Correlation between gene mutation status and selected clinical features
Brain Lower Grade Glioma (Primary solid tumor)
21 August 2015  |  analyses__2015_08_21
Maintainer Information
Citation Information
doi:10.7908/C11J9901
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/C11J9901
Overview
Introduction

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

Summary

Testing the association between mutation status of 84 genes and 8 clinical features across 512 patients, 29 significant findings detected with Q value < 0.25.

  • IDH1 mutation correlated to 'Time to Death',  'YEARS_TO_BIRTH',  'RADIATION_THERAPY',  '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'.

  • SETD2 mutation correlated to 'YEARS_TO_BIRTH'.

  • HTR3A mutation correlated to 'RACE'.

  • WRN mutation correlated to 'ETHNICITY'.

  • TMEM184A mutation correlated to 'Time to Death'.

Results
Overview of the results

Table 1.  Get Full Table Overview of the association between mutation status of 84 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 397 (78%) 115 1.11e-16
(7.46e-14) 		9.38e-09
(1.05e-06) 		1
(1.00) 		0.00895
(0.215) 		0.00252
(0.0769) 		0.00513
(0.138) 		0.0253
(0.437) 		1
(1.00)
TP53 247 (48%) 265 0.054
(0.637) 		2.47e-12
(5.53e-10) 		0.286
(0.927) 		0.000168
(0.00708) 		0.279
(0.922) 		1e-05
(0.000611) 		0.0348
(0.557) 		0.715
(1.00)
CIC 108 (21%) 404 0.000136
(0.00608) 		0.107
(0.72) 		0.328
(0.93) 		3.46e-06
(0.000332) 		0.24
(0.888) 		1e-05
(0.000611) 		0.751
(1.00) 		0.656
(1.00)
PTEN 24 (5%) 488 0.00013
(0.00608) 		0.00176
(0.0623) 		0.297
(0.93) 		0.0671
(0.659) 		0.585
(1.00) 		0.00245
(0.0769) 		0.163
(0.787) 		1
(1.00)
EGFR 35 (7%) 477 1.23e-11
(2.07e-09) 		4.84e-11
(6.5e-09) 		1
(1.00) 		0.0148
(0.317) 		0.00495
(0.138) 		0.0484
(0.608) 		0.181
(0.81) 		0.718
(1.00)
ATRX 194 (38%) 318 0.0886
(0.659) 		1.97e-12
(5.53e-10) 		0.784
(1.00) 		0.0156
(0.317) 		0.797
(1.00) 		1e-05
(0.000611) 		0.436
(0.99) 		1
(1.00)
FUBP1 47 (9%) 465 0.13
(0.751) 		0.00301
(0.0881) 		0.645
(1.00) 		0.0695
(0.659) 		0.236
(0.888) 		1e-05
(0.000611) 		1
(1.00) 		0.1
(0.702)
NOTCH1 42 (8%) 470 0.12
(0.722) 		0.0424
(0.574) 		0.747
(1.00) 		0.392
(0.952) 		0.869
(1.00) 		5e-05
(0.0028) 		0.336
(0.931) 		1
(1.00)
IDH2 20 (4%) 492 0.0594
(0.655) 		0.074
(0.659) 		1
(1.00) 		0.477
(1.00) 		0.621
(1.00) 		0.00065
(0.0243) 		0.45
(0.999) 		0.127
(0.744)
NF1 33 (6%) 479 9.95e-05
(0.00514) 		0.0125
(0.28) 		0.59
(1.00) 		0.454
(1.00) 		0.549
(1.00) 		0.0155
(0.317) 		0.221
(0.883) 		0.258
(0.888)
SMARCA4 26 (5%) 486 0.00715
(0.185) 		0.523
(1.00) 		0.318
(0.93) 		1
(1.00) 		0.432
(0.984) 		0.79
(1.00) 		0.115
(0.72) 		0.644
(1.00)
SETD2 10 (2%) 502 0.56
(1.00) 		0.00794
(0.198) 		1
(1.00) 		0.747
(1.00) 		0.308
(0.93) 		0.362
(0.944) 		0.466
(1.00) 		1
(1.00)
HTR3A 7 (1%) 505 0.403
(0.952) 		0.54
(1.00) 		0.0489
(0.608) 		0.439
(0.99) 		0.0794
(0.659) 		0.9
(1.00) 		0.00927
(0.215) 		1
(1.00)
WRN 5 (1%) 507 0.0842
(0.659) 		0.381
(0.948) 		0.661
(1.00) 		1
(1.00) 		0.0379
(0.559) 		0.552
(1.00) 		0.266
(0.899) 		0.0025
(0.0769)
TMEM184A 3 (1%) 509 0.000525
(0.0207) 		0.151
(0.787) 		1
(1.00) 		1
(1.00) 		1
(1.00) 		0.17
(0.787) 		1
(1.00)
PIK3R1 22 (4%) 490 0.259
(0.888) 		0.0799
(0.659) 		0.275
(0.913) 		0.487
(1.00) 		0.522
(1.00) 		0.354
(0.931) 		0.0455
(0.598) 		0.623
(1.00)
ARID1A 20 (4%) 492 0.0379
(0.559) 		0.648
(1.00) 		0.493
(1.00) 		0.351
(0.931) 		0.964
(1.00) 		0.195
(0.836) 		1
(1.00) 		1
(1.00)
GAGE2A 8 (2%) 504 0.507
(1.00) 		0.733
(1.00) 		0.737
(1.00) 		1
(1.00) 		0.323
(0.93) 		1
(1.00) 		0.054
(0.637) 		0.428
(0.978)
NUDT11 11 (2%) 501 0.525
(1.00) 		0.321
(0.93) 		0.36
(0.941) 		1
(1.00) 		0.641
(1.00) 		0.745
(1.00) 		1
(1.00) 		1
(1.00)
PIK3CA 44 (9%) 468 0.65
(1.00) 		0.0729
(0.659) 		0.875
(1.00) 		0.256
(0.888) 		0.102
(0.705) 		0.0182
(0.34) 		0.628
(1.00) 		0.743
(1.00)
STK19 10 (2%) 502 0.307
(0.93) 		0.311
(0.93) 		0.12
(0.722) 		0.682
(1.00) 		0.23
(0.888) 		0.0754
(0.659) 		1
(1.00) 		0.14
(0.769)
EMG1 6 (1%) 506 0.537
(1.00) 		0.0981
(0.694) 		0.415
(0.952) 		1
(1.00) 		0.366
(0.948) 		0.351
(0.931) 		1
(1.00) 		1
(1.00)
NIPBL 18 (4%) 494 0.0578
(0.654) 		0.176
(0.803) 		0.156
(0.787) 		0.311
(0.93) 		0.604
(1.00) 		0.0697
(0.659) 		0.0756
(0.659) 		0.112
(0.72)
TCF12 15 (3%) 497 0.625
(1.00) 		0.225
(0.888) 		0.601
(1.00) 		1
(1.00) 		0.915
(1.00) 		0.895
(1.00) 		1
(1.00) 		0.613
(1.00)
DNMT3A 10 (2%) 502 0.0364
(0.559) 		0.479
(1.00) 		1
(1.00) 		0.747
(1.00) 		0.992
(1.00) 		0.337
(0.931) 		0.462
(1.00) 		0.503
(1.00)
TRERF1 6 (1%) 506 0.482
(1.00) 		0.285
(0.927) 		0.0941
(0.672) 		0.682
(1.00) 		0.798
(1.00) 		0.167
(0.787) 		1
(1.00) 		1
(1.00)
CREBZF 7 (1%) 505 0.955
(1.00) 		0.171
(0.787) 		0.251
(0.888) 		1
(1.00) 		0.0699
(0.659) 		0.0314
(0.515) 		0.35
(0.931) 		0.386
(0.948)
FAM47C 18 (4%) 494 0.0775
(0.659) 		0.562
(1.00) 		0.47
(1.00) 		0.46
(1.00) 		0.649
(1.00) 		0.595
(1.00) 		1
(1.00) 		1
(1.00)
MYST4 11 (2%) 501 0.0922
(0.666) 		0.108
(0.72) 		1
(1.00) 		1
(1.00) 		0.928
(1.00) 		0.189
(0.831) 		0.147
(0.787) 		0.503
(1.00)
MED9 3 (1%) 509 0.23
(0.888) 		0.871
(1.00) 		0.257
(0.888) 		0.285
(0.927) 		0.0162
(0.32) 		1
(1.00) 		1
(1.00)
IRS4 7 (1%) 505 0.16
(0.787) 		0.495
(1.00) 		1
(1.00) 		1
(1.00) 		0.664
(1.00) 		0.137
(0.769) 		1
(1.00) 		0.386
(0.948)
HTRA2 5 (1%) 507 0.339
(0.931) 		0.0279
(0.469) 		1
(1.00) 		0.39
(0.952) 		0.451
(0.999) 		1
(1.00) 		0.294
(0.927)
NRAS 4 (1%) 508 0.28
(0.922) 		0.883
(1.00) 		1
(1.00) 		0.645
(1.00) 		0.471
(1.00) 		0.023
(0.406) 		1
(1.00) 		1
(1.00)
TNRC18 9 (2%) 503 0.321
(0.93) 		0.948
(1.00) 		0.198
(0.841) 		0.493
(1.00) 		0.915
(1.00) 		0.151
(0.787) 		1
(1.00) 		1
(1.00)
ZNF709 4 (1%) 508 0.0842
(0.659) 		0.595
(1.00) 		0.132
(0.751) 		1
(1.00) 		0.139
(0.769) 		0.22
(0.883) 		0.243
(0.888)
PLXNA3 9 (2%) 503 0.0907
(0.663) 		0.249
(0.888) 		0.311
(0.93) 		0.158
(0.787) 		0.588
(1.00) 		0.834
(1.00) 		0.109
(0.72) 		1
(1.00)
ROBO3 5 (1%) 507 0.49
(1.00) 		0.533
(1.00) 		0.661
(1.00) 		0.645
(1.00) 		0.664
(1.00) 		0.378
(0.948) 		1
(1.00) 		0.294
(0.927)
RB1 6 (1%) 506 0.829
(1.00) 		0.165
(0.787) 		0.415
(0.952) 		1
(1.00) 		0.0807
(0.659) 		0.315
(0.93) 		1
(1.00)
SRPX 4 (1%) 508 0.151
(0.787) 		0.0427
(0.574) 		0.0394
(0.561) 		1
(1.00) 		0.555
(1.00) 		0.377
(0.948) 		0.22
(0.883) 		1
(1.00)
PDGFRA 10 (2%) 502 0.0741
(0.659) 		0.707
(1.00) 		0.354
(0.931) 		0.747
(1.00) 		0.142
(0.775) 		0.115
(0.72) 		1
(1.00) 		0.14
(0.769)
ZNF512B 5 (1%) 507 0.08
(0.659) 		0.301
(0.93) 		1
(1.00) 		1
(1.00) 		1
(1.00) 		1
(1.00) 		0.294
(0.927)
ZMIZ1 9 (2%) 503 0.0712
(0.659) 		0.862
(1.00) 		0.522
(1.00) 		1
(1.00) 		0.149
(0.787) 		0.44
(0.99) 		0.0661
(0.659) 		0.0174
(0.334)
TMEM216 3 (1%) 509 0.771
(1.00) 		0.817
(1.00) 		0.0888
(0.659) 		1
(1.00) 		0.367
(0.948) 		1
(1.00) 		1
(1.00)
ARID2 11 (2%) 501 0.51
(1.00) 		0.109
(0.72) 		1
(1.00) 		0.215
(0.883) 		0.807
(1.00) 		0.206
(0.864) 		0.244
(0.888) 		1
(1.00)
RBPJ 7 (1%) 505 0.873
(1.00) 		0.0538
(0.637) 		1
(1.00) 		0.682
(1.00) 		0.335
(0.931) 		0.274
(0.913) 		1
(1.00) 		1
(1.00)
CUL4B 10 (2%) 502 0.211
(0.882) 		0.824
(1.00) 		0.12
(0.722) 		0.329
(0.93) 		0.641
(1.00) 		0.335
(0.931) 		0.219
(0.883) 		1
(1.00)
SLC6A3 9 (2%) 503 0.642
(1.00) 		0.377
(0.948) 		0.522
(1.00) 		1
(1.00) 		0.761
(1.00) 		1
(1.00) 		0.386
(0.948)
KRT3 4 (1%) 508 0.0883
(0.659) 		0.856
(1.00) 		0.632
(1.00) 		1
(1.00) 		0.105
(0.72) 		0.684
(1.00) 		1
(1.00) 		0.243
(0.888)
MYT1 6 (1%) 506 0.268
(0.899) 		0.408
(0.952) 		1
(1.00) 		0.0861
(0.659) 		0.734
(1.00) 		0.17
(0.787) 		1
(1.00) 		1
(1.00)
SMOC1 3 (1%) 509 0.489
(1.00) 		0.443
(0.993) 		1
(1.00) 		0.523
(1.00) 		0.978
(1.00) 		0.475
(1.00) 		1
(1.00) 		1
(1.00)
ZBTB20 21 (4%) 491 0.229
(0.888) 		0.495
(1.00) 		0.371
(0.948) 		0.161
(0.787) 		0.798
(1.00) 		0.182
(0.81) 		0.127
(0.744) 		0.636
(1.00)
PPL 6 (1%) 506 0.0401
(0.561) 		0.727
(1.00) 		1
(1.00) 		1
(1.00) 		0.798
(1.00) 		0.401
(0.952) 		1
(1.00) 		0.294
(0.927)
PTPN11 7 (1%) 505 0.253
(0.888) 		0.342
(0.931) 		1
(1.00) 		1
(1.00) 		0.755
(1.00) 		0.309
(0.93) 		0.354
(0.931) 		1
(1.00)
RET 7 (1%) 505 0.651
(1.00) 		0.5
(1.00) 		0.251
(0.888) 		0.439
(0.99) 		0.6
(1.00) 		0.0724
(0.659) 		1
(1.00) 		1
(1.00)
ANKRD36 7 (1%) 505 0.0892
(0.659) 		0.593
(1.00) 		0.706
(1.00) 		0.0463
(0.598) 		0.0699
(0.659) 		0.237
(0.888) 		0.0698
(0.659) 		1
(1.00)
NEU2 5 (1%) 507 0.227
(0.888) 		0.168
(0.787) 		1
(1.00) 		1
(1.00) 		0.38
(0.948) 		1
(1.00) 		0.294
(0.927)
PRX 10 (2%) 502 0.761
(1.00) 		0.463
(1.00) 		0.354
(0.931) 		0.329
(0.93) 		0.33
(0.93) 		0.781
(1.00) 		1
(1.00) 		0.503
(1.00)
RBBP6 6 (1%) 506 0.195
(0.836) 		0.321
(0.93) 		1
(1.00) 		0.682
(1.00) 		0.773
(1.00) 		0.125
(0.74) 		1
(1.00)
CIB1 4 (1%) 508 0.407
(0.952) 		1
(1.00) 		1
(1.00) 		1
(1.00) 		0.755
(1.00) 		1
(1.00) 		1
(1.00) 		1
(1.00)
DDX5 5 (1%) 507 0.114
(0.72) 		0.854
(1.00) 		1
(1.00) 		1
(1.00) 		0.289
(0.927) 		0.852
(1.00) 		1
(1.00) 		0.243
(0.888)
NAP1L2 4 (1%) 508 0.267
(0.899) 		0.178
(0.803) 		1
(1.00) 		0.645
(1.00) 		0.195
(0.836) 		1
(1.00) 		1
(1.00)
SCN4A 6 (1%) 506 0.187
(0.827) 		0.26
(0.888) 		0.415
(0.952) 		0.682
(1.00) 		0.333
(0.931) 		0.775
(1.00) 		1
(1.00) 		1
(1.00)
AGBL1 5 (1%) 507 0.254
(0.888) 		0.203
(0.856) 		0.386
(0.948) 		1
(1.00) 		0.192
(0.836) 		1
(1.00) 		1
(1.00)
TPX2 5 (1%) 507 0.233
(0.888) 		0.983
(1.00) 		0.661
(1.00) 		1
(1.00) 		1
(1.00) 		1
(1.00) 		0.0383
(0.559)
KRT15 6 (1%) 506 0.751
(1.00) 		0.116
(0.72) 		0.696
(1.00) 		0.215
(0.883) 		0.41
(0.952) 		0.886
(1.00) 		0.313
(0.93) 		1
(1.00)
C14ORF4 3 (1%) 509 0.467
(1.00) 		0.739
(1.00) 		0.589
(1.00) 		1
(1.00) 		0.786
(1.00) 		0.17
(0.787) 		1
(1.00)
R3HDM1 7 (1%) 505 0.0584
(0.654) 		0.872
(1.00) 		1
(1.00) 		1
(1.00) 		0.755
(1.00) 		0.494
(1.00) 		1
(1.00) 		0.386
(0.948)
G6PC 6 (1%) 506 0.878
(1.00) 		0.401
(0.952) 		0.696
(1.00) 		0.412
(0.952) 		0.51
(1.00) 		0.403
(0.952) 		1
(1.00) 		0.055
(0.638)
DLC1 6 (1%) 506 0.561
(1.00) 		0.553
(1.00) 		0.415
(0.952) 		0.0861
(0.659) 		0.666
(1.00) 		1
(1.00) 		0.342
(0.931)
SLC12A7 7 (1%) 505 0.178
(0.803) 		0.54
(1.00) 		0.706
(1.00) 		0.412
(0.952) 		0.52
(1.00) 		1
(1.00) 		0.35
(0.931) 		1
(1.00)
SMARCB1 4 (1%) 508 0.312
(0.93) 		0.811
(1.00) 		0.632
(1.00) 		0.16
(0.787) 		0.755
(1.00) 		1
(1.00) 		1
(1.00) 		1
(1.00)
LAMA4 4 (1%) 508 0.796
(1.00) 		0.354
(0.931) 		0.132
(0.751) 		1
(1.00) 		0.755
(1.00) 		0.0667
(0.659) 		0.0795
(0.659) 		0.243
(0.888)
MAST2 5 (1%) 507 0.472
(1.00) 		0.705
(1.00) 		0.661
(1.00) 		0.162
(0.787) 		0.45
(0.999) 		1
(1.00) 		1
(1.00)
ZMYM2 7 (1%) 505 0.153
(0.787) 		0.7
(1.00) 		1
(1.00) 		0.255
(0.888) 		0.664
(1.00) 		1
(1.00) 		1
(1.00) 		0.386
(0.948)
SLFN11 4 (1%) 508 0.114
(0.72) 		0.0862
(0.659) 		0.632
(1.00) 		0.645
(1.00) 		0.567
(1.00) 		1
(1.00) 		0.243
(0.888)
C4BPA 6 (1%) 506 0.528
(1.00) 		0.64
(1.00) 		0.415
(0.952) 		0.412
(0.952) 		0.166
(0.787) 		0.885
(1.00) 		0.307
(0.93) 		0.342
(0.931)
KTELC1 5 (1%) 507 0.312
(0.93) 		0.66
(1.00) 		0.386
(0.948) 		0.653
(1.00) 		0.852
(1.00) 		1
(1.00) 		1
(1.00)
ASXL2 3 (1%) 509 0.12
(0.722) 		0.413
(0.952) 		0.589
(1.00) 		1
(1.00) 		0.627
(1.00) 		1
(1.00) 		1
(1.00)
CCDC135 7 (1%) 505 0.236
(0.888) 		0.757
(1.00) 		0.251
(0.888) 		1
(1.00) 		0.706
(1.00) 		1
(1.00) 		0.386
(0.948)
SLC25A5 4 (1%) 508 0.0229
(0.406) 		0.579
(1.00) 		0.329
(0.93) 		1
(1.00) 		0.25
(0.888) 		0.837
(1.00) 		0.221
(0.883) 		1
(1.00)
ABCA7 9 (2%) 503 0.752
(1.00) 		0.163
(0.787) 		0.738
(1.00) 		1
(1.00) 		0.559
(1.00) 		0.534
(1.00) 		1
(1.00) 		1
(1.00)
NKD2 4 (1%) 508 0.989
(1.00) 		0.687
(1.00) 		1
(1.00) 		0.304
(0.93) 		0.456
(1.00) 		1
(1.00) 		1
(1.00)
MAX 4 (1%) 508 0.801
(1.00) 		0.166
(0.787) 		0.329
(0.93) 		0.563
(1.00) 		0.978
(1.00) 		0.838
(1.00) 		1
(1.00) 		1
(1.00)
VSIG4 6 (1%) 506 0.915
(1.00) 		0.946
(1.00) 		0.415
(0.952) 		1
(1.00) 		1
(1.00) 		1
(1.00) 		1
(1.00)
'IDH1 MUTATION STATUS' versus 'Time to Death'

P value = 1.11e-16 (logrank test), Q value = 7.5e-14

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

nPatients nDeath Duration Range (Median), Month
ALL 509 119 0.0 - 211.2 (20.7)
IDH1 MUTATED 394 68 0.0 - 182.3 (23.3)
IDH1 WILD-TYPE 115 51 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 = 9.38e-09 (Wilcoxon-test), Q value = 1.1e-06

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

nPatients Mean (Std.Dev)
ALL 511 42.9 (13.4)
IDH1 MUTATED 396 41.0 (12.4)
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 'RADIATION_THERAPY'

P value = 0.00895 (Fisher's exact test), Q value = 0.21

Table S3.  Gene #1: 'IDH1 MUTATION STATUS' versus Clinical Feature #4: 'RADIATION_THERAPY'

nPatients NO YES
ALL 186 291
IDH1 MUTATED 157 216
IDH1 WILD-TYPE 29 75

Figure S3.  Get High-res Image Gene #1: 'IDH1 MUTATION STATUS' versus Clinical Feature #4: 'RADIATION_THERAPY'

'IDH1 MUTATION STATUS' versus 'KARNOFSKY_PERFORMANCE_SCORE'

P value = 0.00252 (Wilcoxon-test), Q value = 0.077

Table S4.  Gene #1: 'IDH1 MUTATION STATUS' versus Clinical Feature #5: 'KARNOFSKY_PERFORMANCE_SCORE'

nPatients Mean (Std.Dev)
ALL 306 86.7 (12.4)
IDH1 MUTATED 240 87.8 (11.8)
IDH1 WILD-TYPE 66 82.7 (13.8)

Figure S4.  Get High-res Image Gene #1: 'IDH1 MUTATION STATUS' versus Clinical Feature #5: 'KARNOFSKY_PERFORMANCE_SCORE'

'IDH1 MUTATION STATUS' versus 'HISTOLOGICAL_TYPE'

P value = 0.00513 (Fisher's exact test), Q value = 0.14

Table S5.  Gene #1: 'IDH1 MUTATION STATUS' versus Clinical Feature #6: 'HISTOLOGICAL_TYPE'

nPatients ASTROCYTOMA OLIGOASTROCYTOMA OLIGODENDROGLIOMA
ALL 192 130 190
IDH1 MUTATED 134 109 154
IDH1 WILD-TYPE 58 21 36

Figure S5.  Get High-res Image Gene #1: 'IDH1 MUTATION STATUS' versus Clinical Feature #6: 'HISTOLOGICAL_TYPE'

'TP53 MUTATION STATUS' versus 'YEARS_TO_BIRTH'

P value = 2.47e-12 (Wilcoxon-test), Q value = 5.5e-10

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

nPatients Mean (Std.Dev)
ALL 511 42.9 (13.4)
TP53 MUTATED 247 38.6 (11.3)
TP53 WILD-TYPE 264 47.0 (13.9)

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

'TP53 MUTATION STATUS' versus 'RADIATION_THERAPY'

P value = 0.000168 (Fisher's exact test), Q value = 0.0071

Table S7.  Gene #2: 'TP53 MUTATION STATUS' versus Clinical Feature #4: 'RADIATION_THERAPY'

nPatients NO YES
ALL 186 291
TP53 MUTATED 71 163
TP53 WILD-TYPE 115 128

Figure S7.  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 S8.  Gene #2: 'TP53 MUTATION STATUS' versus Clinical Feature #6: 'HISTOLOGICAL_TYPE'

nPatients ASTROCYTOMA OLIGOASTROCYTOMA OLIGODENDROGLIOMA
ALL 192 130 190
TP53 MUTATED 129 74 44
TP53 WILD-TYPE 63 56 146

Figure S8.  Get High-res Image Gene #2: 'TP53 MUTATION STATUS' versus Clinical Feature #6: 'HISTOLOGICAL_TYPE'

'ATRX MUTATION STATUS' versus 'YEARS_TO_BIRTH'

P value = 1.97e-12 (Wilcoxon-test), Q value = 5.5e-10

Table S9.  Gene #3: 'ATRX MUTATION STATUS' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 511 42.9 (13.4)
ATRX MUTATED 194 37.8 (11.9)
ATRX WILD-TYPE 317 46.1 (13.3)

Figure S9.  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 S10.  Gene #3: 'ATRX MUTATION STATUS' versus Clinical Feature #6: 'HISTOLOGICAL_TYPE'

nPatients ASTROCYTOMA OLIGOASTROCYTOMA OLIGODENDROGLIOMA
ALL 192 130 190
ATRX MUTATED 96 64 34
ATRX WILD-TYPE 96 66 156

Figure S10.  Get High-res Image Gene #3: 'ATRX MUTATION STATUS' versus Clinical Feature #6: 'HISTOLOGICAL_TYPE'

'CIC MUTATION STATUS' versus 'Time to Death'

P value = 0.000136 (logrank test), Q value = 0.0061

Table S11.  Gene #4: 'CIC MUTATION STATUS' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 509 119 0.0 - 211.2 (20.7)
CIC MUTATED 107 12 0.1 - 211.2 (23.2)
CIC WILD-TYPE 402 107 0.0 - 172.8 (20.1)

Figure S11.  Get High-res Image Gene #4: 'CIC MUTATION STATUS' versus Clinical Feature #1: 'Time to Death'

'CIC MUTATION STATUS' versus 'RADIATION_THERAPY'

P value = 3.46e-06 (Fisher's exact test), Q value = 0.00033

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

nPatients NO YES
ALL 186 291
CIC MUTATED 60 41
CIC WILD-TYPE 126 250

Figure S12.  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 S13.  Gene #4: 'CIC MUTATION STATUS' versus Clinical Feature #6: 'HISTOLOGICAL_TYPE'

nPatients ASTROCYTOMA OLIGOASTROCYTOMA OLIGODENDROGLIOMA
ALL 192 130 190
CIC MUTATED 3 23 82
CIC WILD-TYPE 189 107 108

Figure S13.  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 S14.  Gene #5: 'NOTCH1 MUTATION STATUS' versus Clinical Feature #6: 'HISTOLOGICAL_TYPE'

nPatients ASTROCYTOMA OLIGOASTROCYTOMA OLIGODENDROGLIOMA
ALL 192 130 190
NOTCH1 MUTATED 6 7 29
NOTCH1 WILD-TYPE 186 123 161

Figure S14.  Get High-res Image Gene #5: 'NOTCH1 MUTATION STATUS' versus Clinical Feature #6: 'HISTOLOGICAL_TYPE'

'IDH2 MUTATION STATUS' versus 'HISTOLOGICAL_TYPE'

P value = 0.00065 (Fisher's exact test), Q value = 0.024

Table S15.  Gene #6: 'IDH2 MUTATION STATUS' versus Clinical Feature #6: 'HISTOLOGICAL_TYPE'

nPatients ASTROCYTOMA OLIGOASTROCYTOMA OLIGODENDROGLIOMA
ALL 192 130 190
IDH2 MUTATED 1 5 14
IDH2 WILD-TYPE 191 125 176

Figure S15.  Get High-res Image Gene #6: 'IDH2 MUTATION STATUS' versus Clinical Feature #6: 'HISTOLOGICAL_TYPE'

'FUBP1 MUTATION STATUS' versus 'YEARS_TO_BIRTH'

P value = 0.00301 (Wilcoxon-test), Q value = 0.088

Table S16.  Gene #8: 'FUBP1 MUTATION STATUS' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 511 42.9 (13.4)
FUBP1 MUTATED 47 47.4 (9.5)
FUBP1 WILD-TYPE 464 42.5 (13.6)

Figure S16.  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 S17.  Gene #8: 'FUBP1 MUTATION STATUS' versus Clinical Feature #6: 'HISTOLOGICAL_TYPE'

nPatients ASTROCYTOMA OLIGOASTROCYTOMA OLIGODENDROGLIOMA
ALL 192 130 190
FUBP1 MUTATED 2 9 36
FUBP1 WILD-TYPE 190 121 154

Figure S17.  Get High-res Image Gene #8: 'FUBP1 MUTATION STATUS' versus Clinical Feature #6: 'HISTOLOGICAL_TYPE'

'NF1 MUTATION STATUS' versus 'Time to Death'

P value = 9.95e-05 (logrank test), Q value = 0.0051

Table S18.  Gene #9: 'NF1 MUTATION STATUS' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 509 119 0.0 - 211.2 (20.7)
NF1 MUTATED 33 15 0.2 - 211.2 (18.6)
NF1 WILD-TYPE 476 104 0.0 - 182.3 (21.3)

Figure S18.  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 = 0.00013 (logrank test), Q value = 0.0061

Table S19.  Gene #11: 'PTEN MUTATION STATUS' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 509 119 0.0 - 211.2 (20.7)
PTEN MUTATED 24 12 0.5 - 211.2 (17.1)
PTEN WILD-TYPE 485 107 0.0 - 182.3 (21.3)

Figure S19.  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 = 0.062

Table S20.  Gene #11: 'PTEN MUTATION STATUS' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 511 42.9 (13.4)
PTEN MUTATED 24 51.0 (12.0)
PTEN WILD-TYPE 487 42.5 (13.3)

Figure S20.  Get High-res Image Gene #11: 'PTEN MUTATION STATUS' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'PTEN MUTATION STATUS' versus 'HISTOLOGICAL_TYPE'

P value = 0.00245 (Fisher's exact test), Q value = 0.077

Table S21.  Gene #11: 'PTEN MUTATION STATUS' versus Clinical Feature #6: 'HISTOLOGICAL_TYPE'

nPatients ASTROCYTOMA OLIGOASTROCYTOMA OLIGODENDROGLIOMA
ALL 192 130 190
PTEN MUTATED 17 4 3
PTEN WILD-TYPE 175 126 187

Figure S21.  Get High-res Image Gene #11: 'PTEN MUTATION STATUS' versus Clinical Feature #6: 'HISTOLOGICAL_TYPE'

'EGFR MUTATION STATUS' versus 'Time to Death'

P value = 1.23e-11 (logrank test), Q value = 2.1e-09

Table S22.  Gene #12: 'EGFR MUTATION STATUS' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 509 119 0.0 - 211.2 (20.7)
EGFR MUTATED 35 21 0.5 - 211.2 (13.1)
EGFR WILD-TYPE 474 98 0.0 - 182.3 (21.5)

Figure S22.  Get High-res Image Gene #12: 'EGFR MUTATION STATUS' versus Clinical Feature #1: 'Time to Death'

'EGFR MUTATION STATUS' versus 'YEARS_TO_BIRTH'

P value = 4.84e-11 (Wilcoxon-test), Q value = 6.5e-09

Table S23.  Gene #12: 'EGFR MUTATION STATUS' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 511 42.9 (13.4)
EGFR MUTATED 35 57.7 (9.1)
EGFR WILD-TYPE 476 41.8 (13.0)

Figure S23.  Get High-res Image Gene #12: 'EGFR MUTATION STATUS' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'EGFR MUTATION STATUS' versus 'KARNOFSKY_PERFORMANCE_SCORE'

P value = 0.00495 (Wilcoxon-test), Q value = 0.14

Table S24.  Gene #12: 'EGFR MUTATION STATUS' versus Clinical Feature #5: 'KARNOFSKY_PERFORMANCE_SCORE'

nPatients Mean (Std.Dev)
ALL 306 86.7 (12.4)
EGFR MUTATED 22 78.2 (16.8)
EGFR WILD-TYPE 284 87.4 (11.8)

Figure S24.  Get High-res Image Gene #12: 'EGFR MUTATION STATUS' versus Clinical Feature #5: 'KARNOFSKY_PERFORMANCE_SCORE'

'SMARCA4 MUTATION STATUS' versus 'Time to Death'

P value = 0.00715 (logrank test), Q value = 0.18

Table S25.  Gene #18: 'SMARCA4 MUTATION STATUS' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 509 119 0.0 - 211.2 (20.7)
SMARCA4 MUTATED 26 1 0.2 - 211.2 (27.2)
SMARCA4 WILD-TYPE 483 118 0.0 - 182.3 (20.7)

Figure S25.  Get High-res Image Gene #18: 'SMARCA4 MUTATION STATUS' versus Clinical Feature #1: 'Time to Death'

'SETD2 MUTATION STATUS' versus 'YEARS_TO_BIRTH'

P value = 0.00794 (Wilcoxon-test), Q value = 0.2

Table S26.  Gene #44: 'SETD2 MUTATION STATUS' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

nPatients Mean (Std.Dev)
ALL 511 42.9 (13.4)
SETD2 MUTATED 10 54.0 (10.9)
SETD2 WILD-TYPE 501 42.7 (13.3)

Figure S26.  Get High-res Image Gene #44: 'SETD2 MUTATION STATUS' versus Clinical Feature #2: 'YEARS_TO_BIRTH'

'HTR3A MUTATION STATUS' versus 'RACE'

P value = 0.00927 (Fisher's exact test), Q value = 0.21

Table S27.  Gene #63: 'HTR3A MUTATION STATUS' versus Clinical Feature #7: 'RACE'

nPatients AMERICAN INDIAN OR ALASKA NATIVE ASIAN BLACK OR AFRICAN AMERICAN WHITE
ALL 1 8 21 472
HTR3A MUTATED 0 2 0 4
HTR3A WILD-TYPE 1 6 21 468

Figure S27.  Get High-res Image Gene #63: 'HTR3A MUTATION STATUS' versus Clinical Feature #7: 'RACE'

'WRN MUTATION STATUS' versus 'ETHNICITY'

P value = 0.0025 (Fisher's exact test), Q value = 0.077

Table S28.  Gene #70: 'WRN MUTATION STATUS' versus Clinical Feature #8: 'ETHNICITY'

nPatients HISPANIC OR LATINO NOT HISPANIC OR LATINO
ALL 32 446
WRN MUTATED 3 2
WRN WILD-TYPE 29 444

Figure S28.  Get High-res Image Gene #70: 'WRN MUTATION STATUS' versus Clinical Feature #8: 'ETHNICITY'

'TMEM184A MUTATION STATUS' versus 'Time to Death'

P value = 0.000525 (logrank test), Q value = 0.021

Table S29.  Gene #76: 'TMEM184A MUTATION STATUS' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 509 119 0.0 - 211.2 (20.7)
TMEM184A MUTATED 3 1 0.3 - 9.2 (6.5)
TMEM184A WILD-TYPE 506 118 0.0 - 211.2 (20.8)

Figure S29.  Get High-res Image Gene #76: 'TMEM184A MUTATION STATUS' versus Clinical Feature #1: 'Time to Death'

Methods & Data
Input

  • Mutation data file = sample_sig_gene_table.txt from Mutsig_2CV pipeline

  • Processed Mutation data file = /xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_Correlate_Genomic_Events_Preprocess/LGG-TP/20067756/transformed.cor.cli.txt

  • Clinical data file = /xchip/cga/gdac-prod/tcga-gdac/jobResults/Append_Data/LGG-TP/19775312/LGG-TP.merged_data.txt

  • Number of patients = 512

  • Number of significantly mutated genes = 84

  • 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)
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