ArticleMolecular oncology2021
Characterization of fragment sizes, copy number aberrations and 4-mer end motifs in cell-free DNA of hepatocellular carcinoma for enhanced liquid biopsy-based cancer detection.
Article in Molecular oncology, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 25 papers, 1 of them a synthesis that pooled it.
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Who cites it
25 citing papers in PubMed, 1 synthesis or guideline pooled it, 43 citations in OpenAlex.
- Pooled it
- Towards liquid biopsy-based analysis of antitumour immunity.Nature reviews. Clinical oncology · 2026Review
- Exploring the Predictive Value of Circulating Cell-Free DNA Within a Multiparameter Panel for Hepatocellular Carcinoma Detection.Life (Basel, Switzerland) · 2026Article
- A comprehensive toolkit for analyzing cell-free DNA genomic sequencing data in liquid biopsy.iScience · 2026Article
- Article
- Machine learning-based cfDNA fragmentation profiling using automated capillary electrophoresis for early detection of hepatocellular carcinoma.Communications medicine · 2026Article
- The emerging clinical relevance of cell-free DNA in lupus: from mechanistic insights to therapeutic opportunities.Frontiers in immunology · 2026Review
- Development and validation of predictive models combining cell-Free DNA motifs and protein biomarkers for early detection of esophageal squamous cell carcinoma and precancerous lesion.Biomarker research · 2025Article
- Multimodal analysis of cell-free DNA enhances differentiation of early-stage breast cancer from benign lesions and healthy individuals.BMC biology · 2025Article
- The Current Role of Circulating Cell-Free DNA in the Management of Hepatocellular Carcinoma.Cancers · 2025Review
- Liquid biopsy in hepatocellular carcinoma: Challenges, advances, and clinical implications.Clinical and molecular hepatology · 2025Review
- Cell-free DNA fragmentomics: a universal framework for early cancer detection and monitoring.American journal of clinical and experimental immunology · 2025Article
- Evaluation of a multimodal ctDNA-based assay for detection of aggressive cancers lacking standard screening tests.Future oncology (London, England) · 2025Article
- Aberrant fragmentomic features of circulating cell-free mitochondrial DNA as novel biomarkers for multi-cancer detection.EMBO molecular medicine · 2024Article
- Cell-free DNA end characteristics enable accurate and sensitive cancer diagnosis.Cell reports methods · 2024Article
- DNA methylation and gene expression as determinants of genome-wide cell-free DNA fragmentation.Nature communications · 2024Article
- Review
- Plasma cell-free DNA as a sensitive biomarker for multi-cancer detection and immunotherapy outcomes prediction.Journal of cancer research and clinical oncology · 2024Article
- Non-invasive detection of lymphoma with circulating tumor DNA features and protein tumor markers.Frontiers in oncology · 2024Article
- Plasma cell-free DNA 5-hydroxymethylcytosine and whole-genome sequencing signatures for early detection of esophageal cancer.Cell death & disease · 2023Article
Corrections and comments
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Authors and funding
18 authors at 6 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Circulating cell-free DNA (cfDNA) fragmentomics, which encompasses the measurement of cfDNA length and short nucleotide motifs at the ends of cfDNA molecules, is an emerging field for cancer diagnosis. The utilization of cfDNA fragmentomics for the diagnosis of patients with hepatocellular carcinoma (HCC) caused by hepatitis B virus (HBV) is currently limited. In this study, we utilized whole-genome sequencing data of cfDNA in samples from patients with HCC (n = 197) and HBV (n = 187) to analyze the association of fragment size selection (< 150 bp) with tumor fraction (TF), copy number variation (CNV) alterations and the change in the proportion of 4-mer end motifs in HCC and HBV samples. Our analyses identified five typical CNV markers (i.e. loss in chr1p, chr4q and chr8p, and gain in chr1q and chr8q) in cfDNA with a cumulatively positive rate of ˜ 95% in HCC samples. Size selection (< 150 bp) significantly enhanced TF and CNV signals in HCC samples. Additionally, three 4-mer end motifs (CCCA, CCTG and CCAG) were identified as preferred end motifs in HCC samples. We identified 139 end motifs significantly associated with fragment size that showed similar patterns of associations between patients with HCC and HBV, suggesting that end motifs might be inherently coupled with fragment size by a ubiquitous mechanism. Here we conclude that CNV markers, fragment size selection and end-motif pattern in cfDNA have potential for effective detection of patients with HCC.
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