Abstract
DNA methylation is a widely studied epigenetic phenomenon. Alterations in methylation patterns influence human phenotypes and risk of disease. The Illumina Infinium HumanMethylation450 (HM450) and MethylationEPIC (EPIC) BeadChip are widely used microarray-based platforms for epigenome-wide association studies (EWASs). In this chapter, we will discuss the use of intraclass correlation coefficient (ICC) for assessing technical variations induced by methylation arrays at single-CpG level. ICC compares variation of methylation levels within- and between-replicate measurements, ranging between 0 and 1. We further characterize the distribution of ICCs using a mixture of truncated normal and normal distributions, and cluster CpG sites on the arrays into low- and high-reliability groups. In practice, we recommend that extra caution needs to be taken for associations at the CpG sites with low ICC values.
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Cao, R., Guan, W. (2022). Evaluating Reliability of DNA Methylation Measurement. In: Guan, W. (eds) Epigenome-Wide Association Studies. Methods in Molecular Biology, vol 2432. Humana, New York, NY. https://doi.org/10.1007/978-1-0716-1994-0_2
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DOI: https://doi.org/10.1007/978-1-0716-1994-0_2
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