Correlation between gene mutation status and selected clinical features
Brain Lower Grade Glioma (Primary solid tumor)
28 January 2016  |  analyses__2016_01_28
Maintainer Information
Citation Information
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/C1DV1J9F
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.

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)