Correlation between copy number variations of arm-level result and selected clinical features

Adrenocortical Carcinoma (Primary solid tumor)

15 January 2014 | analyses__2014_01_15

Maintainer Information

Citation Information

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 copy number variations of arm-level result and selected clinical features. Broad Institute of MIT and Harvard. doi:10.7908/C19W0CVK

Overview

Introduction

This pipeline computes the correlation between significant arm-level copy number variations (cnvs) and selected clinical features.

Summary

Testing the association between copy number variation 34 arm-level events and 5 clinical features across 10 patients, no significant finding detected with Q value < 0.25.

No arm-level cnvs related to clinical features.

Results

Overview of the results

Table 1. Get Full Table Overview of the association between significant copy number variation of 34 arm-level events and 5 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	GENDER
	nCNV (%)	nWild-Type	logrank test	t-test	Fisher's exact test	NULL	Fisher's exact test
4p gain	5 (50%)	5	0.0784 (1.00)	0.971 (1.00)	0.524 (1.00)		0.206 (1.00)
4q gain	5 (50%)	5	0.0784 (1.00)	0.971 (1.00)	0.524 (1.00)		0.206 (1.00)
5p gain	5 (50%)	5	0.0784 (1.00)	0.971 (1.00)	0.524 (1.00)		0.206 (1.00)
5q gain	4 (40%)	6	0.514 (1.00)	0.994 (1.00)	0.714 (1.00)		0.524 (1.00)
7p gain	3 (30%)	7	0.163 (1.00)	0.136 (1.00)	0.714 (1.00)		1 (1.00)
7q gain	3 (30%)	7	0.163 (1.00)	0.136 (1.00)	0.714 (1.00)		1 (1.00)
8p gain	4 (40%)	6	0.28 (1.00)	0.734 (1.00)	1 (1.00)		1 (1.00)
8q gain	5 (50%)	5	0.28 (1.00)	0.658 (1.00)	1 (1.00)		1 (1.00)
10q gain	3 (30%)	7	0.596 (1.00)	0.456 (1.00)			1 (1.00)
12p gain	6 (60%)	4	0.378 (1.00)	0.487 (1.00)	0.381 (1.00)		0.524 (1.00)
12q gain	5 (50%)	5	0.0784 (1.00)	0.971 (1.00)	0.524 (1.00)		0.206 (1.00)
16p gain	5 (50%)	5	0.0784 (1.00)	0.971 (1.00)	0.524 (1.00)		0.206 (1.00)
16q gain	5 (50%)	5	0.0784 (1.00)	0.971 (1.00)	0.524 (1.00)		0.206 (1.00)
19p gain	7 (70%)	3	0.87 (1.00)	0.956 (1.00)	1 (1.00)		1 (1.00)
19q gain	6 (60%)	4	0.467 (1.00)	0.507 (1.00)	1 (1.00)		0.524 (1.00)
20p gain	3 (30%)	7	0.175 (1.00)	0.191 (1.00)			0.167 (1.00)
20q gain	5 (50%)	5	0.0784 (1.00)	0.971 (1.00)	0.524 (1.00)		0.206 (1.00)
21q gain	5 (50%)	5	0.799 (1.00)	0.528 (1.00)	1 (1.00)		1 (1.00)
1p loss	5 (50%)	5	0.799 (1.00)	0.287 (1.00)	1 (1.00)		1 (1.00)
1q loss	4 (40%)	6	0.899 (1.00)	0.113 (1.00)	0.714 (1.00)		1 (1.00)
3p loss	3 (30%)	7	0.0793 (1.00)	0.423 (1.00)			1 (1.00)
8p loss	3 (30%)	7	0.87 (1.00)	0.0886 (1.00)	0.5 (1.00)		1 (1.00)
9p loss	3 (30%)	7	0.596 (1.00)	0.561 (1.00)			1 (1.00)
9q loss	3 (30%)	7	0.596 (1.00)	0.561 (1.00)			1 (1.00)
11p loss	5 (50%)	5	0.899 (1.00)	0.769 (1.00)	0.381 (1.00)		1 (1.00)
11q loss	5 (50%)	5	0.899 (1.00)	0.769 (1.00)	0.381 (1.00)		1 (1.00)
13q loss	5 (50%)	5	0.381 (1.00)	0.883 (1.00)	1 (1.00)		1 (1.00)
15q loss	4 (40%)	6	0.28 (1.00)	0.587 (1.00)	1 (1.00)		0.524 (1.00)
17p loss	5 (50%)	5	0.043 (1.00)	0.797 (1.00)	0.19 (1.00)		1 (1.00)
17q loss	3 (30%)	7	0.497 (1.00)	0.399 (1.00)			1 (1.00)
18p loss	4 (40%)	6	0.987 (1.00)	0.617 (1.00)	0.714 (1.00)		0.524 (1.00)
18q loss	4 (40%)	6	0.987 (1.00)	0.617 (1.00)	0.714 (1.00)		0.524 (1.00)
22q loss	6 (60%)	4	0.994 (1.00)	0.872 (1.00)	1 (1.00)		0.524 (1.00)
xq loss	3 (30%)	7	0.149 (1.00)	0.0324 (1.00)	0.143 (1.00)		1 (1.00)

Methods & Data

Input

Copy number data file = transformed.cor.cli.txt
Clinical data file = ACC-TP.merged_data.txt
Number of patients = 10
Number of significantly arm-level cnvs = 34
Number of selected clinical features = 5
Exclude regions 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

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.

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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