Correlation between gene mutation status and selected clinical features
Head and Neck Squamous Cell Carcinoma (Primary solid tumor)
21 August 2015  |  analyses__2015_08_21
Maintainer Information
Citation Information
doi:10.7908/C1PG1QX8
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/C1PG1QX8
Overview
Introduction

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

Summary

Testing the association between mutation status of 49 genes and 13 clinical features across 510 patients, 17 significant findings detected with Q value < 0.25.

  • TP53 mutation correlated to 'Time to Death' and 'HISTOLOGICAL_TYPE'.

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

  • NSD1 mutation correlated to 'NUMBER_OF_LYMPH_NODES'.

  • FAT1 mutation correlated to 'YEARS_TO_BIRTH'.

  • NOTCH1 mutation correlated to 'YEARS_TO_BIRTH'.

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

  • NFE2L2 mutation correlated to 'YEARS_TO_BIRTH'.

  • FBXW7 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'.

  • CTCF mutation correlated to 'YEARS_TO_BIRTH'.

Results
Overview of the results

Table 1.  Get Full Table Overview of the association between mutation status of 49 genes and 13 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 		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 Wilcoxon-test Wilcoxon-test Wilcoxon-test Fisher's exact test Fisher's exact test
TP53 359 (70%) 151 0.00214
(0.187) 		0.314
(1.00) 		0.428
(1.00) 		0.0256
(0.562) 		0.65
(1.00) 		0.828
(1.00) 		0.503
(1.00) 		0.00351
(0.19) 		0.0355
(0.62) 		0.957
(1.00) 		0.653
(1.00) 		0.551
(1.00) 		0.123
(0.866)
CASP8 55 (11%) 455 0.0517
(0.701) 		3.34e-09
(2.13e-06) 		0.808
(1.00) 		0.381
(1.00) 		0.0715
(0.759) 		0.000336
(0.0535) 		0.257
(1.00) 		1
(1.00) 		0.0857
(0.773) 		0.0146
(0.386) 		0.0186
(0.455) 		0.722
(1.00) 		0.517
(1.00)
JUB 33 (6%) 477 0.0551
(0.716) 		0.00588
(0.234) 		0.642
(1.00) 		0.646
(1.00) 		0.248
(1.00) 		1
(1.00) 		0.543
(1.00) 		1
(1.00) 		0.264
(1.00) 		0.00388
(0.19) 		0.491
(1.00) 		0.193
(0.932) 		0.676
(1.00)
RAC1 15 (3%) 495 0.458
(1.00) 		0.00117
(0.124) 		0.196
(0.932) 		0.185
(0.932) 		0.38
(1.00) 		0.00737
(0.261) 		1
(1.00) 		1
(1.00) 		0.67
(1.00) 		0.00493
(0.224) 		0.189
(0.932) 		0.31
(1.00) 		1
(1.00)
NSD1 63 (12%) 447 0.0593
(0.726) 		0.0389
(0.62) 		0.102
(0.809) 		0.518
(1.00) 		0.0368
(0.62) 		0.0697
(0.758) 		0.879
(1.00) 		1
(1.00) 		0.158
(0.883) 		0.549
(1.00) 		0.000306
(0.0535) 		0.681
(1.00) 		0.349
(1.00)
FAT1 114 (22%) 396 0.634
(1.00) 		8.53e-07
(0.000272) 		0.755
(1.00) 		0.0378
(0.62) 		0.325
(1.00) 		0.0125
(0.362) 		1
(1.00) 		1
(1.00) 		0.15
(0.883) 		0.0168
(0.427) 		0.358
(1.00) 		0.604
(1.00) 		0.472
(1.00)
NOTCH1 87 (17%) 423 0.221
(0.957) 		0.00565
(0.234) 		0.883
(1.00) 		0.458
(1.00) 		0.461
(1.00) 		0.0656
(0.758) 		0.036
(0.62) 		0.677
(1.00) 		0.0802
(0.773) 		0.252
(1.00) 		0.204
(0.938) 		0.862
(1.00) 		0.195
(0.932)
NFE2L2 26 (5%) 484 0.387
(1.00) 		0.00386
(0.19) 		0.647
(1.00) 		0.851
(1.00) 		0.592
(1.00) 		0.112
(0.846) 		0.0757
(0.773) 		1
(1.00) 		0.648
(1.00) 		0.463
(1.00) 		0.342
(1.00) 		0.321
(1.00) 		0.343
(1.00)
FBXW7 33 (6%) 477 0.294
(1.00) 		0.00655
(0.246) 		0.774
(1.00) 		0.399
(1.00) 		0.346
(1.00) 		0.156
(0.883) 		0.427
(1.00) 		1
(1.00) 		0.367
(1.00) 		0.894
(1.00) 		0.187
(0.932) 		0.882
(1.00) 		0.668
(1.00)
RB1 18 (4%) 492 0.0605
(0.728) 		0.567
(1.00) 		0.142
(0.883) 		0.239
(0.99) 		0.579
(1.00) 		0.00239
(0.187) 		1
(1.00) 		1
(1.00) 		0.718
(1.00) 		0.303
(1.00) 		0.215
(0.943) 		0.314
(1.00) 		1
(1.00)
NAP1L2 7 (1%) 503 0.337
(1.00) 		0.905
(1.00) 		0.239
(0.99) 		0.671
(1.00) 		0.146
(0.883) 		1
(1.00) 		1
(1.00) 		0.106
(0.826) 		0.543
(1.00) 		0.844
(1.00) 		0.46
(1.00) 		0.47
(1.00) 		0.00264
(0.187)
MLL4 20 (4%) 490 0.438
(1.00) 		0.00378
(0.19) 		0.202
(0.937) 		0.985
(1.00) 		0.0667
(0.758) 		0.0789
(0.773) 		0.795
(1.00) 		1
(1.00) 		0.688
(1.00) 		0.0562
(0.716) 		0.0968
(0.784) 		0.531
(1.00) 		1
(1.00)
CTCF 16 (3%) 494 0.0696
(0.758) 		0.000999
(0.124) 		0.119
(0.866) 		1
(1.00) 		0.431
(1.00) 		0.0488
(0.676) 		1
(1.00) 		1
(1.00) 		0.657
(1.00) 		0.0418
(0.62) 		0.319
(1.00) 		0.425
(1.00) 		1
(1.00)
CDKN2A 112 (22%) 398 0.818
(1.00) 		0.134
(0.883) 		0.152
(0.883) 		0.835
(1.00) 		0.505
(1.00) 		1
(1.00) 		0.537
(1.00) 		0.498
(1.00) 		0.372
(1.00) 		0.566
(1.00) 		0.449
(1.00) 		0.755
(1.00) 		0.631
(1.00)
HLA-B 24 (5%) 486 0.899
(1.00) 		0.195
(0.932) 		0.753
(1.00) 		0.342
(1.00) 		0.038
(0.62) 		0.157
(0.883) 		0.166
(0.889) 		0.321
(1.00) 		0.205
(0.938) 		0.144
(0.883) 		0.303
(1.00) 		0.514
(1.00) 		0.614
(1.00)
MLL2 78 (15%) 432 0.0661
(0.758) 		0.356
(1.00) 		0.399
(1.00) 		0.2
(0.937) 		0.935
(1.00) 		0.891
(1.00) 		0.887
(1.00) 		0.663
(1.00) 		0.354
(1.00) 		0.933
(1.00) 		0.828
(1.00) 		0.158
(0.883) 		0.402
(1.00)
TGFBR2 23 (5%) 487 0.732
(1.00) 		0.0582
(0.726) 		0.91
(1.00) 		0.727
(1.00) 		0.55
(1.00) 		1
(1.00) 		0.342
(1.00) 		1
(1.00) 		0.386
(1.00) 		0.0911
(0.773) 		0.408
(1.00) 		0.59
(1.00) 		1
(1.00)
ZNF750 19 (4%) 491 0.927
(1.00) 		0.371
(1.00) 		0.281
(1.00) 		0.711
(1.00) 		0.538
(1.00) 		0.304
(1.00) 		1
(1.00) 		1
(1.00) 		0.524
(1.00) 		0.51
(1.00) 		0.0702
(0.758) 		0.407
(1.00) 		0.615
(1.00)
EPHA2 24 (5%) 486 0.247
(1.00) 		0.0851
(0.773) 		0.885
(1.00) 		0.648
(1.00) 		0.491
(1.00) 		0.49
(1.00) 		0.342
(1.00) 		1
(1.00) 		0.0443
(0.627) 		0.164
(0.883) 		0.955
(1.00) 		0.501
(1.00) 		1
(1.00)
HLA-A 22 (4%) 488 0.733
(1.00) 		0.0894
(0.773) 		0.869
(1.00) 		0.0864
(0.773) 		0.338
(1.00) 		1
(1.00) 		0.13
(0.872) 		1
(1.00) 		0.232
(0.988) 		0.0135
(0.373) 		0.739
(1.00) 		0.814
(1.00) 		0.614
(1.00)
HRAS 29 (6%) 481 0.409
(1.00) 		0.291
(1.00) 		0.447
(1.00) 		0.879
(1.00) 		0.128
(0.872) 		0.0897
(0.773) 		0.272
(1.00) 		1
(1.00) 		0.875
(1.00) 		0.589
(1.00) 		0.128
(0.872) 		0.578
(1.00) 		0.392
(1.00)
PIK3CA 94 (18%) 416 0.666
(1.00) 		0.689
(1.00) 		0.459
(1.00) 		0.278
(1.00) 		0.181
(0.932) 		0.0408
(0.62) 		1
(1.00) 		0.476
(1.00) 		0.971
(1.00) 		0.599
(1.00) 		0.349
(1.00) 		0.0289
(0.613) 		1
(1.00)
EP300 39 (8%) 471 0.289
(1.00) 		0.73
(1.00) 		0.94
(1.00) 		0.699
(1.00) 		0.515
(1.00) 		0.455
(1.00) 		1
(1.00) 		1
(1.00) 		0.201
(0.937) 		0.741
(1.00) 		0.822
(1.00) 		0.74
(1.00) 		0.445
(1.00)
PTEN 14 (3%) 496 0.284
(1.00) 		0.318
(1.00) 		0.908
(1.00) 		0.292
(1.00) 		0.463
(1.00) 		1
(1.00) 		1
(1.00) 		1
(1.00) 		0.455
(1.00) 		0.162
(0.883) 		0.518
(1.00) 		0.738
(1.00) 		1
(1.00)
RASA1 17 (3%) 493 0.816
(1.00) 		0.782
(1.00) 		0.756
(1.00) 		0.462
(1.00) 		0.959
(1.00) 		0.58
(1.00) 		0.783
(1.00) 		1
(1.00) 		0.451
(1.00) 		0.973
(1.00) 		0.756
(1.00) 		1
(1.00) 		0.238
(0.99)
MAPK1 9 (2%) 501 0.213
(0.943) 		0.952
(1.00) 		0.864
(1.00) 		0.38
(1.00) 		0.61
(1.00) 		0.711
(1.00) 		1
(1.00) 		1
(1.00) 		0.439
(1.00) 		0.887
(1.00) 		0.233
(0.988) 		1
(1.00)
KEAP1 22 (4%) 488 0.931
(1.00) 		0.0972
(0.784) 		0.109
(0.84) 		0.00791
(0.265) 		0.382
(1.00) 		0.15
(0.883) 		0.0252
(0.562) 		0.0416
(0.62) 		0.114
(0.846) 		0.346
(1.00) 		0.823
(1.00) 		0.484
(1.00) 		0.614
(1.00)
KDM6A 17 (3%) 493 0.344
(1.00) 		0.054
(0.716) 		0.373
(1.00) 		0.264
(1.00) 		0.806
(1.00) 		1
(1.00) 		0.388
(1.00) 		1
(1.00) 		0.169
(0.899) 		0.194
(0.932) 		0.91
(1.00) 		0.286
(1.00) 		0.615
(1.00)
RHOA 10 (2%) 500 0.484
(1.00) 		0.395
(1.00) 		1
(1.00) 		0.416
(1.00) 		0.0331
(0.62) 		0.473
(1.00) 		0.725
(1.00) 		0.145
(0.883) 		0.651
(1.00) 		0.613
(1.00) 		0.315
(1.00) 		1
(1.00) 		1
(1.00)
CREBBP 35 (7%) 475 0.557
(1.00) 		0.0332
(0.62) 		0.744
(1.00) 		0.72
(1.00) 		0.886
(1.00) 		0.561
(1.00) 		0.678
(1.00) 		0.437
(1.00) 		0.805
(1.00) 		0.0438
(0.627) 		0.638
(1.00) 		0.163
(0.883) 		1
(1.00)
NUDT11 8 (2%) 502 0.432
(1.00) 		0.566
(1.00) 		0.644
(1.00) 		0.881
(1.00) 		0.528
(1.00) 		0.114
(0.846) 		0.303
(1.00) 		1
(1.00) 		0.53
(1.00) 		0.559
(1.00) 		0.341
(1.00) 		1
(1.00) 		0.365
(1.00)
EMG1 4 (1%) 506 0.286
(1.00) 		0.492
(1.00) 		1
(1.00) 		0.595
(1.00) 		0.334
(1.00) 		0.303
(1.00) 		0.613
(1.00) 		1
(1.00) 		0.66
(1.00) 		1
(1.00) 		1
(1.00)
SMAD4 13 (3%) 497 0.549
(1.00) 		0.302
(1.00) 		0.737
(1.00) 		1
(1.00) 		0.588
(1.00) 		1
(1.00) 		0.525
(1.00) 		1
(1.00) 		0.378
(1.00) 		0.146
(0.883) 		0.865
(1.00) 		1
(1.00) 		1
(1.00)
CUL3 14 (3%) 496 0.543
(1.00) 		0.259
(1.00) 		0.215
(0.943) 		0.0404
(0.62) 		0.619
(1.00) 		0.369
(1.00) 		0.759
(1.00) 		1
(1.00) 		0.77
(1.00) 		0.162
(0.883) 		0.21
(0.943) 		0.181
(0.932) 		1
(1.00)
TIGD4 7 (1%) 503 0.287
(1.00) 		0.176
(0.92) 		0.27
(1.00) 		0.778
(1.00) 		0.192
(0.932) 		0.68
(1.00) 		0.662
(1.00) 		1
(1.00) 		0.546
(1.00) 		0.439
(1.00) 		0.176
(0.92) 		0.529
(1.00) 		1
(1.00)
MYH9 22 (4%) 488 0.766
(1.00) 		0.604
(1.00) 		0.91
(1.00) 		0.962
(1.00) 		0.762
(1.00) 		0.464
(1.00) 		0.797
(1.00) 		0.3
(1.00) 		0.482
(1.00) 		0.355
(1.00) 		0.613
(1.00) 		0.53
(1.00) 		0.28
(1.00)
C3ORF59 11 (2%) 499 0.884
(1.00) 		0.502
(1.00) 		0.952
(1.00) 		0.758
(1.00) 		0.361
(1.00) 		1
(1.00) 		0.725
(1.00) 		1
(1.00) 		0.944
(1.00) 		0.699
(1.00) 		0.51
(1.00) 		0.698
(1.00) 		1
(1.00)
HUWE1 45 (9%) 465 0.285
(1.00) 		0.344
(1.00) 		0.824
(1.00) 		0.525
(1.00) 		0.451
(1.00) 		0.0236
(0.558) 		1
(1.00) 		1
(1.00) 		0.269
(1.00) 		0.5
(1.00) 		0.569
(1.00) 		0.074
(0.773) 		0.28
(1.00)
SLC9A6 5 (1%) 505 0.00975
(0.296) 		0.792
(1.00) 		0.324
(1.00) 		0.465
(1.00) 		0.106
(0.826) 		0.13
(0.872) 		0.662
(1.00) 		1
(1.00) 		0.825
(1.00) 		0.138
(0.883) 		1
(1.00) 		1
(1.00)
ZNF623 11 (2%) 499 0.272
(1.00) 		0.979
(1.00) 		0.952
(1.00) 		0.758
(1.00) 		0.652
(1.00) 		0.504
(1.00) 		0.505
(1.00) 		1
(1.00) 		0.937
(1.00) 		0.927
(1.00) 		0.219
(0.957) 		0.407
(1.00) 		1
(1.00)
NCOR1 18 (4%) 492 0.747
(1.00) 		0.274
(1.00) 		0.716
(1.00) 		0.523
(1.00) 		0.738
(1.00) 		0.594
(1.00) 		0.572
(1.00) 		1
(1.00) 		0.852
(1.00) 		0.408
(1.00) 		0.363
(1.00) 		0.78
(1.00) 		0.259
(1.00)
PTPN14 15 (3%) 495 0.0903
(0.773) 		0.807
(1.00) 		0.49
(1.00) 		0.785
(1.00) 		0.333
(1.00) 		1
(1.00) 		0.556
(1.00) 		1
(1.00) 		0.365
(1.00) 		0.539
(1.00) 		0.432
(1.00) 		0.0867
(0.773) 		0.577
(1.00)
ITGB1 13 (3%) 497 0.407
(1.00) 		0.124
(0.866) 		0.208
(0.943) 		0.222
(0.957) 		0.559
(1.00) 		0.759
(1.00) 		0.505
(1.00) 		1
(1.00) 		0.745
(1.00) 		0.95
(1.00) 		0.532
(1.00) 		1
(1.00) 		0.524
(1.00)
IRS4 17 (3%) 493 0.794
(1.00) 		0.929
(1.00) 		0.692
(1.00) 		0.759
(1.00) 		0.419
(1.00) 		0.266
(1.00) 		0.555
(1.00) 		1
(1.00) 		0.753
(1.00) 		0.983
(1.00) 		0.154
(0.883) 		0.546
(1.00) 		0.196
(0.932)
SRPX 7 (1%) 503 0.406
(1.00) 		0.329
(1.00) 		0.432
(1.00) 		0.862
(1.00) 		0.152
(0.883) 		0.0939
(0.784) 		1
(1.00) 		1
(1.00) 		0.635
(1.00) 		0.774
(1.00) 		0.0785
(0.773) 		1
(1.00) 		1
(1.00)
KIAA1949 6 (1%) 504 0.238
(0.99) 		0.566
(1.00) 		0.0382
(0.62) 		0.248
(1.00) 		0.334
(1.00) 		1
(1.00) 		1
(1.00) 		1
(1.00) 		0.643
(1.00) 		0.247
(1.00) 		1
(1.00) 		1
(1.00)
NOTCH2 20 (4%) 490 0.692
(1.00) 		0.153
(0.883) 		0.31
(1.00) 		0.811
(1.00) 		0.773
(1.00) 		0.00878
(0.28) 		0.783
(1.00) 		1
(1.00) 		0.211
(0.943) 		0.141
(0.883) 		0.542
(1.00) 		1
(1.00) 		0.617
(1.00)
GAGE2A 5 (1%) 505 0.6
(1.00) 		0.815
(1.00) 		0.151
(0.883) 		0.63
(1.00) 		0.0814
(0.773) 		0.329
(1.00) 		0.123
(0.866) 		1
(1.00) 		0.613
(1.00) 		0.0953
(0.784) 		1
(1.00)
LCP1 15 (3%) 495 0.926
(1.00) 		0.66
(1.00) 		0.26
(1.00) 		0.0825
(0.773) 		1
(1.00) 		1
(1.00) 		0.121
(0.866) 		1
(1.00) 		0.726
(1.00) 		0.374
(1.00) 		0.628
(1.00) 		0.725
(1.00) 		0.577
(1.00)
'TP53 MUTATION STATUS' versus 'Time to Death'

P value = 0.00214 (logrank test), Q value = 0.19

Table S1.  Gene #1: 'TP53 MUTATION STATUS' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 510 217 0.1 - 211.0 (21.1)
TP53 MUTATED 359 169 0.1 - 180.2 (20.6)
TP53 WILD-TYPE 151 48 0.1 - 211.0 (22.3)

Figure S1.  Get High-res Image Gene #1: 'TP53 MUTATION STATUS' versus Clinical Feature #1: 'Time to Death'

'TP53 MUTATION STATUS' versus 'HISTOLOGICAL_TYPE'

P value = 0.00351 (Fisher's exact test), Q value = 0.19

Table S2.  Gene #1: 'TP53 MUTATION STATUS' versus Clinical Feature #8: 'HISTOLOGICAL_TYPE'

nPatients HEAD AND NECK SQUAMOUS CELL CARCINOMA HEAD AND NECK SQUAMOUS CELL CARCINOMA SPINDLE CELL VARIANT HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE
ALL 502 1 7
TP53 MUTATED 357 1 1
TP53 WILD-TYPE 145 0 6

Figure S2.  Get High-res Image Gene #1: 'TP53 MUTATION STATUS' versus Clinical Feature #8: 'HISTOLOGICAL_TYPE'

'CASP8 MUTATION STATUS' versus 'YEARS_TO_BIRTH'

P value = 3.34e-09 (Wilcoxon-test), Q value = 2.1e-06

Table S3.  Gene #3: 'CASP8 MUTATION STATUS' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 510 61.0 (12.0)
CASP8 MUTATED 55 70.2 (13.2)
CASP8 WILD-TYPE 455 59.9 (11.4)

Figure S3.  Get High-res Image Gene #3: 'CASP8 MUTATION STATUS' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'CASP8 MUTATION STATUS' versus 'GENDER'

P value = 0.000336 (Fisher's exact test), Q value = 0.054

Table S4.  Gene #3: 'CASP8 MUTATION STATUS' versus Clinical Feature #6: 'GENDER'

nPatients FEMALE MALE
ALL 140 370
CASP8 MUTATED 27 28
CASP8 WILD-TYPE 113 342

Figure S4.  Get High-res Image Gene #3: 'CASP8 MUTATION STATUS' versus Clinical Feature #6: 'GENDER'

'NSD1 MUTATION STATUS' versus 'NUMBER_OF_LYMPH_NODES'

P value = 0.000306 (Wilcoxon-test), Q value = 0.054

Table S5.  Gene #4: 'NSD1 MUTATION STATUS' versus Clinical Feature #11: 'NUMBER_OF_LYMPH_NODES'

nPatients Mean (Std.Dev)
ALL 400 2.2 (4.3)
NSD1 MUTATED 47 0.8 (1.5)
NSD1 WILD-TYPE 353 2.4 (4.5)

Figure S5.  Get High-res Image Gene #4: 'NSD1 MUTATION STATUS' versus Clinical Feature #11: 'NUMBER_OF_LYMPH_NODES'

'FAT1 MUTATION STATUS' versus 'YEARS_TO_BIRTH'

P value = 8.53e-07 (Wilcoxon-test), Q value = 0.00027

Table S6.  Gene #8: 'FAT1 MUTATION STATUS' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 510 61.0 (12.0)
FAT1 MUTATED 114 66.1 (11.4)
FAT1 WILD-TYPE 396 59.5 (11.8)

Figure S6.  Get High-res Image Gene #8: 'FAT1 MUTATION STATUS' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'NOTCH1 MUTATION STATUS' versus 'YEARS_TO_BIRTH'

P value = 0.00565 (Wilcoxon-test), Q value = 0.23

Table S7.  Gene #9: 'NOTCH1 MUTATION STATUS' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 510 61.0 (12.0)
NOTCH1 MUTATED 87 64.3 (13.3)
NOTCH1 WILD-TYPE 423 60.3 (11.6)

Figure S7.  Get High-res Image Gene #9: 'NOTCH1 MUTATION STATUS' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'JUB MUTATION STATUS' versus 'YEARS_TO_BIRTH'

P value = 0.00588 (Wilcoxon-test), Q value = 0.23

Table S8.  Gene #10: 'JUB MUTATION STATUS' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 510 61.0 (12.0)
JUB MUTATED 33 66.8 (10.5)
JUB WILD-TYPE 477 60.6 (12.0)

Figure S8.  Get High-res Image Gene #10: 'JUB MUTATION STATUS' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'JUB MUTATION STATUS' versus 'YEAR_OF_TOBACCO_SMOKING_ONSET'

P value = 0.00388 (Wilcoxon-test), Q value = 0.19

Table S9.  Gene #10: 'JUB MUTATION STATUS' versus Clinical Feature #10: 'YEAR_OF_TOBACCO_SMOKING_ONSET'

nPatients Mean (Std.Dev)
ALL 274 1967.0 (12.6)
JUB MUTATED 23 1958.7 (12.5)
JUB WILD-TYPE 251 1967.8 (12.4)

Figure S9.  Get High-res Image Gene #10: 'JUB MUTATION STATUS' versus Clinical Feature #10: 'YEAR_OF_TOBACCO_SMOKING_ONSET'

'NFE2L2 MUTATION STATUS' versus 'YEARS_TO_BIRTH'

P value = 0.00386 (Wilcoxon-test), Q value = 0.19

Table S10.  Gene #11: 'NFE2L2 MUTATION STATUS' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 510 61.0 (12.0)
NFE2L2 MUTATED 26 68.1 (11.2)
NFE2L2 WILD-TYPE 484 60.6 (11.9)

Figure S10.  Get High-res Image Gene #11: 'NFE2L2 MUTATION STATUS' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'FBXW7 MUTATION STATUS' versus 'YEARS_TO_BIRTH'

P value = 0.00655 (Wilcoxon-test), Q value = 0.25

Table S11.  Gene #12: 'FBXW7 MUTATION STATUS' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 510 61.0 (12.0)
FBXW7 MUTATED 33 67.5 (13.8)
FBXW7 WILD-TYPE 477 60.6 (11.7)

Figure S11.  Get High-res Image Gene #12: 'FBXW7 MUTATION STATUS' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'RAC1 MUTATION STATUS' versus 'YEARS_TO_BIRTH'

P value = 0.00117 (Wilcoxon-test), Q value = 0.12

Table S12.  Gene #14: '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 (11.9)

Figure S12.  Get High-res Image Gene #14: 'RAC1 MUTATION STATUS' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'RAC1 MUTATION STATUS' versus 'YEAR_OF_TOBACCO_SMOKING_ONSET'

P value = 0.00493 (Wilcoxon-test), Q value = 0.22

Table S13.  Gene #14: 'RAC1 MUTATION STATUS' versus Clinical Feature #10: 'YEAR_OF_TOBACCO_SMOKING_ONSET'

nPatients Mean (Std.Dev)
ALL 274 1967.0 (12.6)
RAC1 MUTATED 9 1954.9 (11.1)
RAC1 WILD-TYPE 265 1967.4 (12.5)

Figure S13.  Get High-res Image Gene #14: 'RAC1 MUTATION STATUS' versus Clinical Feature #10: 'YEAR_OF_TOBACCO_SMOKING_ONSET'

'RB1 MUTATION STATUS' versus 'GENDER'

P value = 0.00239 (Fisher's exact test), Q value = 0.19

Table S14.  Gene #20: 'RB1 MUTATION STATUS' versus Clinical Feature #6: 'GENDER'

nPatients FEMALE MALE
ALL 140 370
RB1 MUTATED 11 7
RB1 WILD-TYPE 129 363

Figure S14.  Get High-res Image Gene #20: 'RB1 MUTATION STATUS' versus Clinical Feature #6: 'GENDER'

'NAP1L2 MUTATION STATUS' versus 'ETHNICITY'

P value = 0.00264 (Fisher's exact test), Q value = 0.19

Table S15.  Gene #24: 'NAP1L2 MUTATION STATUS' versus Clinical Feature #13: 'ETHNICITY'

nPatients HISPANIC OR LATINO NOT HISPANIC OR LATINO
ALL 26 448
NAP1L2 MUTATED 3 3
NAP1L2 WILD-TYPE 23 445

Figure S15.  Get High-res Image Gene #24: 'NAP1L2 MUTATION STATUS' versus Clinical Feature #13: 'ETHNICITY'

'MLL4 MUTATION STATUS' versus 'YEARS_TO_BIRTH'

P value = 0.00378 (Wilcoxon-test), Q value = 0.19

Table S16.  Gene #39: 'MLL4 MUTATION STATUS' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 510 61.0 (12.0)
MLL4 MUTATED 20 68.8 (12.6)
MLL4 WILD-TYPE 490 60.7 (11.9)

Figure S16.  Get High-res Image Gene #39: 'MLL4 MUTATION STATUS' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'CTCF MUTATION STATUS' versus 'YEARS_TO_BIRTH'

P value = 0.000999 (Wilcoxon-test), Q value = 0.12

Table S17.  Gene #40: 'CTCF MUTATION STATUS' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 510 61.0 (12.0)
CTCF MUTATED 16 71.2 (11.1)
CTCF WILD-TYPE 494 60.7 (11.9)

Figure S17.  Get High-res Image Gene #40: 'CTCF MUTATION STATUS' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

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/20203267/transformed.cor.cli.txt

  • Clinical data file = /xchip/cga/gdac-prod/tcga-gdac/jobResults/Append_Data/HNSC-TP/19775211/HNSC-TP.merged_data.txt

  • Number of patients = 510

  • Number of significantly mutated genes = 49

  • 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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