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

Andrew Feber, Paul Guilhamon, Matthias Lechner, Tim Fenton, Gareth A Wilson, Christina Thirlwell, Tiffany J Morris, Adrienne M Flanagan, Andrew E Teschendorff, John D Kelly and Stephan Beck

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Genome Biology 2014, 15:R30  doi:10.1186/gb-2014-15-2-r30

Published: 3 February 2014

Abstract (provisional)

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.

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