Correlation between copy number variation genes and molecular subtypes
Lymphoid Neoplasm Diffuse Large B-cell Lymphoma (Primary solid tumor)
23 September 2013 | analyses__2013_09_23
Maintainer Information
Citation Information
doi:10.7908/C1PK0DFX
Maintained by TCGA GDAC Team (Broad Institute/MD Anderson Cancer Center/Harvard Medical School)
Cite as Broad Institute TCGA Genome Data Analysis Center (2013): Correlation between copy number variation genes and molecular subtypes. Broad Institute of MIT and Harvard. doi:10.7908/C1PK0DFX
Overview
Introduction

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

Summary

Testing the association between copy number variation of 9 peak regions and molecular subtype 'METHLYATION_CNMF' across 18 patients, one significant finding detected with Q value < 0.25.

- Amp Peak 1(2p16.1) cnvs correlated to 'METHLYATION_CNMF'.

Results
Overview of the results

Table 1. Get Full Table Overview of the association between significant copy number variation of 9 regions and 1 molecular subtypes. Shown in the table are P values (Q values). Thresholded by Q value < 0.25, one significant finding detected.

|  | Molecular subtypes | METHLYATION CNMF
| nCNV (%) | nWild-Type | Fisher's exact test
Amp Peak 1(2p16 1) | 0 (0%) | 12 | 0.00905 (0.0814)
Del Peak 2(1q43) | 0 (0%) | 15 | 0.206 (1.00)
Del Peak 3(2q22 3) | 0 (0%) | 14 | 1 (1.00)
Del Peak 4(6q14 1) | 0 (0%) | 14 | 1 (1.00)
Del Peak 5(6q23 3) | 0 (0%) | 15 | 1 (1.00)
Del Peak 7(9p21 3) | 0 (0%) | 14 | 0.576 (1.00)
Del Peak 9(13q33 3) | 0 (0%) | 15 | 1 (1.00)
Del Peak 10(15q15 1) | 0 (0%) | 13 | 1 (1.00)
Del Peak 11(16p13 13) | 0 (0%) | 15 | 0.206 (1.00)

'Amp Peak 1(2p16.1)' versus 'METHLYATION_CNMF'

P value = 0.00905 (Fisher's exact test), Q value = 0.081

Table S1. Gene #1: 'Amp Peak 1(2p16.1)' versus Molecular Subtype #1: 'METHLYATION_CNMF'

nPatients | CLUS_1 | CLUS_2
--- | --- | ---
ALL | 9 | 9
AMP PEAK 1(2P16.1) CNV | 0 | 6
AMP PEAK 1(2P16.1) WILD-TYPE | 9 | 3

Figure S1. Get High-res Image Gene #1: 'Amp Peak 1(2p16.1)' versus Molecular Subtype #1: 'METHLYATION_CNMF'

Methods & Data
Input

- Copy number data file = All Lesions File (all_lesions.conf_##.txt, where ## is the confidence level). The all lesions file is from GISTIC pipeline and summarizes the results from the GISTIC run. It contains data about the significant regions of amplification and deletion as well as which samples are amplified or deleted in each of these regions. The identified regions are listed down the first column, and the samples are listed across the first row, starting in column 10.

- Molecular subtype file = DLBC-TP.transferedmergedcluster.txt

- Number of patients = 18

- Number of copy number variation regions = 9

- Number of molecular subtypes = 1: 'METHLYATION_CNMF'

- Exclude regions 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.

- Analysis Results (MD5 checksum)

- Auxiliary Data (MD5 checksum)

- MAGE-TAB File (MD5 checksum)

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)
[3] GISTIC_version2
Copyright © 2013 Broad Institute TCGA GDAC as part of the TCGA Research Network. All rights reserved.
Made with Nozzle