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

Liver Hepatocellular Carcinoma (Primary solid tumor)

15 July 2014 | analyses__2014_07_15

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 (2014): Correlation between copy number variation genes (focal events) and selected clinical features. Broad Institute of MIT and Harvard. doi:10.7908/C1BG2MR2

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 11 clinical features across 160 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 11 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	HISTOLOGICAL TYPE	COMPLETENESS OF RESECTION	RACE	ETHNICITY
	nCNV (%)	nWild-Type	logrank test	Wilcoxon-test	Fisher's exact test	Fisher's exact test	Fisher's exact test	Fisher's exact test	Fisher's exact test	Fisher's exact test	Fisher's exact test	Fisher's exact test	Fisher's exact test
amp 1p22 3	38 (24%)	122	0.458 (1.00)	0.311 (1.00)	0.173 (1.00)	0.625 (1.00)	0.51 (1.00)	0.184 (1.00)	1 (1.00)	0.666 (1.00)	0.0643 (1.00)	0.399 (1.00)	1 (1.00)
amp 1q22	119 (74%)	41	0.0196 (1.00)	0.329 (1.00)	0.252 (1.00)	0.166 (1.00)	1 (1.00)	0.79 (1.00)	0.578 (1.00)	0.0529 (1.00)	0.734 (1.00)	0.532 (1.00)	1 (1.00)
amp 1q42 3	113 (71%)	47	0.0906 (1.00)	0.882 (1.00)	0.0548 (1.00)	0.0215 (1.00)	0.556 (1.00)	0.631 (1.00)	0.474 (1.00)	0.754 (1.00)	0.868 (1.00)	0.697 (1.00)	1 (1.00)
amp 2p24 1	34 (21%)	126	0.494 (1.00)	0.0608 (1.00)	0.267 (1.00)	0.149 (1.00)	0.101 (1.00)	0.551 (1.00)	0.111 (1.00)	1 (1.00)	0.554 (1.00)	0.75 (1.00)	0.539 (1.00)
amp 2q31 2	31 (19%)	129	0.134 (1.00)	0.42 (1.00)	0.435 (1.00)	0.411 (1.00)	0.435 (1.00)	0.729 (1.00)	0.0125 (1.00)	1 (1.00)	0.486 (1.00)	0.412 (1.00)	0.501 (1.00)
amp 3q26 31	33 (21%)	127	0.355 (1.00)	0.448 (1.00)	0.393 (1.00)	0.282 (1.00)	0.373 (1.00)	0.426 (1.00)	0.841 (1.00)	1 (1.00)	0.935 (1.00)	0.747 (1.00)	1 (1.00)
amp 4q13 3	15 (9%)	145	0.906 (1.00)	0.796 (1.00)	0.557 (1.00)	0.699 (1.00)	1 (1.00)	0.516 (1.00)	0.262 (1.00)	1 (1.00)	0.0174 (1.00)	0.817 (1.00)	1 (1.00)
amp 5p15 33	75 (47%)	85	0.919 (1.00)	0.915 (1.00)	0.0115 (1.00)	0.00788 (1.00)	1 (1.00)	0.284 (1.00)	0.746 (1.00)	0.172 (1.00)	1 (1.00)	0.197 (1.00)	1 (1.00)
amp 5q35 3	58 (36%)	102	0.786 (1.00)	0.207 (1.00)	0.551 (1.00)	0.757 (1.00)	0.549 (1.00)	1 (1.00)	0.398 (1.00)	0.123 (1.00)	0.136 (1.00)	1 (1.00)	1 (1.00)
amp 6p25 2	67 (42%)	93	0.249 (1.00)	0.973 (1.00)	0.552 (1.00)	0.261 (1.00)	1 (1.00)	0.718 (1.00)	0.62 (1.00)	0.149 (1.00)	0.694 (1.00)	0.886 (1.00)	1 (1.00)
amp 6p21 1	67 (42%)	93	0.905 (1.00)	0.24 (1.00)	0.335 (1.00)	0.994 (1.00)	0.286 (1.00)	0.763 (1.00)	0.408 (1.00)	0.15 (1.00)	0.697 (1.00)	0.809 (1.00)	1 (1.00)
amp 6q12	47 (29%)	113	0.967 (1.00)	0.83 (1.00)	0.178 (1.00)	0.94 (1.00)	0.208 (1.00)	0.0998 (1.00)	0.282 (1.00)	0.162 (1.00)	0.524 (1.00)	0.895 (1.00)	1 (1.00)
amp 6q12	34 (21%)	126	0.978 (1.00)	0.233 (1.00)	0.517 (1.00)	0.98 (1.00)	1 (1.00)	0.208 (1.00)	0.426 (1.00)	0.0864 (1.00)	0.282 (1.00)	0.17 (1.00)	0.501 (1.00)
amp 7q21 2	59 (37%)	101	0.827 (1.00)	0.0438 (1.00)	0.172 (1.00)	0.372 (1.00)	0.27 (1.00)	0.544 (1.00)	0.503 (1.00)	0.782 (1.00)	0.604 (1.00)	0.261 (1.00)	1 (1.00)
amp 7q31 2	56 (35%)	104	0.459 (1.00)	0.13 (1.00)	0.174 (1.00)	0.476 (1.00)	0.22 (1.00)	0.695 (1.00)	0.735 (1.00)	0.792 (1.00)	0.763 (1.00)	0.131 (1.00)	1 (1.00)
amp 8q11 1	70 (44%)	90	0.189 (1.00)	0.464 (1.00)	0.124 (1.00)	0.0641 (1.00)	0.286 (1.00)	0.342 (1.00)	0.000942 (0.546)	1 (1.00)	0.758 (1.00)	0.142 (1.00)	0.578 (1.00)
amp 8q24 21	96 (60%)	64	0.778 (1.00)	0.579 (1.00)	0.302 (1.00)	0.903 (1.00)	0.57 (1.00)	0.55 (1.00)	0.0121 (1.00)	0.77 (1.00)	1 (1.00)	0.0439 (1.00)	1 (1.00)
amp 9q34 2	22 (14%)	138	0.644 (1.00)	0.107 (1.00)	0.202 (1.00)	0.269 (1.00)	0.352 (1.00)	0.864 (1.00)	1 (1.00)	0.45 (1.00)	0.247 (1.00)	0.749 (1.00)	1 (1.00)
amp 10p15 1	31 (19%)	129	0.487 (1.00)	0.19 (1.00)	0.0208 (1.00)	0.0139 (1.00)	1 (1.00)	0.0664 (1.00)	0.68 (1.00)	0.579 (1.00)	0.929 (1.00)	0.764 (1.00)	0.475 (1.00)
amp 11q13 3	29 (18%)	131	0.343 (1.00)	0.612 (1.00)	0.0762 (1.00)	0.0366 (1.00)	1 (1.00)	0.249 (1.00)	1 (1.00)	1 (1.00)	0.0903 (1.00)	1 (1.00)	1 (1.00)
amp 13q32 3	25 (16%)	135	0.0899 (1.00)	0.981 (1.00)	0.974 (1.00)	0.902 (1.00)	0.352 (1.00)	0.879 (1.00)	0.504 (1.00)	0.0471 (1.00)	0.32 (1.00)	0.496 (1.00)	1 (1.00)
amp 15q26 3	27 (17%)	133	0.918 (1.00)	0.0995 (1.00)	0.8 (1.00)	0.369 (1.00)	1 (1.00)	1 (1.00)	0.828 (1.00)	0.526 (1.00)	1 (1.00)	0.651 (1.00)	0.404 (1.00)
amp 17p11 2	26 (16%)	134	0.769 (1.00)	0.621 (1.00)	0.167 (1.00)	0.124 (1.00)	1 (1.00)	0.253 (1.00)	0.511 (1.00)	1 (1.00)	0.0209 (1.00)	0.531 (1.00)	0.404 (1.00)
amp 17q25 3	72 (45%)	88	0.396 (1.00)	0.964 (1.00)	0.871 (1.00)	0.55 (1.00)	1 (1.00)	0.725 (1.00)	0.139 (1.00)	0.251 (1.00)	0.0458 (1.00)	0.04 (1.00)	1 (1.00)
amp 19q13 11	45 (28%)	115	0.918 (1.00)	0.554 (1.00)	0.247 (1.00)	0.68 (1.00)	1 (1.00)	0.186 (1.00)	0.719 (1.00)	0.149 (1.00)	0.198 (1.00)	0.928 (1.00)	1 (1.00)
amp 20q13 13	53 (33%)	107	0.293 (1.00)	0.153 (1.00)	0.159 (1.00)	0.587 (1.00)	0.257 (1.00)	0.451 (1.00)	0.731 (1.00)	1 (1.00)	0.596 (1.00)	0.426 (1.00)	0.551 (1.00)
amp 20q13 33	55 (34%)	105	0.818 (1.00)	0.165 (1.00)	0.225 (1.00)	0.622 (1.00)	0.296 (1.00)	0.279 (1.00)	0.169 (1.00)	0.792 (1.00)	0.649 (1.00)	0.451 (1.00)	0.551 (1.00)
amp xq28	39 (24%)	121	0.815 (1.00)	0.194 (1.00)	0.969 (1.00)	0.831 (1.00)	1 (1.00)	1 (1.00)	0.0133 (1.00)	1 (1.00)	1 (1.00)	0.247 (1.00)	1 (1.00)
del 1p36 23	76 (48%)	84	0.371 (1.00)	0.29 (1.00)	0.867 (1.00)	0.437 (1.00)	0.591 (1.00)	0.511 (1.00)	0.259 (1.00)	0.174 (1.00)	0.84 (1.00)	0.402 (1.00)	0.607 (1.00)
del 2q22 1	17 (11%)	143	0.0141 (1.00)	0.78 (1.00)	0.808 (1.00)	0.57 (1.00)	1 (1.00)	1 (1.00)	1 (1.00)	0.364 (1.00)	0.531 (1.00)	0.6 (1.00)	0.246 (1.00)
del 2q37 3	31 (19%)	129	0.86 (1.00)	0.452 (1.00)	0.543 (1.00)	0.0611 (1.00)	0.415 (1.00)	0.459 (1.00)	0.68 (1.00)	0.0746 (1.00)	0.714 (1.00)	0.363 (1.00)	0.076 (1.00)
del 3p13	29 (18%)	131	0.186 (1.00)	0.939 (1.00)	0.125 (1.00)	0.0406 (1.00)	0.454 (1.00)	0.634 (1.00)	0.0354 (1.00)	0.0632 (1.00)	1 (1.00)	0.648 (1.00)	1 (1.00)
del 4p16 3	29 (18%)	131	0.643 (1.00)	0.661 (1.00)	0.252 (1.00)	0.939 (1.00)	0.06 (1.00)	0.566 (1.00)	0.29 (1.00)	0.553 (1.00)	0.238 (1.00)	0.54 (1.00)	1 (1.00)
del 4q24	69 (43%)	91	0.181 (1.00)	0.133 (1.00)	0.0262 (1.00)	0.31 (1.00)	1 (1.00)	0.237 (1.00)	0.869 (1.00)	0.756 (1.00)	0.385 (1.00)	0.05 (1.00)	0.082 (1.00)
del 4q34 1	65 (41%)	95	0.0175 (1.00)	0.0738 (1.00)	0.0437 (1.00)	0.108 (1.00)	1 (1.00)	0.584 (1.00)	0.507 (1.00)	0.765 (1.00)	0.612 (1.00)	0.00088 (0.511)	1 (1.00)
del 4q34 3	65 (41%)	95	0.0333 (1.00)	0.24 (1.00)	0.497 (1.00)	0.558 (1.00)	0.556 (1.00)	0.587 (1.00)	0.507 (1.00)	0.765 (1.00)	0.797 (1.00)	0.00977 (1.00)	1 (1.00)
del 6q27	62 (39%)	98	0.855 (1.00)	0.179 (1.00)	0.218 (1.00)	0.466 (1.00)	0.556 (1.00)	0.0546 (1.00)	0.867 (1.00)	0.771 (1.00)	0.496 (1.00)	0.882 (1.00)	0.277 (1.00)
del 8p23 2	104 (65%)	56	0.33 (1.00)	0.0197 (1.00)	0.628 (1.00)	0.973 (1.00)	0.279 (1.00)	0.339 (1.00)	0.176 (1.00)	0.789 (1.00)	1 (1.00)	0.124 (1.00)	0.298 (1.00)
del 9p21 3	61 (38%)	99	0.181 (1.00)	0.841 (1.00)	0.0961 (1.00)	0.16 (1.00)	0.283 (1.00)	0.232 (1.00)	0.401 (1.00)	0.774 (1.00)	0.132 (1.00)	0.431 (1.00)	0.277 (1.00)
del 10q23 31	44 (28%)	116	0.747 (1.00)	0.813 (1.00)	0.09 (1.00)	0.188 (1.00)	0.162 (1.00)	0.669 (1.00)	0.715 (1.00)	0.063 (1.00)	0.0522 (1.00)	0.309 (1.00)	1 (1.00)
del 10q25 2	43 (27%)	117	0.834 (1.00)	0.679 (1.00)	0.262 (1.00)	0.217 (1.00)	0.162 (1.00)	0.672 (1.00)	0.716 (1.00)	0.0619 (1.00)	0.195 (1.00)	0.229 (1.00)	1 (1.00)
del 11q14 1	28 (18%)	132	0.979 (1.00)	0.235 (1.00)	0.636 (1.00)	0.589 (1.00)	0.0675 (1.00)	1 (1.00)	1 (1.00)	0.143 (1.00)	0.429 (1.00)	0.71 (1.00)	0.419 (1.00)
del 11q23 3	32 (20%)	128	0.974 (1.00)	0.399 (1.00)	0.737 (1.00)	0.555 (1.00)	0.0922 (1.00)	1 (1.00)	1 (1.00)	0.181 (1.00)	0.449 (1.00)	0.907 (1.00)	0.488 (1.00)
del 12p12 1	34 (21%)	126	0.0967 (1.00)	0.562 (1.00)	0.372 (1.00)	0.861 (1.00)	0.11 (1.00)	0.755 (1.00)	0.843 (1.00)	0.621 (1.00)	0.363 (1.00)	0.619 (1.00)	1 (1.00)
del 12q24 33	25 (16%)	135	0.364 (1.00)	0.47 (1.00)	0.0794 (1.00)	0.16 (1.00)	1 (1.00)	0.336 (1.00)	0.824 (1.00)	1 (1.00)	0.839 (1.00)	0.497 (1.00)	1 (1.00)
del 13q14 2	72 (45%)	88	0.368 (1.00)	0.42 (1.00)	0.0479 (1.00)	0.00076 (0.442)	1 (1.00)	0.675 (1.00)	0.331 (1.00)	0.452 (1.00)	0.092 (1.00)	0.0247 (1.00)	1 (1.00)
del 13q22 2	57 (36%)	103	0.802 (1.00)	0.853 (1.00)	0.314 (1.00)	0.00301 (1.00)	0.549 (1.00)	0.541 (1.00)	0.236 (1.00)	1 (1.00)	0.509 (1.00)	0.129 (1.00)	1 (1.00)
del 14q23 3	55 (34%)	105	0.916 (1.00)	0.997 (1.00)	0.314 (1.00)	0.216 (1.00)	1 (1.00)	0.803 (1.00)	0.865 (1.00)	1 (1.00)	0.252 (1.00)	0.218 (1.00)	1 (1.00)
del 14q32 33	56 (35%)	104	0.603 (1.00)	0.617 (1.00)	0.266 (1.00)	0.19 (1.00)	1 (1.00)	0.801 (1.00)	1 (1.00)	1 (1.00)	0.669 (1.00)	0.26 (1.00)	1 (1.00)
del 16q23 2	67 (42%)	93	0.069 (1.00)	0.0942 (1.00)	0.126 (1.00)	0.0787 (1.00)	0.575 (1.00)	0.818 (1.00)	0.408 (1.00)	0.761 (1.00)	0.355 (1.00)	0.00075 (0.437)	0.0782 (1.00)
del 17p11 2	84 (52%)	76	0.0989 (1.00)	0.462 (1.00)	0.312 (1.00)	0.289 (1.00)	0.245 (1.00)	1 (1.00)	0.259 (1.00)	0.747 (1.00)	0.379 (1.00)	0.663 (1.00)	1 (1.00)
del 19p13 3	34 (21%)	126	0.81 (1.00)	0.718 (1.00)	0.211 (1.00)	0.118 (1.00)	0.492 (1.00)	0.433 (1.00)	0.322 (1.00)	1 (1.00)	0.819 (1.00)	0.244 (1.00)	0.539 (1.00)
del 22q13 32	46 (29%)	114	0.216 (1.00)	0.238 (1.00)	0.591 (1.00)	0.112 (1.00)	1 (1.00)	0.571 (1.00)	0.59 (1.00)	0.0723 (1.00)	0.335 (1.00)	0.588 (1.00)	1 (1.00)

Methods & Data

Input

Copy number data file = transformed.cor.cli.txt
Clinical data file = LIHC-TP.merged_data.txt
Number of patients = 160
Number of significantly focal cnvs = 53
Number of selected clinical features = 11
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

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] 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)

[3] 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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