ArticleNature communications2021
Comprehensive cell type decomposition of circulating cell-free DNA with CelFiE.
Article in Nature communications, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 47 papers.
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Who cites it
47 citing papers in PubMed.
- Exercise intensity and training alter the innate immune cell type and chromosomal origins of circulating cell-free DNA in humans.Proceedings of the National Academy of Sciences of the United States of America · 2025Trial
- Cell-free DNA methylation markers in the diagnosis of hepatitis B virus-related- hepatocellular carcinoma: a review.Molecular biology reports · 2026Review
- Strategic Amyotrophic Lateral Sclerosis Australia-Systems Genomics Consortium (SALSA-SGC): cohort profile.BMJ open · 2026Article
- Multimodal analysis of cell-free DNA identifies epigenetic biomarkers for amyotrophic lateral sclerosis diagnosis and progression.The Journal of clinical investigation · 2026Article
- Peripheral Neutrophil Activation and Extracellular Trap Formation in Amyotrophic Lateral Sclerosis.Annals of clinical and translational neurology · 2026Article
- Enriched methylomes of low-input and fragmented DNA using fragment ligation EXclusive methylation sequencing.Nucleic acids research · 2026Article
- Multimodal analysis of cell-free DNA identifies epigenetic biomarkers for amyotrophic lateral sclerosis diagnosis and progression.bioRxiv : the preprint server for biology · 2026Article
- Article
- Cell-Specific DNA Methylation Markers in Plasma cfDNA Reveal Diagnostic Potential for Head and Neck Cancer.Journal of Cancer · 2026Article
- Cell-free DNA in sepsis: from molecular insights to clinical management.Military Medical Research · 2025Review
- Cell type inference in cell-free nucleic acid liquid biopsy.Nature biotechnology · 2025Review
- Epigenetic profiles of tissue informative CpGs inform ALS disease status and progression.Genome medicine · 2025Article
- BLEND: probabilistic cellular deconvolution with individualized single-cell reference integration.Genome biology · 2025Article
- Read-level DNA methylation deconvolution enhances circulating tumor DNA detection.Briefings in bioinformatics · 2025Article
- Review
- Examining cellular heterogeneity in human DNA methylation studies: Overview and recommendations.STAR protocols · 2025Review
- Diagnostic role of circulating cell-free DNA in schizophrenia and neuro-degenerative disorders.Biomarkers in medicine · 2025Review
- Whole-genome bisulfite sequencing of cell-free DNA unveils age-dependent and ALS-associated methylation alterations.Cell & bioscience · 2025Article
- Evaluation of a biomarker for amyotrophic lateral sclerosis derived from a hypomethylated DNA signature of human motor neurons.BMC medical genomics · 2025Article
- Circulating Cell-Free DNA in Metabolic Diseases.Journal of the Endocrine Society · 2025Review
Corrections and comments
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Authors and funding
9 authors.
Funding
Abstract
Circulating cell-free DNA (cfDNA) in the bloodstream originates from dying cells and is a promising noninvasive biomarker for cell death. Here, we propose an algorithm, CelFiE, to accurately estimate the relative abundances of cell types and tissues contributing to cfDNA from epigenetic cfDNA sequencing. In contrast to previous work, CelFiE accommodates low coverage data, does not require CpG site curation, and estimates contributions from multiple unknown cell types that are not available in external reference data. In simulations, CelFiE accurately estimates known and unknown cell type proportions from low coverage and noisy cfDNA mixtures, including from cell types composing less than 1% of the total mixture. When used in two clinically-relevant situations, CelFiE correctly estimates a large placenta component in pregnant women, and an elevated skeletal muscle component in amyotrophic lateral sclerosis (ALS) patients, consistent with the occurrence of muscle wasting typical in these patients. Together, these results show how CelFiE could be a useful tool for biomarker discovery and monitoring the progression of degenerative disease.
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