Brief Communication | Published:

Detecting DNA cytosine methylation using nanopore sequencing

Nature Methods volume 14, pages 407410 (2017) | Download Citation

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.

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European Nucleotide Archive

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Acknowledgements

We thank N. Loman and J. Quick for making the E. coli K12 data set publicly available, and A. Feinberg, K. Hansen and J. McPherson for helpful discussions. J.T.S., P.C.Z., M.D. and L.J.D. are supported by the Ontario Institute for Cancer Research through funds provided by the Government of Ontario. W.T. is supported in part by a Johns Hopkins University Catalyst award.

Author information

Affiliations

  1. Ontario Institute for Cancer Research, Toronto, Ontario, Canada.

    • Jared T Simpson
    • , P C Zuzarte
    • , Matei David
    •  & L J Dursi
  2. Department of Computer Science, University of Toronto, Toronto, Ontario, Canada.

    • Jared T Simpson
  3. Department of Biomedical Engineering, Johns Hopkins University, Baltimore, Maryland, USA.

    • Rachael E Workman
    •  & Winston Timp

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Contributions

J.T.S. and W.T. designed the study; W.T., R.E.W. and P.C.Z. performed the experiments; J.T.S., M.D. and L.J.D. designed and implemented the methylation-training and inference framework; and J.T.S., W.T., R.E.W. and P.C.Z. wrote the paper.

Competing interests

J.T.S. receives research funding from Oxford Nanopore Technologies, and W.T. has two patents licensed to Oxford Nanopore Technologies (US20110226623 A1 and US20120040342 A1). J.T.S. and W.T. have received travel funds to speak at symposia organized by Oxford Nanopore Technologies.

Corresponding authors

Correspondence to Jared T Simpson or Winston Timp.

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    Supplementary Text and Figures

    Supplementary Figures 1–5, Supplementary Note and Supplementary Tables 1–7

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    Supplementary Data 1

    TSS by chromosomes

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    Supplementary Data 3

    Cancer Normal Regions

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    Supplementary Data 4

    Cancer-Normal Strand Data

  5. 5.

    Supplementary Data 2

    CGI bisulfite vs nanopore

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DOI

https://doi.org/10.1038/nmeth.4184

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