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BioMed Central, Genome Biology, 1(16), 2015

DOI: 10.1186/s13059-015-0600-x

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

Journal article published in 2015 by Benjamin Lehne, Alexander W. Drong, Marie Loh ORCID, 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
This paper is made freely available by the publisher.
This paper is made freely available by the publisher.

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Abstract

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.