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

Year: 2015
Type: article
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.
DOI: 10.1186/s13059-015-0600-x
Authors: Benjamin Lehne, Alexander W Drong, Marie Loh, Weihua Zhang, William R Scott, Sian-Tsung Tan, Uzma Afzal, James Scott, Marjo-Riitta Jarvelin, Paul Elliott, Mark I McCarthy, Jaspal S Kooner, John C Chambers
Institutions: Imperial College London, Centre for Human Genetics, University of Oxford, University of Oulu, Ealing Hospital NHS Trust, MRC Centre for Environment and Health, Oxford Centre for Diabetes, Endocrinology and Metabolism, Imperial College Healthcare NHS Trust
Language: English
Open Access status: gold
Estimated APC paid: $5,490
Funders: Wellcome Trust, National Institute for Health Research Health Protection Research Unit, National Institute for Health and Care Research, British Heart Foundation, Imperial College London, Imperial College Healthcare NHS Trust, European Commission, MRC-PHE Centre for Environment and Health, Medical Research Council
Awards: G1606511277, G2050123317, G208506829, Identification of epigenetic markers underlying increased risk of T2D in South Asians, G3841306388, NIHR Senior Investigator Award, G478728645, G4805552703, G5404300429, Identification of genetic variants underlying coronary artery disease and associated phenotypes in Indian Asians., G6815174083, Understanding the genetic basis of common human diseases: core funding for the Wellcome Trust Centre for Human Genetics., Derivation and validation of a risk model for prediction of cardiovascular disease events in UK Indian Asians, G8937465282, Understanding the genetic basis of common human diseases: core funding for the Wellcome Trust Centre for Human Genetics., G8975541179
OpenAlex ID: W4297674379
FWCI: 7.207
Cites: 31
Cited by: 378
Related to: 10