Methylation Analysis by Microarray

  • Daniel E. Deatherage
  • Dustin Potter
  • Pearlly S. Yan
  • Tim H.-M. Huang
  • Shili Lin
Protocol
Part of the Methods in Molecular Biology™ book series (MIMB, volume 556)

Abstract

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.

Key words

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

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Copyright information

© Humana Press, a part of Springer Science+Business Media, LLC 2009

Authors and Affiliations

  • Daniel E. Deatherage
    • 1
  • Dustin Potter
    • 2
  • Pearlly S. Yan
    • 1
  • Tim H.-M. Huang
    • 1
  • Shili Lin
    • 3
  1. 1.Human Cancer Genetics ProgramThe Ohio State University Comprehensive Cancer Center, The Ohio State UniversityColumbusUSA
  2. 2.Human Cancer Genetics ProgramThe Ohio State University Comprehensive Cancer Center and the Mathematical Biosciences Institute, The Ohio State UniversityColumbusUSA
  3. 3.Department of Statistics and the Mathematical Biosciences InstituteThe Ohio State UniversityColumbusUSA

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