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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