Correlation between copy number variations of arm-level result and selected clinical features
Head and Neck Squamous Cell Carcinoma (Primary solid tumor)
16 April 2014  |  analyses__2014_04_16
Maintainer Information
Citation Information
doi:10.7908/C1708025
Maintained by TCGA GDAC Team (Broad Institute/MD Anderson Cancer Center/Harvard Medical School)
Cite as Broad Institute TCGA Genome Data Analysis Center (2014): Correlation between copy number variations of arm-level result and selected clinical features. Broad Institute of MIT and Harvard. doi:10.7908/C1708025
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 80 arm-level events and 12 clinical features across 404 patients, one significant finding detected with Q value < 0.25.

  • 18p gain cnv correlated to 'GENDER'.

Results
Overview of the results

Table 1.  Get Full Table Overview of the association between significant copy number variation of 80 arm-level events and 12 clinical features. Shown in the table are P values (Q values). Thresholded by Q value < 0.25, one significant finding detected.

Clinical
Features 		Time
to
Death 		AGE NEOPLASM
DISEASESTAGE 		PATHOLOGY
T
STAGE 		PATHOLOGY
N
STAGE 		PATHOLOGY
M
STAGE 		GENDER HISTOLOGICAL
TYPE 		RADIATIONS
RADIATION
REGIMENINDICATION 		NUMBERPACKYEARSSMOKED YEAROFTOBACCOSMOKINGONSET NUMBER
OF
LYMPH
NODES
nCNV (%) nWild-Type logrank test t-test Chi-square 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 t-test t-test t-test
18p gain 92 (23%) 312 0.369
(1.00) 		0.0084
(1.00) 		0.195
(1.00) 		0.113
(1.00) 		0.0597
(1.00) 		0.342
(1.00) 		0.00012
(0.116) 		0.493
(1.00) 		0.654
(1.00) 		0.186
(1.00) 		0.408
(1.00) 		0.496
(1.00)
1p gain 53 (13%) 351 0.356
(1.00) 		0.206
(1.00) 		0.844
(1.00) 		0.803
(1.00) 		0.319
(1.00) 		0.0133
(1.00) 		0.415
(1.00) 		0.0258
(1.00) 		0.853
(1.00) 		0.693
(1.00) 		0.186
(1.00) 		0.749
(1.00)
1q gain 94 (23%) 310 0.954
(1.00) 		0.0889
(1.00) 		0.486
(1.00) 		0.307
(1.00) 		0.0881
(1.00) 		0.219
(1.00) 		0.696
(1.00) 		0.0541
(1.00) 		0.3
(1.00) 		1
(1.00) 		0.116
(1.00) 		0.329
(1.00)
2p gain 72 (18%) 332 0.602
(1.00) 		0.273
(1.00) 		0.966
(1.00) 		0.369
(1.00) 		0.483
(1.00) 		0.433
(1.00) 		0.062
(1.00) 		0.668
(1.00) 		0.745
(1.00) 		0.0436
(1.00) 		0.335
(1.00) 		0.471
(1.00)
2q gain 57 (14%) 347 0.825
(1.00) 		0.723
(1.00) 		0.685
(1.00) 		0.666
(1.00) 		0.19
(1.00) 		0.244
(1.00) 		0.344
(1.00) 		0.657
(1.00) 		0.367
(1.00) 		0.237
(1.00) 		0.353
(1.00) 		0.429
(1.00)
3p gain 67 (17%) 337 0.722
(1.00) 		0.326
(1.00) 		0.98
(1.00) 		0.481
(1.00) 		0.816
(1.00) 		0.32
(1.00) 		0.378
(1.00) 		1
(1.00) 		0.504
(1.00) 		0.881
(1.00) 		0.0704
(1.00) 		0.463
(1.00)
3q gain 205 (51%) 199 0.684
(1.00) 		0.178
(1.00) 		0.679
(1.00) 		0.773
(1.00) 		0.0653
(1.00) 		0.718
(1.00) 		0.0989
(1.00) 		0.84
(1.00) 		0.103
(1.00) 		0.496
(1.00) 		0.176
(1.00) 		0.0162
(1.00)
4p gain 34 (8%) 370 0.891
(1.00) 		0.022
(1.00) 		0.546
(1.00) 		0.279
(1.00) 		0.812
(1.00) 		1
(1.00) 		1
(1.00) 		1
(1.00) 		0.505
(1.00) 		0.359
(1.00) 		0.244
(1.00) 		0.118
(1.00)
4q gain 29 (7%) 375 0.283
(1.00) 		0.259
(1.00) 		0.035
(1.00) 		0.599
(1.00) 		0.0702
(1.00) 		1
(1.00) 		1
(1.00) 		0.409
(1.00) 		0.233
(1.00) 		0.53
(1.00) 		0.647
(1.00) 		0.686
(1.00)
5p gain 155 (38%) 249 0.655
(1.00) 		0.0953
(1.00) 		0.338
(1.00) 		0.681
(1.00) 		0.253
(1.00) 		0.269
(1.00) 		0.0557
(1.00) 		0.513
(1.00) 		0.0285
(1.00) 		0.975
(1.00) 		0.849
(1.00) 		0.9
(1.00)
5q gain 51 (13%) 353 0.872
(1.00) 		0.21
(1.00) 		0.366
(1.00) 		0.546
(1.00) 		0.504
(1.00) 		0.102
(1.00) 		0.139
(1.00) 		0.152
(1.00) 		0.0869
(1.00) 		0.186
(1.00) 		0.686
(1.00) 		0.692
(1.00)
6p gain 62 (15%) 342 0.687
(1.00) 		0.169
(1.00) 		0.951
(1.00) 		0.778
(1.00) 		0.49
(1.00) 		0.231
(1.00) 		0.879
(1.00) 		1
(1.00) 		0.0361
(1.00) 		0.128
(1.00) 		0.0534
(1.00) 		0.34
(1.00)
6q gain 46 (11%) 358 0.655
(1.00) 		0.11
(1.00) 		0.67
(1.00) 		0.676
(1.00) 		0.292
(1.00) 		0.268
(1.00) 		0.863
(1.00) 		1
(1.00) 		0.0168
(1.00) 		0.0357
(1.00) 		0.00646
(1.00) 		0.45
(1.00)
7p gain 148 (37%) 256 0.029
(1.00) 		0.28
(1.00) 		0.663
(1.00) 		0.528
(1.00) 		0.598
(1.00) 		0.261
(1.00) 		0.648
(1.00) 		0.0501
(1.00) 		0.604
(1.00) 		0.399
(1.00) 		0.165
(1.00) 		0.993
(1.00)
7q gain 101 (25%) 303 0.173
(1.00) 		0.265
(1.00) 		0.851
(1.00) 		0.867
(1.00) 		0.638
(1.00) 		0.129
(1.00) 		0.703
(1.00) 		0.113
(1.00) 		0.563
(1.00) 		0.372
(1.00) 		0.73
(1.00) 		0.966
(1.00)
8p gain 113 (28%) 291 0.587
(1.00) 		0.345
(1.00) 		0.986
(1.00) 		0.721
(1.00) 		0.916
(1.00) 		1
(1.00) 		0.0859
(1.00) 		0.0202
(1.00) 		0.406
(1.00) 		0.796
(1.00) 		0.757
(1.00) 		0.956
(1.00)
8q gain 235 (58%) 169 0.349
(1.00) 		0.62
(1.00) 		0.374
(1.00) 		0.805
(1.00) 		0.337
(1.00) 		0.276
(1.00) 		0.504
(1.00) 		1
(1.00) 		0.801
(1.00) 		0.777
(1.00) 		0.116
(1.00) 		0.523
(1.00)
9p gain 82 (20%) 322 0.651
(1.00) 		0.248
(1.00) 		0.142
(1.00) 		0.656
(1.00) 		0.0856
(1.00) 		0.825
(1.00) 		0.1
(1.00) 		1
(1.00) 		0.159
(1.00) 		0.0048
(1.00) 		0.35
(1.00) 		0.526
(1.00)
9q gain 109 (27%) 295 0.558
(1.00) 		0.0677
(1.00) 		0.1
(1.00) 		0.203
(1.00) 		0.251
(1.00) 		0.832
(1.00) 		0.902
(1.00) 		0.754
(1.00) 		0.573
(1.00) 		0.0889
(1.00) 		0.956
(1.00) 		0.738
(1.00)
10p gain 27 (7%) 377 0.0858
(1.00) 		0.559
(1.00) 		0.947
(1.00) 		0.889
(1.00) 		0.763
(1.00) 		0.581
(1.00) 		0.515
(1.00) 		0.386
(1.00) 		0.801
(1.00) 		0.452
(1.00) 		0.756
(1.00) 		0.0236
(1.00)
10q gain 26 (6%) 378 0.342
(1.00) 		0.942
(1.00) 		0.675
(1.00) 		0.784
(1.00) 		0.977
(1.00) 		1
(1.00) 		0.656
(1.00) 		1
(1.00) 		0.313
(1.00) 		0.439
(1.00) 		0.482
(1.00) 		0.133
(1.00)
11p gain 54 (13%) 350 0.837
(1.00) 		0.374
(1.00) 		0.59
(1.00) 		0.873
(1.00) 		0.0952
(1.00) 		0.148
(1.00) 		0.63
(1.00) 		1
(1.00) 		0.583
(1.00) 		0.0272
(1.00) 		0.52
(1.00) 		0.847
(1.00)
11q gain 56 (14%) 348 0.46
(1.00) 		0.563
(1.00) 		0.481
(1.00) 		0.6
(1.00) 		0.219
(1.00) 		0.461
(1.00) 		0.265
(1.00) 		1
(1.00) 		0.587
(1.00) 		0.025
(1.00) 		0.267
(1.00) 		0.98
(1.00)
12p gain 114 (28%) 290 0.403
(1.00) 		0.65
(1.00) 		0.914
(1.00) 		0.95
(1.00) 		0.878
(1.00) 		0.679
(1.00) 		0.543
(1.00) 		0.419
(1.00) 		0.889
(1.00) 		0.11
(1.00) 		0.642
(1.00) 		0.871
(1.00)
12q gain 68 (17%) 336 0.809
(1.00) 		0.323
(1.00) 		0.435
(1.00) 		0.768
(1.00) 		0.365
(1.00) 		1
(1.00) 		0.884
(1.00) 		0.663
(1.00) 		0.0296
(1.00) 		0.143
(1.00) 		0.402
(1.00) 		0.0445
(1.00)
13q gain 48 (12%) 356 0.786
(1.00) 		0.0742
(1.00) 		0.565
(1.00) 		0.612
(1.00) 		0.874
(1.00) 		0.784
(1.00) 		1
(1.00) 		1
(1.00) 		0.0821
(1.00) 		0.662
(1.00) 		0.0408
(1.00) 		0.554
(1.00)
14q gain 120 (30%) 284 0.367
(1.00) 		0.833
(1.00) 		0.884
(1.00) 		0.939
(1.00) 		0.97
(1.00) 		0.84
(1.00) 		0.281
(1.00) 		0.239
(1.00) 		0.583
(1.00) 		0.463
(1.00) 		0.77
(1.00) 		0.464
(1.00)
15q gain 62 (15%) 342 0.444
(1.00) 		0.96
(1.00) 		0.94
(1.00) 		0.0567
(1.00) 		0.729
(1.00) 		0.803
(1.00) 		0.761
(1.00) 		0.658
(1.00) 		0.862
(1.00) 		0.691
(1.00) 		0.431
(1.00) 		0.221
(1.00)
16p gain 81 (20%) 323 0.32
(1.00) 		0.0859
(1.00) 		0.444
(1.00) 		0.997
(1.00) 		0.461
(1.00) 		0.794
(1.00) 		0.681
(1.00) 		0.684
(1.00) 		0.754
(1.00) 		0.566
(1.00) 		0.49
(1.00) 		0.0953
(1.00)
16q gain 85 (21%) 319 0.0545
(1.00) 		0.0894
(1.00) 		0.292
(1.00) 		0.675
(1.00) 		0.792
(1.00) 		0.461
(1.00) 		0.139
(1.00) 		1
(1.00) 		0.879
(1.00) 		0.691
(1.00) 		0.322
(1.00) 		0.31
(1.00)
17p gain 51 (13%) 353 0.826
(1.00) 		0.362
(1.00) 		0.406
(1.00) 		0.237
(1.00) 		0.825
(1.00) 		1
(1.00) 		0.413
(1.00) 		0.152
(1.00) 		0.707
(1.00) 		0.919
(1.00) 		0.813
(1.00) 		0.471
(1.00)
17q gain 67 (17%) 337 0.365
(1.00) 		0.78
(1.00) 		0.45
(1.00) 		0.14
(1.00) 		0.291
(1.00) 		0.811
(1.00) 		0.239
(1.00) 		0.149
(1.00) 		0.866
(1.00) 		0.578
(1.00) 		0.656
(1.00) 		0.456
(1.00)
18q gain 36 (9%) 368 0.773
(1.00) 		0.535
(1.00) 		0.551
(1.00) 		0.762
(1.00) 		0.831
(1.00) 		1
(1.00) 		0.00075
(0.719) 		1
(1.00) 		1
(1.00) 		0.412
(1.00) 		0.558
(1.00) 		0.835
(1.00)
19p gain 38 (9%) 366 0.104
(1.00) 		0.237
(1.00) 		0.466
(1.00) 		0.192
(1.00) 		0.375
(1.00) 		0.141
(1.00) 		0.347
(1.00) 		1
(1.00) 		1
(1.00) 		0.516
(1.00) 		0.938
(1.00) 		0.0459
(1.00)
19q gain 56 (14%) 348 0.225
(1.00) 		0.676
(1.00) 		0.999
(1.00) 		0.708
(1.00) 		0.928
(1.00) 		0.168
(1.00) 		0.208
(1.00) 		0.651
(1.00) 		0.717
(1.00) 		0.714
(1.00) 		0.757
(1.00) 		0.201
(1.00)
20p gain 148 (37%) 256 0.912
(1.00) 		0.852
(1.00) 		0.76
(1.00) 		0.796
(1.00) 		0.399
(1.00) 		0.579
(1.00) 		0.733
(1.00) 		1
(1.00) 		0.195
(1.00) 		0.43
(1.00) 		0.444
(1.00) 		0.678
(1.00)
20q gain 156 (39%) 248 0.39
(1.00) 		0.814
(1.00) 		0.598
(1.00) 		0.342
(1.00) 		0.77
(1.00) 		0.581
(1.00) 		0.822
(1.00) 		0.515
(1.00) 		0.25
(1.00) 		0.976
(1.00) 		0.0745
(1.00) 		0.202
(1.00)
21q gain 27 (7%) 377 0.96
(1.00) 		0.914
(1.00) 		0.0906
(1.00) 		0.421
(1.00) 		0.149
(1.00) 		0.42
(1.00) 		0.0455
(1.00) 		0.00363
(1.00) 		0.449
(1.00) 		0.951
(1.00) 		0.935
(1.00) 		0.597
(1.00)
22q gain 88 (22%) 316 0.138
(1.00) 		0.911
(1.00) 		0.754
(1.00) 		0.758
(1.00) 		0.743
(1.00) 		0.18
(1.00) 		0.596
(1.00) 		0.0933
(1.00) 		0.447
(1.00) 		0.132
(1.00) 		0.277
(1.00) 		0.534
(1.00)
xq gain 70 (17%) 334 0.383
(1.00) 		0.132
(1.00) 		0.217
(1.00) 		0.0576
(1.00) 		0.272
(1.00) 		0.601
(1.00) 		0.663
(1.00) 		0.666
(1.00) 		0.00805
(1.00) 		0.187
(1.00) 		0.48
(1.00) 		0.382
(1.00)
1p loss 45 (11%) 359 0.483
(1.00) 		0.0345
(1.00) 		0.552
(1.00) 		0.552
(1.00) 		0.844
(1.00) 		0.396
(1.00) 		0.383
(1.00) 		0.565
(1.00) 		0.69
(1.00) 		0.0189
(1.00) 		0.949
(1.00) 		0.883
(1.00)
1q loss 31 (8%) 373 0.475
(1.00) 		0.49
(1.00) 		0.755
(1.00) 		0.322
(1.00) 		0.878
(1.00) 		1
(1.00) 		0.838
(1.00) 		1
(1.00) 		1
(1.00) 		0.425
(1.00) 		0.604
(1.00) 		0.0463
(1.00)
2p loss 27 (7%) 377 0.949
(1.00) 		0.751
(1.00) 		0.369
(1.00) 		0.932
(1.00) 		0.381
(1.00) 		0.16
(1.00) 		0.0135
(1.00) 		1
(1.00) 		0.131
(1.00) 		0.236
(1.00) 		0.908
(1.00) 		0.00158
(1.00)
2q loss 34 (8%) 370 0.931
(1.00) 		0.877
(1.00) 		0.0488
(1.00) 		0.331
(1.00) 		0.11
(1.00) 		1
(1.00) 		0.00878
(1.00) 		1
(1.00) 		0.04
(1.00) 		0.322
(1.00) 		0.545
(1.00) 		0.279
(1.00)
3p loss 234 (58%) 170 0.00247
(1.00) 		0.665
(1.00) 		0.416
(1.00) 		0.0891
(1.00) 		0.15
(1.00) 		0.146
(1.00) 		0.0453
(1.00) 		0.0869
(1.00) 		0.311
(1.00) 		0.0882
(1.00) 		0.452
(1.00) 		0.037
(1.00)
3q loss 54 (13%) 350 0.00128
(1.00) 		0.283
(1.00) 		0.168
(1.00) 		0.0602
(1.00) 		0.27
(1.00) 		0.232
(1.00) 		0.332
(1.00) 		1
(1.00) 		0.713
(1.00) 		0.131
(1.00) 		0.971
(1.00) 		0.00832
(1.00)
4p loss 153 (38%) 251 0.655
(1.00) 		0.312
(1.00) 		0.694
(1.00) 		0.361
(1.00) 		0.558
(1.00) 		0.187
(1.00) 		0.308
(1.00) 		0.8
(1.00) 		1
(1.00) 		0.367
(1.00) 		0.305
(1.00) 		0.07
(1.00)
4q loss 116 (29%) 288 0.581
(1.00) 		0.402
(1.00) 		0.117
(1.00) 		0.296
(1.00) 		0.105
(1.00) 		0.408
(1.00) 		0.808
(1.00) 		0.77
(1.00) 		0.0959
(1.00) 		0.806
(1.00) 		0.88
(1.00) 		0.137
(1.00)
5p loss 39 (10%) 365 0.983
(1.00) 		0.306
(1.00) 		0.781
(1.00) 		0.651
(1.00) 		0.388
(1.00) 		0.526
(1.00) 		0.577
(1.00) 		1
(1.00) 		0.0553
(1.00) 		0.99
(1.00) 		0.742
(1.00) 		0.321
(1.00)
5q loss 129 (32%) 275 0.546
(1.00) 		0.403
(1.00) 		0.404
(1.00) 		0.0331
(1.00) 		0.394
(1.00) 		0.844
(1.00) 		0.288
(1.00) 		0.775
(1.00) 		1
(1.00) 		0.0424
(1.00) 		0.672
(1.00) 		0.419
(1.00)
6p loss 55 (14%) 349 0.293
(1.00) 		0.606
(1.00) 		0.421
(1.00) 		0.604
(1.00) 		0.601
(1.00) 		0.579
(1.00) 		0.263
(1.00) 		1
(1.00) 		0.714
(1.00) 		0.342
(1.00) 		0.444
(1.00) 		0.196
(1.00)
6q loss 56 (14%) 348 0.325
(1.00) 		0.593
(1.00) 		0.75
(1.00) 		0.59
(1.00) 		0.979
(1.00) 		0.784
(1.00) 		0.0569
(1.00) 		0.651
(1.00) 		0.717
(1.00) 		0.924
(1.00) 		0.635
(1.00) 		0.951
(1.00)
7p loss 19 (5%) 385 0.779
(1.00) 		0.898
(1.00) 		0.652
(1.00) 		0.847
(1.00) 		0.173
(1.00) 		0.42
(1.00) 		1
(1.00) 		1
(1.00) 		1
(1.00) 		0.228
(1.00) 		0.248
(1.00) 		0.906
(1.00)
7q loss 36 (9%) 368 0.829
(1.00) 		0.0956
(1.00) 		0.722
(1.00) 		0.289
(1.00) 		0.701
(1.00) 		0.768
(1.00) 		0.847
(1.00) 		0.482
(1.00) 		0.662
(1.00) 		0.676
(1.00) 		0.0459
(1.00) 		0.238
(1.00)
8p loss 148 (37%) 256 0.0619
(1.00) 		0.81
(1.00) 		0.537
(1.00) 		0.446
(1.00) 		0.328
(1.00) 		1
(1.00) 		0.212
(1.00) 		0.129
(1.00) 		1
(1.00) 		0.273
(1.00) 		0.0874
(1.00) 		0.319
(1.00)
8q loss 25 (6%) 379 0.428
(1.00) 		0.629
(1.00) 		0.854
(1.00) 		0.199
(1.00) 		0.719
(1.00) 		0.748
(1.00) 		0.371
(1.00) 		1
(1.00) 		0.602
(1.00) 		0.00535
(1.00) 		0.0718
(1.00) 		0.739
(1.00)
9p loss 138 (34%) 266 0.09
(1.00) 		0.984
(1.00) 		0.765
(1.00) 		0.654
(1.00) 		0.615
(1.00) 		0.691
(1.00) 		0.299
(1.00) 		0.129
(1.00) 		0.793
(1.00) 		0.00488
(1.00) 		0.886
(1.00) 		0.883
(1.00)
9q loss 63 (16%) 341 0.328
(1.00) 		0.983
(1.00) 		0.788
(1.00) 		0.315
(1.00) 		0.77
(1.00) 		0.619
(1.00) 		1
(1.00) 		0.659
(1.00) 		0.604
(1.00) 		0.22
(1.00) 		0.825
(1.00) 		0.432
(1.00)
10p loss 125 (31%) 279 0.0244
(1.00) 		0.575
(1.00) 		0.424
(1.00) 		0.18
(1.00) 		0.384
(1.00) 		0.563
(1.00) 		0.191
(1.00) 		0.243
(1.00) 		0.344
(1.00) 		0.85
(1.00) 		0.864
(1.00) 		0.429
(1.00)
10q loss 84 (21%) 320 0.37
(1.00) 		0.281
(1.00) 		0.295
(1.00) 		0.668
(1.00) 		0.183
(1.00) 		0.662
(1.00) 		0.105
(1.00) 		0.486
(1.00) 		0.166
(1.00) 		0.591
(1.00) 		0.0774
(1.00) 		0.501
(1.00)
11p loss 105 (26%) 299 0.0402
(1.00) 		0.798
(1.00) 		0.0942
(1.00) 		0.914
(1.00) 		0.013
(1.00) 		0.832
(1.00) 		0.212
(1.00) 		0.743
(1.00) 		0.67
(1.00) 		0.239
(1.00) 		0.738
(1.00) 		0.152
(1.00)
11q loss 129 (32%) 275 0.159
(1.00) 		0.202
(1.00) 		0.382
(1.00) 		0.936
(1.00) 		0.106
(1.00) 		0.241
(1.00) 		0.00212
(1.00) 		1
(1.00) 		0.139
(1.00) 		0.279
(1.00) 		0.344
(1.00) 		0.306
(1.00)
12p loss 27 (7%) 377 0.0143
(1.00) 		0.0751
(1.00) 		0.69
(1.00) 		0.268
(1.00) 		0.581
(1.00) 		1
(1.00) 		0.378
(1.00) 		1
(1.00) 		0.801
(1.00) 		0.148
(1.00) 		0.134
(1.00) 		0.63
(1.00)
12q loss 23 (6%) 381 0.545
(1.00) 		0.361
(1.00) 		0.662
(1.00) 		0.0732
(1.00) 		0.929
(1.00) 		0.694
(1.00) 		1
(1.00) 		1
(1.00) 		0.59
(1.00) 		0.678
(1.00) 		0.512
(1.00) 		0.771
(1.00)
13q loss 127 (31%) 277 0.628
(1.00) 		0.361
(1.00) 		0.199
(1.00) 		0.253
(1.00) 		0.455
(1.00) 		0.844
(1.00) 		0.636
(1.00) 		0.336
(1.00) 		0.893
(1.00) 		0.125
(1.00) 		0.304
(1.00) 		0.369
(1.00)
14q loss 36 (9%) 368 0.206
(1.00) 		0.889
(1.00) 		0.45
(1.00) 		0.176
(1.00) 		0.894
(1.00) 		1
(1.00) 		0.248
(1.00) 		1
(1.00) 		0.382
(1.00) 		0.508
(1.00) 		0.963
(1.00) 		0.005
(1.00)
15q loss 74 (18%) 330 0.0842
(1.00) 		0.0942
(1.00) 		0.856
(1.00) 		0.338
(1.00) 		0.429
(1.00) 		0.212
(1.00) 		0.887
(1.00) 		0.173
(1.00) 		0.259
(1.00) 		0.676
(1.00) 		0.479
(1.00) 		0.383
(1.00)
16p loss 47 (12%) 357 0.0817
(1.00) 		0.0165
(1.00) 		0.802
(1.00) 		0.295
(1.00) 		0.132
(1.00) 		0.295
(1.00) 		0.609
(1.00) 		0.582
(1.00) 		0.119
(1.00) 		0.917
(1.00) 		0.159
(1.00) 		0.893
(1.00)
16q loss 59 (15%) 345 0.425
(1.00) 		0.0657
(1.00) 		0.442
(1.00) 		0.655
(1.00) 		0.11
(1.00) 		0.279
(1.00) 		0.16
(1.00) 		0.329
(1.00) 		0.477
(1.00) 		0.665
(1.00) 		0.184
(1.00) 		0.83
(1.00)
17p loss 90 (22%) 314 0.363
(1.00) 		0.337
(1.00) 		0.401
(1.00) 		0.831
(1.00) 		0.872
(1.00) 		0.398
(1.00) 		0.51
(1.00) 		1
(1.00) 		0.654
(1.00) 		0.69
(1.00) 		0.525
(1.00) 		0.508
(1.00)
17q loss 30 (7%) 374 0.879
(1.00) 		0.856
(1.00) 		0.434
(1.00) 		0.5
(1.00) 		0.346
(1.00) 		0.0792
(1.00) 		1
(1.00) 		0.42
(1.00) 		0.338
(1.00) 		0.747
(1.00) 		0.749
(1.00) 		0.0915
(1.00)
18p loss 83 (21%) 321 0.204
(1.00) 		0.472
(1.00) 		0.883
(1.00) 		0.995
(1.00) 		0.224
(1.00) 		1
(1.00) 		0.415
(1.00) 		0.289
(1.00) 		0.877
(1.00) 		0.829
(1.00) 		0.337
(1.00) 		0.88
(1.00)
18q loss 171 (42%) 233 0.088
(1.00) 		0.0798
(1.00) 		0.946
(1.00) 		0.811
(1.00) 		0.486
(1.00) 		0.464
(1.00) 		0.183
(1.00) 		0.223
(1.00) 		0.528
(1.00) 		0.141
(1.00) 		0.00189
(1.00) 		0.251
(1.00)
19p loss 77 (19%) 327 0.00212
(1.00) 		0.257
(1.00) 		0.213
(1.00) 		0.292
(1.00) 		0.273
(1.00) 		0.0997
(1.00) 		0.266
(1.00) 		0.676
(1.00) 		0.205
(1.00) 		0.376
(1.00) 		0.0198
(1.00) 		0.598
(1.00)
19q loss 65 (16%) 339 0.0921
(1.00) 		0.106
(1.00) 		0.0698
(1.00) 		0.0788
(1.00) 		0.461
(1.00) 		0.31
(1.00) 		0.458
(1.00) 		1
(1.00) 		0.494
(1.00) 		0.949
(1.00) 		0.0459
(1.00) 		0.861
(1.00)
20p loss 42 (10%) 362 0.996
(1.00) 		0.931
(1.00) 		0.813
(1.00) 		0.987
(1.00) 		0.407
(1.00) 		0.232
(1.00) 		0.857
(1.00) 		1
(1.00) 		0.686
(1.00) 		0.312
(1.00) 		0.542
(1.00) 		0.871
(1.00)
20q loss 25 (6%) 379 0.254
(1.00) 		0.177
(1.00) 		0.438
(1.00) 		0.72
(1.00) 		0.726
(1.00) 		1
(1.00) 		0.656
(1.00) 		0.363
(1.00) 		0.798
(1.00) 		0.0821
(1.00) 		0.0078
(1.00) 		0.688
(1.00)
21q loss 153 (38%) 251 0.304
(1.00) 		0.536
(1.00) 		0.809
(1.00) 		0.141
(1.00) 		0.461
(1.00) 		0.069
(1.00) 		0.734
(1.00) 		0.636
(1.00) 		0.518
(1.00) 		0.327
(1.00) 		0.239
(1.00) 		0.674
(1.00)
22q loss 62 (15%) 342 0.899
(1.00) 		0.954
(1.00) 		0.27
(1.00) 		0.383
(1.00) 		0.397
(1.00) 		1
(1.00) 		0.223
(1.00) 		0.658
(1.00) 		0.0827
(1.00) 		0.829
(1.00) 		0.251
(1.00) 		0.00417
(1.00)
xq loss 63 (16%) 341 0.225
(1.00) 		0.102
(1.00) 		0.504
(1.00) 		0.067
(1.00) 		0.485
(1.00) 		0.794
(1.00) 		0.172
(1.00) 		0.357
(1.00) 		0.732
(1.00) 		0.162
(1.00) 		0.935
(1.00) 		0.21
(1.00)
'18p gain' versus 'GENDER'

P value = 0.00012 (Fisher's exact test), Q value = 0.12

Table S1.  Gene #32: '18p gain' versus Clinical Feature #7: 'GENDER'

nPatients FEMALE MALE
ALL 116 288
18P GAIN MUTATED 12 80
18P GAIN WILD-TYPE 104 208

Figure S1.  Get High-res Image Gene #32: '18p gain' versus Clinical Feature #7: 'GENDER'

Methods & Data
Input

  • Copy number data file = transformed.cor.cli.txt

  • Clinical data file = HNSC-TP.merged_data.txt

  • Number of patients = 404

  • Number of significantly arm-level cnvs = 80

  • Number of selected clinical features = 12

  • 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

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

Chi-square test

For multi-class clinical features (nominal or ordinal), Chi-square tests (Greenwood and Nikulin 1996) were used to estimate the P values using the 'chisq.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

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] Lehmann and Romano, Testing Statistical Hypotheses (3E ed.), New York: Springer. ISBN 0387988645 (2005)
[3] Greenwood and Nikulin, A guide to chi-squared testing, Wiley, New York. ISBN 047155779X (1996)
[4] 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)
[5] 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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