Skin Cutaneous Melanoma: Correlation between copy number variations of arm-level result and molecular subtypes<BR>(NF1_Any

Skin Cutaneous Melanoma: Correlation between copy number variations of arm-level result and molecular subtypes
(NF1_Any_Mutants cohort)

Maintained by TCGA GDAC Team (Broad Institute/MD Anderson Cancer Center/Harvard Medical School)

Overview

Introduction

This pipeline computes the correlation between significant arm-level copy number variations (cnvs) and subtypes.

Summary

Testing the association between copy number variation 44 arm-level results and 8 molecular subtypes across 31 patients, no significant finding detected with Q value < 0.25.

No arm-level cnvs related to molecular subtypes.

Results

Overview of the results

Table 1. Get Full Table Overview of the association between significant copy number variation of 44 arm-level results and 8 molecular subtypes. Shown in the table are P values (Q values). Thresholded by Q value < 0.25, no significant finding detected.


		Molecular subtypes	CN CNMF	METHLYATION CNMF	RPPA CNMF	RPPA CHIERARCHICAL	MRNASEQ CNMF	MRNASEQ CHIERARCHICAL	MIRSEQ CNMF	MIRSEQ CHIERARCHICAL
	nCNV (%)	nWild-Type	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	Chi-square test
1p gain	6 (19%)	25	0.394 (1.00)	0.664 (1.00)	0.526 (1.00)	1 (1.00)	0.445 (1.00)	0.331 (1.00)	1 (1.00)	0.786 (1.00)
1q gain	11 (35%)	20	0.0659 (1.00)	0.057 (1.00)	0.657 (1.00)	1 (1.00)	0.328 (1.00)	0.356 (1.00)	0.273 (1.00)	0.267 (1.00)
3p gain	5 (16%)	26	1 (1.00)	1 (1.00)	0.526 (1.00)	1 (1.00)	0.322 (1.00)	0.451 (1.00)	0.654 (1.00)	0.61 (1.00)
3q gain	6 (19%)	25	1 (1.00)	0.664 (1.00)	1 (1.00)	1 (1.00)	0.28 (1.00)	0.812 (1.00)	1 (1.00)	0.786 (1.00)
5p gain	5 (16%)	26	0.654 (1.00)	1 (1.00)	1 (1.00)	1 (1.00)	1 (1.00)	1 (1.00)	0.654 (1.00)	0.521 (1.00)
5q gain	4 (13%)	27	1 (1.00)	1 (1.00)	1 (1.00)	1 (1.00)	0.815 (1.00)	0.813 (1.00)	0.333 (1.00)	0.367 (1.00)
6p gain	12 (39%)	19	0.473 (1.00)	0.724 (1.00)	0.345 (1.00)	0.257 (1.00)	1 (1.00)	0.643 (1.00)	0.473 (1.00)	0.742 (1.00)
7p gain	12 (39%)	19	1 (1.00)	0.724 (1.00)	0.626 (1.00)	1 (1.00)	1 (1.00)	1 (1.00)	1 (1.00)	0.87 (1.00)
7q gain	11 (35%)	20	0.716 (1.00)	1 (1.00)	0.626 (1.00)	1 (1.00)	1 (1.00)	1 (1.00)	0.716 (1.00)	0.866 (1.00)
8p gain	6 (19%)	25	1 (1.00)	0.664 (1.00)	1 (1.00)	1 (1.00)	0.73 (1.00)	1 (1.00)	1 (1.00)	0.786 (1.00)
8q gain	7 (23%)	24	0.394 (1.00)	0.671 (1.00)	1 (1.00)	1 (1.00)	0.871 (1.00)	0.668 (1.00)	0.394 (1.00)	0.286 (1.00)
13q gain	3 (10%)	28	0.6 (1.00)	1 (1.00)	1 (1.00)	1 (1.00)	1 (1.00)	0.388 (1.00)	0.6 (1.00)	0.385 (1.00)
14q gain	5 (16%)	26	0.654 (1.00)	0.0482 (1.00)	0.526 (1.00)	1 (1.00)	1 (1.00)	0.293 (1.00)	0.172 (1.00)	0.478 (1.00)
15q gain	5 (16%)	26	1 (1.00)	1 (1.00)	1 (1.00)	1 (1.00)	0.0509 (1.00)	0.451 (1.00)	1 (1.00)	0.273 (1.00)
17q gain	5 (16%)	26	1 (1.00)	1 (1.00)	0.621 (1.00)	1 (1.00)	0.322 (1.00)	0.337 (1.00)	0.172 (1.00)	0.332 (1.00)
18p gain	4 (13%)	27	1 (1.00)	1 (1.00)	1 (1.00)	1 (1.00)	0.415 (1.00)	0.893 (1.00)	0.333 (1.00)	0.67 (1.00)
19p gain	4 (13%)	27	0.333 (1.00)	0.607 (1.00)	1 (1.00)	1 (1.00)	0.275 (1.00)	0.18 (1.00)	0.333 (1.00)	0.784 (1.00)
19q gain	4 (13%)	27	0.333 (1.00)	0.607 (1.00)	1 (1.00)	1 (1.00)	0.275 (1.00)	0.18 (1.00)	0.333 (1.00)	0.784 (1.00)
20p gain	8 (26%)	23	1 (1.00)	0.698 (1.00)	0.526 (1.00)	1 (1.00)	0.775 (1.00)	0.495 (1.00)	0.22 (1.00)	0.288 (1.00)
20q gain	10 (32%)	21	0.458 (1.00)	1 (1.00)	1 (1.00)	1 (1.00)	0.396 (1.00)	0.482 (1.00)	0.704 (1.00)	0.617 (1.00)
22q gain	11 (35%)	20	0.716 (1.00)	1 (1.00)	1 (1.00)	0.539 (1.00)	0.643 (1.00)	1 (1.00)	1 (1.00)	0.788 (1.00)
1p loss	3 (10%)	28	0.101 (1.00)	1 (1.00)	1 (1.00)	1 (1.00)	0.241 (1.00)	0.101 (1.00)	0.6 (1.00)	0.506 (1.00)
2q loss	3 (10%)	28	1 (1.00)	0.232 (1.00)	0.526 (1.00)	1 (1.00)	1 (1.00)	0.675 (1.00)	0.6 (1.00)	0.919 (1.00)
4p loss	5 (16%)	26	0.654 (1.00)	1 (1.00)	1 (1.00)	1 (1.00)	0.00758 (1.00)	0.13 (1.00)	0.333 (1.00)	0.0118 (1.00)
4q loss	5 (16%)	26	1 (1.00)	0.636 (1.00)	0.273 (1.00)	1 (1.00)	0.0509 (1.00)	0.518 (1.00)	1 (1.00)	0.223 (1.00)
5p loss	5 (16%)	26	0.333 (1.00)	1 (1.00)	0.273 (1.00)	1 (1.00)	0.322 (1.00)	0.911 (1.00)	1 (1.00)	0.162 (1.00)
5q loss	7 (23%)	24	0.394 (1.00)	0.671 (1.00)	1 (1.00)	1 (1.00)	0.225 (1.00)	0.525 (1.00)	0.394 (1.00)	0.15 (1.00)
6q loss	10 (32%)	21	0.135 (1.00)	1 (1.00)	0.626 (1.00)	0.0672 (1.00)	0.207 (1.00)	0.482 (1.00)	1 (1.00)	0.304 (1.00)
8p loss	3 (10%)	28	0.6 (1.00)	1 (1.00)	0.209 (1.00)	0.453 (1.00)	0.241 (1.00)	0.769 (1.00)	0.226 (1.00)	0.333 (1.00)
9p loss	17 (55%)	14	0.0732 (1.00)	0.0759 (1.00)	0.657 (1.00)	1 (1.00)	0.353 (1.00)	0.335 (1.00)	1 (1.00)	0.99 (1.00)
9q loss	15 (48%)	16	0.724 (1.00)	0.285 (1.00)	1 (1.00)	0.317 (1.00)	0.901 (1.00)	0.495 (1.00)	0.289 (1.00)	0.419 (1.00)
10p loss	8 (26%)	23	0.433 (1.00)	0.24 (1.00)	0.366 (1.00)	0.273 (1.00)	0.111 (1.00)	0.332 (1.00)	0.433 (1.00)	0.148 (1.00)
10q loss	8 (26%)	23	0.433 (1.00)	0.24 (1.00)	0.366 (1.00)	0.273 (1.00)	0.111 (1.00)	0.24 (1.00)	1 (1.00)	0.0184 (1.00)
11p loss	11 (35%)	20	0.716 (1.00)	0.258 (1.00)	1 (1.00)	1 (1.00)	1 (1.00)	0.658 (1.00)	1 (1.00)	0.515 (1.00)
11q loss	10 (32%)	21	0.458 (1.00)	0.068 (1.00)	0.657 (1.00)	1 (1.00)	0.443 (1.00)	0.688 (1.00)	0.458 (1.00)	0.183 (1.00)
12p loss	3 (10%)	28	1 (1.00)	0.232 (1.00)	1 (1.00)	1 (1.00)	0.167 (1.00)	0.875 (1.00)	1 (1.00)	0.209 (1.00)
12q loss	4 (13%)	27	1 (1.00)	0.107 (1.00)	1 (1.00)	1 (1.00)	0.648 (1.00)	0.813 (1.00)	1 (1.00)	0.457 (1.00)
13q loss	7 (23%)	24	1 (1.00)	0.198 (1.00)	0.318 (1.00)	1 (1.00)	0.309 (1.00)	0.525 (1.00)	1 (1.00)	0.309 (1.00)
14q loss	4 (13%)	27	1 (1.00)	0.304 (1.00)	1 (1.00)	1 (1.00)	0.16 (1.00)	0.622 (1.00)	1 (1.00)	0.838 (1.00)
16q loss	5 (16%)	26	0.333 (1.00)	0.344 (1.00)	0.526 (1.00)	1 (1.00)	0.487 (1.00)	0.911 (1.00)	1 (1.00)	0.478 (1.00)
17p loss	7 (23%)	24	0.394 (1.00)	1 (1.00)	1 (1.00)	1 (1.00)	0.485 (1.00)	0.606 (1.00)	0.394 (1.00)	0.574 (1.00)
18p loss	5 (16%)	26	0.654 (1.00)	0.344 (1.00)	1 (1.00)	0.539 (1.00)	0.258 (1.00)	0.518 (1.00)	0.654 (1.00)	0.61 (1.00)
18q loss	4 (13%)	27	1 (1.00)	0.607 (1.00)	1 (1.00)	1 (1.00)	1 (1.00)	0.893 (1.00)	1 (1.00)	0.784 (1.00)
21q loss	7 (23%)	24	1 (1.00)	1 (1.00)	0.621 (1.00)	0.539 (1.00)	0.0384 (1.00)	0.325 (1.00)	0.685 (1.00)	0.474 (1.00)

Methods & Data

Input

Mutation data file = broad_values_by_arm.mutsig.cluster.txt
Molecular subtypes file = SKCM-NF1_Any_Mutants.transferedmergedcluster.txt
Number of patients = 31
Number of significantly arm-level cnvs = 44
Number of molecular subtypes = 8
Exclude genes that fewer than K tumors have mutations, K = 3

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

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

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] 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)

[2] Greenwood and Nikulin, A guide to chi-squared testing, Wiley, New York. ISBN 047155779X (1996)

[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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