FinaleMe: Predicting DNA methylation by the fragmentation patterns of plasma cell-free DNA.
basic_science · Level V
Where this comes from
- Record sourced from PubMed, PMID 38555308.
- Also identified by DOI 10.1038/s41467-024-47196-6 and PMC identifier 10981715.
- Licence recorded as CC BY.
- The licence permits redistribution, so the abstract is shown in full and the full text is available from the publisher.
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.
Medical subject headings
- DNA Methylation
- Cell-Free Nucleic Acids