title: A simple algorithm for quantifying DNA methylation levels on multiple independent CpG sites in bisulfite genomic sequencing electropherograms.
abstract: DNA methylation at cytosines is a widely studied epigenetic modification. Methylation is commonly detected using bisulfite modification of DNA followed by PCR and additional techniques such as restriction digestion or sequencing. These additional techniques are either laborious, require specialized equipment, or are not quantitative. Here we describe a simple algorithm that yields quantitative results from analysis of conventional four-dye-trace sequencing. We call this method Mquant and we compare it with the established laboratory method of combined bisulfite restriction assay (COBRA). This analysis of sequencing electropherograms provides a simple, easily applied method to quantify DNA methylation at specific CpG sites.
authors.affiliation: Department of Biochemistry and Molecular Biology, The University of Arkansas for Medical Sciences, Central Arkansas Veterans Health Care Systems, Little Rock AR, USA.
authors.forename: Tatiana I
authors.initials: TI
authors.lastname: Leakey
authors.forename: Jerzy
authors.initials: J
authors.lastname: Zielinski
authors.forename: Rachel N
authors.initials: RN
authors.lastname: Siegfried
authors.forename: Eric R
authors.initials: ER
authors.lastname: Siegel
authors.forename: Chun-Yang
authors.initials: CY
authors.lastname: Fan
authors.forename: Craig A
authors.initials: CA
authors.lastname: Cooney
mesh_terms: D000465:Algorithms; D000818:Animals; D018899:CpG Islands; D019175:DNA Methylation; D004587:Electrophoresis, Agar Gel; D005456:Fluorescent Dyes; D023281:Genomics / Q000379:methods*; D051379:Mice; D016133:Polymerase Chain Reaction; D013447:Sulfites / Q000737:chemistry*; D013941:Thymine / Q000032:analysis
chemical_list: D005456:Fluorescent Dyes; D013447:Sulfites; C042345:hydrogen sulfite; D013941:Thymine