Correlation between copy number variation genes (focal events) and molecular subtypes

Kidney Chromophobe (Primary solid tumor)

17 October 2014 | analyses__2014_10_17

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 molecular subtypes. Broad Institute of MIT and Harvard. doi:10.7908/C1GF0SDS

Overview

Introduction

This pipeline computes the correlation between significant copy number variation (cnv focal) genes and molecular subtypes.

Summary

Testing the association between copy number variation 2 focal events and 8 molecular subtypes across 66 patients, 2 significant findings detected with P value < 0.05 and Q value < 0.25.

amp_8q11.23 cnv correlated to 'MRNASEQ_CNMF'.
amp_15q22.31 cnv correlated to 'MRNASEQ_CNMF'.

Results

Overview of the results

Table 1. Get Full Table Overview of the association between significant copy number variation of 2 focal events and 8 molecular subtypes. Shown in the table are P values (Q values). Thresholded by P value < 0.05 and Q value < 0.25, 2 significant findings detected.


		Clinical Features	CN CNMF	METHLYATION CNMF	MRNASEQ CNMF	MRNASEQ CHIERARCHICAL	MIRSEQ CNMF	MIRSEQ CHIERARCHICAL	MIRSEQ MATURE CNMF	MIRSEQ MATURE 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	Fisher's exact test
amp 8q11 23	19 (29%)	47	0.321 (1.00)	0.625 (1.00)	0.00283 (0.0453)	0.0245 (0.343)	1 (1.00)	0.228 (1.00)	0.363 (1.00)	0.118 (1.00)
amp 15q22 31	23 (35%)	43	0.0534 (0.694)	0.582 (1.00)	0.00627 (0.094)	0.182 (1.00)	0.526 (1.00)	0.301 (1.00)	0.554 (1.00)	0.365 (1.00)

'amp_8q11.23' versus 'MRNASEQ_CNMF'

P value = 0.00283 (Fisher's exact test), Q value = 0.045

Table S1. Gene #1: 'amp_8q11.23' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	19	22	15	10
AMP PEAK 1(8Q11.23) MUTATED	3	13	2	1
AMP PEAK 1(8Q11.23) WILD-TYPE	16	9	13	9

Figure S1. Get High-res Image Gene #1: 'amp_8q11.23' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'amp_15q22.31' versus 'MRNASEQ_CNMF'

P value = 0.00627 (Fisher's exact test), Q value = 0.094

Table S2. Gene #2: 'amp_15q22.31' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	19	22	15	10
AMP PEAK 2(15Q22.31) MUTATED	5	13	5	0
AMP PEAK 2(15Q22.31) WILD-TYPE	14	9	10	10

Figure S2. Get High-res Image Gene #2: 'amp_15q22.31' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

Methods & Data

Input

Copy number data file = transformed.cor.cli.txt
Molecular subtype file = KICH-TP.transferedmergedcluster.txt
Number of patients = 66
Number of significantly focal cnvs = 2
Number of molecular subtypes = 8
Exclude genes that fewer than K tumors have alterations, 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

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] 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] 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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