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Study Description

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 existing datasets, 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 from both cancer patients and healthy controls.

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Study Attribution
  • Principal Investigator
    • Yaping Liu. Division of Human Genetics, Department of Pediatrics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA.
  • Co-Investigators
    • Viktor Adalsteinsson. Gerstner Center for Cancer Diagnostics, Broad Institute, Cambridge, MA, USA.
    • Manolis Kellis. Broad Institute, Cambridge, MA, USA.
    • Atish D. Choudhury. Lank Center for Genitourinary Oncology, Dana-Farber Cancer Institute, Boston, MA, USA.
    • Heather A. Parsons. Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA.
    • Daniel G. Stover. The Ohio State University Comprehensive Cancer Center - James, Columbus, OH, USA.