{"database":"biostudies-literature","file_versions":[],"scores":null,"additional":{"submitter":["Zhou X"],"funding":["National Institute of Environmental Health Sciences","NIEHS NIH HHS","NHGRI NIH HHS","Cincinnati Children's Hospital Medical Center","National Human Genome Research Institute"],"pagination":["138"],"full_dataset_link":["https://www.ebi.ac.uk/biostudies/studies/S-EPMC9733064"],"repository":["biostudies-literature"],"omics_type":["Unknown"],"volume":["14(1)"],"pubmed_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"],"journal":["Genome medicine"],"pubmed_title":["CRAG: de novo characterization of cell-free DNA fragmentation hotspots in plasma whole-genome sequencing."],"pmcid":["PMC9733064"],"funding_grant_id":["start-up grant, Trustee Award, CCTST mentored pilot translational award, and CCHMC innovation grant","R56 HG012360","P30ES006096","R56HG012360","R24 ES028527","P30 ES006096","R24ES028527"],"pubmed_authors":["Liu Y","Zheng H","Fu H","Dillehay McKillip KL","Pinney SM","Zhou X"],"additional_accession":[]},"is_claimable":false,"name":"CRAG: de novo characterization of cell-free DNA fragmentation hotspots in plasma whole-genome sequencing.","description":"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","dates":{"release":"2022-01-01T00:00:00Z","publication":"2022 Dec","modification":"2025-04-19T06:40:01.749Z","creation":"2025-04-19T06:40:01.749Z"},"accession":"S-EPMC9733064","cross_references":{"pubmed":["36482487"],"doi":["10.1186/s13073-022-01141-8"]}}