Skin Cutaneous Melanoma: Correlation between copy number variation genes and selected clinical features
Maintained by TCGA GDAC Team (Broad Institute/Dana-Farber Cancer Institute/Harvard Medical School)
Overview
Introduction

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

Summary

Testing the association between copy number variation of 52 peak regions and 3 clinical features across 138 patients, no significant finding detected with Q value < 0.25.

- No gene 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 52 regions and 3 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
| nCNV (%) | nWild-Type | logrank test | t-test | Fisher's exact test
Amp Peak 1(1p36 11) | 27 (20%) | 111 | 0.112 (1.00) | 0.771 (1.00) | 0.82 (1.00)
Amp Peak 2(1p12) | 40 (29%) | 98 | 0.532 (1.00) | 0.499 (1.00) | 1 (1.00)
Amp Peak 3(1q44) | 73 (53%) | 65 | 0.105 (1.00) | 0.328 (1.00) | 0.369 (1.00)
Amp Peak 4(3p13) | 31 (22%) | 107 | 0.919 (1.00) | 0.201 (1.00) | 0.282 (1.00)
Amp Peak 5(4q12) | 24 (17%) | 114 | 0.474 (1.00) | 0.0376 (1.00) | 0.35 (1.00)
Amp Peak 6(5p15 33) | 40 (29%) | 98 | 0.182 (1.00) | 0.81 (1.00) | 0.843 (1.00)
Amp Peak 7(5q35 3) | 16 (12%) | 122 | 0.907 (1.00) | 0.174 (1.00) | 0.161 (1.00)
Amp Peak 8(6p25 1) | 80 (58%) | 58 | 0.111 (1.00) | 0.218 (1.00) | 1 (1.00)
Amp Peak 9(6q12) | 29 (21%) | 109 | 0.242 (1.00) | 0.97 (1.00) | 0.828 (1.00)
Amp Peak 10(7p22 3) | 81 (59%) | 57 | 0.0648 (1.00) | 0.121 (1.00) | 1 (1.00)
Amp Peak 11(7q34) | 85 (62%) | 53 | 0.4 (1.00) | 0.124 (1.00) | 0.197 (1.00)
Amp Peak 12(8q11 22) | 60 (43%) | 78 | 0.0923 (1.00) | 0.998 (1.00) | 0.363 (1.00)
Amp Peak 13(8q24 3) | 70 (51%) | 68 | 0.0559 (1.00) | 0.496 (1.00) | 0.471 (1.00)
Amp Peak 14(11q13 3) | 17 (12%) | 121 | 0.678 (1.00) | 0.413 (1.00) | 0.177 (1.00)
Amp Peak 15(11q13 4) | 16 (12%) | 122 | 0.272 (1.00) | 0.885 (1.00) | 0.262 (1.00)
Amp Peak 16(12q15) | 17 (12%) | 121 | 0.881 (1.00) | 0.29 (1.00) | 1 (1.00)
Amp Peak 17(15q24 3) | 44 (32%) | 94 | 0.925 (1.00) | 0.546 (1.00) | 0.439 (1.00)
Amp Peak 18(17q25 3) | 54 (39%) | 84 | 0.288 (1.00) | 0.0591 (1.00) | 0.579 (1.00)
Amp Peak 19(19p13 2) | 25 (18%) | 113 | 0.476 (1.00) | 0.976 (1.00) | 0.642 (1.00)
Amp Peak 20(20q13 2) | 72 (52%) | 66 | 0.956 (1.00) | 0.238 (1.00) | 0.286 (1.00)
Amp Peak 21(22q13 2) | 63 (46%) | 75 | 0.268 (1.00) | 0.316 (1.00) | 1 (1.00)
Del Peak 1(1p36 31) | 34 (25%) | 104 | 0.703 (1.00) | 0.778 (1.00) | 0.835 (1.00)
Del Peak 2(1p22 1) | 32 (23%) | 106 | 0.164 (1.00) | 0.378 (1.00) | 0.393 (1.00)
Del Peak 3(2q37 3) | 37 (27%) | 101 | 0.358 (1.00) | 0.69 (1.00) | 0.544 (1.00)
Del Peak 4(3q23) | 20 (14%) | 118 | 0.986 (1.00) | 0.442 (1.00) | 0.305 (1.00)
Del Peak 5(4p16 3) | 28 (20%) | 110 | 0.456 (1.00) | 0.856 (1.00) | 0.265 (1.00)
Del Peak 6(4q34 3) | 36 (26%) | 102 | 0.347 (1.00) | 0.54 (1.00) | 0.106 (1.00)
Del Peak 7(5q11 2) | 41 (30%) | 97 | 0.445 (1.00) | 0.273 (1.00) | 0.693 (1.00)
Del Peak 8(5q31 3) | 56 (41%) | 82 | 0.157 (1.00) | 0.418 (1.00) | 1 (1.00)
Del Peak 9(6q16 3) | 81 (59%) | 57 | 0.829 (1.00) | 0.248 (1.00) | 0.199 (1.00)
Del Peak 10(6q26) | 82 (59%) | 56 | 0.211 (1.00) | 0.524 (1.00) | 0.201 (1.00)
Del Peak 11(6q27) | 82 (59%) | 56 | 0.211 (1.00) | 0.524 (1.00) | 0.0999 (1.00)
Del Peak 12(7q31 1) | 10 (7%) | 128 |  |  | 1 (1.00)
Del Peak 13(8p23 3) | 30 (22%) | 108 |  |  | 0.273 (1.00)
Del Peak 14(9p23) | 92 (67%) | 46 | 0.268 (1.00) | 0.729 (1.00) | 0.126 (1.00)
Del Peak 15(9p21 3) | 107 (78%) | 31 | 0.544 (1.00) | 0.678 (1.00) | 0.0829 (1.00)
Del Peak 16(10p15 3) | 73 (53%) | 65 | 0.625 (1.00) | 0.57 (1.00) | 0.209 (1.00)
Del Peak 17(10q23 31) | 84 (61%) | 54 | 0.964 (1.00) | 0.0552 (1.00) | 0.0282 (1.00)
Del Peak 18(10q26 3) | 84 (61%) | 54 | 0.527 (1.00) | 0.219 (1.00) | 0.0282 (1.00)
Del Peak 19(11q23 3) | 76 (55%) | 62 | 0.589 (1.00) | 0.96 (1.00) | 0.368 (1.00)
Del Peak 20(12p13 31) | 18 (13%) | 120 |  |  | 0.295 (1.00)
Del Peak 21(12q23 3) | 30 (22%) | 108 | 0.193 (1.00) | 0.915 (1.00) | 1 (1.00)
Del Peak 22(12q24 33) | 31 (22%) | 107 | 0.598 (1.00) | 0.821 (1.00) | 0.83 (1.00)
Del Peak 23(13q34) | 33 (24%) | 105 | 0.314 (1.00) | 0.453 (1.00) | 0.677 (1.00)
Del Peak 24(14q32 32) | 43 (31%) | 95 | 0.506 (1.00) | 0.623 (1.00) | 0.437 (1.00)
Del Peak 25(15q13 3) | 35 (25%) | 103 | 0.727 (1.00) | 0.729 (1.00) | 1 (1.00)
Del Peak 26(15q15 2) | 33 (24%) | 105 | 0.839 (1.00) | 0.866 (1.00) | 0.405 (1.00)
Del Peak 27(16p13 3) | 23 (17%) | 115 | 0.297 (1.00) | 0.666 (1.00) | 0.0514 (1.00)
Del Peak 28(16q12 1) | 45 (33%) | 93 | 0.478 (1.00) | 0.887 (1.00) | 0.448 (1.00)
Del Peak 29(16q23 3) | 44 (32%) | 94 | 0.973 (1.00) | 0.218 (1.00) | 0.245 (1.00)
Del Peak 30(17q11 2) | 35 (25%) | 103 | 0.193 (1.00) | 0.952 (1.00) | 0.838 (1.00)
Del Peak 31(19p13 3) | 41 (30%) | 97 |  |  | 0.114 (1.00)

Methods & Data
Input

- Copy number data file = All Lesions File (all_lesions.conf_##.txt, where ## is the confidence level). The all lesions file is from GISTIC pipeline and summarizes the results from the GISTIC run. It contains data about the significant regions of amplification and deletion as well as which samples are amplified or deleted in each of these regions. The identified regions are listed down the first column, and the samples are listed across the first row, starting in column 10.

- Clinical data file = SKCM.clin.merged.picked.txt

- Number of patients = 138

- Number of copy number variation regions = 52

- Number of selected clinical features = 3

- Exclude regions that fewer than K tumors have alterations, K = 3

Survival analysis

For survival clinical features, the Kaplan-Meier survival curves of tumors with and without gene cnvs 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 cnvs 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)
[5] GISTIC_version2
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