SpringerProtocols: Abstract: Methylation Analysis by Microarray

9. Methylation Analysis by Microarray

By: Daniel E. Deatherage², Dustin Potter³, Pearlly S. Yan², Tim H.-M. Huang², Shili Lin⁴

Abstract

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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.

Affiliation(s): (2) Human Cancer Genetics Program, The Ohio State University Comprehensive Cancer Center, The Ohio State University, Columbus, OH, USA
(3) Human Cancer Genetics Program, The Ohio State University Comprehensive Cancer Center and the Mathematical Biosciences Institute, The Ohio State University, Columbus, OH, USA
(4) Department of Statistics and the Mathematical Biosciences Institute, The Ohio State University, Columbus, OH, USA

Book Title: Microarray Analysis of the Physical Genome: Methods and Protocols

Series: Methods in Molecular Biology | Volume: 556 | Pub. Date: Feb-01-2009 | Page Range: 117-139 | DOI: 10.1007/978-1-60327-192-9_9

Subject: Genetics/Genomics

Key Words: DNA methylation - differential methylation hybridization (DMH) - CpG islands (CGI) - microarray

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