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Bioinformatics. 2016 Aug 15;32(16):2505-7. doi: 10.1093/bioinformatics/btw158. Epub 2016 Apr 19.

OxyBS: estimation of 5-methylcytosine and 5-hydroxymethylcytosine from tandem-treated oxidative bisulfite and bisulfite DNA.

Author information

1
School of Biological and Population Health Sciences, College of Public Health and Human Sciences, Oregon State University, Corvallis, OR 97331, USA.
2
Department of Pharmacology and Toxicology Department of Epidemiology, Geisel School of Medicine at Dartmouth, Hanover, NH 03755, USA.

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.

RESULTS:

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.

AVAILABILITY AND IMPLEMENTATION:

OxyBS is an R package available on CRAN.

CONTACT:

Andres.Houseman@oregonstate.edu

SUPPLEMENTARY INFORMATION:

Supplementary data are available at Bioinformatics online.

PMID:
27153596
PMCID:
PMC4978924
DOI:
10.1093/bioinformatics/btw158
[Indexed for MEDLINE]
Free PMC Article

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