title: Comprehensive high-throughput arrays for relative methylation (CHARM).
abstract: DNA methylation (DNAm) is a term used to describe the heritable covalent addition of a methyl group to cytosines at CpG dinucleotides in mammals. While methods for examining DNAm status at specific loci have existed for several years, recent technological advances have begun to enable the examination of DNAm across the genome. In this unit, we describe comprehensive high-throughput arrays for relative methylation (CHARM), a highly sensitive and specific approach to measure DNA methylation across the genome. This method makes no assumptions about where functionally important DNAm occurs, i.e., CpG island or promoter regions, and includes lower-CpG-density regions of the genome. In addition, it uses a novel genome-weighted smoothing algorithm to correct for CpG density and fragment biases present in methyl-enrichment or methyl-depletion DNA-fractionation methods. It can be applied to studying epigenomic changes in DNAm for normal and diseased samples.
authors.affiliation: Department of Medicine, Johns Hopkins University School of Medicine, Center for Epigenetics, Baltimore, Maryland, USA.
authors.forename: Christine
authors.initials: C
authors.lastname: Ladd-Acosta
authors.forename: Martin J
authors.initials: MJ
authors.lastname: Aryee
authors.forename: Jared M
authors.initials: JM
authors.lastname: Ordway
authors.forename: Andrew P
authors.initials: AP
authors.lastname: Feinberg
mesh_terms: D000465:Algorithms; D005591:Chemical Fractionation / Q000379:methods; D018899:CpG Islands / Q000235:genetics; D019175:DNA Methylation; D017931:DNA Primers / Q000235:genetics; D023281:Genomics / Q000379:methods*; D021141:Nucleic Acid Amplification Techniques / Q000379:methods; D020411:Oligonucleotide Array Sequence Analysis / Q000379:methods*
chemical_list: D017931:DNA Primers