Correlation between copy number variation genes (focal) and selected clinical features

Pancreatic Adenocarcinoma (Primary solid tumor)

23 May 2013 | analyses__2013_05_23

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 (2013): Correlation between copy number variation genes (focal) and selected clinical features. Broad Institute of MIT and Harvard. doi:10.7908/C15B00J7

Overview

Introduction

This pipeline computes the correlation between significant copy number variation (cnv focal) genes and selected clinical features.

Summary

Testing the association between copy number variation 28 arm-level results and 10 clinical features across 20 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 28 arm-level results 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	GENDER	HISTOLOGICAL TYPE	DISTANT METASTASIS	LYMPH NODE METASTASIS	COMPLETENESS OF RESECTION	NUMBER OF LYMPH NODES	TUMOR STAGECODE	NEOPLASM DISEASESTAGE
	nCNV (%)	nWild-Type	logrank test	t-test	Fisher's exact test	Fisher's exact test	Fisher's exact test	Fisher's exact test	Fisher's exact test	t-test	t-test	Chi-square test
Amp Peak 1(1p34 3)	0 (0%)	17	0.317 (1.00)	0.136 (1.00)	1 (1.00)	0.404 (1.00)	1 (1.00)	0.242 (1.00)	0.407 (1.00)	0.325 (1.00)		0.798 (1.00)
Amp Peak 2(1p12)	0 (0%)	17	0.317 (1.00)	0.952 (1.00)	1 (1.00)	1 (1.00)	0.193 (1.00)	1 (1.00)	1 (1.00)	0.221 (1.00)		0.226 (1.00)
Amp Peak 3(7q22 1)	0 (0%)	15	0.317 (1.00)	0.905 (1.00)	1 (1.00)	0.601 (1.00)	0.249 (1.00)	0.603 (1.00)	0.0139 (1.00)	0.66 (1.00)		0.328 (1.00)
Amp Peak 4(8q24 21)	0 (0%)	12	1 (1.00)	0.503 (1.00)	1 (1.00)	1 (1.00)	0.728 (1.00)	0.373 (1.00)	0.523 (1.00)	0.219 (1.00)		0.451 (1.00)
Amp Peak 6(12p13 33)	0 (0%)	17	0.317 (1.00)	0.328 (1.00)	1 (1.00)	0.404 (1.00)	1 (1.00)	0.242 (1.00)	0.27 (1.00)	0.387 (1.00)		0.798 (1.00)
Amp Peak 7(12p12 1)	0 (0%)	17	0.317 (1.00)	0.964 (1.00)	1 (1.00)	1 (1.00)	0.193 (1.00)	1 (1.00)	0.27 (1.00)	0.505 (1.00)		0.226 (1.00)
Amp Peak 8(18q11 2)	0 (0%)	16	1 (1.00)	0.0255 (1.00)	0.582 (1.00)	1 (1.00)	0.0134 (1.00)	0.619 (1.00)	0.705 (1.00)	0.479 (1.00)		0.312 (1.00)
Amp Peak 9(20q13 2)	0 (0%)	15	1 (1.00)	0.0507 (1.00)	1 (1.00)	0.601 (1.00)	1 (1.00)	0.0547 (1.00)	0.769 (1.00)	0.143 (1.00)		0.487 (1.00)
Amp Peak 11(Xq27 1)	0 (0%)	16	0.317 (1.00)	0.00959 (1.00)	0.582 (1.00)	0.509 (1.00)	0.624 (1.00)	0.619 (1.00)	0.235 (1.00)	0.608 (1.00)		0.312 (1.00)
Del Peak 1(1p36 22)	0 (0%)	17	0.317 (1.00)	0.0145 (1.00)	0.211 (1.00)	0.404 (1.00)	0.509 (1.00)	0.242 (1.00)	0.27 (1.00)	0.207 (1.00)		0.798 (1.00)
Del Peak 2(1p21 2)	0 (0%)	17	0.317 (1.00)	0.0145 (1.00)	0.211 (1.00)	0.404 (1.00)	0.509 (1.00)	0.242 (1.00)	0.27 (1.00)	0.207 (1.00)		0.798 (1.00)
Del Peak 4(5q14 2)	0 (0%)	15	1 (1.00)	0.0507 (1.00)	1 (1.00)	0.601 (1.00)	1 (1.00)	0.0547 (1.00)	0.769 (1.00)	0.143 (1.00)		0.487 (1.00)
Del Peak 5(6p25 2)	0 (0%)	13	1 (1.00)	0.264 (1.00)	1 (1.00)	1 (1.00)	0.0307 (1.00)	0.642 (1.00)	1 (1.00)	0.537 (1.00)		0.514 (1.00)
Del Peak 6(6p22 3)	0 (0%)	12	1 (1.00)	0.247 (1.00)	1 (1.00)	1 (1.00)	0.0491 (1.00)	0.373 (1.00)	1 (1.00)	0.52 (1.00)		0.451 (1.00)
Del Peak 7(6q22 33)	0 (0%)	10	0.317 (1.00)	0.404 (1.00)	1 (1.00)	1 (1.00)	0.0867 (1.00)	0.65 (1.00)	0.443 (1.00)	0.207 (1.00)		0.34 (1.00)
Del Peak 9(8p23 1)	0 (0%)	13	0.317 (1.00)	0.545 (1.00)	1 (1.00)	1 (1.00)	0.101 (1.00)	0.158 (1.00)	0.281 (1.00)	0.548 (1.00)		0.235 (1.00)
Del Peak 11(9p21 3)	0 (0%)	10	1 (1.00)	0.619 (1.00)	0.656 (1.00)	1 (1.00)	0.0867 (1.00)	0.17 (1.00)	0.443 (1.00)	0.156 (1.00)		0.247 (1.00)
Del Peak 12(9p13 2)	0 (0%)	14	1 (1.00)	0.779 (1.00)	0.628 (1.00)	1 (1.00)	0.0609 (1.00)	0.325 (1.00)	1 (1.00)	0.152 (1.00)		0.296 (1.00)
Del Peak 13(10q23 2)	0 (0%)	16	0.317 (1.00)	0.336 (1.00)	0.582 (1.00)	0.509 (1.00)	0.162 (1.00)	0.117 (1.00)	0.705 (1.00)	0.169 (1.00)		0.649 (1.00)
Del Peak 15(12p12 3)	0 (0%)	17	1 (1.00)	0.599 (1.00)	1 (1.00)	0.404 (1.00)	0.0877 (1.00)	1 (1.00)	0.0421 (1.00)	0.221 (1.00)		0.226 (1.00)
Del Peak 17(12q24 32)	0 (0%)	16	1 (1.00)	0.445 (1.00)	1 (1.00)	0.509 (1.00)	0.624 (1.00)	0.117 (1.00)	0.0367 (1.00)	0.946 (1.00)		0.649 (1.00)
Del Peak 18(15q15 1)	0 (0%)	16	0.317 (1.00)	0.164 (1.00)	0.582 (1.00)	0.509 (1.00)	0.624 (1.00)	0.117 (1.00)	0.705 (1.00)	0.135 (1.00)		0.649 (1.00)
Del Peak 19(17p11 2)	0 (0%)	13	0.317 (1.00)	0.584 (1.00)	1 (1.00)	1 (1.00)	0.69 (1.00)	1 (1.00)	0.0223 (1.00)	0.956 (1.00)		0.375 (1.00)
Del Peak 20(17q23 2)	0 (0%)	15	0.317 (1.00)	0.907 (1.00)	1 (1.00)	0.601 (1.00)	0.249 (1.00)	0.603 (1.00)	0.0307 (1.00)	0.549 (1.00)		0.328 (1.00)
Del Peak 21(18q21 2)	0 (0%)	9	1 (1.00)	0.56 (1.00)	1 (1.00)	0.711 (1.00)	0.142 (1.00)	0.362 (1.00)	0.123 (1.00)	0.306 (1.00)		0.258 (1.00)
Del Peak 22(21q22 11)	0 (0%)	13	1 (1.00)	0.706 (1.00)	0.35 (1.00)	0.681 (1.00)	0.00722 (1.00)	0.158 (1.00)	0.373 (1.00)	0.124 (1.00)		0.235 (1.00)
Del Peak 23(22q13 31)	0 (0%)	17	0.317 (1.00)	0.758 (1.00)	1 (1.00)	1 (1.00)	0.0877 (1.00)	1 (1.00)	0.0132 (1.00)	0.599 (1.00)		0.226 (1.00)
Del Peak 24(Xq21 1)	0 (0%)	17	1 (1.00)	0.755 (1.00)	1 (1.00)	0.404 (1.00)	0.0877 (1.00)	0.242 (1.00)	0.407 (1.00)	0.436 (1.00)		0.798 (1.00)

Methods & Data

Input

Mutation data file = all_lesions.conf_99.cnv.cluster.txt
Clinical data file = PAAD-TP.clin.merged.picked.txt
Number of patients = 20
Number of significantly arm-level cnvs = 28
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

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

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

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] Greenwood and Nikulin, A guide to chi-squared testing, Wiley, New York. ISBN 047155779X (1996)

[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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