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Patterns of reliability: Assessing the reproducibility and integrity of DNA methylation measurement

Research output: Contribution to journalArticle

Karen Sugden, Eilis Hannon, Louise Arseneault, Daniel W. Belsky, David L. Corcoran, Helen Fisher, Renate M Houts, Radhika Kandaswamy, Terrie Moffitt, Richie Poulton, Joseph A Prinz, Line Jee Hartmann Rasmussen, Benjamin Williams, Chloe Wong, Jonathan Mill, Avshalom Caspi

Original languageEnglish
JournalPatterns
Publication statusAccepted/In press - 13 Feb 2020

King's Authors

Abstract

DNA methylation plays an important role in both normal human development and risk of disease. The most utilized method of assessing DNA methylation uses BeadChips, generating an epigenome-wide ‘snapshot’ of >450,000 observations (probe measurements) per assay. However, the reliability of each of these measurements is not equal, and little consideration is paid to consequences for research. We correlated repeat measurements of the same DNA samples using the Illumina HumanMethylation450K and the Infinium MethylationEPIC BeadChips in 350 blood-DNA samples. Probes that were reliably measured were more heritable, and showed consistent associations with environmental exposures, gene expression, and greater cross-tissue concordance. Unreliable probes were less replicable and generated an unknown volume of false negatives. This serves a lesson for working with DNA methylation data, but the lessons are equally applicable to working with other data: as we advance towards generating increasingly greater volumes of data, failure to document reliability risks harming reproducibility.

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