Correlation between gene mutation status and selected clinical features
Head and Neck Squamous Cell Carcinoma (Primary solid tumor)
02 April 2015  |  analyses__2015_04_02
Maintainer Information
Citation Information
doi:10.7908/C10V8BS5
Maintained by TCGA GDAC Team (Broad Institute/MD Anderson Cancer Center/Harvard Medical School)
Cite as Broad Institute TCGA Genome Data Analysis Center (2015): Correlation between gene mutation status and selected clinical features. Broad Institute of MIT and Harvard. doi:10.7908/C10V8BS5
Overview
Introduction

This pipeline computes the correlation between significantly recurrent gene mutations and selected clinical features.

Summary

Testing the association between mutation status of 64 genes and 13 clinical features across 506 patients, 8 significant findings detected with Q value < 0.25.

  • NSD1 mutation correlated to 'NUMBER_OF_LYMPH_NODES'.

  • CASP8 mutation correlated to 'YEARS_TO_BIRTH' and 'GENDER'.

  • FAT1 mutation correlated to 'YEARS_TO_BIRTH'.

  • RAC1 mutation correlated to 'YEARS_TO_BIRTH'.

  • NAP1L2 mutation correlated to 'ETHNICITY'.

  • CTCF mutation correlated to 'YEARS_TO_BIRTH'.

  • SLC9A6 mutation correlated to 'Time to Death'.

Results
Overview of the results

Table 1.  Get Full Table Overview of the association between mutation status of 64 genes and 13 clinical features. Shown in the table are P values (Q values). Thresholded by Q value < 0.25, 8 significant findings detected.

Clinical
Features 		Time
to
Death 		YEARS
TO
BIRTH 		NEOPLASM
DISEASESTAGE 		PATHOLOGY
T
STAGE 		PATHOLOGY
N
STAGE 		GENDER HISTOLOGICAL
TYPE 		RADIATIONS
RADIATION
REGIMENINDICATION 		NUMBER
PACK
YEARS
SMOKED 		YEAR
OF
TOBACCO
SMOKING
ONSET 		NUMBER
OF
LYMPH
NODES 		RACE ETHNICITY
nMutated (%) nWild-Type logrank test Wilcoxon-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 Wilcoxon-test Wilcoxon-test Wilcoxon-test Fisher's exact test Fisher's exact test
CASP8 54 (11%) 452 0.0264
(0.61) 		6.46e-09
(5.38e-06) 		0.889
(1.00) 		0.399
(1.00) 		0.0667
(0.73) 		0.000286
(0.0646) 		1
(1.00) 		0.173
(0.924) 		0.111
(0.888) 		0.0162
(0.465) 		0.0171
(0.473) 		0.724
(1.00) 		0.506
(1.00)
NSD1 63 (12%) 443 0.0308
(0.627) 		0.039
(0.627) 		0.115
(0.888) 		0.571
(1.00) 		0.038
(0.627) 		0.0696
(0.732) 		1
(1.00) 		0.145
(0.888) 		0.0977
(0.854) 		0.6
(1.00) 		0.000311
(0.0646) 		0.676
(1.00) 		0.217
(0.955)
FAT1 113 (22%) 393 0.665
(1.00) 		1.43e-06
(0.000597) 		0.787
(1.00) 		0.0406
(0.627) 		0.328
(1.00) 		0.0118
(0.392) 		1
(1.00) 		1
(1.00) 		0.144
(0.888) 		0.0216
(0.528) 		0.35
(1.00) 		0.598
(1.00) 		0.455
(1.00)
RAC1 15 (3%) 491 0.475
(1.00) 		0.00119
(0.165) 		0.221
(0.968) 		0.188
(0.937) 		0.404
(1.00) 		0.0074
(0.342) 		1
(1.00) 		1
(1.00) 		0.738
(1.00) 		0.00521
(0.31) 		0.19
(0.937) 		0.307
(1.00) 		1
(1.00)
NAP1L2 7 (1%) 499 0.698
(1.00) 		0.909
(1.00) 		0.258
(0.999) 		0.668
(1.00) 		0.148
(0.888) 		1
(1.00) 		0.105
(0.883) 		1
(1.00) 		0.581
(1.00) 		0.863
(1.00) 		0.461
(1.00) 		0.47
(1.00) 		0.0024
(0.25)
CTCF 16 (3%) 490 0.0704
(0.732) 		0.00103
(0.165) 		0.141
(0.888) 		1
(1.00) 		0.45
(1.00) 		0.049
(0.668) 		1
(1.00) 		0.313
(1.00) 		0.709
(1.00) 		0.0438
(0.627) 		0.32
(1.00) 		0.429
(1.00) 		1
(1.00)
SLC9A6 5 (1%) 501 0.00166
(0.198) 		0.796
(1.00) 		0.322
(1.00) 		0.464
(1.00) 		0.129
(0.888) 		0.13
(0.888) 		1
(1.00) 		0.593
(1.00) 		0.861
(1.00) 		0.142
(0.888) 		1
(1.00) 		1
(1.00)
TP53 356 (70%) 150 0.00493
(0.31) 		0.264
(0.999) 		0.52
(1.00) 		0.0275
(0.619) 		0.659
(1.00) 		0.828
(1.00) 		0.00331
(0.296) 		0.361
(1.00) 		0.0834
(0.797) 		0.861
(1.00) 		0.643
(1.00) 		0.61
(1.00) 		0.123
(0.888)
CDKN2A 110 (22%) 396 0.718
(1.00) 		0.143
(0.888) 		0.317
(1.00) 		0.692
(1.00) 		0.664
(1.00) 		0.904
(1.00) 		0.497
(1.00) 		0.149
(0.888) 		0.392
(1.00) 		0.487
(1.00) 		0.43
(1.00) 		0.573
(1.00) 		0.469
(1.00)
PIK3CA 94 (19%) 412 0.548
(1.00) 		0.691
(1.00) 		0.459
(1.00) 		0.306
(1.00) 		0.197
(0.941) 		0.0408
(0.627) 		0.478
(1.00) 		0.644
(1.00) 		0.839
(1.00) 		0.67
(1.00) 		0.346
(1.00) 		0.0326
(0.627) 		1
(1.00)
HRAS 28 (6%) 478 0.546
(1.00) 		0.385
(1.00) 		0.45
(1.00) 		0.939
(1.00) 		0.133
(0.888) 		0.0795
(0.778) 		1
(1.00) 		0.0656
(0.727) 		0.971
(1.00) 		0.623
(1.00) 		0.119
(0.888) 		0.564
(1.00) 		0.387
(1.00)
TGFBR2 23 (5%) 483 0.704
(1.00) 		0.059
(0.707) 		0.861
(1.00) 		0.718
(1.00) 		0.549
(1.00) 		1
(1.00) 		1
(1.00) 		0.0211
(0.528) 		0.344
(1.00) 		0.0948
(0.839) 		0.407
(1.00) 		0.589
(1.00) 		1
(1.00)
NOTCH1 86 (17%) 420 0.298
(1.00) 		0.008
(0.343) 		0.947
(1.00) 		0.426
(1.00) 		0.487
(1.00) 		0.0629
(0.707) 		0.675
(1.00) 		0.873
(1.00) 		0.122
(0.888) 		0.215
(0.955) 		0.198
(0.941) 		0.927
(1.00) 		0.177
(0.924)
EPHA2 23 (5%) 483 0.254
(0.999) 		0.126
(0.888) 		0.827
(1.00) 		0.669
(1.00) 		0.168
(0.924) 		0.474
(1.00) 		1
(1.00) 		1
(1.00) 		0.0559
(0.707) 		0.152
(0.888) 		0.94
(1.00) 		0.399
(1.00) 		1
(1.00)
HLA-B 24 (5%) 482 0.778
(1.00) 		0.197
(0.941) 		0.736
(1.00) 		0.363
(1.00) 		0.0385
(0.627) 		0.157
(0.888) 		0.325
(1.00) 		0.021
(0.528) 		0.245
(0.999) 		0.152
(0.888) 		0.304
(1.00) 		0.517
(1.00) 		0.614
(1.00)
NFE2L2 26 (5%) 480 0.126
(0.888) 		0.00391
(0.296) 		0.789
(1.00) 		0.813
(1.00) 		0.594
(1.00) 		0.112
(0.888) 		1
(1.00) 		0.285
(1.00) 		0.674
(1.00) 		0.216
(0.955) 		0.343
(1.00) 		0.308
(1.00) 		0.329
(1.00)
ZNF750 19 (4%) 487 0.939
(1.00) 		0.372
(1.00) 		0.301
(1.00) 		0.723
(1.00) 		0.557
(1.00) 		0.304
(1.00) 		1
(1.00) 		0.752
(1.00) 		0.47
(1.00) 		0.529
(1.00) 		0.0718
(0.737) 		0.407
(1.00) 		0.614
(1.00)
PTEN 14 (3%) 492 0.184
(0.937) 		0.318
(1.00) 		0.936
(1.00) 		0.301
(1.00) 		0.494
(1.00) 		1
(1.00) 		1
(1.00) 		0.484
(1.00) 		0.419
(1.00) 		0.167
(0.924) 		0.516
(1.00) 		0.736
(1.00) 		1
(1.00)
HLA-A 22 (4%) 484 0.967
(1.00) 		0.0901
(0.821) 		0.901
(1.00) 		0.0894
(0.821) 		0.309
(1.00) 		1
(1.00) 		1
(1.00) 		0.77
(1.00) 		0.209
(0.947) 		0.0144
(0.444) 		0.742
(1.00) 		0.813
(1.00) 		0.614
(1.00)
RB1 17 (3%) 489 0.144
(0.888) 		0.56
(1.00) 		0.147
(0.888) 		0.247
(0.999) 		0.736
(1.00) 		0.00952
(0.345) 		1
(1.00) 		1
(1.00) 		0.661
(1.00) 		0.315
(1.00) 		0.33
(1.00) 		0.358
(1.00) 		1
(1.00)
MAPK1 9 (2%) 497 0.261
(0.999) 		0.95
(1.00) 		0.868
(1.00) 		0.429
(1.00) 		0.652
(1.00) 		0.711
(1.00) 		1
(1.00) 		0.367
(1.00) 		0.427
(1.00) 		0.886
(1.00) 		0.235
(0.987) 		1
(1.00)
KDM6A 17 (3%) 489 0.399
(1.00) 		0.0546
(0.707) 		0.418
(1.00) 		0.256
(0.999) 		0.848
(1.00) 		1
(1.00) 		1
(1.00) 		0.33
(1.00) 		0.151
(0.888) 		0.203
(0.947) 		0.909
(1.00) 		0.285
(1.00) 		1
(1.00)
EP300 39 (8%) 467 0.377
(1.00) 		0.731
(1.00) 		0.909
(1.00) 		0.723
(1.00) 		0.513
(1.00) 		0.455
(1.00) 		1
(1.00) 		0.656
(1.00) 		0.258
(0.999) 		0.692
(1.00) 		0.823
(1.00) 		0.741
(1.00) 		0.435
(1.00)
RASA1 17 (3%) 489 0.991
(1.00) 		0.781
(1.00) 		0.671
(1.00) 		0.436
(1.00) 		0.957
(1.00) 		0.423
(1.00) 		1
(1.00) 		0.0442
(0.627) 		0.407
(1.00) 		0.944
(1.00) 		0.757
(1.00) 		1
(1.00) 		0.227
(0.973)
CREBBP 35 (7%) 471 0.247
(0.999) 		0.0338
(0.627) 		0.689
(1.00) 		0.73
(1.00) 		0.886
(1.00) 		0.562
(1.00) 		0.438
(1.00) 		0.242
(0.998) 		0.712
(1.00) 		0.0483
(0.668) 		0.642
(1.00) 		0.161
(0.907) 		1
(1.00)
KEAP1 22 (4%) 484 0.994
(1.00) 		0.0986
(0.854) 		0.11
(0.888) 		0.00884
(0.343) 		0.384
(1.00) 		0.15
(0.888) 		0.043
(0.627) 		0.0699
(0.732) 		0.0937
(0.838) 		0.365
(1.00) 		0.827
(1.00) 		0.48
(1.00) 		0.614
(1.00)
RHOA 10 (2%) 496 0.318
(1.00) 		0.396
(1.00) 		1
(1.00) 		0.416
(1.00) 		0.0327
(0.627) 		0.473
(1.00) 		0.148
(0.888) 		0.38
(1.00) 		0.707
(1.00) 		0.633
(1.00) 		0.32
(1.00) 		1
(1.00) 		1
(1.00)
FBXW7 33 (7%) 473 0.344
(1.00) 		0.0066
(0.331) 		0.702
(1.00) 		0.404
(1.00) 		0.36
(1.00) 		0.156
(0.888) 		1
(1.00) 		0.631
(1.00) 		0.315
(1.00) 		0.857
(1.00) 		0.187
(0.937) 		0.882
(1.00) 		0.661
(1.00)
TIGD4 7 (1%) 499 0.312
(1.00) 		0.177
(0.924) 		0.268
(0.999) 		0.779
(1.00) 		0.19
(0.937) 		0.68
(1.00) 		1
(1.00) 		0.606
(1.00) 		0.506
(1.00) 		0.454
(1.00) 		0.178
(0.924) 		0.527
(1.00) 		1
(1.00)
KRT5 11 (2%) 495 0.618
(1.00) 		0.262
(0.999) 		0.0539
(0.707) 		0.241
(0.998) 		0.738
(1.00) 		0.504
(1.00) 		1
(1.00) 		0.699
(1.00) 		0.0115
(0.392) 		0.0083
(0.343) 		0.532
(1.00) 		0.261
(0.999) 		1
(1.00)
SMAD4 14 (3%) 492 0.485
(1.00) 		0.42
(1.00) 		0.684
(1.00) 		1
(1.00) 		0.683
(1.00) 		0.767
(1.00) 		1
(1.00) 		0.711
(1.00) 		0.423
(1.00) 		0.192
(0.939) 		0.884
(1.00) 		1
(1.00) 		1
(1.00)
ASXL1 16 (3%) 490 0.239
(0.998) 		0.842
(1.00) 		0.513
(1.00) 		0.171
(0.924) 		0.138
(0.888) 		0.777
(1.00) 		1
(1.00) 		1
(1.00) 		0.936
(1.00) 		0.717
(1.00) 		0.814
(1.00) 		0.577
(1.00) 		1
(1.00)
CES2 11 (2%) 495 0.991
(1.00) 		0.843
(1.00) 		0.617
(1.00) 		0.533
(1.00) 		1
(1.00) 		0.504
(1.00) 		1
(1.00) 		1
(1.00) 		0.579
(1.00) 		0.63
(1.00) 		0.82
(1.00) 		0.0605
(0.707) 		1
(1.00)
IRS4 17 (3%) 489 0.938
(1.00) 		0.931
(1.00) 		0.71
(1.00) 		0.761
(1.00) 		0.421
(1.00) 		0.266
(0.999) 		1
(1.00) 		1
(1.00) 		0.836
(1.00) 		0.986
(1.00) 		0.153
(0.888) 		0.546
(1.00) 		0.187
(0.937)
ARID2 20 (4%) 486 0.25
(0.999) 		0.869
(1.00) 		0.868
(1.00) 		0.478
(1.00) 		0.771
(1.00) 		0.448
(1.00) 		1
(1.00) 		0.223
(0.968) 		0.209
(0.947) 		0.326
(1.00) 		0.208
(0.947) 		0.224
(0.968) 		0.268
(0.999)
CBWD1 5 (1%) 501 0.00907
(0.343) 		0.201
(0.947) 		1
(1.00) 		0.918
(1.00) 		0.688
(1.00) 		0.329
(1.00) 		1
(1.00) 		0.593
(1.00) 		0.312
(1.00) 		1
(1.00) 		1
(1.00)
RGL4 7 (1%) 499 0.123
(0.888) 		0.554
(1.00) 		0.00677
(0.331) 		0.0194
(0.521) 		0.331
(1.00) 		0.4
(1.00) 		1
(1.00) 		0.606
(1.00) 		0.325
(1.00) 		0.389
(1.00) 		0.0358
(0.627) 		0.523
(1.00) 		1
(1.00)
HUWE1 45 (9%) 461 0.206
(0.947) 		0.346
(1.00) 		0.913
(1.00) 		0.559
(1.00) 		0.441
(1.00) 		0.0237
(0.563) 		1
(1.00) 		0.402
(1.00) 		0.374
(1.00) 		0.463
(1.00) 		0.568
(1.00) 		0.0765
(0.767) 		0.271
(1.00)
HNRNPL 11 (2%) 495 0.592
(1.00) 		0.0392
(0.627) 		0.278
(1.00) 		0.427
(1.00) 		0.102
(0.875) 		0.184
(0.937) 		1
(1.00) 		0.699
(1.00) 		0.545
(1.00) 		0.657
(1.00) 		0.217
(0.955) 		1
(1.00) 		1
(1.00)
ITGB1 14 (3%) 492 0.575
(1.00) 		0.12
(0.888) 		0.134
(0.888) 		0.144
(0.888) 		0.383
(1.00) 		1
(1.00) 		1
(1.00) 		0.484
(1.00) 		0.7
(1.00) 		0.973
(1.00) 		0.562
(1.00) 		1
(1.00) 		0.54
(1.00)
B2M 7 (1%) 499 0.605
(1.00) 		0.934
(1.00) 		0.744
(1.00) 		1
(1.00) 		0.436
(1.00) 		1
(1.00) 		1
(1.00) 		0.606
(1.00) 		0.087
(0.821) 		0.729
(1.00) 		0.0338
(0.627) 		1
(1.00) 		1
(1.00)
LRRC37B 16 (3%) 490 0.471
(1.00) 		0.913
(1.00) 		0.969
(1.00) 		0.881
(1.00) 		0.699
(1.00) 		0.395
(1.00) 		0.231
(0.981) 		1
(1.00) 		0.306
(1.00) 		0.587
(1.00) 		0.933
(1.00) 		1
(1.00) 		1
(1.00)
PPFIA4 14 (3%) 492 0.397
(1.00) 		0.859
(1.00) 		0.472
(1.00) 		0.519
(1.00) 		0.0406
(0.627) 		0.225
(0.968) 		1
(1.00) 		0.711
(1.00) 		0.428
(1.00) 		0.696
(1.00) 		0.0043
(0.298) 		1
(1.00) 		1
(1.00)
PIK3R1 9 (2%) 497 0.0445
(0.627) 		0.8
(1.00) 		0.521
(1.00) 		0.801
(1.00) 		0.157
(0.888) 		0.455
(1.00) 		1
(1.00) 		1
(1.00) 		0.775
(1.00) 		0.888
(1.00) 		0.178
(0.924) 		1
(1.00) 		1
(1.00)
VPS33B 7 (1%) 499 0.914
(1.00) 		0.117
(0.888) 		0.173
(0.924) 		0.881
(1.00) 		0.0808
(0.781) 		0.4
(1.00) 		0.104
(0.88) 		1
(1.00) 		0.651
(1.00) 		0.421
(1.00) 		0.688
(1.00) 		0.523
(1.00) 		1
(1.00)
C8ORF31 4 (1%) 502 0.651
(1.00) 		0.195
(0.941) 		0.871
(1.00) 		0.597
(1.00) 		1
(1.00) 		1
(1.00) 		0.513
(1.00) 		0.946
(1.00) 		0.637
(1.00) 		1
(1.00) 		1
(1.00)
NCOR1 18 (4%) 488 0.975
(1.00) 		0.276
(1.00) 		0.752
(1.00) 		0.531
(1.00) 		0.737
(1.00) 		0.594
(1.00) 		1
(1.00) 		0.332
(1.00) 		0.702
(1.00) 		0.426
(1.00) 		0.362
(1.00) 		0.78
(1.00) 		0.247
(0.999)
SEH1L 4 (1%) 502 0.92
(1.00) 		0.587
(1.00) 		0.744
(1.00) 		1
(1.00) 		0.19
(0.937) 		1
(1.00) 		1
(1.00) 		1
(1.00) 		0.0358
(0.627) 		0.13
(0.888) 		1
(1.00)
CUL3 14 (3%) 492 0.457
(1.00) 		0.262
(0.999) 		0.169
(0.924) 		0.0422
(0.627) 		0.618
(1.00) 		0.369
(1.00) 		1
(1.00) 		0.0624
(0.707) 		0.713
(1.00) 		0.171
(0.924) 		0.212
(0.952) 		0.18
(0.93) 		1
(1.00)
NOTCH2 19 (4%) 487 0.946
(1.00) 		0.109
(0.888) 		0.259
(0.999) 		0.751
(1.00) 		0.565
(1.00) 		0.00632
(0.331) 		1
(1.00) 		0.532
(1.00) 		0.303
(1.00) 		0.15
(0.888) 		0.425
(1.00) 		1
(1.00) 		0.614
(1.00)
YTHDF1 6 (1%) 500 0.031
(0.627) 		0.475
(1.00) 		0.904
(1.00) 		0.348
(1.00) 		0.88
(1.00) 		0.668
(1.00) 		0.0908
(0.821) 		0.256
(0.999) 		0.338
(1.00) 		0.689
(1.00) 		0.704
(1.00) 		1
(1.00) 		1
(1.00)
FOSL2 10 (2%) 496 0.00384
(0.296) 		0.878
(1.00) 		0.729
(1.00) 		0.959
(1.00) 		0.881
(1.00) 		0.147
(0.888) 		1
(1.00) 		0.672
(1.00) 		0.646
(1.00) 		0.969
(1.00) 		0.0619
(0.707) 		1
(1.00) 		1
(1.00)
MYH9 22 (4%) 484 0.612
(1.00) 		0.607
(1.00) 		0.86
(1.00) 		0.964
(1.00) 		0.759
(1.00) 		0.464
(1.00) 		0.301
(1.00) 		1
(1.00) 		0.438
(1.00) 		0.369
(1.00) 		0.61
(1.00) 		0.529
(1.00) 		0.268
(0.999)
TP63 12 (2%) 494 0.137
(0.888) 		0.797
(1.00) 		0.33
(1.00) 		0.576
(1.00) 		0.526
(1.00) 		0.744
(1.00) 		1
(1.00) 		0.117
(0.888) 		0.606
(1.00) 		0.652
(1.00) 		0.198
(0.941) 		1
(1.00) 		1
(1.00)
DYSF 21 (4%) 485 0.771
(1.00) 		0.0548
(0.707) 		0.973
(1.00) 		0.692
(1.00) 		0.115
(0.888) 		1
(1.00) 		1
(1.00) 		0.763
(1.00) 		0.0571
(0.707) 		0.114
(0.888) 		0.0783
(0.775) 		1
(1.00) 		0.616
(1.00)
TMEM2 17 (3%) 489 0.792
(1.00) 		0.854
(1.00) 		0.07
(0.732) 		0.2
(0.944) 		0.278
(1.00) 		0.789
(1.00) 		1
(1.00) 		0.0442
(0.627) 		0.978
(1.00) 		0.909
(1.00) 		0.509
(1.00) 		1
(1.00) 		0.54
(1.00)
PTPN14 14 (3%) 492 0.123
(0.888) 		0.976
(1.00) 		0.367
(1.00) 		0.566
(1.00) 		0.26
(0.999) 		1
(1.00) 		1
(1.00) 		0.0624
(0.707) 		0.404
(1.00) 		0.514
(1.00) 		0.408
(1.00) 		0.0739
(0.75) 		0.54
(1.00)
RBM10 4 (1%) 502 0.415
(1.00) 		0.837
(1.00) 		1
(1.00) 		0.535
(1.00) 		0.69
(1.00) 		1
(1.00) 		1
(1.00) 		0.128
(0.888) 		0.525
(1.00) 		1
(1.00) 		0.0153
(0.454)
IRF2 7 (1%) 499 0.298
(1.00) 		0.605
(1.00) 		0.781
(1.00) 		0.465
(1.00) 		0.673
(1.00) 		1
(1.00) 		1
(1.00) 		1
(1.00) 		0.155
(0.888) 		0.0587
(0.707) 		0.831
(1.00) 		1
(1.00) 		1
(1.00)
AMPD1 6 (1%) 500 0.367
(1.00) 		0.998
(1.00) 		0.797
(1.00) 		0.919
(1.00) 		1
(1.00) 		0.668
(1.00) 		1
(1.00) 		1
(1.00) 		0.231
(0.981) 		0.177
(0.924) 		0.91
(1.00) 		1
(1.00) 		1
(1.00)
ZMYM1 9 (2%) 497 0.0624
(0.707) 		0.782
(1.00) 		0.664
(1.00) 		0.782
(1.00) 		0.529
(1.00) 		0.711
(1.00) 		1
(1.00) 		0.646
(1.00) 		0.206
(0.947) 		0.891
(1.00) 		0.442
(1.00) 		1
(1.00) 		1
(1.00)
LCP1 15 (3%) 491 0.737
(1.00) 		0.659
(1.00) 		0.275
(1.00) 		0.0899
(0.821) 		1
(1.00) 		1
(1.00) 		1
(1.00) 		0.285
(1.00) 		0.667
(1.00) 		0.393
(1.00) 		0.628
(1.00) 		0.727
(1.00) 		0.565
(1.00)
CCNG2 3 (1%) 503 0.668
(1.00) 		0.235
(0.987) 		0.48
(1.00) 		1
(1.00) 		0.416
(1.00) 		1
(1.00) 		1
(1.00) 		1
(1.00) 		0.139
(0.888) 		0.0405
(0.627) 		0.0134
(0.428) 		1
(1.00)
TACR2 4 (1%) 502 0.209
(0.947) 		0.671
(1.00) 		0.745
(1.00) 		1
(1.00) 		0.419
(1.00) 		0.579
(1.00) 		1
(1.00) 		0.513
(1.00) 		0.994
(1.00) 		0.242
(0.998) 		1
(1.00) 		1
(1.00)
'NSD1 MUTATION STATUS' versus 'NUMBER_OF_LYMPH_NODES'

P value = 0.000311 (Wilcoxon-test), Q value = 0.065

Table S1.  Gene #4: 'NSD1 MUTATION STATUS' versus Clinical Feature #11: 'NUMBER_OF_LYMPH_NODES'

nPatients Mean (Std.Dev)
ALL 396 2.2 (4.3)
NSD1 MUTATED 47 0.8 (1.5)
NSD1 WILD-TYPE 349 2.4 (4.6)

Figure S1.  Get High-res Image Gene #4: 'NSD1 MUTATION STATUS' versus Clinical Feature #11: 'NUMBER_OF_LYMPH_NODES'

'CASP8 MUTATION STATUS' versus 'YEARS_TO_BIRTH'

P value = 6.46e-09 (Wilcoxon-test), Q value = 5.4e-06

Table S2.  Gene #5: 'CASP8 MUTATION STATUS' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 506 61.0 (12.0)
CASP8 MUTATED 54 70.2 (13.4)
CASP8 WILD-TYPE 452 59.9 (11.4)

Figure S2.  Get High-res Image Gene #5: 'CASP8 MUTATION STATUS' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'CASP8 MUTATION STATUS' versus 'GENDER'

P value = 0.000286 (Fisher's exact test), Q value = 0.065

Table S3.  Gene #5: 'CASP8 MUTATION STATUS' versus Clinical Feature #6: 'GENDER'

nPatients FEMALE MALE
ALL 139 367
CASP8 MUTATED 27 27
CASP8 WILD-TYPE 112 340

Figure S3.  Get High-res Image Gene #5: 'CASP8 MUTATION STATUS' versus Clinical Feature #6: 'GENDER'

'FAT1 MUTATION STATUS' versus 'YEARS_TO_BIRTH'

P value = 1.43e-06 (Wilcoxon-test), Q value = 6e-04

Table S4.  Gene #8: 'FAT1 MUTATION STATUS' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 506 61.0 (12.0)
FAT1 MUTATED 113 66.0 (11.4)
FAT1 WILD-TYPE 393 59.6 (11.8)

Figure S4.  Get High-res Image Gene #8: 'FAT1 MUTATION STATUS' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'RAC1 MUTATION STATUS' versus 'YEARS_TO_BIRTH'

P value = 0.00119 (Wilcoxon-test), Q value = 0.16

Table S5.  Gene #12: 'RAC1 MUTATION STATUS' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 506 61.0 (12.0)
RAC1 MUTATED 15 70.8 (12.6)
RAC1 WILD-TYPE 491 60.7 (11.9)

Figure S5.  Get High-res Image Gene #12: 'RAC1 MUTATION STATUS' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'NAP1L2 MUTATION STATUS' versus 'ETHNICITY'

P value = 0.0024 (Fisher's exact test), Q value = 0.25

Table S6.  Gene #22: 'NAP1L2 MUTATION STATUS' versus Clinical Feature #13: 'ETHNICITY'

nPatients HISPANIC OR LATINO NOT HISPANIC OR LATINO
ALL 25 445
NAP1L2 MUTATED 3 3
NAP1L2 WILD-TYPE 22 442

Figure S6.  Get High-res Image Gene #22: 'NAP1L2 MUTATION STATUS' versus Clinical Feature #13: 'ETHNICITY'

'CTCF MUTATION STATUS' versus 'YEARS_TO_BIRTH'

P value = 0.00103 (Wilcoxon-test), Q value = 0.16

Table S7.  Gene #24: 'CTCF MUTATION STATUS' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 506 61.0 (12.0)
CTCF MUTATED 16 71.2 (11.1)
CTCF WILD-TYPE 490 60.7 (11.9)

Figure S7.  Get High-res Image Gene #24: 'CTCF MUTATION STATUS' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'SLC9A6 MUTATION STATUS' versus 'Time to Death'

P value = 0.00166 (logrank test), Q value = 0.2

Table S8.  Gene #62: 'SLC9A6 MUTATION STATUS' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 504 201 0.1 - 211.0 (18.7)
SLC9A6 MUTATED 5 4 6.1 - 16.0 (13.1)
SLC9A6 WILD-TYPE 499 197 0.1 - 211.0 (18.8)

Figure S8.  Get High-res Image Gene #62: 'SLC9A6 MUTATION STATUS' versus Clinical Feature #1: 'Time to Death'

Methods & Data
Input

  • Mutation data file = sample_sig_gene_table.txt from Mutsig_2CV pipeline

  • Processed Mutation data file = /xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_Correlate_Genomic_Events_Preprocess/HNSC-TP/15648706/transformed.cor.cli.txt

  • Clinical data file = /xchip/cga/gdac-prod/tcga-gdac/jobResults/Append_Data/HNSC-TP/15078978/HNSC-TP.merged_data.txt

  • Number of patients = 506

  • Number of significantly mutated genes = 64

  • Number of selected clinical features = 13

  • 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

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] 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)
[3] 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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