Correlation between copy number variation genes (focal) and selected clinical features
Sarcoma (Primary solid tumor)
23 May 2013 | analyses__2013_05_23
Maintainer Information
Citation Information
doi:10.7908/C1H41PHG
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/C1H41PHG
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 41 arm-level results and 3 clinical features across 22 patients, one significant finding detected with Q value < 0.25.

- Amp Peak 5(6p21.1) cnv correlated to 'AGE'.

Results
Overview of the results

Table 1. Get Full Table Overview of the association between significant copy number variation of 41 arm-level results and 3 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
| nCNV (%) | nWild-Type | logrank test | t-test | Fisher's exact test
Amp Peak 5(6p21 1) | 0 (0%) | 13 | 0.536 (1.00) | 0.000112 (0.0137) | 0.192 (1.00)
Amp Peak 1(1p32 1) | 0 (0%) | 14 | 0.175 (1.00) | 0.789 (1.00) | 1 (1.00)
Amp Peak 2(1q24 3) | 0 (0%) | 13 | 0.724 (1.00) | 0.761 (1.00) | 0.666 (1.00)
Amp Peak 3(4p15 2) | 0 (0%) | 13 | 0.393 (1.00) | 0.123 (1.00) | 0.666 (1.00)
Amp Peak 4(5p15 33) | 0 (0%) | 9 | 0.346 (1.00) | 0.605 (1.00) | 1 (1.00)
Amp Peak 6(6q25 1) | 0 (0%) | 14 | 0.833 (1.00) | 0.236 (1.00) | 1 (1.00)
Amp Peak 7(7p15 3) | 0 (0%) | 14 | 0.712 (1.00) | 0.0039 (0.475) | 1 (1.00)
Amp Peak 8(11q22 2) | 0 (0%) | 16 | 0.0624 (1.00) | 0.966 (1.00) | 1 (1.00)
Amp Peak 9(12p13 32) | 0 (0%) | 16 | 0.165 (1.00) | 0.789 (1.00) | 1 (1.00)
Amp Peak 10(12q15) | 0 (0%) | 8 | 0.683 (1.00) | 0.651 (1.00) | 0.00619 (0.749)
Amp Peak 11(17p12) | 0 (0%) | 14 | 0.654 (1.00) | 0.259 (1.00) | 0.675 (1.00)
Amp Peak 12(19p13 2) | 0 (0%) | 11 | 0.901 (1.00) | 0.63 (1.00) | 0.67 (1.00)
Amp Peak 13(Xq21 1) | 0 (0%) | 15 | 0.525 (1.00) | 0.481 (1.00) | 1 (1.00)
Del Peak 1(1p36 32) | 0 (0%) | 17 | 0.926 (1.00) | 0.723 (1.00) | 0.00957 (1.00)
Del Peak 2(1p32 3) | 0 (0%) | 16 | 0.406 (1.00) | 0.56 (1.00) | 0.348 (1.00)
Del Peak 3(1q44) | 0 (0%) | 10 | 0.99 (1.00) | 0.0582 (1.00) | 0.691 (1.00)
Del Peak 4(2q37 3) | 0 (0%) | 12 | 0.393 (1.00) | 0.0773 (1.00) | 1 (1.00)
Del Peak 5(3p21 31) | 0 (0%) | 15 | 0.0905 (1.00) | 0.0719 (1.00) | 1 (1.00)
Del Peak 6(3q25 1) | 0 (0%) | 13 | 0.254 (1.00) | 0.41 (1.00) | 1 (1.00)
Del Peak 7(4q35 1) | 0 (0%) | 12 | 0.764 (1.00) | 0.192 (1.00) | 0.0836 (1.00)
Del Peak 8(5q23 3) | 0 (0%) | 18 | 0.395 (1.00) | 0.687 (1.00) | 0.0287 (1.00)
Del Peak 9(6q15) | 0 (0%) | 18 | 0.828 (1.00) | 0.622 (1.00) | 1 (1.00)
Del Peak 10(7q36 3) | 0 (0%) | 16 | 0.254 (1.00) | 0.215 (1.00) | 1 (1.00)
Del Peak 11(8p23 2) | 0 (0%) | 14 | 0.452 (1.00) | 0.539 (1.00) | 1 (1.00)
Del Peak 12(9p21 3) | 0 (0%) | 10 | 0.586 (1.00) | 0.162 (1.00) | 0.231 (1.00)
Del Peak 13(9q34 3) | 0 (0%) | 17 | 0.0456 (1.00) | 0.0857 (1.00) | 0.135 (1.00)
Del Peak 14(10p15 3) | 0 (0%) | 11 | 0.603 (1.00) | 0.0164 (1.00) | 0.198 (1.00)
Del Peak 15(11p15 5) | 0 (0%) | 11 | 0.655 (1.00) | 0.0504 (1.00) | 0.67 (1.00)
Del Peak 16(11q22 3) | 0 (0%) | 11 | 0.182 (1.00) | 0.19 (1.00) | 1 (1.00)
Del Peak 17(11q25) | 0 (0%) | 10 | 0.0624 (1.00) | 0.0435 (1.00) | 1 (1.00)
Del Peak 18(12p12 3) | 0 (0%) | 15 | 0.92 (1.00) | 0.347 (1.00) | 0.381 (1.00)
Del Peak 19(13q14 2) | 0 (0%) | 7 | 0.268 (1.00) | 0.937 (1.00) | 0.381 (1.00)
Del Peak 20(13q34) | 0 (0%) | 10 | 0.985 (1.00) | 0.779 (1.00) | 0.691 (1.00)
Del Peak 21(14q24 1) | 0 (0%) | 10 | 0.673 (1.00) | 0.806 (1.00) | 0.691 (1.00)
Del Peak 22(17p13 1) | 0 (0%) | 17 | 0.774 (1.00) | 0.272 (1.00) | 0.624 (1.00)
Del Peak 23(17q25 3) | 0 (0%) | 16 | 0.683 (1.00) | 0.894 (1.00) | 1 (1.00)
Del Peak 24(19p13 3) | 0 (0%) | 17 | 0.0741 (1.00) | 0.555 (1.00) | 0.00957 (1.00)
Del Peak 25(19q13 33) | 0 (0%) | 12 | 0.00757 (0.908) | 0.897 (1.00) | 0.391 (1.00)
Del Peak 26(21q22 3) | 0 (0%) | 14 | 0.696 (1.00) | 0.0797 (1.00) | 0.378 (1.00)
Del Peak 27(Xq21 1) | 0 (0%) | 14 | 0.872 (1.00) | 0.227 (1.00) | 0.378 (1.00)
Del Peak 28(Xq28) | 0 (0%) | 12 | 0.228 (1.00) | 0.187 (1.00) | 0.231 (1.00)

'Amp Peak 5(6p21.1)' versus 'AGE'

P value = 0.000112 (t-test), Q value = 0.014

Table S1. Gene #5: 'Amp Peak 5(6p21.1)' versus Clinical Feature #2: 'AGE'

| nPatients | Mean (Std.Dev)
--- | --- | ---
ALL | 22 | 64.6 (7.7)
AMP PEAK 5(6P21.1) CNV | 9 | 71.8 (5.8)
AMP PEAK 5(6P21.1) WILD-TYPE | 13 | 59.7 (4.0)

Figure S1. Get High-res Image Gene #5: 'Amp Peak 5(6p21.1)' versus Clinical Feature #2: 'AGE'

Methods & Data
Input

- Mutation data file = all_lesions.conf_99.cnv.cluster.txt

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

- Number of patients = 22

- Number of significantly arm-level cnvs = 41

- Number of selected clinical features = 3

- 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)
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