CRAG: de novo characterization of cell-free DNA fragmentation hotspots in plasma whole-genome sequencing.
Genome Med
; 14(1): 138, 2022 12 08.
Article
em En
| MEDLINE
| ID: mdl-36482487
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.
Palavras-chave
Texto completo:
1
Coleções:
01-internacional
Base de dados:
MEDLINE
Assunto principal:
Ácidos Nucleicos Livres
Tipo de estudo:
Screening_studies
Limite:
Humans
Idioma:
En
Revista:
Genome Med
Ano de publicação:
2022
Tipo de documento:
Article