ArticleGenome medicine2022
CRAG: de novo characterization of cell-free DNA fragmentation hotspots in plasma whole-genome sequencing.
Article in Genome medicine, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 22 papers.
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Who cites it
22 citing papers in PubMed, 28 citations in OpenAlex.
- Decoding coupled epigenetic-fragmentomic signals in circulating cell-free DNA for interpretable cancer diagnosis.Genome medicine · 2026Article
- Epigenomic modifications define chromatin states to regulate cell-free DNA fragmentomics.Nature communications · 2026Article
- Circulating DNA reveals nucleosome occupancy patterns that are associated with nucleosome-DNA affinity and are affected in cancer.Genome medicine · 2026Article
- A comprehensive toolkit for analyzing cell-free DNA genomic sequencing data in liquid biopsy.iScience · 2026Article
- cfDECOR: a novel approach for estimating cell type contributions to cfDNA based on chromatin accessibility patterns.Scientific reports · 2026Article
- Early cancer detection via multi-omics cfDNA fragmentation using early-late fusion neural network with sample-modality evaluation.Briefings in bioinformatics · 2025Article
- Circulating Cell-free DNA Fragmentomics Detection and Beyond.Aging and disease · 2025Review
- Promises and pitfalls of multi-cancer early detection using liquid biopsy tests.Nature reviews. Clinical oncology · 2025Review
- Fragment dispersity index analysis of cfDNA fragments reveals chromatin accessibility and enables early cancer detection.Cell reports methods · 2025Article
- GUIDE: a prospective cohort study for blood-based early detection of gastrointestinal cancers using targeted DNA methylation and fragmentomics sequencing.Molecular cancer · 2025Observational
- Genomic and fragmentomic landscapes of cell-free DNA for early cancer detection.Nature reviews. Cancer · 2025Review
- Multi-cancer early detection tests: Attributes for clinical implementation.Cancer biomarkers : section A of Disease markers · 2025Article
- FinaleToolkit: accelerating cell-free DNA fragmentation analysis with a high-speed computational toolkit.Bioinformatics advances · 2025Article
- Dissecting cell-free DNA fragmentation variation in tumors using cell line-derived xenograft mouse.PloS one · 2025Article
- Transformer-based representation learning and multiple-instance learning for cancer diagnosis exclusively from raw sequencing fragments of bisulfite-treated plasma cell-free DNA.Molecular oncology · 2024Article
- Extracting regulatory active chromatin footprint from cell-free DNA.Communications biology · 2024Article
- Systematically Evaluating Cell-Free DNA Fragmentation Patterns for Cancer Diagnosis and Enhanced Cancer Detection via Integrating Multiple Fragmentation Patterns.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2024Article
- Cell type signatures in cell-free DNA fragmentation profiles reveal disease biology.Nature communications · 2024Article
- Cell-free DNA fragmentomics and second malignant neoplasm risk in patients with PTEN hamartoma tumor syndrome.Cell reports. Medicine · 2024Article
- Cancer signature ensemble integrating cfDNA methylation, copy number, and fragmentation facilitates multi-cancer early detection.Experimental & molecular medicine · 2023Article
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Authors and funding
6 authors at 2 institutions in 2 countries.
Funding
Abstract
The fine-scale cell-free DNA fragmentation patterns in early-stage cancers are poorly understood. We developed a de novo approach to characterize the cell-free DNA fragmentation hotspots from plasma whole-genome sequencing. Hotspots are enriched in open chromatin regions, and, interestingly, 3'end of transposons. Hotspots showed global hypo-fragmentation in early-stage liver cancers and are associated with genes involved in the initiation of hepatocellular carcinoma and associated with cancer stem cells. The hotspots varied across multiple early-stage cancers and demonstrated high performance for the diagnosis and identification of tissue-of-origin in early-stage cancers. We further validated the performance with a small number of independent case-control-matched early-stage cancer samples.
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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.