FinaleMe: Predicting DNA Methylation by the Fragmentation Patterns of Plasma Cell-free DNA

Overview

Journal Nat Commun

Specialty Biology

Date 2024 Mar 30

PMID 38555308

Authors

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

Manolis Kellis

Affiliations

Soon will be listed here.

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.

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