ArticleJCI insight2021
Circulating nuclear DNA structural features, origins, and complete size profile revealed by fragmentomics.
Article in JCI insight, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 59 papers.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
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.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
59 citing papers in PubMed, 97 citations in OpenAlex.
- Cell-free DNA dynamics and progression-free survival in metastatic gastroesophageal adenocarcinoma: insights from the REGIRI-PRODIGE 58 ancillary study.NPJ precision oncology · 2026Article
- Cell-free DNA size deconvolution resolves nucleosomal origins and reveals tumor-associated fragmentomic alterations.Nature communications · 2026Article
- Review
- fRagmentomics: an R package for integrating cell-free DNA fragment features with mutational status to support liquid biopsy interpretation.Bioinformatics (Oxford, England) · 2026Article
- Exploring the mechanism of action of abemaciclib in breast cancer through circulating chromatin fragments.Communications medicine · 2026Article
- Non-invasive diagnosis of invasive fungal disease with cell-free DNA PCR.Journal of clinical microbiology · 2026Review
- The emerging clinical relevance of cell-free DNA in lupus: from mechanistic insights to therapeutic opportunities.Frontiers in immunology · 2026Review
- Neutrophil extracellular traps and acute kidney injury: a narrative review.Frontiers in immunology · 2026Review
- Epigenetic profiling of circulating cell-free DNA for early detection and minimal residual disease assessment in lung cancer: a focus on DNA methylation.Frontiers in oncology · 2026Review
- The Clinical Utility of Cell-Free DNA in Brain Tumor Management: A Comprehensive Review.Journal of molecular neuroscience : MN · 2025Review
- Bacterial cell-free DNA profiling reveals the co-elevation of multiple bacteria in newborn foals with suspected sepsis.iScience · 2025Article
- Liquid biopsies across the cancer care continuum.Nature medicine · 2025Review
- Urine cf-nucleosomes: A non-invasive window into human physiology and disease.Cell genomics · 2025Article
- cfDNA Key genomic markers in HCV-Induced hepatocellular carcinoma in Egyptian patients.Journal, genetic engineering & biotechnology · 2025Article
- Paired plus-minus sequencing is an ultra-high throughput and accurate method for dual strand sequencing of DNA molecules.bioRxiv : the preprint server for biology · 2025Article
- Pre-Amplification of Cell-Free DNA: Balancing Amplification Errors with Enhanced Sensitivity.Biomolecules · 2025Article
- Genomic and fragmentomic landscapes of cell-free DNA for early cancer detection.Nature reviews. Cancer · 2025Review
- Cell-Free DNA: Features and Attributes Shaping the Next Frontier in Liquid Biopsy.Molecular diagnosis & therapy · 2025Review
- Clinical application of minimal residual disease detection by ctDNA testing in non-small cell lung cancer: a narrative review.Translational lung cancer research · 2025Review
- Cell-free epigenomes enhanced fragmentomics-based model for early detection of lung cancer.Clinical and translational medicine · 2025Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
9 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
To unequivocally address their unresolved intimate structures in blood, we scrutinized the size distribution of circulating cell-free DNA (cfDNA) using whole-genome sequencing (WGS) from both double- and single-strand DNA library preparations (DSP and SSP, n = 7) and using quantitative PCR (Q-PCR, n = 116). The size profile in healthy individuals was remarkably homogenous when using DSP sequencing or SSP sequencing. CfDNA size profile had a characteristic nucleosome fragmentation pattern. Overall, our data indicate that the proportion of cfDNA inserted in mono-nucleosomes, di-nucleosomes, and chromatin of higher molecular size (>1000 bp) can be estimated as 67.5% to 80%, 9.4% to 11.5%, and 8.5% to 21.0%, respectively. Although DNA on single chromatosomes or mono-nucleosomes is detectable, our data revealed that cfDNA is highly nicked (97%-98%) on those structures, which appear to be subjected to continuous nuclease activity in the bloodstream. Fragments analysis allows the distinction of cfDNA of different origins: first, cfDNA size profile analysis may be useful in cfDNA extract quality control; second, subtle but reliable differences between metastatic colorectal cancer patients and healthy individuals vary with the proportion of malignant cell-derived cfDNA in plasma extracts, pointing to a higher degree of cfDNA fragmentation and nuclease activity in samples with high malignant cell cfDNA content.
Indexed as
Identifiers
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.