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Research Article

Genome-wide detection of cytosine methylation by single molecule real-time sequencing

View ORCID ProfileO. Y. Olivia Tse, View ORCID ProfilePeiyong Jiang, Suk Hang Cheng, Wenlei Peng, Huimin Shang, View ORCID ProfileJohn Wong, View ORCID ProfileStephen L. Chan, Liona C. Y. Poon, Tak Y. Leung, K. C. Allen Chan, View ORCID ProfileRossa W. K. Chiu, and View ORCID ProfileY. M. Dennis Lo
  1. aLi Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong Special Administrative Region, China;
  2. bDepartment of Chemical Pathology, Prince of Wales Hospital, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong Special Administrative Region, China;
  3. cDepartment of Surgery, Prince of Wales Hospital, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong Special Administrative Region, China;
  4. dDepartment of Clinical Oncology, Prince of Wales Hospital, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong Special Administrative Region, China;
  5. eState Key Laboratory of Translational Oncology, Prince of Wales Hospital, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong Special Administrative Region, China;
  6. fDepartment of Obstetrics and Gynaecology, Prince of Wales Hospital, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong Special Administrative Region, China

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PNAS February 2, 2021 118 (5) e2019768118; https://doi.org/10.1073/pnas.2019768118
O. Y. Olivia Tse
aLi Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong Special Administrative Region, China;
bDepartment of Chemical Pathology, Prince of Wales Hospital, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong Special Administrative Region, China;
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  • ORCID record for O. Y. Olivia Tse
Peiyong Jiang
aLi Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong Special Administrative Region, China;
bDepartment of Chemical Pathology, Prince of Wales Hospital, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong Special Administrative Region, China;
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Suk Hang Cheng
aLi Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong Special Administrative Region, China;
bDepartment of Chemical Pathology, Prince of Wales Hospital, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong Special Administrative Region, China;
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Wenlei Peng
aLi Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong Special Administrative Region, China;
bDepartment of Chemical Pathology, Prince of Wales Hospital, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong Special Administrative Region, China;
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Huimin Shang
aLi Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong Special Administrative Region, China;
bDepartment of Chemical Pathology, Prince of Wales Hospital, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong Special Administrative Region, China;
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John Wong
cDepartment of Surgery, Prince of Wales Hospital, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong Special Administrative Region, China;
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Stephen L. Chan
dDepartment of Clinical Oncology, Prince of Wales Hospital, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong Special Administrative Region, China;
eState Key Laboratory of Translational Oncology, Prince of Wales Hospital, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong Special Administrative Region, China;
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Liona C. Y. Poon
fDepartment of Obstetrics and Gynaecology, Prince of Wales Hospital, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong Special Administrative Region, China
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Tak Y. Leung
fDepartment of Obstetrics and Gynaecology, Prince of Wales Hospital, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong Special Administrative Region, China
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K. C. Allen Chan
aLi Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong Special Administrative Region, China;
bDepartment of Chemical Pathology, Prince of Wales Hospital, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong Special Administrative Region, China;
eState Key Laboratory of Translational Oncology, Prince of Wales Hospital, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong Special Administrative Region, China;
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Rossa W. K. Chiu
aLi Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong Special Administrative Region, China;
bDepartment of Chemical Pathology, Prince of Wales Hospital, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong Special Administrative Region, China;
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Y. M. Dennis Lo
aLi Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong Special Administrative Region, China;
bDepartment of Chemical Pathology, Prince of Wales Hospital, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong Special Administrative Region, China;
eState Key Laboratory of Translational Oncology, Prince of Wales Hospital, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong Special Administrative Region, China;
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  • For correspondence: loym@cuhk.edu.hk
  1. Contributed by Y. M. Dennis Lo, December 9, 2020 (sent for review September 25, 2020; reviewed by Shankar Balasubramanian and Andrew P. Feinberg)

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Significance

Single molecule real-time (SMRT) sequencing theoretically offers the opportunity to directly assess certain base modifications of native DNA molecules without any prior chemical/enzymatic conversions and PCR amplification, using kinetic signals of a DNA polymerase. However, the kinetic signal changes caused by 5mC modification are extremely subtle. Hence, the robust genome-wide measurement of 5mC modification has not been achieved. We enhanced 5mC detection using SMRT sequencing by holistically analyzing kinetic signals of a DNA polymerase and sequence context for every base within a measurement window. We employed a convolutional neural network to train a methylation classification model, leading to genome-wide 5mC detection. The sensitivity and specificity reached 90% and 94%, with a 99% correlation of overall methylation level with bisulfite sequencing.

Abstract

5-Methylcytosine (5mC) is an important type of epigenetic modification. Bisulfite sequencing (BS-seq) has limitations, such as severe DNA degradation. Using single molecule real-time sequencing, we developed a methodology to directly examine 5mC. This approach holistically examined kinetic signals of a DNA polymerase (including interpulse duration and pulse width) and sequence context for every nucleotide within a measurement window, termed the holistic kinetic (HK) model. The measurement window of each analyzed double-stranded DNA molecule comprised 21 nucleotides with a cytosine in a CpG site in the center. We used amplified DNA (unmethylated) and M.SssI-treated DNA (methylated) (M.SssI being a CpG methyltransferase) to train a convolutional neural network. The area under the curve for differentiating methylation states using such samples was up to 0.97. The sensitivity and specificity for genome-wide 5mC detection at single-base resolution reached 90% and 94%, respectively. The HK model was then tested on human–mouse hybrid fragments in which each member of the hybrid had a different methylation status. The model was also tested on human genomic DNA molecules extracted from various biological samples, such as buffy coat, placental, and tumoral tissues. The overall methylation levels deduced by the HK model were well correlated with those by BS-seq (r = 0.99; P < 0.0001) and allowed the measurement of allele-specific methylation patterns in imprinted genes. Taken together, this methodology has provided a system for simultaneous genome-wide genetic and epigenetic analyses.

  • third-generation sequencing
  • epigenetics
  • epigenomics
  • base modifications

Footnotes

  • ↵1O.Y.O.T., P.J., and S.H.C. contributed equally to this work.

  • ↵2To whom correspondence may be addressed. Email: loym{at}cuhk.edu.hk.
  • Author contributions: K.C.A.C., R.W.K.C., and Y.M.D.L. designed research; O.Y.O.T., P.J., S.H.C., W.P., and H.S. performed research; O.Y.O.T., P.J., S.H.C., W.P., J.W., S.L.C., L.C.Y.P., and T.Y.L. contributed new reagents/analytic tools; O.Y.O.T., P.J., W.P., K.C.A.C., R.W.K.C., and Y.M.D.L. analyzed data; and P.J., K.C.A.C., R.W.K.C., and Y.M.D.L. wrote the paper.

  • Reviewers: S.B., University of Cambridge; and A.P.F., Johns Hopkins University.

  • Competing interest statement: A patent application on the described technology has been filed and licensed to Take2 Holdings Limited, founded by the research team.

  • This article contains supporting information online at https://www.pnas.org/lookup/suppl/doi:10.1073/pnas.2019768118/-/DCSupplemental.

Data Availability.

Sequence data for the subjects studied in this work have been deposited at the European Genome-Phenome Archive (EGA), https://www.ebi.ac.uk/ega/, hosted by the European Bioinformatics Institute (EBI) (accession no. EGAS00001004642).

  • Copyright © 2021 the Author(s). Published by PNAS.

This open access article is distributed under Creative Commons Attribution-NonCommercial-NoDerivatives License 4.0 (CC BY-NC-ND).

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Genome-wide detection of cytosine methylation by single molecule real-time sequencing
O. Y. Olivia Tse, Peiyong Jiang, Suk Hang Cheng, Wenlei Peng, Huimin Shang, John Wong, Stephen L. Chan, Liona C. Y. Poon, Tak Y. Leung, K. C. Allen Chan, Rossa W. K. Chiu, Y. M. Dennis Lo
Proceedings of the National Academy of Sciences Feb 2021, 118 (5) e2019768118; DOI: 10.1073/pnas.2019768118

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Genome-wide detection of cytosine methylation by single molecule real-time sequencing
O. Y. Olivia Tse, Peiyong Jiang, Suk Hang Cheng, Wenlei Peng, Huimin Shang, John Wong, Stephen L. Chan, Liona C. Y. Poon, Tak Y. Leung, K. C. Allen Chan, Rossa W. K. Chiu, Y. M. Dennis Lo
Proceedings of the National Academy of Sciences Feb 2021, 118 (5) e2019768118; DOI: 10.1073/pnas.2019768118
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