ArticleGenome medicine2024
Multimodal epigenetic sequencing analysis (MESA) of cell-free DNA for non-invasive colorectal cancer detection.
Article in Genome medicine, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 20 papers.
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20 citing papers in PubMed, 18 citations in OpenAlex.
- DNAmBERT: a transformer-based model for non-invasive cancer diagnosis using DNA sequence and methylation data.Briefings in bioinformatics · 2026Article
- Multifeature sequencing-based liquid biopsy for cancer diagnosis and monitoring.Genome medicine · 2026Review
- Integration of breaking-point transition probabilities and specific open chromatin region features for early cancer detection.Cell communication and signaling : CCS · 2026Article
- Multimodal analysis of cell-free DNA identifies epigenetic biomarkers for amyotrophic lateral sclerosis diagnosis and progression.The Journal of clinical investigation · 2026Article
- A comprehensive toolkit for analyzing cell-free DNA genomic sequencing data in liquid biopsy.iScience · 2026Article
- From Spatial Epigenomes to Clinical Diagnostics: Integrative Methylomics Across Scales and Modalities.International journal of molecular sciences · 2026Review
- Multimodal analysis of cell-free DNA identifies epigenetic biomarkers for amyotrophic lateral sclerosis diagnosis and progression.bioRxiv : the preprint server for biology · 2026Article
- Global research trends in diagnostic biomarkers for colorectal cancer: a bibliometric and visualization analysis.Annals of medicine and surgery (2012) · 2026Article
- Harnessing viral footprints in circulating free DNA (cfDNA) for early cancer detection: A focus on liquid-biopsy-based screening.International journal of cancer · 2026Review
- Article
- Early cancer detection via multi-omics cfDNA fragmentation using early-late fusion neural network with sample-modality evaluation.Briefings in bioinformatics · 2025Article
- GUIDE: a prospective cohort study for blood-based early detection of gastrointestinal cancers using targeted DNA methylation and fragmentomics sequencing.Molecular cancer · 2025Observational
- Comparison of enzymatic and bisulfite conversion of circulating cell-free tumor DNA for DNA methylation analyses.Clinical epigenetics · 2025Article
- Artificial intelligence and machine learning in cell-free-DNA-based diagnostics.Genome research · 2025Review
- Circulating tumor DNA methylation detection as biomarker and its application in tumor liquid biopsy: advances and challenges.MedComm · 2024Review
- Methyltransferase DNMT3B promotes colorectal cancer cell proliferation by inhibiting PLCG2.Acta biochimica et biophysica Sinica · 2024Article
- Immune-related gene methylation prognostic instrument for stratification and targeted treatment of ovarian cancer patients toward advanced 3PM approach.The EPMA journal · 2024Article
- Circulating tumor DNA in liquid biopsy: Current diagnostic limitation.World journal of gastroenterology · 2024Article
- Multimodal epigenetic sequencing analysis (MESA) of cell-free DNA for non-invasive colorectal cancer detection.Genome medicine · 2024Article
- Advancements in the clinical application of gene methylation for early cancer detection.Frontiers in epigenetics and epigenomics · 2024Review
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Authors and funding
15 authors at 3 institutions in 2 countries.
Funding
Abstract
backgroundDetecting human cancers through cell-free DNA (cfDNA) in blood is a sensitive and non-invasive option. However, capturing multiple forms of epigenetic information remains a technical and financial challenge.
methodsTo address this, we developed multimodal epigenetic sequencing analysis (MESA), a flexible and sensitive approach to capturing and integrating a diverse range of epigenetic features in cfDNA using a single experimental assay, i.e., non-disruptive bisulfite-free methylation sequencing, such as Enzymatic Methyl-seq. MESA enables simultaneous inference of four epigenetic modalities: cfDNA methylation, nucleosome occupancy, nucleosome fuzziness, and windowed protection score for regions surrounding gene promoters and polyadenylation sites.
resultsWhen applied to 690 cfDNA samples from 3 colorectal cancer clinical cohorts, MESA's novel modalities, which include nucleosome fuzziness, and genomic features, including polyadenylation sites, improve cancer detection beyond the traditional epigenetic markers of promoter DNA methylation.
conclusionsTogether, MESA stands as a major advancement in the field by utilizing comprehensive and complementary epigenetic profiles of cfDNA for effective non-invasive 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.