title: Methylation analysis by microarray.
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.
authors.affiliation: Human Cancer Genetics Program, The Ohio State University Comprehensive Cancer Center, The Ohio State University, Columbus, OH, USA.
authors.forename: Daniel E
authors.initials: DE
authors.lastname: Deatherage
authors.forename: Dustin
authors.initials: D
authors.lastname: Potter
authors.forename: Pearlly S
authors.initials: PS
authors.lastname: Yan
authors.forename: Tim H-M
authors.initials: TH
authors.lastname: Huang
authors.forename: Shili
authors.initials: S
authors.lastname: Lin
mesh_terms: D004247:DNA / Q000032:analysis*; D019175:DNA Methylation; D006801:Humans; D020411:Oligonucleotide Array Sequence Analysis / Q000295:instrumentation / Q000379:methods*; D015203:Reproducibility of Results
chemical_list: D004247:DNA