Correlation between copy number variation genes (focal) and selected clinical features
Head and Neck Squamous Cell Carcinoma (Primary solid tumor)
23 May 2013  |  analyses__2013_05_23
Maintainer Information
Citation Information
doi:10.7908/C1SQ8XFG
Maintained by TCGA GDAC Team (Broad Institute/MD Anderson Cancer Center/Harvard Medical School)
Cite as Broad Institute TCGA Genome Data Analysis Center (2013): Correlation between copy number variation genes (focal) and selected clinical features. Broad Institute of MIT and Harvard. doi:10.7908/C1SQ8XFG
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 71 arm-level results and 11 clinical features across 325 patients, 3 significant findings detected with Q value < 0.25.

  • Amp Peak 22(18p11.31) cnv correlated to 'GENDER'.

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

  • 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 71 arm-level results and 11 clinical features. Shown in the table are P values (Q values). Thresholded by Q value < 0.25, 3 significant findings detected.

Clinical
Features 		Time
to
Death 		AGE GENDER RADIATIONS
RADIATION
REGIMENINDICATION 		NUMBERPACKYEARSSMOKED YEAROFTOBACCOSMOKINGONSET DISTANT
METASTASIS 		LYMPH
NODE
METASTASIS 		NUMBER
OF
LYMPH
NODES 		TUMOR
STAGECODE 		NEOPLASM
DISEASESTAGE
nCNV (%) nWild-Type logrank test t-test Fisher's exact test Fisher's exact test t-test t-test Fisher's exact test Chi-square test t-test t-test Chi-square test
Amp Peak 22(18p11 31) 0 (0%) 223 0.106
(1.00) 		0.0951
(1.00) 		9.64e-05
(0.0684) 		0.401
(1.00) 		0.0728
(1.00) 		0.298
(1.00) 		0.639
(1.00) 		0.835
(1.00) 		0.787
(1.00) 		0.125
(1.00)
Del Peak 7(3p25 3) 0 (0%) 95 0.000228
(0.162) 		0.931
(1.00) 		0.174
(1.00) 		0.887
(1.00) 		0.00304
(1.00) 		0.509
(1.00) 		0.656
(1.00) 		0.187
(1.00) 		0.084
(1.00) 		0.0549
(1.00)
Del Peak 10(3p12 2) 0 (0%) 93 0.000393
(0.278) 		0.613
(1.00) 		0.218
(1.00) 		0.886
(1.00) 		8.08e-05
(0.0574) 		0.978
(1.00) 		1
(1.00) 		0.11
(1.00) 		0.0254
(1.00) 		0.0752
(1.00)
Amp Peak 1(1q21 2) 0 (0%) 250 0.606
(1.00) 		0.0369
(1.00) 		0.56
(1.00) 		0.54
(1.00) 		0.52
(1.00) 		0.692
(1.00) 		0.197
(1.00) 		0.473
(1.00) 		0.12
(1.00) 		0.943
(1.00)
Amp Peak 2(2q11 2) 0 (0%) 255 0.515
(1.00) 		0.595
(1.00) 		0.18
(1.00) 		1
(1.00) 		0.378
(1.00) 		0.654
(1.00) 		1
(1.00) 		0.863
(1.00) 		0.661
(1.00) 		0.153
(1.00)
Amp Peak 3(2q31 2) 0 (0%) 256 0.173
(1.00) 		0.839
(1.00) 		0.764
(1.00) 		1
(1.00) 		0.113
(1.00) 		0.629
(1.00) 		1
(1.00) 		0.447
(1.00) 		0.146
(1.00) 		0.652
(1.00)
Amp Peak 4(3q26 33) 0 (0%) 81 0.133
(1.00) 		0.0615
(1.00) 		0.0221
(1.00) 		0.549
(1.00) 		0.00991
(1.00) 		0.0683
(1.00) 		1
(1.00) 		0.341
(1.00) 		0.118
(1.00) 		0.151
(1.00)
Amp Peak 5(5p15 33) 0 (0%) 177 0.583
(1.00) 		0.0935
(1.00) 		0.0822
(1.00) 		0.192
(1.00) 		0.771
(1.00) 		0.114
(1.00) 		0.399
(1.00) 		0.0564
(1.00) 		0.618
(1.00) 		0.427
(1.00)
Amp Peak 6(6p12 1) 0 (0%) 260 0.724
(1.00) 		0.174
(1.00) 		0.76
(1.00) 		0.147
(1.00) 		0.909
(1.00) 		0.301
(1.00) 		1
(1.00) 		0.828
(1.00) 		0.758
(1.00) 		0.9
(1.00)
Amp Peak 7(6q12) 0 (0%) 265 0.481
(1.00) 		0.66
(1.00) 		0.751
(1.00) 		0.0931
(1.00) 		0.552
(1.00) 		0.0158
(1.00) 		1
(1.00) 		0.955
(1.00) 		0.791
(1.00) 		0.886
(1.00)
Amp Peak 8(7p11 2) 0 (0%) 186 0.0558
(1.00) 		0.0956
(1.00) 		0.619
(1.00) 		1
(1.00) 		0.919
(1.00) 		0.0747
(1.00) 		0.692
(1.00) 		0.452
(1.00) 		0.579
(1.00) 		0.4
(1.00)
Amp Peak 9(7q21 3) 0 (0%) 211 0.0352
(1.00) 		0.92
(1.00) 		0.518
(1.00) 		0.498
(1.00) 		0.113
(1.00) 		0.396
(1.00) 		0.352
(1.00) 		0.191
(1.00) 		0.481
(1.00) 		0.467
(1.00)
Amp Peak 10(8p11 23) 0 (0%) 220 0.161
(1.00) 		0.669
(1.00) 		1
(1.00) 		1
(1.00) 		0.698
(1.00) 		0.667
(1.00) 		1
(1.00) 		0.498
(1.00) 		0.904
(1.00) 		0.116
(1.00)
Amp Peak 11(8q11 21) 0 (0%) 132 0.44
(1.00) 		0.367
(1.00) 		0.803
(1.00) 		0.186
(1.00) 		0.881
(1.00) 		0.0594
(1.00) 		0.0837
(1.00) 		0.881
(1.00) 		0.321
(1.00) 		0.498
(1.00)
Amp Peak 12(8q24 21) 0 (0%) 89 0.523
(1.00) 		0.227
(1.00) 		0.408
(1.00) 		0.885
(1.00) 		0.707
(1.00) 		0.0234
(1.00) 		0.182
(1.00) 		0.024
(1.00) 		0.00235
(1.00) 		0.363
(1.00)
Amp Peak 13(9p23) 0 (0%) 248 0.695
(1.00) 		0.712
(1.00) 		0.0806
(1.00) 		0.542
(1.00) 		0.0903
(1.00) 		0.765
(1.00) 		0.625
(1.00) 		0.598
(1.00) 		0.566
(1.00) 		0.757
(1.00)
Amp Peak 14(9p13 3) 0 (0%) 233 0.871
(1.00) 		0.735
(1.00) 		0.411
(1.00) 		0.885
(1.00) 		0.923
(1.00) 		0.383
(1.00) 		1
(1.00) 		0.493
(1.00) 		0.6
(1.00) 		0.652
(1.00)
Amp Peak 15(11p13) 0 (0%) 262 0.463
(1.00) 		0.102
(1.00) 		0.643
(1.00) 		0.745
(1.00) 		0.00298
(1.00) 		0.17
(1.00) 		0.581
(1.00) 		0.432
(1.00) 		0.242
(1.00) 		0.17
(1.00)
Amp Peak 16(11q13 3) 0 (0%) 175 0.00617
(1.00) 		0.197
(1.00) 		0.901
(1.00) 		0.438
(1.00) 		0.155
(1.00) 		0.366
(1.00) 		0.69
(1.00) 		0.0766
(1.00) 		0.0529
(1.00) 		0.202
(1.00)
Amp Peak 17(12p13 33) 0 (0%) 214 0.976
(1.00) 		0.22
(1.00) 		0.196
(1.00) 		0.683
(1.00) 		0.544
(1.00) 		0.106
(1.00) 		0.17
(1.00) 		0.706
(1.00) 		0.658
(1.00) 		0.856
(1.00)
Amp Peak 18(12q15) 0 (0%) 260 0.373
(1.00) 		0.349
(1.00) 		1
(1.00) 		0.422
(1.00) 		0.218
(1.00) 		0.585
(1.00) 		1
(1.00) 		0.715
(1.00) 		0.967
(1.00) 		0.257
(1.00)
Amp Peak 19(13q22 1) 0 (0%) 254 0.09
(1.00) 		0.0302
(1.00) 		0.456
(1.00) 		0.533
(1.00) 		0.0162
(1.00) 		0.0198
(1.00) 		0.591
(1.00) 		0.157
(1.00) 		0.54
(1.00) 		0.895
(1.00)
Amp Peak 20(15q26 3) 0 (0%) 254 0.0152
(1.00) 		0.481
(1.00) 		0.766
(1.00) 		0.638
(1.00) 		0.657
(1.00) 		0.964
(1.00) 		0.625
(1.00) 		0.774
(1.00) 		0.249
(1.00) 		0.78
(1.00)
Amp Peak 21(17q12) 0 (0%) 269 0.0913
(1.00) 		0.0943
(1.00) 		0.143
(1.00) 		0.492
(1.00) 		0.572
(1.00) 		0.508
(1.00) 		0.571
(1.00) 		0.593
(1.00) 		0.155
(1.00) 		0.343
(1.00)
Amp Peak 23(18q11 2) 0 (0%) 253 0.928
(1.00) 		0.0203
(1.00) 		0.017
(1.00) 		0.35
(1.00) 		0.272
(1.00) 		0.815
(1.00) 		0.331
(1.00) 		0.315
(1.00) 		0.486
(1.00) 		0.688
(1.00)
Amp Peak 24(20q11 22) 0 (0%) 178 0.837
(1.00) 		0.149
(1.00) 		0.323
(1.00) 		0.515
(1.00) 		0.824
(1.00) 		0.0605
(1.00) 		0.206
(1.00) 		0.159
(1.00) 		0.381
(1.00) 		0.352
(1.00)
Del Peak 1(1p36 13) 0 (0%) 256 0.104
(1.00) 		0.0588
(1.00) 		0.366
(1.00) 		0.203
(1.00) 		0.0182
(1.00) 		0.471
(1.00) 		0.337
(1.00) 		0.492
(1.00) 		0.128
(1.00) 		0.224
(1.00)
Del Peak 2(1p13 2) 0 (0%) 243 0.267
(1.00) 		0.123
(1.00) 		1
(1.00) 		0.181
(1.00) 		0.0122
(1.00) 		0.701
(1.00) 		0.104
(1.00) 		0.903
(1.00) 		0.801
(1.00) 		0.643
(1.00)
Del Peak 3(1q44) 0 (0%) 297 0.101
(1.00) 		0.292
(1.00) 		1
(1.00) 		1
(1.00) 		0.578
(1.00) 		0.226
(1.00) 		0.133
(1.00) 		0.44
(1.00) 		0.0787
(1.00) 		0.848
(1.00)
Del Peak 4(2q21 2) 0 (0%) 285 0.48
(1.00) 		0.099
(1.00) 		0.038
(1.00) 		0.429
(1.00) 		0.592
(1.00) 		0.638
(1.00) 		0.585
(1.00) 		0.507
(1.00) 		0.0359
(1.00) 		0.987
(1.00)
Del Peak 5(2q22 1) 0 (0%) 257 0.556
(1.00) 		0.218
(1.00) 		0.229
(1.00) 		1
(1.00) 		0.106
(1.00) 		0.999
(1.00) 		0.182
(1.00) 		0.0719
(1.00) 		0.639
(1.00) 		0.201
(1.00)
Del Peak 6(2q36 2) 0 (0%) 228 0.184
(1.00) 		0.719
(1.00) 		0.686
(1.00) 		0.572
(1.00) 		0.038
(1.00) 		0.582
(1.00) 		0.662
(1.00) 		0.387
(1.00) 		0.732
(1.00) 		0.0616
(1.00)
Del Peak 8(3p14 2) 0 (0%) 79 0.00052
(0.366) 		0.425
(1.00) 		0.0141
(1.00) 		0.449
(1.00) 		0.0044
(1.00) 		0.444
(1.00) 		0.668
(1.00) 		0.178
(1.00) 		0.0358
(1.00) 		0.0406
(1.00)
Del Peak 9(3p14 2) 0 (0%) 79 0.00048
(0.339) 		0.472
(1.00) 		0.0304
(1.00) 		0.65
(1.00) 		0.00267
(1.00) 		0.456
(1.00) 		1
(1.00) 		0.177
(1.00) 		0.0314
(1.00) 		0.0406
(1.00)
Del Peak 11(4p15 2) 0 (0%) 185 0.116
(1.00) 		0.0676
(1.00) 		0.32
(1.00) 		1
(1.00) 		0.201
(1.00) 		0.449
(1.00) 		0.674
(1.00) 		0.449
(1.00) 		0.0762
(1.00) 		0.836
(1.00)
Del Peak 12(4q22 1) 0 (0%) 221 0.616
(1.00) 		0.564
(1.00) 		0.793
(1.00) 		0.58
(1.00) 		0.397
(1.00) 		0.155
(1.00) 		0.352
(1.00) 		0.748
(1.00) 		0.16
(1.00) 		0.621
(1.00)
Del Peak 13(4q35 2) 0 (0%) 192 0.172
(1.00) 		0.868
(1.00) 		0.103
(1.00) 		0.692
(1.00) 		0.617
(1.00) 		0.0491
(1.00) 		0.204
(1.00) 		0.896
(1.00) 		0.119
(1.00) 		0.327
(1.00)
Del Peak 14(5q11 2) 0 (0%) 191 0.51
(1.00) 		0.494
(1.00) 		0.105
(1.00) 		0.51
(1.00) 		0.00343
(1.00) 		0.924
(1.00) 		1
(1.00) 		0.11
(1.00) 		0.123
(1.00) 		0.575
(1.00)
Del Peak 15(5q15) 0 (0%) 187 0.58
(1.00) 		0.475
(1.00) 		0.263
(1.00) 		0.511
(1.00) 		0.00146
(1.00) 		0.413
(1.00) 		1
(1.00) 		0.276
(1.00) 		0.358
(1.00) 		0.654
(1.00)
Del Peak 16(5q35 3) 0 (0%) 198 0.506
(1.00) 		0.617
(1.00) 		0.166
(1.00) 		0.895
(1.00) 		0.114
(1.00) 		0.988
(1.00) 		1
(1.00) 		0.0525
(1.00) 		0.652
(1.00) 		0.229
(1.00)
Del Peak 17(6p25 3) 0 (0%) 261 0.178
(1.00) 		0.175
(1.00) 		0.277
(1.00) 		0.625
(1.00) 		0.366
(1.00) 		0.0669
(1.00) 		0.581
(1.00) 		0.96
(1.00) 		0.602
(1.00) 		0.378
(1.00)
Del Peak 18(6q12) 0 (0%) 266 0.65
(1.00) 		0.783
(1.00) 		0.038
(1.00) 		0.74
(1.00) 		0.402
(1.00) 		0.604
(1.00) 		1
(1.00) 		0.272
(1.00) 		0.972
(1.00) 		0.938
(1.00)
Del Peak 19(7q31 1) 0 (0%) 276 0.784
(1.00) 		0.0127
(1.00) 		0.608
(1.00) 		0.276
(1.00) 		0.265
(1.00) 		0.00962
(1.00) 		0.581
(1.00) 		0.522
(1.00) 		0.807
(1.00) 		0.392
(1.00)
Del Peak 20(7q36 1) 0 (0%) 244 0.0155
(1.00) 		0.474
(1.00) 		0.201
(1.00) 		0.881
(1.00) 		0.458
(1.00) 		0.118
(1.00) 		1
(1.00) 		0.375
(1.00) 		0.195
(1.00) 		0.202
(1.00)
Del Peak 21(8p23 2) 0 (0%) 140 0.00824
(1.00) 		0.115
(1.00) 		0.456
(1.00) 		0.896
(1.00) 		0.0339
(1.00) 		0.943
(1.00) 		1
(1.00) 		0.328
(1.00) 		0.17
(1.00) 		0.746
(1.00)
Del Peak 22(9p23) 0 (0%) 171 0.734
(1.00) 		0.351
(1.00) 		0.622
(1.00) 		0.363
(1.00) 		0.136
(1.00) 		0.717
(1.00) 		0.417
(1.00) 		0.952
(1.00) 		0.369
(1.00) 		0.903
(1.00)
Del Peak 23(9p21 3) 0 (0%) 133 0.0235
(1.00) 		0.201
(1.00) 		0.452
(1.00) 		0.293
(1.00) 		0.295
(1.00) 		0.335
(1.00) 		0.206
(1.00) 		0.423
(1.00) 		0.38
(1.00) 		0.87
(1.00)
Del Peak 24(9q21 11) 0 (0%) 263 0.867
(1.00) 		0.604
(1.00) 		0.875
(1.00) 		0.51
(1.00) 		0.256
(1.00) 		0.333
(1.00) 		1
(1.00) 		0.347
(1.00) 		0.134
(1.00) 		0.542
(1.00)
Del Peak 25(9q34 3) 0 (0%) 272 0.576
(1.00) 		0.79
(1.00) 		0.182
(1.00) 		0.862
(1.00) 		0.34
(1.00) 		0.927
(1.00) 		0.571
(1.00) 		0.953
(1.00) 		0.165
(1.00) 		0.998
(1.00)
Del Peak 26(10p15 3) 0 (0%) 216 0.156
(1.00) 		0.537
(1.00) 		1
(1.00) 		0.13
(1.00) 		0.547
(1.00) 		0.559
(1.00) 		1
(1.00) 		0.094
(1.00) 		0.0777
(1.00) 		0.475
(1.00)
Del Peak 27(10p11 21) 0 (0%) 222 0.254
(1.00) 		0.475
(1.00) 		0.508
(1.00) 		0.0506
(1.00) 		0.322
(1.00) 		0.297
(1.00) 		0.662
(1.00) 		0.328
(1.00) 		0.913
(1.00) 		0.635
(1.00)
Del Peak 28(10q23 31) 0 (0%) 241 0.265
(1.00) 		0.479
(1.00) 		0.158
(1.00) 		0.458
(1.00) 		0.28
(1.00) 		0.0239
(1.00) 		0.662
(1.00) 		0.955
(1.00) 		0.173
(1.00) 		0.65
(1.00)
Del Peak 29(11p15 4) 0 (0%) 222 0.0595
(1.00) 		0.397
(1.00) 		0.353
(1.00) 		0.677
(1.00) 		0.277
(1.00) 		0.741
(1.00) 		0.611
(1.00) 		0.000815
(0.573) 		0.406
(1.00) 		0.136
(1.00)
Del Peak 30(11q14 2) 0 (0%) 206 0.196
(1.00) 		0.14
(1.00) 		0.0207
(1.00) 		0.105
(1.00) 		0.414
(1.00) 		0.0403
(1.00) 		1
(1.00) 		0.0439
(1.00) 		0.0833
(1.00) 		0.22
(1.00)
Del Peak 31(11q23 1) 0 (0%) 170 0.768
(1.00) 		0.181
(1.00) 		0.00635
(1.00) 		0.242
(1.00) 		0.266
(1.00) 		0.171
(1.00) 		1
(1.00) 		0.107
(1.00) 		0.0385
(1.00) 		0.737
(1.00)
Del Peak 32(12q24 33) 0 (0%) 286 0.568
(1.00) 		0.611
(1.00) 		0.85
(1.00) 		0.842
(1.00) 		0.565
(1.00) 		0.436
(1.00) 		0.571
(1.00) 		0.17
(1.00) 		0.919
(1.00) 		0.857
(1.00)
Del Peak 33(13q12 11) 0 (0%) 180 0.737
(1.00) 		0.992
(1.00) 		0.174
(1.00) 		1
(1.00) 		0.118
(1.00) 		0.81
(1.00) 		0.683
(1.00) 		0.269
(1.00) 		0.0741
(1.00) 		0.0514
(1.00)
Del Peak 34(13q14 2) 0 (0%) 188 0.0122
(1.00) 		0.644
(1.00) 		0.317
(1.00) 		0.432
(1.00) 		0.275
(1.00) 		0.351
(1.00) 		0.674
(1.00) 		0.58
(1.00) 		0.587
(1.00) 		0.393
(1.00)
Del Peak 35(14q11 2) 0 (0%) 278 0.262
(1.00) 		0.234
(1.00) 		0.488
(1.00) 		1
(1.00) 		0.0259
(1.00) 		0.279
(1.00) 		1
(1.00) 		0.423
(1.00) 		0.00921
(1.00) 		0.262
(1.00)
Del Peak 36(14q32 32) 0 (0%) 277 0.357
(1.00) 		0.427
(1.00) 		0.163
(1.00) 		0.364
(1.00) 		0.432
(1.00) 		0.427
(1.00) 		1
(1.00) 		0.193
(1.00) 		0.176
(1.00) 		0.524
(1.00)
Del Peak 37(15q15 1) 0 (0%) 252 0.67
(1.00) 		0.874
(1.00) 		0.375
(1.00) 		0.28
(1.00) 		0.759
(1.00) 		0.96
(1.00) 		1
(1.00) 		0.267
(1.00) 		0.168
(1.00) 		0.634
(1.00)
Del Peak 38(16q12 1) 0 (0%) 270 0.233
(1.00) 		0.521
(1.00) 		0.511
(1.00) 		0.493
(1.00) 		0.533
(1.00) 		0.383
(1.00) 		0.337
(1.00) 		0.0919
(1.00) 		0.935
(1.00) 		0.633
(1.00)
Del Peak 39(16q23 3) 0 (0%) 260 0.176
(1.00) 		0.236
(1.00) 		0.54
(1.00) 		1
(1.00) 		0.817
(1.00) 		0.114
(1.00) 		0.164
(1.00) 		0.0483
(1.00) 		0.751
(1.00) 		0.276
(1.00)
Del Peak 40(17q25 3) 0 (0%) 284 0.956
(1.00) 		0.92
(1.00) 		1
(1.00) 		0.241
(1.00) 		0.884
(1.00) 		0.72
(1.00) 		1
(1.00) 		0.00257
(1.00) 		0.975
(1.00) 		0.167
(1.00)
Del Peak 41(18q21 2) 0 (0%) 152 0.136
(1.00) 		0.452
(1.00) 		0.0131
(1.00) 		0.795
(1.00) 		0.000569
(0.401) 		0.298
(1.00) 		0.674
(1.00) 		0.444
(1.00) 		0.03
(1.00) 		0.841
(1.00)
Del Peak 42(18q23) 0 (0%) 139 0.111
(1.00) 		0.179
(1.00) 		0.0467
(1.00) 		0.793
(1.00) 		0.00242
(1.00) 		0.117
(1.00) 		0.222
(1.00) 		0.53
(1.00) 		0.0347
(1.00) 		0.935
(1.00)
Del Peak 43(19p13 3) 0 (0%) 216 0.0398
(1.00) 		0.318
(1.00) 		1
(1.00) 		0.492
(1.00) 		0.322
(1.00) 		0.207
(1.00) 		1
(1.00) 		0.703
(1.00) 		0.475
(1.00) 		0.727
(1.00)
Del Peak 44(19q13 43) 0 (0%) 260 0.156
(1.00) 		0.593
(1.00) 		0.877
(1.00) 		0.746
(1.00) 		0.795
(1.00) 		0.0361
(1.00) 		0.266
(1.00) 		0.978
(1.00) 		0.271
(1.00) 		0.331
(1.00)
Del Peak 45(Xp21 3) 0 (0%) 217 0.0556
(1.00) 		0.336
(1.00) 		0.794
(1.00) 		0.272
(1.00) 		0.0902
(1.00) 		0.564
(1.00) 		0.352
(1.00) 		0.186
(1.00) 		0.163
(1.00) 		0.487
(1.00)
Del Peak 46(Xp11 3) 0 (0%) 216 0.00219
(1.00) 		0.964
(1.00) 		0.433
(1.00) 		0.336
(1.00) 		0.0172
(1.00) 		0.433
(1.00) 		0.352
(1.00) 		0.386
(1.00) 		0.101
(1.00) 		0.584
(1.00)
Del Peak 47(Xq21 33) 0 (0%) 270 0.436
(1.00) 		0.45
(1.00) 		0.87
(1.00) 		0.493
(1.00) 		0.961
(1.00) 		0.573
(1.00) 		0.571
(1.00) 		0.572
(1.00) 		0.187
(1.00) 		0.272
(1.00)
'Amp Peak 22(18p11.31)' versus 'GENDER'

P value = 9.64e-05 (Fisher's exact test), Q value = 0.068

Table S1.  Gene #22: 'Amp Peak 22(18p11.31)' versus Clinical Feature #3: 'GENDER'

nPatients FEMALE MALE
ALL 91 234
AMP PEAK 22(18P11.31) CNV 14 88
AMP PEAK 22(18P11.31) WILD-TYPE 77 146

Figure S1.  Get High-res Image Gene #22: 'Amp Peak 22(18p11.31)' versus Clinical Feature #3: 'GENDER'

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

P value = 0.000228 (logrank test), Q value = 0.16

Table S2.  Gene #31: 'Del Peak 7(3p25.3)' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 321 121 0.1 - 210.9 (13.9)
DEL PEAK 7(3P25.3) CNV 226 100 0.1 - 210.9 (13.2)
DEL PEAK 7(3P25.3) WILD-TYPE 95 21 0.8 - 156.5 (19.8)

Figure S2.  Get High-res Image Gene #31: 'Del Peak 7(3p25.3)' versus Clinical Feature #1: 'Time to Death'

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

P value = 8.08e-05 (t-test), Q value = 0.057

Table S3.  Gene #34: 'Del Peak 10(3p12.2)' versus Clinical Feature #5: 'NUMBERPACKYEARSSMOKED'

nPatients Mean (Std.Dev)
ALL 181 50.2 (40.6)
DEL PEAK 10(3P12.2) CNV 136 55.5 (43.5)
DEL PEAK 10(3P12.2) WILD-TYPE 45 34.2 (24.7)

Figure S3.  Get High-res Image Gene #34: 'Del Peak 10(3p12.2)' versus Clinical Feature #5: '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 = 325

  • Number of significantly arm-level cnvs = 71

  • Number of selected clinical features = 11

  • 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

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

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] Greenwood and Nikulin, A guide to chi-squared testing, Wiley, New York. ISBN 047155779X (1996)
[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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