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Targeted next-generation sequencing-based sequencing of cell-free DNA in cerebrospinal fluid uncovers cancer-specific

Alexander Köpp1, Peter Westarp2, Marta Nowak3

  • 1Department of Neurology, Clinical Neuroscience Center, University Hospital Zurich and University of Zurich, Zurich, Switzerland.

Neuro-Oncology Advances
|February 10, 2026
PubMed
Abstract

Insights

Targeted sequencing of cell-free DNA in cerebrospinal fluid (CSF) shows promise for diagnosing brain tumors when biopsies are not feasible. This liquid biopsy approach aids in detecting cancer-specific mutations, facilitating timely diagnosis and treatment.

Area of Science:

  • Neuro-oncology
  • Genomics
  • Molecular Diagnostics

Background:

  • Neurosurgical biopsies are the standard for brain tumor diagnosis but can be limited by tumor location.
  • Alternative diagnostic methods are needed for inaccessible brain tumors.
  • Cell-free DNA (cfDNA) analysis offers a potential non-invasive diagnostic approach.

Purpose of the Study:

  • To evaluate the clinical utility of targeted sequencing of cfDNA in cerebrospinal fluid (CSF) and blood for brain tumor detection.
  • To assess if this method can identify cancer-specific mutations using a standard gene panel.
  • To determine if cfDNA sequencing can aid in diagnosing brain tumors, especially when biopsies are challenging.

Main Methods:

  • Patients with suspected or confirmed CNS tumors or leptomeningeal metastasis were enrolled.
  • CSF and blood samples were collected for cfDNA extraction.
  • Next-generation sequencing (NGS) was used for targeted sequencing of cfDNA, with matched tissue sequencing when available.

Main Results:

  • Sequencing was successful in 55% of CSF samples and 100% of blood samples.
  • CSF cfDNA analysis detected more tumor-specific mutations than blood analysis on average.
  • Successful CSF sequencing correlated with tumors closer to the CSF space and larger tumor size.
  • CSF sequencing aided diagnosis in two high-surgical-risk cases, identifying primary CNS lymphoma and H3 K27M diffuse midline glioma.

Conclusions:

  • NGS-based targeted sequencing of cfDNA in CSF holds significant potential for diagnosing brain tumors.
  • This approach can facilitate diagnosis in patients with new cerebral lesions, particularly when conventional biopsies are not feasible.
  • CSF cfDNA sequencing represents a promising advancement in neuro-oncology diagnostics.
Keywords:
cell-free DNAcerebrospinal fluidliquid biopsytargeted sequencing

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