Jared T. Simpson, Rachael E. Workman, P. C. Zuzarte, Matei David, L. J. Dursi, Winston Timp. Detecting DNA cytosine methylation using nanopore sequencing. Nature methods, 14(4):407-410. 2017. Supplement https://media.nature.com/original/nature-assets/nmeth/journal/v14/n4/extref/nmeth.4184-S1.pdf.
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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.