Detecting DNA cytosine methylation using nanopore sequencing

Detecting DNA cytosine methylation using nanopore sequencing. Simpson, J. T., Workman, R. E., Zuzarte, P. C., David, M., Dursi, L. J., & Timp, W. Nature Methods, 14(4):407–410, April, 2017.

Paper doi abstract bibtex

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.

@article{simpson_detecting_2017,
	title = {Detecting {DNA} cytosine methylation using nanopore sequencing},
	volume = {14},
	copyright = {© 2017 Nature Publishing Group, a division of Macmillan Publishers Limited. All Rights Reserved.},
	issn = {1548-7091},
	url = {http://www.nature.com/nmeth/journal/v14/n4/full/nmeth.4184.html},
	doi = {10.1038/nmeth.4184},
	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.},
	number = {4},
	journal = {Nature Methods},
	author = {Simpson, Jared T. and Workman, Rachael E. and Zuzarte, P. C. and David, Matei and Dursi, L. J. and Timp, Winston},
	month = apr,
	year = {2017},
	keywords = {DNA sequencing, Epigenomics, nanopores, Software},
	pages = {407--410},
    author+an = {1=corresponding; 2=student; 6=pi, corresponding}
}

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