Detecting DNA cytosine methylation using nanopore sequencing

Jared T. Simpson; Rachael E. Workman; P. C. Zuzarte; Matei David; L. J. Dursi; Winston Timp

doi:10.1038/nmeth.4184

Detecting DNA cytosine methylation using nanopore sequencing

Jared T. Simpson
, Rachael E. Workman
, P. C. Zuzarte
, Matei David
, L. J. Dursi
, Winston Timp

Whiting School of Engineering

Research output: Contribution to journal › Article › peer-review

Abstract

In nanopore sequencing devices, electrolytic current signals are sensitive to base modifcations, such as 5-methylcytosine (5-mc). here we quantifed 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.

Original language	English (US)
Pages (from-to)	407-410
Number of pages	4
Journal	Nature Methods
Volume	14
Issue number	4
DOIs	https://doi.org/10.1038/nmeth.4184
State	Published - Feb 20 2017

ASJC Scopus subject areas

Biotechnology
Biochemistry
Molecular Biology
Cell Biology

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10.1038/nmeth.4184

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AU - Dursi, L. J.

AU - Timp, Winston

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AB - In nanopore sequencing devices, electrolytic current signals are sensitive to base modifcations, such as 5-methylcytosine (5-mc). here we quantifed 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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Detecting DNA cytosine methylation using nanopore sequencing

Abstract

ASJC Scopus subject areas

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