ArticleGenome research2020
Detection and characterization of jagged ends of double-stranded DNA in plasma.
Article in Genome research, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 62 papers.
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Who cites it
62 citing papers in PubMed.
- Cell-free DNA fragmentomics for preeclampsia risk assessment.Nature communications · 2026Article
- Holistic determination of ends of cfDNA molecules.Cell genomics · 2026Article
- End-repair causes methylation underestimation in cell-free DNA sequencing libraries.The journal of liquid biopsy · 2026Article
- The emerging clinical relevance of cell-free DNA in lupus: from mechanistic insights to therapeutic opportunities.Frontiers in immunology · 2026Review
- Liquid biopsies across the cancer care continuum.Nature medicine · 2025Review
- Tracing the tissue origin of cell-free DNA through open chromatin footprint.Communications biology · 2025Article
- Seminal plasma cfDNA fragmentomics landscape delineates male infertility subtypes.Clinical epigenetics · 2025Article
- Circulating Cell-free DNA Fragmentomics Detection and Beyond.Aging and disease · 2025Review
- 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
- Fragment dispersity index analysis of cfDNA fragments reveals chromatin accessibility and enables early cancer detection.Cell reports methods · 2025Article
- Genomic and fragmentomic landscapes of cell-free DNA for early cancer detection.Nature reviews. Cancer · 2025Review
- High tissue specificity of lncRNAs maximises the prediction of tissue of origin of circulating DNA.Scientific reports · 2025Article
- Transformer-based deep learning for accurate detection of multiple base modifications using single molecule real-time sequencing.Communications biology · 2025Article
- DAGIP: alleviating cell-free DNA sequencing biases with optimal transport.Genome biology · 2025Article
- Application of Digital Polymerase Chain Reaction (dPCR) in Non-Invasive Prenatal Testing (NIPT).Biomolecules · 2025Review
- Application of plasma cell-free DNA in screening of advanced colorectal adenoma.European journal of medical research · 2025Review
- Artificial intelligence and machine learning in cell-free-DNA-based diagnostics.Genome research · 2025Review
- Exploration of cfDNA landscape in NIPT and clinical utilities of cfDNA based gene expression inference in prenatal diagnostics.Frontiers in genetics · 2025Article
- LBFextract: Unveiling transcription factor dynamics from liquid biopsy data.Computational and structural biotechnology journal · 2024Article
- Cell-free placental DNA: What do we really know?PLoS genetics · 2024Review
2 more citing papers are in PubMed but not listed here.
Corrections and comments
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Authors and funding
17 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Cell-free DNA in plasma has been used for noninvasive prenatal testing and cancer liquid biopsy. The physical properties of cell-free DNA fragments in plasma, such as fragment sizes and ends, have attracted much recent interest, leading to the emerging field of cell-free DNA fragmentomics. However, one aspect of plasma DNA fragmentomics as to whether double-stranded plasma molecules might carry single-stranded ends, termed a jagged end in this study, remains underexplored. We have developed two approaches for investigating the presence of jagged ends in a plasma DNA pool. These approaches utilized DNA end repair to introduce differential methylation signals between the original sequence and the jagged ends, depending on whether unmethylated or methylated cytosines were used in the DNA end-repair procedure. The majority of plasma DNA molecules (87.8%) were found to bear jagged ends. The jaggedness varied according to plasma DNA fragment sizes and appeared to be in association with nucleosomal patterns. In the plasma of pregnant women, the jaggedness of fetal DNA molecules was higher than that of the maternal counterparts. The jaggedness of plasma DNA correlated with the fetal DNA fraction. Similarly, in the plasma of cancer patients, tumor-derived DNA molecules in patients with hepatocellular carcinoma showed an elevated jaggedness compared with nontumoral DNA. In mouse models, knocking out of the
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