title: OxyBS: estimation of 5-methylcytosine and 5-hydroxymethylcytosine from tandem-treated oxidative bisulfite and bisulfite DNA.
abstract: The use of sodium bisulfite (BS) treatment followed by hybridization to an Illumina Infinium BeadChip (HumanMethylation450 and MethylationEPIC) is a common method for interrogating 5-methylcytosine (5mC) at single nucleotide resolution. However, standard treatment of DNA with BS does not allow disambiguation of 5mC from an additional cytosine modification, 5-hydroxymethylcytosine (5hmC). Recently, it has been demonstrated that paired BS and oxidative bisulfite (oxBS) treatment on the same sample followed by hybridization to an Infinium microarray permits the differentiation of 5hmC from 5mC. Nevertheless, estimation of 5hmC and 5mC from tandem-treated arrays has been shown to produce irregular estimates of cytosine modifications.
  
  
  
  We present a novel method using maximum likelihood estimation to accurately estimate the parameters of unmethylated cytosine (5C), 5mC and 5hmC from Infinium microarray data given the signal intensities from the oxBS and BS replicates.
  
  
  
  OxyBS is an R package available on CRAN.
  
  
  
  Andres.Houseman@oregonstate.edu
  
  
  
  Supplementary data are available at Bioinformatics online.
authors.affiliation: School of Biological and Population Health Sciences, College of Public Health and Human Sciences, Oregon State University, Corvallis, OR 97331, USA.
authors.forename: E Andres
authors.initials: EA
authors.lastname: Houseman
authors.affiliation: Department of Pharmacology and Toxicology Department of Epidemiology, Geisel School of Medicine at Dartmouth, Hanover, NH 03755, USA.
authors.forename: Kevin C
authors.initials: KC
authors.lastname: Johnson
authors.affiliation: Department of Pharmacology and Toxicology Department of Epidemiology, Geisel School of Medicine at Dartmouth, Hanover, NH 03755, USA.
authors.forename: Brock C
authors.initials: BC
authors.lastname: Christensen
mesh_terms: D044503:5-Methylcytosine; D003596:Cytosine; D004247:DNA; D019175:DNA Methylation; D006801:Humans; D016013:Likelihood Functions; D046228:Microarray Analysis; D017422:Sequence Analysis, DNA
chemical_list: D044503:5-Methylcytosine; D003596:Cytosine; D004247:DNA