ArticleeLife2022
Unsupervised detection of fragment length signatures of circulating tumor DNA using non-negative matrix factorization.
Article in eLife, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 15 papers.
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Who cites it
15 citing papers in PubMed, 24 citations in OpenAlex.
- Decomposition-driven biomarker identification enhances non-invasive early cancer detection.iScience · 2026Article
- Evolving role of biomarkers beyond prostate‑specific antigen in refining prostate cancer screening: From blood‑based tests to urinary and genetic markers (Review).Molecular medicine reports · 2026Review
- Cell-free DNA size deconvolution resolves nucleosomal origins and reveals tumor-associated fragmentomic alterations.Nature communications · 2026Article
- Nanopore-based consensus sequencing enables accurate multimodal tumor cell-free DNA profiling.Genome research · 2025Article
- A perspective review on the systematic implementation of ctDNA in phase I clinical trial drug development.Journal of experimental & clinical cancer research : CR · 2025Review
- A deep-learning model for quantifying circulating tumour DNA from the density distribution of DNA-fragment lengths.Nature biomedical engineering · 2025Article
- Artificial intelligence and machine learning in cell-free-DNA-based diagnostics.Genome research · 2025Review
- Advances of nanopore direct sequencing technology and bioinformatics analysis for cell-free DNA detection and its clinical applications in cancer liquid biopsy.Frontiers in molecular biosciences · 2025Review
- Early Detection of Malignant and Premalignant Peripheral Nerve Tumors Using Cell-Free DNA Fragmentomics.Clinical cancer research : an official journal of the American Association for Cancer Research · 2024Article
- Early Changes in Tumor-Naive Cell-Free Methylomes and Fragmentomes Predict Outcomes in Pembrolizumab-Treated Solid Tumors.Cancer discovery · 2024Article
- Ultrasensitive plasma-based monitoring of tumor burden using machine-learning-guided signal enrichment.Nature medicine · 2024Article
- Circulating tumor DNA in liquid biopsy: Current diagnostic limitation.World journal of gastroenterology · 2024Article
- Early detection of malignant and pre-malignant peripheral nerve tumors using cell-free DNA fragmentomics.medRxiv : the preprint server for health sciences · 2024Article
- Cancer signature ensemble integrating cfDNA methylation, copy number, and fragmentation facilitates multi-cancer early detection.Experimental & molecular medicine · 2023Article
- Cell-Free DNA Fragmentomics: The Novel Promising Biomarker.International journal of molecular sciences · 2023Review
Corrections and comments
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Authors and funding
11 authors at 4 institutions in 3 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Sequencing of cell-free DNA (cfDNA) is currently being used to detect cancer by searching both for mutational and non-mutational alterations. Recent work has shown that the length distribution of cfDNA fragments from a cancer patient can inform tumor load and type. Here, we propose non-negative matrix factorization (NMF) of fragment length distributions as a novel and completely unsupervised method for studying fragment length patterns in cfDNA. Using shallow whole-genome sequencing (sWGS) of cfDNA from a cohort of patients with metastatic castration-resistant prostate cancer (mCRPC), we demonstrate how NMF accurately infers the true tumor fragment length distribution as an NMF component - and that the sample weights of this component correlate with ctDNA levels (
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Registered trials
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