ArticleBMC genomics2015
Non-random fragmentation patterns in circulating cell-free DNA reflect epigenetic regulation.
Article in BMC genomics, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 123 papers.
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Who cites it
123 citing papers in PubMed, 223 citations in OpenAlex.
- A cfDNA fragmentomics classifier for noninvasive differentiation of benign and malignant renal masses.Molecular biomedicine · 2026Article
- Non-Invasive Diagnosis of Early Breast Cancer: Current and Emerging Liquid Biopsy Biomarkers.Cancers · 2026Review
- Off-Target-Based Tumor Fraction Estimation from Targeted Sequencing Shows Concordance with Orthogonal Methods Across Advanced Solid Tumors.International journal of molecular sciences · 2026Article
- Circulating Tumour DNA and Extracellular Vesicle-Associated DNA as Biomarkers for Cancer Detection: A Systematic Review and Meta-Analysis.Journal of extracellular biology · 2026Article
- Exploring the mechanism of action of abemaciclib in breast cancer through circulating chromatin fragments.Communications medicine · 2026Article
- Deep learning-based non-invasive profiling of tumor transcriptomes from cell-free DNA for precision oncology.bioRxiv : the preprint server for biology · 2026Article
- A pan-cancer compendium of 1,294 plasma cell-free DNA methylomes and fragmentomes enabling multicancer detection.Nature cancer · 2026Article
- Cell-Free DNA (cfDNA), Its Applications in Cancer Diagnosis and Monitoring, and Its Potential Role in Regulating Cancer Metabolism.Advances in experimental medicine and biology · 2026Review
- Circulating extracellular vesicle DNA (EV-DNA) and cell-free DNA in ovarian cancer: pathological relevance and diagnostic applications.Extracellular vesicles and circulating nucleic acids · 2026Review
- DeepFRAG: a method for cancer detection based on DNA fragmentomics and deep learning.Bioinformatics advances · 2026Article
- Liquid biopsies across the cancer care continuum.Nature medicine · 2025Review
- RECAP-seq: restriction enzyme-based CpG-methylated fragment amplification for early cancer detection.Scientific reports · 2025Article
- A chromatin fiber model explains cell-free DNA fragmentation signatures of active regulatory elements.bioRxiv : the preprint server for biology · 2025Article
- Engineered crRNA Drives RPA-T7-CRISPR/Cas14a Cascade for Ultrasensitive Detection of ctDNA PIK3CA H1047R.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2025Article
- Article
- Analysis of cfDNA fragmentomics metrics and commercial targeted sequencing panels.Nature communications · 2025Article
- Urine cf-nucleosomes: A non-invasive window into human physiology and disease.Cell genomics · 2025Article
- Circulating Cell-free DNA Fragmentomics Detection and Beyond.Aging and disease · 2025Review
- Characterization of Ultra-Short plasma Cell-Free DNA in maternal blood and its preliminary potential as a screening marker for preeclampsia.Molecular medicine (Cambridge, Mass.) · 2025Article
- Evaluation of automatic cell free DNA extraction metrics using different blood collection tubes.Scientific reports · 2025Article
63 more citing papers are in PubMed but not listed here.
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Authors and funding
5 authors at 3 institutions in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundThe assessment of cell-free circulating DNA fragments, also known as a "liquid biopsy" of the patient's plasma, is an important source for the discovery and subsequent non-invasive monitoring of cancer and other pathological conditions. Although the nucleosome-guided fragmentation patterns of cell-free DNA (cfDNA) have not yet been studied in detail, non-random representation of cfDNA sequencies may reflect chromatin features in the tissue of origin at gene-regulation level.
resultsIn this study, we investigated the association between epigenetic landscapes of human tissues evident in the patterns of cfDNA in plasma by deep sequencing of human cfDNA samples. We have demonstrated that baseline characteristics of cfDNA fragmentation pattern are in concordance with the ones corresponding to cell lines-derived. To identify the loci differentially represented in cfDNA fragment, we mapped the transcription start sites within the sequenced cfDNA fragments and tested for association of these genomic coordinates with the relative strength and the patterns of gene expressions. Preselected sets of house-keeping and tissue specific genes were used as models for actively expressed and silenced genes. Developed measure of gene regulation was able to differentiate these two sets based on sequencing coverage near gene transcription start site.
conclusionExperimental outcomes suggest that cfDNA retains characteristics previously noted in genome-wide analysis of chromatin structure, in particular, in MNase-seq assays. Thus far the analysis of the DNA fragmentation pattern may aid further developing of cfDNA based biomarkers for a variety of human conditions.
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