ArticleCommunications biology2025
Tracing the tissue origin of cell-free DNA through open chromatin footprint.
Article in Communications biology, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 4 papers.
What it found
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
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Who cites it
4 citing papers in PubMed.
- Inferring tissue origin from cell-free DNA in metastatic cancer.Cancer metastasis reviews · 2026Review
- Circulating Cell-free DNA as a biomarker for radiation-induced injury: From mechanistic insights to clinical translation.Cancer metastasis reviews · 2026Review
- Low-Pass Nanopore Sequencing of Plasma cfDNA Reveals Fragmentomic, Epigenomic, and Age-Associated Signatures Under Ultra-Low-Coverage Conditions.International journal of molecular sciences · 2026Article
- DADA-EV: domain-adaptive diffusion autoencoder for estimating tissue- and cell-type-specific origin in extracellular vesicle transcriptomes.Briefings in bioinformatics · 2026Article
Corrections and comments
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Authors and funding
10 authors.
Funding
Abstract
Plasma cell-free DNA (cfDNA) is a promising biomarker for liquid biopsy, essential for diagnosing and monitoring diseases. Current methods for estimating tissue contributions primarily rely on methylation markers, which can damage cfDNA, limiting clinical use. While research shows cfDNA coverage near transcription start sites (TSS) of actively transcribed genes decreases due to open chromatin, a comprehensive cross-tissue atlas has been lacking. Here, we identify 2549 tissue-specific, highly expressed genes across 12 human tissues and develop the Tissue Contribution Index (TCI) to quantify tissue contributions to plasma cfDNA using TSS coverage. TCI is validated in cfDNA origin models, including pregnant women and transplant recipients, demonstrating high accuracy. We establish reference intervals using plasma cfDNA from 460 healthy individuals and explore TCI's diagnostic utility in monitoring tissue damage and predicting outcomes. This study presents a simple, cost-effective method for tissue deconvolution of cfDNA, advancing liquid biopsy for disease detection and personalized medicine.
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Registered trials
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