5(3Q26.33) MUTATED 0 0 108
AMP PEAK 5(3Q26.33) WILD-TYPE 28 18 417

Figure S2.  Get High-res Image Gene #5: 'amp_3q26.33' versus Clinical Feature #6: 'HISTOLOGICAL_TYPE'

'amp_7p11.2' versus 'Time to Death'

P value = 5.03e-07 (logrank test), Q value = 3.6e-05

Table S3.  Gene #8: 'amp_7p11.2' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 570 470 0.1 - 127.6 (12.2)
AMP PEAK 8(7P11.2) MUTATED 500 422 0.1 - 127.6 (11.8)
AMP PEAK 8(7P11.2) WILD-TYPE 70 48 0.2 - 115.9 (17.1)

Figure S3.  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 = 9.44e-13 (Wilcoxon-test), Q value = 5.4e-10

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

nPatients Mean (Std.Dev)
ALL 571 57.7 (14.5)
AMP PEAK 8(7P11.2) MUTATED 501 59.8 (12.5)
AMP PEAK 8(7P11.2) WILD-TYPE 70 43.1 (18.8)

Figure S4.  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 = 1.89e-05 (logrank test), Q value = 0.00086

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

nPatients nDeath Duration Range (Median), Month
ALL 570 470 0.1 - 127.6 (12.2)
AMP PEAK 9(7Q11.21) MUTATED 458 384 0.1 - 127.6 (11.8)
AMP PEAK 9(7Q11.21) WILD-TYPE 112 86 0.2 - 120.6 (15.2)

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 = 1.02e-07 (Wilcoxon-test), Q value = 1.2e-05

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

nPatients Mean (Std.Dev)
ALL 571 57.7 (14.5)
AMP PEAK 9(7Q11.21) MUTATED 459 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 = 0.0133 (Fisher's exact test), Q value = 0.24

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 28 18 525
AMP PEAK 9(7Q11.21) MUTATED 20 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 = 8.47e-05 (logrank test), Q value = 0.003

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

nPatients nDeath Duration Range (Median), Month
ALL 570 470 0.1 - 127.6 (12.2)
AMP PEAK 10(7Q21.2) MUTATED 473 398 0.1 - 127.6 (11.8)
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 = 3.81e-06 (Wilcoxon-test), Q value = 0.00024

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

nPatients Mean (Std.Dev)
ALL 571 57.7 (14.5)
AMP PEAK 10(7Q21.2) MUTATED 474 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 = 0.00115 (logrank test), Q value = 0.034

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

nPatients nDeath Duration Range (Median), Month
ALL 570 470 0.1 - 127.6 (12.2)
AMP PEAK 11(7Q31.2) MUTATED 466 390 0.1 - 127.6 (11.8)
AMP PEAK 11(7Q31.2) WILD-TYPE 104 80 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 = 0.000958 (Wilcoxon-test), Q value = 0.03

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

nPatients Mean (Std.Dev)
ALL 571 57.7 (14.5)
AMP PEAK 11(7Q31.2) MUTATED 467 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 = 0.00533 (Wilcoxon-test), Q value = 0.14

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

nPatients Mean (Std.Dev)
ALL 571 57.7 (14.5)
AMP PEAK 19(14Q32.33) MUTATED 36 63.4 (14.4)
AMP PEAK 19(14Q32.33) WILD-TYPE 535 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 = 0.00843 (Wilcoxon-test), Q value = 0.18

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

nPatients Mean (Std.Dev)
ALL 571 57.7 (14.5)
AMP PEAK 21(17Q25.1) MUTATED 83 61.2 (13.6)
AMP PEAK 21(17Q25.1) WILD-TYPE 488 57.1 (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 = 0.00982 (Wilcoxon-test), Q value = 0.21

Table S14.  Gene #25: 'amp_21q21.1' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 571 57.7 (14.5)
AMP PEAK 25(21Q21.1) MUTATED 69 62.0 (13.3)
AMP PEAK 25(21Q21.1) WILD-TYPE 502 57.2 (14.6)

Figure S14.  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 = 0.22

Table S15.  Gene #27: 'del_1p36.23' versus Clinical Feature #3: 'GENDER'

nPatients FEMALE MALE
ALL 224 347
DEL PEAK 2(1P36.23) MUTATED 39 93
DEL PEAK 2(1P36.23) WILD-TYPE 185 254

Figure S15.  Get High-res Image Gene #27: 'del_1p36.23' versus Clinical Feature #3: 'GENDER'

'del_1q42.11' versus 'KARNOFSKY_PERFORMANCE_SCORE'

P value = 0.00641 (Wilcoxon-test), Q value = 0.15

Table S16.  Gene #30: 'del_1q42.11' versus Clinical Feature #5: 'KARNOFSKY_PERFORMANCE_SCORE'

nPatients Mean (Std.Dev)
ALL 424 77.4 (14.9)
DEL PEAK 5(1Q42.11) MUTATED 39 69.7 (18.6)
DEL PEAK 5(1Q42.11) WILD-TYPE 385 78.2 (14.3)

Figure S16.  Get High-res Image Gene #30: 'del_1q42.11' versus Clinical Feature #5: 'KARNOFSKY_PERFORMANCE_SCORE'

'del_9p21.3' versus 'YEARS_TO_BIRTH'

P value = 6.29e-05 (Wilcoxon-test), Q value = 0.0026

Table S17.  Gene #44: 'del_9p21.3' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 571 57.7 (14.5)
DEL PEAK 19(9P21.3) MUTATED 418 59.1 (13.8)
DEL PEAK 19(9P21.3) WILD-TYPE 153 53.9 (15.7)

Figure S17.  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 = 1.98e-05 (logrank test), Q value = 0.00086

Table S18.  Gene #46: 'del_10p15.3' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 570 470 0.1 - 127.6 (12.2)
DEL PEAK 21(10P15.3) MUTATED 463 391 0.1 - 120.6 (12.0)
DEL PEAK 21(10P15.3) WILD-TYPE 107 79 0.1 - 127.6 (14.1)

Figure S18.  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 = 1.07e-08 (Wilcoxon-test), Q value = 2e-06

Table S19.  Gene #46: 'del_10p15.3' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 571 57.7 (14.5)
DEL PEAK 21(10P15.3) MUTATED 464 59.8 (12.6)
DEL PEAK 21(10P15.3) WILD-TYPE 107 48.8 (18.5)

Figure S19.  Get High-res Image Gene #46: 'del_10p15.3' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'del_10p13' versus 'Time to Death'

P value = 6.55e-06 (logrank test), Q value = 0.00037

Table S20.  Gene #47: 'del_10p13' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 570 470 0.1 - 127.6 (12.2)
DEL PEAK 22(10P13) MUTATED 464 392 0.1 - 120.6 (12.0)
DEL PEAK 22(10P13) WILD-TYPE 106 78 0.1 - 127.6 (14.3)

Figure S20.  Get High-res Image Gene #47: 'del_10p13' versus Clinical Feature #1: 'Time to Death'

'del_10p13' versus 'YEARS_TO_BIRTH'

P value = 2.25e-08 (Wilcoxon-test), Q value = 3.2e-06

Table S21.  Gene #47: 'del_10p13' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 571 57.7 (14.5)
DEL PEAK 22(10P13) MUTATED 465 59.8 (12.4)
DEL PEAK 22(10P13) WILD-TYPE 106 48.8 (19.1)

Figure S21.  Get High-res Image Gene #47: 'del_10p13' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'del_10p13' versus 'HISTOLOGICAL_TYPE'

P value = 0.0117 (Fisher's exact test), Q value = 0.23

Table S22.  Gene #47: 'del_10p13' versus Clinical Feature #6: 'HISTOLOGICAL_TYPE'

nPatients GLIOBLASTOMA MULTIFORME (GBM) TREATED PRIMARY GBM UNTREATED PRIMARY (DE NOVO) GBM
ALL 28 18 525
DEL PEAK 22(10P13) MUTATED 19 11 435
DEL PEAK 22(10P13) WILD-TYPE 9 7 90

Figure S22.  Get High-res Image Gene #47: 'del_10p13' versus Clinical Feature #6: 'HISTOLOGICAL_TYPE'

'del_10p11.23' versus 'Time to Death'

P value = 5.07e-07 (logrank test), Q value = 3.6e-05

Table S23.  Gene #48: 'del_10p11.23' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 570 470 0.1 - 127.6 (12.2)
DEL PEAK 23(10P11.23) MUTATED 469 396 0.1 - 120.6 (11.8)
DEL PEAK 23(10P11.23) WILD-TYPE 101 74 0.1 - 127.6 (16.1)

Figure S23.  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 = 7.43e-11 (Wilcoxon-test), Q value = 2.1e-08

Table S24.  Gene #48: 'del_10p11.23' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 571 57.7 (14.5)
DEL PEAK 23(10P11.23) MUTATED 470 60.0 (12.3)
DEL PEAK 23(10P11.23) WILD-TYPE 101 47.3 (18.8)

Figure S24.  Get High-res Image Gene #48: 'del_10p11.23' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'del_10p11.23' versus 'HISTOLOGICAL_TYPE'

P value = 0.00431 (Fisher's exact test), Q value = 0.12

Table S25.  Gene #48: 'del_10p11.23' versus Clinical Feature #6: 'HISTOLOGICAL_TYPE'

nPatients GLIOBLASTOMA MULTIFORME (GBM) TREATED PRIMARY GBM UNTREATED PRIMARY (DE NOVO) GBM
ALL 28 18 525
DEL PEAK 23(10P11.23) MUTATED 20 10 440
DEL PEAK 23(10P11.23) WILD-TYPE 8 8 85

Figure S25.  Get High-res Image Gene #48: 'del_10p11.23' versus Clinical Feature #6: 'HISTOLOGICAL_TYPE'

'del_10q23.31' versus 'Time to Death'

P value = 7.48e-05 (logrank test), Q value = 0.0028

Table S26.  Gene #49: 'del_10q23.31' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 570 470 0.1 - 127.6 (12.2)
DEL PEAK 24(10Q23.31) MUTATED 507 424 0.1 - 127.6 (12.1)
DEL PEAK 24(10Q23.31) WILD-TYPE 63 46 0.4 - 115.9 (14.1)

Figure S26.  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 = 2.24e-07 (Wilcoxon-test), Q value = 2.1e-05

Table S27.  Gene #49: 'del_10q23.31' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 571 57.7 (14.5)
DEL PEAK 24(10Q23.31) MUTATED 508 59.1 (13.4)
DEL PEAK 24(10Q23.31) WILD-TYPE 63 47.2 (18.6)

Figure S27.  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 = 0.00396 (logrank test), Q value = 0.11

Table S28.  Gene #50: 'del_10q26.3' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 570 470 0.1 - 127.6 (12.2)
DEL PEAK 25(10Q26.3) MUTATED 508 423 0.1 - 127.6 (12.1)
DEL PEAK 25(10Q26.3) WILD-TYPE 62 47 0.4 - 100.0 (12.8)

Figure S28.  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 = 8.97e-06 (Wilcoxon-test), Q value = 0.00046

Table S29.  Gene #50: 'del_10q26.3' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 571 57.7 (14.5)
DEL PEAK 25(10Q26.3) MUTATED 509 58.9 (13.5)
DEL PEAK 25(10Q26.3) WILD-TYPE 62 48.3 (18.7)

Figure S29.  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 = 0.00591 (Wilcoxon-test), Q value = 0.15

Table S30.  Gene #51: 'del_11p15.5' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 571 57.7 (14.5)
DEL PEAK 26(11P15.5) MUTATED 129 53.9 (16.4)
DEL PEAK 26(11P15.5) WILD-TYPE 442 58.9 (13.7)

Figure S30.  Get High-res Image Gene #51: 'del_11p15.5' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'del_19q13.41' versus 'Time to Death'

P value = 0.00747 (logrank test), Q value = 0.17

Table S31.  Gene #68: 'del_19q13.41' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 570 470 0.1 - 127.6 (12.2)
DEL PEAK 43(19Q13.41) MUTATED 99 82 0.2 - 127.6 (13.6)
DEL PEAK 43(19Q13.41) WILD-TYPE 471 388 0.1 - 92.7 (11.8)

Figure S31.  Get High-res Image Gene #68: '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/19791355/transformed.cor.cli.txt

  • Clinical data file = /xchip/cga/gdac-prod/tcga-gdac/jobResults/Append_Data/GBM-TP/19775175/GBM-TP.merged_data.txt

  • Number of patients = 571

  • 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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