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DNA methylation plays a fundamental role in the regulation of the genome, but the optimal strategy for analysis of genome-wide DNA methylation data remains to be determined. We developed a comprehensive analysis pipeline for epigenome-wide association studies (EWAS) using the Illumina Infinium HumanMethylation450 BeadChip, based on 2,687 individuals, with 36 samples measured in duplicate. We propose new approaches to quality control, data normalisation and batch correction through control-probe adjustment and establish a null hypothesis for EWAS using permutation testing. Our analysis pipeline outperforms existing approaches, enabling accurate identification of methylation quantitative trait loci for hypothesis driven follow-up experiments.

Original publication

DOI

10.1186/s13059-015-0600-x

Type

Journal article

Journal

Genome Biol

Publication Date

15/02/2015

Volume

16

Keywords

CpG Islands, DNA Methylation, Epigenesis, Genetic, Epigenomics, Genome, Human, Genome-Wide Association Study, Humans, Oligonucleotide Array Sequence Analysis, Quantitative Trait Loci, Software