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- Title
CRAG: de novo characterization of cell-free DNA fragmentation hotspots in plasma whole-genome sequencing.
- Authors
Zhou, Xionghui; Zheng, Haizi; Fu, Hailu; Dillehay McKillip, Kelsey L.; Pinney, Susan M.; Liu, Yaping
- Abstract
The fine-scale cell-free DNA fragmentation patterns in early-stage cancers are poorly understood. We developed a de novo approach to characterize the cell-free DNA fragmentation hotspots from plasma whole-genome sequencing. Hotspots are enriched in open chromatin regions, and, interestingly, 3′end of transposons. Hotspots showed global hypo-fragmentation in early-stage liver cancers and are associated with genes involved in the initiation of hepatocellular carcinoma and associated with cancer stem cells. The hotspots varied across multiple early-stage cancers and demonstrated high performance for the diagnosis and identification of tissue-of-origin in early-stage cancers. We further validated the performance with a small number of independent case–control-matched early-stage cancer samples.
- Subjects
CELL-free DNA; NUCLEOTIDE sequencing; CANCER stem cells; LIVER cancer; HEPATOCELLULAR carcinoma
- Publication
Genome Medicine, 2022, Vol 14, Issue 1, p1
- ISSN
1756-994X
- Publication type
Article
- DOI
10.1186/s13073-022-01141-8