Using high-density DNA methylation arrays to profile copy number alterations

The integration of genomic and epigenomic data is an increasingly popular approach for studying the complex mechanisms driving cancer development. We have developed a method for evaluating both methylation and copy number from high-density DNA methylation arrays. Comparing copy number data from Infi...

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Bibliographic Details
Published in:Genome biology 2014-02, Vol.15 (2), p.R30-R30, Article R30
Main Authors: Feber, Andrew, Guilhamon, Paul, Lechner, Matthias, Fenton, Tim, Wilson, Gareth A, Thirlwell, Christina, Morris, Tiffany J, Flanagan, Adrienne M, Teschendorff, Andrew E, Kelly, John D, Beck, Stephan
Format: Article
Language:English
Subjects:
Algorithms
carcinogenesis
DNA Copy Number Variations - genetics
DNA methylation
DNA Methylation - genetics
Genome, Human
Humans
Method
neoplasms
Oligonucleotide Array Sequence Analysis - methods
Polymorphism, Single Nucleotide
single nucleotide polymorphism
Software
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Summary:The integration of genomic and epigenomic data is an increasingly popular approach for studying the complex mechanisms driving cancer development. We have developed a method for evaluating both methylation and copy number from high-density DNA methylation arrays. Comparing copy number data from Infinium HumanMethylation450 BeadChips and SNP arrays, we demonstrate that Infinium arrays detect copy number alterations with the sensitivity of SNP platforms. These results show that high-density methylation arrays provide a robust and economic platform for detecting copy number and methylation changes in a single experiment. Our method is available in the ChAMP Bioconductor package: http://www.bioconductor.org/packages/2.13/bioc/html/ChAMP.html.
ISSN:1474-760X
1465-6906
1474-760X
1465-6914
DOI:10.1186/gb-2014-15-2-r30