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

Thyroid Adenocarcinoma (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/C1028QBZ

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 30 focal events and 17 clinical features across 486 patients, one significant finding detected with Q value < 0.25.

del_9q21.13 cnv correlated to 'NEOPLASM.DISEASESTAGE'.

Results

Overview of the results

Table 1. Get Full Table Overview of the association between significant copy number variation of 30 focal events and 17 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	NEOPLASM DISEASESTAGE	PATHOLOGY T STAGE	PATHOLOGY N STAGE	PATHOLOGY M STAGE	GENDER	HISTOLOGICAL TYPE	RADIATIONS RADIATION REGIMENINDICATION	RADIATIONEXPOSURE	EXTRATHYROIDAL EXTENSION	COMPLETENESS OF RESECTION	NUMBER OF LYMPH NODES	MULTIFOCALITY	TUMOR SIZE	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	Fisher's exact test	Wilcoxon-test	Fisher's exact test	Wilcoxon-test	Fisher's exact test	Fisher's exact test
del 9q21 13	23 (5%)	463	0.0433 (1.00)	0.00485 (1.00)	0.00049 (0.245)	0.227 (1.00)	0.493 (1.00)	0.026 (1.00)	0.343 (1.00)	0.723 (1.00)	0.498 (1.00)	0.601 (1.00)	0.0776 (1.00)	0.679 (1.00)	0.507 (1.00)	0.528 (1.00)	0.0513 (1.00)	0.784 (1.00)	1 (1.00)
amp xq22 3	15 (3%)	471	0.118 (1.00)	0.357 (1.00)	0.188 (1.00)	0.565 (1.00)	0.416 (1.00)	0.698 (1.00)	0.0147 (1.00)	0.532 (1.00)	1 (1.00)	1 (1.00)	0.0128 (1.00)	0.79 (1.00)	0.357 (1.00)	0.302 (1.00)	0.781 (1.00)	0.745 (1.00)	1 (1.00)
del 1q24 2	3 (1%)	483	0.608 (1.00)	0.816 (1.00)	0.332 (1.00)	0.693 (1.00)	0.499 (1.00)	0.133 (1.00)	0.569 (1.00)	0.232 (1.00)	1 (1.00)	1 (1.00)	0.607 (1.00)	1 (1.00)		1 (1.00)	0.11 (1.00)		1 (1.00)
del 2p23 1	12 (2%)	474	0.695 (1.00)	0.699 (1.00)	0.0545 (1.00)	0.892 (1.00)	0.0201 (1.00)	0.0243 (1.00)	0.528 (1.00)	0.00401 (1.00)	1 (1.00)	1 (1.00)	0.0801 (1.00)	0.533 (1.00)	0.00867 (1.00)	0.779 (1.00)	0.911 (1.00)	1 (1.00)	1 (1.00)
del 2q35	12 (2%)	474	0.252 (1.00)	0.142 (1.00)	0.0102 (1.00)	0.684 (1.00)	0.00732 (1.00)	0.0237 (1.00)	0.528 (1.00)	0.0222 (1.00)	1 (1.00)	0.365 (1.00)	0.291 (1.00)	0.268 (1.00)	0.005 (1.00)	1 (1.00)	0.0722 (1.00)	1 (1.00)	1 (1.00)
del 5p15 2	4 (1%)	482	0.894 (1.00)	0.175 (1.00)	0.227 (1.00)	0.63 (1.00)	0.372 (1.00)	0.197 (1.00)	0.578 (1.00)	0.0291 (1.00)	1 (1.00)	1 (1.00)	0.414 (1.00)	0.0691 (1.00)	0.783 (1.00)	0.338 (1.00)	0.204 (1.00)	0.271 (1.00)	0.346 (1.00)
del 6q22 31	7 (1%)	479	0.00749 (1.00)	0.0784 (1.00)	0.202 (1.00)	0.792 (1.00)	0.372 (1.00)	0.00952 (1.00)	0.389 (1.00)	0.821 (1.00)	0.186 (1.00)	0.218 (1.00)	0.383 (1.00)	0.751 (1.00)	0.202 (1.00)	0.46 (1.00)	0.00834 (1.00)	1 (1.00)	1 (1.00)
del 7q34	4 (1%)	482	0.748 (1.00)	0.744 (1.00)	0.473 (1.00)	0.554 (1.00)	0.623 (1.00)	1 (1.00)	1 (1.00)	0.123 (1.00)	1 (1.00)	1 (1.00)	0.637 (1.00)	1 (1.00)	0.511 (1.00)	0.628 (1.00)	0.0903 (1.00)	1 (1.00)	1 (1.00)
del 8p23 2	4 (1%)	482	0.873 (1.00)	0.903 (1.00)	0.173 (1.00)	1 (1.00)	0.248 (1.00)	0.373 (1.00)	0.0591 (1.00)	0.461 (1.00)	1 (1.00)	1 (1.00)	0.639 (1.00)	1 (1.00)	0.0485 (1.00)	1 (1.00)	0.728 (1.00)		1 (1.00)
del 8p22	4 (1%)	482	0.873 (1.00)	0.903 (1.00)	0.177 (1.00)	1 (1.00)	0.248 (1.00)	0.373 (1.00)	0.0591 (1.00)	0.461 (1.00)	1 (1.00)	1 (1.00)	0.637 (1.00)	1 (1.00)	0.0485 (1.00)	1 (1.00)	0.728 (1.00)		1 (1.00)
del 8p12	4 (1%)	482	0.873 (1.00)	0.903 (1.00)	0.174 (1.00)	1 (1.00)	0.248 (1.00)	0.371 (1.00)	0.0591 (1.00)	0.461 (1.00)	1 (1.00)	1 (1.00)	0.639 (1.00)	1 (1.00)	0.0485 (1.00)	1 (1.00)	0.728 (1.00)		1 (1.00)
del 8q24 22	7 (1%)	479	0.844 (1.00)	0.396 (1.00)	0.122 (1.00)	0.79 (1.00)	0.0611 (1.00)	0.74 (1.00)	0.0161 (1.00)	0.135 (1.00)	1 (1.00)	1 (1.00)	0.752 (1.00)	0.522 (1.00)	0.0271 (1.00)	1 (1.00)	0.261 (1.00)	1 (1.00)	1 (1.00)
del 10q21 2	12 (2%)	474	0.515 (1.00)	0.989 (1.00)	0.827 (1.00)	0.708 (1.00)	0.338 (1.00)	0.508 (1.00)	0.528 (1.00)	0.555 (1.00)	0.299 (1.00)	1 (1.00)	1 (1.00)	1 (1.00)	0.408 (1.00)	0.761 (1.00)	0.0335 (1.00)	0.662 (1.00)	0.611 (1.00)
del 10q23 31	12 (2%)	474	0.511 (1.00)	0.194 (1.00)	0.0501 (1.00)	0.781 (1.00)	0.0201 (1.00)	0.0712 (1.00)	0.317 (1.00)	0.339 (1.00)	1 (1.00)	1 (1.00)	0.696 (1.00)	0.626 (1.00)	0.0349 (1.00)	1 (1.00)	0.0021 (1.00)	1 (1.00)	0.607 (1.00)
del 11p15 1	7 (1%)	479	0.00114 (0.57)	0.000622 (0.311)	0.00637 (1.00)	0.218 (1.00)	0.449 (1.00)	0.0966 (1.00)	0.0161 (1.00)	0.819 (1.00)	0.186 (1.00)	1 (1.00)	0.545 (1.00)	0.523 (1.00)	0.242 (1.00)	0.708 (1.00)	0.00714 (1.00)	0.421 (1.00)	1 (1.00)
del 13q12 3	16 (3%)	470	0.613 (1.00)	0.00118 (0.585)	0.149 (1.00)	0.556 (1.00)	0.0875 (1.00)	0.107 (1.00)	0.147 (1.00)	0.529 (1.00)	0.378 (1.00)	0.00182 (0.904)	0.767 (1.00)	0.788 (1.00)	0.067 (1.00)	0.802 (1.00)	0.223 (1.00)	0.347 (1.00)	0.607 (1.00)
del 13q21 31	18 (4%)	468	0.625 (1.00)	0.0587 (1.00)	0.776 (1.00)	0.737 (1.00)	0.0322 (1.00)	0.303 (1.00)	0.275 (1.00)	0.608 (1.00)	0.0906 (1.00)	0.00237 (1.00)	0.569 (1.00)	0.651 (1.00)	0.021 (1.00)	0.474 (1.00)	0.382 (1.00)	0.709 (1.00)	0.379 (1.00)
del 15q25 3	9 (2%)	477	0.56 (1.00)	0.892 (1.00)	0.285 (1.00)	0.53 (1.00)	0.0678 (1.00)	0.0424 (1.00)	0.456 (1.00)	0.0888 (1.00)	1 (1.00)	1 (1.00)	1 (1.00)	1 (1.00)	0.091 (1.00)	1 (1.00)	0.14 (1.00)	0.633 (1.00)	0.412 (1.00)
del 16q23 3	6 (1%)	480	0.0841 (1.00)	0.0471 (1.00)	0.00224 (1.00)	0.0116 (1.00)	0.449 (1.00)	0.142 (1.00)	1 (1.00)	0.169 (1.00)	1 (1.00)	0.218 (1.00)	0.0578 (1.00)	0.0713 (1.00)	0.918 (1.00)	1 (1.00)	0.414 (1.00)	0.419 (1.00)	1 (1.00)
del 17p13 1	7 (1%)	479	0.579 (1.00)	0.838 (1.00)	0.259 (1.00)	0.143 (1.00)	0.449 (1.00)	0.343 (1.00)	0.681 (1.00)	0.133 (1.00)	0.0149 (1.00)	0.25 (1.00)	0.183 (1.00)	0.753 (1.00)	0.589 (1.00)	1 (1.00)	0.04 (1.00)	0.553 (1.00)	1 (1.00)
del 18p11 21	4 (1%)	482	0.76 (1.00)	0.681 (1.00)	0.176 (1.00)	0.344 (1.00)	1 (1.00)	0.374 (1.00)	1 (1.00)	0.461 (1.00)	1 (1.00)	1 (1.00)	0.639 (1.00)	1 (1.00)	0.202 (1.00)	0.628 (1.00)	0.657 (1.00)		0.191 (1.00)
del 18q22 2	5 (1%)	481	0.71 (1.00)	0.366 (1.00)	0.253 (1.00)	0.186 (1.00)	0.623 (1.00)	0.687 (1.00)	1 (1.00)	0.568 (1.00)	1 (1.00)	1 (1.00)	0.441 (1.00)	1 (1.00)	0.113 (1.00)	0.38 (1.00)	0.85 (1.00)		0.0276 (1.00)
del 19p13 2	7 (1%)	479	0.13 (1.00)	0.159 (1.00)	0.526 (1.00)	0.926 (1.00)	1 (1.00)	0.743 (1.00)	0.389 (1.00)	1 (1.00)	1 (1.00)	0.028 (1.00)	1 (1.00)	0.187 (1.00)		0.46 (1.00)	0.00264 (1.00)	0.729 (1.00)	1 (1.00)
del 21q21 1	9 (2%)	477	0.84 (1.00)	0.0992 (1.00)	0.00709 (1.00)	0.288 (1.00)	1 (1.00)	0.592 (1.00)	0.705 (1.00)	0.658 (1.00)	1 (1.00)	1 (1.00)	0.613 (1.00)	0.393 (1.00)	0.787 (1.00)	0.313 (1.00)	0.449 (1.00)	0.486 (1.00)	1 (1.00)
del 22q13 1	85 (17%)	401	0.506 (1.00)	0.771 (1.00)	0.553 (1.00)	0.476 (1.00)	0.261 (1.00)	0.579 (1.00)	0.502 (1.00)	0.273 (1.00)	0.481 (1.00)	0.332 (1.00)	0.3 (1.00)	0.485 (1.00)	0.482 (1.00)	0.276 (1.00)	0.82 (1.00)	0.663 (1.00)	1 (1.00)
del 22q13 2	85 (17%)	401	0.506 (1.00)	0.771 (1.00)	0.555 (1.00)	0.476 (1.00)	0.261 (1.00)	0.578 (1.00)	0.502 (1.00)	0.272 (1.00)	0.481 (1.00)	0.332 (1.00)	0.295 (1.00)	0.481 (1.00)	0.482 (1.00)	0.276 (1.00)	0.82 (1.00)	0.663 (1.00)	1 (1.00)
del 22q13 31	85 (17%)	401	0.506 (1.00)	0.771 (1.00)	0.554 (1.00)	0.474 (1.00)	0.261 (1.00)	0.582 (1.00)	0.502 (1.00)	0.271 (1.00)	0.481 (1.00)	0.332 (1.00)	0.296 (1.00)	0.483 (1.00)	0.482 (1.00)	0.276 (1.00)	0.82 (1.00)	0.659 (1.00)	1 (1.00)
del 22q13 32	86 (18%)	400	0.503 (1.00)	0.807 (1.00)	0.555 (1.00)	0.462 (1.00)	0.214 (1.00)	0.622 (1.00)	0.591 (1.00)	0.2 (1.00)	0.481 (1.00)	0.218 (1.00)	0.256 (1.00)	0.482 (1.00)	0.406 (1.00)	0.228 (1.00)	0.82 (1.00)	0.711 (1.00)	1 (1.00)
del xq22 1	6 (1%)	480	0.731 (1.00)	0.165 (1.00)	0.0135 (1.00)	0.216 (1.00)	0.685 (1.00)	0.19 (1.00)	0.0453 (1.00)	1 (1.00)	1 (1.00)	0.185 (1.00)	0.351 (1.00)	0.317 (1.00)	0.387 (1.00)	0.421 (1.00)	0.778 (1.00)	1 (1.00)	1 (1.00)
del xq22 3	4 (1%)	482	0.754 (1.00)	0.213 (1.00)	0.00108 (0.539)	0.0582 (1.00)	0.123 (1.00)	0.106 (1.00)	0.0591 (1.00)	1 (1.00)	1 (1.00)	0.115 (1.00)	0.638 (1.00)	0.312 (1.00)	0.0485 (1.00)	1 (1.00)	0.645 (1.00)		1 (1.00)

'del_9q21.13' versus 'NEOPLASM.DISEASESTAGE'

P value = 0.00049 (Fisher's exact test), Q value = 0.25

Table S1. Gene #12: 'del_9q21.13' versus Clinical Feature #3: 'NEOPLASM.DISEASESTAGE'

nPatients	STAGE I	STAGE II	STAGE III	STAGE IV	STAGE IVA	STAGE IVC
ALL	275	50	107	2	44	6
DEL PEAK 13(9Q21.13) MUTATED	8	5	4	2	3	1
DEL PEAK 13(9Q21.13) WILD-TYPE	267	45	103	0	41	5

Figure S1. Get High-res Image Gene #12: 'del_9q21.13' versus Clinical Feature #3: 'NEOPLASM.DISEASESTAGE'

Methods & Data

Input

Copy number data file = transformed.cor.cli.txt
Clinical data file = THCA-TP.merged_data.txt
Number of patients = 486
Number of significantly focal cnvs = 30
Number of selected clinical features = 17
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)

Made with Nozzle