ArticleNucleic acids research2018
CancerDetector: ultrasensitive and non-invasive cancer detection at the resolution of individual reads using cell-free DNA methylation sequencing data.
Article in Nucleic acids research, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 125 papers.
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Who cites it
125 citing papers in PubMed, 209 citations in OpenAlex.
- Cell-free DNA Methylation as a Predictive Biomarker of Response to Neoadjuvant Chemotherapy for Patients with Muscle-invasive Bladder Cancer in SWOG S1314.European urology oncology · 2023Trial
- Sensitive detection of tumor mutations from blood and its application to immunotherapy prognosis.Nature communications · 2021Trial
- DNAmBERT: a transformer-based model for non-invasive cancer diagnosis using DNA sequence and methylation data.Briefings in bioinformatics · 2026Article
- Off-Target-Based Tumor Fraction Estimation from Targeted Sequencing Shows Concordance with Orthogonal Methods Across Advanced Solid Tumors.International journal of molecular sciences · 2026Article
- MethylSense: high accuracy machine learning-based diagnostics forJournal of clinical microbiology · 2026Article
- Cell-free DNA methylation biomarkers for the early detection and tumor burden monitoring of gastric cancer.NPJ precision oncology · 2026Article
- Epigenetic Instability-Based Metrics in Cell-Free DNA for Early Cancer Detection.Clinical cancer research : an official journal of the American Association for Cancer Research · 2026Article
- Comprehensive molecular characterization of cfDNA as predictive and monitoring biomarkers in advanced gastric cancer receiving immunotherapy.Journal for immunotherapy of cancer · 2026Article
- Toward the simultaneous detection of multiple diseases with a highly cost-effective cell-free DNA methylome test.Proceedings of the National Academy of Sciences of the United States of America · 2026Article
- Article
- Circulating tumor DNA methylation-based method for noninvasive detection and stage stratification of colorectal tumor.Clinical epigenetics · 2026Article
- Genome-wide classification of tumor-derived reads from bulk long-read sequencing.bioRxiv : the preprint server for biology · 2026Article
- MPCI: A novel metric for quantifying DNA methylation patterns in NGS data.PLoS computational biology · 2026Article
- A computational framework for sensitive tumor detection and accurate subtyping using shallow cell-free DNA methylome sequencing.Genome medicine · 2026Article
- Article
- Circulating neuron-derived cfDNA for blood-based detection of Alzheimer's and other neurodegenerative conditions.Frontiers in neurology · 2026Article
- Review
- 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
- Open chromatin-guided interpretable machine learning reveals cancer-specific chromatin features in cell-free DNA.Communications biology · 2025Article
- Multi-omics data integration for enhanced cancer subtyping via interactive multi-kernel learning.Briefings in bioinformatics · 2025Article
65 more citing papers are in PubMed but not listed here.
Corrections and comments
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Authors and funding
12 authors at 7 institutions in 2 countries.
Funding
Abstract
The detection of tumor-derived cell-free DNA in plasma is one of the most promising directions in cancer diagnosis. The major challenge in such an approach is how to identify the tiny amount of tumor DNAs out of total cell-free DNAs in blood. Here we propose an ultrasensitive cancer detection method, termed 'CancerDetector', using the DNA methylation profiles of cell-free DNAs. The key of our method is to probabilistically model the joint methylation states of multiple adjacent CpG sites on an individual sequencing read, in order to exploit the pervasive nature of DNA methylation for signal amplification. Therefore, CancerDetector can sensitively identify a trace amount of tumor cfDNAs in plasma, at the level of individual reads. We evaluated CancerDetector on the simulated data, and showed a high concordance of the predicted and true tumor fraction. Testing CancerDetector on real plasma data demonstrated its high sensitivity and specificity in detecting tumor cfDNAs. In addition, the predicted tumor fraction showed great consistency with tumor size and survival outcome. Note that all of those testing were performed on sequencing data at low to medium coverage (1× to 10×). Therefore, CancerDetector holds the great potential to detect cancer early and cost-effectively.
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Registered trials
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.