Correlation between gene mutation status and selected clinical features
Overview
Introduction

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

Summary

Testing the association between mutation status of 70 genes and 13 clinical features across 784 patients, 21 significant findings detected with Q value < 0.25.

  • TP53 mutation correlated to 'PATHOLOGIC_STAGE',  'PATHOLOGY_T_STAGE', and 'HISTOLOGICAL_TYPE'.

  • PBRM1 mutation correlated to 'HISTOLOGICAL_TYPE'.

  • VHL mutation correlated to 'Time to Death',  'HISTOLOGICAL_TYPE', and 'RACE'.

  • NF2 mutation correlated to 'PATHOLOGY_N_STAGE'.

  • MET mutation correlated to 'HISTOLOGICAL_TYPE'.

  • KDM5C mutation correlated to 'HISTOLOGICAL_TYPE'.

  • MTOR mutation correlated to 'GENDER' and 'HISTOLOGICAL_TYPE'.

  • ZNF814 mutation correlated to 'HISTOLOGICAL_TYPE'.

  • AR mutation correlated to 'HISTOLOGICAL_TYPE'.

  • CACNA1C mutation correlated to 'PATHOLOGY_M_STAGE'.

  • PCF11 mutation correlated to 'HISTOLOGICAL_TYPE'.

  • KDM6A mutation correlated to 'YEARS_TO_BIRTH'.

  • FAM178A mutation correlated to 'Time to Death'.

  • FAM47A mutation correlated to 'Time to Death'.

  • MLL3 mutation correlated to 'HISTOLOGICAL_TYPE' and 'RACE'.

Results
Overview of the results

Table 1.  Get Full Table Overview of the association between mutation status of 70 genes and 13 clinical features. Shown in the table are P values (Q values). Thresholded by Q value < 0.25, 21 significant findings detected.

Clinical
Features 		Time
to
Death 		YEARS
TO
BIRTH 		PATHOLOGIC
STAGE 		PATHOLOGY
T
STAGE 		PATHOLOGY
N
STAGE 		PATHOLOGY
M
STAGE 		GENDER KARNOFSKY
PERFORMANCE
SCORE 		HISTOLOGICAL
TYPE 		NUMBER
PACK
YEARS
SMOKED 		YEAR
OF
TOBACCO
SMOKING
ONSET 		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 Wilcoxon-test Fisher's exact test Wilcoxon-test Wilcoxon-test Fisher's exact test Fisher's exact test
TP53 38 (5%) 746 0.605
(1.00) 		0.268
(1.00) 		0.0031
(0.166) 		0.00241
(0.166) 		0.0223
(0.422) 		0.768
(1.00) 		0.38
(1.00) 		0.464
(1.00) 		1e-05
(0.00152) 		0.378
(1.00) 		0.802
(1.00) 		0.204
(1.00) 		1
(1.00)
VHL 196 (25%) 588 0.0045
(0.214) 		0.282
(1.00) 		0.409
(1.00) 		0.205
(1.00) 		0.0262
(0.461) 		0.704
(1.00) 		0.0964
(0.794) 		0.651
(1.00) 		1e-05
(0.00152) 		1e-05
(0.00152) 		1
(1.00)
MTOR 34 (4%) 750 0.0745
(0.77) 		0.117
(0.853) 		0.323
(1.00) 		0.607
(1.00) 		1
(1.00) 		0.181
(1.00) 		0.00493
(0.214) 		0.0109
(0.337) 		0.00253
(0.166) 		0.795
(1.00) 		0.713
(1.00)
MLL3 42 (5%) 742 0.791
(1.00) 		0.982
(1.00) 		0.0931
(0.794) 		0.0825
(0.794) 		1
(1.00) 		1
(1.00) 		0.177
(1.00) 		0.655
(1.00) 		0.00301
(0.166) 		0.489
(1.00) 		0.327
(1.00) 		0.00464
(0.214) 		0.713
(1.00)
PBRM1 143 (18%) 641 0.094
(0.794) 		0.023
(0.428) 		0.222
(1.00) 		0.225
(1.00) 		0.055
(0.659) 		0.482
(1.00) 		0.768
(1.00) 		0.298
(1.00) 		1e-05
(0.00152) 		0.26
(1.00) 		0.0139
(0.337) 		0.819
(1.00)
NF2 16 (2%) 768 0.0783
(0.778) 		0.341
(1.00) 		0.0137
(0.337) 		0.0672
(0.71) 		0.00025
(0.0253) 		0.155
(0.967) 		0.789
(1.00) 		0.896
(1.00) 		0.09
(0.794) 		0.394
(1.00) 		0.796
(1.00) 		0.202
(1.00) 		0.533
(1.00)
MET 25 (3%) 759 0.78
(1.00) 		0.497
(1.00) 		0.514
(1.00) 		0.633
(1.00) 		0.14
(0.912) 		1
(1.00) 		0.671
(1.00) 		0.0918
(0.794) 		1e-05
(0.00152) 		0.416
(1.00) 		0.184
(1.00) 		0.822
(1.00) 		1
(1.00)
KDM5C 27 (3%) 757 0.0171
(0.362) 		0.0574
(0.67) 		0.536
(1.00) 		0.6
(1.00) 		0.769
(1.00) 		0.775
(1.00) 		0.0583
(0.67) 		8e-05
(0.0104) 		0.636
(1.00) 		0.631
(1.00)
ZNF814 14 (2%) 770 0.346
(1.00) 		0.439
(1.00) 		0.135
(0.912) 		0.455
(1.00) 		0.434
(1.00) 		1
(1.00) 		0.567
(1.00) 		0.00301
(0.166) 		0.185
(1.00) 		0.75
(1.00) 		1
(1.00)
AR 15 (2%) 769 0.599
(1.00) 		0.373
(1.00) 		0.534
(1.00) 		0.542
(1.00) 		0.579
(1.00) 		1
(1.00) 		0.584
(1.00) 		0.464
(1.00) 		0.00014
(0.0159) 		0.993
(1.00) 		0.943
(1.00) 		1
(1.00) 		1
(1.00)
CACNA1C 15 (2%) 769 0.482
(1.00) 		0.51
(1.00) 		0.0154
(0.359) 		0.249
(1.00) 		0.0169
(0.362) 		0.00494
(0.214) 		1
(1.00) 		0.139
(0.912) 		1
(1.00) 		0.469
(1.00)
PCF11 13 (2%) 771 0.848
(1.00) 		0.2
(1.00) 		0.501
(1.00) 		0.407
(1.00) 		0.621
(1.00) 		0.562
(1.00) 		0.0015
(0.124) 		0.651
(1.00) 		0.731
(1.00) 		0.469
(1.00)
KDM6A 13 (2%) 771 0.406
(1.00) 		0.000542
(0.0493) 		0.567
(1.00) 		0.94
(1.00) 		1
(1.00) 		0.371
(1.00) 		0.767
(1.00) 		0.481
(1.00) 		0.0125
(0.337) 		0.164
(0.997) 		0.0515
(0.633) 		1
(1.00)
FAM178A 8 (1%) 776 1.48e-09
(1.35e-06) 		0.089
(0.794) 		0.373
(1.00) 		0.597
(1.00) 		0.6
(1.00) 		0.123
(0.858) 		0.748
(1.00) 		1
(1.00) 		0.315
(1.00)
FAM47A 6 (1%) 778 0.00299
(0.166) 		0.406
(1.00) 		0.576
(1.00) 		0.474
(1.00) 		0.456
(1.00) 		0.0165
(0.362) 		0.426
(1.00) 		1
(1.00) 		1
(1.00)
PTEN 28 (4%) 756 0.727
(1.00) 		0.578
(1.00) 		0.268
(1.00) 		0.278
(1.00) 		0.16
(0.99) 		0.343
(1.00) 		0.539
(1.00) 		0.787
(1.00) 		0.0443
(0.601) 		0.434
(1.00) 		0.731
(1.00) 		0.324
(1.00) 		1
(1.00)
SETD2 61 (8%) 723 0.0347
(0.535) 		0.0537
(0.652) 		0.00619
(0.256) 		0.00845
(0.31) 		1
(1.00) 		0.142
(0.915) 		0.478
(1.00) 		0.91
(1.00) 		0.0414
(0.601) 		0.918
(1.00) 		0.509
(1.00) 		0.507
(1.00)
NEFH 12 (2%) 772 0.525
(1.00) 		0.695
(1.00) 		0.283
(1.00) 		0.624
(1.00) 		1
(1.00) 		0.639
(1.00) 		0.117
(0.853) 		0.733
(1.00) 		0.598
(1.00) 		1
(1.00) 		1
(1.00)
STAG2 15 (2%) 769 0.906
(1.00) 		0.0132
(0.337) 		0.0279
(0.462) 		0.0181
(0.366) 		0.514
(1.00) 		0.659
(1.00) 		0.273
(1.00) 		0.474
(1.00) 		0.733
(1.00) 		1
(1.00)
KRAS 6 (1%) 778 0.296
(1.00) 		0.649
(1.00) 		0.689
(1.00) 		0.559
(1.00) 		1
(1.00) 		0.0165
(0.362) 		0.0589
(0.67) 		0.00713
(0.282) 		1
(1.00)
SLC6A14 4 (1%) 780 0.359
(1.00) 		0.203
(1.00) 		0.0478
(0.613) 		0.0419
(0.601) 		0.0459
(0.612) 		1
(1.00) 		0.602
(1.00) 		0.512
(1.00) 		1
(1.00) 		1
(1.00)
SMARCA4 20 (3%) 764 0.719
(1.00) 		0.494
(1.00) 		0.832
(1.00) 		0.964
(1.00) 		1
(1.00) 		0.681
(1.00) 		0.334
(1.00) 		0.469
(1.00) 		0.422
(1.00) 		0.663
(1.00) 		0.616
(1.00)
NFE2L2 12 (2%) 772 0.924
(1.00) 		0.0131
(0.337) 		0.768
(1.00) 		0.669
(1.00) 		0.633
(1.00) 		1
(1.00) 		0.76
(1.00) 		0.598
(1.00) 		0.138
(0.912) 		1
(1.00)
ARID1A 18 (2%) 766 0.633
(1.00) 		0.942
(1.00) 		0.0951
(0.794) 		0.343
(1.00) 		0.279
(1.00) 		0.704
(1.00) 		0.616
(1.00) 		0.553
(1.00) 		0.506
(1.00) 		0.0122
(0.337) 		0.207
(1.00)
BCLAF1 10 (1%) 774 0.357
(1.00) 		0.353
(1.00) 		0.0432
(0.601) 		0.14
(0.912) 		0.175
(1.00) 		1
(1.00) 		1
(1.00) 		0.0386
(0.585) 		0.688
(1.00) 		1
(1.00)
ATM 20 (3%) 764 0.386
(1.00) 		0.228
(1.00) 		0.0821
(0.794) 		0.0764
(0.778) 		1
(1.00) 		0.455
(1.00) 		0.48
(1.00) 		0.464
(1.00) 		0.341
(1.00) 		0.98
(1.00) 		0.313
(1.00) 		0.589
(1.00)
PARD6B 8 (1%) 776 0.482
(1.00) 		0.0091
(0.31) 		0.618
(1.00) 		0.803
(1.00) 		1
(1.00) 		0.0582
(0.67) 		0.0968
(0.794) 		0.0922
(0.794) 		1
(1.00)
CUL3 16 (2%) 768 0.0996
(0.803) 		0.964
(1.00) 		0.978
(1.00) 		0.655
(1.00) 		0.0656
(0.705) 		1
(1.00) 		0.106
(0.803) 		0.464
(1.00) 		0.0887
(0.794) 		0.0105
(0.337) 		0.218
(1.00) 		0.785
(1.00) 		0.589
(1.00)
PIK3CA 15 (2%) 769 0.745
(1.00) 		0.195
(1.00) 		0.15
(0.953) 		0.0965
(0.794) 		1
(1.00) 		0.192
(1.00) 		0.273
(1.00) 		0.624
(1.00) 		1
(1.00) 		0.562
(1.00)
SMARCB1 9 (1%) 775 0.764
(1.00) 		0.0613
(0.683) 		0.203
(1.00) 		0.0965
(0.794) 		0.51
(1.00) 		1
(1.00) 		0.725
(1.00) 		0.0874
(0.794) 		1
(1.00) 		1
(1.00)
WASL 8 (1%) 776 0.971
(1.00) 		0.251
(1.00) 		0.51
(1.00) 		0.729
(1.00) 		1
(1.00) 		1
(1.00) 		1
(1.00) 		0.535
(1.00) 		0.672
(1.00) 		1
(1.00)
DNMT3A 11 (1%) 773 0.282
(1.00) 		0.603
(1.00) 		0.305
(1.00) 		0.33
(1.00) 		0.577
(1.00) 		1
(1.00) 		0.757
(1.00) 		0.723
(1.00) 		1
(1.00) 		0.469
(1.00)
KIAA0922 7 (1%) 777 0.895
(1.00) 		0.163
(0.997) 		0.182
(1.00) 		0.155
(0.967) 		1
(1.00) 		0.103
(0.803) 		0.206
(1.00) 		0.566
(1.00) 		1
(1.00)
GPR50 5 (1%) 779 0.37
(1.00) 		0.366
(1.00) 		0.825
(1.00) 		0.855
(1.00) 		1
(1.00) 		0.338
(1.00) 		0.46
(1.00) 		0.502
(1.00) 		1
(1.00)
ACSF2 11 (1%) 773 0.00919
(0.31) 		0.727
(1.00) 		0.254
(1.00) 		0.459
(1.00) 		0.435
(1.00) 		0.089
(0.794) 		1
(1.00) 		0.787
(1.00) 		0.725
(1.00) 		0.0616
(0.683) 		1
(1.00)
WDR52 9 (1%) 775 0.749
(1.00) 		0.102
(0.803) 		0.319
(1.00) 		0.282
(1.00) 		1
(1.00) 		0.202
(1.00) 		1
(1.00) 		0.772
(1.00) 		0.391
(1.00) 		0.434
(1.00)
ALMS1 14 (2%) 770 0.363
(1.00) 		0.242
(1.00) 		0.81
(1.00) 		1
(1.00) 		1
(1.00) 		0.314
(1.00) 		0.0436
(0.601) 		0.265
(1.00) 		0.281
(1.00) 		0.162
(0.997)
TXNIP 8 (1%) 776 0.763
(1.00) 		0.743
(1.00) 		0.034
(0.535) 		0.0343
(0.535) 		0.00912
(0.31) 		0.258
(1.00) 		0.723
(1.00) 		1
(1.00) 		1
(1.00) 		0.357
(1.00)
NUDT11 5 (1%) 779 0.521
(1.00) 		0.221
(1.00) 		0.608
(1.00) 		0.473
(1.00) 		1
(1.00) 		1
(1.00) 		0.778
(1.00) 		1
(1.00) 		1
(1.00)
PCK1 9 (1%) 775 0.626
(1.00) 		0.479
(1.00) 		0.949
(1.00) 		0.261
(1.00) 		1
(1.00) 		1
(1.00) 		1
(1.00) 		0.419
(1.00) 		1
(1.00) 		1
(1.00)
RAI1 11 (1%) 773 0.808
(1.00) 		0.379
(1.00) 		0.279
(1.00) 		0.107
(0.803) 		0.366
(1.00) 		0.355
(1.00) 		0.102
(0.803) 		0.689
(1.00) 		1
(1.00)
PAM 4 (1%) 780 0.236
(1.00) 		0.896
(1.00) 		0.677
(1.00) 		1
(1.00) 		0.351
(1.00) 		1
(1.00) 		1
(1.00) 		0.402
(1.00) 		0.448
(1.00) 		0.342
(1.00) 		1
(1.00)
GLS 9 (1%) 775 0.829
(1.00) 		0.931
(1.00) 		0.948
(1.00) 		0.0658
(0.705) 		0.6
(1.00) 		1
(1.00) 		0.349
(1.00) 		1
(1.00) 		1
(1.00)
EPS15L1 10 (1%) 774 0.961
(1.00) 		0.0265
(0.461) 		0.0268
(0.461) 		0.119
(0.856) 		1
(1.00) 		0.601
(1.00) 		0.511
(1.00) 		0.796
(1.00) 		0.204
(1.00) 		0.0464
(0.612)
NOM1 6 (1%) 778 0.327
(1.00) 		0.464
(1.00) 		1
(1.00) 		0.0948
(0.794) 		0.437
(1.00) 		1
(1.00) 		0.67
(1.00) 		0.537
(1.00) 		0.567
(1.00) 		1
(1.00)
CDK12 8 (1%) 776 0.995
(1.00) 		0.0498
(0.621) 		0.592
(1.00) 		0.727
(1.00) 		1
(1.00) 		0.314
(1.00) 		0.45
(1.00) 		0.313
(1.00) 		1
(1.00) 		1
(1.00)
ARHGAP35 7 (1%) 777 0.123
(0.858) 		0.745
(1.00) 		0.104
(0.803) 		0.206
(1.00) 		1
(1.00) 		0.202
(1.00) 		0.69
(1.00) 		0.395
(1.00) 		0.0428
(0.601) 		1
(1.00)
RIMBP3 5 (1%) 779 0.277
(1.00) 		0.358
(1.00) 		0.667
(1.00) 		0.0786
(0.778) 		1
(1.00) 		1
(1.00) 		0.338
(1.00) 		0.0336
(0.535) 		1
(1.00) 		1
(1.00)
FAT1 20 (3%) 764 0.775
(1.00) 		0.337
(1.00) 		0.303
(1.00) 		0.38
(1.00) 		0.23
(1.00) 		0.659
(1.00) 		1
(1.00) 		0.896
(1.00) 		0.0779
(0.778) 		0.687
(1.00) 		0.403
(1.00) 		0.523
(1.00) 		0.616
(1.00)
TCEB1 4 (1%) 780 0.195
(1.00) 		0.0887
(0.794) 		0.806
(1.00) 		0.406
(1.00) 		1
(1.00) 		1
(1.00) 		1
(1.00) 		0.427
(1.00) 		0.223
(1.00)
PODXL 6 (1%) 778 0.247
(1.00) 		0.0406
(0.601) 		0.322
(1.00) 		0.476
(1.00) 		1
(1.00) 		1
(1.00) 		0.67
(1.00) 		0.539
(1.00) 		0.568
(1.00) 		0.172
(1.00) 		0.11
(0.815) 		1
(1.00)
DNAJA3 3 (0%) 781 0.391
(1.00) 		0.874
(1.00) 		0.558
(1.00) 		0.288
(1.00) 		1
(1.00) 		0.253
(1.00) 		0.667
(1.00) 		1
(1.00)
NASP 5 (1%) 779 0.434
(1.00) 		0.317
(1.00) 		0.326
(1.00) 		0.473
(1.00) 		1
(1.00) 		0.338
(1.00) 		0.0492
(0.621) 		1
(1.00) 		0.27
(1.00)
SLC23A1 6 (1%) 778 0.123
(0.858) 		0.963
(1.00) 		0.435
(1.00) 		0.297
(1.00) 		1
(1.00) 		0.533
(1.00) 		0.401
(1.00) 		1
(1.00) 		0.239
(1.00) 		1
(1.00)
RILPL1 5 (1%) 779 0.572
(1.00) 		0.99
(1.00) 		0.122
(0.858) 		0.33
(1.00) 		0.348
(1.00) 		0.456
(1.00) 		1
(1.00) 		0.0478
(0.613) 		0.189
(1.00) 		1
(1.00)
NIPBL 15 (2%) 769 0.875
(1.00) 		0.617
(1.00) 		0.139
(0.912) 		0.0636
(0.697) 		0.513
(1.00) 		0.371
(1.00) 		0.408
(1.00) 		0.787
(1.00) 		0.153
(0.967) 		0.179
(1.00) 		0.302
(1.00) 		1
(1.00) 		1
(1.00)
RHEB 3 (0%) 781 0.745
(1.00) 		0.951
(1.00) 		0.455
(1.00) 		0.574
(1.00) 		0.262
(1.00) 		0.253
(1.00) 		1
(1.00) 		0.341
(1.00) 		1
(1.00)
BRAF 5 (1%) 779 0.667
(1.00) 		0.601
(1.00) 		0.865
(1.00) 		1
(1.00) 		0.366
(1.00) 		0.666
(1.00) 		0.201
(1.00) 		1
(1.00) 		1
(1.00)
ANK3 22 (3%) 762 0.128
(0.883) 		0.638
(1.00) 		0.462
(1.00) 		0.567
(1.00) 		0.579
(1.00) 		0.712
(1.00) 		0.106
(0.803) 		0.32
(1.00) 		0.846
(1.00) 		0.136
(0.912) 		0.389
(1.00) 		0.54
(1.00) 		1
(1.00)
EMG1 4 (1%) 780 0.212
(1.00) 		0.829
(1.00) 		0.589
(1.00) 		0.402
(1.00) 		1
(1.00) 		1
(1.00) 		0.295
(1.00) 		1
(1.00) 		1
(1.00)
LHX1 4 (1%) 780 0.729
(1.00) 		0.812
(1.00) 		0.0241
(0.438) 		0.175
(1.00) 		1
(1.00) 		0.107
(0.803) 		0.511
(1.00) 		1
(1.00) 		0.172
(1.00)
SCARB2 4 (1%) 780 0.192
(1.00) 		0.0274
(0.461) 		0.146
(0.933) 		0.136
(0.912) 		1
(1.00) 		1
(1.00) 		0.295
(1.00) 		1
(1.00) 		1
(1.00)
C1ORF25 6 (1%) 778 0.0679
(0.71) 		0.0141
(0.337) 		0.576
(1.00) 		0.0833
(0.794) 		1
(1.00) 		1
(1.00) 		1
(1.00) 		0.541
(1.00) 		1
(1.00) 		1
(1.00)
KDELR3 7 (1%) 777 0.249
(1.00) 		0.495
(1.00) 		0.236
(1.00) 		0.0126
(0.337) 		1
(1.00) 		1
(1.00) 		0.436
(1.00) 		0.108
(0.803) 		0.622
(1.00) 		1
(1.00)
TTLL6 4 (1%) 780 0.813
(1.00) 		0.517
(1.00) 		0.0123
(0.337) 		0.0176
(0.364) 		1
(1.00) 		0.107
(0.803) 		0.0204
(0.403) 		1
(1.00) 		1
(1.00)
STXBP3 5 (1%) 779 0.727
(1.00) 		0.789
(1.00) 		0.41
(1.00) 		0.189
(1.00) 		0.366
(1.00) 		1
(1.00) 		0.605
(1.00) 		1
(1.00) 		0.27
(1.00)
FAM20C 5 (1%) 779 0.446
(1.00) 		0.526
(1.00) 		0.453
(1.00) 		0.389
(1.00) 		1
(1.00) 		1
(1.00) 		0.338
(1.00) 		0.0208
(0.403) 		1
(1.00) 		1
(1.00)
CCBL2 3 (0%) 781 0.196
(1.00) 		0.313
(1.00) 		0.557
(1.00) 		0.289
(1.00) 		1
(1.00) 		0.253
(1.00) 		0.667
(1.00) 		0.34
(1.00) 		1
(1.00)
B3GNT6 3 (0%) 781 0.736
(1.00) 		0.511
(1.00) 		0.805
(1.00) 		0.733
(1.00) 		1
(1.00) 		0.555
(1.00) 		0.669
(1.00) 		0.341
(1.00) 		0.118
(0.854)
HNF1B 4 (1%) 780 0.173
(1.00) 		0.704
(1.00) 		0.322
(1.00) 		0.322
(1.00) 		0.262
(1.00) 		0.602
(1.00) 		0.511
(1.00) 		1
(1.00) 		1
(1.00)
'TP53 MUTATION STATUS' versus 'PATHOLOGIC_STAGE'

P value = 0.0031 (Fisher's exact test), Q value = 0.17

Table S1.  Gene #1: 'TP53 MUTATION STATUS' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

nPatients STAGE I STAGE II STAGE III STAGE IV
ALL 399 89 175 93
TP53 MUTATED 12 10 6 8
TP53 WILD-TYPE 387 79 169 85

Figure S1.  Get High-res Image Gene #1: 'TP53 MUTATION STATUS' versus Clinical Feature #3: 'PATHOLOGIC_STAGE'

'TP53 MUTATION STATUS' versus 'PATHOLOGY_T_STAGE'

P value = 0.00241 (Fisher's exact test), Q value = 0.17

Table S2.  Gene #1: 'TP53 MUTATION STATUS' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

nPatients T1 T2 T3 T4
ALL 423 111 237 11
TP53 MUTATED 13 12 11 2
TP53 WILD-TYPE 410 99 226 9

Figure S2.  Get High-res Image Gene #1: 'TP53 MUTATION STATUS' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'

'TP53 MUTATION STATUS' versus 'HISTOLOGICAL_TYPE'

P value = 1e-05 (Fisher's exact test), Q value = 0.0015

Table S3.  Gene #1: 'TP53 MUTATION STATUS' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'

nPatients KIDNEY CHROMOPHOBE KIDNEY CLEAR CELL RENAL CARCINOMA KIDNEY PAPILLARY RENAL CELL CARCINOMA
ALL 66 436 282
TP53 MUTATED 22 9 7
TP53 WILD-TYPE 44 427 275

Figure S3.  Get High-res Image Gene #1: 'TP53 MUTATION STATUS' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'

'PBRM1 MUTATION STATUS' versus 'HISTOLOGICAL_TYPE'

P value = 1e-05 (Fisher's exact test), Q value = 0.0015

Table S4.  Gene #4: 'PBRM1 MUTATION STATUS' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'

nPatients KIDNEY CHROMOPHOBE KIDNEY CLEAR CELL RENAL CARCINOMA KIDNEY PAPILLARY RENAL CELL CARCINOMA
ALL 66 436 282
PBRM1 MUTATED 1 131 11
PBRM1 WILD-TYPE 65 305 271

Figure S4.  Get High-res Image Gene #4: 'PBRM1 MUTATION STATUS' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'

'VHL MUTATION STATUS' versus 'Time to Death'

P value = 0.0045 (logrank test), Q value = 0.21

Table S5.  Gene #6: 'VHL MUTATION STATUS' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 780 202 0.1 - 194.8 (37.0)
VHL MUTATED 196 69 0.4 - 149.2 (41.7)
VHL WILD-TYPE 584 133 0.1 - 194.8 (36.0)

Figure S5.  Get High-res Image Gene #6: 'VHL MUTATION STATUS' versus Clinical Feature #1: 'Time to Death'

'VHL MUTATION STATUS' versus 'HISTOLOGICAL_TYPE'

P value = 1e-05 (Fisher's exact test), Q value = 0.0015

Table S6.  Gene #6: 'VHL MUTATION STATUS' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'

nPatients KIDNEY CHROMOPHOBE KIDNEY CLEAR CELL RENAL CARCINOMA KIDNEY PAPILLARY RENAL CELL CARCINOMA
ALL 66 436 282
VHL MUTATED 1 192 3
VHL WILD-TYPE 65 244 279

Figure S6.  Get High-res Image Gene #6: 'VHL MUTATION STATUS' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'

'VHL MUTATION STATUS' versus 'RACE'

P value = 1e-05 (Fisher's exact test), Q value = 0.0015

Table S7.  Gene #6: 'VHL MUTATION STATUS' versus Clinical Feature #12: 'RACE'

nPatients AMERICAN INDIAN OR ALASKA NATIVE ASIAN BLACK OR AFRICAN AMERICAN WHITE
ALL 2 14 83 663
VHL MUTATED 0 2 2 190
VHL WILD-TYPE 2 12 81 473

Figure S7.  Get High-res Image Gene #6: 'VHL MUTATION STATUS' versus Clinical Feature #12: 'RACE'

'NF2 MUTATION STATUS' versus 'PATHOLOGY_N_STAGE'

P value = 0.00025 (Fisher's exact test), Q value = 0.025

Table S8.  Gene #7: 'NF2 MUTATION STATUS' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

nPatients N0 N1 N2
ALL 293 40 5
NF2 MUTATED 1 5 0
NF2 WILD-TYPE 292 35 5

Figure S8.  Get High-res Image Gene #7: 'NF2 MUTATION STATUS' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'

'MET MUTATION STATUS' versus 'HISTOLOGICAL_TYPE'

P value = 1e-05 (Fisher's exact test), Q value = 0.0015

Table S9.  Gene #8: 'MET MUTATION STATUS' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'

nPatients KIDNEY CHROMOPHOBE KIDNEY CLEAR CELL RENAL CARCINOMA KIDNEY PAPILLARY RENAL CELL CARCINOMA
ALL 66 436 282
MET MUTATED 0 4 21
MET WILD-TYPE 66 432 261

Figure S9.  Get High-res Image Gene #8: 'MET MUTATION STATUS' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'

'KDM5C MUTATION STATUS' versus 'HISTOLOGICAL_TYPE'

P value = 8e-05 (Fisher's exact test), Q value = 0.01

Table S10.  Gene #9: 'KDM5C MUTATION STATUS' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'

nPatients KIDNEY CHROMOPHOBE KIDNEY CLEAR CELL RENAL CARCINOMA KIDNEY PAPILLARY RENAL CELL CARCINOMA
ALL 66 436 282
KDM5C MUTATED 1 25 1
KDM5C WILD-TYPE 65 411 281

Figure S10.  Get High-res Image Gene #9: 'KDM5C MUTATION STATUS' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'

'MTOR MUTATION STATUS' versus 'GENDER'

P value = 0.00493 (Fisher's exact test), Q value = 0.21

Table S11.  Gene #10: 'MTOR MUTATION STATUS' versus Clinical Feature #7: 'GENDER'

nPatients FEMALE MALE
ALL 258 526
MTOR MUTATED 19 15
MTOR WILD-TYPE 239 511

Figure S11.  Get High-res Image Gene #10: 'MTOR MUTATION STATUS' versus Clinical Feature #7: 'GENDER'

'MTOR MUTATION STATUS' versus 'HISTOLOGICAL_TYPE'

P value = 0.00253 (Fisher's exact test), Q value = 0.17

Table S12.  Gene #10: 'MTOR MUTATION STATUS' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'

nPatients KIDNEY CHROMOPHOBE KIDNEY CLEAR CELL RENAL CARCINOMA KIDNEY PAPILLARY RENAL CELL CARCINOMA
ALL 66 436 282
MTOR MUTATED 2 28 4
MTOR WILD-TYPE 64 408 278

Figure S12.  Get High-res Image Gene #10: 'MTOR MUTATION STATUS' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'

'ZNF814 MUTATION STATUS' versus 'HISTOLOGICAL_TYPE'

P value = 0.00301 (Fisher's exact test), Q value = 0.17

Table S13.  Gene #11: 'ZNF814 MUTATION STATUS' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'

nPatients KIDNEY CHROMOPHOBE KIDNEY CLEAR CELL RENAL CARCINOMA KIDNEY PAPILLARY RENAL CELL CARCINOMA
ALL 66 436 282
ZNF814 MUTATED 3 2 9
ZNF814 WILD-TYPE 63 434 273

Figure S13.  Get High-res Image Gene #11: 'ZNF814 MUTATION STATUS' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'

'AR MUTATION STATUS' versus 'HISTOLOGICAL_TYPE'

P value = 0.00014 (Fisher's exact test), Q value = 0.016

Table S14.  Gene #12: 'AR MUTATION STATUS' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'

nPatients KIDNEY CHROMOPHOBE KIDNEY CLEAR CELL RENAL CARCINOMA KIDNEY PAPILLARY RENAL CELL CARCINOMA
ALL 66 436 282
AR MUTATED 1 1 13
AR WILD-TYPE 65 435 269

Figure S14.  Get High-res Image Gene #12: 'AR MUTATION STATUS' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'

'CACNA1C MUTATION STATUS' versus 'PATHOLOGY_M_STAGE'

P value = 0.00494 (Fisher's exact test), Q value = 0.21

Table S15.  Gene #21: 'CACNA1C MUTATION STATUS' versus Clinical Feature #6: 'PATHOLOGY_M_STAGE'

nPatients 0 1
ALL 494 81
CACNA1C MUTATED 7 6
CACNA1C WILD-TYPE 487 75

Figure S15.  Get High-res Image Gene #21: 'CACNA1C MUTATION STATUS' versus Clinical Feature #6: 'PATHOLOGY_M_STAGE'

'PCF11 MUTATION STATUS' versus 'HISTOLOGICAL_TYPE'

P value = 0.0015 (Fisher's exact test), Q value = 0.12

Table S16.  Gene #26: 'PCF11 MUTATION STATUS' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'

nPatients KIDNEY CHROMOPHOBE KIDNEY CLEAR CELL RENAL CARCINOMA KIDNEY PAPILLARY RENAL CELL CARCINOMA
ALL 66 436 282
PCF11 MUTATED 0 2 11
PCF11 WILD-TYPE 66 434 271

Figure S16.  Get High-res Image Gene #26: 'PCF11 MUTATION STATUS' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'

'KDM6A MUTATION STATUS' versus 'YEARS_TO_BIRTH'

P value = 0.000542 (Wilcoxon-test), Q value = 0.049

Table S17.  Gene #39: 'KDM6A MUTATION STATUS' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 779 60.1 (12.6)
KDM6A MUTATED 11 72.4 (6.7)
KDM6A WILD-TYPE 768 59.9 (12.5)

Figure S17.  Get High-res Image Gene #39: 'KDM6A MUTATION STATUS' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'FAM178A MUTATION STATUS' versus 'Time to Death'

P value = 1.48e-09 (logrank test), Q value = 1.3e-06

Table S18.  Gene #47: 'FAM178A MUTATION STATUS' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 780 202 0.1 - 194.8 (37.0)
FAM178A MUTATED 8 6 0.5 - 52.1 (10.4)
FAM178A WILD-TYPE 772 196 0.1 - 194.8 (37.2)

Figure S18.  Get High-res Image Gene #47: 'FAM178A MUTATION STATUS' versus Clinical Feature #1: 'Time to Death'

'FAM47A MUTATION STATUS' versus 'Time to Death'

P value = 0.00299 (logrank test), Q value = 0.17

Table S19.  Gene #55: 'FAM47A MUTATION STATUS' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 780 202 0.1 - 194.8 (37.0)
FAM47A MUTATED 6 4 2.5 - 84.3 (22.3)
FAM47A WILD-TYPE 774 198 0.1 - 194.8 (37.2)

Figure S19.  Get High-res Image Gene #55: 'FAM47A MUTATION STATUS' versus Clinical Feature #1: 'Time to Death'

'MLL3 MUTATION STATUS' versus 'HISTOLOGICAL_TYPE'

P value = 0.00301 (Fisher's exact test), Q value = 0.17

Table S20.  Gene #58: 'MLL3 MUTATION STATUS' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'

nPatients KIDNEY CHROMOPHOBE KIDNEY CLEAR CELL RENAL CARCINOMA KIDNEY PAPILLARY RENAL CELL CARCINOMA
ALL 66 436 282
MLL3 MUTATED 9 15 18
MLL3 WILD-TYPE 57 421 264

Figure S20.  Get High-res Image Gene #58: 'MLL3 MUTATION STATUS' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'

'MLL3 MUTATION STATUS' versus 'RACE'

P value = 0.00464 (Fisher's exact test), Q value = 0.21

Table S21.  Gene #58: 'MLL3 MUTATION STATUS' versus Clinical Feature #12: 'RACE'

nPatients AMERICAN INDIAN OR ALASKA NATIVE ASIAN BLACK OR AFRICAN AMERICAN WHITE
ALL 2 14 83 663
MLL3 MUTATED 0 1 12 28
MLL3 WILD-TYPE 2 13 71 635

Figure S21.  Get High-res Image Gene #58: 'MLL3 MUTATION STATUS' versus Clinical Feature #12: 'RACE'

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/KIPAN-TP/22815577/transformed.cor.cli.txt

  • Clinical data file = /xchip/cga/gdac-prod/tcga-gdac/jobResults/Append_Data/KIPAN-TP/22506733/KIPAN-TP.merged_data.txt

  • Number of patients = 784

  • Number of significantly mutated genes = 70

  • 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.

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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