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.
| Original language | English (US) |
|---|---|
| Title of host publication | Methods in Molecular Biology |
| Publisher | Humana Press Inc. |
| Pages | 15-24 |
| Number of pages | 10 |
| Volume | 2432 |
| DOIs | |
| State | Published - 2022 |
Publication series
| Name | Methods in Molecular Biology |
|---|---|
| Volume | 2432 |
| ISSN (Print) | 1064-3745 |
| ISSN (Electronic) | 1940-6029 |
Bibliographical note
Publisher Copyright:© 2022, Springer Science+Business Media, LLC, part of Springer Nature.
Keywords
- 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
