ArticleGenome medicine2020
cfNOMe - A single assay for comprehensive epigenetic analyses of cell-free DNA.
Article in Genome medicine, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 44 papers.
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Who cites it
44 citing papers in PubMed.
- MethylSense: high accuracy machine learning-based diagnostics forJournal of clinical microbiology · 2026Article
- Detection of known gene fusions in cancer cell lines using whole-genome bisulfite sequencing data.Scientific reports · 2026Article
- Urine-Based cfDNA Ensemble Modeling for Early Detection of Bladder Cancer Using Whole-Genome Methylation Sequencing.Cancers · 2026Article
- Cell-Specific DNA Methylation Markers in Plasma cfDNA Reveal Diagnostic Potential for Head and Neck Cancer.Journal of Cancer · 2026Article
- The Clinical Utility of Cell-Free DNA in Brain Tumor Management: A Comprehensive Review.Journal of molecular neuroscience : MN · 2025Review
- Read-level DNA methylation deconvolution enhances circulating tumor DNA detection.Briefings in bioinformatics · 2025Article
- GUIDE: a prospective cohort study for blood-based early detection of gastrointestinal cancers using targeted DNA methylation and fragmentomics sequencing.Molecular cancer · 2025Observational
- Comparison of enzymatic and bisulfite conversion of circulating cell-free tumor DNA for DNA methylation analyses.Clinical epigenetics · 2025Article
- Comparative performance evaluation of bisulfite- and enzyme-based DNA conversion methods.Clinical epigenetics · 2025Article
- Detection of an intestinal cell DNA methylation signature in blood samples from neonates with necrotizing enterocolitis.Epigenomics · 2025Article
- Circulating Cell-Free DNA in Metabolic Diseases.Journal of the Endocrine Society · 2025Review
- Genomic and Epigenomic Analysis of Plasma Cell-Free DNA Identifies Stemness Features Associated with Worse Survival in Lethal Prostate Cancer.Clinical cancer research : an official journal of the American Association for Cancer Research · 2025Article
- Systematic evaluation of methylation-based cell type deconvolution methods for plasma cell-free DNA.Genome biology · 2024Article
- Mining nucleic acid "omics" to boost liquid biopsy in cancer.Cell reports. Medicine · 2024Review
- MetDecode: methylation-based deconvolution of cell-free DNA for noninvasive multi-cancer typing.Bioinformatics (Oxford, England) · 2024Article
- Article
- FinaleMe: Predicting DNA methylation by the fragmentation patterns of plasma cell-free DNA.Nature communications · 2024Article
- Multimodal epigenetic sequencing analysis (MESA) of cell-free DNA for non-invasive colorectal cancer detection.Genome medicine · 2024Article
- cfDNA UniFlow: a unified preprocessing pipeline for cell-free DNA data from liquid biopsies.GigaScience · 2024Article
- FinaleMe: Predicting DNA methylation by the fragmentation patterns of plasma cell-free DNA.bioRxiv : the preprint server for biology · 2024Article
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Authors and funding
13 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Cell-free DNA (cfDNA) analysis has become essential in cancer diagnostics and prenatal testing. We present cfNOMe, a two-in-one method of measuring cfDNA cytosine methylation and nucleosome occupancy in a single assay using non-disruptive enzymatic cytosine conversion and a custom bioinformatic pipeline. We show that enzymatic cytosine conversion better preserves cfDNA fragmentation information than does bisulfite conversion. Whereas previously separate experiments were required to study either epigenetic marking, cfNOMe delivers reliable results for both, enabling more comprehensive and inexpensive epigenetic cfDNA profiling. cfNOMe has the potential to advance biomarker discovery and diagnostic usage in diseases with systemic perturbations of cfDNA composition.
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