Your browser doesn't support javascript.
loading
FinaleMe: Predicting DNA methylation by the fragmentation patterns of plasma cell-free DNA.
Liu, Yaping; Reed, Sarah C; Lo, Christopher; Choudhury, Atish D; Parsons, Heather A; Stover, Daniel G; Ha, Gavin; Gydush, Gregory; Rhoades, Justin; Rotem, Denisse; Freeman, Samuel; Katz, David; Bandaru, Ravi; Zheng, Haizi; Fu, Hailu; Adalsteinsson, Viktor A; Kellis, Manolis.
Afiliação
  • Liu Y; Department of Biochemistry and Molecular Genetics, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611.
  • Reed SC; Robert H. Lurie Comprehensive Cancer Center of Northwestern University, Chicago, IL 60611.
  • Lo C; Division of Human Genetics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229.
  • Choudhury AD; Division of Biomedical Informatics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229.
  • Parsons HA; Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH 45229.
  • Stover DG; University of Cincinnati Center for Environmental Genetics, Cincinnati, OH 45229.
  • Ha G; University of Cincinnati Cancer Center, Cincinnati, OH 45229.
  • Gydush G; Broad Institute of MIT and Harvard, Cambridge, MA 02142.
  • Rhoades J; Massachusetts Institute of Technology, Computer Science and Artificial Intelligence Laboratory, Cambridge, MA 02139.
  • Rotem D; Broad Institute of MIT and Harvard, Cambridge, MA 02142.
  • Freeman S; Broad Institute of MIT and Harvard, Cambridge, MA 02142.
  • Katz D; Broad Institute of MIT and Harvard, Cambridge, MA 02142.
  • Bandaru R; Dana-Farber Cancer Institute, Boston, MA, USA.
  • Zheng H; Dana-Farber Cancer Institute, Boston, MA, USA.
  • Fu H; Dana-Farber Cancer Institute, Boston, MA, USA.
  • Adalsteinsson VA; Broad Institute of MIT and Harvard, Cambridge, MA 02142.
  • Kellis M; Broad Institute of MIT and Harvard, Cambridge, MA 02142.
bioRxiv ; 2024 Jan 02.
Article em En | MEDLINE | ID: mdl-38260558
ABSTRACT
Analysis of DNA methylation in cell-free DNA (cfDNA) reveals clinically relevant biomarkers but requires specialized protocols and sufficient input material that limits its applicability. Millions of cfDNA samples have been profiled by genomic sequencing. To maximize the gene regulation information from the existing dataset, we developed FinaleMe, a non-homogeneous Hidden Markov Model (HMM), to predict DNA methylation of cfDNA and, therefore, tissues-of-origin directly from plasma whole-genome sequencing (WGS). We validated the performance with 80 pairs of deep and shallow-coverage WGS and whole-genome bisulfite sequencing (WGBS) data.
Palavras-chave
Texto completo
Imprimir
XML
PubMed Links
Buscar no Google

Texto completo: 1 Coleções: 01-internacional Base de dados: MEDLINE Tipo de estudo: Guideline / Prognostic_studies / Risk_factors_studies Idioma: En Revista: BioRxiv Ano de publicação: 2024 Tipo de documento: Article
Texto completo
Imprimir
XML
PubMed Links
Buscar no Google

Texto completo: 1 Coleções: 01-internacional Base de dados: MEDLINE Tipo de estudo: Guideline / Prognostic_studies / Risk_factors_studies Idioma: En Revista: BioRxiv Ano de publicação: 2024 Tipo de documento: Article