Open AccessComprehensive High‐Throughput Arrays for Relative Methylation (CHARM)
Author(s) -
LaddAcosta Christine,
J. Aryee Martin,
Ordway Jared M.,
Feinberg Andrew P.
Publication year - 2010
Publication title -
current protocols in human genetics
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 1.282
H-Index - 30
eISSN - 1934-8258
pISSN - 1934-8266
DOI - 10.1002/0471142905.hg2001s65
Subject(s) - charm (quantum number) , throughput , computational biology , methylation , computer science , biology , chemistry , physics , particle physics , genetics , operating system , dna , wireless
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. Curr. Protoc. Hum. Genet . 65:20.0.1‐20.0.19. © 2010 by John Wiley & Sons, Inc.