Head and Neck Squamous Cell Carcinoma: Correlation between copy number variation genes (focal) and selected clinical features
(primary solid tumor cohort)
Maintained by TCGA GDAC Team (Broad Institute/MD Anderson Cancer Center/Harvard Medical School)
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 70 arm-level results and 12 clinical features across 321 patients, 5 significant findings detected with Q value < 0.25.

  • Amp Peak 23(18p11.31) cnv correlated to 'GENDER'.

  • Del Peak 7(3p25.3) cnv correlated to 'Time to Death'.

  • Del Peak 8(3p14.2) cnv correlated to 'TOBACCOSMOKINGHISTORYINDICATOR'.

  • Del Peak 9(3p14.2) cnv correlated to 'TOBACCOSMOKINGHISTORYINDICATOR'.

  • Del Peak 10(3p12.2) cnv correlated to 'NUMBERPACKYEARSSMOKED'.

Results
Overview of the results

Table 1.  Get Full Table Overview of the association between significant copy number variation of 70 arm-level results and 12 clinical features. Shown in the table are P values (Q values). Thresholded by Q value < 0.25, 5 significant findings detected.

Clinical
Features 		Time
to
Death 		AGE GENDER PATHOLOGY
T 		PATHOLOGY
N 		PATHOLOGICSPREAD(M) TUMOR
STAGE 		RADIATIONS
RADIATION
REGIMENINDICATION 		NUMBERPACKYEARSSMOKED TOBACCOSMOKINGHISTORYINDICATOR YEAROFTOBACCOSMOKINGONSET NUMBER
OF
LYMPH
NODES
nCNV (%) nWild-Type logrank test t-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 Fisher's exact test t-test t-test
Amp Peak 23(18p11 31) 102 (32%) 219 0.105
(1.00) 		0.0824
(1.00) 		9.24e-05
(0.0773) 		0.266
(1.00) 		0.772
(1.00) 		0.666
(1.00) 		0.0773
(1.00) 		0.576
(1.00) 		0.0965
(1.00) 		0.0534
(1.00) 		0.176
(1.00) 		0.768
(1.00)
Del Peak 7(3p25 3) 227 (71%) 94 0.000229
(0.191) 		0.967
(1.00) 		0.221
(1.00) 		0.0299
(1.00) 		0.124
(1.00) 		0.655
(1.00) 		0.0654
(1.00) 		0.566
(1.00) 		0.0023
(1.00) 		0.00192
(1.00) 		0.59
(1.00) 		0.0673
(1.00)
Del Peak 8(3p14 2) 242 (75%) 79 0.000502
(0.417) 		0.499
(1.00) 		0.0302
(1.00) 		0.0756
(1.00) 		0.0602
(1.00) 		0.662
(1.00) 		0.0349
(1.00) 		0.289
(1.00) 		0.00305
(1.00) 		8.79e-05
(0.0737) 		0.564
(1.00) 		0.0232
(1.00)
Del Peak 9(3p14 2) 242 (75%) 79 0.000463
(0.386) 		0.551
(1.00) 		0.0604
(1.00) 		0.0756
(1.00) 		0.0602
(1.00) 		1
(1.00) 		0.0349
(1.00) 		0.449
(1.00) 		0.00182
(1.00) 		8.79e-05
(0.0737) 		0.574
(1.00) 		0.0202
(1.00)
Del Peak 10(3p12 2) 228 (71%) 93 0.000379
(0.316) 		0.515
(1.00) 		0.338
(1.00) 		0.109
(1.00) 		0.113
(1.00) 		1
(1.00) 		0.075
(1.00) 		0.885
(1.00) 		4.83e-05
(0.0406) 		0.00697
(1.00) 		0.839
(1.00) 		0.017
(1.00)
Amp Peak 1(1q21 2) 75 (23%) 246 0.614
(1.00) 		0.0503
(1.00) 		0.56
(1.00) 		0.741
(1.00) 		0.236
(1.00) 		0.228
(1.00) 		0.939
(1.00) 		0.215
(1.00) 		0.575
(1.00) 		0.0696
(1.00) 		0.852
(1.00) 		0.129
(1.00)
Amp Peak 2(2q11 2) 69 (21%) 252 0.518
(1.00) 		0.505
(1.00) 		0.365
(1.00) 		0.00633
(1.00) 		0.546
(1.00) 		1
(1.00) 		0.106
(1.00) 		1
(1.00) 		0.394
(1.00) 		0.103
(1.00) 		0.559
(1.00) 		0.634
(1.00)
Amp Peak 3(2q31 2) 67 (21%) 254 0.189
(1.00) 		0.846
(1.00) 		0.879
(1.00) 		0.327
(1.00) 		0.318
(1.00) 		1
(1.00) 		0.696
(1.00) 		0.872
(1.00) 		0.12
(1.00) 		0.00287
(1.00) 		0.51
(1.00) 		0.134
(1.00)
Amp Peak 4(3q26 33) 240 (75%) 81 0.132
(1.00) 		0.0804
(1.00) 		0.0451
(1.00) 		0.558
(1.00) 		0.275
(1.00) 		1
(1.00) 		0.153
(1.00) 		0.368
(1.00) 		0.0067
(1.00) 		0.118
(1.00) 		0.108
(1.00) 		0.0862
(1.00)
Amp Peak 5(5p15 33) 146 (45%) 175 0.583
(1.00) 		0.147
(1.00) 		0.105
(1.00) 		0.277
(1.00) 		0.118
(1.00) 		0.395
(1.00) 		0.127
(1.00) 		0.0645
(1.00) 		0.796
(1.00) 		0.218
(1.00) 		0.166
(1.00) 		0.617
(1.00)
Amp Peak 6(5p12) 121 (38%) 200 0.672
(1.00) 		0.331
(1.00) 		0.249
(1.00) 		0.412
(1.00) 		0.344
(1.00) 		0.662
(1.00) 		0.532
(1.00) 		0.0145
(1.00) 		0.498
(1.00) 		0.276
(1.00) 		0.993
(1.00) 		0.792
(1.00)
Amp Peak 7(6p12 1) 64 (20%) 257 0.729
(1.00) 		0.208
(1.00) 		0.641
(1.00) 		0.54
(1.00) 		0.921
(1.00) 		1
(1.00) 		0.632
(1.00) 		0.192
(1.00) 		0.723
(1.00) 		0.649
(1.00) 		0.4
(1.00) 		0.77
(1.00)
Amp Peak 8(6q12) 59 (18%) 262 0.479
(1.00) 		0.652
(1.00) 		0.874
(1.00) 		0.597
(1.00) 		0.973
(1.00) 		1
(1.00) 		0.561
(1.00) 		0.0433
(1.00) 		0.733
(1.00) 		0.557
(1.00) 		0.0245
(1.00) 		0.784
(1.00)
Amp Peak 9(7p11 2) 137 (43%) 184 0.0564
(1.00) 		0.126
(1.00) 		0.708
(1.00) 		0.0531
(1.00) 		0.404
(1.00) 		0.686
(1.00) 		0.739
(1.00) 		0.692
(1.00) 		0.796
(1.00) 		0.249
(1.00) 		0.126
(1.00) 		0.535
(1.00)
Amp Peak 10(7q22 1) 114 (36%) 207 0.0561
(1.00) 		0.453
(1.00) 		0.364
(1.00) 		0.0241
(1.00) 		0.226
(1.00) 		0.335
(1.00) 		0.276
(1.00) 		0.276
(1.00) 		0.0603
(1.00) 		0.00114
(0.943) 		0.668
(1.00) 		0.685
(1.00)
Amp Peak 11(8p11 23) 102 (32%) 219 0.161
(1.00) 		0.711
(1.00) 		0.895
(1.00) 		0.102
(1.00) 		0.472
(1.00) 		1
(1.00) 		0.177
(1.00) 		0.888
(1.00) 		0.62
(1.00) 		0.619
(1.00) 		0.839
(1.00) 		0.989
(1.00)
Amp Peak 12(8q11 21) 189 (59%) 132 0.444
(1.00) 		0.48
(1.00) 		0.802
(1.00) 		0.962
(1.00) 		0.432
(1.00) 		0.0772
(1.00) 		0.4
(1.00) 		0.351
(1.00) 		0.825
(1.00) 		0.0873
(1.00) 		0.114
(1.00) 		0.396
(1.00)
Amp Peak 13(8q24 21) 232 (72%) 89 0.52
(1.00) 		0.288
(1.00) 		0.581
(1.00) 		0.715
(1.00) 		0.00146
(1.00) 		0.175
(1.00) 		0.348
(1.00) 		0.883
(1.00) 		0.773
(1.00) 		0.709
(1.00) 		0.0404
(1.00) 		0.00193
(1.00)
Amp Peak 14(9p23) 76 (24%) 245 0.69
(1.00) 		0.65
(1.00) 		0.108
(1.00) 		0.924
(1.00) 		0.329
(1.00) 		0.631
(1.00) 		0.723
(1.00) 		0.877
(1.00) 		0.104
(1.00) 		0.546
(1.00) 		0.84
(1.00) 		0.557
(1.00)
Amp Peak 15(9p13 3) 90 (28%) 231 0.877
(1.00) 		0.989
(1.00) 		0.49
(1.00) 		0.757
(1.00) 		0.722
(1.00) 		1
(1.00) 		0.774
(1.00) 		0.884
(1.00) 		0.795
(1.00) 		0.339
(1.00) 		0.611
(1.00) 		0.579
(1.00)
Amp Peak 16(11p13) 63 (20%) 258 0.466
(1.00) 		0.08
(1.00) 		0.642
(1.00) 		0.434
(1.00) 		0.224
(1.00) 		0.579
(1.00) 		0.541
(1.00) 		0.742
(1.00) 		0.00242
(1.00) 		0.326
(1.00) 		0.131
(1.00) 		0.263
(1.00)
Amp Peak 17(11q13 3) 146 (45%) 175 0.00597
(1.00) 		0.298
(1.00) 		0.901
(1.00) 		0.329
(1.00) 		0.0777
(1.00) 		1
(1.00) 		0.16
(1.00) 		0.187
(1.00) 		0.12
(1.00) 		0.0244
(1.00) 		0.604
(1.00) 		0.0494
(1.00)
Amp Peak 18(12p13 33) 109 (34%) 212 0.967
(1.00) 		0.298
(1.00) 		0.241
(1.00) 		0.417
(1.00) 		0.471
(1.00) 		0.169
(1.00) 		0.825
(1.00) 		0.679
(1.00) 		0.411
(1.00) 		0.212
(1.00) 		0.212
(1.00) 		0.634
(1.00)
Amp Peak 19(12q15) 63 (20%) 258 0.374
(1.00) 		0.355
(1.00) 		0.877
(1.00) 		0.629
(1.00) 		0.556
(1.00) 		1
(1.00) 		0.288
(1.00) 		0.323
(1.00) 		0.136
(1.00) 		0.403
(1.00) 		0.332
(1.00) 		0.96
(1.00)
Amp Peak 20(13q22 1) 68 (21%) 253 0.0889
(1.00) 		0.0566
(1.00) 		0.447
(1.00) 		0.519
(1.00) 		0.602
(1.00) 		0.579
(1.00) 		0.63
(1.00) 		0.341
(1.00) 		0.0451
(1.00) 		0.355
(1.00) 		0.0793
(1.00) 		0.499
(1.00)
Amp Peak 21(15q26 3) 71 (22%) 250 0.0155
(1.00) 		0.406
(1.00) 		1
(1.00) 		0.37
(1.00) 		0.973
(1.00) 		0.631
(1.00) 		0.828
(1.00) 		0.431
(1.00) 		0.711
(1.00) 		0.398
(1.00) 		0.895
(1.00) 		0.256
(1.00)
Amp Peak 22(17q12) 56 (17%) 265 0.0924
(1.00) 		0.12
(1.00) 		0.142
(1.00) 		0.501
(1.00) 		0.654
(1.00) 		1
(1.00) 		0.296
(1.00) 		0.302
(1.00) 		0.529
(1.00) 		0.0242
(1.00) 		0.599
(1.00) 		0.152
(1.00)
Amp Peak 24(18q11 2) 71 (22%) 250 0.937
(1.00) 		0.0288
(1.00) 		0.0509
(1.00) 		0.496
(1.00) 		0.755
(1.00) 		0.335
(1.00) 		0.978
(1.00) 		0.431
(1.00) 		0.266
(1.00) 		0.136
(1.00) 		0.977
(1.00) 		0.495
(1.00)
Amp Peak 25(20q11 22) 145 (45%) 176 0.841
(1.00) 		0.189
(1.00) 		0.263
(1.00) 		0.823
(1.00) 		0.48
(1.00) 		0.213
(1.00) 		0.934
(1.00) 		0.511
(1.00) 		0.722
(1.00) 		0.792
(1.00) 		0.104
(1.00) 		0.402
(1.00)
Del Peak 1(1p36 13) 68 (21%) 253 0.107
(1.00) 		0.0601
(1.00) 		0.287
(1.00) 		0.245
(1.00) 		0.605
(1.00) 		0.591
(1.00) 		0.562
(1.00) 		0.26
(1.00) 		0.0138
(1.00) 		0.0793
(1.00) 		0.353
(1.00) 		0.127
(1.00)
Del Peak 2(1p13 2) 81 (25%) 240 0.269
(1.00) 		0.158
(1.00) 		0.775
(1.00) 		0.281
(1.00) 		0.58
(1.00) 		0.108
(1.00) 		0.443
(1.00) 		0.549
(1.00) 		0.0126
(1.00) 		0.128
(1.00) 		0.816
(1.00) 		0.772
(1.00)
Del Peak 3(1q44) 27 (8%) 294 0.0989
(1.00) 		0.309
(1.00) 		0.826
(1.00) 		0.413
(1.00) 		0.578
(1.00) 		0.122
(1.00) 		0.845
(1.00) 		1
(1.00) 		0.575
(1.00) 		0.704
(1.00) 		0.228
(1.00) 		0.101
(1.00)
Del Peak 4(2q21 2) 40 (12%) 281 0.478
(1.00) 		0.117
(1.00) 		0.038
(1.00) 		0.601
(1.00) 		0.151
(1.00) 		0.579
(1.00) 		0.954
(1.00) 		0.427
(1.00) 		0.643
(1.00) 		0.464
(1.00) 		0.735
(1.00) 		0.0299
(1.00)
Del Peak 5(2q22 1) 66 (21%) 255 0.553
(1.00) 		0.258
(1.00) 		0.17
(1.00) 		0.197
(1.00) 		0.181
(1.00) 		0.327
(1.00) 		0.366
(1.00) 		0.516
(1.00) 		0.103
(1.00) 		0.207
(1.00) 		0.998
(1.00) 		0.574
(1.00)
Del Peak 6(2q36 2) 96 (30%) 225 0.189
(1.00) 		0.846
(1.00) 		0.418
(1.00) 		0.00358
(1.00) 		0.478
(1.00) 		0.657
(1.00) 		0.17
(1.00) 		0.887
(1.00) 		0.0345
(1.00) 		0.165
(1.00) 		0.463
(1.00) 		0.764
(1.00)
Del Peak 11(4p15 2) 138 (43%) 183 0.115
(1.00) 		0.0793
(1.00) 		0.381
(1.00) 		0.305
(1.00) 		0.573
(1.00) 		0.668
(1.00) 		0.405
(1.00) 		0.427
(1.00) 		0.2
(1.00) 		0.00342
(1.00) 		0.547
(1.00) 		0.0655
(1.00)
Del Peak 12(4q22 1) 102 (32%) 219 0.621
(1.00) 		0.667
(1.00) 		1
(1.00) 		0.535
(1.00) 		0.949
(1.00) 		0.335
(1.00) 		0.584
(1.00) 		0.481
(1.00) 		0.406
(1.00) 		0.065
(1.00) 		0.181
(1.00) 		0.136
(1.00)
Del Peak 13(4q35 2) 131 (41%) 190 0.172
(1.00) 		0.722
(1.00) 		0.0431
(1.00) 		0.0816
(1.00) 		0.915
(1.00) 		0.194
(1.00) 		0.263
(1.00) 		0.596
(1.00) 		0.59
(1.00) 		0.0222
(1.00) 		0.0324
(1.00) 		0.0973
(1.00)
Del Peak 14(5q11 2) 134 (42%) 187 0.519
(1.00) 		0.37
(1.00) 		0.168
(1.00) 		0.0869
(1.00) 		0.234
(1.00) 		1
(1.00) 		0.537
(1.00) 		0.287
(1.00) 		0.00402
(1.00) 		0.0124
(1.00) 		0.828
(1.00) 		0.118
(1.00)
Del Peak 15(5q35 3) 127 (40%) 194 0.512
(1.00) 		0.483
(1.00) 		0.255
(1.00) 		0.0346
(1.00) 		0.362
(1.00) 		1
(1.00) 		0.259
(1.00) 		0.502
(1.00) 		0.129
(1.00) 		0.0262
(1.00) 		0.786
(1.00) 		0.668
(1.00)
Del Peak 16(6p25 3) 64 (20%) 257 0.179
(1.00) 		0.22
(1.00) 		0.276
(1.00) 		0.00941
(1.00) 		0.856
(1.00) 		0.579
(1.00) 		0.289
(1.00) 		0.746
(1.00) 		0.365
(1.00) 		0.328
(1.00) 		0.102
(1.00) 		0.595
(1.00)
Del Peak 17(7q31 1) 49 (15%) 272 0.782
(1.00) 		0.00946
(1.00) 		0.608
(1.00) 		0.989
(1.00) 		0.381
(1.00) 		0.579
(1.00) 		0.578
(1.00) 		0.368
(1.00) 		0.293
(1.00) 		0.0486
(1.00) 		0.00522
(1.00) 		0.765
(1.00)
Del Peak 18(7q36 1) 80 (25%) 241 0.0152
(1.00) 		0.516
(1.00) 		0.151
(1.00) 		0.74
(1.00) 		0.092
(1.00) 		1
(1.00) 		0.247
(1.00) 		1
(1.00) 		0.431
(1.00) 		0.262
(1.00) 		0.129
(1.00) 		0.205
(1.00)
Del Peak 19(8p23 2) 183 (57%) 138 0.00809
(1.00) 		0.0854
(1.00) 		0.381
(1.00) 		0.799
(1.00) 		0.524
(1.00) 		1
(1.00) 		0.919
(1.00) 		0.692
(1.00) 		0.0333
(1.00) 		0.582
(1.00) 		0.947
(1.00) 		0.145
(1.00)
Del Peak 20(9p23) 151 (47%) 170 0.734
(1.00) 		0.384
(1.00) 		1
(1.00) 		0.407
(1.00) 		0.982
(1.00) 		0.395
(1.00) 		0.98
(1.00) 		0.358
(1.00) 		0.137
(1.00) 		0.00251
(1.00) 		0.788
(1.00) 		0.318
(1.00)
Del Peak 21(9p21 3) 189 (59%) 132 0.0231
(1.00) 		0.159
(1.00) 		0.377
(1.00) 		0.572
(1.00) 		0.982
(1.00) 		0.197
(1.00) 		0.831
(1.00) 		0.351
(1.00) 		0.321
(1.00) 		0.000591
(0.491) 		0.322
(1.00) 		0.32
(1.00)
Del Peak 22(9q21 11) 61 (19%) 260 0.87
(1.00) 		0.671
(1.00) 		0.754
(1.00) 		0.811
(1.00) 		0.73
(1.00) 		1
(1.00) 		0.583
(1.00) 		1
(1.00) 		0.281
(1.00) 		0.206
(1.00) 		0.383
(1.00) 		0.155
(1.00)
Del Peak 23(9q34 3) 53 (17%) 268 0.572
(1.00) 		0.707
(1.00) 		0.182
(1.00) 		0.664
(1.00) 		0.912
(1.00) 		0.51
(1.00) 		0.947
(1.00) 		0.479
(1.00) 		0.378
(1.00) 		0.537
(1.00) 		0.755
(1.00) 		0.163
(1.00)
Del Peak 24(10p15 3) 108 (34%) 213 0.157
(1.00) 		0.448
(1.00) 		1
(1.00) 		0.335
(1.00) 		0.0531
(1.00) 		1
(1.00) 		0.51
(1.00) 		0.0949
(1.00) 		0.55
(1.00) 		0.79
(1.00) 		0.505
(1.00) 		0.0788
(1.00)
Del Peak 25(10p11 21) 101 (31%) 220 0.256
(1.00) 		0.384
(1.00) 		0.594
(1.00) 		0.392
(1.00) 		0.598
(1.00) 		1
(1.00) 		0.658
(1.00) 		0.0489
(1.00) 		0.352
(1.00) 		0.329
(1.00) 		0.208
(1.00) 		0.828
(1.00)
Del Peak 26(10q23 31) 82 (26%) 239 0.27
(1.00) 		0.358
(1.00) 		0.319
(1.00) 		0.753
(1.00) 		0.974
(1.00) 		1
(1.00) 		0.599
(1.00) 		0.653
(1.00) 		0.224
(1.00) 		0.25
(1.00) 		0.00822
(1.00) 		0.214
(1.00)
Del Peak 27(11p15 4) 101 (31%) 220 0.0594
(1.00) 		0.485
(1.00) 		0.594
(1.00) 		0.877
(1.00) 		0.0604
(1.00) 		0.591
(1.00) 		0.56
(1.00) 		1
(1.00) 		0.289
(1.00) 		0.0615
(1.00) 		0.805
(1.00) 		0.336
(1.00)
Del Peak 28(11q14 1) 101 (31%) 220 0.0736
(1.00) 		0.696
(1.00) 		0.032
(1.00) 		0.164
(1.00) 		0.00446
(1.00) 		1
(1.00) 		0.00162
(1.00) 		0.0245
(1.00) 		0.348
(1.00) 		0.016
(1.00) 		0.244
(1.00) 		0.0331
(1.00)
Del Peak 29(11q23 1) 152 (47%) 169 0.774
(1.00) 		0.273
(1.00) 		0.00422
(1.00) 		0.966
(1.00) 		0.0393
(1.00) 		1
(1.00) 		0.601
(1.00) 		0.434
(1.00) 		0.242
(1.00) 		0.149
(1.00) 		0.262
(1.00) 		0.0362
(1.00)
Del Peak 30(12q24 33) 38 (12%) 283 0.563
(1.00) 		0.654
(1.00) 		1
(1.00) 		0.467
(1.00) 		0.674
(1.00) 		0.561
(1.00) 		0.734
(1.00) 		0.687
(1.00) 		0.585
(1.00) 		0.14
(1.00) 		0.46
(1.00) 		0.87
(1.00)
Del Peak 31(13q12 11) 144 (45%) 177 0.73
(1.00) 		0.831
(1.00) 		0.318
(1.00) 		0.0656
(1.00) 		0.147
(1.00) 		0.686
(1.00) 		0.0254
(1.00) 		1
(1.00) 		0.124
(1.00) 		0.151
(1.00) 		0.615
(1.00) 		0.0662
(1.00)
Del Peak 32(13q14 2) 136 (42%) 185 0.0121
(1.00) 		0.509
(1.00) 		0.453
(1.00) 		0.907
(1.00) 		0.282
(1.00) 		0.686
(1.00) 		0.469
(1.00) 		1
(1.00) 		0.281
(1.00) 		0.703
(1.00) 		0.244
(1.00) 		0.59
(1.00)
Del Peak 33(14q11 2) 46 (14%) 275 0.261
(1.00) 		0.264
(1.00) 		0.596
(1.00) 		0.09
(1.00) 		0.672
(1.00) 		1
(1.00) 		0.232
(1.00) 		1
(1.00) 		0.0267
(1.00) 		0.552
(1.00) 		0.291
(1.00) 		0.0118
(1.00)
Del Peak 34(14q32 32) 48 (15%) 273 0.356
(1.00) 		0.358
(1.00) 		0.163
(1.00) 		0.0541
(1.00) 		0.692
(1.00) 		1
(1.00) 		0.382
(1.00) 		0.358
(1.00) 		0.417
(1.00) 		0.472
(1.00) 		0.528
(1.00) 		0.181
(1.00)
Del Peak 35(15q15 1) 73 (23%) 248 0.667
(1.00) 		0.987
(1.00) 		0.374
(1.00) 		0.112
(1.00) 		0.241
(1.00) 		1
(1.00) 		0.625
(1.00) 		0.159
(1.00) 		0.816
(1.00) 		0.183
(1.00) 		0.842
(1.00) 		0.166
(1.00)
Del Peak 36(16q12 1) 54 (17%) 267 0.238
(1.00) 		0.577
(1.00) 		0.512
(1.00) 		0.86
(1.00) 		0.473
(1.00) 		0.591
(1.00) 		0.498
(1.00) 		0.221
(1.00) 		0.564
(1.00) 		0.00998
(1.00) 		0.415
(1.00) 		0.959
(1.00)
Del Peak 37(16q23 3) 64 (20%) 257 0.179
(1.00) 		0.278
(1.00) 		0.641
(1.00) 		0.399
(1.00) 		0.161
(1.00) 		0.155
(1.00) 		0.313
(1.00) 		0.87
(1.00) 		0.802
(1.00) 		0.0154
(1.00) 		0.124
(1.00) 		0.678
(1.00)
Del Peak 38(17q25 3) 41 (13%) 280 0.954
(1.00) 		0.993
(1.00) 		1
(1.00) 		0.49
(1.00) 		0.103
(1.00) 		1
(1.00) 		0.356
(1.00) 		0.237
(1.00) 		0.918
(1.00) 		0.204
(1.00) 		0.818
(1.00) 		0.981
(1.00)
Del Peak 39(18q21 2) 170 (53%) 151 0.134
(1.00) 		0.597
(1.00) 		0.00901
(1.00) 		0.655
(1.00) 		0.591
(1.00) 		0.427
(1.00) 		0.829
(1.00) 		0.512
(1.00) 		0.000344
(0.287) 		0.0121
(1.00) 		0.449
(1.00) 		0.0275
(1.00)
Del Peak 40(18q23) 182 (57%) 139 0.109
(1.00) 		0.254
(1.00) 		0.0461
(1.00) 		0.492
(1.00) 		0.617
(1.00) 		0.205
(1.00) 		0.87
(1.00) 		0.508
(1.00) 		0.0014
(1.00) 		0.0562
(1.00) 		0.216
(1.00) 		0.0269
(1.00)
Del Peak 41(19p13 3) 110 (34%) 211 0.0517
(1.00) 		0.454
(1.00) 		1
(1.00) 		0.798
(1.00) 		0.556
(1.00) 		1
(1.00) 		0.455
(1.00) 		0.411
(1.00) 		0.274
(1.00) 		0.819
(1.00) 		0.302
(1.00) 		0.459
(1.00)
Del Peak 42(19q13 43) 64 (20%) 257 0.156
(1.00) 		0.743
(1.00) 		0.757
(1.00) 		0.00522
(1.00) 		0.977
(1.00) 		0.228
(1.00) 		0.176
(1.00) 		0.622
(1.00) 		0.826
(1.00) 		0.382
(1.00) 		0.05
(1.00) 		0.277
(1.00)
Del Peak 43(Xp21 3) 106 (33%) 215 0.0552
(1.00) 		0.257
(1.00) 		0.895
(1.00) 		0.0217
(1.00) 		0.045
(1.00) 		0.347
(1.00) 		0.521
(1.00) 		0.209
(1.00) 		0.0933
(1.00) 		0.29
(1.00) 		0.623
(1.00) 		0.155
(1.00)
Del Peak 44(Xp11 3) 108 (34%) 213 0.00222
(1.00) 		0.861
(1.00) 		0.6
(1.00) 		0.0826
(1.00) 		0.0862
(1.00) 		0.361
(1.00) 		0.643
(1.00) 		0.164
(1.00) 		0.0197
(1.00) 		0.016
(1.00) 		0.422
(1.00) 		0.115
(1.00)
Del Peak 45(Xq21 33) 55 (17%) 266 0.441
(1.00) 		0.512
(1.00) 		0.622
(1.00) 		0.232
(1.00) 		0.815
(1.00) 		1
(1.00) 		0.107
(1.00) 		0.602
(1.00) 		0.867
(1.00) 		0.223
(1.00) 		0.436
(1.00) 		0.214
(1.00)
'Amp Peak 23(18p11.31) mutation analysis' versus 'GENDER'

P value = 9.24e-05 (Fisher's exact test), Q value = 0.077

Table S1.  Gene #23: 'Amp Peak 23(18p11.31) mutation analysis' versus Clinical Feature #3: 'GENDER'

nPatients FEMALE MALE
ALL 90 231
AMP PEAK 23(18P11.31) MUTATED 14 88
AMP PEAK 23(18P11.31) WILD-TYPE 76 143

Figure S1.  Get High-res Image Gene #23: 'Amp Peak 23(18p11.31) mutation analysis' versus Clinical Feature #3: 'GENDER'

'Del Peak 7(3p25.3) mutation analysis' versus 'Time to Death'

P value = 0.000229 (logrank test), Q value = 0.19

Table S2.  Gene #32: 'Del Peak 7(3p25.3) mutation analysis' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 317 121 0.1 - 210.9 (14.0)
DEL PEAK 7(3P25.3) MUTATED 223 100 0.1 - 210.9 (13.3)
DEL PEAK 7(3P25.3) WILD-TYPE 94 21 0.8 - 156.5 (20.4)

Figure S2.  Get High-res Image Gene #32: 'Del Peak 7(3p25.3) mutation analysis' versus Clinical Feature #1: 'Time to Death'

'Del Peak 8(3p14.2) mutation analysis' versus 'TOBACCOSMOKINGHISTORYINDICATOR'

P value = 8.79e-05 (Fisher's exact test), Q value = 0.074

Table S3.  Gene #33: 'Del Peak 8(3p14.2) mutation analysis' versus Clinical Feature #10: 'TOBACCOSMOKINGHISTORYINDICATOR'

nPatients CURRENT REFORMED SMOKER FOR < OR = 15 YEARS CURRENT REFORMED SMOKER FOR > 15 YEARS CURRENT SMOKER LIFELONG NON-SMOKER
ALL 84 57 103 66
DEL PEAK 8(3P14.2) MUTATED 73 35 84 40
DEL PEAK 8(3P14.2) WILD-TYPE 11 22 19 26

Figure S3.  Get High-res Image Gene #33: 'Del Peak 8(3p14.2) mutation analysis' versus Clinical Feature #10: 'TOBACCOSMOKINGHISTORYINDICATOR'

'Del Peak 9(3p14.2) mutation analysis' versus 'TOBACCOSMOKINGHISTORYINDICATOR'

P value = 8.79e-05 (Fisher's exact test), Q value = 0.074

Table S4.  Gene #34: 'Del Peak 9(3p14.2) mutation analysis' versus Clinical Feature #10: 'TOBACCOSMOKINGHISTORYINDICATOR'

nPatients CURRENT REFORMED SMOKER FOR < OR = 15 YEARS CURRENT REFORMED SMOKER FOR > 15 YEARS CURRENT SMOKER LIFELONG NON-SMOKER
ALL 84 57 103 66
DEL PEAK 9(3P14.2) MUTATED 73 35 84 40
DEL PEAK 9(3P14.2) WILD-TYPE 11 22 19 26

Figure S4.  Get High-res Image Gene #34: 'Del Peak 9(3p14.2) mutation analysis' versus Clinical Feature #10: 'TOBACCOSMOKINGHISTORYINDICATOR'

'Del Peak 10(3p12.2) mutation analysis' versus 'NUMBERPACKYEARSSMOKED'

P value = 4.83e-05 (t-test), Q value = 0.041

Table S5.  Gene #35: 'Del Peak 10(3p12.2) mutation analysis' versus Clinical Feature #9: 'NUMBERPACKYEARSSMOKED'

nPatients Mean (Std.Dev)
ALL 175 50.8 (41.1)
DEL PEAK 10(3P12.2) MUTATED 130 56.6 (44.1)
DEL PEAK 10(3P12.2) WILD-TYPE 45 34.2 (24.7)

Figure S5.  Get High-res Image Gene #35: 'Del Peak 10(3p12.2) mutation analysis' versus Clinical Feature #9: 'NUMBERPACKYEARSSMOKED'

Methods & Data
Input

  • Mutation data file = all_lesions.conf_99.cnv.cluster.txt

  • Clinical data file = HNSC-TP.clin.merged.picked.txt

  • Number of patients = 321

  • Number of significantly arm-level cnvs = 70

  • 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

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

This is an experimental feature. The full results of the analysis summarized in this report can be downloaded from the TCGA Data Coordination Center.

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] 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)
[4] 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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