A method for finding novel associations between genome-wide copy number and dna methylation patterns

Tang, M. H. E., Varadan, V., Kamalakaran, S., Zhang, M. Q., Dimitrova, N., Hicks, J. (2011) A method for finding novel associations between genome-wide copy number and dna methylation patterns. 2011 IEEE International Workshop on Genomic Signal Processing and Statistics, GENSIPS'11 . IEEE, pp. 78-82. ISBN 21503001 (ISSN); 9781467304900 (ISBN)

URL: http://ieeexplore.ieee.org/xpl/login.jsp?tp=&arnum...

Abstract

We present a computational method that combines genome-wide DNA methylation and copy number variation data in an integrated fashion with the aim of finding mechanistic associations between genome instability and local DNA methylation changes. The method is applied to Luminal A breast cancer early-stage tumour samples and focuses on methylation events occurring at frequently rearranged genome locations. Our method accommodates array and sequencing platforms for methylation and DNA copy number estimates. We find significant local methylation changes in tumours tend to occur in the viscinity of breakpoint rich regions, with 80% of the differentially methylated regions occurring within 2Mb from a breakpoint rich locus. ©2011 IEEE.

Item Type: Book
Uncontrolled Keywords: Breast cancer DNA methylation Genome instability Breakpoint Copy number DNA methylation pattern Integrated fashion Alkylation Diseases Gene encoding Signal processing Tumors Methylation
Subjects: diseases & disorders > cancer
bioinformatics > genomics and proteomics > genetics & nucleic acid processing > DNA, RNA structure, function, modification > DNA methylation
bioinformatics > genomics and proteomics > genetics & nucleic acid processing > DNA, RNA structure, function, modification
diseases & disorders
bioinformatics > genomics and proteomics > genetics & nucleic acid processing
diseases & disorders > cancer > cancer types > breast cancer
bioinformatics > genomics and proteomics > genetics & nucleic acid processing > DNA, RNA structure, function, modification > copy number variants
bioinformatics > genomics and proteomics > genetics & nucleic acid processing > genomes
CSHL Authors:
Communities: CSHL labs > Hicks lab
CSHL labs > Zhang lab
Depositing User: Matt Covey
Date Deposited: 09 Aug 2013 20:58
Last Modified: 12 Aug 2013 13:43
URI: http://repository.cshl.edu/id/eprint/28478

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