Correlation between gene mutation status and selected clinical features
Rectum Adenocarcinoma (Primary solid tumor)
23 September 2013 | analyses__2013_09_23
Maintainer Information
Citation Information
doi:10.7908/C16971ZN
Maintained by TCGA GDAC Team (Broad Institute/MD Anderson Cancer Center/Harvard Medical School)
Cite as Broad Institute TCGA Genome Data Analysis Center (2013): Correlation between gene mutation status and selected clinical features. Broad Institute of MIT and Harvard. doi:10.7908/C16971ZN
Overview
Introduction

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

Summary

Testing the association between mutation status of 3 genes and 10 clinical features across 69 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 3 genes and 10 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 | NEOPLASM DISEASESTAGE | PATHOLOGY T STAGE | PATHOLOGY N STAGE | PATHOLOGY M STAGE | GENDER | HISTOLOGICAL TYPE | COMPLETENESS OF RESECTION | NUMBER OF LYMPH NODES
| nMutated (%) | nWild-Type | logrank test | t-test | Chi-square test | Fisher's exact test | Fisher's exact test | Fisher's exact test | Fisher's exact test | Fisher's exact test | Fisher's exact test | t-test
APC | 57 (83%) | 12 | 0.535 (1.00) | 0.897 (1.00) | 0.202 (1.00) | 0.0753 (1.00) | 0.813 (1.00) | 0.362 (1.00) | 1 (1.00) | 0.634 (1.00) | 0.693 (1.00) | 0.536 (1.00)
KRAS | 38 (55%) | 31 | 0.0233 (0.698) | 0.534 (1.00) | 0.7 (1.00) | 0.0973 (1.00) | 0.832 (1.00) | 0.327 (1.00) | 0.329 (1.00) | 0.27 (1.00) | 0.0405 (1.00) | 0.363 (1.00)
TP53 | 45 (65%) | 24 | 0.886 (1.00) | 0.976 (1.00) | 0.488 (1.00) | 0.0498 (1.00) | 0.935 (1.00) | 0.73 (1.00) | 0.803 (1.00) | 0.238 (1.00) | 0.624 (1.00) | 0.51 (1.00)

Methods & Data
Input

- Mutation data file = READ-TP.mutsig.cluster.txt

- Clinical data file = READ-TP.clin.merged.picked.txt

- Number of patients = 69

- Number of significantly mutated genes = 3

- Number of selected clinical features = 10

- 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

Chi-square test

For multi-class clinical features (nominal or ordinal), Chi-square tests (Greenwood and Nikulin 1996) were used to estimate the P values using the 'chisq.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

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] Lehmann and Romano, Testing Statistical Hypotheses (3E ed.), New York: Springer. ISBN 0387988645 (2005)
[3] Greenwood and Nikulin, A guide to chi-squared testing, Wiley, New York. ISBN 047155779X (1996)
[4] 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)
[5] 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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