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

Liver Hepatocellular Carcinoma (Primary solid tumor)

21 April 2013 | analyses__2013_04_21

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): Liver Hepatocellular Carcinoma (Primary solid tumor cohort) - 21 April 2013: Correlation between copy number variation genes (focal) and selected clinical features. Broad Institute of MIT and Harvard. doi:10.7908/C1154F1F

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 53 arm-level results and 4 clinical features across 72 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 53 arm-level results and 4 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	COMPLETENESS OF RESECTION
	nCNV (%)	nWild-Type	logrank test	t-test	Fisher's exact test	Fisher's exact test
Amp Peak 1(1p22 3)	0 (0%)	52	0.77 (1.00)	0.235 (1.00)	1 (1.00)	0.142 (1.00)
Amp Peak 2(1q22)	0 (0%)	16	0.503 (1.00)	0.92 (1.00)	0.392 (1.00)	0.915 (1.00)
Amp Peak 3(1q42 3)	0 (0%)	25	0.308 (1.00)	0.52 (1.00)	0.605 (1.00)	1 (1.00)
Amp Peak 4(2p24 1)	0 (0%)	55	0.632 (1.00)	0.779 (1.00)	0.253 (1.00)	0.793 (1.00)
Amp Peak 5(2q33 1)	0 (0%)	56	0.499 (1.00)	0.27 (1.00)	0.0715 (1.00)	0.616 (1.00)
Amp Peak 6(3q26 31)	0 (0%)	57	0.35 (1.00)	0.481 (1.00)	0.762 (1.00)	0.758 (1.00)
Amp Peak 7(4q31 3)	0 (0%)	64	0.68 (1.00)	0.883 (1.00)	1 (1.00)	0.371 (1.00)
Amp Peak 8(5p15 33)	0 (0%)	38	0.955 (1.00)	0.745 (1.00)	0.805 (1.00)	1 (1.00)
Amp Peak 9(5q35 3)	0 (0%)	46	0.801 (1.00)	0.694 (1.00)	0.44 (1.00)	0.109 (1.00)
Amp Peak 10(6p25 2)	0 (0%)	42	0.31 (1.00)	0.688 (1.00)	0.806 (1.00)	0.834 (1.00)
Amp Peak 11(6p21 1)	0 (0%)	41	0.833 (1.00)	0.956 (1.00)	1 (1.00)	0.839 (1.00)
Amp Peak 12(6q12)	0 (0%)	49	0.883 (1.00)	0.677 (1.00)	0.606 (1.00)	0.557 (1.00)
Amp Peak 13(7q21 2)	0 (0%)	45	0.726 (1.00)	0.14 (1.00)	0.45 (1.00)	0.855 (1.00)
Amp Peak 14(8q13 1)	0 (0%)	35	0.888 (1.00)	0.746 (1.00)	0.0829 (1.00)	0.845 (1.00)
Amp Peak 15(8q24 13)	0 (0%)	29	0.709 (1.00)	0.764 (1.00)	0.0763 (1.00)	0.953 (1.00)
Amp Peak 16(10p15 1)	0 (0%)	58	0.435 (1.00)	0.708 (1.00)	0.539 (1.00)	1 (1.00)
Amp Peak 17(11q13 3)	0 (0%)	60	0.503 (1.00)	0.464 (1.00)	0.524 (1.00)	0.0179 (1.00)
Amp Peak 18(12q23 1)	0 (0%)	59	0.384 (1.00)	0.247 (1.00)	0.757 (1.00)	0.211 (1.00)
Amp Peak 19(13q32 3)	0 (0%)	57	0.58 (1.00)	0.177 (1.00)	0.762 (1.00)	0.214 (1.00)
Amp Peak 20(15q21 3)	0 (0%)	60	0.729 (1.00)	0.146 (1.00)	0.0947 (1.00)	1 (1.00)
Amp Peak 21(15q26 3)	0 (0%)	60	0.142 (1.00)	0.789 (1.00)	0.32 (1.00)	1 (1.00)
Amp Peak 22(17p11 2)	0 (0%)	61	0.0963 (1.00)	0.533 (1.00)	0.173 (1.00)	0.218 (1.00)
Amp Peak 23(17q23 1)	0 (0%)	38	0.382 (1.00)	0.799 (1.00)	1 (1.00)	0.515 (1.00)
Amp Peak 24(17q25 3)	0 (0%)	36	0.23 (1.00)	0.45 (1.00)	0.322 (1.00)	0.173 (1.00)
Amp Peak 25(19q13 11)	0 (0%)	49	0.387 (1.00)	0.863 (1.00)	0.121 (1.00)	0.297 (1.00)
Amp Peak 26(20q13 13)	0 (0%)	48	0.158 (1.00)	0.252 (1.00)	0.795 (1.00)	0.137 (1.00)
Del Peak 1(1p36 32)	0 (0%)	37	0.558 (1.00)	0.434 (1.00)	1 (1.00)	0.274 (1.00)
Del Peak 2(2q22 1)	0 (0%)	65	0.328 (1.00)	0.847 (1.00)	0.688 (1.00)	0.844 (1.00)
Del Peak 3(2q37 3)	0 (0%)	60	0.193 (1.00)	0.669 (1.00)	0.741 (1.00)	0.89 (1.00)
Del Peak 4(3p13)	0 (0%)	57	0.464 (1.00)	0.643 (1.00)	0.128 (1.00)	0.915 (1.00)
Del Peak 5(4q24)	0 (0%)	39	0.0679 (1.00)	0.249 (1.00)	0.62 (1.00)	0.274 (1.00)
Del Peak 6(4q35 1)	0 (0%)	39	0.00769 (1.00)	0.0682 (1.00)	0.62 (1.00)	0.541 (1.00)
Del Peak 7(5q23 1)	0 (0%)	63	0.392 (1.00)	0.772 (1.00)	0.482 (1.00)	0.483 (1.00)
Del Peak 8(6q16 3)	0 (0%)	47	0.129 (1.00)	0.662 (1.00)	1 (1.00)	0.622 (1.00)
Del Peak 9(6q26)	0 (0%)	45	0.293 (1.00)	0.463 (1.00)	0.611 (1.00)	0.48 (1.00)
Del Peak 10(8p23 2)	0 (0%)	28	0.462 (1.00)	0.073 (1.00)	0.312 (1.00)	1 (1.00)
Del Peak 11(9p21 3)	0 (0%)	41	0.15 (1.00)	0.348 (1.00)	0.805 (1.00)	0.333 (1.00)
Del Peak 12(10p15 3)	0 (0%)	67	0.0147 (1.00)	0.851 (1.00)	0.156 (1.00)	1 (1.00)
Del Peak 13(10q23 31)	0 (0%)	47	0.654 (1.00)	0.564 (1.00)	1 (1.00)	0.357 (1.00)
Del Peak 14(10q24 33)	0 (0%)	51	0.326 (1.00)	0.807 (1.00)	1 (1.00)	0.464 (1.00)
Del Peak 15(11q14 1)	0 (0%)	57	0.816 (1.00)	0.0525 (1.00)	1 (1.00)	0.596 (1.00)
Del Peak 16(12p12 1)	0 (0%)	57	0.249 (1.00)	0.356 (1.00)	0.553 (1.00)	0.141 (1.00)
Del Peak 17(12q24 33)	0 (0%)	61	0.19 (1.00)	0.0899 (1.00)	0.497 (1.00)	0.681 (1.00)
Del Peak 18(13q14 2)	0 (0%)	38	0.295 (1.00)	0.772 (1.00)	1 (1.00)	0.236 (1.00)
Del Peak 19(14q23 3)	0 (0%)	42	0.0927 (1.00)	0.869 (1.00)	1 (1.00)	0.582 (1.00)
Del Peak 20(15q15 1)	0 (0%)	56	0.37 (1.00)	0.302 (1.00)	0.552 (1.00)	0.915 (1.00)
Del Peak 21(16q23 1)	0 (0%)	39	0.223 (1.00)	0.276 (1.00)	0.809 (1.00)	0.148 (1.00)
Del Peak 22(17p12)	0 (0%)	28	0.14 (1.00)	0.653 (1.00)	1 (1.00)	0.943 (1.00)
Del Peak 23(18q21 2)	0 (0%)	58	0.0656 (1.00)	0.273 (1.00)	0.539 (1.00)	1 (1.00)
Del Peak 24(19p13 3)	0 (0%)	54	0.922 (1.00)	0.224 (1.00)	0.575 (1.00)	1 (1.00)
Del Peak 25(22q12 1)	0 (0%)	58	0.322 (1.00)	0.763 (1.00)	0.0645 (1.00)	0.399 (1.00)
Del Peak 26(22q13 32)	0 (0%)	54	0.476 (1.00)	0.78 (1.00)	0.155 (1.00)	0.543 (1.00)
Del Peak 27(Xq27 3)	0 (0%)	60	0.0649 (1.00)	0.754 (1.00)	0.741 (1.00)	0.533 (1.00)

Methods & Data

Input

Mutation data file = all_lesions.conf_99.cnv.cluster.txt
Clinical data file = LIHC-TP.clin.merged.picked.txt
Number of patients = 72
Number of significantly arm-level cnvs = 53
Number of selected clinical features = 4
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.

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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