Ovarian Serous Cystadenocarcinoma: Correlation between gene mutation status and selected clinical features

Maintained by TCGA GDAC Team (Broad Institute/Dana-Farber Cancer Institute/Harvard Medical School)

Overview

Introduction

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

Summary

Testing the association between mutation status of 12 genes and 4 clinical features across 316 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 12 genes and 4 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	AGE	KARNOFSKY PERFORMANCE SCORE	NEOADJUVANT THERAPY
	nMutated (%)	nWild-Type	logrank test	t-test	t-test	Fisher's exact test
TP53	276 (87%)	40	0.389 (1.00)	0.649 (1.00)	0.585 (1.00)	0.505 (1.00)
SRC	4 (1%)	312	0.197 (1.00)	0.621 (1.00)		0.536 (1.00)
BRCA1	12 (4%)	304	0.957 (1.00)	0.65 (1.00)		1 (1.00)
TBP	4 (1%)	312	0.323 (1.00)	0.191 (1.00)		0.141 (1.00)
CSMD3	18 (6%)	298	0.262 (1.00)	0.61 (1.00)	0.285 (1.00)	0.53 (1.00)
NF1	14 (4%)	302	0.2 (1.00)	0.606 (1.00)		0.478 (1.00)
RB1	9 (3%)	307	0.241 (1.00)	0.204 (1.00)		0.658 (1.00)
C9ORF171	5 (2%)	311	0.895 (1.00)	0.121 (1.00)	0.746 (1.00)	0.591 (1.00)
GABRA6	6 (2%)	310	0.815 (1.00)	0.0121 (0.496)		0.595 (1.00)
CDK12	9 (3%)	307	0.367 (1.00)	0.214 (1.00)	0.0171 (0.684)	0.193 (1.00)
FAT3	19 (6%)	297	0.139 (1.00)	0.743 (1.00)	0.643 (1.00)	0.215 (1.00)
ARHGEF9	5 (2%)	311	0.0717 (1.00)	0.428 (1.00)		1 (1.00)

Methods & Data

Input

Mutation data file = OV.mutsig.cluster.txt
Clinical data file = OV.clin.merged.picked.txt
Number of patients = 316
Number of significantly mutated genes = 12
Number of selected clinical features = 4
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

Student's t-test analysis

For continuous numerical clinical features, two-tailed Student's t test with unequal variance (Lehmann and Romano 2005) was applied to compare the clinical values between tumors with and without gene mutations using 't.test' 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

This is an experimental feature. The full results of the analysis summarized in this report can be downloaded from the TCGA Data Coordination Center.

References

[1] Bland and Altman, Statistics notes: The logrank test, BMJ 328(7447):1073 (2004)

[2] Lehmann and Romano, Testing Statistical Hypotheses (3E ed.), New York: Springer. ISBN 0387988645 (2005)

[3] 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)

[4] 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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