Kidney Renal Papillary Cell Carcinoma: Correlation between gene mutation status and selected clinical features
(primary solid tumor cohort)
Maintained by TCGA GDAC Team (Broad Institute/MD Anderson Cancer Center/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 7 genes and 8 clinical features across 99 patients, one significant finding detected with Q value < 0.25.

- IL32 mutation correlated to 'Time to Death'.

Results
Overview of the results

Table 1. Get Full Table Overview of the association between mutation status of 7 genes and 8 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 | GENDER | KARNOFSKY PERFORMANCE SCORE | PATHOLOGY T | PATHOLOGY N | PATHOLOGICSPREAD(M) | TUMOR STAGE
| nMutated (%) | nWild-Type | logrank test | t-test | Fisher's exact test | t-test | Fisher's exact test | Fisher's exact test | Fisher's exact test | Fisher's exact test
IL32 | 4 (4%) | 95 | 9.44e-15 (4.25e-13) | 0.37 (1.00) | 0.301 (1.00) |  | 0.783 (1.00) |  | 0.222 (1.00) | 0.671 (1.00)
CDC27 | 4 (4%) | 95 | 0.598 (1.00) | 0.782 (1.00) | 0.593 (1.00) |  | 0.783 (1.00) |  | 0.129 (1.00) | 0.452 (1.00)
MET | 7 (7%) | 92 | 0.695 (1.00) | 0.877 (1.00) | 1 (1.00) |  | 1 (1.00) |  | 1 (1.00) | 0.892 (1.00)
PCF11 | 7 (7%) | 92 | 0.834 (1.00) | 0.399 (1.00) | 0.423 (1.00) |  | 0.749 (1.00) | 0.202 (1.00) | 0.58 (1.00) | 1 (1.00)
SFRS2IP | 5 (5%) | 94 | 0.226 (1.00) | 0.121 (1.00) | 0.657 (1.00) |  | 0.107 (1.00) | 1 (1.00) | 0.0839 (1.00) | 0.328 (1.00)
NF2 | 6 (6%) | 93 | 0.598 (1.00) | 0.139 (1.00) | 1 (1.00) |  | 0.301 (1.00) | 0.0583 (1.00) | 0.0252 (1.00) | 0.0619 (1.00)
LGI4 | 4 (4%) | 95 | 0.19 (1.00) | 0.913 (1.00) | 0.301 (1.00) |  | 0.783 (1.00) |  | 0.707 (1.00) | 0.671 (1.00)

'IL32 MUTATION STATUS' versus 'Time to Death'

P value = 9.44e-15 (logrank test), Q value = 4.2e-13

Table S1. Gene #3: 'IL32 MUTATION STATUS' versus Clinical Feature #1: 'Time to Death'

| nPatients | nDeath | Duration Range (Median), Month
--- | --- | --- | ---
ALL | 92 | 14 | 0.0 - 182.7 (14.4)
IL32 MUTATED | 4 | 1 | 3.6 - 7.9 (4.8)
IL32 WILD-TYPE | 88 | 13 | 0.0 - 182.7 (15.1)

Figure S1. Get High-res Image Gene #3: 'IL32 MUTATION STATUS' versus Clinical Feature #1: 'Time to Death'

Methods & Data
Input

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

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

- Number of patients = 99

- Number of significantly mutated genes = 7

- Number of selected clinical features = 8

- 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.

- 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] 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)
Copyright © 2013 Broad Institute TCGA GDAC as part of the TCGA Research Network. All rights reserved.
Made with Nozzle