Detecting DNA cytosine methylation using nanopore sequencing | Zendy

Jared T. Simpson | Zendy; Rachael E. Workman | Zendy; Philip C. Zuzarte | Zendy; Matei David | Zendy; Lewis Jonathan Dursi | Zendy; Winston Timp | Zendy

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Detecting DNA cytosine methylation using nanopore sequencing

Author(s) -

Jared T. Simpson,

Rachael E. Workman,

Philip C. Zuzarte,

Matei David,

Lewis Jonathan Dursi,

Winston Timp

Publication year - 2017

Publication title -

nature methods

Language(s) - English

Resource type - Journals

SCImago Journal Rank - 19.469

H-Index - 318

eISSN - 1548-7105

pISSN - 1548-7091

DOI - 10.1038/nmeth.4184

Subject(s) - minion , nanopore sequencing , nanopore , 5 methylcytosine , dna sequencer , dna methylation , cytosine , dna , computational biology , dna sequencing , hidden markov model , sequencing by ligation , genomic dna , human genome , computer science , biology , genetics , genome , genomic library , nanotechnology , gene , base sequence , materials science , artificial intelligence , gene expression

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.

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