Methylation analysis by microarray

Daniel E. Deatherage, Dustin Potter, Pearlly S. Yan, Tim H.M. Huang, Shili Lin

Research output: Chapter in Book/Report/Conference proceedingChapter

9 Scopus citations


Differential methylation hybridization (DMH) is a high-throughput DNA methylation screening tool that utilizes methylation-sensitive restriction enzymes to profile methylated fragments by hybridizing them to a CpG island microarray. This array contains probes spanning all the 27,800 islands annotated in the UCSC Genome Browser. Herein we describe a DMH protocol with clearly identified quality control points. In this manner, samples that are unlikely to provide good read-outs for differential methylation profiles between the test and the control samples will be identified and repeated with appropriate modifications. The step-by-step laboratory DMH protocol is described. In addition, we provide descriptions regarding DMH data analysis, including image quantification, background correction, and statistical procedures for both exploratory analysis and more formal inferences. Issues regarding quality control are addressed as well.

Original languageEnglish (US)
Title of host publicationMicroarray Analysis of the Physical Genome
Subtitle of host publicationMethods and Protocols
EditorsJonathan Pollack
Number of pages23
StatePublished - 2009
Externally publishedYes

Publication series

NameMethods in Molecular Biology
ISSN (Print)1064-3745


  • CpG islands (CGI)
  • DNA methylation
  • differential methylation hybridization (DMH)
  • microarray

ASJC Scopus subject areas

  • Genetics
  • Molecular Biology


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