ArticleNature communications2024
Cell type signatures in cell-free DNA fragmentation profiles reveal disease biology.
Article in Nature communications, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 56 papers.
What it found
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Who cites it
56 citing papers in PubMed.
- ctDNA and tumor-based biomarkers of giredestrant response in acelERA breast cancer.Nature communications · 2026Trial
- Reappraising the topology of cell-free fetal DNA in maternal blood toward improved prenatal genetic diagnostics.Science advances · 2026Review
- Circulating Cell-free DNA as a biomarker for radiation-induced injury: From mechanistic insights to clinical translation.Cancer metastasis reviews · 2026Review
- Advancing the applications of liquid biopsies in oncology.Nature reviews. Genetics · 2026Review
- First-trimester multi-modal cell-free DNA analysis for prediction of preterm and term preeclampsia.AJOG global reports · 2026Article
- Circulating DNA reveals nucleosome occupancy patterns that are associated with nucleosome-DNA affinity and are affected in cancer.Genome medicine · 2026Article
- Detection of recurrence of HPV-driven oropharyngeal cancer by HPV cell-free DNA.Scientific reports · 2026Article
- MethylSense: high accuracy machine learning-based diagnostics forJournal of clinical microbiology · 2026Article
- Frequency-Domain Transformation of cfDNA End-Motif Profiles Enhances Robust Cancer Detection.Genes · 2026Article
- Engineered M2 macrophage-derived vesicles deliver DNase I for cfDNA clearance and multi-organ protection in sepsis.International journal of pharmaceutics: X · 2026Article
- Biological basis and clinical translation prospects of circulating cell-free DNA in precision management of breast cancer (Review).Oncology letters · 2026Review
- From Spatial Epigenomes to Clinical Diagnostics: Integrative Methylomics Across Scales and Modalities.International journal of molecular sciences · 2026Review
- cfDECOR: a novel approach for estimating cell type contributions to cfDNA based on chromatin accessibility patterns.Scientific reports · 2026Article
- Longitudinal cell-free DNA methylome and fragmentome profiles in health uncover signatures of cell type and demographic origin.Genome medicine · 2026Article
- Cell-Based and Cell-Free Non-Invasive Prenatal Analysis of Preeclampsia: An Updated Review of Liquid Biopsy.Biomedicines · 2026Review
- Cell-Free DNA-Derived Immune Cell Ratios Uncover Cancer-Associated Systemic Changes.Cancer research communications · 2026Article
- Liquid biopsy epigenetics: establishing a molecular profile based on cell-free DNA.Molecular oncology · 2026Review
- A computational framework for sensitive tumor detection and accurate subtyping using shallow cell-free DNA methylome sequencing.Genome medicine · 2026Article
- Cell-free DNA fragmentation signatures link cancer and autoimmunity.Nature reviews. Rheumatology · 2026Article
- Leveraging cfDNA fragmentomic features for the early detection of colorectal cancer.Frontiers in immunology · 2026Article
Corrections and comments
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Authors and funding
18 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Circulating cell-free DNA (cfDNA) fragments have characteristics that are specific to the cell types that release them. Current methods for cfDNA deconvolution typically use disease tailored marker selection in a limited number of bulk tissues or cell lines. Here, we utilize single cell transcriptome data as a comprehensive cellular reference set for disease-agnostic cfDNA cell-of-origin analysis. We correlate cfDNA-inferred nucleosome spacing with gene expression to rank the relative contribution of over 490 cell types to plasma cfDNA. In 744 healthy individuals and patients, we uncover cell type signatures in support of emerging disease paradigms in oncology and prenatal care. We train predictive models that can differentiate patients with colorectal cancer (84.7%), early-stage breast cancer (90.1%), multiple myeloma (AUC 95.0%), and preeclampsia (88.3%) from matched controls. Importantly, our approach performs well in ultra-low coverage cfDNA datasets and can be readily transferred to diverse clinical settings for the expansion of liquid biopsy.
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.