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.

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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