Correlation between gene mutation status and selected clinical features
Uveal Melanoma (Primary solid tumor)
02 April 2015 | analyses__2015_04_02
Maintainer Information
Citation Information
doi:10.7908/C1MG7NPZ
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/C1MG7NPZ
Overview
Introduction

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

Summary

Testing the association between mutation status of 7 genes and 6 clinical features across 80 patients, one significant finding detected with Q value < 0.25.

- GNAQ mutation correlated to 'NEOPLASM_DISEASESTAGE'.

Results
Overview of the results

Table 1. Get Full Table Overview of the association between mutation status of 7 genes and 6 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 | NEOPLASM DISEASESTAGE | PATHOLOGY T STAGE | PATHOLOGY M STAGE | GENDER
| nMutated (%) | nWild-Type | logrank test | Wilcoxon-test | Fisher's exact test | Fisher's exact test | Fisher's exact test | Fisher's exact test
GNAQ | 40 (50%) | 40 | 0.229 (1.00) | 0.467 (1.00) | 0.00181 (0.076) | 0.801 (1.00) | 0.0515 (0.756) | 1 (1.00)
GNA11 | 36 (45%) | 44 | 0.286 (1.00) | 0.749 (1.00) | 0.0575 (0.756) | 0.834 (1.00) | 0.307 (1.00) | 0.653 (1.00)
EIF1AX | 10 (12%) | 70 | 0.43 (1.00) | 0.419 (1.00) | 1 (1.00) | 0.667 (1.00) | 1 (1.00) | 0.32 (1.00)
SF3B1 | 18 (22%) | 62 | 0.115 (0.799) | 0.231 (1.00) | 0.883 (1.00) | 0.878 (1.00) | 0.573 (1.00) | 0.596 (1.00)
BAP1 | 16 (20%) | 64 | 0.849 (1.00) | 0.072 (0.756) | 0.483 (1.00) | 0.812 (1.00) | 1 (1.00) | 1 (1.00)
PRMT8 | 5 (6%) | 75 | 0.402 (1.00) | 0.133 (0.799) | 0.114 (0.799) | 0.388 (1.00) | 1 (1.00) | 0.649 (1.00)
CYSLTR2 | 3 (4%) | 77 | 0.464 (1.00) | 0.425 (1.00) | 0.684 (1.00) | 0.783 (1.00) | 1 (1.00) | 1 (1.00)

'GNAQ MUTATION STATUS' versus 'NEOPLASM_DISEASESTAGE'

P value = 0.00181 (Fisher's exact test), Q value = 0.076

Table S1. Gene #1: 'GNAQ MUTATION STATUS' versus Clinical Feature #3: 'NEOPLASM_DISEASESTAGE'

nPatients | STAGE IIA | STAGE IIB | STAGE IIIA | STAGE IIIB | STAGE IIIC | STAGE IV
--- | --- | --- | --- | --- | --- | ---
ALL | 12 | 27 | 25 | 10 | 1 | 4
GNAQ MUTATED | 8 | 11 | 19 | 2 | 0 | 0
GNAQ WILD-TYPE | 4 | 16 | 6 | 8 | 1 | 4

Figure S1. Get High-res Image Gene #1: 'GNAQ MUTATION STATUS' versus Clinical Feature #3: 'NEOPLASM_DISEASESTAGE'

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/UVM-TP/15890468/transformed.cor.cli.txt

- Clinical data file = /xchip/cga/gdac-prod/tcga-gdac/jobResults/Append_Data/UVM-TP/15096076/UVM-TP.merged_data.txt

- Number of patients = 80

- Number of significantly mutated genes = 7

- Number of selected clinical features = 6

- 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.

- Analysis Results (MD5 checksum)

- Auxiliary Data (MD5 checksum)

- MAGE-TAB File (MD5 checksum)

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)
Copyright © 2015 Broad Institute TCGA GDAC as part of the TCGA Research Network. All rights reserved.
Made with Nozzle