ArticleScience translational medicine2023
Genome-wide analysis of aberrant position and sequence of plasma DNA fragment ends in patients with cancer.
Article in Science translational medicine, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 42 papers.
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Who cites it
42 citing papers in PubMed.
- A cfDNA fragmentomics classifier for noninvasive differentiation of benign and malignant renal masses.Molecular biomedicine · 2026Article
- Generalizable cancer detection from ultra-low-pass WGS via deep contextual modeling of cfDNA sequences.Molecular biomedicine · 2026Article
- A scalable deep-learning framework for cancer detection using cell-free DNA shallow whole-genome sequencing.Science advances · 2026Article
- Exploring per-base quality scores as a surrogate marker of cell-free DNA fragmentome.Briefings in bioinformatics · 2026Article
- Enriched methylomes of low-input and fragmented DNA using fragment ligation EXclusive methylation sequencing.Nucleic acids research · 2026Article
- Long-read sequencing identifies aberrant fragmentation patterns linked to elevated cell-free DNA levels in cancer.Genome biology · 2026Article
- Holistic determination of ends of cfDNA molecules.Cell genomics · 2026Article
- Liquid biopsy epigenetics: establishing a molecular profile based on cell-free DNA.Molecular oncology · 2026Review
- Comparative Analysis of Cell-Free DNA Fragmentation Patterns in Canines with Sarcoma and Tumor-Free Canines and Humans.Cancer research communications · 2026Article
- Detection of primary cancer types via fragment size selection in circulating cell-free extrachromosomal circular DNA.Genome medicine · 2026Article
- Liquid biopsy, multi-cancer early detection, and artificial intelligence: new frontiers in cancer screening from a technological and immunological perspective.Frontiers in immunology · 2026Review
- Leveraging cfDNA fragmentomic features for the early detection of colorectal cancer.Frontiers in immunology · 2026Article
- Cross-dataset pan-cancer detection by correlating cell-free DNA fragment coverage with open chromatin sites across cell types.Nature communications · 2025Article
- Genomics and Epigenomics Approaches for the Quantification of Circulating Tumor DNA in Liquid Biopsy: Relevance of a Multimodal Strategy.International journal of molecular sciences · 2025Review
- Longitudinal profiling of hormone receptor positive, HER2 negative metastatic breast cancer through droplet digital PCR-based circulating tumor DNA fragmentomics.Translational oncology · 2025Article
- Fragmentation signatures in cancer patients resemble those of patients with vascular or autoimmune diseases.Proceedings of the National Academy of Sciences of the United States of America · 2025Article
- Minimizing and quantifying uncertainty in AI-informed decisions: Applications in medicine.Proceedings of the National Academy of Sciences of the United States of America · 2025Article
- A standardized framework for robust fragmentomic feature extraction from cell-free DNA sequencing data.Genome biology · 2025Article
- Cost-effective shallow genome-wide sequencing for profiling plasma cfDNA signatures to enhance lung cancer detection.Future oncology (London, England) · 2025Article
- Genomic and fragmentomic landscapes of cell-free DNA for early cancer detection.Nature reviews. Cancer · 2025Review
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22 authors.
Funding
Abstract
Genome-wide fragmentation patterns in cell-free DNA (cfDNA) in plasma are strongly influenced by cellular origin due to variation in chromatin accessibility across cell types. Such differences between healthy and cancer cells provide the opportunity for development of novel cancer diagnostics. Here, we investigated whether analysis of cfDNA fragment end positions and their surrounding DNA sequences reveals the presence of tumor-derived DNA in blood. We performed genome-wide analysis of cfDNA from 521 samples and analyzed sequencing data from an additional 2147 samples, including healthy individuals and patients with 11 different cancer types. We developed a metric based on genome-wide differences in fragment positioning, weighted by fragment length and GC content [information-weighted fraction of aberrant fragments (iwFAF)]. We observed that iwFAF strongly correlated with tumor fraction, was higher for DNA fragments carrying somatic mutations, and was higher within genomic regions affected by copy number amplifications. We also calculated sample-level means of nucleotide frequencies observed at genomic positions spanning fragment ends. Using a combination of iwFAF and nine nucleotide frequencies from three positions surrounding fragment ends, we developed a machine learning model to differentiate healthy individuals from patients with cancer. We observed an area under the receiver operative characteristic curve (AUC) of 0.91 for detection of cancer at any stage and an AUC of 0.87 for detection of stage I cancer. Our findings remained robust with as few as 1 million fragments analyzed per sample, demonstrating that analysis of fragment ends can become a cost-effective and accessible approach for cancer detection and monitoring.
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