Cell-free DNA fragmentomics: from chromatin biology to clinical stratification.

Authors

Tien-Dung Bui, Minh-Thu Phung, Teh-Ying Chou, Nguyen Quoc Khanh Le

Published in

Epigenomics. Pages 1-13. Oct 03, 2026. Epub Oct 03, 2026.

Abstract

Plasma cell-free DNA (cfDNA) is fragmented nonrandomly, reflecting the chromatin architecture of its source cells and the nucleases that process it. The fragmentome can therefore provide an indirect readout of cellular regulatory state. This review examines how DNA methylation, chromatin accessibility, nucleosome positioning, protein occupancy, and nuclease activity shape cfDNA fragmentation and considers their implications for oncology. We organize fragmentomic measurements into four classes: coverage and protection, fragment size, fragment-end properties, and diversity and entropy metrics. We discuss the genomic contexts in which these features are informative, including repetitive and transposable elements, and compare platforms by sequencing requirements, feature portability, and the fragment populations captured by different library chemistries. We then review applications in cancer screening, tissue-of-origin inference, molecular subtyping, prognosis, minimal residual disease detection, and treatment response monitoring. A central challenge for clinical translation is attributing fragmentomic changes to their tissue of origin.

PMID:
42829334
Bibliographic data and abstract were imported from PubMed on 04 Oct 2026.

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