Correlation between gene mutation status and selected clinical features
Kidney Renal Clear Cell Carcinoma (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/C1SQ8ZSC
Overview
Introduction

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

Summary

Testing the association between mutation status of 25 genes and 12 clinical features across 436 patients, no significant finding detected with Q value < 0.25.

  • No gene mutations related to clinical features.

Results
Overview of the results

Table 1.  Get Full Table Overview of the association between mutation status of 25 genes and 12 clinical features. Shown in the table are P values (Q values). Thresholded by Q value < 0.25, no significant finding detected.

Clinical
Features
Time
to
Death
YEARS
TO
BIRTH
PATHOLOGIC
STAGE
PATHOLOGY
T
STAGE
PATHOLOGY
N
STAGE
PATHOLOGY
M
STAGE
GENDER KARNOFSKY
PERFORMANCE
SCORE
NUMBER
PACK
YEARS
SMOKED
YEAR
OF
TOBACCO
SMOKING
ONSET
RACE ETHNICITY
nMutated (%) nWild-Type logrank test Wilcoxon-test Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test Wilcoxon-test Wilcoxon-test Wilcoxon-test Fisher's exact test Fisher's exact test
SETD2 43 (10%) 393 0.374
(1.00)
0.198
(1.00)
0.279
(1.00)
0.144
(1.00)
0.373
(1.00)
0.381
(1.00)
0.505
(1.00)
0.398
(1.00)
0.689
(1.00)
0.705
(1.00)
PBRM1 131 (30%) 305 0.495
(1.00)
0.277
(1.00)
0.959
(1.00)
0.275
(1.00)
0.245
(1.00)
0.777
(1.00)
0.587
(1.00)
0.732
(1.00)
0.327
(1.00)
0.804
(1.00)
KDM5C 25 (6%) 411 0.0782
(1.00)
0.13
(1.00)
0.848
(1.00)
0.946
(1.00)
1
(1.00)
1
(1.00)
0.00972
(0.719)
1
(1.00)
0.379
(1.00)
VHL 192 (44%) 244 0.481
(1.00)
0.422
(1.00)
0.232
(1.00)
0.106
(1.00)
0.597
(1.00)
0.694
(1.00)
0.365
(1.00)
0.454
(1.00)
0.00234
(0.702)
0.821
(1.00)
MTOR 28 (6%) 408 0.186
(1.00)
0.137
(1.00)
0.293
(1.00)
0.383
(1.00)
0.328
(1.00)
0.186
(1.00)
0.106
(1.00)
0.0399
(1.00)
0.245
(1.00)
1
(1.00)
TP53 9 (2%) 427 0.53
(1.00)
0.554
(1.00)
0.746
(1.00)
0.199
(1.00)
1
(1.00)
1
(1.00)
0.291
(1.00)
0.435
(1.00)
1
(1.00)
PTEN 15 (3%) 421 0.834
(1.00)
0.905
(1.00)
0.132
(1.00)
0.396
(1.00)
0.143
(1.00)
0.483
(1.00)
0.0973
(1.00)
0.763
(1.00)
0.614
(1.00)
1
(1.00)
NEFH 6 (1%) 430 0.828
(1.00)
0.448
(1.00)
0.0595
(1.00)
0.219
(1.00)
1
(1.00)
0.248
(1.00)
0.429
(1.00)
1
(1.00)
1
(1.00)
NF2 6 (1%) 430 0.128
(1.00)
0.312
(1.00)
0.498
(1.00)
0.468
(1.00)
0.0127
(0.719)
0.248
(1.00)
1
(1.00)
0.313
(1.00)
0.347
(1.00)
ATM 12 (3%) 424 0.432
(1.00)
0.52
(1.00)
0.141
(1.00)
0.101
(1.00)
0.478
(1.00)
0.419
(1.00)
0.361
(1.00)
1
(1.00)
0.392
(1.00)
NUDT11 4 (1%) 432 0.511
(1.00)
0.14
(1.00)
0.537
(1.00)
0.395
(1.00)
0.0685
(1.00)
1
(1.00)
0.302
(1.00)
1
(1.00)
1
(1.00)
PIK3CA 10 (2%) 426 0.584
(1.00)
0.402
(1.00)
0.173
(1.00)
0.207
(1.00)
1
(1.00)
0.666
(1.00)
0.0387
(1.00)
1
(1.00)
0.474
(1.00)
GPR50 3 (1%) 433 0.248
(1.00)
0.921
(1.00)
1
(1.00)
1
(1.00)
1
(1.00)
1
(1.00)
0.289
(1.00)
0.171
(1.00)
1
(1.00)
TFDP2 4 (1%) 432 0.694
(1.00)
0.0514
(1.00)
0.768
(1.00)
1
(1.00)
0.193
(1.00)
1
(1.00)
0.618
(1.00)
1
(1.00)
1
(1.00)
FAM200A 4 (1%) 432 0.156
(1.00)
0.239
(1.00)
0.882
(1.00)
0.804
(1.00)
1
(1.00)
1
(1.00)
0.0156
(0.719)
1
(1.00)
1
(1.00)
DPCR1 6 (1%) 430 0.665
(1.00)
0.541
(1.00)
0.114
(1.00)
0.877
(1.00)
1
(1.00)
0.0553
(1.00)
1
(1.00)
0.315
(1.00)
1
(1.00)
EGFR 6 (1%) 430 0.12
(1.00)
0.226
(1.00)
0.0168
(0.719)
0.00518
(0.719)
0.249
(1.00)
0.248
(1.00)
0.429
(1.00)
1
(1.00)
1
(1.00)
SH3KBP1 3 (1%) 433 0.685
(1.00)
0.222
(1.00)
0.477
(1.00)
0.733
(1.00)
1
(1.00)
1
(1.00)
0.289
(1.00)
0.17
(1.00)
0.191
(1.00)
EMG1 4 (1%) 432 0.155
(1.00)
0.799
(1.00)
0.47
(1.00)
0.237
(1.00)
1
(1.00)
1
(1.00)
1
(1.00)
1
(1.00)
1
(1.00)
ARID1A 10 (2%) 426 0.791
(1.00)
0.89
(1.00)
0.0207
(0.775)
0.0593
(1.00)
1
(1.00)
1
(1.00)
0.749
(1.00)
1
(1.00)
0.0962
(1.00)
ARAP3 3 (1%) 433 0.711
(1.00)
0.517
(1.00)
0.824
(1.00)
0.735
(1.00)
0.409
(1.00)
0.289
(1.00)
0.17
(1.00)
1
(1.00)
SLC16A9 4 (1%) 432 0.336
(1.00)
0.724
(1.00)
0.372
(1.00)
0.629
(1.00)
0.505
(1.00)
0.618
(1.00)
1
(1.00)
1
(1.00)
PCK1 4 (1%) 432 0.184
(1.00)
0.374
(1.00)
0.609
(1.00)
0.629
(1.00)
1
(1.00)
1
(1.00)
0.618
(1.00)
1
(1.00)
1
(1.00)
CUL9 7 (2%) 429 0.383
(1.00)
0.714
(1.00)
0.535
(1.00)
0.53
(1.00)
0.193
(1.00)
1
(1.00)
1
(1.00)
1
(1.00)
0.347
(1.00)
ZDHHC1 4 (1%) 432 0.169
(1.00)
0.864
(1.00)
0.123
(1.00)
0.181
(1.00)
1
(1.00)
1
(1.00)
1
(1.00)
0.222
(1.00)
0.0127
(0.719)
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/KIRC-TP/22815438/transformed.cor.cli.txt

  • Clinical data file = /xchip/cga/gdac-prod/tcga-gdac/jobResults/Append_Data/KIRC-TP/22506714/KIRC-TP.merged_data.txt

  • Number of patients = 436

  • Number of significantly mutated genes = 25

  • Number of selected clinical features = 12

  • 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)