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

Andrew Feber1*, Paul Guilhamon1, Matthias Lechner1, Tim Fenton1, Gareth A Wilson1, Christina Thirlwell1, Tiffany J Morris1, Adrienne M Flanagan12, Andrew E Teschendorff1, John D Kelly13 and Stephan Beck1

Author Affiliations

1 UCL Cancer Institute, University College London, 72 Huntley Street, London WC1E 6BT, UK

2 Royal National Orthopaedic Hospital, Stanmore, Brockly Hill, Middlesex HA7 4LP, UK

3 Division of Surgery and Interventional Science, UCL Medical School, University College London, London WC1E 6BT, UK

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

Published: 3 February 2014


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: webcite.