A coherent approach for analysis of the Illumina HumanMethylation450 BeadChip improves data quality and performance in epigenome-wide association studies.

TitleA coherent approach for analysis of the Illumina HumanMethylation450 BeadChip improves data quality and performance in epigenome-wide association studies.
Publication TypeJournal Article
Year of Publication2015
AuthorsLehne B, Drong AW, Loh M, Zhang W, Scott WR, Tan S-T, Afzal U, Scott J, Jarvelin M-R, Elliott P, McCarthy MI, Kooner JS, Chambers JC
JournalGenome Biol
Volume16
Pagination37
Date Published02/2015
ISSN1474-760X
Abstract

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.

DOI10.1186/s13059-015-0600-x
Alternate JournalGenome Biol.
PubMed ID25853392
PubMed Central IDPMC4365767
Grant ListG0601966 / / Medical Research Council / United Kingdom
G0700931 / / Medical Research Council / United Kingdom