Evaluating Reliability of DNA Methylation Measurement

Rui Cao, Weihua Guan

Research output: Chapter in Book/Report/Conference proceedingChapter


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.

Original languageEnglish (US)
Title of host publicationMethods in Molecular Biology
PublisherHumana Press Inc.
Number of pages10
StatePublished - 2022

Publication series

NameMethods in Molecular Biology
ISSN (Print)1064-3745
ISSN (Electronic)1940-6029

Bibliographical note

Publisher Copyright:
© 2022, Springer Science+Business Media, LLC, part of Springer Nature.


  • DNA methylation
  • Intraclass correlation
  • Normal mixture models
  • Technical error
  • DNA Methylation
  • Reproducibility of Results
  • Epigenomics
  • Oligonucleotide Array Sequence Analysis
  • CpG Islands

PubMed: MeSH publication types

  • Journal Article


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