Correlation between copy number variations of arm-level result and selected clinical features
Head and Neck Squamous Cell Carcinoma (Primary solid tumor)
15 January 2014  |  analyses__2014_01_15
Maintainer Information
Citation Information
doi:10.7908/C17P8WTP
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/C17P8WTP
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 373 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 84 (23%) 289 0.282
(1.00) 		0.0328
(1.00) 		0.312
(1.00) 		0.279
(1.00) 		0.133
(1.00) 		1
(1.00) 		6.09e-05
(0.0585) 		0.673
(1.00) 		0.645
(1.00) 		0.122
(1.00) 		0.634
(1.00) 		0.44
(1.00)
1p gain 47 (13%) 326 0.379
(1.00) 		0.167
(1.00) 		0.414
(1.00) 		0.733
(1.00) 		0.316
(1.00) 		0.13
(1.00) 		0.392
(1.00) 		0.0579
(1.00) 		0.845
(1.00) 		0.878
(1.00) 		0.612
(1.00) 		0.601
(1.00)
1q gain 86 (23%) 287 0.974
(1.00) 		0.11
(1.00) 		0.591
(1.00) 		0.26
(1.00) 		0.0588
(1.00) 		0.119
(1.00) 		0.686
(1.00) 		0.261
(1.00) 		0.359
(1.00) 		0.693
(1.00) 		0.181
(1.00) 		0.308
(1.00)
2p gain 71 (19%) 302 0.557
(1.00) 		0.35
(1.00) 		0.863
(1.00) 		0.372
(1.00) 		0.303
(1.00) 		0.391
(1.00) 		0.0796
(1.00) 		1
(1.00) 		0.869
(1.00) 		0.0377
(1.00) 		0.282
(1.00) 		0.836
(1.00)
2q gain 56 (15%) 317 0.425
(1.00) 		0.723
(1.00) 		0.612
(1.00) 		0.657
(1.00) 		0.13
(1.00) 		0.349
(1.00) 		0.261
(1.00) 		1
(1.00) 		0.719
(1.00) 		0.137
(1.00) 		0.46
(1.00) 		0.745
(1.00)
3p gain 62 (17%) 311 0.712
(1.00) 		0.331
(1.00) 		0.989
(1.00) 		0.234
(1.00) 		0.587
(1.00) 		0.774
(1.00) 		0.444
(1.00) 		0.599
(1.00) 		0.383
(1.00) 		0.772
(1.00) 		0.136
(1.00) 		0.458
(1.00)
3q gain 190 (51%) 183 0.82
(1.00) 		0.142
(1.00) 		0.293
(1.00) 		0.667
(1.00) 		0.0571
(1.00) 		0.669
(1.00) 		0.0877
(1.00) 		0.808
(1.00) 		0.0192
(1.00) 		0.561
(1.00) 		0.26
(1.00) 		0.0103
(1.00)
4p gain 31 (8%) 342 0.599
(1.00) 		0.0132
(1.00) 		0.387
(1.00) 		0.269
(1.00) 		0.557
(1.00) 		0.336
(1.00) 		1
(1.00) 		1
(1.00) 		0.643
(1.00) 		0.54
(1.00) 		0.238
(1.00) 		0.111
(1.00)
4q gain 26 (7%) 347 0.408
(1.00) 		0.723
(1.00) 		0.137
(1.00) 		0.681
(1.00) 		0.0799
(1.00) 		0.333
(1.00) 		1
(1.00) 		1
(1.00) 		0.13
(1.00) 		0.68
(1.00) 		0.64
(1.00) 		0.764
(1.00)
5p gain 144 (39%) 229 0.864
(1.00) 		0.158
(1.00) 		0.256
(1.00) 		0.886
(1.00) 		0.141
(1.00) 		1
(1.00) 		0.0599
(1.00) 		0.572
(1.00) 		0.016
(1.00) 		0.577
(1.00) 		0.748
(1.00) 		0.831
(1.00)
5q gain 52 (14%) 321 0.573
(1.00) 		0.286
(1.00) 		0.331
(1.00) 		0.877
(1.00) 		0.528
(1.00) 		0.369
(1.00) 		0.136
(1.00) 		0.222
(1.00) 		0.0229
(1.00) 		0.187
(1.00) 		0.864
(1.00) 		0.379
(1.00)
6p gain 54 (14%) 319 0.506
(1.00) 		0.18
(1.00) 		0.975
(1.00) 		0.912
(1.00) 		0.685
(1.00) 		0.55
(1.00) 		0.745
(1.00) 		1
(1.00) 		0.097
(1.00) 		0.127
(1.00) 		0.033
(1.00) 		0.482
(1.00)
6q gain 41 (11%) 332 0.73
(1.00) 		0.148
(1.00) 		0.201
(1.00) 		0.718
(1.00) 		0.267
(1.00) 		0.478
(1.00) 		0.856
(1.00) 		1
(1.00) 		0.0366
(1.00) 		0.0129
(1.00) 		0.00472
(1.00) 		0.614
(1.00)
7p gain 138 (37%) 235 0.0464
(1.00) 		0.436
(1.00) 		0.257
(1.00) 		0.599
(1.00) 		0.201
(1.00) 		0.367
(1.00) 		0.906
(1.00) 		0.123
(1.00) 		0.688
(1.00) 		0.475
(1.00) 		0.106
(1.00) 		0.94
(1.00)
7q gain 96 (26%) 277 0.262
(1.00) 		0.315
(1.00) 		0.675
(1.00) 		0.633
(1.00) 		0.192
(1.00) 		0.0674
(1.00) 		0.897
(1.00) 		0.189
(1.00) 		1
(1.00) 		0.477
(1.00) 		0.993
(1.00) 		0.851
(1.00)
8p gain 104 (28%) 269 0.342
(1.00) 		0.908
(1.00) 		0.998
(1.00) 		0.637
(1.00) 		0.759
(1.00) 		0.804
(1.00) 		0.0296
(1.00) 		0.0227
(1.00) 		0.385
(1.00) 		0.954
(1.00) 		0.568
(1.00) 		0.939
(1.00)
8q gain 220 (59%) 153 0.75
(1.00) 		0.205
(1.00) 		0.282
(1.00) 		0.888
(1.00) 		0.22
(1.00) 		0.662
(1.00) 		0.727
(1.00) 		0.791
(1.00) 		0.693
(1.00) 		0.51
(1.00) 		0.0886
(1.00) 		0.55
(1.00)
9p gain 71 (19%) 302 0.433
(1.00) 		0.185
(1.00) 		0.481
(1.00) 		0.842
(1.00) 		0.45
(1.00) 		1
(1.00) 		0.0294
(1.00) 		1
(1.00) 		0.408
(1.00) 		0.024
(1.00) 		0.383
(1.00) 		0.371
(1.00)
9q gain 94 (25%) 279 0.694
(1.00) 		0.163
(1.00) 		0.352
(1.00) 		0.0774
(1.00) 		0.808
(1.00) 		0.779
(1.00) 		1
(1.00) 		1
(1.00) 		1
(1.00) 		0.118
(1.00) 		0.9
(1.00) 		0.454
(1.00)
10p gain 26 (7%) 347 0.0987
(1.00) 		0.604
(1.00) 		0.953
(1.00) 		0.938
(1.00) 		0.567
(1.00) 		0.563
(1.00) 		0.655
(1.00) 		0.305
(1.00) 		1
(1.00) 		0.473
(1.00) 		0.823
(1.00) 		0.0188
(1.00)
10q gain 24 (6%) 349 0.254
(1.00) 		0.602
(1.00) 		0.683
(1.00) 		0.87
(1.00) 		0.888
(1.00) 		1
(1.00) 		0.817
(1.00) 		1
(1.00) 		0.595
(1.00) 		0.405
(1.00) 		0.349
(1.00) 		0.13
(1.00)
11p gain 45 (12%) 328 0.535
(1.00) 		0.131
(1.00) 		0.497
(1.00) 		0.738
(1.00) 		0.113
(1.00) 		0.0685
(1.00) 		0.726
(1.00) 		1
(1.00) 		0.691
(1.00) 		0.101
(1.00) 		0.805
(1.00) 		0.206
(1.00)
11q gain 50 (13%) 323 0.541
(1.00) 		0.227
(1.00) 		0.489
(1.00) 		0.768
(1.00) 		0.29
(1.00) 		0.557
(1.00) 		0.402
(1.00) 		1
(1.00) 		0.342
(1.00) 		0.139
(1.00) 		0.509
(1.00) 		0.0637
(1.00)
12p gain 107 (29%) 266 0.419
(1.00) 		0.768
(1.00) 		0.872
(1.00) 		0.945
(1.00) 		0.787
(1.00) 		0.628
(1.00) 		0.378
(1.00) 		0.702
(1.00) 		0.886
(1.00) 		0.124
(1.00) 		0.58
(1.00) 		0.781
(1.00)
12q gain 65 (17%) 308 0.885
(1.00) 		0.217
(1.00) 		0.47
(1.00) 		0.774
(1.00) 		0.473
(1.00) 		1
(1.00) 		0.881
(1.00) 		1
(1.00) 		0.0883
(1.00) 		0.152
(1.00) 		0.438
(1.00) 		0.047
(1.00)
13q gain 45 (12%) 328 0.854
(1.00) 		0.0671
(1.00) 		0.514
(1.00) 		0.6
(1.00) 		0.686
(1.00) 		0.754
(1.00) 		0.861
(1.00) 		1
(1.00) 		0.113
(1.00) 		0.769
(1.00) 		0.0357
(1.00) 		0.523
(1.00)
14q gain 108 (29%) 265 0.32
(1.00) 		0.878
(1.00) 		0.634
(1.00) 		0.97
(1.00) 		0.916
(1.00) 		0.141
(1.00) 		0.451
(1.00) 		0.522
(1.00) 		0.775
(1.00) 		0.656
(1.00) 		0.503
(1.00) 		0.365
(1.00)
15q gain 61 (16%) 312 0.387
(1.00) 		0.88
(1.00) 		0.791
(1.00) 		0.0657
(1.00) 		0.602
(1.00) 		0.27
(1.00) 		0.645
(1.00) 		1
(1.00) 		0.861
(1.00) 		0.599
(1.00) 		0.423
(1.00) 		0.139
(1.00)
16p gain 76 (20%) 297 0.7
(1.00) 		0.033
(1.00) 		0.245
(1.00) 		1
(1.00) 		0.315
(1.00) 		0.759
(1.00) 		0.777
(1.00) 		0.67
(1.00) 		0.749
(1.00) 		0.424
(1.00) 		0.208
(1.00) 		0.0817
(1.00)
16q gain 82 (22%) 291 0.124
(1.00) 		0.0755
(1.00) 		0.24
(1.00) 		0.68
(1.00) 		0.647
(1.00) 		0.396
(1.00) 		0.131
(1.00) 		1
(1.00) 		1
(1.00) 		0.635
(1.00) 		0.271
(1.00) 		0.244
(1.00)
17p gain 49 (13%) 324 0.802
(1.00) 		0.343
(1.00) 		0.34
(1.00) 		0.304
(1.00) 		0.698
(1.00) 		0.754
(1.00) 		0.397
(1.00) 		0.206
(1.00) 		0.7
(1.00) 		0.862
(1.00) 		0.768
(1.00) 		0.526
(1.00)
17q gain 62 (17%) 311 0.378
(1.00) 		0.805
(1.00) 		0.509
(1.00) 		0.188
(1.00) 		0.448
(1.00) 		0.566
(1.00) 		0.167
(1.00) 		0.179
(1.00) 		1
(1.00) 		0.595
(1.00) 		0.562
(1.00) 		0.461
(1.00)
18q gain 34 (9%) 339 0.803
(1.00) 		0.576
(1.00) 		0.586
(1.00) 		0.751
(1.00) 		0.875
(1.00) 		1
(1.00) 		0.00115
(1.00) 		1
(1.00) 		1
(1.00) 		0.414
(1.00) 		0.318
(1.00) 		0.784
(1.00)
19p gain 35 (9%) 338 0.0694
(1.00) 		0.23
(1.00) 		0.617
(1.00) 		0.234
(1.00) 		0.395
(1.00) 		0.298
(1.00) 		0.326
(1.00) 		1
(1.00) 		1
(1.00) 		0.259
(1.00) 		0.819
(1.00) 		0.0454
(1.00)
19q gain 51 (14%) 322 0.106
(1.00) 		0.543
(1.00) 		0.984
(1.00) 		0.562
(1.00) 		0.738
(1.00) 		0.349
(1.00) 		0.136
(1.00) 		0.523
(1.00) 		1
(1.00) 		0.902
(1.00) 		0.519
(1.00) 		0.183
(1.00)
20p gain 134 (36%) 239 0.798
(1.00) 		0.875
(1.00) 		0.351
(1.00) 		0.645
(1.00) 		0.258
(1.00) 		0.372
(1.00) 		0.722
(1.00) 		1
(1.00) 		0.104
(1.00) 		0.181
(1.00) 		0.712
(1.00) 		0.752
(1.00)
20q gain 144 (39%) 229 0.655
(1.00) 		0.78
(1.00) 		0.185
(1.00) 		0.301
(1.00) 		0.27
(1.00) 		0.381
(1.00) 		0.907
(1.00) 		1
(1.00) 		0.109
(1.00) 		0.65
(1.00) 		0.185
(1.00) 		0.419
(1.00)
21q gain 25 (7%) 348 0.959
(1.00) 		0.801
(1.00) 		0.0702
(1.00) 		0.427
(1.00) 		0.225
(1.00) 		0.592
(1.00) 		0.0668
(1.00) 		0.0167
(1.00) 		1
(1.00) 		0.948
(1.00) 		0.733
(1.00) 		0.632
(1.00)
22q gain 82 (22%) 291 0.261
(1.00) 		0.891
(1.00) 		0.904
(1.00) 		0.845
(1.00) 		0.679
(1.00) 		0.603
(1.00) 		0.407
(1.00) 		0.155
(1.00) 		0.433
(1.00) 		0.281
(1.00) 		0.482
(1.00) 		0.604
(1.00)
xq gain 64 (17%) 309 0.349
(1.00) 		0.0269
(1.00) 		0.166
(1.00) 		0.126
(1.00) 		0.0872
(1.00) 		0.754
(1.00) 		0.225
(1.00) 		1
(1.00) 		0.00895
(1.00) 		0.202
(1.00) 		0.209
(1.00) 		0.349
(1.00)
1p loss 41 (11%) 332 0.265
(1.00) 		0.0523
(1.00) 		0.69
(1.00) 		0.654
(1.00) 		0.871
(1.00) 		0.289
(1.00) 		0.364
(1.00) 		1
(1.00) 		0.836
(1.00) 		0.0186
(1.00) 		0.845
(1.00) 		0.901
(1.00)
1q loss 27 (7%) 346 0.409
(1.00) 		0.564
(1.00) 		0.683
(1.00) 		0.422
(1.00) 		0.729
(1.00) 		0.678
(1.00) 		0.828
(1.00) 		1
(1.00) 		1
(1.00) 		0.463
(1.00) 		0.438
(1.00) 		0.0924
(1.00)
2p loss 24 (6%) 349 0.978
(1.00) 		0.681
(1.00) 		0.285
(1.00) 		0.964
(1.00) 		0.177
(1.00) 		0.672
(1.00) 		0.0637
(1.00) 		1
(1.00) 		0.189
(1.00) 		0.34
(1.00) 		0.888
(1.00) 		0.00382
(1.00)
2q loss 32 (9%) 341 0.966
(1.00) 		0.62
(1.00) 		0.0269
(1.00) 		0.297
(1.00) 		0.0432
(1.00) 		1
(1.00) 		0.0238
(1.00) 		1
(1.00) 		0.0602
(1.00) 		0.337
(1.00) 		0.526
(1.00) 		0.303
(1.00)
3p loss 218 (58%) 155 0.00745
(1.00) 		0.842
(1.00) 		0.236
(1.00) 		0.0148
(1.00) 		0.158
(1.00) 		0.279
(1.00) 		0.0494
(1.00) 		0.0291
(1.00) 		0.512
(1.00) 		0.145
(1.00) 		0.527
(1.00) 		0.0502
(1.00)
3q loss 49 (13%) 324 0.00901
(1.00) 		0.501
(1.00) 		0.268
(1.00) 		0.256
(1.00) 		0.566
(1.00) 		0.456
(1.00) 		0.397
(1.00) 		1
(1.00) 		0.181
(1.00) 		0.225
(1.00) 		0.88
(1.00) 		0.000652
(0.624)
4p loss 146 (39%) 227 0.55
(1.00) 		0.218
(1.00) 		0.73
(1.00) 		0.198
(1.00) 		0.745
(1.00) 		0.117
(1.00) 		0.412
(1.00) 		1
(1.00) 		0.69
(1.00) 		0.368
(1.00) 		0.354
(1.00) 		0.0862
(1.00)
4q loss 112 (30%) 261 0.698
(1.00) 		0.296
(1.00) 		0.213
(1.00) 		0.145
(1.00) 		0.277
(1.00) 		0.331
(1.00) 		1
(1.00) 		0.524
(1.00) 		0.202
(1.00) 		0.916
(1.00) 		0.908
(1.00) 		0.161
(1.00)
5p loss 35 (9%) 338 0.704
(1.00) 		0.221
(1.00) 		0.844
(1.00) 		0.527
(1.00) 		0.482
(1.00) 		0.248
(1.00) 		0.698
(1.00) 		1
(1.00) 		0.00619
(1.00) 		0.509
(1.00) 		0.79
(1.00) 		0.324
(1.00)
5q loss 118 (32%) 255 0.76
(1.00) 		0.538
(1.00) 		0.574
(1.00) 		0.0699
(1.00) 		0.355
(1.00) 		0.642
(1.00) 		0.176
(1.00) 		0.53
(1.00) 		0.403
(1.00) 		0.0527
(1.00) 		0.401
(1.00) 		0.381
(1.00)
6p loss 51 (14%) 322 0.154
(1.00) 		0.554
(1.00) 		0.433
(1.00) 		0.478
(1.00) 		0.519
(1.00) 		0.508
(1.00) 		0.248
(1.00) 		1
(1.00) 		0.709
(1.00) 		0.241
(1.00) 		0.421
(1.00) 		0.206
(1.00)
6q loss 50 (13%) 323 0.396
(1.00) 		0.544
(1.00) 		0.505
(1.00) 		0.326
(1.00) 		0.983
(1.00) 		0.508
(1.00) 		0.0922
(1.00) 		1
(1.00) 		0.447
(1.00) 		0.535
(1.00) 		0.683
(1.00) 		0.94
(1.00)
7p loss 17 (5%) 356 0.686
(1.00) 		0.828
(1.00) 		0.659
(1.00) 		0.887
(1.00) 		0.267
(1.00) 		1
(1.00) 		0.787
(1.00) 		1
(1.00) 		0.542
(1.00) 		0.234
(1.00) 		0.263
(1.00) 		0.821
(1.00)
7q loss 32 (9%) 341 0.914
(1.00) 		0.184
(1.00) 		0.726
(1.00) 		0.153
(1.00) 		0.607
(1.00) 		0.728
(1.00) 		0.689
(1.00) 		0.363
(1.00) 		0.486
(1.00) 		0.68
(1.00) 		0.0469
(1.00) 		0.354
(1.00)
8p loss 140 (38%) 233 0.0932
(1.00) 		0.419
(1.00) 		0.485
(1.00) 		0.459
(1.00) 		0.344
(1.00) 		0.828
(1.00) 		0.124
(1.00) 		0.302
(1.00) 		0.689
(1.00) 		0.221
(1.00) 		0.435
(1.00) 		0.42
(1.00)
8q loss 22 (6%) 351 0.429
(1.00) 		0.944
(1.00) 		0.823
(1.00) 		0.12
(1.00) 		0.542
(1.00) 		1
(1.00) 		0.632
(1.00) 		1
(1.00) 		0.407
(1.00) 		0.000461
(0.442) 		0.137
(1.00) 		0.842
(1.00)
9p loss 131 (35%) 242 0.0369
(1.00) 		0.86
(1.00) 		0.903
(1.00) 		0.505
(1.00) 		0.902
(1.00) 		0.492
(1.00) 		0.19
(1.00) 		0.411
(1.00) 		0.892
(1.00) 		0.0154
(1.00) 		0.795
(1.00) 		0.785
(1.00)
9q loss 60 (16%) 313 0.507
(1.00) 		0.729
(1.00) 		0.69
(1.00) 		0.113
(1.00) 		0.727
(1.00) 		1
(1.00) 		0.758
(1.00) 		1
(1.00) 		0.481
(1.00) 		0.23
(1.00) 		0.804
(1.00) 		0.374
(1.00)
10p loss 115 (31%) 258 0.0651
(1.00) 		0.551
(1.00) 		0.64
(1.00) 		0.319
(1.00) 		0.657
(1.00) 		0.366
(1.00) 		0.107
(1.00) 		0.527
(1.00) 		0.4
(1.00) 		0.828
(1.00) 		0.97
(1.00) 		0.378
(1.00)
10q loss 80 (21%) 293 0.383
(1.00) 		0.169
(1.00) 		0.44
(1.00) 		0.604
(1.00) 		0.273
(1.00) 		0.21
(1.00) 		0.0263
(1.00) 		0.671
(1.00) 		0.207
(1.00) 		0.501
(1.00) 		0.0642
(1.00) 		0.432
(1.00)
11p loss 100 (27%) 273 0.0606
(1.00) 		0.521
(1.00) 		0.115
(1.00) 		0.955
(1.00) 		0.00893
(1.00) 		1
(1.00) 		0.247
(1.00) 		0.691
(1.00) 		0.77
(1.00) 		0.237
(1.00) 		0.918
(1.00) 		0.0685
(1.00)
11q loss 120 (32%) 253 0.291
(1.00) 		0.233
(1.00) 		0.4
(1.00) 		0.972
(1.00) 		0.0725
(1.00) 		1
(1.00) 		0.00491
(1.00) 		1
(1.00) 		0.165
(1.00) 		0.564
(1.00) 		0.2
(1.00) 		0.0927
(1.00)
12p loss 26 (7%) 347 0.0463
(1.00) 		0.0336
(1.00) 		0.602
(1.00) 		0.302
(1.00) 		0.446
(1.00) 		1
(1.00) 		0.504
(1.00) 		1
(1.00) 		0.617
(1.00) 		0.211
(1.00) 		0.125
(1.00) 		0.615
(1.00)
12q loss 22 (6%) 351 0.457
(1.00) 		0.213
(1.00) 		0.72
(1.00) 		0.102
(1.00) 		0.914
(1.00) 		0.672
(1.00) 		0.632
(1.00) 		1
(1.00) 		0.588
(1.00) 		0.799
(1.00) 		0.492
(1.00) 		0.768
(1.00)
13q loss 120 (32%) 253 0.455
(1.00) 		0.278
(1.00) 		0.182
(1.00) 		0.267
(1.00) 		0.261
(1.00) 		0.487
(1.00) 		1
(1.00) 		0.168
(1.00) 		0.89
(1.00) 		0.25
(1.00) 		0.421
(1.00) 		0.361
(1.00)
14q loss 36 (10%) 337 0.337
(1.00) 		0.903
(1.00) 		0.454
(1.00) 		0.156
(1.00) 		0.833
(1.00) 		1
(1.00) 		0.12
(1.00) 		1
(1.00) 		0.387
(1.00) 		0.481
(1.00) 		0.883
(1.00) 		0.00212
(1.00)
15q loss 66 (18%) 307 0.288
(1.00) 		0.109
(1.00) 		0.795
(1.00) 		0.33
(1.00) 		0.14
(1.00) 		0.74
(1.00) 		0.881
(1.00) 		0.192
(1.00) 		0.5
(1.00) 		0.944
(1.00) 		0.506
(1.00) 		0.282
(1.00)
16p loss 45 (12%) 328 0.175
(1.00) 		0.0156
(1.00) 		0.979
(1.00) 		0.581
(1.00) 		0.222
(1.00) 		0.235
(1.00) 		0.294
(1.00) 		1
(1.00) 		0.161
(1.00) 		0.786
(1.00) 		0.305
(1.00) 		0.807
(1.00)
16q loss 55 (15%) 318 0.211
(1.00) 		0.0791
(1.00) 		0.664
(1.00) 		0.743
(1.00) 		0.284
(1.00) 		0.0968
(1.00) 		0.26
(1.00) 		0.552
(1.00) 		0.361
(1.00) 		0.803
(1.00) 		0.242
(1.00) 		0.737
(1.00)
17p loss 83 (22%) 290 0.426
(1.00) 		0.234
(1.00) 		0.426
(1.00) 		0.849
(1.00) 		1
(1.00) 		0.8
(1.00) 		0.493
(1.00) 		1
(1.00) 		0.437
(1.00) 		0.77
(1.00) 		0.455
(1.00) 		0.558
(1.00)
17q loss 28 (8%) 345 0.791
(1.00) 		0.712
(1.00) 		0.795
(1.00) 		0.522
(1.00) 		0.679
(1.00) 		0.039
(1.00) 		1
(1.00) 		0.325
(1.00) 		0.224
(1.00) 		0.926
(1.00) 		0.424
(1.00) 		0.0803
(1.00)
18p loss 78 (21%) 295 0.359
(1.00) 		0.462
(1.00) 		0.939
(1.00) 		1
(1.00) 		0.337
(1.00) 		0.795
(1.00) 		0.483
(1.00) 		0.233
(1.00) 		0.75
(1.00) 		0.722
(1.00) 		0.343
(1.00) 		0.832
(1.00)
18q loss 159 (43%) 214 0.137
(1.00) 		0.0912
(1.00) 		0.985
(1.00) 		0.955
(1.00) 		0.278
(1.00) 		0.667
(1.00) 		0.0835
(1.00) 		0.455
(1.00) 		0.793
(1.00) 		0.0892
(1.00) 		0.00702
(1.00) 		0.258
(1.00)
19p loss 74 (20%) 299 0.00584
(1.00) 		0.192
(1.00) 		0.414
(1.00) 		0.191
(1.00) 		0.571
(1.00) 		0.275
(1.00) 		0.568
(1.00) 		0.67
(1.00) 		0.745
(1.00) 		0.27
(1.00) 		0.0174
(1.00) 		0.453
(1.00)
19q loss 62 (17%) 311 0.0451
(1.00) 		0.0764
(1.00) 		0.113
(1.00) 		0.0625
(1.00) 		0.652
(1.00) 		0.759
(1.00) 		0.879
(1.00) 		1
(1.00) 		0.862
(1.00) 		0.558
(1.00) 		0.0579
(1.00) 		0.984
(1.00)
20p loss 40 (11%) 333 0.888
(1.00) 		0.707
(1.00) 		0.769
(1.00) 		0.966
(1.00) 		0.521
(1.00) 		0.186
(1.00) 		0.46
(1.00) 		1
(1.00) 		1
(1.00) 		0.393
(1.00) 		0.508
(1.00) 		0.862
(1.00)
20q loss 25 (7%) 348 0.272
(1.00) 		0.35
(1.00) 		0.296
(1.00) 		0.73
(1.00) 		0.666
(1.00) 		1
(1.00) 		0.819
(1.00) 		1
(1.00) 		0.797
(1.00) 		0.0785
(1.00) 		0.0118
(1.00) 		0.746
(1.00)
21q loss 136 (36%) 237 0.383
(1.00) 		0.599
(1.00) 		0.575
(1.00) 		0.271
(1.00) 		0.136
(1.00) 		0.275
(1.00) 		0.721
(1.00) 		0.301
(1.00) 		0.5
(1.00) 		0.194
(1.00) 		0.237
(1.00) 		0.89
(1.00)
22q loss 56 (15%) 317 0.945
(1.00) 		0.921
(1.00) 		0.475
(1.00) 		0.366
(1.00) 		0.62
(1.00) 		1
(1.00) 		0.341
(1.00) 		1
(1.00) 		0.15
(1.00) 		0.802
(1.00) 		0.276
(1.00) 		0.00821
(1.00)
xq loss 61 (16%) 312 0.333
(1.00) 		0.0794
(1.00) 		0.579
(1.00) 		0.0747
(1.00) 		0.659
(1.00) 		0.759
(1.00) 		0.0914
(1.00) 		0.593
(1.00) 		0.598
(1.00) 		0.177
(1.00) 		0.806
(1.00) 		0.26
(1.00)
'18p gain' versus 'GENDER'

P value = 6.09e-05 (Fisher's exact test), Q value = 0.058

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

nPatients FEMALE MALE
ALL 107 266
18P GAIN MUTATED 10 74
18P GAIN WILD-TYPE 97 192

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 = 373

  • 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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