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 92 genes and 8 clinical features across 515 patients, 29 significant findings detected with Q value < 0.25.

  • IDH1 mutation correlated to 'Time to Death',  'YEARS_TO_BIRTH',  'KARNOFSKY_PERFORMANCE_SCORE', and 'HISTOLOGICAL_TYPE'.

  • TP53 mutation correlated to 'YEARS_TO_BIRTH',  'RADIATION_THERAPY', and 'HISTOLOGICAL_TYPE'.

  • ATRX mutation correlated to 'YEARS_TO_BIRTH' and 'HISTOLOGICAL_TYPE'.

  • CIC mutation correlated to 'Time to Death',  'RADIATION_THERAPY', and 'HISTOLOGICAL_TYPE'.

  • NOTCH1 mutation correlated to 'HISTOLOGICAL_TYPE'.

  • IDH2 mutation correlated to 'HISTOLOGICAL_TYPE'.

  • FUBP1 mutation correlated to 'YEARS_TO_BIRTH' and 'HISTOLOGICAL_TYPE'.

  • NF1 mutation correlated to 'Time to Death'.

  • PTEN mutation correlated to 'Time to Death',  'YEARS_TO_BIRTH', and 'HISTOLOGICAL_TYPE'.

  • EGFR mutation correlated to 'Time to Death',  'YEARS_TO_BIRTH', and 'KARNOFSKY_PERFORMANCE_SCORE'.

  • SMARCA4 mutation correlated to 'Time to Death'.

  • ZNF292 mutation correlated to 'YEARS_TO_BIRTH'.

  • PLCG1 mutation correlated to 'Time to Death'.

  • SETD2 mutation correlated to 'YEARS_TO_BIRTH'.

  • TMEM184A mutation correlated to 'Time to Death'.

  • WRN mutation correlated to 'ETHNICITY'.

Results
Overview of the results

Table 1.  Get Full Table Overview of the association between mutation status of 92 genes and 8 clinical features. Shown in the table are P values (Q values). Thresholded by Q value < 0.25, 29 significant findings detected.

Clinical
Features 		Time
to
Death 		YEARS
TO
BIRTH 		GENDER RADIATION
THERAPY 		KARNOFSKY
PERFORMANCE
SCORE 		HISTOLOGICAL
TYPE 		RACE ETHNICITY
nMutated (%) nWild-Type logrank test Wilcoxon-test Fisher's exact test Fisher's exact test Wilcoxon-test Fisher's exact test Fisher's exact test Fisher's exact test
IDH1 400 (78%) 115 0
(0) 		9.81e-09
(1.2e-06) 		1
(1.00) 		0.0123
(0.289) 		0.00286
(0.0914) 		0.00555
(0.151) 		0.025
(0.439) 		1
(1.00)
TP53 250 (49%) 265 0.0444
(0.597) 		3.07e-12
(7.54e-10) 		0.25
(0.9) 		0.000182
(0.0079) 		0.366
(0.921) 		1e-05
(0.000613) 		0.0322
(0.526) 		0.715
(1.00)
CIC 108 (21%) 407 8.16e-05
(0.00429) 		0.109
(0.737) 		0.328
(0.921) 		6.82e-06
(0.000613) 		0.236
(0.9) 		1e-05
(0.000613) 		0.748
(1.00) 		0.655
(1.00)
PTEN 24 (5%) 491 0.000127
(0.00583) 		0.00176
(0.0646) 		0.297
(0.916) 		0.0684
(0.668) 		0.592
(1.00) 		0.00276
(0.0914) 		0.163
(0.803) 		1
(1.00)
EGFR 35 (7%) 480 1.88e-11
(3.45e-09) 		4.92e-11
(7.25e-09) 		1
(1.00) 		0.0227
(0.414) 		0.00535
(0.151) 		0.0503
(0.65) 		0.178
(0.808) 		0.717
(1.00)
ATRX 197 (38%) 318 0.0813
(0.682) 		2.71e-12
(7.54e-10) 		0.784
(1.00) 		0.0123
(0.289) 		0.939
(1.00) 		1e-05
(0.000613) 		0.396
(0.936) 		1
(1.00)
FUBP1 47 (9%) 468 0.133
(0.787) 		0.00305
(0.0934) 		0.645
(1.00) 		0.0728
(0.668) 		0.234
(0.9) 		1e-05
(0.000613) 		1
(1.00) 		0.0998
(0.718)
NOTCH1 42 (8%) 473 0.21
(0.863) 		0.043
(0.596) 		0.747
(1.00) 		0.504
(1.00) 		0.879
(1.00) 		5e-05
(0.00283) 		0.334
(0.921) 		1
(1.00)
IDH2 20 (4%) 495 0.0597
(0.668) 		0.0739
(0.668) 		1
(1.00) 		0.474
(0.992) 		0.617
(1.00) 		0.00093
(0.036) 		0.45
(0.982) 		0.125
(0.761)
NF1 33 (6%) 482 9.59e-05
(0.00471) 		0.0126
(0.289) 		0.59
(1.00) 		0.568
(1.00) 		0.555
(1.00) 		0.0158
(0.324) 		0.219
(0.875) 		0.257
(0.9)
SMARCA4 26 (5%) 489 0.00516
(0.151) 		0.525
(1.00) 		0.318
(0.921) 		1
(1.00) 		0.431
(0.956) 		0.816
(1.00) 		0.114
(0.746) 		0.643
(1.00)
ZNF292 14 (3%) 501 0.985
(1.00) 		0.00654
(0.172) 		0.174
(0.808) 		0.576
(1.00) 		0.625
(1.00) 		0.889
(1.00) 		0.14
(0.802) 		0.596
(1.00)
PLCG1 6 (1%) 509 1.08e-07
(1.13e-05) 		0.0147
(0.319) 		0.415
(0.936) 		0.413
(0.936) 		0.311
(0.916) 		0.299
(0.916) 		0.31
(0.916) 		1
(1.00)
SETD2 10 (2%) 505 0.559
(1.00) 		0.00798
(0.202) 		1
(1.00) 		0.748
(1.00) 		0.311
(0.916) 		0.367
(0.921) 		0.464
(0.987) 		1
(1.00)
TMEM184A 3 (1%) 512 0.000469
(0.0192) 		0.152
(0.803) 		1
(1.00) 		1
(1.00) 		1
(1.00) 		0.165
(0.803) 		1
(1.00)
WRN 5 (1%) 510 0.0836
(0.682) 		0.378
(0.921) 		0.66
(1.00) 		1
(1.00) 		0.0387
(0.566) 		0.549
(1.00) 		0.264
(0.9) 		0.00245
(0.0859)
PIK3R1 22 (4%) 493 0.36
(0.921) 		0.0806
(0.682) 		0.275
(0.916) 		0.37
(0.921) 		0.754
(1.00) 		0.353
(0.921) 		0.0446
(0.597) 		0.623
(1.00)
TCF12 15 (3%) 500 0.61
(1.00) 		0.227
(0.9) 		0.601
(1.00) 		1
(1.00) 		0.909
(1.00) 		0.894
(1.00) 		1
(1.00) 		0.613
(1.00)
ARID1A 20 (4%) 495 0.0363
(0.566) 		0.647
(1.00) 		0.493
(1.00) 		0.349
(0.921) 		0.958
(1.00) 		0.196
(0.836) 		1
(1.00) 		1
(1.00)
GAGE2A 8 (2%) 507 0.518
(1.00) 		0.734
(1.00) 		0.737
(1.00) 		1
(1.00) 		0.328
(0.921) 		1
(1.00) 		0.054
(0.667) 		0.426
(0.95)
NUDT11 11 (2%) 504 0.475
(0.992) 		0.322
(0.921) 		0.36
(0.921) 		1
(1.00) 		0.639
(1.00) 		0.74
(1.00) 		1
(1.00) 		1
(1.00)
PIK3CA 44 (9%) 471 0.648
(1.00) 		0.0733
(0.668) 		0.875
(1.00) 		0.198
(0.836) 		0.106
(0.737) 		0.0176
(0.342) 		0.629
(1.00) 		0.741
(1.00)
STK19 10 (2%) 505 0.301
(0.916) 		0.311
(0.916) 		0.119
(0.75) 		0.681
(1.00) 		0.233
(0.9) 		0.0742
(0.668) 		1
(1.00) 		0.138
(0.802)
NIPBL 18 (3%) 497 0.056
(0.668) 		0.175
(0.808) 		0.157
(0.803) 		0.31
(0.916) 		0.601
(1.00) 		0.0691
(0.668) 		0.0744
(0.668) 		0.11
(0.737)
TRERF1 6 (1%) 509 0.258
(0.9) 		0.283
(0.916) 		0.0938
(0.691) 		0.681
(1.00) 		0.801
(1.00) 		0.168
(0.803) 		1
(1.00) 		1
(1.00)
CREBZF 7 (1%) 508 0.965
(1.00) 		0.171
(0.803) 		0.251
(0.9) 		1
(1.00) 		0.0726
(0.668) 		0.0311
(0.521) 		0.354
(0.921) 		0.384
(0.921)
DNMT3A 11 (2%) 504 0.0333
(0.533) 		0.666
(1.00) 		1
(1.00) 		0.542
(1.00) 		0.946
(1.00) 		0.208
(0.862) 		0.495
(1.00) 		0.535
(1.00)
EMG1 5 (1%) 510 0.535
(1.00) 		0.0839
(0.682) 		0.178
(0.808) 		1
(1.00) 		0.142
(0.803) 		0.851
(1.00) 		1
(1.00) 		1
(1.00)
IRS4 8 (2%) 507 0.139
(0.802) 		0.887
(1.00) 		1
(1.00) 		1
(1.00) 		0.242
(0.9) 		0.092
(0.685) 		1
(1.00) 		0.426
(0.95)
MYST4 11 (2%) 504 0.163
(0.803) 		0.109
(0.737) 		1
(1.00) 		1
(1.00) 		0.925
(1.00) 		0.19
(0.836) 		0.147
(0.803) 		0.501
(1.00)
MED9 3 (1%) 512 0.305
(0.916) 		0.868
(1.00) 		0.257
(0.9) 		0.288
(0.916) 		0.0159
(0.324) 		1
(1.00) 		1
(1.00)
FAM47C 19 (4%) 496 0.0687
(0.668) 		0.704
(1.00) 		0.25
(0.9) 		0.461
(0.986) 		0.632
(1.00) 		0.763
(1.00) 		1
(1.00) 		1
(1.00)
NRAS 4 (1%) 511 0.43
(0.956) 		0.885
(1.00) 		1
(1.00) 		0.642
(1.00) 		0.471
(0.99) 		0.0223
(0.414) 		1
(1.00) 		1
(1.00)
PLXNA3 9 (2%) 506 0.0701
(0.668) 		0.249
(0.9) 		0.197
(0.836) 		0.16
(0.803) 		0.59
(1.00) 		0.834
(1.00) 		0.105
(0.737) 		1
(1.00)
TNRC18 10 (2%) 505 0.361
(0.921) 		0.742
(1.00) 		0.197
(0.836) 		0.33
(0.921) 		0.417
(0.939) 		0.366
(0.921) 		1
(1.00) 		1
(1.00)
HTRA2 5 (1%) 510 0.344
(0.921) 		0.0277
(0.474) 		1
(1.00) 		0.386
(0.921) 		0.452
(0.982) 		1
(1.00) 		0.292
(0.916)
ZMIZ1 9 (2%) 506 0.0693
(0.668) 		0.858
(1.00) 		0.522
(1.00) 		1
(1.00) 		0.15
(0.803) 		0.436
(0.964) 		0.0653
(0.668) 		0.0171
(0.34)
CUL4B 10 (2%) 505 0.168
(0.803) 		0.822
(1.00) 		0.119
(0.75) 		0.163
(0.803) 		0.639
(1.00) 		0.335
(0.921) 		0.218
(0.875) 		1
(1.00)
DLX6 4 (1%) 511 0.312
(0.916) 		0.976
(1.00) 		0.632
(1.00) 		1
(1.00) 		0.457
(0.982) 		1
(1.00) 		1
(1.00)
RB1 6 (1%) 509 0.834
(1.00) 		0.164
(0.803) 		0.415
(0.936) 		1
(1.00) 		0.0965
(0.703) 		0.308
(0.916) 		1
(1.00)
ROBO3 5 (1%) 510 0.365
(0.921) 		0.531
(1.00) 		0.66
(1.00) 		0.642
(1.00) 		0.669
(1.00) 		0.38
(0.921) 		1
(1.00) 		0.292
(0.916)
SRPX 4 (1%) 511 0.199
(0.836) 		0.0429
(0.596) 		0.0392
(0.566) 		1
(1.00) 		0.554
(1.00) 		0.374
(0.921) 		0.22
(0.876) 		1
(1.00)
RBPJ 7 (1%) 508 0.869
(1.00) 		0.0539
(0.667) 		1
(1.00) 		0.681
(1.00) 		0.338
(0.921) 		0.274
(0.916) 		1
(1.00) 		1
(1.00)
TMEM216 3 (1%) 512 0.741
(1.00) 		0.817
(1.00) 		0.0884
(0.682) 		1
(1.00) 		0.368
(0.921) 		1
(1.00) 		1
(1.00)
ARID2 11 (2%) 504 0.502
(1.00) 		0.108
(0.737) 		1
(1.00) 		0.217
(0.875) 		0.803
(1.00) 		0.208
(0.862) 		0.245
(0.9) 		1
(1.00)
SLC6A3 9 (2%) 506 0.605
(1.00) 		0.378
(0.921) 		0.522
(1.00) 		1
(1.00) 		0.759
(1.00) 		1
(1.00) 		0.384
(0.921)
PDGFRA 10 (2%) 505 0.156
(0.803) 		0.707
(1.00) 		0.353
(0.921) 		0.748
(1.00) 		0.146
(0.803) 		0.115
(0.746) 		1
(1.00) 		0.138
(0.802)
PTPN11 7 (1%) 508 0.288
(0.916) 		0.342
(0.921) 		1
(1.00) 		1
(1.00) 		0.753
(1.00) 		0.307
(0.916) 		0.351
(0.921) 		1
(1.00)
MYT1 6 (1%) 509 0.263
(0.9) 		0.408
(0.936) 		1
(1.00) 		0.0865
(0.682) 		0.733
(1.00) 		0.166
(0.803) 		1
(1.00) 		1
(1.00)
PPL 6 (1%) 509 0.0383
(0.566) 		0.725
(1.00) 		1
(1.00) 		1
(1.00) 		0.801
(1.00) 		0.458
(0.982) 		1
(1.00) 		0.292
(0.916)
CIB1 4 (1%) 511 0.408
(0.936) 		1
(1.00) 		1
(1.00) 		1
(1.00) 		0.753
(1.00) 		1
(1.00) 		1
(1.00) 		1
(1.00)
ANKRD36 7 (1%) 508 0.0921
(0.685) 		0.59
(1.00) 		0.706
(1.00) 		0.0469
(0.616) 		0.0711
(0.668) 		0.235
(0.9) 		0.0693
(0.668) 		1
(1.00)
NAP1L2 4 (1%) 511 0.263
(0.9) 		0.177
(0.808) 		1
(1.00) 		0.642
(1.00) 		0.191
(0.836) 		1
(1.00) 		1
(1.00)
SMOC1 3 (1%) 512 0.338
(0.921) 		0.443
(0.974) 		1
(1.00) 		0.288
(0.916) 		0.471
(0.99) 		0.476
(0.992) 		1
(1.00) 		1
(1.00)
ABCA7 10 (2%) 505 0.925
(1.00) 		0.311
(0.916) 		0.523
(1.00) 		1
(1.00) 		0.639
(1.00) 		0.61
(1.00) 		1
(1.00) 		0.501
(1.00)
ZNF512B 5 (1%) 510 0.0782
(0.682) 		0.299
(0.916) 		1
(1.00) 		1
(1.00) 		1
(1.00) 		1
(1.00) 		0.292
(0.916)
PRX 10 (2%) 505 0.771
(1.00) 		0.462
(0.986) 		0.353
(0.921) 		0.33
(0.921) 		0.328
(0.921) 		0.78
(1.00) 		1
(1.00) 		0.501
(1.00)
SMARCB1 4 (1%) 511 0.305
(0.916) 		0.809
(1.00) 		0.632
(1.00) 		0.303
(0.916) 		0.753
(1.00) 		1
(1.00) 		1
(1.00) 		1
(1.00)
C9ORF79 10 (2%) 505 0.111
(0.739) 		0.275
(0.916) 		1
(1.00) 		0.16
(0.803) 		0.169
(0.803) 		0.566
(1.00) 		0.458
(0.982) 		1
(1.00)
KRT3 4 (1%) 511 0.0899
(0.682) 		0.856
(1.00) 		0.632
(1.00) 		1
(1.00) 		0.107
(0.737) 		0.682
(1.00) 		1
(1.00) 		0.241
(0.9)
ELF4 4 (1%) 511 0.0879
(0.682) 		0.816
(1.00) 		0.0392
(0.566) 		0.642
(1.00) 		0.683
(1.00) 		1
(1.00) 		1
(1.00)
NEU2 6 (1%) 509 0.526
(1.00) 		0.307
(0.916) 		1
(1.00) 		1
(1.00) 		0.457
(0.982) 		1
(1.00) 		0.34
(0.921)
ZNF709 3 (1%) 512 0.503
(1.00) 		0.608
(1.00) 		0.257
(0.9) 		1
(1.00) 		0.367
(0.921) 		0.169
(0.803) 		1
(1.00)
R3HDM1 7 (1%) 508 0.0576
(0.668) 		0.871
(1.00) 		1
(1.00) 		1
(1.00) 		0.753
(1.00) 		0.491
(1.00) 		1
(1.00) 		0.384
(0.921)
C14ORF4 3 (1%) 512 0.466
(0.989) 		0.742
(1.00) 		0.589
(1.00) 		1
(1.00) 		0.787
(1.00) 		0.167
(0.803) 		1
(1.00)
ZBTB20 21 (4%) 494 0.411
(0.936) 		0.498
(1.00) 		0.372
(0.921) 		0.159
(0.803) 		0.804
(1.00) 		0.183
(0.817) 		0.127
(0.767) 		0.635
(1.00)
C4BPA 6 (1%) 509 0.521
(1.00) 		0.642
(1.00) 		0.415
(0.936) 		0.413
(0.936) 		0.171
(0.803) 		0.888
(1.00) 		0.309
(0.916) 		0.34
(0.921)
ENGASE 5 (1%) 510 0.506
(1.00) 		0.886
(1.00) 		0.66
(1.00) 		0.162
(0.803) 		0.991
(1.00) 		0.262
(0.9) 		1
(1.00) 		1
(1.00)
DLC1 6 (1%) 509 0.547
(1.00) 		0.549
(1.00) 		0.415
(0.936) 		0.0865
(0.682) 		0.662
(1.00) 		1
(1.00) 		0.34
(0.921)
G6PC 6 (1%) 509 0.866
(1.00) 		0.4
(0.936) 		0.696
(1.00) 		0.413
(0.936) 		0.514
(1.00) 		0.456
(0.982) 		1
(1.00) 		0.0544
(0.667)
SLC12A7 7 (1%) 508 0.238
(0.9) 		0.538
(1.00) 		0.706
(1.00) 		0.413
(0.936) 		0.519
(1.00) 		1
(1.00) 		0.352
(0.921) 		1
(1.00)
RET 7 (1%) 508 0.645
(1.00) 		0.5
(1.00) 		0.251
(0.9) 		0.438
(0.964) 		0.602
(1.00) 		0.0713
(0.668) 		1
(1.00) 		1
(1.00)
ZC3H11A 6 (1%) 509 0.613
(1.00) 		0.195
(0.836) 		0.696
(1.00) 		1
(1.00) 		0.338
(0.921) 		0.665
(1.00) 		1
(1.00) 		1
(1.00)
USP6 7 (1%) 508 0.0846
(0.682) 		0.522
(1.00) 		1
(1.00) 		0.258
(0.9) 		0.0725
(0.668) 		0.306
(0.916) 		0.351
(0.921) 		1
(1.00)
RBBP6 6 (1%) 509 0.194
(0.836) 		0.321
(0.921) 		1
(1.00) 		0.681
(1.00) 		0.774
(1.00) 		0.124
(0.761) 		1
(1.00)
SLFN11 6 (1%) 509 0.0895
(0.682) 		0.0583
(0.668) 		0.696
(1.00) 		1
(1.00) 		0.471
(0.99) 		0.35
(0.921) 		1
(1.00) 		0.34
(0.921)
ASXL2 3 (1%) 512 0.118
(0.75) 		0.413
(0.936) 		0.589
(1.00) 		1
(1.00) 		0.628
(1.00) 		1
(1.00) 		1
(1.00)
KRT15 6 (1%) 509 0.75
(1.00) 		0.116
(0.746) 		0.696
(1.00) 		0.211
(0.864) 		0.412
(0.936) 		0.888
(1.00) 		0.309
(0.916) 		1
(1.00)
FMR1 5 (1%) 510 0.0687
(0.668) 		0.181
(0.817) 		1
(1.00) 		0.653
(1.00) 		0.356
(0.921) 		0.125
(0.761) 		1
(1.00) 		1
(1.00)
DDX5 5 (1%) 510 0.331
(0.921) 		0.854
(1.00) 		1
(1.00) 		1
(1.00) 		0.292
(0.916) 		0.852
(1.00) 		1
(1.00) 		0.241
(0.9)
SCN4A 6 (1%) 509 0.182
(0.817) 		0.26
(0.9) 		0.415
(0.936) 		0.681
(1.00) 		0.34
(0.921) 		0.774
(1.00) 		1
(1.00) 		1
(1.00)
CCDC135 7 (1%) 508 0.233
(0.9) 		0.755
(1.00) 		0.251
(0.9) 		1
(1.00) 		0.705
(1.00) 		1
(1.00) 		0.384
(0.921)
MYOCD 9 (2%) 506 0.146
(0.803) 		0.41
(0.936) 		1
(1.00) 		0.163
(0.803) 		0.503
(1.00) 		0.0143
(0.319) 		0.426
(0.95) 		1
(1.00)
KTELC1 5 (1%) 510 0.308
(0.916) 		0.661
(1.00) 		0.387
(0.921) 		0.653
(1.00) 		0.849
(1.00) 		1
(1.00) 		1
(1.00)
GPR133 4 (1%) 511 0.271
(0.916) 		0.514
(1.00) 		1
(1.00) 		1
(1.00) 		1
(1.00) 		1
(1.00) 		0.241
(0.9)
CDH3 3 (1%) 512 0.294
(0.916) 		0.627
(1.00) 		0.0884
(0.682) 		1
(1.00) 		0.632
(1.00) 		1
(1.00) 		1
(1.00)
SLC25A5 4 (1%) 511 0.0231
(0.414) 		0.577
(1.00) 		0.329
(0.921) 		1
(1.00) 		0.255
(0.9) 		0.84
(1.00) 		0.218
(0.875) 		1
(1.00)
LAMA4 4 (1%) 511 0.792
(1.00) 		0.355
(0.921) 		0.132
(0.787) 		1
(1.00) 		0.753
(1.00) 		0.0666
(0.668) 		0.0785
(0.682) 		0.241
(0.9)
NKD2 4 (1%) 511 0.968
(1.00) 		0.689
(1.00) 		1
(1.00) 		0.162
(0.803) 		0.457
(0.982) 		1
(1.00) 		1
(1.00)
PHF3 8 (2%) 507 0.693
(1.00) 		0.608
(1.00) 		1
(1.00) 		0.16
(0.803) 		0.12
(0.75) 		0.606
(1.00) 		0.387
(0.921) 		0.384
(0.921)
AGBL1 5 (1%) 510 0.241
(0.9) 		0.205
(0.856) 		0.387
(0.921) 		1
(1.00) 		0.19
(0.836) 		1
(1.00) 		1
(1.00)
ZNF148 4 (1%) 511 0.101
(0.718) 		0.668
(1.00) 		1
(1.00) 		0.162
(0.803) 		0.378
(0.921) 		0.0797
(0.682) 		1
(1.00)
'IDH1 MUTATION STATUS' versus 'Time to Death'

P value = 0 (logrank test), Q value = 0

Table S1.  Gene #1: 'IDH1 MUTATION STATUS' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 511 125 0.0 - 211.2 (22.3)
IDH1 MUTATED 396 73 0.0 - 182.3 (25.7)
IDH1 WILD-TYPE 115 52 0.1 - 211.2 (16.2)

Figure S1.  Get High-res Image Gene #1: 'IDH1 MUTATION STATUS' versus Clinical Feature #1: 'Time to Death'

'IDH1 MUTATION STATUS' versus 'YEARS_TO_BIRTH'

P value = 9.81e-09 (Wilcoxon-test), Q value = 1.2e-06

Table S2.  Gene #1: 'IDH1 MUTATION STATUS' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 514 42.9 (13.4)
IDH1 MUTATED 399 41.0 (12.3)
IDH1 WILD-TYPE 115 49.6 (14.6)

Figure S2.  Get High-res Image Gene #1: 'IDH1 MUTATION STATUS' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'IDH1 MUTATION STATUS' versus 'KARNOFSKY_PERFORMANCE_SCORE'

P value = 0.00286 (Wilcoxon-test), Q value = 0.091

Table S3.  Gene #1: 'IDH1 MUTATION STATUS' versus Clinical Feature #5: 'KARNOFSKY_PERFORMANCE_SCORE'

nPatients Mean (Std.Dev)
ALL 307 86.6 (12.6)
IDH1 MUTATED 241 87.7 (12.0)
IDH1 WILD-TYPE 66 82.7 (13.8)

Figure S3.  Get High-res Image Gene #1: 'IDH1 MUTATION STATUS' versus Clinical Feature #5: 'KARNOFSKY_PERFORMANCE_SCORE'

'IDH1 MUTATION STATUS' versus 'HISTOLOGICAL_TYPE'

P value = 0.00555 (Fisher's exact test), Q value = 0.15

Table S4.  Gene #1: 'IDH1 MUTATION STATUS' versus Clinical Feature #6: 'HISTOLOGICAL_TYPE'

nPatients ASTROCYTOMA OLIGOASTROCYTOMA OLIGODENDROGLIOMA
ALL 194 130 191
IDH1 MUTATED 136 109 155
IDH1 WILD-TYPE 58 21 36

Figure S4.  Get High-res Image Gene #1: 'IDH1 MUTATION STATUS' versus Clinical Feature #6: 'HISTOLOGICAL_TYPE'

'TP53 MUTATION STATUS' versus 'YEARS_TO_BIRTH'

P value = 3.07e-12 (Wilcoxon-test), Q value = 7.5e-10

Table S5.  Gene #2: 'TP53 MUTATION STATUS' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 514 42.9 (13.4)
TP53 MUTATED 250 38.6 (11.3)
TP53 WILD-TYPE 264 47.0 (13.9)

Figure S5.  Get High-res Image Gene #2: 'TP53 MUTATION STATUS' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'TP53 MUTATION STATUS' versus 'RADIATION_THERAPY'

P value = 0.000182 (Fisher's exact test), Q value = 0.0079

Table S6.  Gene #2: 'TP53 MUTATION STATUS' versus Clinical Feature #4: 'RADIATION_THERAPY'

nPatients NO YES
ALL 186 296
TP53 MUTATED 71 165
TP53 WILD-TYPE 115 131

Figure S6.  Get High-res Image Gene #2: 'TP53 MUTATION STATUS' versus Clinical Feature #4: 'RADIATION_THERAPY'

'TP53 MUTATION STATUS' versus 'HISTOLOGICAL_TYPE'

P value = 1e-05 (Fisher's exact test), Q value = 0.00061

Table S7.  Gene #2: 'TP53 MUTATION STATUS' versus Clinical Feature #6: 'HISTOLOGICAL_TYPE'

nPatients ASTROCYTOMA OLIGOASTROCYTOMA OLIGODENDROGLIOMA
ALL 194 130 191
TP53 MUTATED 131 74 45
TP53 WILD-TYPE 63 56 146

Figure S7.  Get High-res Image Gene #2: 'TP53 MUTATION STATUS' versus Clinical Feature #6: 'HISTOLOGICAL_TYPE'

'ATRX MUTATION STATUS' versus 'YEARS_TO_BIRTH'

P value = 2.71e-12 (Wilcoxon-test), Q value = 7.5e-10

Table S8.  Gene #3: 'ATRX MUTATION STATUS' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 514 42.9 (13.4)
ATRX MUTATED 197 37.9 (11.9)
ATRX WILD-TYPE 317 46.1 (13.3)

Figure S8.  Get High-res Image Gene #3: 'ATRX MUTATION STATUS' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'ATRX MUTATION STATUS' versus 'HISTOLOGICAL_TYPE'

P value = 1e-05 (Fisher's exact test), Q value = 0.00061

Table S9.  Gene #3: 'ATRX MUTATION STATUS' versus Clinical Feature #6: 'HISTOLOGICAL_TYPE'

nPatients ASTROCYTOMA OLIGOASTROCYTOMA OLIGODENDROGLIOMA
ALL 194 130 191
ATRX MUTATED 98 64 35
ATRX WILD-TYPE 96 66 156

Figure S9.  Get High-res Image Gene #3: 'ATRX MUTATION STATUS' versus Clinical Feature #6: 'HISTOLOGICAL_TYPE'

'CIC MUTATION STATUS' versus 'Time to Death'

P value = 8.16e-05 (logrank test), Q value = 0.0043

Table S10.  Gene #4: 'CIC MUTATION STATUS' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 511 125 0.0 - 211.2 (22.3)
CIC MUTATED 107 12 0.1 - 211.2 (24.6)
CIC WILD-TYPE 404 113 0.0 - 172.8 (21.3)

Figure S10.  Get High-res Image Gene #4: 'CIC MUTATION STATUS' versus Clinical Feature #1: 'Time to Death'

'CIC MUTATION STATUS' versus 'RADIATION_THERAPY'

P value = 6.82e-06 (Fisher's exact test), Q value = 0.00061

Table S11.  Gene #4: 'CIC MUTATION STATUS' versus Clinical Feature #4: 'RADIATION_THERAPY'

nPatients NO YES
ALL 186 296
CIC MUTATED 60 43
CIC WILD-TYPE 126 253

Figure S11.  Get High-res Image Gene #4: 'CIC MUTATION STATUS' versus Clinical Feature #4: 'RADIATION_THERAPY'

'CIC MUTATION STATUS' versus 'HISTOLOGICAL_TYPE'

P value = 1e-05 (Fisher's exact test), Q value = 0.00061

Table S12.  Gene #4: 'CIC MUTATION STATUS' versus Clinical Feature #6: 'HISTOLOGICAL_TYPE'

nPatients ASTROCYTOMA OLIGOASTROCYTOMA OLIGODENDROGLIOMA
ALL 194 130 191
CIC MUTATED 3 23 82
CIC WILD-TYPE 191 107 109

Figure S12.  Get High-res Image Gene #4: 'CIC MUTATION STATUS' versus Clinical Feature #6: 'HISTOLOGICAL_TYPE'

'NOTCH1 MUTATION STATUS' versus 'HISTOLOGICAL_TYPE'

P value = 5e-05 (Fisher's exact test), Q value = 0.0028

Table S13.  Gene #5: 'NOTCH1 MUTATION STATUS' versus Clinical Feature #6: 'HISTOLOGICAL_TYPE'

nPatients ASTROCYTOMA OLIGOASTROCYTOMA OLIGODENDROGLIOMA
ALL 194 130 191
NOTCH1 MUTATED 6 7 29
NOTCH1 WILD-TYPE 188 123 162

Figure S13.  Get High-res Image Gene #5: 'NOTCH1 MUTATION STATUS' versus Clinical Feature #6: 'HISTOLOGICAL_TYPE'

'IDH2 MUTATION STATUS' versus 'HISTOLOGICAL_TYPE'

P value = 0.00093 (Fisher's exact test), Q value = 0.036

Table S14.  Gene #6: 'IDH2 MUTATION STATUS' versus Clinical Feature #6: 'HISTOLOGICAL_TYPE'

nPatients ASTROCYTOMA OLIGOASTROCYTOMA OLIGODENDROGLIOMA
ALL 194 130 191
IDH2 MUTATED 1 5 14
IDH2 WILD-TYPE 193 125 177

Figure S14.  Get High-res Image Gene #6: 'IDH2 MUTATION STATUS' versus Clinical Feature #6: 'HISTOLOGICAL_TYPE'

'FUBP1 MUTATION STATUS' versus 'YEARS_TO_BIRTH'

P value = 0.00305 (Wilcoxon-test), Q value = 0.093

Table S15.  Gene #8: 'FUBP1 MUTATION STATUS' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 514 42.9 (13.4)
FUBP1 MUTATED 47 47.4 (9.5)
FUBP1 WILD-TYPE 467 42.5 (13.6)

Figure S15.  Get High-res Image Gene #8: 'FUBP1 MUTATION STATUS' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'FUBP1 MUTATION STATUS' versus 'HISTOLOGICAL_TYPE'

P value = 1e-05 (Fisher's exact test), Q value = 0.00061

Table S16.  Gene #8: 'FUBP1 MUTATION STATUS' versus Clinical Feature #6: 'HISTOLOGICAL_TYPE'

nPatients ASTROCYTOMA OLIGOASTROCYTOMA OLIGODENDROGLIOMA
ALL 194 130 191
FUBP1 MUTATED 2 9 36
FUBP1 WILD-TYPE 192 121 155

Figure S16.  Get High-res Image Gene #8: 'FUBP1 MUTATION STATUS' versus Clinical Feature #6: 'HISTOLOGICAL_TYPE'

'NF1 MUTATION STATUS' versus 'Time to Death'

P value = 9.59e-05 (logrank test), Q value = 0.0047

Table S17.  Gene #9: 'NF1 MUTATION STATUS' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 511 125 0.0 - 211.2 (22.3)
NF1 MUTATED 33 15 0.2 - 211.2 (18.6)
NF1 WILD-TYPE 478 110 0.0 - 182.3 (23.4)

Figure S17.  Get High-res Image Gene #9: 'NF1 MUTATION STATUS' versus Clinical Feature #1: 'Time to Death'

'PTEN MUTATION STATUS' versus 'Time to Death'

P value = 0.000127 (logrank test), Q value = 0.0058

Table S18.  Gene #11: 'PTEN MUTATION STATUS' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 511 125 0.0 - 211.2 (22.3)
PTEN MUTATED 24 12 0.5 - 211.2 (17.1)
PTEN WILD-TYPE 487 113 0.0 - 182.3 (23.2)

Figure S18.  Get High-res Image Gene #11: 'PTEN MUTATION STATUS' versus Clinical Feature #1: 'Time to Death'

'PTEN MUTATION STATUS' versus 'YEARS_TO_BIRTH'

P value = 0.00176 (Wilcoxon-test), Q value = 0.065

Table S19.  Gene #11: 'PTEN MUTATION STATUS' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 514 42.9 (13.4)
PTEN MUTATED 24 51.0 (12.0)
PTEN WILD-TYPE 490 42.5 (13.3)

Figure S19.  Get High-res Image Gene #11: 'PTEN MUTATION STATUS' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'PTEN MUTATION STATUS' versus 'HISTOLOGICAL_TYPE'

P value = 0.00276 (Fisher's exact test), Q value = 0.091

Table S20.  Gene #11: 'PTEN MUTATION STATUS' versus Clinical Feature #6: 'HISTOLOGICAL_TYPE'

nPatients ASTROCYTOMA OLIGOASTROCYTOMA OLIGODENDROGLIOMA
ALL 194 130 191
PTEN MUTATED 17 4 3
PTEN WILD-TYPE 177 126 188

Figure S20.  Get High-res Image Gene #11: 'PTEN MUTATION STATUS' versus Clinical Feature #6: 'HISTOLOGICAL_TYPE'

'EGFR MUTATION STATUS' versus 'Time to Death'

P value = 1.88e-11 (logrank test), Q value = 3.5e-09

Table S21.  Gene #13: 'EGFR MUTATION STATUS' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 511 125 0.0 - 211.2 (22.3)
EGFR MUTATED 35 21 0.5 - 211.2 (13.8)
EGFR WILD-TYPE 476 104 0.0 - 182.3 (23.6)

Figure S21.  Get High-res Image Gene #13: 'EGFR MUTATION STATUS' versus Clinical Feature #1: 'Time to Death'

'EGFR MUTATION STATUS' versus 'YEARS_TO_BIRTH'

P value = 4.92e-11 (Wilcoxon-test), Q value = 7.2e-09

Table S22.  Gene #13: 'EGFR MUTATION STATUS' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 514 42.9 (13.4)
EGFR MUTATED 35 57.7 (9.1)
EGFR WILD-TYPE 479 41.9 (13.0)

Figure S22.  Get High-res Image Gene #13: 'EGFR MUTATION STATUS' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'EGFR MUTATION STATUS' versus 'KARNOFSKY_PERFORMANCE_SCORE'

P value = 0.00535 (Wilcoxon-test), Q value = 0.15

Table S23.  Gene #13: 'EGFR MUTATION STATUS' versus Clinical Feature #5: 'KARNOFSKY_PERFORMANCE_SCORE'

nPatients Mean (Std.Dev)
ALL 307 86.6 (12.6)
EGFR MUTATED 22 78.2 (16.8)
EGFR WILD-TYPE 285 87.3 (12.0)

Figure S23.  Get High-res Image Gene #13: 'EGFR MUTATION STATUS' versus Clinical Feature #5: 'KARNOFSKY_PERFORMANCE_SCORE'

'SMARCA4 MUTATION STATUS' versus 'Time to Death'

P value = 0.00516 (logrank test), Q value = 0.15

Table S24.  Gene #18: 'SMARCA4 MUTATION STATUS' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 511 125 0.0 - 211.2 (22.3)
SMARCA4 MUTATED 26 1 0.2 - 211.2 (29.1)
SMARCA4 WILD-TYPE 485 124 0.0 - 182.3 (21.5)

Figure S24.  Get High-res Image Gene #18: 'SMARCA4 MUTATION STATUS' versus Clinical Feature #1: 'Time to Death'

'ZNF292 MUTATION STATUS' versus 'YEARS_TO_BIRTH'

P value = 0.00654 (Wilcoxon-test), Q value = 0.17

Table S25.  Gene #45: 'ZNF292 MUTATION STATUS' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 514 42.9 (13.4)
ZNF292 MUTATED 14 52.6 (12.3)
ZNF292 WILD-TYPE 500 42.7 (13.3)

Figure S25.  Get High-res Image Gene #45: 'ZNF292 MUTATION STATUS' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'PLCG1 MUTATION STATUS' versus 'Time to Death'

P value = 1.08e-07 (logrank test), Q value = 1.1e-05

Table S26.  Gene #61: 'PLCG1 MUTATION STATUS' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 511 125 0.0 - 211.2 (22.3)
PLCG1 MUTATED 6 4 6.7 - 23.7 (11.3)
PLCG1 WILD-TYPE 505 121 0.0 - 211.2 (22.5)

Figure S26.  Get High-res Image Gene #61: 'PLCG1 MUTATION STATUS' versus Clinical Feature #1: 'Time to Death'

'SETD2 MUTATION STATUS' versus 'YEARS_TO_BIRTH'

P value = 0.00798 (Wilcoxon-test), Q value = 0.2

Table S27.  Gene #70: 'SETD2 MUTATION STATUS' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 514 42.9 (13.4)
SETD2 MUTATED 10 54.0 (10.9)
SETD2 WILD-TYPE 504 42.7 (13.3)

Figure S27.  Get High-res Image Gene #70: 'SETD2 MUTATION STATUS' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'TMEM184A MUTATION STATUS' versus 'Time to Death'

P value = 0.000469 (logrank test), Q value = 0.019

Table S28.  Gene #82: 'TMEM184A MUTATION STATUS' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 511 125 0.0 - 211.2 (22.3)
TMEM184A MUTATED 3 1 0.3 - 9.2 (6.5)
TMEM184A WILD-TYPE 508 124 0.0 - 211.2 (22.5)

Figure S28.  Get High-res Image Gene #82: 'TMEM184A MUTATION STATUS' versus Clinical Feature #1: 'Time to Death'

'WRN MUTATION STATUS' versus 'ETHNICITY'

P value = 0.00245 (Fisher's exact test), Q value = 0.086

Table S29.  Gene #89: 'WRN MUTATION STATUS' versus Clinical Feature #8: 'ETHNICITY'

nPatients HISPANIC OR LATINO NOT HISPANIC OR LATINO
ALL 32 449
WRN MUTATED 3 2
WRN WILD-TYPE 29 447

Figure S29.  Get High-res Image Gene #89: 'WRN MUTATION STATUS' versus Clinical Feature #8: 'ETHNICITY'

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/LGG-TP/22813356/transformed.cor.cli.txt

  • Clinical data file = /xchip/cga/gdac-prod/tcga-gdac/jobResults/Append_Data/LGG-TP/22506744/LGG-TP.merged_data.txt

  • Number of patients = 515

  • Number of significantly mutated genes = 92

  • Number of selected clinical features = 8

  • 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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