Correlation between gene mutation status and selected clinical features
Lymphoid Neoplasm Diffuse Large B-cell Lymphoma (Primary solid tumor)
21 August 2015  |  analyses__2015_08_21
Maintainer Information
Citation Information
doi:10.7908/C1W0954D
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/C1W0954D
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 7 clinical features across 40 patients, one significant finding detected with Q value < 0.25.

  • KCNN3 mutation correlated to 'Time to Death'.

Results
Overview of the results

Table 1.  Get Full Table Overview of the association between mutation status of 92 genes and 7 clinical features. Shown in the table are P values (Q values). Thresholded by Q value < 0.25, one significant finding detected.

Clinical
Features 		Time
to
Death 		YEARS
TO
BIRTH 		GENDER RADIATION
THERAPY 		HISTOLOGICAL
TYPE 		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
KCNN3 7 (18%) 33 2.19e-05
(0.0141) 		0.618
(1.00) 		0.681
(1.00) 		0.568
(1.00) 		0.763
(1.00) 		0.063
(0.841) 		0.652
(1.00)
MYD88 3 (8%) 37 0.0413
(0.841) 		1
(1.00) 		0.553
(1.00) 		1
(1.00) 		0.236
(0.939) 		0.617
(1.00) 		0.541
(1.00)
FRG1 8 (20%) 32 0.877
(1.00) 		0.648
(1.00) 		0.69
(1.00) 		0.313
(0.954) 		1
(1.00) 		1
(1.00) 		0.079
(0.841)
MLL2 14 (35%) 26 0.944
(1.00) 		0.294
(0.939) 		0.329
(0.981) 		0.0705
(0.841) 		0.137
(0.903) 		0.299
(0.939) 		0.157
(0.903)
TPPP 5 (12%) 35 0.291
(0.939) 		0.854
(1.00) 		1
(1.00) 		0.574
(1.00) 		1
(1.00) 		1
(1.00) 		0.298
(0.939)
CHIT1 6 (15%) 34 0.0449
(0.841) 		0.155
(0.903) 		0.195
(0.939) 		0.564
(1.00) 		1
(1.00) 		0.00756
(0.841) 		0.153
(0.903)
B2M 8 (20%) 32 0.207
(0.939) 		0.25
(0.939) 		0.114
(0.903) 		0.29
(0.939) 		0.0146
(0.841) 		0.761
(1.00) 		1
(1.00)
TPTE2 11 (28%) 29 0.689
(1.00) 		0.575
(1.00) 		0.295
(0.939) 		0.655
(1.00) 		0.157
(0.903) 		0.4
(1.00) 		1
(1.00)
RHPN2 6 (15%) 34 0.888
(1.00) 		0.12
(0.903) 		0.668
(1.00) 		1
(1.00) 		0.712
(1.00) 		0.0434
(0.841) 		0.648
(1.00)
FOXD4L1 7 (18%) 33 0.431
(1.00) 		0.569
(1.00) 		0.681
(1.00) 		1
(1.00) 		1
(1.00) 		0.144
(0.903) 		0.652
(1.00)
DND1 4 (10%) 36 0.377
(0.993) 		0.191
(0.939) 		0.638
(1.00) 		1
(1.00) 		1
(1.00) 		0.199
(0.939) 		0.297
(0.939)
ATXN1 7 (18%) 33 0.757
(1.00) 		0.165
(0.906) 		0.681
(1.00) 		1
(1.00) 		1
(1.00) 		0.257
(0.939) 		0.652
(1.00)
TP53 6 (15%) 34 0.291
(0.939) 		0.519
(1.00) 		0.0645
(0.841) 		1
(1.00) 		0.276
(0.939) 		0.719
(1.00) 		0.341
(0.988)
CDC27 10 (25%) 30 0.618
(1.00) 		0.341
(0.988) 		0.711
(1.00) 		0.607
(1.00) 		1
(1.00) 		0.0519
(0.841) 		0.693
(1.00)
EPB41L4A 4 (10%) 36 0.378
(0.993) 		0.169
(0.906) 		0.638
(1.00) 		0.502
(1.00) 		0.553
(1.00) 		1
(1.00) 		1
(1.00)
NOTCH2NL 4 (10%) 36 0.607
(1.00) 		0.787
(1.00) 		0.638
(1.00) 		0.502
(1.00) 		0.315
(0.954) 		0.0233
(0.841) 		0.57
(1.00)
KRT3 4 (10%) 36 0.0511
(0.841) 		0.857
(1.00) 		0.136
(0.903) 		1
(1.00) 		1
(1.00) 		0.0916
(0.875) 		1
(1.00)
OR1S2 10 (25%) 30 0.624
(1.00) 		0.803
(1.00) 		0.482
(1.00) 		1
(1.00) 		0.618
(1.00) 		0.286
(0.939) 		0.231
(0.939)
RGPD5 5 (12%) 35 0.00451
(0.841) 		0.26
(0.939) 		1
(1.00) 		1
(1.00) 		0.639
(1.00) 		0.12
(0.903) 		0.627
(1.00)
TNFAIP3 6 (15%) 34 0.183
(0.937) 		0.256
(0.939) 		0.668
(1.00) 		1
(1.00) 		0.15
(0.903) 		0.117
(0.903) 		0.648
(1.00)
RBMXL1 4 (10%) 36 0.363
(0.993) 		0.207
(0.939) 		1
(1.00) 		0.104
(0.903) 		0.55
(1.00) 		1
(1.00) 		0.57
(1.00)
CCDC66 4 (10%) 36 0.0896
(0.875) 		0.636
(1.00) 		1
(1.00) 		1
(1.00) 		1
(1.00) 		0.0924
(0.875) 		0.297
(0.939)
NOTCH2 7 (18%) 33 0.807
(1.00) 		0.206
(0.939) 		1
(1.00) 		0.568
(1.00) 		0.531
(1.00) 		0.518
(1.00) 		0.652
(1.00)
PCMTD1 6 (15%) 34 0.996
(1.00) 		0.88
(1.00) 		0.373
(0.993) 		1
(1.00) 		0.278
(0.939) 		0.216
(0.939) 		1
(1.00)
FAM120B 5 (12%) 35 0.302
(0.939) 		0.743
(1.00) 		1
(1.00) 		0.574
(1.00) 		1
(1.00) 		0.266
(0.939) 		0.298
(0.939)
SMARCA2 4 (10%) 36 0.392
(1.00) 		0.332
(0.981) 		0.136
(0.903) 		1
(1.00) 		1
(1.00) 		1
(1.00) 		0.297
(0.939)
C11ORF40 4 (10%) 36 0.567
(1.00) 		0.543
(1.00) 		1
(1.00) 		1
(1.00) 		1
(1.00) 		0.00934
(0.841) 		0.297
(0.939)
ZSCAN5A 3 (8%) 37 0.345
(0.988) 		0.98
(1.00) 		1
(1.00) 		1
(1.00) 		1
(1.00) 		1
(1.00) 		1
(1.00)
KRTAP4-5 4 (10%) 36 0.752
(1.00) 		0.3
(0.939) 		0.638
(1.00) 		1
(1.00) 		0.314
(0.954) 		0.0233
(0.841) 		0.297
(0.939)
DEFA1 4 (10%) 36 0.119
(0.903) 		0.62
(1.00) 		1
(1.00) 		1
(1.00) 		1
(1.00) 		0.135
(0.903) 		0.297
(0.939)
SIRPA 5 (12%) 35 0.173
(0.908) 		0.357
(0.992) 		0.373
(0.993) 		0.574
(1.00) 		0.203
(0.939) 		0.17
(0.906) 		1
(1.00)
TMPRSS13 3 (8%) 37 0.57
(1.00) 		0.504
(1.00) 		0.553
(1.00) 		1
(1.00) 		1
(1.00) 		1
(1.00) 		0.541
(1.00)
CYP2A6 4 (10%) 36 0.377
(0.993) 		0.0202
(0.841) 		0.283
(0.939) 		0.502
(1.00) 		1
(1.00) 		1
(1.00) 		1
(1.00)
AR 7 (18%) 33 0.615
(1.00) 		0.0841
(0.86) 		0.681
(1.00) 		1
(1.00) 		0.204
(0.939) 		0.0987
(0.903) 		1
(1.00)
ARHGEF5 3 (8%) 37 0.653
(1.00) 		0.607
(1.00) 		0.262
(0.939) 		1
(1.00) 		1
(1.00) 		0.0366
(0.841) 		0.541
(1.00)
RNF39 3 (8%) 37 0.653
(1.00) 		0.292
(0.939) 		0.553
(1.00) 		1
(1.00) 		0.235
(0.939) 		0.0358
(0.841) 		1
(1.00)
ABCA1 5 (12%) 35 0.315
(0.954) 		0.5
(1.00) 		0.373
(0.993) 		0.574
(1.00) 		1
(1.00) 		0.169
(0.906) 		0.298
(0.939)
CS 3 (8%) 37 0.653
(1.00) 		0.218
(0.939) 		0.262
(0.939) 		0.403
(1.00) 		0.447
(1.00) 		0.0362
(0.841) 		1
(1.00)
IFITM3 4 (10%) 36 0.731
(1.00) 		0.367
(0.993) 		0.638
(1.00) 		1
(1.00) 		0.555
(1.00) 		0.00875
(0.841) 		0.297
(0.939)
RANBP2 5 (12%) 35 0.105
(0.903) 		0.0751
(0.841) 		0.0712
(0.841) 		1
(1.00) 		0.639
(1.00) 		0.12
(0.903) 		0.627
(1.00)
KLHL6 6 (15%) 34 0.284
(0.939) 		0.471
(1.00) 		0.373
(0.993) 		0.564
(1.00) 		1
(1.00) 		0.478
(1.00) 		0.153
(0.903)
ZNF814 10 (25%) 30 0.865
(1.00) 		0.348
(0.99) 		0.711
(1.00) 		0.163
(0.906) 		0.376
(0.993) 		0.354
(0.99) 		0.133
(0.903)
CYP4A11 4 (10%) 36 0.11
(0.903) 		0.0748
(0.841) 		0.283
(0.939) 		1
(1.00) 		1
(1.00) 		0.00832
(0.841) 		0.297
(0.939)
PIM1 8 (20%) 32 0.905
(1.00) 		0.447
(1.00) 		0.229
(0.939) 		1
(1.00) 		0.117
(0.903) 		0.543
(1.00) 		0.677
(1.00)
POTEE 7 (18%) 33 0.868
(1.00) 		0.345
(0.988) 		1
(1.00) 		0.568
(1.00) 		1
(1.00) 		0.256
(0.939) 		0.081
(0.841)
OR52E6 3 (8%) 37 0.0778
(0.841) 		0.0424
(0.841) 		0.553
(1.00) 		1
(1.00) 		1
(1.00) 		0.0761
(0.841) 		0.541
(1.00)
NBPF10 8 (20%) 32 0.589
(1.00) 		0.787
(1.00) 		0.229
(0.939) 		1
(1.00) 		0.118
(0.903) 		1
(1.00) 		1
(1.00)
PRB2 8 (20%) 32 0.292
(0.939) 		0.735
(1.00) 		0.439
(1.00) 		0.583
(1.00) 		0.172
(0.906) 		0.121
(0.903) 		0.211
(0.939)
MUC6 21 (52%) 19 0.9
(1.00) 		0.481
(1.00) 		0.755
(1.00) 		1
(1.00) 		0.484
(1.00) 		0.201
(0.939) 		0.494
(1.00)
SALL1 5 (12%) 35 0.149
(0.903) 		0.39
(1.00) 		1
(1.00) 		1
(1.00) 		0.642
(1.00) 		0.17
(0.906) 		1
(1.00)
PAK2 7 (18%) 33 0.848
(1.00) 		0.285
(0.939) 		0.0295
(0.841) 		1
(1.00) 		0.126
(0.903) 		0.146
(0.903) 		1
(1.00)
FLG 17 (42%) 23 0.625
(1.00) 		0.691
(1.00) 		0.747
(1.00) 		0.679
(1.00) 		0.319
(0.959) 		0.0804
(0.841) 		0.505
(1.00)
MUC17 12 (30%) 28 0.382
(0.997) 		0.275
(0.939) 		0.49
(1.00) 		0.151
(0.903) 		0.538
(1.00) 		0.331
(0.981) 		0.725
(1.00)
OR2T4 8 (20%) 32 0.388
(1.00) 		0.946
(1.00) 		1
(1.00) 		1
(1.00) 		1
(1.00) 		0.291
(0.939) 		1
(1.00)
AMAC1L3 5 (12%) 35 0.76
(1.00) 		0.595
(1.00) 		1
(1.00) 		0.574
(1.00) 		1
(1.00) 		0.0533
(0.841) 		0.298
(0.939)
APOB 3 (8%) 37 0.752
(1.00) 		0.0181
(0.841) 		1
(1.00) 		0.403
(1.00) 		0.45
(1.00) 		0.0367
(0.841) 		1
(1.00)
KRTAP4-7 8 (20%) 32 0.302
(0.939) 		0.0317
(0.841) 		1
(1.00) 		1
(1.00) 		0.259
(0.939) 		0.0103
(0.841) 		0.396
(1.00)
MUC16 12 (30%) 28 0.0603
(0.841) 		0.4
(1.00) 		0.49
(1.00) 		0.645
(1.00) 		0.434
(1.00) 		0.0345
(0.841) 		0.0674
(0.841)
NEFH 6 (15%) 34 0.335
(0.981) 		0.343
(0.988) 		1
(1.00) 		0.564
(1.00) 		0.714
(1.00) 		0.478
(1.00) 		0.153
(0.903)
RNASEH2B 3 (8%) 37 0.462
(1.00) 		0.898
(1.00) 		0.0567
(0.841) 		0.403
(1.00) 		1
(1.00) 		0.617
(1.00) 		1
(1.00)
OTOP1 4 (10%) 36 0.0243
(0.841) 		0.528
(1.00) 		0.638
(1.00) 		1
(1.00) 		1
(1.00) 		0.0571
(0.841) 		0.297
(0.939)
AATK 3 (8%) 37 0.0454
(0.841) 		0.59
(1.00) 		1
(1.00) 		1
(1.00) 		1
(1.00) 		0.0764
(0.841) 		0.541
(1.00)
ARID1A 5 (12%) 35 0.976
(1.00) 		0.5
(1.00) 		0.0712
(0.841) 		0.574
(1.00) 		1
(1.00) 		0.014
(0.841) 		0.298
(0.939)
GUCA1C 3 (8%) 37 0.0778
(0.841) 		0.0424
(0.841) 		0.553
(1.00) 		1
(1.00) 		1
(1.00) 		0.0743
(0.841) 		0.541
(1.00)
TRIM48 8 (20%) 32 0.061
(0.841) 		0.577
(1.00) 		0.69
(1.00) 		0.583
(1.00) 		1
(1.00) 		0.226
(0.939) 		1
(1.00)
CSGALNACT2 5 (12%) 35 0.256
(0.939) 		0.141
(0.903) 		0.631
(1.00) 		0.574
(1.00) 		0.639
(1.00) 		0.0517
(0.841) 		0.298
(0.939)
CRIPAK 6 (15%) 34 0.878
(1.00) 		0.353
(0.99) 		1
(1.00) 		0.564
(1.00) 		1
(1.00) 		0.0726
(0.841) 		0.153
(0.903)
DHRS4 4 (10%) 36 0.0896
(0.875) 		0.636
(1.00) 		1
(1.00) 		1
(1.00) 		1
(1.00) 		0.0912
(0.875) 		0.297
(0.939)
FAM21A 4 (10%) 36 0.163
(0.906) 		0.155
(0.903) 		1
(1.00) 		1
(1.00) 		1
(1.00) 		0.136
(0.903) 		0.297
(0.939)
KIAA1529 4 (10%) 36 0.844
(1.00) 		0.241
(0.939) 		1
(1.00) 		1
(1.00) 		1
(1.00) 		0.134
(0.903) 		0.297
(0.939)
OR2M5 4 (10%) 36 0.434
(1.00) 		0.735
(1.00) 		1
(1.00) 		1
(1.00) 		1
(1.00) 		1
(1.00) 		0.297
(0.939)
KRT6A 4 (10%) 36 0.459
(1.00) 		0.183
(0.937) 		0.638
(1.00) 		1
(1.00) 		1
(1.00) 		0.0567
(0.841) 		0.297
(0.939)
CYP2F1 4 (10%) 36 0.639
(1.00) 		0.131
(0.903) 		0.638
(1.00) 		1
(1.00) 		1
(1.00) 		0.134
(0.903) 		0.297
(0.939)
FCGBP 5 (12%) 35 0.315
(0.954) 		0.177
(0.919) 		0.373
(0.993) 		0.574
(1.00) 		1
(1.00) 		0.169
(0.906) 		0.298
(0.939)
ZNF493 4 (10%) 36 0.915
(1.00) 		0.804
(1.00) 		1
(1.00) 		0.502
(1.00) 		1
(1.00) 		0.0234
(0.841) 		1
(1.00)
HLA-B 6 (15%) 34 0.998
(1.00) 		0.191
(0.939) 		0.668
(1.00) 		1
(1.00) 		0.153
(0.903) 		0.217
(0.939) 		0.648
(1.00)
FCRLA 3 (8%) 37 0.752
(1.00) 		0.355
(0.99) 		1
(1.00) 		1
(1.00) 		1
(1.00) 		0.0362
(0.841) 		0.541
(1.00)
KLRC2 5 (12%) 35 0.334
(0.981) 		0.539
(1.00) 		1
(1.00) 		0.574
(1.00) 		1
(1.00) 		0.429
(1.00) 		0.298
(0.939)
CD79B 5 (12%) 35 0.403
(1.00) 		0.197
(0.939) 		0.373
(0.993) 		0.574
(1.00) 		0.055
(0.841) 		0.69
(1.00) 		0.627
(1.00)
TMSB4X 5 (12%) 35 0.718
(1.00) 		0.513
(1.00) 		0.631
(1.00) 		0.161
(0.906) 		0.105
(0.903) 		0.69
(1.00) 		0.627
(1.00)
PRB1 5 (12%) 35 0.277
(0.939) 		0.623
(1.00) 		1
(1.00) 		1
(1.00) 		0.637
(1.00) 		0.121
(0.903) 		0.627
(1.00)
PCDHA7 4 (10%) 36 0.455
(1.00) 		0.12
(0.903) 		1
(1.00) 		1
(1.00) 		0.314
(0.954) 		1
(1.00) 		1
(1.00)
OR5H14 3 (8%) 37 0.413
(1.00) 		0.382
(0.997) 		0.262
(0.939) 		0.403
(1.00) 		0.448
(1.00) 		0.616
(1.00) 		1
(1.00)
PER3 4 (10%) 36 0.812
(1.00) 		0.839
(1.00) 		0.638
(1.00) 		0.502
(1.00) 		0.552
(1.00) 		0.133
(0.903) 		1
(1.00)
PABPC1 7 (18%) 33 0.919
(1.00) 		0.327
(0.981) 		0.681
(1.00) 		0.568
(1.00) 		0.354
(0.99) 		0.0205
(0.841) 		0.652
(1.00)
ITGA6 3 (8%) 37 0.653
(1.00) 		0.13
(0.903) 		1
(1.00) 		1
(1.00) 		1
(1.00) 		0.0757
(0.841) 		0.541
(1.00)
IGSF3 6 (15%) 34 0.746
(1.00) 		0.609
(1.00) 		1
(1.00) 		1
(1.00) 		0.461
(1.00) 		0.715
(1.00) 		0.648
(1.00)
KRTAP1-1 3 (8%) 37 0.653
(1.00) 		0.0509
(0.841) 		0.553
(1.00) 		1
(1.00) 		1
(1.00) 		0.0739
(0.841) 		0.541
(1.00)
C15ORF39 3 (8%) 37 0.653
(1.00) 		0.292
(0.939) 		0.553
(1.00) 		1
(1.00) 		0.233
(0.939) 		0.0354
(0.841) 		1
(1.00)
ZNF880 8 (20%) 32 0.541
(1.00) 		0.8
(1.00) 		1
(1.00) 		1
(1.00) 		1
(1.00) 		0.226
(0.939) 		0.396
(1.00)
NBPF15 4 (10%) 36 0.378
(0.993) 		0.839
(1.00) 		0.136
(0.903) 		1
(1.00) 		1
(1.00) 		1
(1.00) 		0.297
(0.939)
SLC22A16 3 (8%) 37 0.752
(1.00) 		0.355
(0.99) 		1
(1.00) 		1
(1.00) 		1
(1.00) 		0.0378
(0.841) 		0.541
(1.00)
'KCNN3 MUTATION STATUS' versus 'Time to Death'

P value = 2.19e-05 (logrank test), Q value = 0.014

Table S1.  Gene #59: 'KCNN3 MUTATION STATUS' versus Clinical Feature #1: 'Time to Death'

nPatients nDeath Duration Range (Median), Month
ALL 40 6 0.0 - 128.1 (25.5)
KCNN3 MUTATED 7 4 1.9 - 31.7 (12.8)
KCNN3 WILD-TYPE 33 2 0.0 - 128.1 (27.4)

Figure S1.  Get High-res Image Gene #59: 'KCNN3 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/DLBC-TP/19899504/transformed.cor.cli.txt

  • Clinical data file = /xchip/cga/gdac-prod/tcga-gdac/jobResults/Append_Data/DLBC-TP/19775131/DLBC-TP.merged_data.txt

  • Number of patients = 40

  • Number of significantly mutated genes = 92

  • Number of selected clinical features = 7

  • 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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