Correlation between gene mutation status and selected clinical features
Head and Neck Squamous Cell Carcinoma (Primary solid tumor)
28 January 2016  |  analyses__2016_01_28
Maintainer Information
Citation Information
doi:10.7908/C16H4GSQ
Maintained by TCGA GDAC Team (Broad Institute/MD Anderson Cancer Center/Harvard Medical School)
Cite as Broad Institute TCGA Genome Data Analysis Center (2016): Correlation between gene mutation status and selected clinical features. Broad Institute of MIT and Harvard. doi:10.7908/C16H4GSQ
Overview
Introduction

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

Summary

Testing the association between mutation status of 62 genes and 14 clinical features across 511 patients, 17 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' and 'GENDER'.

  • JUB mutation correlated to 'YEARS_TO_BIRTH' and 'YEAR_OF_TOBACCO_SMOKING_ONSET'.

  • NFE2L2 mutation correlated to 'YEARS_TO_BIRTH'.

  • RAC1 mutation correlated to 'YEARS_TO_BIRTH' and 'YEAR_OF_TOBACCO_SMOKING_ONSET'.

  • RB1 mutation correlated to 'GENDER'.

  • NAP1L2 mutation correlated to 'ETHNICITY'.

  • MLL4 mutation correlated to 'YEARS_TO_BIRTH'.

  • THSD7A mutation correlated to 'NUMBER_PACK_YEARS_SMOKED'.

  • CTCF mutation correlated to 'YEARS_TO_BIRTH'.

  • NOTCH2 mutation correlated to 'GENDER'.

  • AK5 mutation correlated to 'Time to Death'.

Results
Overview of the results

Table 1.  Get Full Table Overview of the association between mutation status of 62 genes and 14 clinical features. Shown in the table are P values (Q values). Thresholded by Q value < 0.25, 17 significant findings detected.

Clinical
Features 		Time
to
Death 		YEARS
TO
BIRTH 		PATHOLOGIC
STAGE 		PATHOLOGY
T
STAGE 		PATHOLOGY
N
STAGE 		PATHOLOGY
M
STAGE 		GENDER RADIATION
THERAPY 		HISTOLOGICAL
TYPE 		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 Fisher's exact test Wilcoxon-test Wilcoxon-test Wilcoxon-test Fisher's exact test Fisher's exact test
CASP8 54 (11%) 457 0.0632
(0.773) 		7.62e-09
(6.61e-06) 		0.725
(1.00) 		0.463
(1.00) 		0.0824
(0.836) 		1
(1.00) 		0.000523
(0.113) 		0.0854
(0.842) 		0.65
(1.00) 		0.0629
(0.773) 		0.0199
(0.479) 		0.0232
(0.503) 		0.435
(1.00) 		0.34
(1.00)
FAT1 112 (22%) 399 0.389
(1.00) 		2.31e-07
(1e-04) 		0.354
(1.00) 		0.0228
(0.503) 		0.207
(0.933) 		0.229
(0.933) 		0.00365
(0.227) 		0.719
(1.00) 		0.766
(1.00) 		0.0799
(0.83) 		0.00871
(0.293) 		0.36
(1.00) 		0.587
(1.00) 		0.45
(1.00)
JUB 34 (7%) 477 0.0245
(0.518) 		0.00254
(0.184) 		0.651
(1.00) 		0.606
(1.00) 		0.224
(0.933) 		1
(1.00) 		0.695
(1.00) 		0.847
(1.00) 		1
(1.00) 		0.214
(0.933) 		0.0029
(0.194) 		0.47
(1.00) 		0.275
(0.983) 		0.674
(1.00)
RAC1 15 (3%) 496 0.485
(1.00) 		0.00117
(0.113) 		0.216
(0.933) 		0.18
(0.907) 		0.359
(1.00) 		1
(1.00) 		0.00653
(0.287) 		1
(1.00) 		1
(1.00) 		0.708
(1.00) 		0.00434
(0.235) 		0.179
(0.907) 		0.208
(0.933) 		1
(1.00)
NSD1 62 (12%) 449 0.0379
(0.6) 		0.0912
(0.851) 		0.162
(0.907) 		0.404
(1.00) 		0.0335
(0.6) 		0.141
(0.907) 		0.171
(0.907) 		1
(1.00) 		0.427
(1.00) 		0.115
(0.87) 		0.401
(1.00) 		0.000124
(0.0358) 		0.765
(1.00) 		0.206
(0.933)
NFE2L2 27 (5%) 484 0.283
(0.986) 		0.00183
(0.158) 		0.726
(1.00) 		0.73
(1.00) 		0.667
(1.00) 		1
(1.00) 		0.118
(0.87) 		0.09
(0.851) 		1
(1.00) 		0.497
(1.00) 		0.377
(1.00) 		0.51
(1.00) 		0.417
(1.00) 		0.346
(1.00)
RB1 17 (3%) 494 0.072
(0.791) 		0.353
(1.00) 		0.154
(0.907) 		0.226
(0.933) 		0.58
(1.00) 		1
(1.00) 		0.00104
(0.113) 		0.796
(1.00) 		1
(1.00) 		0.686
(1.00) 		0.281
(0.985) 		0.201
(0.933) 		0.245
(0.961) 		0.586
(1.00)
NAP1L2 7 (1%) 504 0.932
(1.00) 		0.259
(0.961) 		0.78
(1.00) 		1
(1.00) 		0.773
(1.00) 		1
(1.00) 		0.394
(1.00) 		1
(1.00) 		0.142
(0.907) 		0.249
(0.961) 		0.423
(1.00) 		0.887
(1.00) 		1
(1.00) 		0.00234
(0.184)
MLL4 19 (4%) 492 0.312
(1.00) 		0.000866
(0.113) 		0.194
(0.926) 		0.923
(1.00) 		0.0864
(0.843) 		1
(1.00) 		0.184
(0.907) 		0.451
(1.00) 		1
(1.00) 		0.642
(1.00) 		0.0502
(0.722) 		0.144
(0.907) 		0.441
(1.00) 		0.614
(1.00)
THSD7A 32 (6%) 479 0.676
(1.00) 		0.704
(1.00) 		0.951
(1.00) 		0.215
(0.933) 		0.902
(1.00) 		1
(1.00) 		0.41
(1.00) 		0.31
(1.00) 		0.511
(1.00) 		0.00466
(0.238) 		0.521
(1.00) 		0.069
(0.791) 		0.55
(1.00) 		0.674
(1.00)
CTCF 15 (3%) 496 0.0355
(0.6) 		0.00107
(0.113) 		0.161
(0.907) 		1
(1.00) 		0.412
(1.00) 		1
(1.00) 		0.0338
(0.6) 		0.774
(1.00) 		1
(1.00) 		0.981
(1.00) 		0.038
(0.6) 		0.326
(1.00) 		0.343
(1.00) 		1
(1.00)
NOTCH2 21 (4%) 490 0.545
(1.00) 		0.147
(0.907) 		0.333
(1.00) 		0.78
(1.00) 		0.692
(1.00) 		1
(1.00) 		0.00398
(0.23) 		0.609
(1.00) 		1
(1.00) 		0.129
(0.876) 		0.158
(0.907) 		0.514
(1.00) 		0.831
(1.00) 		0.618
(1.00)
AK5 13 (3%) 498 0.000923
(0.113) 		0.326
(1.00) 		0.768
(1.00) 		0.383
(1.00) 		0.657
(1.00) 		1
(1.00) 		0.351
(1.00) 		1
(1.00) 		1
(1.00) 		0.816
(1.00) 		0.543
(1.00) 		0.456
(1.00) 		0.5
(1.00) 		0.0927
(0.851)
TP53 364 (71%) 147 0.00696
(0.287) 		0.53
(1.00) 		0.502
(1.00) 		0.0187
(0.476) 		0.627
(1.00) 		1
(1.00) 		0.913
(1.00) 		0.328
(1.00) 		0.00728
(0.287) 		0.114
(0.87) 		0.723
(1.00) 		0.603
(1.00) 		0.328
(1.00) 		0.0685
(0.791)
CDKN2A 112 (22%) 399 0.996
(1.00) 		0.112
(0.87) 		0.168
(0.907) 		0.812
(1.00) 		0.398
(1.00) 		1
(1.00) 		0.904
(1.00) 		0.548
(1.00) 		0.254
(0.961) 		0.648
(1.00) 		0.402
(1.00) 		0.224
(0.933) 		0.495
(1.00) 		0.474
(1.00)
MLL2 81 (16%) 430 0.125
(0.876) 		0.289
(0.986) 		0.355
(1.00) 		0.215
(0.933) 		0.769
(1.00) 		1
(1.00) 		1
(1.00) 		0.789
(1.00) 		0.477
(1.00) 		0.449
(1.00) 		0.866
(1.00) 		0.945
(1.00) 		0.113
(0.87) 		0.401
(1.00)
TGFBR2 24 (5%) 487 0.862
(1.00) 		0.109
(0.87) 		0.949
(1.00) 		0.705
(1.00) 		0.704
(1.00) 		1
(1.00) 		1
(1.00) 		0.484
(1.00) 		1
(1.00) 		0.386
(1.00) 		0.23
(0.933) 		0.49
(1.00) 		0.846
(1.00) 		1
(1.00)
HLA-B 24 (5%) 487 0.963
(1.00) 		0.197
(0.933) 		0.751
(1.00) 		0.371
(1.00) 		0.0302
(0.6) 		1
(1.00) 		0.104
(0.87) 		0.167
(0.907) 		0.415
(1.00) 		0.225
(0.933) 		0.129
(0.876) 		0.287
(0.986) 		0.604
(1.00) 		0.614
(1.00)
FBXW7 33 (6%) 478 0.318
(1.00) 		0.00668
(0.287) 		0.748
(1.00) 		0.42
(1.00) 		0.324
(1.00) 		1
(1.00) 		0.107
(0.87) 		0.326
(1.00) 		1
(1.00) 		0.323
(1.00) 		0.967
(1.00) 		0.17
(0.907) 		1
(1.00) 		0.66
(1.00)
NOTCH1 90 (18%) 421 0.1
(0.87) 		0.00878
(0.293) 		0.354
(1.00) 		0.296
(0.991) 		0.674
(1.00) 		0.172
(0.907) 		0.0894
(0.851) 		0.0204
(0.479) 		1
(1.00) 		0.0551
(0.736) 		0.185
(0.907) 		0.36
(1.00) 		0.933
(1.00) 		0.188
(0.909)
ZNF750 21 (4%) 490 0.974
(1.00) 		0.135
(0.893) 		0.21
(0.933) 		0.559
(1.00) 		0.227
(0.933) 		1
(1.00) 		0.217
(0.933) 		0.473
(1.00) 		0.373
(1.00) 		0.765
(1.00) 		0.541
(1.00) 		0.0348
(0.6) 		0.178
(0.907) 		0.618
(1.00)
HLA-A 22 (4%) 489 0.755
(1.00) 		0.0758
(0.812) 		0.884
(1.00) 		0.0737
(0.8) 		0.416
(1.00) 		1
(1.00) 		1
(1.00) 		0.13
(0.876) 		1
(1.00) 		0.439
(1.00) 		0.0117
(0.377) 		0.559
(1.00) 		0.67
(1.00) 		0.614
(1.00)
EPHA2 24 (5%) 487 0.293
(0.991) 		0.0846
(0.842) 		0.874
(1.00) 		0.653
(1.00) 		0.518
(1.00) 		1
(1.00) 		0.484
(1.00) 		0.167
(0.907) 		1
(1.00) 		0.0478
(0.703) 		0.184
(0.907) 		0.933
(1.00) 		0.587
(1.00) 		1
(1.00)
HRAS 31 (6%) 480 0.247
(0.961) 		0.397
(1.00) 		0.409
(1.00) 		0.65
(1.00) 		0.141
(0.907) 		1
(1.00) 		0.0614
(0.773) 		0.22
(0.933) 		0.5
(1.00) 		0.733
(1.00) 		0.464
(1.00) 		0.0801
(0.83) 		0.388
(1.00) 		0.395
(1.00)
EP300 38 (7%) 473 0.247
(0.961) 		0.541
(1.00) 		0.988
(1.00) 		0.504
(1.00) 		0.388
(1.00) 		1
(1.00) 		0.569
(1.00) 		0.705
(1.00) 		0.579
(1.00) 		0.115
(0.87) 		0.911
(1.00) 		0.695
(1.00) 		0.824
(1.00) 		1
(1.00)
OR6C65 16 (3%) 495 0.243
(0.961) 		0.985
(1.00) 		0.528
(1.00) 		0.937
(1.00) 		0.874
(1.00) 		1
(1.00) 		0.257
(0.961) 		0.278
(0.985) 		1
(1.00) 		0.58
(1.00) 		0.443
(1.00) 		0.917
(1.00) 		0.573
(1.00) 		1
(1.00)
PIK3CA 94 (18%) 417 0.828
(1.00) 		0.879
(1.00) 		0.29
(0.986) 		0.324
(1.00) 		0.104
(0.87) 		1
(1.00) 		0.0545
(0.736) 		0.899
(1.00) 		0.753
(1.00) 		0.803
(1.00) 		0.797
(1.00) 		0.508
(1.00) 		0.0909
(0.851) 		0.595
(1.00)
PTEN 14 (3%) 497 0.205
(0.933) 		0.32
(1.00) 		0.935
(1.00) 		0.29
(0.986) 		0.491
(1.00) 		1
(1.00) 		1
(1.00) 		0.779
(1.00) 		1
(1.00) 		0.426
(1.00) 		0.15
(0.907) 		0.496
(1.00) 		0.563
(1.00) 		1
(1.00)
RASA1 18 (4%) 493 0.507
(1.00) 		0.347
(1.00) 		0.118
(0.87) 		0.376
(1.00) 		0.733
(1.00) 		0.0365
(0.6) 		0.423
(1.00) 		0.306
(1.00) 		1
(1.00) 		0.162
(0.907) 		0.853
(1.00) 		0.361
(1.00) 		0.62
(1.00) 		1
(1.00)
MAPK1 9 (2%) 502 0.161
(0.907) 		0.95
(1.00) 		0.869
(1.00) 		0.412
(1.00) 		0.65
(1.00) 		1
(1.00) 		0.708
(1.00) 		0.726
(1.00) 		1
(1.00) 		0.46
(1.00) 		0.865
(1.00) 		0.239
(0.961) 		1
(1.00)
NUDT11 9 (2%) 502 0.254
(0.961) 		0.351
(1.00) 		0.58
(1.00) 		0.758
(1.00) 		0.649
(1.00) 		1
(1.00) 		0.122
(0.876) 		0.0961
(0.851) 		1
(1.00) 		0.584
(1.00) 		0.295
(0.991) 		0.504
(1.00) 		1
(1.00) 		0.389
(1.00)
KDM6A 17 (3%) 494 0.26
(0.961) 		0.0534
(0.736) 		0.399
(1.00) 		0.258
(0.961) 		0.804
(1.00) 		1
(1.00) 		1
(1.00) 		0.784
(1.00) 		1
(1.00) 		0.146
(0.907) 		0.179
(0.907) 		0.876
(1.00) 		0.491
(1.00) 		1
(1.00)
KEAP1 22 (4%) 489 0.765
(1.00) 		0.096
(0.851) 		0.151
(0.907) 		0.00782
(0.293) 		0.37
(1.00) 		1
(1.00) 		0.144
(0.907) 		0.0159
(0.454) 		0.105
(0.87) 		0.0943
(0.851) 		0.302
(1.00) 		0.871
(1.00) 		0.69
(1.00) 		0.614
(1.00)
KRT17 6 (1%) 505 0.21
(0.933) 		0.643
(1.00) 		0.259
(0.961) 		0.186
(0.907) 		0.0507
(0.722) 		0.351
(1.00) 		0.614
(1.00) 		1
(1.00) 		0.901
(1.00) 		0.945
(1.00) 		0.122
(0.876) 		0.536
(1.00) 		1
(1.00)
RHOA 10 (2%) 501 0.512
(1.00) 		0.39
(1.00) 		1
(1.00) 		0.386
(1.00) 		0.0367
(0.6) 		1
(1.00) 		0.47
(1.00) 		0.505
(1.00) 		0.199
(0.933) 		0.696
(1.00) 		0.572
(1.00) 		0.343
(1.00) 		0.691
(1.00) 		1
(1.00)
PTPN14 16 (3%) 495 0.154
(0.907) 		0.828
(1.00) 		0.0409
(0.623) 		0.852
(1.00) 		0.249
(0.961) 		0.0365
(0.6) 		0.775
(1.00) 		0.591
(1.00) 		1
(1.00) 		0.738
(1.00) 		0.592
(1.00) 		0.412
(1.00) 		0.0619
(0.773) 		0.586
(1.00)
KRTAP5-5 4 (1%) 507 0.73
(1.00) 		0.425
(1.00) 		0.0649
(0.783) 		0.192
(0.919) 		1
(1.00) 		1
(1.00) 		0.296
(0.991) 		1
(1.00) 		1
(1.00) 		0.584
(1.00) 		0.267
(0.97) 		0.804
(1.00) 		1
(1.00) 		1
(1.00)
ZNF623 12 (2%) 499 0.311
(1.00) 		0.643
(1.00) 		1
(1.00) 		0.787
(1.00) 		0.794
(1.00) 		1
(1.00) 		0.742
(1.00) 		0.754
(1.00) 		1
(1.00) 		0.803
(1.00) 		0.578
(1.00) 		0.243
(0.961) 		0.499
(1.00) 		1
(1.00)
TIGD4 7 (1%) 504 0.32
(1.00) 		0.175
(0.907) 		0.253
(0.961) 		0.776
(1.00) 		0.171
(0.907) 		1
(1.00) 		0.68
(1.00) 		0.662
(1.00) 		1
(1.00) 		0.501
(1.00) 		0.403
(1.00) 		0.167
(0.907) 		0.589
(1.00) 		1
(1.00)
CUL3 16 (3%) 495 0.924
(1.00) 		0.377
(1.00) 		0.24
(0.961) 		0.16
(0.907) 		0.948
(1.00) 		1
(1.00) 		0.257
(0.961) 		0.784
(1.00) 		1
(1.00) 		0.776
(1.00) 		0.336
(1.00) 		0.285
(0.986) 		0.0366
(0.6) 		1
(1.00)
CREBBP 34 (7%) 477 0.507
(1.00) 		0.0168
(0.454) 		0.753
(1.00) 		0.73
(1.00) 		0.887
(1.00) 		1
(1.00) 		0.548
(1.00) 		1
(1.00) 		0.537
(1.00) 		0.715
(1.00) 		0.0351
(0.6) 		0.689
(1.00) 		0.104
(0.87) 		1
(1.00)
VEZF1 8 (2%) 503 0.53
(1.00) 		0.944
(1.00) 		0.0129
(0.386) 		0.0167
(0.454) 		0.066
(0.784) 		1
(1.00) 		1
(1.00) 		0.0535
(0.736) 		0.161
(0.907) 		0.707
(1.00) 		0.558
(1.00) 		0.189
(0.912) 		1
(1.00) 		0.354
(1.00)
IRS4 17 (3%) 494 0.733
(1.00) 		0.931
(1.00) 		0.698
(1.00) 		0.786
(1.00) 		0.389
(1.00) 		1
(1.00) 		0.263
(0.961) 		0.556
(1.00) 		1
(1.00) 		0.802
(1.00) 		0.911
(1.00) 		0.144
(0.907) 		0.758
(1.00) 		0.184
(0.907)
HUWE1 46 (9%) 465 0.417
(1.00) 		0.419
(1.00) 		0.842
(1.00) 		0.619
(1.00) 		0.492
(1.00) 		1
(1.00) 		0.0352
(0.6) 		0.863
(1.00) 		1
(1.00) 		0.261
(0.961) 		0.581
(1.00) 		0.52
(1.00) 		0.0396
(0.614) 		0.275
(0.983)
C3ORF59 10 (2%) 501 0.947
(1.00) 		0.391
(1.00) 		0.954
(1.00) 		0.757
(1.00) 		0.359
(1.00) 		1
(1.00) 		0.734
(1.00) 		0.271
(0.981) 		1
(1.00) 		0.65
(1.00) 		0.727
(1.00) 		0.539
(1.00) 		1
(1.00) 		1
(1.00)
DYSF 20 (4%) 491 0.733
(1.00) 		0.0614
(0.773) 		0.96
(1.00) 		0.658
(1.00) 		0.0942
(0.851) 		1
(1.00) 		0.798
(1.00) 		1
(1.00) 		1
(1.00) 		0.0265
(0.548) 		0.107
(0.87) 		0.0718
(0.791) 		0.823
(1.00) 		0.614
(1.00)
ZNF233 9 (2%) 502 0.314
(1.00) 		0.281
(0.985) 		0.392
(1.00) 		0.468
(1.00) 		0.228
(0.933) 		1
(1.00) 		1
(1.00) 		1
(1.00) 		0.0702
(0.791) 		0.116
(0.87) 		0.00841
(0.293) 		0.684
(1.00) 		1
(1.00)
KIAA1267 11 (2%) 500 0.458
(1.00) 		0.263
(0.961) 		0.474
(1.00) 		0.22
(0.933) 		0.889
(1.00) 		1
(1.00) 		0.498
(1.00) 		0.754
(1.00) 		1
(1.00) 		0.884
(1.00) 		0.469
(1.00) 		0.489
(1.00) 		0.696
(1.00) 		0.11
(0.87)
ASXL1 16 (3%) 495 0.288
(0.986) 		0.837
(1.00) 		0.517
(1.00) 		0.175
(0.907) 		0.124
(0.876) 		1
(1.00) 		0.775
(1.00) 		0.00557
(0.269) 		1
(1.00) 		0.949
(1.00) 		0.782
(1.00) 		0.836
(1.00) 		0.772
(1.00) 		1
(1.00)
SMAD4 13 (3%) 498 0.602
(1.00) 		0.304
(1.00) 		0.771
(1.00) 		1
(1.00) 		0.618
(1.00) 		1
(1.00) 		1
(1.00) 		0.526
(1.00) 		1
(1.00) 		0.402
(1.00) 		0.171
(0.907) 		0.902
(1.00) 		1
(1.00) 		1
(1.00)
GAGE2A 4 (1%) 507 0.904
(1.00) 		0.307
(1.00) 		0.642
(1.00) 		0.797
(1.00) 		1
(1.00) 		1
(1.00) 		0.578
(1.00) 		0.28
(0.985) 		1
(1.00) 		0.755
(1.00) 		0.397
(1.00) 		1
(1.00)
EMG1 3 (1%) 508 0.663
(1.00) 		0.812
(1.00) 		0.817
(1.00) 		0.85
(1.00) 		0.118
(0.87) 		1
(1.00) 		0.179
(0.907) 		0.28
(0.985) 		1
(1.00) 		0.578
(1.00) 		1
(1.00) 		1
(1.00)
PIK3R1 8 (2%) 503 0.129
(0.876) 		0.936
(1.00) 		0.521
(1.00) 		0.797
(1.00) 		0.156
(0.907) 		1
(1.00) 		0.689
(1.00) 		0.719
(1.00) 		1
(1.00) 		0.914
(1.00) 		0.962
(1.00) 		0.167
(0.907) 		1
(1.00) 		1
(1.00)
KRTAP5-7 5 (1%) 506 0.169
(0.907) 		0.495
(1.00) 		0.405
(1.00) 		0.782
(1.00) 		0.689
(1.00) 		1
(1.00) 		0.125
(0.876) 		0.348
(1.00) 		1
(1.00) 		0.959
(1.00) 		0.772
(1.00) 		0.347
(1.00) 		0.184
(0.907) 		1
(1.00)
SLC9A6 5 (1%) 506 0.0129
(0.386) 		0.778
(1.00) 		0.326
(1.00) 		0.456
(1.00) 		0.13
(0.876) 		1
(1.00) 		0.125
(0.876) 		0.662
(1.00) 		1
(1.00) 		0.849
(1.00) 		0.15
(0.907) 		1
(1.00) 		1
(1.00)
ELF4 7 (1%) 504 0.374
(1.00) 		0.922
(1.00) 		0.0174
(0.457) 		0.072
(0.791) 		0.217
(0.933) 		1
(1.00) 		0.68
(1.00) 		0.0213
(0.486) 		1
(1.00) 		0.423
(1.00) 		0.874
(1.00) 		0.0605
(0.773) 		1
(1.00) 		1
(1.00)
HNRNPL 11 (2%) 500 0.48
(1.00) 		0.105
(0.87) 		0.302
(1.00) 		0.319
(1.00) 		0.104
(0.87) 		1
(1.00) 		0.177
(0.907) 		1
(1.00) 		0.213
(0.933) 		0.261
(0.961) 		0.792
(1.00) 		0.214
(0.933) 		1
(1.00) 		1
(1.00)
ZFP36L2 8 (2%) 503 0.131
(0.878) 		0.552
(1.00) 		0.766
(1.00) 		0.881
(1.00) 		0.307
(1.00) 		0.451
(1.00) 		1
(1.00) 		1
(1.00) 		0.661
(1.00) 		0.201
(0.933) 		0.868
(1.00) 		1
(1.00) 		0.354
(1.00)
MYH9 21 (4%) 490 0.765
(1.00) 		0.819
(1.00) 		0.862
(1.00) 		0.384
(1.00) 		0.893
(1.00) 		1
(1.00) 		0.217
(0.933) 		0.473
(1.00) 		0.373
(1.00) 		0.468
(1.00) 		0.361
(1.00) 		0.862
(1.00) 		0.44
(1.00) 		0.244
(0.961)
NCOR1 17 (3%) 494 0.878
(1.00) 		0.178
(0.907) 		0.759
(1.00) 		0.569
(1.00) 		0.686
(1.00) 		1
(1.00) 		0.415
(1.00) 		0.39
(1.00) 		1
(1.00) 		0.8
(1.00) 		0.261
(0.961) 		0.346
(1.00) 		0.788
(1.00) 		0.224
(0.933)
SPTY2D1 10 (2%) 501 0.471
(1.00) 		0.0197
(0.479) 		0.867
(1.00) 		0.624
(1.00) 		0.786
(1.00) 		1
(1.00) 		0.734
(1.00) 		0.329
(1.00) 		1
(1.00) 		0.0421
(0.63) 		0.221
(0.933) 		0.225
(0.933) 		1
(1.00) 		0.421
(1.00)
PIWIL2 8 (2%) 503 0.555
(1.00) 		0.275
(0.983) 		0.566
(1.00) 		0.711
(1.00) 		1
(1.00) 		1
(1.00) 		1
(1.00) 		0.699
(1.00) 		1
(1.00) 		0.0828
(0.836) 		0.0804
(0.83) 		0.554
(1.00) 		1
(1.00) 		1
(1.00)
'NSD1 MUTATION STATUS' versus 'NUMBER_OF_LYMPH_NODES'

P value = 0.000124 (Wilcoxon-test), Q value = 0.036

Table S1.  Gene #3: 'NSD1 MUTATION STATUS' versus Clinical Feature #12: 'NUMBER_OF_LYMPH_NODES'

nPatients Mean (Std.Dev)
ALL 402 2.1 (3.8)
NSD1 MUTATED 45 0.7 (1.2)
NSD1 WILD-TYPE 357 2.3 (3.9)

Figure S1.  Get High-res Image Gene #3: 'NSD1 MUTATION STATUS' versus Clinical Feature #12: 'NUMBER_OF_LYMPH_NODES'

'CASP8 MUTATION STATUS' versus 'YEARS_TO_BIRTH'

P value = 7.62e-09 (Wilcoxon-test), Q value = 6.6e-06

Table S2.  Gene #4: 'CASP8 MUTATION STATUS' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 510 61.0 (12.0)
CASP8 MUTATED 54 70.1 (13.3)
CASP8 WILD-TYPE 456 60.0 (11.3)

Figure S2.  Get High-res Image Gene #4: 'CASP8 MUTATION STATUS' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'CASP8 MUTATION STATUS' versus 'GENDER'

P value = 0.000523 (Fisher's exact test), Q value = 0.11

Table S3.  Gene #4: 'CASP8 MUTATION STATUS' versus Clinical Feature #7: 'GENDER'

nPatients FEMALE MALE
ALL 138 373
CASP8 MUTATED 26 28
CASP8 WILD-TYPE 112 345

Figure S3.  Get High-res Image Gene #4: 'CASP8 MUTATION STATUS' versus Clinical Feature #7: 'GENDER'

'FAT1 MUTATION STATUS' versus 'YEARS_TO_BIRTH'

P value = 2.31e-07 (Wilcoxon-test), Q value = 1e-04

Table S4.  Gene #10: 'FAT1 MUTATION STATUS' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 510 61.0 (12.0)
FAT1 MUTATED 112 66.4 (11.2)
FAT1 WILD-TYPE 398 59.5 (11.7)

Figure S4.  Get High-res Image Gene #10: 'FAT1 MUTATION STATUS' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'FAT1 MUTATION STATUS' versus 'GENDER'

P value = 0.00365 (Fisher's exact test), Q value = 0.23

Table S5.  Gene #10: 'FAT1 MUTATION STATUS' versus Clinical Feature #7: 'GENDER'

nPatients FEMALE MALE
ALL 138 373
FAT1 MUTATED 43 69
FAT1 WILD-TYPE 95 304

Figure S5.  Get High-res Image Gene #10: 'FAT1 MUTATION STATUS' versus Clinical Feature #7: 'GENDER'

'JUB MUTATION STATUS' versus 'YEARS_TO_BIRTH'

P value = 0.00254 (Wilcoxon-test), Q value = 0.18

Table S6.  Gene #11: 'JUB MUTATION STATUS' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 510 61.0 (12.0)
JUB MUTATED 34 67.3 (10.8)
JUB WILD-TYPE 476 60.6 (11.9)

Figure S6.  Get High-res Image Gene #11: 'JUB MUTATION STATUS' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'JUB MUTATION STATUS' versus 'YEAR_OF_TOBACCO_SMOKING_ONSET'

P value = 0.0029 (Wilcoxon-test), Q value = 0.19

Table S7.  Gene #11: 'JUB MUTATION STATUS' versus Clinical Feature #11: 'YEAR_OF_TOBACCO_SMOKING_ONSET'

nPatients Mean (Std.Dev)
ALL 276 1967.3 (12.8)
JUB MUTATED 23 1958.7 (12.5)
JUB WILD-TYPE 253 1968.1 (12.6)

Figure S7.  Get High-res Image Gene #11: 'JUB MUTATION STATUS' versus Clinical Feature #11: 'YEAR_OF_TOBACCO_SMOKING_ONSET'

'NFE2L2 MUTATION STATUS' versus 'YEARS_TO_BIRTH'

P value = 0.00183 (Wilcoxon-test), Q value = 0.16

Table S8.  Gene #13: 'NFE2L2 MUTATION STATUS' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 510 61.0 (12.0)
NFE2L2 MUTATED 27 68.5 (11.2)
NFE2L2 WILD-TYPE 483 60.6 (11.9)

Figure S8.  Get High-res Image Gene #13: 'NFE2L2 MUTATION STATUS' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'RAC1 MUTATION STATUS' versus 'YEARS_TO_BIRTH'

P value = 0.00117 (Wilcoxon-test), Q value = 0.11

Table S9.  Gene #16: 'RAC1 MUTATION STATUS' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 510 61.0 (12.0)
RAC1 MUTATED 15 70.8 (12.6)
RAC1 WILD-TYPE 495 60.7 (11.8)

Figure S9.  Get High-res Image Gene #16: 'RAC1 MUTATION STATUS' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'RAC1 MUTATION STATUS' versus 'YEAR_OF_TOBACCO_SMOKING_ONSET'

P value = 0.00434 (Wilcoxon-test), Q value = 0.24

Table S10.  Gene #16: 'RAC1 MUTATION STATUS' versus Clinical Feature #11: 'YEAR_OF_TOBACCO_SMOKING_ONSET'

nPatients Mean (Std.Dev)
ALL 276 1967.3 (12.8)
RAC1 MUTATED 9 1954.9 (11.1)
RAC1 WILD-TYPE 267 1967.8 (12.7)

Figure S10.  Get High-res Image Gene #16: 'RAC1 MUTATION STATUS' versus Clinical Feature #11: 'YEAR_OF_TOBACCO_SMOKING_ONSET'

'RB1 MUTATION STATUS' versus 'GENDER'

P value = 0.00104 (Fisher's exact test), Q value = 0.11

Table S11.  Gene #26: 'RB1 MUTATION STATUS' versus Clinical Feature #7: 'GENDER'

nPatients FEMALE MALE
ALL 138 373
RB1 MUTATED 11 6
RB1 WILD-TYPE 127 367

Figure S11.  Get High-res Image Gene #26: 'RB1 MUTATION STATUS' versus Clinical Feature #7: 'GENDER'

'NAP1L2 MUTATION STATUS' versus 'ETHNICITY'

P value = 0.00234 (Fisher's exact test), Q value = 0.18

Table S12.  Gene #34: 'NAP1L2 MUTATION STATUS' versus Clinical Feature #14: 'ETHNICITY'

nPatients HISPANIC OR LATINO NOT HISPANIC OR LATINO
ALL 25 449
NAP1L2 MUTATED 3 3
NAP1L2 WILD-TYPE 22 446

Figure S12.  Get High-res Image Gene #34: 'NAP1L2 MUTATION STATUS' versus Clinical Feature #14: 'ETHNICITY'

'MLL4 MUTATION STATUS' versus 'YEARS_TO_BIRTH'

P value = 0.000866 (Wilcoxon-test), Q value = 0.11

Table S13.  Gene #38: 'MLL4 MUTATION STATUS' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 510 61.0 (12.0)
MLL4 MUTATED 19 70.2 (11.3)
MLL4 WILD-TYPE 491 60.7 (11.8)

Figure S13.  Get High-res Image Gene #38: 'MLL4 MUTATION STATUS' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'THSD7A MUTATION STATUS' versus 'NUMBER_PACK_YEARS_SMOKED'

P value = 0.00466 (Wilcoxon-test), Q value = 0.24

Table S14.  Gene #41: 'THSD7A MUTATION STATUS' versus Clinical Feature #10: 'NUMBER_PACK_YEARS_SMOKED'

nPatients Mean (Std.Dev)
ALL 290 45.7 (35.1)
THSD7A MUTATED 23 54.1 (17.7)
THSD7A WILD-TYPE 267 45.0 (36.1)

Figure S14.  Get High-res Image Gene #41: 'THSD7A MUTATION STATUS' versus Clinical Feature #10: 'NUMBER_PACK_YEARS_SMOKED'

'CTCF MUTATION STATUS' versus 'YEARS_TO_BIRTH'

P value = 0.00107 (Wilcoxon-test), Q value = 0.11

Table S15.  Gene #54: 'CTCF MUTATION STATUS' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 510 61.0 (12.0)
CTCF MUTATED 15 71.7 (11.4)
CTCF WILD-TYPE 495 60.7 (11.8)

Figure S15.  Get High-res Image Gene #54: 'CTCF MUTATION STATUS' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'NOTCH2 MUTATION STATUS' versus 'GENDER'

P value = 0.00398 (Fisher's exact test), Q value = 0.23

Table S16.  Gene #58: 'NOTCH2 MUTATION STATUS' versus Clinical Feature #7: 'GENDER'

nPatients FEMALE MALE
ALL 138 373
NOTCH2 MUTATED 12 9
NOTCH2 WILD-TYPE 126 364

Figure S16.  Get High-res Image Gene #58: 'NOTCH2 MUTATION STATUS' versus Clinical Feature #7: 'GENDER'

'AK5 MUTATION STATUS' versus 'Time to Death'

P value = 0.000923 (logrank test), Q value = 0.11

Table S17.  Gene #60: 'AK5 MUTATION STATUS' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 509 220 0.1 - 211.0 (20.9)
AK5 MUTATED 13 9 1.1 - 32.6 (12.9)
AK5 WILD-TYPE 496 211 0.1 - 211.0 (21.1)

Figure S17.  Get High-res Image Gene #60: 'AK5 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/22815324/transformed.cor.cli.txt

  • Clinical data file = /xchip/cga/gdac-prod/tcga-gdac/jobResults/Append_Data/HNSC-TP/22506490/HNSC-TP.merged_data.txt

  • Number of patients = 511

  • Number of significantly mutated genes = 62

  • Number of selected clinical features = 14

  • 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)
Copyright © 2016 Broad Institute TCGA GDAC as part of the TCGA Research Network. All rights reserved.
Made with Nozzle