ArticleCell2016
Cell-free DNA Comprises an In Vivo Nucleosome Footprint that Informs Its Tissues-Of-Origin.
Article in Cell, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. It is linked to 4 registered trials, which are not on this map. Cited by 876 papers, 1 of them a synthesis that pooled it.
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
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
AlloSure Test Characteristics in Immunologically Quiescent and Immunologically Active Heart Transplant Recipients: Does Maximal Cardiopulmonary Stress Testing Prior to Assay Preserve Test Specificity While Enhancing Sensitivity?
A Prospective Study of Plasma Cell-free DNA Fragmentomics for Early Detection of Pancreatic Neuroendocrine Tumors and Differential Diagnosis of Solid Pancreatic Tumors
Multi-center Prospective Validation of the SPOT-MAS Lung Test Using Circulating Tumor DNA for the Detection of Lung Cancer
Pulmonary Hypertension (PH) Biorepository for Translational Research
Who cites it
876 citing papers in PubMed, 1 synthesis or guideline pooled it, 1,480 citations in OpenAlex.
- Precision medicine in diagnosis, prognosis, and disease monitoring of bone and soft tissue sarcomas using liquid biopsy: a systematic review.Archives of orthopaedic and trauma surgery · 2025Pooled it
- Genome-wide variation in cell-free DNA end-motif entropy predicts immunotherapy response in head and neck cancer.The Journal of clinical investigation · 2026Trial
- Inferring tissue origin from cell-free DNA in metastatic cancer.Cancer metastasis reviews · 2026Review
- Decoding coupled epigenetic-fragmentomic signals in circulating cell-free DNA for interpretable cancer diagnosis.Genome medicine · 2026Article
- Reappraising the topology of cell-free fetal DNA in maternal blood toward improved prenatal genetic diagnostics.Science advances · 2026Review
- Circulating tumour DNA and extrachromosomal DNA in prostate and bladder cancer: biology, clinical applications and future perspectives.World journal of urology · 2026Review
- Analysis of cell-free DNA in lymphomas: from sample collection to genotyping and minimal residual disease monitoring.Blood advances · 2026Review
- Review
- Circulating Cell-free DNA as a biomarker for radiation-induced injury: From mechanistic insights to clinical translation.Cancer metastasis reviews · 2026Review
- Article
- Article
- Liquid biopsy in bladder cancer: towards precision oncology.Journal of translational medicine · 2026Review
- Fragmentation patterns of human telomeric chromatin in plasma cfDNA.Nature communications · 2026Article
- From Tumour to Bloodstream: Advancing PD-L1 Testing With Liquid Biopsies in Non-Small Cell Lung Cancer.Cytopathology : official journal of the British Society for Clinical Cytology · 2026Review
- Advancing the applications of liquid biopsies in oncology.Nature reviews. Genetics · 2026Review
- DNAmBERT: a transformer-based model for non-invasive cancer diagnosis using DNA sequence and methylation data.Briefings in bioinformatics · 2026Article
- Biomarkers of partial remission in paediatric type 1 diabetes: β-cell stress, immune-metabolic remodelling, and translational priorities-a narrative review.Translational pediatrics · 2026Review
- Digital PCR in forensic genetics: principles, applications, and challenges.International journal of legal medicine · 2026Review
- Generalizable cancer detection from ultra-low-pass WGS via deep contextual modeling of cfDNA sequences.Molecular biomedicine · 2026Article
- Circulating Tumor DNA-Guided Adjuvant and Post-Adjuvant Therapy in Resected Colorectal Cancer: From Molecular Residual Disease Detection to Proven Clinical Utility.Biomedicines · 2026Review
816 more citing papers are in PubMed but not listed here.
Corrections and comments
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Authors and funding
5 authors at 2 institutions in 1 country.
Funding
Abstract
Nucleosome positioning varies between cell types. By deep sequencing cell-free DNA (cfDNA), isolated from circulating blood plasma, we generated maps of genome-wide in vivo nucleosome occupancy and found that short cfDNA fragments harbor footprints of transcription factors. The cfDNA nucleosome occupancies correlate well with the nuclear architecture, gene structure, and expression observed in cells, suggesting that they could inform the cell type of origin. Nucleosome spacing inferred from cfDNA in healthy individuals correlates most strongly with epigenetic features of lymphoid and myeloid cells, consistent with hematopoietic cell death as the normal source of cfDNA. We build on this observation to show how nucleosome footprints can be used to infer cell types contributing to cfDNA in pathological states such as cancer. Since this strategy does not rely on genetic differences to distinguish between contributing tissues, it may enable the noninvasive monitoring of a much broader set of clinical conditions than currently possible.
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What OpenQuestion holds
Registered trials
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.