Correlation between copy number variation genes (focal events) 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/C13X853R
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 variation genes (focal events) and selected clinical features. Broad Institute of MIT and Harvard. doi:10.7908/C13X853R
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 75 focal events and 12 clinical features across 373 patients, 7 significant findings detected with Q value < 0.25.

  • amp_18p11.31 cnv correlated to 'GENDER'.

  • del_3p25.3 cnv correlated to 'Time to Death'.

  • del_3p14.2 cnv correlated to 'Time to Death'.

  • del_3p14.2 cnv correlated to 'Time to Death'.

  • del_3p12.2 cnv correlated to 'Time to Death' and 'NUMBERPACKYEARSSMOKED'.

  • del_11q23.1 cnv correlated to 'GENDER'.

Results
Overview of the results

Table 1.  Get Full Table Overview of the association between significant copy number variation of 75 focal events and 12 clinical features. Shown in the table are P values (Q values). Thresholded by Q value < 0.25, 7 significant findings 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
del 3p12 2 262 (70%) 111 0.000266
(0.238) 		0.557
(1.00) 		0.0837
(1.00) 		0.0925
(1.00) 		0.0963
(1.00) 		0.254
(1.00) 		0.0456
(1.00) 		0.0808
(1.00) 		0.778
(1.00) 		4.87e-05
(0.0439) 		0.983
(1.00) 		0.0117
(1.00)
amp 18p11 31 111 (30%) 262 0.0741
(1.00) 		0.183
(1.00) 		0.0987
(1.00) 		0.261
(1.00) 		0.186
(1.00) 		0.8
(1.00) 		0.000159
(0.143) 		0.709
(1.00) 		0.478
(1.00) 		0.0441
(1.00) 		0.384
(1.00) 		0.913
(1.00)
del 3p25 3 259 (69%) 114 0.00025
(0.224) 		0.832
(1.00) 		0.114
(1.00) 		0.00672
(1.00) 		0.123
(1.00) 		0.361
(1.00) 		0.0467
(1.00) 		0.00841
(1.00) 		0.676
(1.00) 		0.00356
(1.00) 		0.342
(1.00) 		0.0233
(1.00)
del 3p14 2 278 (75%) 95 0.00015
(0.135) 		0.395
(1.00) 		0.0325
(1.00) 		0.029
(1.00) 		0.0207
(1.00) 		0.232
(1.00) 		0.00254
(1.00) 		0.00401
(1.00) 		0.458
(1.00) 		0.00425
(1.00) 		0.352
(1.00) 		0.0021
(1.00)
del 3p14 2 278 (75%) 95 0.000119
(0.107) 		0.437
(1.00) 		0.0325
(1.00) 		0.029
(1.00) 		0.0207
(1.00) 		0.153
(1.00) 		0.00583
(1.00) 		0.00401
(1.00) 		0.656
(1.00) 		0.00264
(1.00) 		0.369
(1.00) 		0.00171
(1.00)
del 11q23 1 175 (47%) 198 0.654
(1.00) 		0.142
(1.00) 		0.983
(1.00) 		0.829
(1.00) 		0.00715
(1.00) 		1
(1.00) 		0.000229
(0.206) 		0.477
(1.00) 		0.194
(1.00) 		0.143
(1.00) 		0.484
(1.00) 		0.0243
(1.00)
amp 2q11 2 80 (21%) 293 0.272
(1.00) 		0.984
(1.00) 		0.106
(1.00) 		0.00183
(1.00) 		0.432
(1.00) 		0.779
(1.00) 		0.124
(1.00) 		0.671
(1.00) 		1
(1.00) 		0.186
(1.00) 		0.667
(1.00) 		0.509
(1.00)
amp 2q31 2 79 (21%) 294 0.115
(1.00) 		0.976
(1.00) 		0.412
(1.00) 		0.332
(1.00) 		0.228
(1.00) 		0.391
(1.00) 		0.21
(1.00) 		0.671
(1.00) 		1
(1.00) 		0.102
(1.00) 		0.876
(1.00) 		0.118
(1.00)
amp 3q26 33 277 (74%) 96 0.0853
(1.00) 		0.0958
(1.00) 		0.0475
(1.00) 		0.447
(1.00) 		0.0711
(1.00) 		0.341
(1.00) 		0.00383
(1.00) 		0.11
(1.00) 		0.458
(1.00) 		0.0316
(1.00) 		0.042
(1.00) 		0.0447
(1.00)
amp 5p15 33 169 (45%) 204 0.904
(1.00) 		0.0724
(1.00) 		0.571
(1.00) 		0.379
(1.00) 		0.14
(1.00) 		1
(1.00) 		0.0382
(1.00) 		0.468
(1.00) 		0.192
(1.00) 		0.882
(1.00) 		0.169
(1.00) 		0.516
(1.00)
amp 6p12 1 72 (19%) 301 0.77
(1.00) 		0.305
(1.00) 		0.973
(1.00) 		0.544
(1.00) 		0.975
(1.00) 		1
(1.00) 		0.886
(1.00) 		1
(1.00) 		0.326
(1.00) 		0.785
(1.00) 		0.325
(1.00) 		0.531
(1.00)
amp 6q12 68 (18%) 305 0.603
(1.00) 		0.772
(1.00) 		0.944
(1.00) 		0.433
(1.00) 		0.991
(1.00) 		1
(1.00) 		0.462
(1.00) 		1
(1.00) 		0.178
(1.00) 		0.416
(1.00) 		0.0219
(1.00) 		0.908
(1.00)
amp 7p11 2 160 (43%) 213 0.00853
(1.00) 		0.488
(1.00) 		0.393
(1.00) 		0.0978
(1.00) 		0.358
(1.00) 		1
(1.00) 		0.645
(1.00) 		0.0787
(1.00) 		1
(1.00) 		0.957
(1.00) 		0.15
(1.00) 		0.45
(1.00)
amp 7q21 3 132 (35%) 241 0.00491
(1.00) 		0.485
(1.00) 		0.512
(1.00) 		0.076
(1.00) 		0.0683
(1.00) 		0.348
(1.00) 		0.55
(1.00) 		0.117
(1.00) 		0.498
(1.00) 		0.168
(1.00) 		0.562
(1.00) 		0.609
(1.00)
amp 8p11 23 117 (31%) 256 0.457
(1.00) 		0.555
(1.00) 		0.12
(1.00) 		0.143
(1.00) 		0.576
(1.00) 		1
(1.00) 		0.805
(1.00) 		0.25
(1.00) 		0.675
(1.00) 		0.439
(1.00) 		0.645
(1.00) 		0.866
(1.00)
amp 8q11 21 217 (58%) 156 0.601
(1.00) 		0.856
(1.00) 		0.156
(1.00) 		0.461
(1.00) 		0.245
(1.00) 		0.509
(1.00) 		1
(1.00) 		1
(1.00) 		0.601
(1.00) 		0.644
(1.00) 		0.154
(1.00) 		0.231
(1.00)
amp 8q24 21 271 (73%) 102 0.195
(1.00) 		0.374
(1.00) 		0.453
(1.00) 		0.578
(1.00) 		0.00375
(1.00) 		0.331
(1.00) 		0.7
(1.00) 		1
(1.00) 		1
(1.00) 		0.916
(1.00) 		0.0185
(1.00) 		0.308
(1.00)
amp 9p24 1 90 (24%) 283 0.764
(1.00) 		0.125
(1.00) 		0.85
(1.00) 		0.855
(1.00) 		0.643
(1.00) 		0.612
(1.00) 		0.000746
(0.665) 		0.678
(1.00) 		0.172
(1.00) 		0.0326
(1.00) 		0.492
(1.00) 		0.35
(1.00)
amp 9p23 89 (24%) 284 0.867
(1.00) 		0.247
(1.00) 		0.836
(1.00) 		1
(1.00) 		0.486
(1.00) 		0.447
(1.00) 		0.007
(1.00) 		0.677
(1.00) 		0.451
(1.00) 		0.0292
(1.00) 		0.54
(1.00) 		0.535
(1.00)
amp 9p13 3 100 (27%) 273 0.665
(1.00) 		0.667
(1.00) 		0.446
(1.00) 		0.944
(1.00) 		0.904
(1.00) 		0.476
(1.00) 		0.196
(1.00) 		0.691
(1.00) 		0.661
(1.00) 		0.866
(1.00) 		0.268
(1.00) 		0.473
(1.00)
amp 9q34 3 122 (33%) 251 0.452
(1.00) 		0.0643
(1.00) 		0.336
(1.00) 		0.0623
(1.00) 		0.69
(1.00) 		0.476
(1.00) 		0.903
(1.00) 		1
(1.00) 		0.582
(1.00) 		0.924
(1.00) 		0.789
(1.00) 		0.492
(1.00)
amp 11p13 73 (20%) 300 0.431
(1.00) 		0.19
(1.00) 		0.279
(1.00) 		0.529
(1.00) 		0.18
(1.00) 		0.184
(1.00) 		0.886
(1.00) 		1
(1.00) 		0.625
(1.00) 		0.00257
(1.00) 		0.507
(1.00) 		0.215
(1.00)
amp 11q13 3 170 (46%) 203 0.0347
(1.00) 		0.353
(1.00) 		0.245
(1.00) 		0.468
(1.00) 		0.0762
(1.00) 		0.0819
(1.00) 		0.566
(1.00) 		0.129
(1.00) 		0.298
(1.00) 		0.147
(1.00) 		0.704
(1.00) 		0.0503
(1.00)
amp 12p13 33 120 (32%) 253 0.682
(1.00) 		0.504
(1.00) 		0.925
(1.00) 		0.973
(1.00) 		0.666
(1.00) 		0.813
(1.00) 		0.22
(1.00) 		1
(1.00) 		1
(1.00) 		0.516
(1.00) 		0.331
(1.00) 		0.933
(1.00)
amp 12q15 75 (20%) 298 0.709
(1.00) 		0.105
(1.00) 		0.259
(1.00) 		0.713
(1.00) 		0.457
(1.00) 		0.558
(1.00) 		0.887
(1.00) 		0.67
(1.00) 		0.332
(1.00) 		0.215
(1.00) 		0.43
(1.00) 		0.6
(1.00)
amp 13q22 1 83 (22%) 290 0.0903
(1.00) 		0.0914
(1.00) 		0.772
(1.00) 		0.37
(1.00) 		0.745
(1.00) 		0.789
(1.00) 		0.337
(1.00) 		0.673
(1.00) 		0.277
(1.00) 		0.493
(1.00) 		0.0837
(1.00) 		0.654
(1.00)
amp 17q12 61 (16%) 312 0.205
(1.00) 		0.0514
(1.00) 		0.659
(1.00) 		0.538
(1.00) 		0.863
(1.00) 		1
(1.00) 		0.215
(1.00) 		0.176
(1.00) 		1
(1.00) 		0.236
(1.00) 		0.152
(1.00) 		0.195
(1.00)
amp 18q11 2 75 (20%) 298 0.851
(1.00) 		0.0142
(1.00) 		0.616
(1.00) 		0.521
(1.00) 		0.633
(1.00) 		1
(1.00) 		0.0152
(1.00) 		0.223
(1.00) 		0.628
(1.00) 		0.169
(1.00) 		0.902
(1.00) 		0.434
(1.00)
amp 20p12 2 134 (36%) 239 0.858
(1.00) 		0.978
(1.00) 		0.632
(1.00) 		0.97
(1.00) 		0.414
(1.00) 		0.0751
(1.00) 		0.553
(1.00) 		1
(1.00) 		0.176
(1.00) 		0.151
(1.00) 		0.91
(1.00) 		0.948
(1.00)
amp 20q11 22 164 (44%) 209 0.656
(1.00) 		0.28
(1.00) 		0.156
(1.00) 		0.35
(1.00) 		0.449
(1.00) 		0.124
(1.00) 		0.492
(1.00) 		0.795
(1.00) 		0.191
(1.00) 		0.433
(1.00) 		0.154
(1.00) 		0.292
(1.00)
amp xq28 107 (29%) 266 0.501
(1.00) 		0.542
(1.00) 		0.914
(1.00) 		0.141
(1.00) 		0.136
(1.00) 		0.447
(1.00) 		0.529
(1.00) 		1
(1.00) 		0.114
(1.00) 		0.329
(1.00) 		0.579
(1.00) 		0.552
(1.00)
del 1p36 13 74 (20%) 299 0.0708
(1.00) 		0.0336
(1.00) 		0.236
(1.00) 		0.497
(1.00) 		0.579
(1.00) 		0.759
(1.00) 		0.392
(1.00) 		1
(1.00) 		0.192
(1.00) 		0.00646
(1.00) 		0.186
(1.00) 		0.107
(1.00)
del 1p13 2 94 (25%) 279 0.152
(1.00) 		0.0486
(1.00) 		0.706
(1.00) 		0.644
(1.00) 		0.719
(1.00) 		1
(1.00) 		1
(1.00) 		0.451
(1.00) 		0.181
(1.00) 		0.0269
(1.00) 		0.732
(1.00) 		0.977
(1.00)
del 1q44 33 (9%) 340 0.243
(1.00) 		0.254
(1.00) 		0.824
(1.00) 		0.779
(1.00) 		0.875
(1.00) 		0.728
(1.00) 		0.548
(1.00) 		1
(1.00) 		0.821
(1.00) 		0.644
(1.00) 		0.112
(1.00) 		0.0508
(1.00)
del 2q21 2 51 (14%) 322 0.692
(1.00) 		0.189
(1.00) 		0.811
(1.00) 		0.835
(1.00) 		0.216
(1.00) 		1
(1.00) 		0.00744
(1.00) 		1
(1.00) 		0.344
(1.00) 		0.897
(1.00) 		0.645
(1.00) 		0.00642
(1.00)
del 2q22 1 81 (22%) 292 0.345
(1.00) 		0.218
(1.00) 		0.189
(1.00) 		0.231
(1.00) 		0.257
(1.00) 		0.327
(1.00) 		0.212
(1.00) 		0.672
(1.00) 		1
(1.00) 		0.334
(1.00) 		0.433
(1.00) 		0.975
(1.00)
del 2q37 1 116 (31%) 257 0.419
(1.00) 		0.518
(1.00) 		0.0167
(1.00) 		0.000736
(0.657) 		0.336
(1.00) 		0.35
(1.00) 		0.711
(1.00) 		0.528
(1.00) 		0.0508
(1.00) 		0.268
(1.00) 		0.36
(1.00) 		0.54
(1.00)
del 3p14 3 281 (75%) 92 0.00155
(1.00) 		0.236
(1.00) 		0.102
(1.00) 		0.0338
(1.00) 		0.0653
(1.00) 		0.153
(1.00) 		0.00133
(1.00) 		0.00352
(1.00) 		0.55
(1.00) 		0.00122
(1.00) 		0.342
(1.00) 		0.0425
(1.00)
del 4p16 3 156 (42%) 217 0.0639
(1.00) 		0.293
(1.00) 		0.646
(1.00) 		0.354
(1.00) 		0.511
(1.00) 		0.509
(1.00) 		0.132
(1.00) 		0.792
(1.00) 		0.794
(1.00) 		0.505
(1.00) 		0.773
(1.00) 		0.151
(1.00)
del 4q22 1 120 (32%) 253 0.826
(1.00) 		0.894
(1.00) 		0.497
(1.00) 		0.502
(1.00) 		0.929
(1.00) 		0.241
(1.00) 		0.807
(1.00) 		0.532
(1.00) 		0.781
(1.00) 		0.381
(1.00) 		0.32
(1.00) 		0.117
(1.00)
del 4q35 2 154 (41%) 219 0.392
(1.00) 		0.959
(1.00) 		0.124
(1.00) 		0.0207
(1.00) 		0.911
(1.00) 		0.517
(1.00) 		0.131
(1.00) 		0.213
(1.00) 		0.513
(1.00) 		0.844
(1.00) 		0.0592
(1.00) 		0.132
(1.00)
del 5q11 2 155 (42%) 218 0.561
(1.00) 		0.211
(1.00) 		0.636
(1.00) 		0.0314
(1.00) 		0.0835
(1.00) 		0.659
(1.00) 		0.0363
(1.00) 		0.0776
(1.00) 		0.599
(1.00) 		0.00375
(1.00) 		0.981
(1.00) 		0.107
(1.00)
del 5q15 162 (43%) 211 0.536
(1.00) 		0.246
(1.00) 		0.67
(1.00) 		0.0403
(1.00) 		0.517
(1.00) 		1
(1.00) 		0.106
(1.00) 		0.0792
(1.00) 		0.695
(1.00) 		0.00601
(1.00) 		0.963
(1.00) 		0.313
(1.00)
del 5q35 3 146 (39%) 227 0.882
(1.00) 		0.294
(1.00) 		0.511
(1.00) 		0.0396
(1.00) 		0.148
(1.00) 		1
(1.00) 		0.0784
(1.00) 		0.0766
(1.00) 		1
(1.00) 		0.0892
(1.00) 		0.92
(1.00) 		0.808
(1.00)
del 6p25 3 69 (18%) 304 0.14
(1.00) 		0.317
(1.00) 		0.264
(1.00) 		0.0449
(1.00) 		0.471
(1.00) 		1
(1.00) 		0.185
(1.00) 		1
(1.00) 		0.503
(1.00) 		0.481
(1.00) 		0.0794
(1.00) 		0.45
(1.00)
del 7q31 1 60 (16%) 313 0.629
(1.00) 		0.0817
(1.00) 		0.701
(1.00) 		0.924
(1.00) 		0.103
(1.00) 		0.779
(1.00) 		0.758
(1.00) 		0.586
(1.00) 		0.29
(1.00) 		0.197
(1.00) 		0.0289
(1.00) 		0.561
(1.00)
del 7q36 1 95 (25%) 278 0.0594
(1.00) 		0.936
(1.00) 		0.497
(1.00) 		0.991
(1.00) 		0.168
(1.00) 		0.8
(1.00) 		0.115
(1.00) 		1
(1.00) 		1
(1.00) 		0.385
(1.00) 		0.162
(1.00) 		0.351
(1.00)
del 8p23 2 216 (58%) 157 0.00364
(1.00) 		0.0412
(1.00) 		0.829
(1.00) 		0.601
(1.00) 		0.543
(1.00) 		0.0469
(1.00) 		0.49
(1.00) 		0.0127
(1.00) 		0.895
(1.00) 		0.123
(1.00) 		0.836
(1.00) 		0.265
(1.00)
del 9p23 169 (45%) 204 0.232
(1.00) 		0.25
(1.00) 		0.668
(1.00) 		0.661
(1.00) 		0.617
(1.00) 		1
(1.00) 		0.107
(1.00) 		0.13
(1.00) 		0.365
(1.00) 		0.0674
(1.00) 		0.51
(1.00) 		0.232
(1.00)
del 9p21 3 215 (58%) 158 0.00947
(1.00) 		0.401
(1.00) 		0.627
(1.00) 		0.387
(1.00) 		0.759
(1.00) 		0.828
(1.00) 		1
(1.00) 		0.315
(1.00) 		0.359
(1.00) 		0.239
(1.00) 		0.518
(1.00) 		0.231
(1.00)
del 9q21 11 66 (18%) 307 0.329
(1.00) 		0.617
(1.00) 		0.723
(1.00) 		0.584
(1.00) 		0.894
(1.00) 		0.238
(1.00) 		0.653
(1.00) 		1
(1.00) 		0.233
(1.00) 		0.249
(1.00) 		0.502
(1.00) 		0.243
(1.00)
del 9q34 3 55 (15%) 318 0.866
(1.00) 		0.524
(1.00) 		0.91
(1.00) 		0.605
(1.00) 		0.916
(1.00) 		0.508
(1.00) 		0.747
(1.00) 		1
(1.00) 		0.715
(1.00) 		0.19
(1.00) 		0.629
(1.00) 		0.423
(1.00)
del 10p15 3 123 (33%) 250 0.0361
(1.00) 		0.687
(1.00) 		0.496
(1.00) 		0.311
(1.00) 		0.0793
(1.00) 		0.652
(1.00) 		0.331
(1.00) 		0.535
(1.00) 		0.216
(1.00) 		0.626
(1.00) 		0.896
(1.00) 		0.0848
(1.00)
del 10p11 21 116 (31%) 257 0.0905
(1.00) 		0.329
(1.00) 		0.674
(1.00) 		0.525
(1.00) 		0.486
(1.00) 		0.472
(1.00) 		0.217
(1.00) 		0.161
(1.00) 		0.122
(1.00) 		0.386
(1.00) 		0.36
(1.00) 		0.791
(1.00)
del 10q23 31 94 (25%) 279 0.25
(1.00) 		0.531
(1.00) 		0.522
(1.00) 		0.401
(1.00) 		0.776
(1.00) 		0.453
(1.00) 		0.0359
(1.00) 		1
(1.00) 		0.765
(1.00) 		0.193
(1.00) 		0.03
(1.00) 		0.292
(1.00)
del 11p15 5 116 (31%) 257 0.0288
(1.00) 		0.495
(1.00) 		0.158
(1.00) 		0.977
(1.00) 		0.0318
(1.00) 		1
(1.00) 		0.324
(1.00) 		1
(1.00) 		0.889
(1.00) 		0.362
(1.00) 		0.884
(1.00) 		0.267
(1.00)
del 11q14 2 139 (37%) 234 0.0745
(1.00) 		0.206
(1.00) 		0.326
(1.00) 		0.866
(1.00) 		0.00946
(1.00) 		1
(1.00) 		0.000932
(0.829) 		0.562
(1.00) 		0.179
(1.00) 		0.317
(1.00) 		0.122
(1.00) 		0.0655
(1.00)
del 12q24 33 47 (13%) 326 0.714
(1.00) 		0.776
(1.00) 		0.84
(1.00) 		0.45
(1.00) 		0.386
(1.00) 		0.235
(1.00) 		0.731
(1.00) 		1
(1.00) 		1
(1.00) 		0.634
(1.00) 		0.727
(1.00) 		0.672
(1.00)
del 13q12 11 161 (43%) 212 0.573
(1.00) 		0.924
(1.00) 		0.0213
(1.00) 		0.109
(1.00) 		0.00906
(1.00) 		0.826
(1.00) 		0.106
(1.00) 		0.0789
(1.00) 		0.794
(1.00) 		0.102
(1.00) 		0.801
(1.00) 		0.0253
(1.00)
del 13q14 2 153 (41%) 220 0.156
(1.00) 		0.388
(1.00) 		0.19
(1.00) 		0.529
(1.00) 		0.0595
(1.00) 		0.826
(1.00) 		0.13
(1.00) 		0.593
(1.00) 		0.511
(1.00) 		0.278
(1.00) 		0.536
(1.00) 		0.241
(1.00)
del 14q11 2 50 (13%) 323 0.11
(1.00) 		0.193
(1.00) 		0.279
(1.00) 		0.0389
(1.00) 		0.888
(1.00) 		0.728
(1.00) 		0.315
(1.00) 		1
(1.00) 		0.704
(1.00) 		0.0181
(1.00) 		0.271
(1.00) 		0.0223
(1.00)
del 14q32 32 52 (14%) 321 0.452
(1.00) 		0.295
(1.00) 		0.443
(1.00) 		0.0212
(1.00) 		0.654
(1.00) 		0.672
(1.00) 		0.0679
(1.00) 		1
(1.00) 		0.189
(1.00) 		0.418
(1.00) 		0.361
(1.00) 		0.143
(1.00)
del 15q15 1 85 (23%) 288 0.73
(1.00) 		0.491
(1.00) 		0.673
(1.00) 		0.192
(1.00) 		0.298
(1.00) 		0.369
(1.00) 		0.275
(1.00) 		0.162
(1.00) 		0.537
(1.00) 		0.978
(1.00) 		0.697
(1.00) 		0.165
(1.00)
del 16q23 3 75 (20%) 298 0.115
(1.00) 		0.113
(1.00) 		0.191
(1.00) 		0.237
(1.00) 		0.215
(1.00) 		0.235
(1.00) 		0.775
(1.00) 		1
(1.00) 		0.872
(1.00) 		0.738
(1.00) 		0.336
(1.00) 		0.726
(1.00)
del 17q25 3 53 (14%) 320 0.826
(1.00) 		0.789
(1.00) 		0.291
(1.00) 		0.247
(1.00) 		0.115
(1.00) 		0.0843
(1.00) 		0.329
(1.00) 		0.073
(1.00) 		0.356
(1.00) 		0.654
(1.00) 		0.999
(1.00) 		0.977
(1.00)
del 18q21 2 196 (53%) 177 0.115
(1.00) 		0.214
(1.00) 		0.891
(1.00) 		0.817
(1.00) 		0.459
(1.00) 		1
(1.00) 		0.0117
(1.00) 		0.349
(1.00) 		1
(1.00) 		0.000625
(0.558) 		0.158
(1.00) 		0.0296
(1.00)
del 18q23 210 (56%) 163 0.0822
(1.00) 		0.0552
(1.00) 		0.951
(1.00) 		0.597
(1.00) 		0.485
(1.00) 		0.83
(1.00) 		0.0379
(1.00) 		0.0357
(1.00) 		1
(1.00) 		0.00297
(1.00) 		0.0335
(1.00) 		0.0196
(1.00)
del 19p13 3 122 (33%) 251 0.0263
(1.00) 		0.287
(1.00) 		0.644
(1.00) 		0.828
(1.00) 		0.536
(1.00) 		0.487
(1.00) 		0.903
(1.00) 		0.534
(1.00) 		0.333
(1.00) 		0.349
(1.00) 		0.0787
(1.00) 		0.211
(1.00)
del 19q13 43 73 (20%) 300 0.117
(1.00) 		0.187
(1.00) 		0.597
(1.00) 		0.0361
(1.00) 		0.713
(1.00) 		0.765
(1.00) 		1
(1.00) 		1
(1.00) 		0.744
(1.00) 		0.973
(1.00) 		0.017
(1.00) 		0.203
(1.00)
del 21q22 3 146 (39%) 227 0.62
(1.00) 		0.539
(1.00) 		0.526
(1.00) 		0.171
(1.00) 		0.173
(1.00) 		0.264
(1.00) 		0.725
(1.00) 		0.215
(1.00) 		0.352
(1.00) 		0.267
(1.00) 		0.438
(1.00) 		0.677
(1.00)
del 22q13 31 69 (18%) 304 0.754
(1.00) 		0.443
(1.00) 		0.817
(1.00) 		0.373
(1.00) 		0.43
(1.00) 		0.779
(1.00) 		0.377
(1.00) 		1
(1.00) 		0.134
(1.00) 		0.561
(1.00) 		0.545
(1.00) 		0.26
(1.00)
del xp22 2 108 (29%) 265 0.00911
(1.00) 		0.422
(1.00) 		0.494
(1.00) 		0.00552
(1.00) 		0.0145
(1.00) 		0.794
(1.00) 		0.377
(1.00) 		1
(1.00) 		0.318
(1.00) 		0.0573
(1.00) 		0.377
(1.00) 		0.0244
(1.00)
del xp21 3 112 (30%) 261 0.073
(1.00) 		0.612
(1.00) 		0.468
(1.00) 		0.0283
(1.00) 		0.0119
(1.00) 		0.804
(1.00) 		0.62
(1.00) 		1
(1.00) 		0.322
(1.00) 		0.113
(1.00) 		0.385
(1.00) 		0.105
(1.00)
del xp11 3 113 (30%) 260 0.00678
(1.00) 		0.709
(1.00) 		0.762
(1.00) 		0.105
(1.00) 		0.0298
(1.00) 		0.804
(1.00) 		0.213
(1.00) 		1
(1.00) 		0.325
(1.00) 		0.0232
(1.00) 		0.286
(1.00) 		0.0789
(1.00)
del xq21 33 58 (16%) 315 0.898
(1.00) 		0.929
(1.00) 		0.489
(1.00) 		0.573
(1.00) 		0.22
(1.00) 		1
(1.00) 		1
(1.00) 		0.573
(1.00) 		0.282
(1.00) 		0.96
(1.00) 		0.361
(1.00) 		0.141
(1.00)
'amp_18p11.31' versus 'GENDER'

P value = 0.000159 (Fisher's exact test), Q value = 0.14

Table S1.  Gene #22: 'amp_18p11.31' versus Clinical Feature #7: 'GENDER'

nPatients FEMALE MALE
ALL 107 266
AMP PEAK 22(18P11.31) MUTATED 17 94
AMP PEAK 22(18P11.31) WILD-TYPE 90 172

Figure S1.  Get High-res Image Gene #22: 'amp_18p11.31' versus Clinical Feature #7: 'GENDER'

'del_3p25.3' versus 'Time to Death'

P value = 0.00025 (logrank test), Q value = 0.22

Table S2.  Gene #33: 'del_3p25.3' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 368 138 0.1 - 210.9 (15.8)
DEL PEAK 7(3P25.3) MUTATED 256 113 0.1 - 210.9 (15.1)
DEL PEAK 7(3P25.3) WILD-TYPE 112 25 0.1 - 156.5 (19.2)

Figure S2.  Get High-res Image Gene #33: 'del_3p25.3' versus Clinical Feature #1: 'Time to Death'

'del_3p14.2' versus 'Time to Death'

P value = 0.00015 (logrank test), Q value = 0.13

Table S3.  Gene #35: 'del_3p14.2' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 368 138 0.1 - 210.9 (15.8)
DEL PEAK 9(3P14.2) MUTATED 275 118 0.1 - 210.9 (15.1)
DEL PEAK 9(3P14.2) WILD-TYPE 93 20 0.1 - 156.5 (19.8)

Figure S3.  Get High-res Image Gene #35: 'del_3p14.2' versus Clinical Feature #1: 'Time to Death'

'del_3p14.2' versus 'Time to Death'

P value = 0.000119 (logrank test), Q value = 0.11

Table S4.  Gene #36: 'del_3p14.2' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 368 138 0.1 - 210.9 (15.8)
DEL PEAK 10(3P14.2) MUTATED 275 118 0.1 - 210.9 (15.0)
DEL PEAK 10(3P14.2) WILD-TYPE 93 20 0.1 - 156.5 (21.0)

Figure S4.  Get High-res Image Gene #36: 'del_3p14.2' versus Clinical Feature #1: 'Time to Death'

'del_3p12.2' versus 'Time to Death'

P value = 0.000266 (logrank test), Q value = 0.24

Table S5.  Gene #37: 'del_3p12.2' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 368 138 0.1 - 210.9 (15.8)
DEL PEAK 11(3P12.2) MUTATED 259 111 0.1 - 210.9 (14.7)
DEL PEAK 11(3P12.2) WILD-TYPE 109 27 0.1 - 156.5 (20.4)

Figure S5.  Get High-res Image Gene #37: 'del_3p12.2' versus Clinical Feature #1: 'Time to Death'

'del_3p12.2' versus 'NUMBERPACKYEARSSMOKED'

P value = 4.87e-05 (t-test), Q value = 0.044

Table S6.  Gene #37: 'del_3p12.2' versus Clinical Feature #10: 'NUMBERPACKYEARSSMOKED'

nPatients Mean (Std.Dev)
ALL 209 47.5 (38.8)
DEL PEAK 11(3P12.2) MUTATED 156 52.4 (41.7)
DEL PEAK 11(3P12.2) WILD-TYPE 53 33.0 (23.6)

Figure S6.  Get High-res Image Gene #37: 'del_3p12.2' versus Clinical Feature #10: 'NUMBERPACKYEARSSMOKED'

'del_11q23.1' versus 'GENDER'

P value = 0.000229 (Fisher's exact test), Q value = 0.21

Table S7.  Gene #57: 'del_11q23.1' versus Clinical Feature #7: 'GENDER'

nPatients FEMALE MALE
ALL 107 266
DEL PEAK 31(11Q23.1) MUTATED 34 141
DEL PEAK 31(11Q23.1) WILD-TYPE 73 125

Figure S7.  Get High-res Image Gene #57: 'del_11q23.1' 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 focal cnvs = 75

  • Number of selected clinical features = 12

  • 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

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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