Cerebrospinal Fluid cfDNA Sequencing for Classification of Central Nervous System Glioma

Clin Cancer Res. 2024 Jul 15;30(14):2974-2985. doi: 10.1158/1078-0432.CCR-23-2907.

Abstract

Purpose: Primary central nervous system (CNS) gliomas can be classified by characteristic genetic alterations. In addition to solid tissue obtained via surgery or biopsy, cell-free DNA (cfDNA) from cerebrospinal fluid (CSF) is an alternative source of material for genomic analyses.

Experimental design: We performed targeted next-generation sequencing of CSF cfDNA in a representative cohort of 85 patients presenting at two neurooncological centers with suspicion of primary or recurrent glioma. Copy-number variation (CNV) profiles, single-nucleotide variants (SNV), and small insertions/deletions (indel) were combined into a molecular-guided tumor classification. Comparison with the solid tumor was performed for 38 cases with matching solid tissue available.

Results: Cases were stratified into four groups: glioblastoma (n = 32), other glioma (n = 19), nonmalignant (n = 17), and nondiagnostic (n = 17). We introduced a molecular-guided tumor classification, which enabled identification of tumor entities and/or cancer-specific alterations in 75.0% (n = 24) of glioblastoma and 52.6% (n = 10) of other glioma cases. The overlap between CSF and matching solid tissue was highest for CNVs (26%-48%) and SNVs at predefined gene loci (44%), followed by SNVs/indels identified via uninformed variant calling (8%-14%). A molecular-guided tumor classification was possible for 23.5% (n = 4) of nondiagnostic cases.

Conclusions: We developed a targeted sequencing workflow for CSF cfDNA as well as a strategy for interpretation and reporting of sequencing results based on a molecular-guided tumor classification in glioma. See related commentary by Abdullah, p. 2860.

MeSH terms

  • Adult
  • Aged
  • Aged, 80 and over
  • Biomarkers, Tumor* / cerebrospinal fluid
  • Biomarkers, Tumor* / genetics
  • Brain Neoplasms / cerebrospinal fluid
  • Brain Neoplasms / diagnosis
  • Brain Neoplasms / genetics
  • Brain Neoplasms / pathology
  • Cell-Free Nucleic Acids* / cerebrospinal fluid
  • Cell-Free Nucleic Acids* / genetics
  • Central Nervous System Neoplasms / cerebrospinal fluid
  • Central Nervous System Neoplasms / diagnosis
  • Central Nervous System Neoplasms / genetics
  • Central Nervous System Neoplasms / pathology
  • DNA Copy Number Variations*
  • Female
  • Glioma* / cerebrospinal fluid
  • Glioma* / diagnosis
  • Glioma* / genetics
  • Glioma* / pathology
  • High-Throughput Nucleotide Sequencing* / methods
  • Humans
  • Male
  • Middle Aged
  • Polymorphism, Single Nucleotide
  • Young Adult

Substances

  • Biomarkers, Tumor
  • Cell-Free Nucleic Acids