Correlation between gene mutation status and selected clinical features
Kidney Chromophobe (Primary solid tumor)
15 July 2014 | analyses__2014_07_15
Maintainer Information
Citation Information
doi:10.7908/C1PN94CT
Maintained by TCGA GDAC Team (Broad Institute/MD Anderson Cancer Center/Harvard Medical School)
Cite as Broad Institute TCGA Genome Data Analysis Center (2014): Correlation between gene mutation status and selected clinical features. Broad Institute of MIT and Harvard. doi:10.7908/C1PN94CT
Overview
Introduction

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

Summary

Testing the association between mutation status of 4 genes and 11 clinical features across 66 patients, one significant finding detected with Q value < 0.25.

- PABPC1 mutation correlated to 'NEOPLASM.DISEASESTAGE'.

Results
Overview of the results

Table 1. Get Full Table Overview of the association between mutation status of 4 genes and 11 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 | AGE | NEOPLASM DISEASESTAGE | PATHOLOGY T STAGE | PATHOLOGY N STAGE | PATHOLOGY M STAGE | GENDER | KARNOFSKY PERFORMANCE SCORE | NUMBERPACKYEARSSMOKED | 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 | Fisher's exact test | Fisher's exact test
PABPC1 | 7 (11%) | 59 | 100 (1.00) | 0.252 (1.00) | 0.00471 (0.165) | 0.0462 (1.00) | 0.0874 (1.00) | 1 (1.00) | 0.226 (1.00) |  |  | 0.0142 (0.483) | 1 (1.00)
TP53 | 22 (33%) | 44 | 100 (1.00) | 0.935 (1.00) | 0.306 (1.00) | 0.37 (1.00) | 0.036 (1.00) | 0.108 (1.00) | 1 (1.00) |  | 0.394 (1.00) | 0.195 (1.00) | 1 (1.00)
PTEN | 6 (9%) | 60 | 100 (1.00) | 0.422 (1.00) | 0.0493 (1.00) | 0.0321 (1.00) | 0.0874 (1.00) | 0.66 (1.00) | 0.217 (1.00) |  |  | 0.216 (1.00) | 0.213 (1.00)
URGCP | 3 (5%) | 63 |  | 0.841 (1.00) | 1 (1.00) | 1 (1.00) | 1 (1.00) |  | 1 (1.00) |  |  | 1 (1.00) | 1 (1.00)

'PABPC1 MUTATION STATUS' versus 'NEOPLASM.DISEASESTAGE'

P value = 0.00471 (Fisher's exact test), Q value = 0.16

Table S1. Gene #3: 'PABPC1 MUTATION STATUS' versus Clinical Feature #3: 'NEOPLASM.DISEASESTAGE'

nPatients | STAGE I | STAGE II | STAGE III | STAGE IV
--- | --- | --- | --- | ---
ALL | 21 | 25 | 14 | 6
PABPC1 MUTATED | 3 | 0 | 1 | 3
PABPC1 WILD-TYPE | 18 | 25 | 13 | 3

Figure S1. Get High-res Image Gene #3: 'PABPC1 MUTATION STATUS' versus Clinical Feature #3: 'NEOPLASM.DISEASESTAGE'

Methods & Data
Input

- Mutation data file = transformed.cor.cli.txt

- Clinical data file = KICH-TP.merged_data.txt

- Number of patients = 66

- Number of significantly mutated genes = 4

- Number of selected clinical features = 11

- 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)
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