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

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, Ravi Bandaru, Haizi Zheng, Hailu Fu, Viktor A. Adalsteinsson () and Manolis Kellis ()
Additional contact information
Yaping Liu: Northwestern University
Sarah C. Reed: Broad Institute of MIT and Harvard
Christopher Lo: Broad Institute of MIT and Harvard
Atish D. Choudhury: Broad Institute of MIT and Harvard
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
Ravi Bandaru: Northwestern University
Haizi Zheng: Cincinnati Children’s Hospital Medical Center
Hailu Fu: Northwestern University
Viktor A. Adalsteinsson: Broad Institute of MIT and Harvard
Manolis Kellis: Broad Institute of MIT and Harvard

Nature Communications, 2024, vol. 15, issue 1, 1-9

Abstract: 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.

Date: 2024
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DOI: 10.1038/s41467-024-47196-6

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