Correlation between copy number variation genes (focal events) 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/C13777BF
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/C13777BF
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 73 focal events and 12 clinical features across 404 patients, 4 significant findings detected with Q value < 0.25.

  • amp_18p11.31 cnv correlated to 'GENDER'.

  • del_3p24.1 cnv correlated to 'Time to Death'.

  • del_3p12.1 cnv correlated to 'Time to Death'.

  • 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 73 focal events and 12 clinical features. Shown in the table are P values (Q values). Thresholded by Q value < 0.25, 4 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
amp 18p11 31 119 (29%) 285 0.105
(1.00) 		0.0667
(1.00) 		0.0883
(1.00) 		0.0923
(1.00) 		0.266
(1.00) 		0.29
(1.00) 		0.000183
(0.159) 		1
(1.00) 		0.584
(1.00) 		0.0472
(1.00) 		0.344
(1.00) 		0.945
(1.00)
del 3p24 1 293 (73%) 111 5.84e-05
(0.0511) 		0.644
(1.00) 		0.162
(1.00) 		0.00769
(1.00) 		0.0363
(1.00) 		0.241
(1.00) 		0.00442
(1.00) 		0.00684
(1.00) 		0.889
(1.00) 		0.000553
(0.482) 		0.459
(1.00) 		0.00166
(1.00)
del 3p12 1 274 (68%) 130 9.41e-05
(0.0822) 		0.697
(1.00) 		0.136
(1.00) 		0.259
(1.00) 		0.0726
(1.00) 		0.703
(1.00) 		0.0136
(1.00) 		0.119
(1.00) 		0.421
(1.00) 		0.0757
(1.00) 		0.778
(1.00) 		0.0112
(1.00)
del 11q23 1 188 (47%) 216 0.411
(1.00) 		0.139
(1.00) 		0.945
(1.00) 		0.947
(1.00) 		0.0111
(1.00) 		0.468
(1.00) 		7.13e-05
(0.0624) 		0.548
(1.00) 		0.132
(1.00) 		0.0816
(1.00) 		0.518
(1.00) 		0.024
(1.00)
amp 2q11 2 84 (21%) 320 0.303
(1.00) 		0.93
(1.00) 		0.0583
(1.00) 		0.000709
(0.617) 		0.294
(1.00) 		0.632
(1.00) 		0.282
(1.00) 		0.486
(1.00) 		0.644
(1.00) 		0.21
(1.00) 		0.595
(1.00) 		0.501
(1.00)
amp 2q31 2 88 (22%) 316 0.155
(1.00) 		0.776
(1.00) 		0.382
(1.00) 		0.181
(1.00) 		0.203
(1.00) 		0.0379
(1.00) 		0.288
(1.00) 		1
(1.00) 		1
(1.00) 		0.233
(1.00) 		0.583
(1.00) 		0.139
(1.00)
amp 3q26 33 300 (74%) 104 0.072
(1.00) 		0.152
(1.00) 		0.075
(1.00) 		0.478
(1.00) 		0.0985
(1.00) 		0.685
(1.00) 		0.00364
(1.00) 		0.197
(1.00) 		0.391
(1.00) 		0.0219
(1.00) 		0.029
(1.00) 		0.0424
(1.00)
amp 5p15 33 183 (45%) 221 0.979
(1.00) 		0.0451
(1.00) 		0.627
(1.00) 		0.474
(1.00) 		0.176
(1.00) 		0.276
(1.00) 		0.0365
(1.00) 		0.681
(1.00) 		0.131
(1.00) 		0.999
(1.00) 		0.257
(1.00) 		0.578
(1.00)
amp 5p12 158 (39%) 246 0.76
(1.00) 		0.046
(1.00) 		0.883
(1.00) 		0.579
(1.00) 		0.461
(1.00) 		0.269
(1.00) 		0.176
(1.00) 		0.641
(1.00) 		0.0211
(1.00) 		0.451
(1.00) 		0.711
(1.00) 		0.722
(1.00)
amp 6p12 1 80 (20%) 324 0.824
(1.00) 		0.232
(1.00) 		0.975
(1.00) 		0.282
(1.00) 		0.836
(1.00) 		0.635
(1.00) 		1
(1.00) 		1
(1.00) 		0.159
(1.00) 		0.788
(1.00) 		0.435
(1.00) 		0.477
(1.00)
amp 6q12 73 (18%) 331 0.713
(1.00) 		0.72
(1.00) 		0.948
(1.00) 		0.526
(1.00) 		0.963
(1.00) 		1
(1.00) 		0.255
(1.00) 		0.67
(1.00) 		0.103
(1.00) 		0.602
(1.00) 		0.0471
(1.00) 		0.979
(1.00)
amp 7p11 2 172 (43%) 232 0.00598
(1.00) 		0.306
(1.00) 		0.818
(1.00) 		0.0867
(1.00) 		0.831
(1.00) 		0.468
(1.00) 		0.912
(1.00) 		0.0207
(1.00) 		0.8
(1.00) 		0.848
(1.00) 		0.22
(1.00) 		0.5
(1.00)
amp 7q21 3 139 (34%) 265 0.00241
(1.00) 		0.56
(1.00) 		0.732
(1.00) 		0.0793
(1.00) 		0.386
(1.00) 		0.241
(1.00) 		0.418
(1.00) 		0.0471
(1.00) 		0.235
(1.00) 		0.155
(1.00) 		0.772
(1.00) 		0.502
(1.00)
amp 8p11 23 125 (31%) 279 0.26
(1.00) 		0.445
(1.00) 		0.0659
(1.00) 		0.0965
(1.00) 		0.377
(1.00) 		0.84
(1.00) 		0.905
(1.00) 		0.17
(1.00) 		0.499
(1.00) 		0.456
(1.00) 		0.691
(1.00) 		0.851
(1.00)
amp 8q11 21 234 (58%) 170 0.915
(1.00) 		0.868
(1.00) 		0.116
(1.00) 		0.345
(1.00) 		0.298
(1.00) 		0.359
(1.00) 		0.911
(1.00) 		0.826
(1.00) 		0.704
(1.00) 		0.807
(1.00) 		0.103
(1.00) 		0.229
(1.00)
amp 8q24 21 294 (73%) 110 0.14
(1.00) 		0.485
(1.00) 		0.511
(1.00) 		0.406
(1.00) 		0.00969
(1.00) 		0.544
(1.00) 		0.902
(1.00) 		0.757
(1.00) 		0.778
(1.00) 		0.687
(1.00) 		0.00959
(1.00) 		0.33
(1.00)
amp 9p24 1 101 (25%) 303 0.705
(1.00) 		0.105
(1.00) 		0.507
(1.00) 		0.593
(1.00) 		0.285
(1.00) 		0.408
(1.00) 		0.00335
(1.00) 		1
(1.00) 		0.111
(1.00) 		0.00922
(1.00) 		0.534
(1.00) 		0.41
(1.00)
amp 9p23 99 (25%) 305 0.966
(1.00) 		0.212
(1.00) 		0.455
(1.00) 		0.857
(1.00) 		0.173
(1.00) 		0.4
(1.00) 		0.0209
(1.00) 		1
(1.00) 		0.383
(1.00) 		0.00829
(1.00) 		0.52
(1.00) 		0.573
(1.00)
amp 9p13 3 112 (28%) 292 0.713
(1.00) 		0.439
(1.00) 		0.149
(1.00) 		0.996
(1.00) 		0.455
(1.00) 		0.844
(1.00) 		0.269
(1.00) 		0.763
(1.00) 		0.675
(1.00) 		0.478
(1.00) 		0.317
(1.00) 		0.529
(1.00)
amp 9q34 3 136 (34%) 268 0.517
(1.00) 		0.0521
(1.00) 		0.0634
(1.00) 		0.0183
(1.00) 		0.211
(1.00) 		0.845
(1.00) 		0.907
(1.00) 		1
(1.00) 		0.511
(1.00) 		0.445
(1.00) 		0.823
(1.00) 		0.568
(1.00)
amp 11p13 84 (21%) 320 0.418
(1.00) 		0.206
(1.00) 		0.213
(1.00) 		0.763
(1.00) 		0.281
(1.00) 		0.673
(1.00) 		0.591
(1.00) 		1
(1.00) 		1
(1.00) 		0.000667
(0.581) 		0.451
(1.00) 		0.261
(1.00)
amp 11q13 3 183 (45%) 221 0.0264
(1.00) 		0.601
(1.00) 		0.536
(1.00) 		0.564
(1.00) 		0.303
(1.00) 		0.0996
(1.00) 		0.583
(1.00) 		0.0342
(1.00) 		0.131
(1.00) 		0.0701
(1.00) 		0.716
(1.00) 		0.0549
(1.00)
amp 12p13 33 127 (31%) 277 0.542
(1.00) 		0.413
(1.00) 		0.974
(1.00) 		0.943
(1.00) 		0.661
(1.00) 		1
(1.00) 		0.478
(1.00) 		0.774
(1.00) 		1
(1.00) 		0.455
(1.00) 		0.228
(1.00) 		0.746
(1.00)
amp 12q15 79 (20%) 325 0.717
(1.00) 		0.128
(1.00) 		0.256
(1.00) 		0.754
(1.00) 		0.249
(1.00) 		0.807
(1.00) 		0.782
(1.00) 		0.68
(1.00) 		0.27
(1.00) 		0.154
(1.00) 		0.382
(1.00) 		0.595
(1.00)
amp 13q22 1 88 (22%) 316 0.0452
(1.00) 		0.0621
(1.00) 		0.814
(1.00) 		0.392
(1.00) 		0.591
(1.00) 		0.49
(1.00) 		0.426
(1.00) 		0.489
(1.00) 		0.171
(1.00) 		0.445
(1.00) 		0.097
(1.00) 		0.645
(1.00)
amp 13q34 82 (20%) 322 0.12
(1.00) 		0.124
(1.00) 		0.114
(1.00) 		0.157
(1.00) 		0.144
(1.00) 		0.655
(1.00) 		0.274
(1.00) 		0.485
(1.00) 		0.353
(1.00) 		0.309
(1.00) 		0.185
(1.00) 		0.397
(1.00)
amp 15q26 3 86 (21%) 318 0.00901
(1.00) 		0.986
(1.00) 		0.954
(1.00) 		0.201
(1.00) 		0.974
(1.00) 		0.828
(1.00) 		0.788
(1.00) 		1
(1.00) 		1
(1.00) 		0.442
(1.00) 		0.451
(1.00) 		0.342
(1.00)
amp 17q12 65 (16%) 339 0.277
(1.00) 		0.0876
(1.00) 		0.639
(1.00) 		0.559
(1.00) 		0.679
(1.00) 		1
(1.00) 		0.298
(1.00) 		0.143
(1.00) 		0.866
(1.00) 		0.238
(1.00) 		0.156
(1.00) 		0.185
(1.00)
amp 18q11 2 80 (20%) 324 0.933
(1.00) 		0.013
(1.00) 		0.392
(1.00) 		0.63
(1.00) 		0.418
(1.00) 		0.619
(1.00) 		0.055
(1.00) 		0.275
(1.00) 		0.753
(1.00) 		0.159
(1.00) 		0.987
(1.00) 		0.423
(1.00)
amp 20p12 2 148 (37%) 256 0.963
(1.00) 		0.925
(1.00) 		0.923
(1.00) 		0.952
(1.00) 		0.41
(1.00) 		0.263
(1.00) 		0.57
(1.00) 		1
(1.00) 		0.3
(1.00) 		0.327
(1.00) 		0.463
(1.00) 		0.993
(1.00)
amp 20q11 22 177 (44%) 227 0.849
(1.00) 		0.372
(1.00) 		0.464
(1.00) 		0.36
(1.00) 		0.877
(1.00) 		0.206
(1.00) 		0.74
(1.00) 		0.313
(1.00) 		0.312
(1.00) 		0.7
(1.00) 		0.0755
(1.00) 		0.299
(1.00)
amp xq28 115 (28%) 289 0.286
(1.00) 		0.739
(1.00) 		0.83
(1.00) 		0.0704
(1.00) 		0.199
(1.00) 		0.205
(1.00) 		0.903
(1.00) 		0.77
(1.00) 		0.0727
(1.00) 		0.311
(1.00) 		0.882
(1.00) 		0.505
(1.00)
del 1p36 21 77 (19%) 327 0.256
(1.00) 		0.0454
(1.00) 		0.324
(1.00) 		0.567
(1.00) 		0.759
(1.00) 		0.615
(1.00) 		0.266
(1.00) 		0.184
(1.00) 		0.0369
(1.00) 		0.00926
(1.00) 		0.141
(1.00) 		0.0962
(1.00)
del 1p13 2 102 (25%) 302 0.223
(1.00) 		0.0571
(1.00) 		0.822
(1.00) 		0.763
(1.00) 		0.95
(1.00) 		0.515
(1.00) 		0.899
(1.00) 		0.382
(1.00) 		0.471
(1.00) 		0.0293
(1.00) 		0.592
(1.00) 		0.962
(1.00)
del 1q44 37 (9%) 367 0.296
(1.00) 		0.266
(1.00) 		0.708
(1.00) 		0.686
(1.00) 		0.901
(1.00) 		1
(1.00) 		0.573
(1.00) 		1
(1.00) 		1
(1.00) 		0.733
(1.00) 		0.11
(1.00) 		0.0407
(1.00)
del 2q21 2 54 (13%) 350 0.798
(1.00) 		0.283
(1.00) 		0.803
(1.00) 		0.639
(1.00) 		0.158
(1.00) 		1
(1.00) 		0.00918
(1.00) 		1
(1.00) 		0.268
(1.00) 		0.761
(1.00) 		0.485
(1.00) 		0.00744
(1.00)
del 2q22 1 85 (21%) 319 0.463
(1.00) 		0.245
(1.00) 		0.348
(1.00) 		0.128
(1.00) 		0.539
(1.00) 		0.204
(1.00) 		0.139
(1.00) 		0.487
(1.00) 		0.879
(1.00) 		0.332
(1.00) 		0.564
(1.00) 		0.89
(1.00)
del 2q36 2 121 (30%) 283 0.0973
(1.00) 		0.682
(1.00) 		0.069
(1.00) 		0.00142
(1.00) 		0.699
(1.00) 		0.69
(1.00) 		0.472
(1.00) 		0.771
(1.00) 		0.497
(1.00) 		0.0734
(1.00) 		0.503
(1.00) 		0.728
(1.00)
del 4p15 2 169 (42%) 235 0.115
(1.00) 		0.361
(1.00) 		0.825
(1.00) 		0.526
(1.00) 		0.579
(1.00) 		0.266
(1.00) 		0.0592
(1.00) 		0.825
(1.00) 		0.525
(1.00) 		0.163
(1.00) 		0.626
(1.00) 		0.0513
(1.00)
del 4q22 1 129 (32%) 275 0.838
(1.00) 		0.995
(1.00) 		0.281
(1.00) 		0.664
(1.00) 		0.629
(1.00) 		0.426
(1.00) 		0.724
(1.00) 		0.775
(1.00) 		0.687
(1.00) 		0.384
(1.00) 		0.125
(1.00) 		0.12
(1.00)
del 4q35 2 164 (41%) 240 0.563
(1.00) 		0.847
(1.00) 		0.0548
(1.00) 		0.0313
(1.00) 		0.635
(1.00) 		0.459
(1.00) 		0.145
(1.00) 		0.408
(1.00) 		1
(1.00) 		0.866
(1.00) 		0.0974
(1.00) 		0.0991
(1.00)
del 5q11 2 165 (41%) 239 0.58
(1.00) 		0.189
(1.00) 		0.542
(1.00) 		0.0114
(1.00) 		0.0741
(1.00) 		0.346
(1.00) 		0.0733
(1.00) 		0.217
(1.00) 		0.252
(1.00) 		0.00526
(1.00) 		0.904
(1.00) 		0.0898
(1.00)
del 5q15 174 (43%) 230 0.494
(1.00) 		0.187
(1.00) 		0.513
(1.00) 		0.0125
(1.00) 		0.505
(1.00) 		0.578
(1.00) 		0.149
(1.00) 		0.155
(1.00) 		0.315
(1.00) 		0.00808
(1.00) 		0.957
(1.00) 		0.285
(1.00)
del 5q35 3 155 (38%) 249 0.782
(1.00) 		0.305
(1.00) 		0.406
(1.00) 		0.0381
(1.00) 		0.165
(1.00) 		1
(1.00) 		0.175
(1.00) 		0.288
(1.00) 		0.368
(1.00) 		0.0871
(1.00) 		0.869
(1.00) 		0.877
(1.00)
del 6p25 3 76 (19%) 328 0.181
(1.00) 		0.39
(1.00) 		0.183
(1.00) 		0.0764
(1.00) 		0.472
(1.00) 		1
(1.00) 		0.122
(1.00) 		1
(1.00) 		0.521
(1.00) 		0.698
(1.00) 		0.144
(1.00) 		0.467
(1.00)
del 7q31 1 65 (16%) 339 0.86
(1.00) 		0.103
(1.00) 		0.652
(1.00) 		0.892
(1.00) 		0.0928
(1.00) 		0.811
(1.00) 		0.882
(1.00) 		1
(1.00) 		0.494
(1.00) 		0.106
(1.00) 		0.0704
(1.00) 		0.579
(1.00)
del 7q36 1 103 (25%) 301 0.0413
(1.00) 		0.865
(1.00) 		0.748
(1.00) 		0.95
(1.00) 		0.343
(1.00) 		0.525
(1.00) 		0.103
(1.00) 		1
(1.00) 		0.776
(1.00) 		0.237
(1.00) 		0.16
(1.00) 		0.366
(1.00)
del 8p23 2 234 (58%) 170 0.00179
(1.00) 		0.021
(1.00) 		0.936
(1.00) 		0.556
(1.00) 		0.429
(1.00) 		0.194
(1.00) 		0.436
(1.00) 		0.0396
(1.00) 		0.8
(1.00) 		0.0991
(1.00) 		0.945
(1.00) 		0.212
(1.00)
del 9p23 181 (45%) 223 0.415
(1.00) 		0.22
(1.00) 		0.525
(1.00) 		0.842
(1.00) 		0.491
(1.00) 		0.713
(1.00) 		0.15
(1.00) 		0.231
(1.00) 		0.801
(1.00) 		0.0239
(1.00) 		0.773
(1.00) 		0.2
(1.00)
del 9p21 3 231 (57%) 173 0.0102
(1.00) 		0.522
(1.00) 		0.357
(1.00) 		0.531
(1.00) 		0.601
(1.00) 		0.282
(1.00) 		0.58
(1.00) 		0.0882
(1.00) 		0.613
(1.00) 		0.144
(1.00) 		0.422
(1.00) 		0.193
(1.00)
del 9q21 11 71 (18%) 333 0.161
(1.00) 		0.854
(1.00) 		0.648
(1.00) 		0.565
(1.00) 		0.561
(1.00) 		0.633
(1.00) 		0.564
(1.00) 		0.667
(1.00) 		0.324
(1.00) 		0.119
(1.00) 		0.551
(1.00) 		0.271
(1.00)
del 9q34 3 60 (15%) 344 0.742
(1.00) 		0.546
(1.00) 		0.879
(1.00) 		0.681
(1.00) 		0.932
(1.00) 		0.579
(1.00) 		0.44
(1.00) 		0.658
(1.00) 		1
(1.00) 		0.109
(1.00) 		0.922
(1.00) 		0.477
(1.00)
del 10p15 3 133 (33%) 271 0.0158
(1.00) 		0.71
(1.00) 		0.259
(1.00) 		0.135
(1.00) 		0.0348
(1.00) 		0.334
(1.00) 		0.484
(1.00) 		0.184
(1.00) 		0.185
(1.00) 		0.656
(1.00) 		0.79
(1.00) 		0.0732
(1.00)
del 10p11 21 125 (31%) 279 0.0757
(1.00) 		0.281
(1.00) 		0.598
(1.00) 		0.26
(1.00) 		0.42
(1.00) 		0.842
(1.00) 		0.405
(1.00) 		0.334
(1.00) 		0.0793
(1.00) 		0.272
(1.00) 		0.343
(1.00) 		0.721
(1.00)
del 10q23 31 98 (24%) 306 0.175
(1.00) 		0.568
(1.00) 		0.518
(1.00) 		0.547
(1.00) 		0.891
(1.00) 		0.831
(1.00) 		0.125
(1.00) 		1
(1.00) 		0.464
(1.00) 		0.162
(1.00) 		0.0251
(1.00) 		0.35
(1.00)
del 11p15 5 125 (31%) 279 0.024
(1.00) 		0.752
(1.00) 		0.114
(1.00) 		0.885
(1.00) 		0.0493
(1.00) 		0.312
(1.00) 		0.405
(1.00) 		0.572
(1.00) 		0.893
(1.00) 		0.659
(1.00) 		0.962
(1.00) 		0.261
(1.00)
del 12q24 33 49 (12%) 355 0.729
(1.00) 		0.852
(1.00) 		0.725
(1.00) 		0.267
(1.00) 		0.638
(1.00) 		0.279
(1.00) 		1
(1.00) 		1
(1.00) 		0.849
(1.00) 		0.704
(1.00) 		0.691
(1.00) 		0.646
(1.00)
del 13q12 11 173 (43%) 231 0.315
(1.00) 		0.985
(1.00) 		0.0739
(1.00) 		0.295
(1.00) 		0.0107
(1.00) 		0.579
(1.00) 		0.0593
(1.00) 		0.156
(1.00) 		0.801
(1.00) 		0.0626
(1.00) 		0.958
(1.00) 		0.0266
(1.00)
del 13q14 2 165 (41%) 239 0.467
(1.00) 		0.411
(1.00) 		0.398
(1.00) 		0.415
(1.00) 		0.183
(1.00) 		0.853
(1.00) 		0.117
(1.00) 		0.523
(1.00) 		0.702
(1.00) 		0.125
(1.00) 		0.901
(1.00) 		0.264
(1.00)
del 14q11 2 51 (13%) 353 0.088
(1.00) 		0.296
(1.00) 		0.274
(1.00) 		0.0425
(1.00) 		0.948
(1.00) 		0.758
(1.00) 		0.413
(1.00) 		1
(1.00) 		0.707
(1.00) 		0.0205
(1.00) 		0.326
(1.00) 		0.0365
(1.00)
del 14q32 32 53 (13%) 351 0.537
(1.00) 		0.196
(1.00) 		0.48
(1.00) 		0.0337
(1.00) 		0.752
(1.00) 		0.723
(1.00) 		0.104
(1.00) 		1
(1.00) 		0.0951
(1.00) 		0.434
(1.00) 		0.433
(1.00) 		0.197
(1.00)
del 15q15 1 93 (23%) 311 0.32
(1.00) 		0.417
(1.00) 		0.613
(1.00) 		0.173
(1.00) 		0.657
(1.00) 		0.153
(1.00) 		0.516
(1.00) 		0.1
(1.00) 		0.297
(1.00) 		0.691
(1.00) 		0.675
(1.00) 		0.199
(1.00)
del 16q23 3 80 (20%) 324 0.298
(1.00) 		0.114
(1.00) 		0.122
(1.00) 		0.202
(1.00) 		0.0928
(1.00) 		0.32
(1.00) 		0.491
(1.00) 		0.471
(1.00) 		0.876
(1.00) 		0.568
(1.00) 		0.35
(1.00) 		0.885
(1.00)
del 17q25 3 56 (14%) 348 0.692
(1.00) 		0.702
(1.00) 		0.629
(1.00) 		0.13
(1.00) 		0.29
(1.00) 		0.219
(1.00) 		0.426
(1.00) 		0.114
(1.00) 		0.278
(1.00) 		0.766
(1.00) 		0.843
(1.00) 		0.963
(1.00)
del 18q21 2 211 (52%) 193 0.0646
(1.00) 		0.323
(1.00) 		0.653
(1.00) 		0.557
(1.00) 		0.443
(1.00) 		0.856
(1.00) 		0.037
(1.00) 		0.431
(1.00) 		0.707
(1.00) 		0.000913
(0.793) 		0.12
(1.00) 		0.0313
(1.00)
del 18q23 225 (56%) 179 0.029
(1.00) 		0.0743
(1.00) 		0.876
(1.00) 		0.253
(1.00) 		0.628
(1.00) 		0.718
(1.00) 		0.0979
(1.00) 		0.0922
(1.00) 		0.705
(1.00) 		0.00601
(1.00) 		0.0208
(1.00) 		0.0167
(1.00)
del 19p13 3 134 (33%) 270 0.00751
(1.00) 		0.325
(1.00) 		0.513
(1.00) 		0.849
(1.00) 		0.373
(1.00) 		0.703
(1.00) 		0.484
(1.00) 		0.184
(1.00) 		0.351
(1.00) 		0.259
(1.00) 		0.16
(1.00) 		0.225
(1.00)
del 19q13 43 77 (19%) 327 0.0931
(1.00) 		0.323
(1.00) 		0.418
(1.00) 		0.0724
(1.00) 		0.635
(1.00) 		0.613
(1.00) 		0.889
(1.00) 		1
(1.00) 		0.526
(1.00) 		0.799
(1.00) 		0.0303
(1.00) 		0.167
(1.00)
del 21q22 3 161 (40%) 243 0.603
(1.00) 		0.54
(1.00) 		0.764
(1.00) 		0.104
(1.00) 		0.443
(1.00) 		0.0944
(1.00) 		0.823
(1.00) 		0.519
(1.00) 		0.442
(1.00) 		0.457
(1.00) 		0.413
(1.00) 		0.558
(1.00)
del 22q13 31 72 (18%) 332 0.447
(1.00) 		0.337
(1.00) 		0.726
(1.00) 		0.406
(1.00) 		0.378
(1.00) 		0.461
(1.00) 		0.25
(1.00) 		0.668
(1.00) 		0.25
(1.00) 		0.652
(1.00) 		0.541
(1.00) 		0.294
(1.00)
del xp22 2 115 (28%) 289 0.00736
(1.00) 		0.291
(1.00) 		0.571
(1.00) 		0.00595
(1.00) 		0.0248
(1.00) 		1
(1.00) 		0.394
(1.00) 		1
(1.00) 		0.0727
(1.00) 		0.0825
(1.00) 		0.691
(1.00) 		0.0188
(1.00)
del xp21 3 119 (29%) 285 0.0689
(1.00) 		0.594
(1.00) 		0.584
(1.00) 		0.0325
(1.00) 		0.0192
(1.00) 		1
(1.00) 		0.631
(1.00) 		1
(1.00) 		0.0738
(1.00) 		0.123
(1.00) 		0.692
(1.00) 		0.0803
(1.00)
del xq21 33 60 (15%) 344 0.866
(1.00) 		0.926
(1.00) 		0.44
(1.00) 		0.71
(1.00) 		0.156
(1.00) 		1
(1.00) 		0.759
(1.00) 		0.336
(1.00) 		0.601
(1.00) 		0.945
(1.00) 		0.429
(1.00) 		0.123
(1.00)
'amp_18p11.31' versus 'GENDER'

P value = 0.000183 (Fisher's exact test), Q value = 0.16

Table S1.  Gene #25: 'amp_18p11.31' versus Clinical Feature #7: 'GENDER'

nPatients FEMALE MALE
ALL 116 288
AMP PEAK 25(18P11.31) MUTATED 19 100
AMP PEAK 25(18P11.31) WILD-TYPE 97 188

Figure S1.  Get High-res Image Gene #25: 'amp_18p11.31' versus Clinical Feature #7: 'GENDER'

'del_3p24.1' versus 'Time to Death'

P value = 5.84e-05 (logrank test), Q value = 0.051

Table S2.  Gene #36: 'del_3p24.1' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 399 152 0.1 - 211.0 (16.1)
DEL PEAK 7(3P24.1) MUTATED 289 127 0.1 - 211.0 (15.8)
DEL PEAK 7(3P24.1) WILD-TYPE 110 25 0.1 - 169.4 (21.0)

Figure S2.  Get High-res Image Gene #36: 'del_3p24.1' versus Clinical Feature #1: 'Time to Death'

'del_3p12.1' versus 'Time to Death'

P value = 9.41e-05 (logrank test), Q value = 0.082

Table S3.  Gene #37: 'del_3p12.1' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 399 152 0.1 - 211.0 (16.1)
DEL PEAK 8(3P12.1) MUTATED 271 121 0.1 - 211.0 (15.2)
DEL PEAK 8(3P12.1) WILD-TYPE 128 31 0.1 - 169.4 (19.8)

Figure S3.  Get High-res Image Gene #37: 'del_3p12.1' versus Clinical Feature #1: 'Time to Death'

'del_11q23.1' versus 'GENDER'

P value = 7.13e-05 (Fisher's exact test), Q value = 0.062

Table S4.  Gene #56: 'del_11q23.1' versus Clinical Feature #7: 'GENDER'

nPatients FEMALE MALE
ALL 116 288
DEL PEAK 27(11Q23.1) MUTATED 36 152
DEL PEAK 27(11Q23.1) WILD-TYPE 80 136

Figure S4.  Get High-res Image Gene #56: '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 = 404

  • Number of significantly focal cnvs = 73

  • 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)
Copyright © 2014 Broad Institute TCGA GDAC as part of the TCGA Research Network. All rights reserved.
Made with Nozzle