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

Genome Biology
Andrew FeberStephan Beck

Abstract

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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Methods Mentioned

BETA
immunoprecipitation
PCR
exome-sequencing
exome sequencing
exome-seq
genotyping

Software Mentioned

GenomeStudio
Bioconductor
Bioconductor package
R package DNAcopy
Infinium
glm
Picard
ChAMP Bioconductor
CytoSNP
gam

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