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

Lymphoid Neoplasm Diffuse Large B-cell Lymphoma (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 molecular subtypes. Broad Institute of MIT and Harvard. doi:10.7908/C1XS5T40

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 24 focal events and 7 molecular subtypes across 28 patients, one significant finding detected with P value < 0.05 and Q value < 0.25.

amp_2p15 cnv correlated to 'METHLYATION_CNMF'.

Results

Overview of the results

Table 1. Get Full Table Overview of the association between significant copy number variation of 24 focal events and 7 molecular subtypes. Shown in the table are P values (Q values). Thresholded by P value < 0.05 and Q value < 0.25, one significant finding detected.


		Clinical Features	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
amp 2p15	8 (29%)	20	0.000414 (0.0696)	0.686 (1.00)	0.75 (1.00)	1 (1.00)	0.106 (1.00)	0.434 (1.00)	0.231 (1.00)
amp 1q31 1	9 (32%)	19	0.435 (1.00)	0.228 (1.00)	0.0768 (1.00)	0.0461 (1.00)	0.636 (1.00)	0.871 (1.00)	0.327 (1.00)
amp 3q27 3	7 (25%)	21	1 (1.00)	0.396 (1.00)	0.718 (1.00)	0.385 (1.00)	0.112 (1.00)	0.419 (1.00)	0.0164 (1.00)
amp 8q24 12	6 (21%)	22	0.372 (1.00)	1 (1.00)	0.424 (1.00)	1 (1.00)	0.258 (1.00)	0.292 (1.00)	0.576 (1.00)
amp 12q13 12	5 (18%)	23	0.153 (1.00)	1 (1.00)	0.122 (1.00)	0.326 (1.00)	0.453 (1.00)	1 (1.00)	1 (1.00)
amp 16p11 2	6 (21%)	22	0.0691 (1.00)	0.173 (1.00)	0.34 (1.00)	0.648 (1.00)	0.79 (1.00)	0.843 (1.00)	0.871 (1.00)
amp xq27 3	6 (21%)	22	0.0691 (1.00)	0.655 (1.00)	0.705 (1.00)	0.648 (1.00)	0.889 (1.00)	0.844 (1.00)	0.994 (1.00)
del 1p22 1	4 (14%)	24	0.6 (1.00)	1 (1.00)	0.81 (1.00)	0.326 (1.00)	1 (1.00)	1 (1.00)	0.853 (1.00)
del 1p13 1	7 (25%)	21	0.396 (1.00)	0.67 (1.00)	0.277 (1.00)	0.0329 (1.00)	0.504 (1.00)	0.418 (1.00)	0.504 (1.00)
del 1q43	7 (25%)	21	0.198 (1.00)	1 (1.00)	1 (1.00)	1 (1.00)	0.898 (1.00)	1 (1.00)	0.98 (1.00)
del 2q23 1	6 (21%)	22	1 (1.00)	1 (1.00)	0.518 (1.00)	0.648 (1.00)	1 (1.00)	1 (1.00)	0.711 (1.00)
del 6q14 1	9 (32%)	19	0.689 (1.00)	0.435 (1.00)	0.329 (1.00)	0.103 (1.00)	0.176 (1.00)	0.872 (1.00)	0.544 (1.00)
del 6q23 3	7 (25%)	21	0.198 (1.00)	0.0836 (1.00)	0.0225 (1.00)	0.385 (1.00)	0.114 (1.00)	1 (1.00)	0.627 (1.00)
del 8p23 1	4 (14%)	24	1 (1.00)	0.311 (1.00)	0.354 (1.00)	0.326 (1.00)	0.513 (1.00)	1 (1.00)	0.0658 (1.00)
del 8q12 1	4 (14%)	24	1 (1.00)	0.311 (1.00)	0.354 (1.00)	0.326 (1.00)	1 (1.00)	1 (1.00)	0.856 (1.00)
del 9p21 3	9 (32%)	19	0.0418 (1.00)	0.114 (1.00)	0.33 (1.00)	0.42 (1.00)	0.00932 (1.00)	0.282 (1.00)	0.0197 (1.00)
del 10q23 31	5 (18%)	23	1 (1.00)	0.639 (1.00)	0.0398 (1.00)	0.648 (1.00)	0.958 (1.00)	1 (1.00)	0.358 (1.00)
del 13q14 2	3 (11%)	25	0.583 (1.00)	1 (1.00)	0.761 (1.00)	1 (1.00)	0.487 (1.00)	0.751 (1.00)	0.182 (1.00)
del 13q33 3	4 (14%)	24	1 (1.00)	0.102 (1.00)	0.28 (1.00)	0.222 (1.00)	0.12 (1.00)	0.75 (1.00)	0.0309 (1.00)
del 15q15 1	8 (29%)	20	0.221 (1.00)	1 (1.00)	0.647 (1.00)	0.678 (1.00)	0.229 (1.00)	1 (1.00)	0.0195 (1.00)
del 15q21 1	9 (32%)	19	0.435 (1.00)	1 (1.00)	0.659 (1.00)	1 (1.00)	0.561 (1.00)	1 (1.00)	0.0777 (1.00)
del 16p13 13	4 (14%)	24	0.311 (1.00)	0.311 (1.00)	0.808 (1.00)	0.326 (1.00)	0.161 (1.00)	0.279 (1.00)	0.287 (1.00)
del 16q23 1	5 (18%)	23	1 (1.00)	0.639 (1.00)	0.45 (1.00)	0.648 (1.00)	0.567 (1.00)	1 (1.00)	0.611 (1.00)
del 17q24 1	4 (14%)	24	0.0349 (1.00)	1 (1.00)	0.044 (1.00)	1 (1.00)	0.546 (1.00)	0.499 (1.00)	0.285 (1.00)

'amp_2p15' versus 'METHLYATION_CNMF'

P value = 0.000414 (Fisher's exact test), Q value = 0.07

Table S1. Gene #2: 'amp_2p15' versus Molecular Subtype #1: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2
ALL	15	13
AMP PEAK 2(2P15) MUTATED	0	8
AMP PEAK 2(2P15) WILD-TYPE	15	5

Figure S1. Get High-res Image Gene #2: 'amp_2p15' versus Molecular Subtype #1: 'METHLYATION_CNMF'

Methods & Data

Input

Copy number data file = transformed.cor.cli.txt
Molecular subtype file = DLBC-TP.transferedmergedcluster.txt
Number of patients = 28
Number of significantly focal cnvs = 24
Number of molecular subtypes = 7
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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