ArticleNeuro-oncology2023
Cerebrospinal fluid methylome-based liquid biopsies for accurate malignant brain neoplasm classification.
Article in Neuro-oncology, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 41 papers, 1 of them a synthesis that pooled it.
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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.
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Who cites it
41 citing papers in PubMed, 1 synthesis or guideline pooled it, 66 citations in OpenAlex.
- Utility and clinical effectiveness of liquid biopsy-based DNA methylation testing in early tumor screening and diagnosis, emphasizing older adult populations: a systematic review and meta-analysis.Frontiers in oncology · 2025Pooled it
- Cerebrospinal fluid cell-free DNA sequencing in pediatric CNS tumors: towards liquid molecular neuropathology.Acta neuropathologica · 2026Review
- Advances in the management of pediatric low-grade glioma.Neurotherapeutics : the journal of the American Society for Experimental NeuroTherapeutics · 2026Review
- Spatially resolved single-cell analyses of human meningioma identify novel cell states influencing tumor microenvironment and progression.Nature genetics · 2026Article
- Circulating cell-free methylated DNA immunoprecipitation sequencing (cfMeDIP-seq) in oncology: from technological advances to clinical applications.NPJ precision oncology · 2026Review
- M-PACT leverages cell-free DNA methylomes to achieve robust classification of pediatric brain tumors.Nature cancer · 2026Article
- Clinical validation of a tissue-agnostic genome-wide methylome enrichment assay to monitor response to pembrolizumab.NPJ precision oncology · 2026Article
- Research progress in imaging detection of brain metastases.Frontiers in medicine · 2026Review
- SNAP: Streamlined Nextflow Analysis Pipeline for Immunoprecipitation-Based Epigenomic Profiling of Circulating Chromatin.bioRxiv : the preprint server for biology · 2025Article
- Unveiling the role of EGR1 and hub senescence-related genes in type II alveolar epithelial cells senescence for obstructive sleep apnea.BMC biotechnology · 2025Article
- Review
- Co-detection of mutations and methylations in cerebrospinal fluid ctdna for minimally-invasive diagnosis of brainstem glioma.Journal of experimental & clinical cancer research : CR · 2025Article
- Detection of Human Brain Cancers using Genomic and Immune Cell Characterization of Cerebrospinal Fluid through CSF-BAM.Cancer discovery · 2025Article
- Cerebrospinal Fluid-Derived Small Extracellular Vesicles May Better Reflect Medulloblastoma Proteomes than Those from Blood Plasma.International journal of molecular sciences · 2025Article
- Next-Generation Sequencing of Intraoperatively Acquired Cerebrospinal Fluid and Matched Tumor Tissue in Patients Undergoing Surgical Resection for Glioblastoma.JCO precision oncology · 2025Article
- Liquid Biopsy and Epigenetic Signatures in AML, ALL, and CNS Tumors: Diagnostic and Monitoring Perspectives.International journal of molecular sciences · 2025Review
- Molecular-based decision-making in glioblastoma surgery: When to aim for supramaximal resection.Neuro-oncology · 2025Review
- Epigenetic Profiling of Cell-Free DNA in Cerebrospinal Fluid: A Novel Biomarker Approach for Metabolic Brain Diseases.Life (Basel, Switzerland) · 2025Review
- Ultra-low-input cell-free DNA sequencing for tumor detection and characterization in a real-world pediatric brain tumor cohort.Acta neuropathologica communications · 2025Article
- A hitchhiker's guide to cerebrospinal fluid biomarkers for neuro-oncology.Neuro-oncology · 2025Review
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15 authors at 3 institutions in 2 countries.
Funding
Abstract
backgroundResolving the differential diagnosis between brain metastases (BM), glioblastomas (GBM), and central nervous system lymphomas (CNSL) is an important dilemma for the clinical management of the main three intra-axial brain tumor types. Currently, treatment decisions require invasive diagnostic surgical biopsies that carry risks and morbidity. This study aimed to utilize methylomes from cerebrospinal fluid (CSF), a biofluid proximal to brain tumors, for reliable non-invasive classification that addresses limitations associated with low target abundance in existing approaches.
methodsBinomial GLMnet classifiers of tumor type were built, in fifty iterations of 80% discovery sets, using CSF methylomes obtained from 57 BM, GBM, CNSL, and non-neoplastic control patients. Publicly-available tissue methylation profiles (N = 197) on these entities and normal brain parenchyma were used for validation and model optimization.
resultsModels reliably distinguished between BM (area under receiver operating characteristic curve [AUROC] = 0.93, 95% confidence interval [CI]: 0.71-1.0), GBM (AUROC = 0.83, 95% CI: 0.63-1.0), and CNSL (AUROC = 0.91, 95% CI: 0.66-1.0) in independent 20% validation sets. For validation, CSF-based methylome signatures reliably distinguished between tumor types within external tissue samples and tumors from non-neoplastic controls in CSF and tissue. CSF methylome signals were observed to align closely with tissue signatures for each entity. An additional set of optimized CSF-based models, built using tumor-specific features present in tissue data, showed enhanced classification accuracy.
conclusionsCSF methylomes are reliable for liquid biopsy-based classification of the major three malignant brain tumor types. We discuss how liquid biopsies may impact brain cancer management in the future by avoiding surgical risks, classifying unbiopsiable tumors, and guiding surgical planning when resection is indicated.
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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.