Correlation between copy number variations of arm-level result and selected clinical features
Head and Neck Squamous Cell Carcinoma (Primary solid tumor)
28 January 2016  |  analyses__2016_01_28
Maintainer Information
Citation Information
doi:10.7908/C1QJ7GPH
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 variations of arm-level result and selected clinical features. Broad Institute of MIT and Harvard. doi:10.7908/C1QJ7GPH
Overview
Introduction

This pipeline computes the correlation between significant arm-level copy number variations (cnvs) and selected clinical features.

Summary

Testing the association between copy number variation 82 arm-level events and 14 clinical features across 522 patients, 9 significant findings detected with Q value < 0.25.

  • 1q gain cnv correlated to 'RACE'.

  • 3q gain cnv correlated to 'NUMBER_OF_LYMPH_NODES'.

  • 7p gain cnv correlated to 'Time to Death'.

  • 18p gain cnv correlated to 'GENDER'.

  • 18q gain cnv correlated to 'GENDER'.

  • 9p loss cnv correlated to 'NUMBER_PACK_YEARS_SMOKED'.

  • 11q loss cnv correlated to 'GENDER',  'RADIATION_THERAPY', and 'NUMBER_OF_LYMPH_NODES'.

Results
Overview of the results

Table 1.  Get Full Table Overview of the association between significant copy number variation of 82 arm-level events and 14 clinical features. Shown in the table are P values (Q values). Thresholded by Q value < 0.25, 9 significant findings detected.

Clinical
Features 		Time
to
Death 		YEARS
TO
BIRTH 		PATHOLOGIC
STAGE 		PATHOLOGY
T
STAGE 		PATHOLOGY
N
STAGE 		PATHOLOGY
M
STAGE 		GENDER RADIATION
THERAPY 		HISTOLOGICAL
TYPE 		NUMBER
PACK
YEARS
SMOKED 		YEAR
OF
TOBACCO
SMOKING
ONSET 		NUMBER
OF
LYMPH
NODES 		RACE ETHNICITY
nCNV (%) nWild-Type logrank test Wilcoxon-test Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test Wilcoxon-test Wilcoxon-test Wilcoxon-test Fisher's exact test Fisher's exact test
11q loss 172 (33%) 350 0.923
(1.00) 		0.0177
(0.448) 		0.0991
(0.645) 		0.897
(1.00) 		0.00944
(0.417) 		1
(1.00) 		0.000141
(0.081) 		0.000399
(0.114) 		0.119
(0.671) 		0.383
(0.925) 		0.231
(0.805) 		0.000498
(0.114) 		0.0434
(0.514) 		0.0833
(0.618)
1q gain 124 (24%) 398 0.425
(0.935) 		0.183
(0.745) 		0.642
(1.00) 		0.234
(0.805) 		0.129
(0.68) 		1
(1.00) 		0.247
(0.819) 		0.0216
(0.479) 		0.00496
(0.334) 		0.501
(0.963) 		0.335
(0.922) 		0.374
(0.922) 		0.00136
(0.223) 		0.64
(1.00)
3q gain 257 (49%) 265 0.574
(1.00) 		0.124
(0.678) 		0.867
(1.00) 		0.959
(1.00) 		0.0155
(0.448) 		0.466
(0.95) 		0.0378
(0.499) 		0.242
(0.813) 		0.539
(0.989) 		0.935
(1.00) 		0.859
(1.00) 		0.00176
(0.224) 		0.946
(1.00) 		1
(1.00)
7p gain 184 (35%) 338 0.00109
(0.208) 		0.891
(1.00) 		0.928
(1.00) 		0.357
(0.922) 		0.83
(1.00) 		1
(1.00) 		1
(1.00) 		0.68
(1.00) 		0.292
(0.878) 		0.0839
(0.618) 		0.524
(0.977) 		0.65
(1.00) 		0.367
(0.922) 		1
(1.00)
18p gain 124 (24%) 398 0.188
(0.748) 		0.113
(0.663) 		0.138
(0.688) 		0.0809
(0.618) 		0.0466
(0.527) 		0.199
(0.762) 		0.000298
(0.114) 		0.484
(0.961) 		1
(1.00) 		0.276
(0.869) 		0.466
(0.95) 		0.155
(0.714) 		0.506
(0.964) 		0.353
(0.922)
18q gain 53 (10%) 469 0.887
(1.00) 		0.616
(1.00) 		0.226
(0.801) 		0.645
(1.00) 		0.893
(1.00) 		0.0838
(0.618) 		0.00169
(0.224) 		0.74
(1.00) 		0.345
(0.922) 		0.984
(1.00) 		0.995
(1.00) 		0.949
(1.00) 		0.691
(1.00) 		1
(1.00)
9p loss 186 (36%) 336 0.487
(0.963) 		0.967
(1.00) 		0.839
(1.00) 		0.742
(1.00) 		0.898
(1.00) 		0.356
(0.922) 		0.18
(0.745) 		0.837
(1.00) 		1
(1.00) 		1.09e-05
(0.0125) 		0.343
(0.922) 		0.764
(1.00) 		0.0556
(0.561) 		0.673
(1.00)
1p gain 74 (14%) 448 0.0686
(0.601) 		0.732
(1.00) 		0.756
(1.00) 		0.456
(0.95) 		0.0636
(0.58) 		1
(1.00) 		0.888
(1.00) 		0.0959
(0.644) 		0.0282
(0.484) 		0.21
(0.777) 		0.45
(0.948) 		0.103
(0.647) 		0.0713
(0.606) 		0.565
(1.00)
2p gain 96 (18%) 426 0.436
(0.941) 		0.314
(0.904) 		0.979
(1.00) 		0.624
(1.00) 		0.699
(1.00) 		1
(1.00) 		0.0297
(0.484) 		0.194
(0.759) 		0.515
(0.968) 		0.00881
(0.417) 		0.478
(0.954) 		0.75
(1.00) 		0.0833
(0.618) 		1
(1.00)
2q gain 73 (14%) 449 0.416
(0.934) 		0.476
(0.952) 		0.816
(1.00) 		0.919
(1.00) 		0.225
(0.801) 		1
(1.00) 		0.119
(0.671) 		0.389
(0.925) 		0.459
(0.95) 		0.0813
(0.618) 		0.756
(1.00) 		0.626
(1.00) 		0.233
(0.805) 		0.771
(1.00)
3p gain 82 (16%) 440 0.683
(1.00) 		0.128
(0.68) 		0.491
(0.963) 		0.362
(0.922) 		0.424
(0.935) 		0.115
(0.668) 		0.787
(1.00) 		1
(1.00) 		0.714
(1.00) 		0.812
(1.00) 		0.0446
(0.517) 		0.15
(0.714) 		1
(1.00) 		1
(1.00)
4p gain 41 (8%) 481 0.809
(1.00) 		0.00931
(0.417) 		0.388
(0.925) 		0.071
(0.606) 		0.438
(0.942) 		1
(1.00) 		0.855
(1.00) 		1
(1.00) 		1
(1.00) 		0.742
(1.00) 		0.116
(0.669) 		0.34
(0.922) 		0.024
(0.484) 		0.118
(0.671)
4q gain 37 (7%) 485 0.51
(0.965) 		0.354
(0.922) 		0.0126
(0.437) 		0.37
(0.922) 		0.169
(0.724) 		1
(1.00) 		0.565
(1.00) 		1
(1.00) 		0.557
(1) 		0.578
(1.00) 		0.599
(1.00) 		0.35
(0.922) 		0.0245
(0.484) 		0.0912
(0.631)
5p gain 201 (39%) 321 0.853
(1.00) 		0.102
(0.647) 		0.138
(0.688) 		0.787
(1.00) 		0.0185
(0.448) 		0.377
(0.922) 		0.187
(0.745) 		0.0739
(0.606) 		0.186
(0.745) 		0.146
(0.708) 		0.853
(1.00) 		0.0229
(0.479) 		0.276
(0.869) 		0.0606
(0.566)
5q gain 75 (14%) 447 0.732
(1.00) 		0.391
(0.93) 		0.165
(0.719) 		0.562
(1.00) 		0.101
(0.645) 		1
(1.00) 		0.264
(0.841) 		0.13
(0.68) 		0.0892
(0.624) 		0.808
(1.00) 		0.497
(0.963) 		0.0131
(0.437) 		0.815
(1.00) 		0.0876
(0.621)
6p gain 85 (16%) 437 0.233
(0.805) 		0.0373
(0.498) 		0.658
(1.00) 		0.349
(0.922) 		0.889
(1.00) 		1
(1.00) 		0.35
(0.922) 		0.516
(0.968) 		0.723
(1.00) 		0.353
(0.922) 		0.0692
(0.601) 		0.411
(0.934) 		0.0289
(0.484) 		0.585
(1.00)
6q gain 64 (12%) 458 0.598
(1.00) 		0.0752
(0.606) 		0.182
(0.745) 		0.426
(0.935) 		0.303
(0.899) 		1
(1.00) 		0.88
(1.00) 		0.0584
(0.564) 		0.431
(0.936) 		0.115
(0.668) 		0.00591
(0.339) 		0.0522
(0.561) 		0.454
(0.95) 		0.028
(0.484)
7q gain 128 (25%) 394 0.0597
(0.566) 		0.0964
(0.644) 		0.838
(1.00) 		0.745
(1.00) 		0.553
(0.996) 		1
(1.00) 		0.819
(1.00) 		0.907
(1.00) 		0.344
(0.922) 		0.165
(0.719) 		0.379
(0.922) 		0.734
(1.00) 		0.28
(0.877) 		0.481
(0.958)
8p gain 158 (30%) 364 0.417
(0.934) 		0.734
(1.00) 		0.803
(1.00) 		0.16
(0.714) 		0.716
(1.00) 		1
(1.00) 		0.132
(0.68) 		0.287
(0.878) 		0.105
(0.648) 		0.579
(1.00) 		0.891
(1.00) 		0.848
(1.00) 		0.601
(1.00) 		0.659
(1.00)
8q gain 318 (61%) 204 0.288
(0.878) 		0.456
(0.95) 		0.444
(0.948) 		0.684
(1.00) 		0.325
(0.919) 		0.372
(0.922) 		0.92
(1.00) 		0.0364
(0.498) 		1
(1.00) 		0.863
(1.00) 		0.314
(0.904) 		0.168
(0.724) 		0.723
(1.00) 		0.217
(0.792)
9p gain 102 (20%) 420 0.495
(0.963) 		0.127
(0.68) 		0.669
(1.00) 		0.609
(1.00) 		0.246
(0.819) 		1
(1.00) 		0.0183
(0.448) 		0.714
(1.00) 		0.753
(1.00) 		0.0137
(0.437) 		0.224
(0.801) 		0.584
(1.00) 		0.606
(1.00) 		0.449
(0.948)
9q gain 145 (28%) 377 0.452
(0.949) 		0.0696
(0.601) 		0.175
(0.738) 		0.0755
(0.606) 		0.574
(1.00) 		1
(1.00) 		0.509
(0.965) 		0.662
(1.00) 		1
(1.00) 		0.425
(0.935) 		0.71
(1.00) 		0.695
(1.00) 		0.915
(1.00) 		0.112
(0.663)
10p gain 42 (8%) 480 0.158
(0.714) 		0.619
(1.00) 		0.583
(1.00) 		0.404
(0.934) 		0.155
(0.714) 		1
(1.00) 		0.72
(1.00) 		1
(1.00) 		0.604
(1.00) 		0.153
(0.714) 		0.726
(1.00) 		0.0414
(0.501) 		0.93
(1.00) 		0.714
(1.00)
10q gain 34 (7%) 488 0.588
(1.00) 		0.971
(1.00) 		0.418
(0.934) 		0.592
(1.00) 		0.618
(1.00) 		1
(1.00) 		1
(1.00) 		1
(1.00) 		1
(1.00) 		0.643
(1.00) 		0.562
(1.00) 		0.84
(1.00) 		0.904
(1.00) 		0.694
(1.00)
11p gain 68 (13%) 454 0.31
(0.904) 		0.554
(0.996) 		0.251
(0.825) 		0.342
(0.922) 		0.0558
(0.561) 		1
(1.00) 		0.66
(1.00) 		0.2
(0.762) 		0.457
(0.95) 		0.846
(1.00) 		0.352
(0.922) 		0.094
(0.642) 		0.129
(0.68) 		1
(1.00)
11q gain 71 (14%) 451 0.603
(1.00) 		0.798
(1.00) 		0.332
(0.922) 		0.649
(1.00) 		0.0855
(0.618) 		1
(1.00) 		0.153
(0.714) 		0.0923
(0.635) 		0.456
(0.95) 		0.443
(0.948) 		0.503
(0.963) 		0.0134
(0.437) 		0.802
(1.00) 		1
(1.00)
12p gain 148 (28%) 374 0.664
(1.00) 		0.966
(1.00) 		0.95
(1.00) 		0.91
(1.00) 		0.914
(1.00) 		1
(1.00) 		0.229
(0.805) 		1
(1.00) 		0.805
(1.00) 		0.173
(0.735) 		0.623
(1.00) 		0.99
(1.00) 		0.181
(0.745) 		0.657
(1.00)
12q gain 92 (18%) 430 0.701
(1.00) 		0.118
(0.671) 		0.671
(1.00) 		0.728
(1.00) 		0.465
(0.95) 		1
(1.00) 		0.699
(1.00) 		0.699
(1.00) 		1
(1.00) 		0.141
(0.697) 		0.586
(1.00) 		0.314
(0.904) 		0.937
(1.00) 		0.792
(1.00)
13q gain 57 (11%) 465 0.45
(0.948) 		0.0567
(0.561) 		0.344
(0.922) 		0.285
(0.878) 		0.953
(1.00) 		1
(1.00) 		0.874
(1.00) 		0.634
(1.00) 		1
(1.00) 		0.889
(1.00) 		0.117
(0.669) 		0.925
(1.00) 		0.601
(1.00) 		0.512
(0.965)
14q gain 153 (29%) 369 0.0575
(0.564) 		0.77
(1.00) 		0.936
(1.00) 		0.774
(1.00) 		0.818
(1.00) 		1
(1.00) 		0.388
(0.925) 		0.335
(0.922) 		0.501
(0.963) 		0.288
(0.878) 		0.695
(1.00) 		0.818
(1.00) 		0.0357
(0.498) 		0.658
(1.00)
15q gain 72 (14%) 450 0.636
(1.00) 		0.429
(0.935) 		0.868
(1.00) 		0.0222
(0.479) 		0.748
(1.00) 		1
(1.00) 		0.474
(0.952) 		0.887
(1.00) 		0.685
(1.00) 		0.465
(0.95) 		0.202
(0.762) 		0.384
(0.925) 		0.874
(1.00) 		0.232
(0.805)
16p gain 109 (21%) 413 0.356
(0.922) 		0.524
(0.977) 		0.675
(1.00) 		0.771
(1.00) 		0.318
(0.908) 		1
(1.00) 		0.628
(1.00) 		0.334
(0.922) 		1
(1.00) 		0.165
(0.719) 		1
(1.00) 		0.0581
(0.564) 		0.129
(0.68) 		0.618
(1.00)
16q gain 105 (20%) 417 0.201
(0.762) 		0.493
(0.963) 		0.543
(0.992) 		0.772
(1.00) 		0.743
(1.00) 		1
(1.00) 		0.538
(0.989) 		0.535
(0.987) 		1
(1.00) 		0.684
(1.00) 		0.845
(1.00) 		0.429
(0.935) 		0.177
(0.744) 		0.612
(1.00)
17p gain 67 (13%) 455 0.666
(1.00) 		0.514
(0.968) 		0.11
(0.659) 		0.0312
(0.484) 		0.594
(1.00) 		1
(1.00) 		0.301
(0.896) 		0.885
(1.00) 		0.0719
(0.606) 		0.819
(1.00) 		0.492
(0.963) 		0.34
(0.922) 		0.753
(1.00) 		0.0361
(0.498)
17q gain 86 (16%) 436 0.315
(0.904) 		0.722
(1.00) 		0.0998
(0.645) 		0.0187
(0.448) 		0.471
(0.952) 		0.178
(0.745) 		0.506
(0.964) 		0.361
(0.922) 		0.167
(0.724) 		0.11
(0.659) 		0.767
(1.00) 		0.883
(1.00) 		0.73
(1.00) 		0.0263
(0.484)
19p gain 56 (11%) 466 0.627
(1.00) 		0.305
(0.902) 		0.543
(0.992) 		0.29
(0.878) 		0.123
(0.678) 		1
(1.00) 		0.0565
(0.561) 		0.208
(0.774) 		0.372
(0.922) 		0.0385
(0.499) 		0.335
(0.922) 		0.0365
(0.498) 		0.762
(1.00) 		0.756
(1.00)
19q gain 77 (15%) 445 0.29
(0.878) 		0.629
(1.00) 		0.866
(1.00) 		1
(1.00) 		0.385
(0.925) 		1
(1.00) 		0.0364
(0.498) 		0.778
(1.00) 		0.7
(1.00) 		0.378
(0.922) 		0.679
(1.00) 		0.205
(0.766) 		0.261
(0.837) 		0.782
(1.00)
20p gain 192 (37%) 330 0.931
(1.00) 		0.937
(1.00) 		0.585
(1.00) 		0.539
(0.989) 		0.142
(0.7) 		1
(1.00) 		0.838
(1.00) 		0.92
(1.00) 		1
(1.00) 		0.575
(1.00) 		0.493
(0.963) 		0.552
(0.996) 		0.787
(1.00) 		0.144
(0.704)
20q gain 204 (39%) 318 0.805
(1.00) 		0.53
(0.981) 		0.488
(0.963) 		0.378
(0.922) 		0.8
(1.00) 		1
(1.00) 		0.762
(1.00) 		0.618
(1.00) 		0.847
(1.00) 		0.716
(1.00) 		0.201
(0.762) 		0.914
(1.00) 		0.496
(0.963) 		0.415
(0.934)
21q gain 35 (7%) 487 0.783
(1.00) 		0.646
(1.00) 		0.0419
(0.501) 		0.467
(0.95) 		0.338
(0.922) 		1
(1.00) 		0.031
(0.484) 		0.705
(1.00) 		0.0119
(0.437) 		0.398
(0.932) 		0.767
(1.00) 		0.57
(1.00) 		0.451
(0.948) 		0.0832
(0.618)
22q gain 112 (21%) 410 0.133
(0.68) 		0.944
(1.00) 		0.985
(1.00) 		0.721
(1.00) 		0.836
(1.00) 		1
(1.00) 		0.185
(0.745) 		0.634
(1.00) 		0.245
(0.817) 		0.0198
(0.455) 		0.153
(0.714) 		0.789
(1.00) 		0.416
(0.934) 		0.138
(0.688)
xp gain 51 (10%) 471 0.583
(1.00) 		0.689
(1.00) 		0.789
(1.00) 		0.29
(0.878) 		0.365
(0.922) 		1
(1.00) 		0.182
(0.745) 		0.87
(1.00) 		0.647
(1.00) 		0.5
(0.963) 		0.0296
(0.484) 		0.16
(0.714) 		0.538
(0.989) 		1
(1.00)
xq gain 96 (18%) 426 0.351
(0.922) 		0.245
(0.817) 		0.836
(1.00) 		0.185
(0.745) 		0.551
(0.996) 		1
(1.00) 		0.526
(0.977) 		0.531
(0.981) 		0.754
(1.00) 		0.611
(1.00) 		0.642
(1.00) 		0.17
(0.724) 		0.258
(0.834) 		0.8
(1.00)
1p loss 56 (11%) 466 0.154
(0.714) 		0.0176
(0.448) 		0.596
(1.00) 		0.821
(1.00) 		0.761
(1.00) 		1
(1.00) 		0.873
(1.00) 		0.11
(0.659) 		0.37
(0.922) 		0.00524
(0.334) 		0.863
(1.00) 		0.291
(0.878) 		0.568
(1.00) 		1
(1.00)
1q loss 39 (7%) 483 0.076
(0.606) 		0.373
(0.922) 		0.649
(1.00) 		0.475
(0.952) 		0.986
(1.00) 		1
(1.00) 		0.708
(1.00) 		0.00263
(0.302) 		1
(1.00) 		0.787
(1.00) 		0.393
(0.93) 		0.74
(1.00) 		0.131
(0.68) 		0.71
(1.00)
2p loss 32 (6%) 490 0.739
(1.00) 		0.793
(1.00) 		0.364
(0.922) 		0.502
(0.963) 		0.274
(0.866) 		1
(1.00) 		0.0125
(0.437) 		0.848
(1.00) 		1
(1.00) 		0.259
(0.834) 		0.922
(1.00) 		0.315
(0.904) 		0.647
(1.00) 		0.0683
(0.601)
2q loss 44 (8%) 478 0.774
(1.00) 		0.92
(1.00) 		0.0251
(0.484) 		0.395
(0.932) 		0.0606
(0.566) 		1
(1.00) 		0.00678
(0.371) 		0.62
(1.00) 		0.27
(0.86) 		0.311
(0.904) 		0.322
(0.915) 		0.828
(1.00) 		0.137
(0.688) 		0.262
(0.839)
3p loss 296 (57%) 226 0.0283
(0.484) 		0.704
(1.00) 		0.521
(0.975) 		0.1
(0.645) 		0.508
(0.965) 		0.419
(0.934) 		0.00943
(0.417) 		0.922
(1.00) 		0.109
(0.659) 		0.00429
(0.334) 		0.0152
(0.448) 		0.613
(1.00) 		0.0104
(0.425) 		0.551
(0.996)
3q loss 58 (11%) 464 0.016
(0.448) 		0.555
(0.996) 		0.179
(0.745) 		0.447
(0.948) 		0.547
(0.996) 		1
(1.00) 		0.345
(0.922) 		0.436
(0.941) 		0.656
(1.00) 		0.169
(0.724) 		0.8
(1.00) 		0.336
(0.922) 		0.307
(0.902) 		0.342
(0.922)
4p loss 193 (37%) 329 0.67
(1.00) 		0.375
(0.922) 		0.413
(0.934) 		0.0749
(0.606) 		0.419
(0.934) 		0.325
(0.919) 		0.125
(0.678) 		0.546
(0.996) 		0.695
(1.00) 		0.0445
(0.517) 		0.133
(0.68) 		0.24
(0.812) 		0.149
(0.714) 		0.677
(1.00)
4q loss 151 (29%) 371 0.562
(1.00) 		0.75
(1.00) 		0.104
(0.648) 		0.129
(0.68) 		0.136
(0.688) 		0.236
(0.805) 		0.663
(1.00) 		0.163
(0.718) 		0.81
(1.00) 		0.191
(0.755) 		0.29
(0.878) 		0.174
(0.737) 		0.105
(0.648) 		0.512
(0.965)
5p loss 51 (10%) 471 0.937
(1.00) 		0.234
(0.805) 		0.927
(1.00) 		0.44
(0.944) 		0.751
(1.00) 		1
(1.00) 		0.739
(1.00) 		1
(1.00) 		0.329
(0.922) 		0.697
(1.00) 		0.631
(1.00) 		0.893
(1.00) 		0.432
(0.936) 		0.474
(0.952)
5q loss 160 (31%) 362 0.184
(0.745) 		0.35
(0.922) 		0.795
(1.00) 		0.156
(0.714) 		0.699
(1.00) 		1
(1.00) 		0.239
(0.812) 		0.596
(1.00) 		0.657
(1.00) 		0.0948
(0.644) 		0.924
(1.00) 		0.67
(1.00) 		0.0619
(0.568) 		0.829
(1.00)
6p loss 67 (13%) 455 0.592
(1.00) 		0.47
(0.952) 		0.415
(0.934) 		0.678
(1.00) 		0.465
(0.95) 		1
(1.00) 		0.301
(0.896) 		0.768
(1.00) 		1
(1.00) 		0.15
(0.714) 		0.372
(0.922) 		0.827
(1.00) 		0.0868
(0.62) 		0.113
(0.663)
6q loss 70 (13%) 452 0.61
(1.00) 		0.981
(1.00) 		0.711
(1.00) 		0.593
(1.00) 		0.72
(1.00) 		1
(1.00) 		0.111
(0.659) 		1
(1.00) 		1
(1.00) 		0.789
(1.00) 		0.794
(1.00) 		0.721
(1.00) 		0.026
(0.484) 		0.762
(1.00)
7p loss 29 (6%) 493 0.83
(1.00) 		0.906
(1.00) 		0.162
(0.718) 		0.643
(1.00) 		0.0843
(0.618) 		0.0524
(0.561) 		0.666
(1.00) 		0.526
(0.977) 		0.473
(0.952) 		0.317
(0.906) 		0.253
(0.828) 		0.354
(0.922) 		1
(1.00) 		1
(1.00)
7q loss 41 (8%) 481 0.24
(0.812) 		0.124
(0.678) 		0.87
(1.00) 		0.102
(0.647) 		0.124
(0.678) 		1
(1.00) 		0.466
(0.95) 		0.863
(1.00) 		0.248
(0.819) 		0.626
(1.00) 		0.0614
(0.568) 		0.92
(1.00) 		0.788
(1.00) 		0.713
(1.00)
8p loss 185 (35%) 337 0.0272
(0.484) 		0.592
(1.00) 		0.225
(0.801) 		0.0898
(0.625) 		0.402
(0.934) 		0.393
(0.93) 		0.215
(0.787) 		0.686
(1.00) 		0.681
(1.00) 		0.845
(1.00) 		0.379
(0.922) 		0.326
(0.919) 		0.0857
(0.618) 		0.833
(1.00)
8q loss 25 (5%) 497 0.339
(0.922) 		0.431
(0.936) 		0.838
(1.00) 		0.852
(1.00) 		0.965
(1.00) 		1
(1.00) 		0.822
(1.00) 		0.823
(1.00) 		0.417
(0.934) 		0.0492
(0.538) 		0.214
(0.786) 		0.19
(0.753) 		1
(1.00) 		1
(1.00)
9q loss 83 (16%) 439 0.768
(1.00) 		0.802
(1.00) 		0.374
(0.922) 		0.292
(0.878) 		0.747
(1.00) 		0.183
(0.745) 		0.788
(1.00) 		0.893
(1.00) 		0.475
(0.952) 		0.0869
(0.62) 		0.768
(1.00) 		0.38
(0.922) 		0.132
(0.68) 		0.257
(0.834)
10p loss 156 (30%) 366 0.0419
(0.501) 		0.718
(1.00) 		0.361
(0.922) 		0.0605
(0.566) 		0.606
(1.00) 		1
(1.00) 		0.0401
(0.501) 		0.594
(1.00) 		0.0472
(0.527) 		0.663
(1.00) 		0.888
(1.00) 		0.667
(1.00) 		0.0733
(0.606) 		0.829
(1.00)
10q loss 114 (22%) 408 0.764
(1.00) 		0.919
(1.00) 		0.55
(0.996) 		0.156
(0.714) 		0.12
(0.674) 		1
(1.00) 		0.0231
(0.479) 		0.157
(0.714) 		0.254
(0.828) 		0.418
(0.934) 		0.498
(0.963) 		0.749
(1.00) 		0.368
(0.922) 		0.474
(0.952)
11p loss 137 (26%) 385 0.499
(0.963) 		0.645
(1.00) 		0.00881
(0.417) 		0.885
(1.00) 		0.0297
(0.484) 		1
(1.00) 		0.313
(0.904) 		0.0563
(0.561) 		0.0366
(0.498) 		0.484
(0.961) 		0.88
(1.00) 		0.0185
(0.448) 		0.1
(0.645) 		0.16
(0.714)
12p loss 36 (7%) 486 0.0233
(0.479) 		0.041
(0.501) 		0.568
(1.00) 		0.62
(1.00) 		0.379
(0.922) 		1
(1.00) 		0.565
(1.00) 		0.351
(0.922) 		1
(1.00) 		0.422
(0.935) 		0.0233
(0.479) 		0.552
(0.996) 		0.285
(0.878) 		0.415
(0.934)
12q loss 31 (6%) 491 0.966
(1.00) 		0.203
(0.762) 		0.801
(1.00) 		0.208
(0.774) 		0.715
(1.00) 		1
(1.00) 		1
(1.00) 		0.684
(1.00) 		0.494
(0.963) 		0.404
(0.934) 		0.0891
(0.624) 		0.272
(0.864) 		0.0999
(0.645) 		0.0683
(0.601)
13q loss 168 (32%) 354 0.911
(1.00) 		0.661
(1.00) 		0.417
(0.934) 		0.933
(1.00) 		0.874
(1.00) 		0.314
(0.904) 		0.597
(1.00) 		0.835
(1.00) 		0.528
(0.979) 		0.445
(0.948) 		0.322
(0.915) 		0.337
(0.922) 		0.0403
(0.501) 		0.195
(0.762)
14q loss 56 (11%) 466 0.939
(1.00) 		0.924
(1.00) 		0.412
(0.934) 		0.868
(1.00) 		0.776
(1.00) 		1
(1.00) 		0.15
(0.714) 		0.0186
(0.448) 		0.369
(0.922) 		0.994
(1.00) 		0.836
(1.00) 		0.16
(0.714) 		0.554
(0.996) 		1
(1.00)
15q loss 103 (20%) 419 0.122
(0.678) 		0.236
(0.805) 		0.711
(1.00) 		0.465
(0.95) 		0.295
(0.883) 		1
(1.00) 		1
(1.00) 		0.461
(0.95) 		0.0683
(0.601) 		0.956
(1.00) 		0.485
(0.961) 		0.368
(0.922) 		0.386
(0.925) 		0.132
(0.68)
16p loss 62 (12%) 460 0.0844
(0.618) 		0.028
(0.484) 		0.958
(1.00) 		0.00525
(0.334) 		0.0356
(0.498) 		1
(1.00) 		0.45
(0.948) 		0.3
(0.896) 		0.416
(0.934) 		0.949
(1.00) 		0.614
(1.00) 		0.0141
(0.438) 		0.611
(1.00) 		0.0306
(0.484)
16q loss 82 (16%) 440 0.437
(0.941) 		0.0791
(0.618) 		0.846
(1.00) 		0.233
(0.805) 		0.0733
(0.606) 		1
(1.00) 		0.135
(0.684) 		0.292
(0.878) 		0.106
(0.651) 		0.961
(1.00) 		0.147
(0.711) 		0.0542
(0.561) 		0.77
(1.00) 		0.284
(0.878)
17p loss 107 (20%) 415 0.332
(0.922) 		0.227
(0.801) 		0.0804
(0.618) 		0.408
(0.934) 		0.656
(1.00) 		0.183
(0.745) 		0.715
(1.00) 		0.809
(1.00) 		1
(1.00) 		0.429
(0.935) 		0.821
(1.00) 		0.522
(0.976) 		0.408
(0.934) 		0.0841
(0.618)
17q loss 32 (6%) 490 0.884
(1.00) 		0.643
(1.00) 		0.745
(1.00) 		0.396
(0.932) 		0.355
(0.922) 		1
(1.00) 		1
(1.00) 		0.848
(1.00) 		0.505
(0.964) 		0.892
(1.00) 		0.734
(1.00) 		0.998
(1.00) 		0.714
(1.00) 		0.198
(0.762)
18p loss 103 (20%) 419 0.0964
(0.644) 		0.458
(0.95) 		0.887
(1.00) 		0.936
(1.00) 		0.7
(1.00) 		1
(1.00) 		0.0466
(0.527) 		0.714
(1.00) 		0.163
(0.719) 		0.945
(1.00) 		0.941
(1.00) 		0.984
(1.00) 		0.203
(0.762) 		0.0192
(0.45)
18q loss 211 (40%) 311 0.101
(0.645) 		0.289
(0.878) 		0.955
(1.00) 		0.928
(1.00) 		0.396
(0.932) 		1
(1.00) 		0.764
(1.00) 		0.842
(1.00) 		0.0335
(0.498) 		0.157
(0.714) 		0.0555
(0.561) 		0.147
(0.711) 		0.0169
(0.448) 		0.306
(0.902)
19p loss 100 (19%) 422 0.0135
(0.437) 		0.186
(0.745) 		0.0676
(0.601) 		0.192
(0.755) 		0.105
(0.648) 		1
(1.00) 		0.259
(0.834) 		0.381
(0.922) 		0.369
(0.922) 		0.223
(0.801) 		0.0387
(0.499) 		0.42
(0.934) 		0.199
(0.762) 		0.2
(0.762)
19q loss 88 (17%) 434 0.0554
(0.561) 		0.0848
(0.618) 		0.00372
(0.334) 		0.0404
(0.501) 		0.353
(0.922) 		1
(1.00) 		0.428
(0.935) 		0.2
(0.762) 		0.735
(1.00) 		0.646
(1.00) 		0.0373
(0.498) 		0.687
(1.00) 		0.00485
(0.334) 		0.414
(0.934)
20p loss 46 (9%) 476 0.73
(1.00) 		0.937
(1.00) 		0.631
(1.00) 		0.959
(1.00) 		0.352
(0.922) 		1
(1.00) 		1
(1.00) 		0.231
(0.805) 		1
(1.00) 		0.371
(0.922) 		0.929
(1.00) 		0.213
(0.783) 		0.753
(1.00) 		0.497
(0.963)
20q loss 27 (5%) 495 0.25
(0.822) 		0.409
(0.934) 		0.213
(0.783) 		0.426
(0.935) 		0.958
(1.00) 		1
(1.00) 		0.662
(1.00) 		0.5
(0.963) 		0.448
(0.948) 		0.031
(0.484) 		0.00552
(0.334) 		0.312
(0.904) 		0.868
(1.00) 		0.386
(0.925)
21q loss 185 (35%) 337 0.248
(0.819) 		0.926
(1.00) 		0.856
(1.00) 		0.0554
(0.561) 		0.282
(0.878) 		1
(1.00) 		0.607
(1.00) 		0.41
(0.934) 		0.837
(1.00) 		0.00482
(0.334) 		0.698
(1.00) 		0.616
(1.00) 		0.00514
(0.334) 		0.833
(1.00)
22q loss 74 (14%) 448 0.72
(1.00) 		0.833
(1.00) 		0.471
(0.952) 		0.222
(0.801) 		0.494
(0.963) 		1
(1.00) 		0.258
(0.834) 		1
(1.00) 		0.46
(0.95) 		0.647
(1.00) 		0.398
(0.932) 		0.221
(0.801) 		0.144
(0.704) 		0.241
(0.812)
xp loss 136 (26%) 386 0.0484
(0.534) 		0.837
(1.00) 		0.425
(0.935) 		0.0115
(0.437) 		0.613
(1.00) 		0.241
(0.812) 		0.368
(0.922) 		0.582
(1.00) 		0.223
(0.801) 		0.0103
(0.425) 		0.924
(1.00) 		0.0473
(0.527) 		0.449
(0.948) 		0.821
(1.00)
xq loss 82 (16%) 440 0.196
(0.762) 		0.379
(0.922) 		0.0729
(0.606) 		0.0337
(0.498) 		0.225
(0.801) 		0.152
(0.714) 		0.417
(0.934) 		0.507
(0.965) 		0.107
(0.656) 		0.125
(0.678) 		0.51
(0.965) 		0.0349
(0.498) 		0.963
(1.00) 		0.782
(1.00)
'1q gain' versus 'RACE'

P value = 0.00136 (Fisher's exact test), Q value = 0.22

Table S1.  Gene #2: '1q gain' versus Clinical Feature #13: 'RACE'

nPatients AMERICAN INDIAN OR ALASKA NATIVE ASIAN BLACK OR AFRICAN AMERICAN WHITE
ALL 2 11 48 446
1Q GAIN MUTATED 0 0 21 98
1Q GAIN WILD-TYPE 2 11 27 348

Figure S1.  Get High-res Image Gene #2: '1q gain' versus Clinical Feature #13: 'RACE'

'3q gain' versus 'NUMBER_OF_LYMPH_NODES'

P value = 0.00176 (Wilcoxon-test), Q value = 0.22

Table S2.  Gene #6: '3q gain' versus Clinical Feature #12: 'NUMBER_OF_LYMPH_NODES'

nPatients Mean (Std.Dev)
ALL 408 2.2 (4.3)
3Q GAIN MUTATED 206 2.7 (5.3)
3Q GAIN WILD-TYPE 202 1.7 (2.8)

Figure S2.  Get High-res Image Gene #6: '3q gain' versus Clinical Feature #12: 'NUMBER_OF_LYMPH_NODES'

'7p gain' versus 'Time to Death'

P value = 0.00109 (logrank test), Q value = 0.21

Table S3.  Gene #13: '7p gain' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 520 219 0.1 - 211.0 (21.1)
7P GAIN MUTATED 183 97 0.8 - 172.7 (18.9)
7P GAIN WILD-TYPE 337 122 0.1 - 211.0 (22.4)

Figure S3.  Get High-res Image Gene #13: '7p gain' versus Clinical Feature #1: 'Time to Death'

'18p gain' versus 'GENDER'

P value = 0.000298 (Fisher's exact test), Q value = 0.11

Table S4.  Gene #32: '18p gain' versus Clinical Feature #7: 'GENDER'

nPatients FEMALE MALE
ALL 140 382
18P GAIN MUTATED 18 106
18P GAIN WILD-TYPE 122 276

Figure S4.  Get High-res Image Gene #32: '18p gain' versus Clinical Feature #7: 'GENDER'

'18q gain' versus 'GENDER'

P value = 0.00169 (Fisher's exact test), Q value = 0.22

Table S5.  Gene #33: '18q gain' versus Clinical Feature #7: 'GENDER'

nPatients FEMALE MALE
ALL 140 382
18Q GAIN MUTATED 5 48
18Q GAIN WILD-TYPE 135 334

Figure S5.  Get High-res Image Gene #33: '18q gain' versus Clinical Feature #7: 'GENDER'

'9p loss' versus 'NUMBER_PACK_YEARS_SMOKED'

P value = 1.09e-05 (Wilcoxon-test), Q value = 0.013

Table S6.  Gene #58: '9p loss' versus Clinical Feature #10: 'NUMBER_PACK_YEARS_SMOKED'

nPatients Mean (Std.Dev)
ALL 293 45.9 (35.3)
9P LOSS MUTATED 114 53.2 (30.6)
9P LOSS WILD-TYPE 179 41.2 (37.4)

Figure S6.  Get High-res Image Gene #58: '9p loss' versus Clinical Feature #10: 'NUMBER_PACK_YEARS_SMOKED'

'11q loss' versus 'GENDER'

P value = 0.000141 (Fisher's exact test), Q value = 0.081

Table S7.  Gene #63: '11q loss' versus Clinical Feature #7: 'GENDER'

nPatients FEMALE MALE
ALL 140 382
11Q LOSS MUTATED 28 144
11Q LOSS WILD-TYPE 112 238

Figure S7.  Get High-res Image Gene #63: '11q loss' versus Clinical Feature #7: 'GENDER'

'11q loss' versus 'RADIATION_THERAPY'

P value = 0.000399 (Fisher's exact test), Q value = 0.11

Table S8.  Gene #63: '11q loss' versus Clinical Feature #8: 'RADIATION_THERAPY'

nPatients NO YES
ALL 162 301
11Q LOSS MUTATED 36 116
11Q LOSS WILD-TYPE 126 185

Figure S8.  Get High-res Image Gene #63: '11q loss' versus Clinical Feature #8: 'RADIATION_THERAPY'

'11q loss' versus 'NUMBER_OF_LYMPH_NODES'

P value = 0.000498 (Wilcoxon-test), Q value = 0.11

Table S9.  Gene #63: '11q loss' versus Clinical Feature #12: 'NUMBER_OF_LYMPH_NODES'

nPatients Mean (Std.Dev)
ALL 408 2.2 (4.3)
11Q LOSS MUTATED 128 2.9 (4.9)
11Q LOSS WILD-TYPE 280 1.9 (4.0)

Figure S9.  Get High-res Image Gene #63: '11q loss' versus Clinical Feature #12: 'NUMBER_OF_LYMPH_NODES'

Methods & Data
Input

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

  • Processed Copy number data file = /xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_Correlate_Genomic_Events_Preprocess/HNSC-TP/22508725/transformed.cor.cli.txt

  • Clinical data file = /xchip/cga/gdac-prod/tcga-gdac/jobResults/Append_Data/HNSC-TP/22506490/HNSC-TP.merged_data.txt

  • Number of patients = 522

  • Number of significantly arm-level cnvs = 82

  • Number of selected clinical features = 14

  • Exclude regions 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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