Correlation between copy number variation genes (focal) and selected clinical features
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 70 arm-level results and 6 clinical features across 552 patients, 15 significant findings detected with Q value < 0.25.

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

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

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

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

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

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

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

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

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

Results
Overview of the results

Table 1.  Get Full Table Overview of the association between significant copy number variation of 70 arm-level results and 6 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 		HISTOLOGICAL
TYPE 		RADIATIONS
RADIATION
REGIMENINDICATION
nCNV (%) nWild-Type logrank test t-test Fisher's exact test t-test Fisher's exact test Fisher's exact test
Amp Peak 8(7p11 2) 0 (0%) 68 4.01e-06
(0.00166) 		3.88e-09
(1.63e-06) 		0.428
(1.00) 		0.0351
(1.00) 		0.0463
(1.00) 		0.0505
(1.00)
Amp Peak 9(7q11 21) 0 (0%) 108 0.000284
(0.115) 		1.32e-07
(5.5e-05) 		0.273
(1.00) 		0.658
(1.00) 		0.0105
(1.00) 		0.0629
(1.00)
Del Peak 21(10p15 3) 0 (0%) 102 2.29e-05
(0.00939) 		7.27e-08
(3.04e-05) 		0.0927
(1.00) 		0.596
(1.00) 		0.0223
(1.00) 		0.41
(1.00)
Del Peak 22(10p13) 0 (0%) 100 1.49e-05
(0.00613) 		3.45e-07
(0.000143) 		0.0415
(1.00) 		0.884
(1.00) 		0.0199
(1.00) 		0.905
(1.00)
Del Peak 23(10p11 23) 0 (0%) 96 2.23e-06
(0.000927) 		2.12e-08
(8.86e-06) 		0.109
(1.00) 		0.232
(1.00) 		0.00327
(1.00) 		0.545
(1.00)
Del Peak 24(10q23 31) 0 (0%) 61 6.15e-05
(0.0251) 		5.66e-06
(0.00234) 		0.677
(1.00) 		0.0751
(1.00) 		0.00512
(1.00) 		0.661
(1.00)
Amp Peak 10(7q21 2) 0 (0%) 94 0.00181
(0.732) 		1.54e-05
(0.00635) 		0.563
(1.00) 		0.49
(1.00) 		0.0369
(1.00) 		0.143
(1.00)
Del Peak 19(9p21 3) 0 (0%) 149 0.037
(1.00) 		0.000356
(0.145) 		0.493
(1.00) 		0.0926
(1.00) 		0.195
(1.00) 		0.536
(1.00)
Del Peak 25(10q26 3) 0 (0%) 60 0.00319
(1.00) 		5.33e-05
(0.0218) 		0.576
(1.00) 		0.0613
(1.00) 		0.0188
(1.00) 		1
(1.00)
Amp Peak 1(1p36 21) 0 (0%) 465 0.0947
(1.00) 		0.348
(1.00) 		0.283
(1.00) 		0.653
(1.00) 		0.314
(1.00) 		0.801
(1.00)
Amp Peak 2(1q32 1) 0 (0%) 404 0.48
(1.00) 		0.299
(1.00) 		0.624
(1.00) 		0.279
(1.00) 		0.275
(1.00) 		0.917
(1.00)
Amp Peak 3(1q44) 0 (0%) 458 0.534
(1.00) 		0.857
(1.00) 		0.297
(1.00) 		0.599
(1.00) 		0.627
(1.00) 		0.808
(1.00)
Amp Peak 4(2p24 3) 0 (0%) 507 0.0986
(1.00) 		0.175
(1.00) 		0.341
(1.00) 		0.583
(1.00) 		0.69
(1.00) 		0.867
(1.00)
Amp Peak 5(3q26 33) 0 (0%) 447 0.312
(1.00) 		0.0358
(1.00) 		0.825
(1.00) 		0.688
(1.00) 		0.0328
(1.00) 		0.907
(1.00)
Amp Peak 6(4p16 3) 0 (0%) 507 0.525
(1.00) 		0.514
(1.00) 		0.526
(1.00) 		0.429
(1.00) 		1
(1.00) 		0.239
(1.00)
Amp Peak 7(4q12) 0 (0%) 449 0.663
(1.00) 		0.575
(1.00) 		0.22
(1.00) 		0.597
(1.00) 		0.416
(1.00) 		0.346
(1.00)
Amp Peak 11(7q31 2) 0 (0%) 101 0.0371
(1.00) 		0.00184
(0.742) 		0.369
(1.00) 		0.513
(1.00) 		0.143
(1.00) 		0.0565
(1.00)
Amp Peak 12(7q36 1) 0 (0%) 96 0.0873
(1.00) 		0.00282
(1.00) 		0.492
(1.00) 		0.732
(1.00) 		0.115
(1.00) 		0.276
(1.00)
Amp Peak 13(8q24 21) 0 (0%) 489 0.359
(1.00) 		0.13
(1.00) 		0.275
(1.00) 		0.804
(1.00) 		0.885
(1.00) 		0.472
(1.00)
Amp Peak 14(11p13) 0 (0%) 527 0.958
(1.00) 		0.217
(1.00) 		0.406
(1.00) 		0.316
(1.00) 		0.226
(1.00) 		0.513
(1.00)
Amp Peak 15(12p13 32) 0 (0%) 473 0.664
(1.00) 		0.0932
(1.00) 		1
(1.00) 		0.695
(1.00) 		1
(1.00) 		1
(1.00)
Amp Peak 16(12q14 1) 0 (0%) 424 0.201
(1.00) 		0.684
(1.00) 		0.409
(1.00) 		0.808
(1.00) 		0.745
(1.00) 		0.827
(1.00)
Amp Peak 17(12q15) 0 (0%) 463 0.861
(1.00) 		0.679
(1.00) 		0.346
(1.00) 		0.911
(1.00) 		0.683
(1.00) 		0.21
(1.00)
Amp Peak 18(13q34) 0 (0%) 522 0.803
(1.00) 		0.824
(1.00) 		0.339
(1.00) 		0.838
(1.00) 		0.529
(1.00) 		0.688
(1.00)
Amp Peak 19(14q32 33) 0 (0%) 520 0.159
(1.00) 		0.0224
(1.00) 		0.582
(1.00) 		0.254
(1.00) 		0.209
(1.00) 		1
(1.00)
Amp Peak 20(17p13 2) 0 (0%) 508 0.932
(1.00) 		0.541
(1.00) 		0.336
(1.00) 		0.109
(1.00) 		0.685
(1.00) 		0.615
(1.00)
Amp Peak 21(17q25 1) 0 (0%) 477 0.139
(1.00) 		0.0873
(1.00) 		0.255
(1.00) 		0.837
(1.00) 		1
(1.00) 		0.687
(1.00)
Amp Peak 22(19p13 2) 0 (0%) 318 0.101
(1.00) 		0.821
(1.00) 		1
(1.00) 		0.441
(1.00) 		0.517
(1.00) 		1
(1.00)
Amp Peak 23(19q12) 0 (0%) 353 0.261
(1.00) 		0.529
(1.00) 		0.587
(1.00) 		0.996
(1.00) 		0.718
(1.00) 		0.774
(1.00)
Amp Peak 24(21q21 1) 0 (0%) 488 0.526
(1.00) 		0.0198
(1.00) 		0.684
(1.00) 		0.549
(1.00) 		0.374
(1.00) 		0.566
(1.00)
Del Peak 1(1p36 32) 0 (0%) 457 0.374
(1.00) 		0.867
(1.00) 		0.0508
(1.00) 		0.999
(1.00) 		0.43
(1.00) 		0.808
(1.00)
Del Peak 2(1p36 23) 0 (0%) 421 0.943
(1.00) 		0.0255
(1.00) 		0.0104
(1.00) 		0.193
(1.00) 		0.263
(1.00) 		0.665
(1.00)
Del Peak 3(1p32 3) 0 (0%) 493 0.735
(1.00) 		0.0677
(1.00) 		0.159
(1.00) 		0.687
(1.00) 		1
(1.00) 		0.101
(1.00)
Del Peak 4(1p22 1) 0 (0%) 506 0.257
(1.00) 		0.345
(1.00) 		1
(1.00) 		0.585
(1.00) 		0.0899
(1.00) 		1
(1.00)
Del Peak 5(1q42 11) 0 (0%) 507 0.0965
(1.00) 		0.0679
(1.00) 		1
(1.00) 		0.0102
(1.00) 		1
(1.00) 		0.181
(1.00)
Del Peak 6(1q44) 0 (0%) 521 0.315
(1.00) 		0.301
(1.00) 		0.851
(1.00) 		0.0669
(1.00) 		1
(1.00) 		0.844
(1.00)
Del Peak 7(2q22 1) 0 (0%) 509 0.33
(1.00) 		0.102
(1.00) 		0.198
(1.00) 		0.686
(1.00) 		0.816
(1.00) 		0.123
(1.00)
Del Peak 8(2q37 1) 0 (0%) 497 0.73
(1.00) 		0.327
(1.00) 		0.146
(1.00) 		0.657
(1.00) 		1
(1.00) 		0.36
(1.00)
Del Peak 9(3p21 1) 0 (0%) 500 0.021
(1.00) 		0.0109
(1.00) 		0.883
(1.00) 		0.698
(1.00) 		0.501
(1.00) 		0.0591
(1.00)
Del Peak 10(3q13 31) 0 (0%) 497 0.504
(1.00) 		0.0586
(1.00) 		0.384
(1.00) 		0.306
(1.00) 		0.872
(1.00) 		0.128
(1.00)
Del Peak 11(3q22 1) 0 (0%) 497 0.625
(1.00) 		0.128
(1.00) 		1
(1.00) 		0.49
(1.00) 		0.872
(1.00) 		0.442
(1.00)
Del Peak 12(3q29) 0 (0%) 489 0.277
(1.00) 		0.233
(1.00) 		1
(1.00) 		0.459
(1.00) 		1
(1.00) 		0.246
(1.00)
Del Peak 13(4p16 3) 0 (0%) 476 0.295
(1.00) 		0.0281
(1.00) 		0.255
(1.00) 		0.154
(1.00) 		0.507
(1.00) 		0.084
(1.00)
Del Peak 14(4q34 3) 0 (0%) 463 0.149
(1.00) 		0.0849
(1.00) 		0.0585
(1.00) 		0.66
(1.00) 		0.561
(1.00) 		0.105
(1.00)
Del Peak 15(5q35 3) 0 (0%) 500 0.0167
(1.00) 		0.171
(1.00) 		1
(1.00) 		0.564
(1.00) 		1
(1.00) 		0.431
(1.00)
Del Peak 16(6q22 31) 0 (0%) 400 0.0543
(1.00) 		0.353
(1.00) 		0.0974
(1.00) 		0.454
(1.00) 		0.122
(1.00) 		0.838
(1.00)
Del Peak 17(6q26) 0 (0%) 380 0.214
(1.00) 		0.713
(1.00) 		0.189
(1.00) 		0.702
(1.00) 		0.128
(1.00) 		0.692
(1.00)
Del Peak 18(8p23 2) 0 (0%) 486 0.171
(1.00) 		0.0355
(1.00) 		0.595
(1.00) 		0.634
(1.00) 		0.782
(1.00) 		0.571
(1.00)
Del Peak 20(9q34 2) 0 (0%) 482 0.417
(1.00) 		0.768
(1.00) 		1
(1.00) 		0.498
(1.00) 		0.615
(1.00) 		0.681
(1.00)
Del Peak 26(11p15 5) 0 (0%) 427 0.0326
(1.00) 		0.00539
(1.00) 		0.177
(1.00) 		0.242
(1.00) 		0.436
(1.00) 		0.742
(1.00)
Del Peak 27(11p11 2) 0 (0%) 452 0.0771
(1.00) 		0.64
(1.00) 		0.144
(1.00) 		0.796
(1.00) 		0.197
(1.00) 		0.812
(1.00)
Del Peak 28(11q14 1) 0 (0%) 458 0.763
(1.00) 		0.815
(1.00) 		0.297
(1.00) 		0.538
(1.00) 		0.382
(1.00) 		0.0658
(1.00)
Del Peak 29(12p13 1) 0 (0%) 478 0.356
(1.00) 		0.859
(1.00) 		0.523
(1.00) 		0.846
(1.00) 		0.713
(1.00) 		0.893
(1.00)
Del Peak 30(12q12) 0 (0%) 477 0.667
(1.00) 		0.736
(1.00) 		1
(1.00) 		0.81
(1.00) 		1
(1.00) 		0.227
(1.00)
Del Peak 31(12q15) 0 (0%) 476 0.635
(1.00) 		0.717
(1.00) 		0.451
(1.00) 		0.186
(1.00) 		0.394
(1.00) 		0.181
(1.00)
Del Peak 32(13q14 2) 0 (0%) 320 0.55
(1.00) 		0.648
(1.00) 		0.792
(1.00) 		0.828
(1.00) 		0.515
(1.00) 		0.577
(1.00)
Del Peak 33(14q13 1) 0 (0%) 379 0.817
(1.00) 		0.591
(1.00) 		0.223
(1.00) 		0.262
(1.00) 		0.162
(1.00) 		0.767
(1.00)
Del Peak 34(14q24 2) 0 (0%) 384 0.806
(1.00) 		0.397
(1.00) 		0.395
(1.00) 		0.605
(1.00) 		0.112
(1.00) 		0.484
(1.00)
Del Peak 35(14q31 3) 0 (0%) 397 0.977
(1.00) 		0.663
(1.00) 		0.628
(1.00) 		0.647
(1.00) 		0.0532
(1.00) 		0.609
(1.00)
Del Peak 36(15q14) 0 (0%) 405 0.447
(1.00) 		0.0681
(1.00) 		0.695
(1.00) 		0.808
(1.00) 		0.77
(1.00) 		0.211
(1.00)
Del Peak 37(16p12 2) 0 (0%) 463 0.359
(1.00) 		0.339
(1.00) 		0.238
(1.00) 		0.808
(1.00) 		0.287
(1.00) 		0.534
(1.00)
Del Peak 38(16q23 3) 0 (0%) 459 0.243
(1.00) 		0.91
(1.00) 		0.486
(1.00) 		0.266
(1.00) 		0.569
(1.00) 		0.0141
(1.00)
Del Peak 39(17p13 2) 0 (0%) 470 0.626
(1.00) 		0.504
(1.00) 		0.272
(1.00) 		0.189
(1.00) 		1
(1.00) 		0.519
(1.00)
Del Peak 40(17p13 1) 0 (0%) 460 0.807
(1.00) 		0.164
(1.00) 		0.0802
(1.00) 		0.797
(1.00) 		1
(1.00) 		0.0832
(1.00)
Del Peak 41(17q11 2) 0 (0%) 484 0.585
(1.00) 		0.518
(1.00) 		0.895
(1.00) 		0.245
(1.00) 		1
(1.00) 		0.035
(1.00)
Del Peak 42(18q22 3) 0 (0%) 473 0.744
(1.00) 		0.63
(1.00) 		0.805
(1.00) 		0.128
(1.00) 		1
(1.00) 		0.896
(1.00)
Del Peak 43(19q13 41) 0 (0%) 454 0.058
(1.00) 		0.415
(1.00) 		1
(1.00) 		0.264
(1.00) 		0.441
(1.00) 		1
(1.00)
Del Peak 44(21q22 3) 0 (0%) 493 0.699
(1.00) 		0.0576
(1.00) 		0.325
(1.00) 		0.198
(1.00) 		0.883
(1.00) 		0.882
(1.00)
Del Peak 45(22q13 32) 0 (0%) 346 0.634
(1.00) 		0.307
(1.00) 		0.928
(1.00) 		0.518
(1.00) 		0.79
(1.00) 		1
(1.00)
Del Peak 46(Xp22 2) 0 (0%) 430 0.252
(1.00) 		0.429
(1.00) 		0.676
(1.00) 		0.825
(1.00) 		0.308
(1.00) 		0.438
(1.00)
'Amp Peak 8(7p11.2)' versus 'Time to Death'

P value = 4.01e-06 (logrank test), Q value = 0.0017

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

nPatients nDeath Duration Range (Median), Month
ALL 552 419 0.1 - 127.6 (9.6)
AMP PEAK 8(7P11.2) CNV 484 373 0.1 - 127.6 (9.2)
AMP PEAK 8(7P11.2) WILD-TYPE 68 46 0.2 - 108.8 (13.2)

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

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

P value = 3.88e-09 (t-test), Q value = 1.6e-06

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

nPatients Mean (Std.Dev)
ALL 552 57.9 (14.4)
AMP PEAK 8(7P11.2) CNV 484 59.8 (12.5)
AMP PEAK 8(7P11.2) WILD-TYPE 68 44.2 (18.8)

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

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

P value = 0.000284 (logrank test), Q value = 0.12

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

nPatients nDeath Duration Range (Median), Month
ALL 552 419 0.1 - 127.6 (9.6)
AMP PEAK 9(7Q11.21) CNV 444 338 0.1 - 127.6 (9.2)
AMP PEAK 9(7Q11.21) WILD-TYPE 108 81 0.2 - 108.8 (11.9)

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

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

P value = 1.32e-07 (t-test), Q value = 5.5e-05

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

nPatients Mean (Std.Dev)
ALL 552 57.9 (14.4)
AMP PEAK 9(7Q11.21) CNV 444 59.9 (12.4)
AMP PEAK 9(7Q11.21) WILD-TYPE 108 49.6 (18.3)

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

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

P value = 1.54e-05 (t-test), Q value = 0.0063

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

nPatients Mean (Std.Dev)
ALL 552 57.9 (14.4)
AMP PEAK 10(7Q21.2) CNV 458 59.5 (12.4)
AMP PEAK 10(7Q21.2) WILD-TYPE 94 49.9 (19.9)

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

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

P value = 0.000356 (t-test), Q value = 0.14

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

nPatients Mean (Std.Dev)
ALL 552 57.9 (14.4)
DEL PEAK 19(9P21.3) CNV 403 59.3 (13.6)
DEL PEAK 19(9P21.3) WILD-TYPE 149 54.0 (15.8)

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

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

P value = 2.29e-05 (logrank test), Q value = 0.0094

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

nPatients nDeath Duration Range (Median), Month
ALL 552 419 0.1 - 127.6 (9.6)
DEL PEAK 21(10P15.3) CNV 450 347 0.1 - 92.6 (9.4)
DEL PEAK 21(10P15.3) WILD-TYPE 102 72 0.1 - 127.6 (10.6)

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

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

P value = 7.27e-08 (t-test), Q value = 3e-05

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

nPatients Mean (Std.Dev)
ALL 552 57.9 (14.4)
DEL PEAK 21(10P15.3) CNV 450 59.9 (12.4)
DEL PEAK 21(10P15.3) WILD-TYPE 102 48.9 (18.4)

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

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

P value = 1.49e-05 (logrank test), Q value = 0.0061

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

nPatients nDeath Duration Range (Median), Month
ALL 552 419 0.1 - 127.6 (9.6)
DEL PEAK 22(10P13) CNV 452 348 0.1 - 92.6 (9.4)
DEL PEAK 22(10P13) WILD-TYPE 100 71 0.1 - 127.6 (10.2)

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

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

P value = 3.45e-07 (t-test), Q value = 0.00014

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

nPatients Mean (Std.Dev)
ALL 552 57.9 (14.4)
DEL PEAK 22(10P13) CNV 452 59.8 (12.4)
DEL PEAK 22(10P13) WILD-TYPE 100 49.1 (18.9)

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

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

P value = 2.23e-06 (logrank test), Q value = 0.00093

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

nPatients nDeath Duration Range (Median), Month
ALL 552 419 0.1 - 127.6 (9.6)
DEL PEAK 23(10P11.23) CNV 456 350 0.1 - 92.6 (9.4)
DEL PEAK 23(10P11.23) WILD-TYPE 96 69 0.1 - 127.6 (11.7)

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

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

P value = 2.12e-08 (t-test), Q value = 8.9e-06

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

nPatients Mean (Std.Dev)
ALL 552 57.9 (14.4)
DEL PEAK 23(10P11.23) CNV 456 60.0 (12.3)
DEL PEAK 23(10P11.23) WILD-TYPE 96 47.9 (18.8)

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

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

P value = 6.15e-05 (logrank test), Q value = 0.025

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

nPatients nDeath Duration Range (Median), Month
ALL 552 419 0.1 - 127.6 (9.6)
DEL PEAK 24(10Q23.31) CNV 491 377 0.1 - 127.6 (9.5)
DEL PEAK 24(10Q23.31) WILD-TYPE 61 42 0.2 - 108.8 (10.7)

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

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

P value = 5.66e-06 (t-test), Q value = 0.0023

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

nPatients Mean (Std.Dev)
ALL 552 57.9 (14.4)
DEL PEAK 24(10Q23.31) CNV 491 59.3 (13.1)
DEL PEAK 24(10Q23.31) WILD-TYPE 61 47.0 (18.9)

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

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

P value = 5.33e-05 (t-test), Q value = 0.022

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

nPatients Mean (Std.Dev)
ALL 552 57.9 (14.4)
DEL PEAK 25(10Q26.3) CNV 492 59.1 (13.3)
DEL PEAK 25(10Q26.3) WILD-TYPE 60 48.2 (19.0)

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

Methods & Data
Input

  • Mutation data file = all_lesions.conf_99.cnv.cluster.txt

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

  • Number of patients = 552

  • Number of significantly arm-level cnvs = 70

  • Number of selected clinical features = 6

  • 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

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 mutations 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.

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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