title: Detecting DNA cytosine methylation using nanopore sequencing.
abstract: In nanopore sequencing devices, electrolytic current signals are sensitive to base modifications, such as 5-methylcytosine (5-mC). Here we quantified the strength of this effect for the Oxford Nanopore Technologies MinION sequencer. By using synthetically methylated DNA, we were able to train a hidden Markov model to distinguish 5-mC from unmethylated cytosine. We applied our method to sequence the methylome of human DNA, without requiring special steps for library preparation.
authors.affiliation: Ontario Institute for Cancer Research, Toronto, Ontario, Canada.|Department of Computer Science, University of Toronto, Toronto, Ontario, Canada.
authors.forename: Jared T
authors.initials: JT
authors.lastname: Simpson
authors.affiliation: Department of Biomedical Engineering, Johns Hopkins University, Baltimore, Maryland, USA.
authors.forename: Rachael E
authors.initials: RE
authors.lastname: Workman
authors.affiliation: Ontario Institute for Cancer Research, Toronto, Ontario, Canada.
authors.forename: P C
authors.initials: PC
authors.lastname: Zuzarte
authors.affiliation: Ontario Institute for Cancer Research, Toronto, Ontario, Canada.
authors.forename: Matei
authors.initials: M
authors.lastname: David
authors.affiliation: Ontario Institute for Cancer Research, Toronto, Ontario, Canada.
authors.forename: L J
authors.identifier: http://orcid.org/0000-0002-4697-798X
authors.initials: LJ
authors.lastname: Dursi
authors.affiliation: Department of Biomedical Engineering, Johns Hopkins University, Baltimore, Maryland, USA.
authors.forename: Winston
authors.identifier: http://orcid.org/0000-0003-2083-6027
authors.initials: W
authors.lastname: Timp
mesh_terms: D044503:5-Methylcytosine / Q000032:analysis*; D045744:Cell Line, Tumor; D018899:CpG Islands; D003596:Cytosine / Q000032:analysis / Q000378:metabolism*; D019175:DNA Methylation; D004926:Escherichia coli / Q000235:genetics; D015894:Genome, Human; D006801:Humans; D008390:Markov Chains; D058608:Nanopores
chemical_list: D044503:5-Methylcytosine; D003596:Cytosine