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FinaleMe: Predicting DNA methylation by the fragmentation patterns of plasma cell-free DNA

Author

Listed:
  • Yaping Liu

    (Northwestern University
    Robert H. Lurie Comprehensive Cancer Center of Northwestern University
    Cincinnati Children’s Hospital Medical Center
    Cincinnati Children’s Hospital Medical Center)

  • Sarah C. Reed

    (Broad Institute of MIT and Harvard
    Vanderbilt University School of Medicine)

  • Christopher Lo

    (Broad Institute of MIT and Harvard)

  • Atish D. Choudhury

    (Broad Institute of MIT and Harvard
    Dana-Farber Cancer Institute)

  • Heather A. Parsons

    (Dana-Farber Cancer Institute)

  • Daniel G. Stover

    (Dana-Farber Cancer Institute)

  • Gavin Ha

    (Broad Institute of MIT and Harvard)

  • Gregory Gydush

    (Broad Institute of MIT and Harvard)

  • Justin Rhoades

    (Broad Institute of MIT and Harvard)

  • Denisse Rotem

    (Broad Institute of MIT and Harvard)

  • Samuel Freeman

    (Broad Institute of MIT and Harvard)

  • David W. Katz

    (Northwestern University
    Robert H. Lurie Comprehensive Cancer Center of Northwestern University
    Cincinnati Children’s Hospital Medical Center)

  • Ravi Bandaru

    (Northwestern University
    Robert H. Lurie Comprehensive Cancer Center of Northwestern University
    Cincinnati Children’s Hospital Medical Center)

  • Haizi Zheng

    (Cincinnati Children’s Hospital Medical Center)

  • Hailu Fu

    (Northwestern University
    Robert H. Lurie Comprehensive Cancer Center of Northwestern University
    Cincinnati Children’s Hospital Medical Center)

  • Viktor A. Adalsteinsson

    (Broad Institute of MIT and Harvard)

  • Manolis Kellis

    (Broad Institute of MIT and Harvard
    Computer Science and Artificial Intelligence Laboratory)

Abstract

Analysis of DNA methylation in cell-free DNA reveals clinically relevant biomarkers but requires specialized protocols such as whole-genome bisulfite sequencing. Meanwhile, millions of cell-free DNA samples are being profiled by whole-genome sequencing. Here, we develop FinaleMe, a non-homogeneous Hidden Markov Model, to predict DNA methylation of cell-free DNA and, therefore, tissues-of-origin, directly from plasma whole-genome sequencing. We validate the performance with 80 pairs of deep and shallow-coverage whole-genome sequencing and whole-genome bisulfite sequencing data.

Suggested Citation

  • Yaping Liu & Sarah C. Reed & Christopher Lo & Atish D. Choudhury & Heather A. Parsons & Daniel G. Stover & Gavin Ha & Gregory Gydush & Justin Rhoades & Denisse Rotem & Samuel Freeman & David W. Katz &, 2024. "FinaleMe: Predicting DNA methylation by the fragmentation patterns of plasma cell-free DNA," Nature Communications, Nature, vol. 15(1), pages 1-9, December.
    • Handle: RePEc:nat:natcom:v:15:y:2024:i:1:d:10.1038_s41467-024-47196-6
    DOI: 10.1038/s41467-024-47196-6
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    References listed on IDEAS

    as
    1. Viktor A. Adalsteinsson & Gavin Ha & Samuel S. Freeman & Atish D. Choudhury & Daniel G. Stover & Heather A. Parsons & Gregory Gydush & Sarah C. Reed & Denisse Rotem & Justin Rhoades & Denis Loginov & , 2017. "Scalable whole-exome sequencing of cell-free DNA reveals high concordance with metastatic tumors," Nature Communications, Nature, vol. 8(1), pages 1-13, December.
    2. Joshua Moss & Judith Magenheim & Daniel Neiman & Hai Zemmour & Netanel Loyfer & Amit Korach & Yaacov Samet & Myriam Maoz & Henrik Druid & Peter Arner & Keng-Yeh Fu & Endre Kiss & Kirsty L. Spalding & , 2018. "Comprehensive human cell-type methylation atlas reveals origins of circulating cell-free DNA in health and disease," Nature Communications, Nature, vol. 9(1), pages 1-12, December.
    3. Yunyun An & Xin Zhao & Ziteng Zhang & Zhaohua Xia & Mengqi Yang & Li Ma & Yu Zhao & Gang Xu & Shunda Du & Xiang’an Wu & Shuowen Zhang & Xin Hong & Xin Jin & Kun Sun, 2023. "DNA methylation analysis explores the molecular basis of plasma cell-free DNA fragmentation," Nature Communications, Nature, vol. 14(1), pages 1-12, December.
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