title: A coherent approach for analysis of the Illumina HumanMethylation450 BeadChip improves data quality and performance in epigenome-wide association studies.
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.
authors: Benjamin
authors: B
authors: Lehne
authors: Alexander W
authors: AW
authors: Drong
authors: Marie
authors: M
authors: Loh
authors: Weihua
authors: W
authors: Zhang
authors: William R
authors: WR
authors: Scott
authors: Sian-Tsung
authors: ST
authors: Tan
authors: Uzma
authors: U
authors: Afzal
authors: James
authors: J
authors: Scott
authors: Marjo-Riitta
authors: MR
authors: Jarvelin
authors: Paul
authors: P
authors: Elliott
authors: Mark I
authors: MI
authors: McCarthy
authors: Jaspal S
authors: JS
authors: Kooner
authors: John C
authors: JC
authors: Chambers
mesh_terms: D018899:CpG Islands / Q000235:genetics; D019175:DNA Methylation / Q000235:genetics*; D044127:Epigenesis, Genetic / Q000235:genetics*; D057890:Epigenomics / Q000379:methods*; D015894:Genome, Human; D055106:Genome-Wide Association Study / Q000379:methods*; D006801:Humans; D020411:Oligonucleotide Array Sequence Analysis; D040641:Quantitative Trait Loci / Q000235:genetics; D012984:Software