Determination of DNA methylation levels using illumina humanmethylation450 beadchips

Melanie A. Carless

Research output: Chapter in Book/Report/Conference proceedingChapter

3 Scopus citations

Abstract

DNA methylation is a modifiable epigenetic phenomenon that has a strong influence over transcriptional regulation and as such has been consistently implicated in development and disease. Several platforms are targeted toward the identification of DNA methylation changes that might be pertinent to the disease process and include regional analysis (e.g., pyrosequencing) as well as genome-wide analysis (e.g., next- generation sequencing and microarray). The Illumina HumanMethylation450 BeadChip is one of the most comprehensive microarray platforms available, and due to the high costs associated with next- generation sequencing, it is becoming a widely used tool for the analysis of genome-wide DNA methylation levels. Providing quantitative DNA methylation levels at 482,421 CpG sites within CpG islands, shores, and shelves, as well as intergenic regions, the HumanMethylation450 BeadChip can allow accurate assessment of differential methylation across large studies. This chapter outlines the laboratory methodologies associated with performing the Illumina Infinium Methylation Assay, including bisulfite conversion, whole-genome amplification, BeadChip hybridization, XStain procedures, and imaging systems. Furthermore, this chapter provides an outline of data analysis tools, including the GenomeStudio pipeline, quality control measures, and additional statistical considerations. This comprehensive overview can aid not only in performing the Illumina Infinium Methylation Assay but also in the interpretation of data derived from this platform.

Original languageEnglish (US)
Title of host publicationChromatin Protocols: Third Edition
PublisherSpringer New York
Pages143-192
Number of pages50
ISBN (Print)9781493924745, 9781493924738
DOIs
StatePublished - Mar 31 2015
Externally publishedYes

Keywords

  • Bisulfite conversion
  • CpG site
  • DNA methylation
  • GenomeStudio
  • Infinium assay

ASJC Scopus subject areas

  • Biochemistry, Genetics and Molecular Biology(all)

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  • Cite this

    Carless, M. A. (2015). Determination of DNA methylation levels using illumina humanmethylation450 beadchips. In Chromatin Protocols: Third Edition (pp. 143-192). Springer New York. https://doi.org/10.1007/978-1-4939-2474-5_10