Glioblastoma Multiforme: Correlation between copy number variation genes and selected clinical features
(primary solid tumor cohort)
Maintained by TCGA GDAC Team (Broad Institute/MD Anderson Cancer Center/Harvard Medical School)
Overview
Introduction

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

Summary

Testing the association between copy number variation of 70 peak regions and 5 clinical features across 544 patients, 15 significant findings detected with Q value < 0.25.

  • Amp Peak 8(7p11.2) cnvs correlated to 'Time to Death' and 'AGE'.

  • Amp Peak 9(7q11.21) cnvs correlated to 'Time to Death' and 'AGE'.

  • Amp Peak 10(7q21.2) cnvs correlated to 'AGE'.

  • Del Peak 19(9p21.3) cnvs correlated to 'AGE'.

  • Del Peak 21(10p15.3) cnvs correlated to 'Time to Death' and 'AGE'.

  • Del Peak 22(10p13) cnvs correlated to 'Time to Death' and 'AGE'.

  • Del Peak 23(10p11.23) cnvs correlated to 'Time to Death' and 'AGE'.

  • Del Peak 24(10q23.31) cnvs correlated to 'Time to Death' and 'AGE'.

  • Del Peak 25(10q26.3) cnvs correlated to 'AGE'.

Results
Overview of the results

Table 1.  Get Full Table Overview of the association between significant copy number variation of 70 regions and 5 clinical features. Shown in the table are P values (Q values). Thresholded by Q value < 0.25, 15 significant findings detected.

Clinical
Features 		Time
to
Death 		AGE GENDER KARNOFSKY
PERFORMANCE
SCORE 		RADIATIONS
RADIATION
REGIMENINDICATION
nCNV (%) nWild-Type logrank test t-test Fisher's exact test t-test Fisher's exact test
Amp Peak 8(7p11 2) 478 (88%) 66 2.57e-06
(0.000885) 		5.95e-09
(2.08e-06) 		0.502
(1.00) 		0.0351
(1.00) 		0.0239
(1.00)
Amp Peak 9(7q11 21) 439 (81%) 105 0.000152
(0.0513) 		8.05e-08
(2.79e-05) 		0.224
(1.00) 		0.658
(1.00) 		0.0268
(1.00)
Del Peak 21(10p15 3) 445 (82%) 99 1.06e-05
(0.00361) 		4.22e-08
(1.47e-05) 		0.088
(1.00) 		0.596
(1.00) 		0.0427
(1.00)
Del Peak 22(10p13) 447 (82%) 97 6.7e-06
(0.00229) 		2.12e-07
(7.33e-05) 		0.0297
(1.00) 		0.884
(1.00) 		0.151
(1.00)
Del Peak 23(10p11 23) 451 (83%) 93 9.14e-07
(0.000315) 		1.16e-08
(4.04e-06) 		0.103
(1.00) 		0.232
(1.00) 		0.18
(1.00)
Del Peak 24(10q23 31) 486 (89%) 58 2.27e-05
(0.0077) 		2.71e-06
(0.000931) 		0.572
(1.00) 		0.0751
(1.00) 		0.302
(1.00)
Amp Peak 10(7q21 2) 453 (83%) 91 0.000974
(0.326) 		1.06e-05
(0.0036) 		0.483
(1.00) 		0.49
(1.00) 		0.0851
(1.00)
Del Peak 19(9p21 3) 399 (73%) 145 0.0223
(1.00) 		0.000156
(0.0524) 		0.552
(1.00) 		0.0926
(1.00) 		0.255
(1.00)
Del Peak 25(10q26 3) 487 (90%) 57 0.00151
(0.501) 		2.89e-05
(0.00976) 		0.478
(1.00) 		0.0613
(1.00) 		0.551
(1.00)
Amp Peak 1(1p36 21) 87 (16%) 457 0.0861
(1.00) 		0.316
(1.00) 		0.283
(1.00) 		0.653
(1.00) 		0.618
(1.00)
Amp Peak 2(1q32 1) 148 (27%) 396 0.436
(1.00) 		0.261
(1.00) 		0.624
(1.00) 		0.279
(1.00) 		0.837
(1.00)
Amp Peak 3(1q44) 94 (17%) 450 0.497
(1.00) 		0.903
(1.00) 		0.297
(1.00) 		0.599
(1.00) 		0.903
(1.00)
Amp Peak 4(2p24 3) 44 (8%) 500 0.151
(1.00) 		0.268
(1.00) 		0.424
(1.00) 		0.583
(1.00) 		1
(1.00)
Amp Peak 5(3q26 33) 105 (19%) 439 0.286
(1.00) 		0.0296
(1.00) 		0.824
(1.00) 		0.688
(1.00) 		0.353
(1.00)
Amp Peak 6(4p16 3) 45 (8%) 499 0.554
(1.00) 		0.539
(1.00) 		0.526
(1.00) 		0.429
(1.00) 		0.0943
(1.00)
Amp Peak 7(4q12) 103 (19%) 441 0.619
(1.00) 		0.532
(1.00) 		0.219
(1.00) 		0.597
(1.00) 		0.292
(1.00)
Amp Peak 11(7q31 2) 446 (82%) 98 0.0246
(1.00) 		0.00146
(0.486) 		0.362
(1.00) 		0.513
(1.00) 		0.0234
(1.00)
Amp Peak 12(7q36 1) 451 (83%) 93 0.061
(1.00) 		0.00223
(0.74) 		0.485
(1.00) 		0.732
(1.00) 		0.18
(1.00)
Amp Peak 13(8q24 21) 63 (12%) 481 0.381
(1.00) 		0.14
(1.00) 		0.275
(1.00) 		0.804
(1.00) 		0.667
(1.00)
Amp Peak 14(11p13) 24 (4%) 520 0.911
(1.00) 		0.237
(1.00) 		0.528
(1.00) 		0.316
(1.00) 		0.269
(1.00)
Amp Peak 15(12p13 32) 78 (14%) 466 0.839
(1.00) 		0.145
(1.00) 		0.901
(1.00) 		0.695
(1.00) 		0.795
(1.00)
Amp Peak 16(12q14 1) 127 (23%) 417 0.125
(1.00) 		0.87
(1.00) 		0.468
(1.00) 		0.808
(1.00) 		0.665
(1.00)
Amp Peak 17(12q15) 87 (16%) 457 0.945
(1.00) 		0.697
(1.00) 		0.339
(1.00) 		0.911
(1.00) 		0.135
(1.00)
Amp Peak 18(13q34) 30 (6%) 514 0.828
(1.00) 		0.847
(1.00) 		0.338
(1.00) 		0.838
(1.00) 		1
(1.00)
Amp Peak 19(14q32 33) 31 (6%) 513 0.0676
(1.00) 		0.00493
(1.00) 		0.453
(1.00) 		0.254
(1.00) 		1
(1.00)
Amp Peak 20(17p13 2) 43 (8%) 501 0.847
(1.00) 		0.749
(1.00) 		0.255
(1.00) 		0.109
(1.00) 		0.497
(1.00)
Amp Peak 21(17q25 1) 74 (14%) 470 0.0765
(1.00) 		0.0404
(1.00) 		0.202
(1.00) 		0.837
(1.00) 		0.593
(1.00)
Amp Peak 22(19p13 2) 231 (42%) 313 0.143
(1.00) 		0.658
(1.00) 		0.859
(1.00) 		0.441
(1.00) 		0.853
(1.00)
Amp Peak 23(19q12) 196 (36%) 348 0.333
(1.00) 		0.397
(1.00) 		0.649
(1.00) 		0.996
(1.00) 		0.849
(1.00)
Amp Peak 24(21q21 1) 62 (11%) 482 0.582
(1.00) 		0.0125
(1.00) 		0.681
(1.00) 		0.549
(1.00) 		0.565
(1.00)
Del Peak 1(1p36 32) 95 (17%) 449 0.403
(1.00) 		0.817
(1.00) 		0.0503
(1.00) 		0.999
(1.00) 		1
(1.00)
Del Peak 2(1p36 23) 131 (24%) 413 0.996
(1.00) 		0.02
(1.00) 		0.0102
(1.00) 		0.193
(1.00) 		0.915
(1.00)
Del Peak 3(1p32 3) 59 (11%) 485 0.761
(1.00) 		0.06
(1.00) 		0.159
(1.00) 		0.687
(1.00) 		0.0786
(1.00)
Del Peak 4(1p22 1) 46 (8%) 498 0.272
(1.00) 		0.321
(1.00) 		1
(1.00) 		0.585
(1.00) 		1
(1.00)
Del Peak 5(1q42 11) 45 (8%) 499 0.0871
(1.00) 		0.0607
(1.00) 		1
(1.00) 		0.0102
(1.00) 		0.137
(1.00)
Del Peak 6(1q44) 31 (6%) 513 0.3
(1.00) 		0.286
(1.00) 		0.851
(1.00) 		0.0669
(1.00) 		0.695
(1.00)
Del Peak 7(2q22 1) 43 (8%) 501 0.311
(1.00) 		0.0941
(1.00) 		0.198
(1.00) 		0.686
(1.00) 		0.174
(1.00)
Del Peak 8(2q37 1) 55 (10%) 489 0.76
(1.00) 		0.345
(1.00) 		0.146
(1.00) 		0.657
(1.00) 		0.361
(1.00)
Del Peak 9(3p21 1) 52 (10%) 492 0.0237
(1.00) 		0.0119
(1.00) 		0.883
(1.00) 		0.698
(1.00) 		0.086
(1.00)
Del Peak 10(3q13 31) 55 (10%) 489 0.528
(1.00) 		0.063
(1.00) 		0.383
(1.00) 		0.306
(1.00) 		0.29
(1.00)
Del Peak 11(3q22 1) 55 (10%) 489 0.656
(1.00) 		0.136
(1.00) 		1
(1.00) 		0.49
(1.00) 		0.29
(1.00)
Del Peak 12(3q29) 62 (11%) 482 0.26
(1.00) 		0.194
(1.00) 		0.891
(1.00) 		0.459
(1.00) 		0.193
(1.00)
Del Peak 13(4p16 3) 76 (14%) 468 0.313
(1.00) 		0.0312
(1.00) 		0.209
(1.00) 		0.154
(1.00) 		0.427
(1.00)
Del Peak 14(4q34 3) 89 (16%) 455 0.165
(1.00) 		0.0944
(1.00) 		0.0581
(1.00) 		0.66
(1.00) 		0.174
(1.00)
Del Peak 15(5q35 3) 52 (10%) 492 0.0182
(1.00) 		0.181
(1.00) 		1
(1.00) 		0.564
(1.00) 		0.438
(1.00)
Del Peak 16(6q22 31) 152 (28%) 392 0.0438
(1.00) 		0.31
(1.00) 		0.0965
(1.00) 		0.454
(1.00) 		0.683
(1.00)
Del Peak 17(6q26) 171 (31%) 373 0.215
(1.00) 		0.665
(1.00) 		0.186
(1.00) 		0.702
(1.00) 		0.767
(1.00)
Del Peak 18(8p23 2) 65 (12%) 479 0.181
(1.00) 		0.0441
(1.00) 		0.589
(1.00) 		0.634
(1.00) 		0.48
(1.00)
Del Peak 20(9q34 2) 70 (13%) 474 0.441
(1.00) 		0.806
(1.00) 		1
(1.00) 		0.498
(1.00) 		0.784
(1.00)
Del Peak 26(11p15 5) 124 (23%) 420 0.0325
(1.00) 		0.00446
(1.00) 		0.145
(1.00) 		0.242
(1.00) 		0.827
(1.00)
Del Peak 27(11p11 2) 99 (18%) 445 0.0736
(1.00) 		0.595
(1.00) 		0.139
(1.00) 		0.796
(1.00) 		0.342
(1.00)
Del Peak 28(11q14 1) 93 (17%) 451 0.747
(1.00) 		0.865
(1.00) 		0.245
(1.00) 		0.538
(1.00) 		0.0201
(1.00)
Del Peak 29(12p13 1) 73 (13%) 471 0.338
(1.00) 		0.795
(1.00) 		0.442
(1.00) 		0.846
(1.00) 		1
(1.00)
Del Peak 30(12q12) 74 (14%) 470 0.641
(1.00) 		0.798
(1.00) 		0.898
(1.00) 		0.81
(1.00) 		0.285
(1.00)
Del Peak 31(12q15) 74 (14%) 470 0.516
(1.00) 		0.952
(1.00) 		0.371
(1.00) 		0.186
(1.00) 		0.285
(1.00)
Del Peak 32(13q14 2) 230 (42%) 314 0.586
(1.00) 		0.538
(1.00) 		0.929
(1.00) 		0.828
(1.00) 		0.355
(1.00)
Del Peak 33(14q13 1) 173 (32%) 371 0.756
(1.00) 		0.529
(1.00) 		0.222
(1.00) 		0.262
(1.00) 		0.694
(1.00)
Del Peak 34(14q24 2) 168 (31%) 376 0.867
(1.00) 		0.443
(1.00) 		0.394
(1.00) 		0.605
(1.00) 		0.843
(1.00)
Del Peak 35(14q31 3) 155 (28%) 389 0.924
(1.00) 		0.721
(1.00) 		0.628
(1.00) 		0.647
(1.00) 		0.685
(1.00)
Del Peak 36(15q14) 146 (27%) 398 0.459
(1.00) 		0.0774
(1.00) 		0.622
(1.00) 		0.808
(1.00) 		0.149
(1.00)
Del Peak 37(16p12 2) 89 (16%) 455 0.333
(1.00) 		0.31
(1.00) 		0.237
(1.00) 		0.808
(1.00) 		0.804
(1.00)
Del Peak 38(16q23 3) 93 (17%) 451 0.219
(1.00) 		0.956
(1.00) 		0.485
(1.00) 		0.266
(1.00) 		0.0288
(1.00)
Del Peak 39(17p13 2) 81 (15%) 463 0.601
(1.00) 		0.554
(1.00) 		0.221
(1.00) 		0.189
(1.00) 		0.609
(1.00)
Del Peak 40(17p13 1) 91 (17%) 453 0.826
(1.00) 		0.183
(1.00) 		0.0613
(1.00) 		0.797
(1.00) 		0.11
(1.00)
Del Peak 41(17q11 2) 67 (12%) 477 0.605
(1.00) 		0.583
(1.00) 		1
(1.00) 		0.245
(1.00) 		0.0498
(1.00)
Del Peak 42(18q22 3) 78 (14%) 466 0.918
(1.00) 		0.448
(1.00) 		0.708
(1.00) 		0.128
(1.00) 		0.603
(1.00)
Del Peak 43(19q13 41) 98 (18%) 446 0.066
(1.00) 		0.449
(1.00) 		1
(1.00) 		0.264
(1.00) 		0.406
(1.00)
Del Peak 44(21q22 3) 58 (11%) 486 0.757
(1.00) 		0.0758
(1.00) 		0.258
(1.00) 		0.198
(1.00) 		0.883
(1.00)
Del Peak 45(22q13 32) 204 (38%) 340 0.581
(1.00) 		0.387
(1.00) 		0.856
(1.00) 		0.518
(1.00) 		0.705
(1.00)
Del Peak 46(Xp22 2) 122 (22%) 422 0.277
(1.00) 		0.467
(1.00) 		0.675
(1.00) 		0.825
(1.00) 		1
(1.00)
'Amp Peak 8(7p11.2) mutation analysis' versus 'Time to Death'

P value = 2.57e-06 (logrank test), Q value = 0.00088

Table S1.  Gene #8: 'Amp Peak 8(7p11.2) mutation analysis' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 544 411 0.1 - 127.6 (9.6)
AMP PEAK 8(7P11.2) MUTATED 478 367 0.1 - 127.6 (9.2)
AMP PEAK 8(7P11.2) WILD-TYPE 66 44 0.2 - 108.8 (13.5)

Figure S1.  Get High-res Image Gene #8: 'Amp Peak 8(7p11.2) mutation analysis' versus Clinical Feature #1: 'Time to Death'

'Amp Peak 8(7p11.2) mutation analysis' versus 'AGE'

P value = 5.95e-09 (t-test), Q value = 2.1e-06

Table S2.  Gene #8: 'Amp Peak 8(7p11.2) mutation analysis' versus Clinical Feature #2: 'AGE'

nPatients Mean (Std.Dev)
ALL 544 57.8 (14.3)
AMP PEAK 8(7P11.2) MUTATED 478 59.7 (12.4)
AMP PEAK 8(7P11.2) WILD-TYPE 66 43.9 (19.0)

Figure S2.  Get High-res Image Gene #8: 'Amp Peak 8(7p11.2) mutation analysis' versus Clinical Feature #2: 'AGE'

'Amp Peak 9(7q11.21) mutation analysis' versus 'Time to Death'

P value = 0.000152 (logrank test), Q value = 0.051

Table S3.  Gene #9: 'Amp Peak 9(7q11.21) mutation analysis' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 544 411 0.1 - 127.6 (9.6)
AMP PEAK 9(7Q11.21) MUTATED 439 333 0.1 - 127.6 (9.2)
AMP PEAK 9(7Q11.21) WILD-TYPE 105 78 0.2 - 108.8 (12.4)

Figure S3.  Get High-res Image Gene #9: 'Amp Peak 9(7q11.21) mutation analysis' versus Clinical Feature #1: 'Time to Death'

'Amp Peak 9(7q11.21) mutation analysis' versus 'AGE'

P value = 8.05e-08 (t-test), Q value = 2.8e-05

Table S4.  Gene #9: 'Amp Peak 9(7q11.21) mutation analysis' versus Clinical Feature #2: 'AGE'

nPatients Mean (Std.Dev)
ALL 544 57.8 (14.3)
AMP PEAK 9(7Q11.21) MUTATED 439 59.9 (12.3)
AMP PEAK 9(7Q11.21) WILD-TYPE 105 49.2 (18.3)

Figure S4.  Get High-res Image Gene #9: 'Amp Peak 9(7q11.21) mutation analysis' versus Clinical Feature #2: 'AGE'

'Amp Peak 10(7q21.2) mutation analysis' versus 'AGE'

P value = 1.06e-05 (t-test), Q value = 0.0036

Table S5.  Gene #10: 'Amp Peak 10(7q21.2) mutation analysis' versus Clinical Feature #2: 'AGE'

nPatients Mean (Std.Dev)
ALL 544 57.8 (14.3)
AMP PEAK 10(7Q21.2) MUTATED 453 59.5 (12.2)
AMP PEAK 10(7Q21.2) WILD-TYPE 91 49.5 (19.9)

Figure S5.  Get High-res Image Gene #10: 'Amp Peak 10(7q21.2) mutation analysis' versus Clinical Feature #2: 'AGE'

'Del Peak 19(9p21.3) mutation analysis' versus 'AGE'

P value = 0.000156 (t-test), Q value = 0.052

Table S6.  Gene #43: 'Del Peak 19(9p21.3) mutation analysis' versus Clinical Feature #2: 'AGE'

nPatients Mean (Std.Dev)
ALL 544 57.8 (14.3)
DEL PEAK 19(9P21.3) MUTATED 399 59.3 (13.5)
DEL PEAK 19(9P21.3) WILD-TYPE 145 53.7 (15.7)

Figure S6.  Get High-res Image Gene #43: 'Del Peak 19(9p21.3) mutation analysis' versus Clinical Feature #2: 'AGE'

'Del Peak 21(10p15.3) mutation analysis' versus 'Time to Death'

P value = 1.06e-05 (logrank test), Q value = 0.0036

Table S7.  Gene #45: 'Del Peak 21(10p15.3) mutation analysis' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 544 411 0.1 - 127.6 (9.6)
DEL PEAK 21(10P15.3) MUTATED 445 342 0.1 - 92.6 (9.4)
DEL PEAK 21(10P15.3) WILD-TYPE 99 69 0.1 - 127.6 (10.6)

Figure S7.  Get High-res Image Gene #45: 'Del Peak 21(10p15.3) mutation analysis' versus Clinical Feature #1: 'Time to Death'

'Del Peak 21(10p15.3) mutation analysis' versus 'AGE'

P value = 4.22e-08 (t-test), Q value = 1.5e-05

Table S8.  Gene #45: 'Del Peak 21(10p15.3) mutation analysis' versus Clinical Feature #2: 'AGE'

nPatients Mean (Std.Dev)
ALL 544 57.8 (14.3)
DEL PEAK 21(10P15.3) MUTATED 445 59.9 (12.3)
DEL PEAK 21(10P15.3) WILD-TYPE 99 48.5 (18.4)

Figure S8.  Get High-res Image Gene #45: 'Del Peak 21(10p15.3) mutation analysis' versus Clinical Feature #2: 'AGE'

'Del Peak 22(10p13) mutation analysis' versus 'Time to Death'

P value = 6.7e-06 (logrank test), Q value = 0.0023

Table S9.  Gene #46: 'Del Peak 22(10p13) mutation analysis' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 544 411 0.1 - 127.6 (9.6)
DEL PEAK 22(10P13) MUTATED 447 343 0.1 - 92.6 (9.4)
DEL PEAK 22(10P13) WILD-TYPE 97 68 0.1 - 127.6 (9.8)

Figure S9.  Get High-res Image Gene #46: 'Del Peak 22(10p13) mutation analysis' versus Clinical Feature #1: 'Time to Death'

'Del Peak 22(10p13) mutation analysis' versus 'AGE'

P value = 2.12e-07 (t-test), Q value = 7.3e-05

Table S10.  Gene #46: 'Del Peak 22(10p13) mutation analysis' versus Clinical Feature #2: 'AGE'

nPatients Mean (Std.Dev)
ALL 544 57.8 (14.3)
DEL PEAK 22(10P13) MUTATED 447 59.8 (12.2)
DEL PEAK 22(10P13) WILD-TYPE 97 48.7 (18.9)

Figure S10.  Get High-res Image Gene #46: 'Del Peak 22(10p13) mutation analysis' versus Clinical Feature #2: 'AGE'

'Del Peak 23(10p11.23) mutation analysis' versus 'Time to Death'

P value = 9.14e-07 (logrank test), Q value = 0.00032

Table S11.  Gene #47: 'Del Peak 23(10p11.23) mutation analysis' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 544 411 0.1 - 127.6 (9.6)
DEL PEAK 23(10P11.23) MUTATED 451 345 0.1 - 92.6 (9.4)
DEL PEAK 23(10P11.23) WILD-TYPE 93 66 0.1 - 127.6 (12.4)

Figure S11.  Get High-res Image Gene #47: 'Del Peak 23(10p11.23) mutation analysis' versus Clinical Feature #1: 'Time to Death'

'Del Peak 23(10p11.23) mutation analysis' versus 'AGE'

P value = 1.16e-08 (t-test), Q value = 4e-06

Table S12.  Gene #47: 'Del Peak 23(10p11.23) mutation analysis' versus Clinical Feature #2: 'AGE'

nPatients Mean (Std.Dev)
ALL 544 57.8 (14.3)
DEL PEAK 23(10P11.23) MUTATED 451 60.0 (12.1)
DEL PEAK 23(10P11.23) WILD-TYPE 93 47.4 (18.8)

Figure S12.  Get High-res Image Gene #47: 'Del Peak 23(10p11.23) mutation analysis' versus Clinical Feature #2: 'AGE'

'Del Peak 24(10q23.31) mutation analysis' versus 'Time to Death'

P value = 2.27e-05 (logrank test), Q value = 0.0077

Table S13.  Gene #48: 'Del Peak 24(10q23.31) mutation analysis' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 544 411 0.1 - 127.6 (9.6)
DEL PEAK 24(10Q23.31) MUTATED 486 372 0.1 - 127.6 (9.6)
DEL PEAK 24(10Q23.31) WILD-TYPE 58 39 0.2 - 108.8 (10.9)

Figure S13.  Get High-res Image Gene #48: 'Del Peak 24(10q23.31) mutation analysis' versus Clinical Feature #1: 'Time to Death'

'Del Peak 24(10q23.31) mutation analysis' versus 'AGE'

P value = 2.71e-06 (t-test), Q value = 0.00093

Table S14.  Gene #48: 'Del Peak 24(10q23.31) mutation analysis' versus Clinical Feature #2: 'AGE'

nPatients Mean (Std.Dev)
ALL 544 57.8 (14.3)
DEL PEAK 24(10Q23.31) MUTATED 486 59.2 (13.0)
DEL PEAK 24(10Q23.31) WILD-TYPE 58 46.2 (18.7)

Figure S14.  Get High-res Image Gene #48: 'Del Peak 24(10q23.31) mutation analysis' versus Clinical Feature #2: 'AGE'

'Del Peak 25(10q26.3) mutation analysis' versus 'AGE'

P value = 2.89e-05 (t-test), Q value = 0.0098

Table S15.  Gene #49: 'Del Peak 25(10q26.3) mutation analysis' versus Clinical Feature #2: 'AGE'

nPatients Mean (Std.Dev)
ALL 544 57.8 (14.3)
DEL PEAK 25(10Q26.3) MUTATED 487 59.0 (13.1)
DEL PEAK 25(10Q26.3) WILD-TYPE 57 47.4 (19.0)

Figure S15.  Get High-res Image Gene #49: 'Del Peak 25(10q26.3) mutation analysis' versus Clinical Feature #2: 'AGE'

Methods & Data
Input

  • Copy number data file = All Lesions File (all_lesions.conf_##.txt, where ## is the confidence level). The all lesions file is from GISTIC pipeline and summarizes the results from the GISTIC run. It contains data about the significant regions of amplification and deletion as well as which samples are amplified or deleted in each of these regions. The identified regions are listed down the first column, and the samples are listed across the first row, starting in column 10.

  • Clinical data file = GBM-TP.clin.merged.picked.txt

  • Number of patients = 544

  • Number of copy number variation regions = 70

  • Number of selected clinical features = 5

  • Exclude regions that fewer than K tumors have alterations, K = 3

Survival analysis

For survival clinical features, the Kaplan-Meier survival curves of tumors with and without gene cnvs were plotted and the statistical significance P values were estimated by logrank test (Bland and Altman 2004) using the 'survdiff' function in R

Student's t-test analysis

For continuous numerical clinical features, two-tailed Student's t test with unequal variance (Lehmann and Romano 2005) was applied to compare the clinical values between tumors with and without gene cnvs using 't.test' 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

This is an experimental feature. The full results of the analysis summarized in this report can be downloaded from the TCGA Data Coordination Center.

References
[1] Bland and Altman, Statistics notes: The logrank test, BMJ 328(7447):1073 (2004)
[2] Lehmann and Romano, Testing Statistical Hypotheses (3E ed.), New York: Springer. ISBN 0387988645 (2005)
[3] 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)
[4] 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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