ArticleNature communications2023
Multimodal analysis of cell-free DNA whole-methylome sequencing for cancer detection and localization.
Article in Nature communications, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 60 papers, 2 of them syntheses that pooled it.
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Who cites it
60 citing papers in PubMed, 2 syntheses or guidelines pooled it.
- Diagnostic performance of SHOX2 and RASSF1A gene methylation assays in malignant pleural effusion: A systematic review and meta-analysis.Cancer cytopathology · 2025Pooled it
- Value of Machine Learning Models for Cell-Free DNA-Based Multi-Cancer Early Detection: A Systematic Review and Meta-Analysis.Technology in cancer research & treatmentPooled it
- Trial
- Decoding coupled epigenetic-fragmentomic signals in circulating cell-free DNA for interpretable cancer diagnosis.Genome medicine · 2026Article
- Review
- DNAmBERT: a transformer-based model for non-invasive cancer diagnosis using DNA sequence and methylation data.Briefings in bioinformatics · 2026Article
- Multidimensional 5-hydroxymethylcytosine features in cell-free DNA enable the detection, staging and subtyping of pancreatic ductal adenocarcinoma.Biomarker research · 2026Article
- DNA Methylation as a Programmable Information Layer: From Molecular Marks to Disease State Engineering.International journal of molecular sciences · 2026Review
- Multifeature sequencing-based liquid biopsy for cancer diagnosis and monitoring.Genome medicine · 2026Review
- Non-Invasive Diagnosis of Early Breast Cancer: Current and Emerging Liquid Biopsy Biomarkers.Cancers · 2026Review
- Epigenomic modifications define chromatin states to regulate cell-free DNA fragmentomics.Nature communications · 2026Article
- Integration of breaking-point transition probabilities and specific open chromatin region features for early cancer detection.Cell communication and signaling : CCS · 2026Article
- cfMethDB: A Comprehensive cfDNA Methylation Data Resource for Cancer Biomarkers.Genomics, proteomics & bioinformatics · 2026Article
- TiSMeD: A tissue-specific methylation and expression database for biomarker and translational applications.Molecular therapy. Nucleic acids · 2026Article
- Access to diagnosis using liquid biopsy (ADLiB): Identifying lymphoma in a tuberculosis-endemic setting.HemaSphere · 2026Article
- Pan-cancer differentially methylated regions are promising biomarkers for non-invasive diagnosis in multiple cancers.iScience · 2026Article
- From Spatial Epigenomes to Clinical Diagnostics: Integrative Methylomics Across Scales and Modalities.International journal of molecular sciences · 2026Review
- Beyond Circulating Tumor DNA for Efficacy: Can We Use Cell-Free DNA to Detect and Monitor Toxicity Signals?JCO precision oncology · 2026Article
- cfDECOR: a novel approach for estimating cell type contributions to cfDNA based on chromatin accessibility patterns.Scientific reports · 2026Article
- Artificial intelligence-powered liquid biopsy in cancer: a paradigm shift in cancer detection and personalized care.Cancer cell international · 2026Review
Corrections and comments
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Authors and funding
25 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Multimodal epigenetic characterization of cell-free DNA (cfDNA) could improve the performance of blood-based early cancer detection. However, integrative profiling of cfDNA methylome and fragmentome has been technologically challenging. Here, we adapt an enzyme-mediated methylation sequencing method for comprehensive analysis of genome-wide cfDNA methylation, fragmentation, and copy number alteration (CNA) characteristics for enhanced cancer detection. We apply this method to plasma samples of 497 healthy controls and 780 patients of seven cancer types and develop an ensemble classifier by incorporating methylation, fragmentation, and CNA features. In the test cohort, our approach achieves an area under the curve value of 0.966 for overall cancer detection. Detection sensitivity for early-stage patients achieves 73% at 99% specificity. Finally, we demonstrate the feasibility to accurately localize the origin of cancer signals with combined methylation and fragmentation profiling of tissue-specific accessible chromatin regions. Overall, this proof-of-concept study provides a technical platform to utilize multimodal cfDNA features for improved cancer detection.
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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.