ReviewComputational and structural biotechnology journal2022
Computational challenges in detection of cancer using cell-free DNA methylation.
Review in Computational and structural biotechnology journal, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 29 papers, 1 of them a synthesis that pooled it.
What it found
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
29 citing papers in PubMed, 1 synthesis or guideline pooled it, 38 citations in OpenAlex.
- 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
- Multifeature sequencing-based liquid biopsy for cancer diagnosis and monitoring.Genome medicine · 2026Review
- Genome-wide methylome profiling of cell-free DNA enables prognostication of patients with castration-resistant prostate cancer.British journal of cancer · 2026Article
- Methylated circulating tumor DNA: technical challenges and clinical applications in non-small cell lung cancer patients-a narrative review.Translational lung cancer research · 2026Review
- 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
- Integrating liquid biopsy and mutational signatures to advance precision oncology.NPJ precision oncology · 2026Review
- Detection of primary cancer types via fragment size selection in circulating cell-free extrachromosomal circular DNA.Genome medicine · 2026Article
- Clinical Relevance of USP44 Expression and DNA Methylation Status in Breast Cancer Cell Lines, Tumor Tissues, and Circulating Tumor DNA.Breast cancer (Dove Medical Press) · 2026Article
- SNAP: Streamlined Nextflow Analysis Pipeline for Immunoprecipitation-Based Epigenomic Profiling of Circulating Chromatin.bioRxiv : the preprint server for biology · 2025Article
- Article
- From multi-omics to deep learning: advances in cfDNA-based liquid biopsy for multi-cancer screening.Biomarker research · 2025Review
- Cell-free DNA methylation and fragmentomics-based liquid biopsy for accurate esophageal cancer detection.BMC cancer · 2025Article
- Read-level DNA methylation deconvolution enhances circulating tumor DNA detection.Briefings in bioinformatics · 2025Article
- Monitoring breast cancer progression through circulating methylated GCM2 and TMEM240 detection.Clinical epigenetics · 2025Article
- DNA methylation in breast cancer: early detection and biomarker discovery through current and emerging approaches.Journal of translational medicine · 2025Review
- Unravelling mutational signatures with plasma circulating tumour DNA.Nature communications · 2024Article
- Transformer-based representation learning and multiple-instance learning for cancer diagnosis exclusively from raw sequencing fragments of bisulfite-treated plasma cell-free DNA.Molecular oncology · 2024Article
- Plasma cell-free DNA methylome-based liquid biopsy for accurate gastric cancer detection.Cancer science · 2024Article
- PathMethy: an interpretable AI framework for cancer origin tracing based on DNA methylation.Briefings in bioinformatics · 2024Article
- Discovery and Validation of Methylation Signatures in Circulating Cell-Free DNA for the Detection of Colorectal Cancer.Biomolecules · 2024Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
4 authors at 2 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Cell-free DNA(cfDNA) methylation profiling is considered promising and potentially reliable for liquid biopsy to study progress of diseases and develop reliable and consistent diagnostic and prognostic biomarkers. There are several different mechanisms responsible for the release of cfDNA in blood plasma, and henceforth it can provide information regarding dynamic changes in the human body. Due to the fragmented nature, low concentration of cfDNA, and high background noise, there are several challenges in its analysis for regular use in diagnosis of cancer. Such challenges in the analysis of the methylation profile of cfDNA are further aggravated due to heterogeneity, biomarker sensitivity, platform biases, and batch effects. This review delineates the origin of cfDNA methylation, its profiling, and associated computational problems in analysis for diagnosis. Here we also contemplate upon the multi-marker approach to handle the scenario of cancer heterogeneity and explore the utility of markers for 5hmC based cfDNA methylation pattern. Further, we provide a critical overview of deconvolution and machine learning methods for cfDNA methylation analysis. Our review of current methods reveals the potential for further improvement in analysis strategies for detecting early cancer using cfDNA methylation.
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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.