Patterns of Reliability: Assessing the Reproducibility and Integrity of DNA Methylation Measurement | Zendy

Karen Sugden | Zendy; Eilís Han | Zendy; Louise Arseneault | Zendy; Daniel W. Belsky | Zendy; David L. Corcoran | Zendy; Helen L. Fisher | Zendy; Renate Houts | Zendy; Radhika Kandaswamy | Zendy; Terrie E. Moffitt | Zendy; Richie Poulton | Zendy; Joseph A. Prinz | Zendy; Line Jee Hartmann Rasmussen | Zendy; Benjamin Williams | Zendy; Chloe C. Y. Wong | Zendy; Jonathan Mill | Zendy; Avshalom Caspi | Zendy

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Patterns of Reliability: Assessing the Reproducibility and Integrity of DNA Methylation Measurement

Author(s) -

Karen Sugden,

Eilís Han,

Louise Arseneault,

Daniel W. Belsky,

David L. Corcoran,

Helen L. Fisher,

Renate Houts,

Radhika Kandaswamy,

Terrie E. Moffitt,

Richie Poulton,

Joseph A. Prinz,

Line Jee Hartmann Rasmussen,

Benjamin Williams,

Chloe C. Y. Wong,

Jonathan Mill,

Avshalom Caspi

Publication year - 2020

Publication title -

patterns

Language(s) - English

Resource type - Journals

ISSN - 2666-3899

DOI - 10.1016/j.patter.2020.100014

Subject(s) - reproducibility , reliability (semiconductor) , reliability engineering , dna methylation , computer science , computational biology , biology , chemistry , engineering , genetics , chromatography , physics , gene , gene expression , power (physics) , quantum mechanics

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 as a lesson for working with DNA methylation data, but the lessons are equally applicable to working with other data: as we advance toward generating increasingly greater volumes of data, failure to document reliability risks harming reproducibility.

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