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

Esophageal Carcinoma (Primary solid tumor)

23 September 2013 | analyses__2013_09_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 events) and selected clinical features. Broad Institute of MIT and Harvard. doi:10.7908/C1SB4418

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 63 focal events and 7 clinical features across 19 patients, no significant finding detected with Q value < 0.25.

No focal 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 63 focal events and 7 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	PATHOLOGY N STAGE	GENDER	NUMBERPACKYEARSSMOKED
	nCNV (%)	nWild-Type	logrank test	t-test	Chi-square test	Fisher's exact test	Fisher's exact test	Fisher's exact test	t-test
AMP PEAK 1(1P34 2) MUTATION ANALYSIS	7 (37%)	12	0.195 (1.00)	0.0573 (1.00)	0.803 (1.00)	0.201 (1.00)	1 (1.00)	0.523 (1.00)	0.797 (1.00)
AMP PEAK 2(1Q42 3) MUTATION ANALYSIS	11 (58%)	8	0.405 (1.00)	0.0378 (1.00)	0.383 (1.00)	0.417 (1.00)	1 (1.00)	0.546 (1.00)	0.956 (1.00)
AMP PEAK 3(2Q14 2) MUTATION ANALYSIS	6 (32%)	13	0.318 (1.00)	0.441 (1.00)	0.415 (1.00)	1 (1.00)	1 (1.00)	1 (1.00)	0.684 (1.00)
AMP PEAK 4(3Q26 2) MUTATION ANALYSIS	16 (84%)	3	0.446 (1.00)	0.693 (1.00)	0.296 (1.00)	0.278 (1.00)	0.263 (1.00)	0.422 (1.00)
AMP PEAK 5(5P15 33) MUTATION ANALYSIS	7 (37%)	12	0.811 (1.00)	0.379 (1.00)	0.238 (1.00)	0.704 (1.00)	0.326 (1.00)	0.523 (1.00)	0.882 (1.00)
AMP PEAK 6(6P21 1) MUTATION ANALYSIS	8 (42%)	11	0.73 (1.00)	0.711 (1.00)	0.842 (1.00)	0.494 (1.00)	1 (1.00)	0.0578 (1.00)	0.95 (1.00)
AMP PEAK 7(6Q12) MUTATION ANALYSIS	6 (32%)	13	0.124 (1.00)	0.939 (1.00)	0.797 (1.00)	0.827 (1.00)	1 (1.00)	1 (1.00)	0.749 (1.00)
AMP PEAK 8(7P11 2) MUTATION ANALYSIS	14 (74%)	5	0.619 (1.00)	0.0937 (1.00)	0.638 (1.00)	0.663 (1.00)	1 (1.00)	0.53 (1.00)	0.921 (1.00)
AMP PEAK 9(7Q21 2) MUTATION ANALYSIS	14 (74%)	5	0.836 (1.00)	0.0889 (1.00)	0.416 (1.00)	1 (1.00)	1 (1.00)	0.53 (1.00)	0.414 (1.00)
AMP PEAK 10(8P11 21) MUTATION ANALYSIS	12 (63%)	7	0.252 (1.00)	0.0508 (1.00)	0.215 (1.00)	0.105 (1.00)	1 (1.00)	1 (1.00)	0.0703 (1.00)
AMP PEAK 11(8Q24 21) MUTATION ANALYSIS	16 (84%)	3	0.214 (1.00)	0.796 (1.00)	0.663 (1.00)	1 (1.00)	1 (1.00)	1 (1.00)
AMP PEAK 13(11P13) MUTATION ANALYSIS	4 (21%)	15	0.221 (1.00)	0.536 (1.00)	0.576 (1.00)	0.155 (1.00)	0.603 (1.00)	0.53 (1.00)	0.975 (1.00)
AMP PEAK 14(11Q13 3) MUTATION ANALYSIS	11 (58%)	8	0.143 (1.00)	0.922 (1.00)	0.842 (1.00)	1 (1.00)	0.633 (1.00)	1 (1.00)	0.0823 (1.00)
AMP PEAK 15(12P13 33) MUTATION ANALYSIS	8 (42%)	11	0.731 (1.00)	0.473 (1.00)	0.253 (1.00)	0.208 (1.00)	0.377 (1.00)	1 (1.00)	0.747 (1.00)
AMP PEAK 16(12P12 1) MUTATION ANALYSIS	8 (42%)	11	0.167 (1.00)	0.858 (1.00)	0.383 (1.00)	0.208 (1.00)	0.633 (1.00)	1 (1.00)	0.151 (1.00)
AMP PEAK 17(14Q22 1) MUTATION ANALYSIS	6 (32%)	13	0.0383 (1.00)	0.287 (1.00)	0.797 (1.00)	0.827 (1.00)	0.129 (1.00)	1 (1.00)	0.394 (1.00)
AMP PEAK 18(17Q12) MUTATION ANALYSIS	9 (47%)	10	0.385 (1.00)	0.0974 (1.00)	0.489 (1.00)	0.714 (1.00)	0.35 (1.00)	0.582 (1.00)	0.422 (1.00)
AMP PEAK 19(17Q24 3) MUTATION ANALYSIS	9 (47%)	10	0.701 (1.00)	0.84 (1.00)	0.213 (1.00)	0.714 (1.00)	1 (1.00)	0.211 (1.00)	0.0178 (1.00)
AMP PEAK 20(18P11 32) MUTATION ANALYSIS	5 (26%)	14	0.0157 (1.00)	0.663 (1.00)	0.0574 (1.00)	0.364 (1.00)	1 (1.00)	0.155 (1.00)	0.993 (1.00)
AMP PEAK 21(18Q11 2) MUTATION ANALYSIS	5 (26%)	14	0.657 (1.00)	0.471 (1.00)	0.263 (1.00)	0.663 (1.00)	0.603 (1.00)	0.53 (1.00)	0.101 (1.00)
AMP PEAK 22(19P13 2) MUTATION ANALYSIS	3 (16%)	16		0.206 (1.00)	0.48 (1.00)	0.278 (1.00)	1 (1.00)	0.422 (1.00)
AMP PEAK 23(19P13 11) MUTATION ANALYSIS	4 (21%)	15	0.122 (1.00)	0.0646 (1.00)	0.276 (1.00)	0.372 (1.00)	1 (1.00)	1 (1.00)	0.201 (1.00)
AMP PEAK 24(19Q12) MUTATION ANALYSIS	8 (42%)	11	0.856 (1.00)	0.00231 (0.985)	0.233 (1.00)	0.417 (1.00)	0.147 (1.00)	1 (1.00)	0.283 (1.00)
AMP PEAK 25(XP11 4) MUTATION ANALYSIS	4 (21%)	15	0.00123 (0.526)	0.794 (1.00)	0.805 (1.00)	0.111 (1.00)	0.603 (1.00)	0.53 (1.00)	0.706 (1.00)
DEL PEAK 1(1P36 13) MUTATION ANALYSIS	8 (42%)	11	0.701 (1.00)	0.661 (1.00)	0.207 (1.00)	1 (1.00)	0.633 (1.00)	1 (1.00)	0.651 (1.00)
DEL PEAK 2(1P13 2) MUTATION ANALYSIS	8 (42%)	11	0.856 (1.00)	0.55 (1.00)	0.291 (1.00)	0.24 (1.00)	0.633 (1.00)	1 (1.00)	0.973 (1.00)
DEL PEAK 3(1Q44) MUTATION ANALYSIS	3 (16%)	16	0.492 (1.00)	0.0314 (1.00)	0.00192 (0.823)	0.191 (1.00)	0.263 (1.00)	1 (1.00)
DEL PEAK 4(2Q22 1) MUTATION ANALYSIS	7 (37%)	12	0.446 (1.00)	0.82 (1.00)	0.394 (1.00)	0.24 (1.00)	0.173 (1.00)	1 (1.00)	0.403 (1.00)
DEL PEAK 5(2Q34) MUTATION ANALYSIS	6 (32%)	13	0.709 (1.00)	0.513 (1.00)	0.646 (1.00)	0.164 (1.00)	1 (1.00)	0.222 (1.00)	0.614 (1.00)
DEL PEAK 6(3P26 1) MUTATION ANALYSIS	11 (58%)	8	0.954 (1.00)	0.989 (1.00)	0.534 (1.00)	0.494 (1.00)	0.633 (1.00)	0.228 (1.00)	0.407 (1.00)
DEL PEAK 7(3P14 3) MUTATION ANALYSIS	13 (68%)	6	0.175 (1.00)	0.0328 (1.00)	0.457 (1.00)	0.682 (1.00)	0.617 (1.00)	1 (1.00)	0.396 (1.00)
DEL PEAK 8(3P14 2) MUTATION ANALYSIS	14 (74%)	5	0.24 (1.00)	0.12 (1.00)	0.345 (1.00)	0.364 (1.00)	0.305 (1.00)	1 (1.00)	0.156 (1.00)
DEL PEAK 10(3Q26 31) MUTATION ANALYSIS	3 (16%)	16	0.211 (1.00)	0.959 (1.00)	0.759 (1.00)	0.278 (1.00)	0.263 (1.00)	1 (1.00)	0.52 (1.00)
DEL PEAK 11(4P15 2) MUTATION ANALYSIS	11 (58%)	8	0.208 (1.00)	0.402 (1.00)	0.4 (1.00)	0.494 (1.00)	0.633 (1.00)	1 (1.00)	0.306 (1.00)
DEL PEAK 12(4Q22 1) MUTATION ANALYSIS	9 (47%)	10	0.221 (1.00)	0.00937 (1.00)	0.296 (1.00)	0.714 (1.00)	0.35 (1.00)	0.582 (1.00)	0.471 (1.00)
DEL PEAK 13(5Q11 2) MUTATION ANALYSIS	12 (63%)	7	0.76 (1.00)	0.323 (1.00)	0.484 (1.00)	0.471 (1.00)	1 (1.00)	0.263 (1.00)	0.397 (1.00)
DEL PEAK 14(5Q12 3) MUTATION ANALYSIS	12 (63%)	7	0.76 (1.00)	0.323 (1.00)	0.484 (1.00)	0.471 (1.00)	1 (1.00)	0.263 (1.00)	0.397 (1.00)
DEL PEAK 15(6P25 3) MUTATION ANALYSIS	8 (42%)	11	0.0427 (1.00)	0.957 (1.00)	0.842 (1.00)	1 (1.00)	0.633 (1.00)	1 (1.00)	0.145 (1.00)
DEL PEAK 16(6Q14 2) MUTATION ANALYSIS	3 (16%)	16	0.0515 (1.00)	0.96 (1.00)	0.0691 (1.00)	1 (1.00)	0.0361 (1.00)	1 (1.00)
DEL PEAK 17(7Q31 1) MUTATION ANALYSIS	8 (42%)	11	0.592 (1.00)	0.497 (1.00)	0.514 (1.00)	0.146 (1.00)	0.377 (1.00)	1 (1.00)	0.112 (1.00)
DEL PEAK 18(7Q36 2) MUTATION ANALYSIS	9 (47%)	10	0.118 (1.00)	0.51 (1.00)	0.18 (1.00)	0.0611 (1.00)	0.65 (1.00)	0.582 (1.00)	0.896 (1.00)
DEL PEAK 19(8P23 2) MUTATION ANALYSIS	10 (53%)	9	0.813 (1.00)	0.615 (1.00)	0.365 (1.00)	0.247 (1.00)	0.17 (1.00)	0.0867 (1.00)	0.793 (1.00)
DEL PEAK 20(9P21 3) MUTATION ANALYSIS	15 (79%)	4	0.0337 (1.00)	0.135 (1.00)	0.652 (1.00)	0.798 (1.00)	1 (1.00)	1 (1.00)	0.322 (1.00)
DEL PEAK 21(10P11 21) MUTATION ANALYSIS	4 (21%)	15	0.646 (1.00)	0.801 (1.00)	0.805 (1.00)	0.624 (1.00)	0.603 (1.00)	1 (1.00)	0.667 (1.00)
DEL PEAK 22(10Q23 31) MUTATION ANALYSIS	8 (42%)	11	0.954 (1.00)	0.122 (1.00)	0.821 (1.00)	0.417 (1.00)	1 (1.00)	0.546 (1.00)	0.676 (1.00)
DEL PEAK 23(11P15 4) MUTATION ANALYSIS	5 (26%)	14	0.266 (1.00)	0.47 (1.00)	0.166 (1.00)	0.122 (1.00)	0.305 (1.00)	0.53 (1.00)
DEL PEAK 24(11Q24 3) MUTATION ANALYSIS	9 (47%)	10	0.475 (1.00)	0.914 (1.00)	0.19 (1.00)	0.361 (1.00)	0.65 (1.00)	1 (1.00)	0.357 (1.00)
DEL PEAK 25(12Q12) MUTATION ANALYSIS	5 (26%)	14	0.589 (1.00)	0.477 (1.00)	0.394 (1.00)	0.663 (1.00)	0.106 (1.00)	0.155 (1.00)
DEL PEAK 26(13Q12 11) MUTATION ANALYSIS	11 (58%)	8	0.592 (1.00)	0.582 (1.00)	0.156 (1.00)	0.208 (1.00)	0.0128 (1.00)	0.546 (1.00)	0.185 (1.00)
DEL PEAK 27(15Q13 1) MUTATION ANALYSIS	4 (21%)	15	0.17 (1.00)	0.385 (1.00)	0.0351 (1.00)	0.213 (1.00)	0.603 (1.00)	0.53 (1.00)	0.165 (1.00)
DEL PEAK 28(16Q23 1) MUTATION ANALYSIS	9 (47%)	10	0.378 (1.00)	0.0506 (1.00)	0.127 (1.00)	0.607 (1.00)	0.35 (1.00)	0.582 (1.00)	0.994 (1.00)
DEL PEAK 29(17Q25 3) MUTATION ANALYSIS	3 (16%)	16	0.86 (1.00)	0.703 (1.00)	0.582 (1.00)	1 (1.00)	0.523 (1.00)	1 (1.00)
DEL PEAK 30(18Q12 2) MUTATION ANALYSIS	9 (47%)	10	0.73 (1.00)	0.0405 (1.00)	0.469 (1.00)	0.0866 (1.00)	1 (1.00)	0.211 (1.00)	0.922 (1.00)
DEL PEAK 31(18Q21 2) MUTATION ANALYSIS	10 (53%)	9	0.73 (1.00)	0.222 (1.00)	0.634 (1.00)	0.204 (1.00)	0.65 (1.00)	0.0867 (1.00)	0.797 (1.00)
DEL PEAK 32(19P13 3) MUTATION ANALYSIS	12 (63%)	7	0.666 (1.00)	0.905 (1.00)	0.616 (1.00)	0.844 (1.00)	0.0449 (1.00)	1 (1.00)	0.649 (1.00)
DEL PEAK 33(19Q13 31) MUTATION ANALYSIS	4 (21%)	15	0.214 (1.00)	0.772 (1.00)	0.805 (1.00)	1 (1.00)	0.603 (1.00)	0.097 (1.00)
DEL PEAK 34(20P12 1) MUTATION ANALYSIS	3 (16%)	16	0.492 (1.00)	0.441 (1.00)	0.118 (1.00)	0.393 (1.00)	0.263 (1.00)	1 (1.00)
DEL PEAK 35(21Q22 12) MUTATION ANALYSIS	11 (58%)	8	0.582 (1.00)	0.533 (1.00)	0.4 (1.00)	1 (1.00)	0.633 (1.00)	0.228 (1.00)	0.0686 (1.00)
DEL PEAK 36(22Q11 1) MUTATION ANALYSIS	9 (47%)	10	0.447 (1.00)	0.188 (1.00)	0.489 (1.00)	1 (1.00)	0.35 (1.00)	0.582 (1.00)	0.726 (1.00)
DEL PEAK 37(XP22 2) MUTATION ANALYSIS	7 (37%)	12	0.719 (1.00)	0.6 (1.00)	0.353 (1.00)	0.393 (1.00)	0.656 (1.00)	0.263 (1.00)	0.923 (1.00)
DEL PEAK 38(XP21 1) MUTATION ANALYSIS	10 (53%)	9	0.725 (1.00)	0.699 (1.00)	0.489 (1.00)	0.298 (1.00)	1 (1.00)	0.582 (1.00)	0.156 (1.00)
DEL PEAK 39(XP11 3) MUTATION ANALYSIS	10 (53%)	9	0.592 (1.00)	0.297 (1.00)	0.634 (1.00)	0.298 (1.00)	0.35 (1.00)	0.582 (1.00)	0.438 (1.00)
DEL PEAK 40(XQ21 33) MUTATION ANALYSIS	4 (21%)	15	0.266 (1.00)	0.584 (1.00)	0.0104 (1.00)	0.372 (1.00)	0.00903 (1.00)	0.53 (1.00)

Methods & Data

Input

Copy number data file = transformed.cor.cli.txt
Clinical data file = ESCA-TP.clin.merged.picked.txt
Number of patients = 19
Number of significantly focal cnvs = 63
Number of selected clinical features = 7
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

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

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

[4] 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)

[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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