Correlation between copy number variation genes (focal events) and selected clinical features
Liver Hepatocellular 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/C1RB72ZC
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 focal events and 8 clinical features across 117 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 53 focal events and 8 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 |
PATHOLOGY M STAGE |
GENDER |
COMPLETENESS OF RESECTION |
||
| nCNV (%) | nWild-Type | logrank test | t-test | Chi-square test | Fisher's exact test | Fisher's exact test | Fisher's exact test | Fisher's exact test | Fisher's exact test | |
| AMP PEAK 1(1P22 3) MUTATION ANALYSIS | 31 (26%) | 86 |
0.372 (1.00) |
0.439 (1.00) |
0.248 (1.00) |
0.814 (1.00) |
0.532 (1.00) |
0.0785 (1.00) |
0.832 (1.00) |
0.0671 (1.00) |
| AMP PEAK 2(1Q22) MUTATION ANALYSIS | 86 (74%) | 31 |
0.056 (1.00) |
0.381 (1.00) |
0.665 (1.00) |
0.66 (1.00) |
1 (1.00) |
0.894 (1.00) |
0.388 (1.00) |
0.692 (1.00) |
| AMP PEAK 3(1Q42 3) MUTATION ANALYSIS | 79 (68%) | 38 |
0.0831 (1.00) |
0.432 (1.00) |
0.138 (1.00) |
0.0269 (1.00) |
0.548 (1.00) |
1 (1.00) |
0.543 (1.00) |
0.852 (1.00) |
| AMP PEAK 4(2P24 1) MUTATION ANALYSIS | 26 (22%) | 91 |
0.968 (1.00) |
0.433 (1.00) |
0.186 (1.00) |
0.113 (1.00) |
0.108 (1.00) |
0.305 (1.00) |
0.648 (1.00) |
0.529 (1.00) |
| AMP PEAK 5(2Q31 2) MUTATION ANALYSIS | 27 (23%) | 90 |
0.355 (1.00) |
0.443 (1.00) |
0.163 (1.00) |
0.398 (1.00) |
0.508 (1.00) |
0.581 (1.00) |
0.112 (1.00) |
0.576 (1.00) |
| AMP PEAK 6(3Q26 31) MUTATION ANALYSIS | 22 (19%) | 95 |
0.216 (1.00) |
0.495 (1.00) |
0.723 (1.00) |
0.455 (1.00) |
0.345 (1.00) |
0.371 (1.00) |
0.808 (1.00) |
1 (1.00) |
| AMP PEAK 7(5P15 33) MUTATION ANALYSIS | 58 (50%) | 59 |
0.665 (1.00) |
0.904 (1.00) |
0.151 (1.00) |
0.104 (1.00) |
0.605 (1.00) |
0.0795 (1.00) |
0.849 (1.00) |
1 (1.00) |
| AMP PEAK 8(5Q35 3) MUTATION ANALYSIS | 43 (37%) | 74 |
0.387 (1.00) |
0.378 (1.00) |
0.549 (1.00) |
0.681 (1.00) |
0.547 (1.00) |
1 (1.00) |
0.239 (1.00) |
0.193 (1.00) |
| AMP PEAK 9(6P25 2) MUTATION ANALYSIS | 49 (42%) | 68 |
0.132 (1.00) |
0.688 (1.00) |
0.454 (1.00) |
0.326 (1.00) |
1 (1.00) |
0.343 (1.00) |
0.181 (1.00) |
0.851 (1.00) |
| AMP PEAK 10(6P21 1) MUTATION ANALYSIS | 49 (42%) | 68 |
0.46 (1.00) |
0.406 (1.00) |
0.324 (1.00) |
0.937 (1.00) |
0.286 (1.00) |
0.252 (1.00) |
0.181 (1.00) |
0.851 (1.00) |
| AMP PEAK 11(7Q21 2) MUTATION ANALYSIS | 45 (38%) | 72 |
0.632 (1.00) |
0.0497 (1.00) |
0.546 (1.00) |
0.489 (1.00) |
0.28 (1.00) |
0.691 (1.00) |
0.557 (1.00) |
0.46 (1.00) |
| AMP PEAK 12(8Q13 1) MUTATION ANALYSIS | 61 (52%) | 56 |
0.725 (1.00) |
0.759 (1.00) |
0.176 (1.00) |
0.37 (1.00) |
0.615 (1.00) |
0.91 (1.00) |
0.00393 (1.00) |
0.773 (1.00) |
| AMP PEAK 13(8Q24 13) MUTATION ANALYSIS | 70 (60%) | 47 |
0.553 (1.00) |
0.912 (1.00) |
0.36 (1.00) |
0.953 (1.00) |
0.567 (1.00) |
1 (1.00) |
0.00626 (1.00) |
0.956 (1.00) |
| AMP PEAK 14(9Q34 2) MUTATION ANALYSIS | 15 (13%) | 102 |
0.76 (1.00) |
0.268 (1.00) |
0.19 (1.00) |
0.476 (1.00) |
0.284 (1.00) |
0.478 (1.00) |
0.783 (1.00) |
0.0348 (1.00) |
| AMP PEAK 15(10P15 1) MUTATION ANALYSIS | 24 (21%) | 93 |
0.37 (1.00) |
0.469 (1.00) |
0.19 (1.00) |
0.073 (1.00) |
1 (1.00) |
0.334 (1.00) |
0.814 (1.00) |
0.922 (1.00) |
| AMP PEAK 16(11Q13 3) MUTATION ANALYSIS | 21 (18%) | 96 |
0.98 (1.00) |
0.614 (1.00) |
0.0639 (1.00) |
0.0099 (1.00) |
1 (1.00) |
0.247 (1.00) |
0.805 (1.00) |
0.0572 (1.00) |
| AMP PEAK 17(12Q23 1) MUTATION ANALYSIS | 22 (19%) | 95 |
0.792 (1.00) |
0.103 (1.00) |
0.123 (1.00) |
0.259 (1.00) |
0.457 (1.00) |
0.307 (1.00) |
0.224 (1.00) |
0.257 (1.00) |
| AMP PEAK 18(13Q32 3) MUTATION ANALYSIS | 22 (19%) | 95 |
0.205 (1.00) |
0.868 (1.00) |
0.93 (1.00) |
0.792 (1.00) |
0.403 (1.00) |
0.855 (1.00) |
0.466 (1.00) |
0.133 (1.00) |
| AMP PEAK 19(15Q26 3) MUTATION ANALYSIS | 19 (16%) | 98 |
0.344 (1.00) |
0.594 (1.00) |
0.918 (1.00) |
0.282 (1.00) |
1 (1.00) |
1 (1.00) |
0.195 (1.00) |
1 (1.00) |
| AMP PEAK 20(17P11 2) MUTATION ANALYSIS | 18 (15%) | 99 |
0.578 (1.00) |
0.538 (1.00) |
0.0742 (1.00) |
0.0777 (1.00) |
1 (1.00) |
0.243 (1.00) |
0.795 (1.00) |
0.0466 (1.00) |
| AMP PEAK 21(17Q23 1) MUTATION ANALYSIS | 50 (43%) | 67 |
0.598 (1.00) |
0.604 (1.00) |
0.287 (1.00) |
0.69 (1.00) |
1 (1.00) |
0.348 (1.00) |
0.848 (1.00) |
0.27 (1.00) |
| AMP PEAK 22(17Q25 3) MUTATION ANALYSIS | 54 (46%) | 63 |
0.258 (1.00) |
0.981 (1.00) |
0.451 (1.00) |
0.255 (1.00) |
1 (1.00) |
0.33 (1.00) |
0.126 (1.00) |
0.0797 (1.00) |
| AMP PEAK 23(19P13 12) MUTATION ANALYSIS | 32 (27%) | 85 |
0.679 (1.00) |
0.467 (1.00) |
0.101 (1.00) |
0.693 (1.00) |
0.556 (1.00) |
0.0156 (1.00) |
0.133 (1.00) |
0.346 (1.00) |
| AMP PEAK 24(19Q13 11) MUTATION ANALYSIS | 38 (32%) | 79 |
0.596 (1.00) |
0.638 (1.00) |
0.0067 (1.00) |
0.0322 (1.00) |
1 (1.00) |
0.0123 (1.00) |
0.311 (1.00) |
0.216 (1.00) |
| AMP PEAK 25(20Q13 33) MUTATION ANALYSIS | 43 (37%) | 74 |
0.846 (1.00) |
0.117 (1.00) |
0.239 (1.00) |
0.959 (1.00) |
0.28 (1.00) |
0.244 (1.00) |
0.323 (1.00) |
0.532 (1.00) |
| DEL PEAK 1(1P36 32) MUTATION ANALYSIS | 54 (46%) | 63 |
0.398 (1.00) |
0.196 (1.00) |
0.592 (1.00) |
0.0547 (1.00) |
0.573 (1.00) |
0.403 (1.00) |
0.342 (1.00) |
0.209 (1.00) |
| DEL PEAK 2(1P35 2) MUTATION ANALYSIS | 44 (38%) | 73 |
0.545 (1.00) |
0.128 (1.00) |
0.234 (1.00) |
0.365 (1.00) |
0.0355 (1.00) |
0.12 (1.00) |
0.694 (1.00) |
0.361 (1.00) |
| DEL PEAK 3(2Q22 1) MUTATION ANALYSIS | 13 (11%) | 104 |
0.124 (1.00) |
0.832 (1.00) |
0.593 (1.00) |
0.138 (1.00) |
1 (1.00) |
1 (1.00) |
1 (1.00) |
0.734 (1.00) |
| DEL PEAK 4(2Q37 3) MUTATION ANALYSIS | 23 (20%) | 94 |
0.517 (1.00) |
0.962 (1.00) |
0.602 (1.00) |
0.213 (1.00) |
0.508 (1.00) |
0.612 (1.00) |
0.149 (1.00) |
0.917 (1.00) |
| DEL PEAK 5(3P13) MUTATION ANALYSIS | 20 (17%) | 97 |
0.423 (1.00) |
0.733 (1.00) |
0.126 (1.00) |
0.143 (1.00) |
0.43 (1.00) |
0.282 (1.00) |
0.217 (1.00) |
0.742 (1.00) |
| DEL PEAK 6(4P16 1) MUTATION ANALYSIS | 22 (19%) | 95 |
0.437 (1.00) |
0.861 (1.00) |
0.241 (1.00) |
0.927 (1.00) |
0.0722 (1.00) |
0.438 (1.00) |
0.333 (1.00) |
0.222 (1.00) |
| DEL PEAK 7(4Q25) MUTATION ANALYSIS | 54 (46%) | 63 |
0.212 (1.00) |
0.42 (1.00) |
0.461 (1.00) |
0.844 (1.00) |
0.0976 (1.00) |
0.33 (1.00) |
0.849 (1.00) |
0.254 (1.00) |
| DEL PEAK 8(4Q35 1) MUTATION ANALYSIS | 49 (42%) | 68 |
0.0255 (1.00) |
0.279 (1.00) |
0.695 (1.00) |
1 (1.00) |
0.573 (1.00) |
0.252 (1.00) |
0.699 (1.00) |
0.336 (1.00) |
| DEL PEAK 9(5Q23 1) MUTATION ANALYSIS | 16 (14%) | 101 |
0.123 (1.00) |
0.714 (1.00) |
0.465 (1.00) |
0.116 (1.00) |
0.345 (1.00) |
1 (1.00) |
0.782 (1.00) |
0.695 (1.00) |
| DEL PEAK 10(6Q16 3) MUTATION ANALYSIS | 42 (36%) | 75 |
0.798 (1.00) |
0.602 (1.00) |
0.499 (1.00) |
0.431 (1.00) |
0.28 (1.00) |
0.336 (1.00) |
0.429 (1.00) |
0.644 (1.00) |
| DEL PEAK 11(6Q26) MUTATION ANALYSIS | 47 (40%) | 70 |
0.724 (1.00) |
0.64 (1.00) |
0.414 (1.00) |
0.315 (1.00) |
0.561 (1.00) |
0.0288 (1.00) |
1 (1.00) |
0.665 (1.00) |
| DEL PEAK 12(8P23 2) MUTATION ANALYSIS | 75 (64%) | 42 |
0.0603 (1.00) |
0.0376 (1.00) |
0.414 (1.00) |
0.649 (1.00) |
0.269 (1.00) |
0.834 (1.00) |
0.429 (1.00) |
1 (1.00) |
| DEL PEAK 13(8P11 22) MUTATION ANALYSIS | 60 (51%) | 57 |
0.0487 (1.00) |
0.0345 (1.00) |
0.397 (1.00) |
0.526 (1.00) |
0.0976 (1.00) |
0.213 (1.00) |
0.572 (1.00) |
1 (1.00) |
| DEL PEAK 14(9P21 3) MUTATION ANALYSIS | 45 (38%) | 72 |
0.4 (1.00) |
0.92 (1.00) |
0.0878 (1.00) |
0.16 (1.00) |
0.55 (1.00) |
0.038 (1.00) |
0.557 (1.00) |
0.0448 (1.00) |
| DEL PEAK 15(9Q34 3) MUTATION ANALYSIS | 43 (37%) | 74 |
0.998 (1.00) |
0.573 (1.00) |
0.151 (1.00) |
0.561 (1.00) |
0.05 (1.00) |
0.1 (1.00) |
0.554 (1.00) |
0.467 (1.00) |
| DEL PEAK 16(10Q23 31) MUTATION ANALYSIS | 36 (31%) | 81 |
0.95 (1.00) |
0.964 (1.00) |
0.14 (1.00) |
0.104 (1.00) |
0.211 (1.00) |
0.584 (1.00) |
1 (1.00) |
0.139 (1.00) |
| DEL PEAK 17(11Q23 3) MUTATION ANALYSIS | 24 (21%) | 93 |
0.99 (1.00) |
0.0236 (1.00) |
0.316 (1.00) |
0.236 (1.00) |
0.0952 (1.00) |
0.862 (1.00) |
0.645 (1.00) |
0.421 (1.00) |
| DEL PEAK 18(12P12 1) MUTATION ANALYSIS | 26 (22%) | 91 |
0.103 (1.00) |
0.923 (1.00) |
0.234 (1.00) |
0.74 (1.00) |
0.121 (1.00) |
0.565 (1.00) |
0.82 (1.00) |
0.106 (1.00) |
| DEL PEAK 19(12Q24 33) MUTATION ANALYSIS | 20 (17%) | 97 |
0.451 (1.00) |
0.461 (1.00) |
0.0585 (1.00) |
0.441 (1.00) |
1 (1.00) |
0.144 (1.00) |
0.217 (1.00) |
1 (1.00) |
| DEL PEAK 20(13Q14 2) MUTATION ANALYSIS | 54 (46%) | 63 |
0.129 (1.00) |
0.614 (1.00) |
0.285 (1.00) |
0.00179 (0.758) |
1 (1.00) |
0.753 (1.00) |
0.342 (1.00) |
0.661 (1.00) |
| DEL PEAK 21(13Q22 2) MUTATION ANALYSIS | 43 (37%) | 74 |
0.533 (1.00) |
0.115 (1.00) |
0.572 (1.00) |
0.00143 (0.608) |
0.548 (1.00) |
0.834 (1.00) |
0.323 (1.00) |
0.57 (1.00) |
| DEL PEAK 22(14Q23 3) MUTATION ANALYSIS | 41 (35%) | 76 |
0.759 (1.00) |
0.978 (1.00) |
0.239 (1.00) |
0.235 (1.00) |
1 (1.00) |
0.545 (1.00) |
0.69 (1.00) |
0.251 (1.00) |
| DEL PEAK 23(16Q23 1) MUTATION ANALYSIS | 50 (43%) | 67 |
0.0629 (1.00) |
0.203 (1.00) |
0.527 (1.00) |
0.378 (1.00) |
0.615 (1.00) |
0.912 (1.00) |
0.25 (1.00) |
0.0773 (1.00) |
| DEL PEAK 24(17P13 3) MUTATION ANALYSIS | 64 (55%) | 53 |
0.177 (1.00) |
0.231 (1.00) |
0.229 (1.00) |
0.566 (1.00) |
1 (1.00) |
0.16 (1.00) |
0.705 (1.00) |
0.184 (1.00) |
| DEL PEAK 25(17P11 2) MUTATION ANALYSIS | 64 (55%) | 53 |
0.355 (1.00) |
0.895 (1.00) |
0.285 (1.00) |
0.343 (1.00) |
0.262 (1.00) |
0.911 (1.00) |
0.449 (1.00) |
0.25 (1.00) |
| DEL PEAK 26(18Q21 2) MUTATION ANALYSIS | 24 (21%) | 93 |
0.142 (1.00) |
0.217 (1.00) |
0.616 (1.00) |
0.934 (1.00) |
0.43 (1.00) |
0.543 (1.00) |
0.167 (1.00) |
0.922 (1.00) |
| DEL PEAK 27(19P13 3) MUTATION ANALYSIS | 27 (23%) | 90 |
0.873 (1.00) |
0.497 (1.00) |
0.146 (1.00) |
0.153 (1.00) |
1 (1.00) |
0.153 (1.00) |
1 (1.00) |
0.858 (1.00) |
| DEL PEAK 28(22Q13 32) MUTATION ANALYSIS | 30 (26%) | 87 |
0.112 (1.00) |
0.883 (1.00) |
0.747 (1.00) |
0.118 (1.00) |
1 (1.00) |
0.347 (1.00) |
0.277 (1.00) |
0.163 (1.00) |
Methods & Data
Input
-
Copy number data file = transformed.cor.cli.txt
-
Clinical data file = LIHC-TP.clin.merged.picked.txt
-
Number of patients = 117
-
Number of significantly focal cnvs = 53
-
Number of selected clinical features = 8
-
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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Broad Institute TCGA GDAC as part of the TCGA Research Network.
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