title: Accurate genome-scale percentage DNA methylation estimates from microarray data.
abstract: DNA methylation is a key regulator of gene function in a multitude of both normal and abnormal biological processes, but tools to elucidate its roles on a genome-wide scale are still in their infancy. Methylation sensitive restriction enzymes and microarrays provide a potential high-throughput, low-cost platform to allow methylation profiling. However, accurate absolute methylation estimates have been elusive due to systematic errors and unwanted variability. Previous microarray preprocessing procedures, mostly developed for expression arrays, fail to adequately normalize methylation-related data since they rely on key assumptions that are violated in the case of DNA methylation. We develop a normalization strategy tailored to DNA methylation data and an empirical Bayes percentage methylation estimator that together yield accurate absolute methylation estimates that can be compared across samples. We illustrate the method on data generated to detect methylation differences between tissues and between normal and tumor colon samples.
authors.affiliation: Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University and Department of Biostatistics, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD 21231, USA. aryee@jhu.edu
authors.forename: Martin J
authors.initials: MJ
authors.lastname: Aryee
authors.forename: Zhijin
authors.initials: Z
authors.lastname: Wu
authors.forename: Christine
authors.initials: C
authors.lastname: Ladd-Acosta
authors.forename: Brian
authors.initials: B
authors.lastname: Herb
authors.forename: Andrew P
authors.initials: AP
authors.lastname: Feinberg
authors.forename: Srinivasan
authors.initials: S
authors.lastname: Yegnasubramanian
authors.forename: Rafael A
authors.initials: RA
authors.lastname: Irizarry
mesh_terms: D000465:Algorithms; D001499:Bayes Theorem; D001923:Brain Chemistry / Q000235:genetics; D003106:Colon / Q000737:chemistry; D003110:Colonic Neoplasms / Q000737:chemistry; D004247:DNA / Q000737:chemistry / Q000378:metabolism; D019175:DNA Methylation; D004262:DNA Restriction Enzymes / Q000378:metabolism; D004273:DNA, Neoplasm / Q000737:chemistry / Q000378:metabolism; D057890:Epigenomics / Q000379:methods; D016678:Genome; D006801:Humans; D008099:Liver / Q000737:chemistry; D020411:Oligonucleotide Array Sequence Analysis / Q000379:methods*; D017422:Sequence Analysis, DNA; D013154:Spleen / Q000737:chemistry; D013447:Sulfites / Q000737:chemistry
chemical_list: D004273:DNA, Neoplasm; D013447:Sulfites; D004247:DNA; D004262:DNA Restriction Enzymes; C120301:McrBC endonuclease; C042345:hydrogen sulfite