Detection of Tumor-Specific Variants in CSF of Children With Brain Tumors, Including Low-Grade and Cytology-Negative Cases.
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OBJECTIVE: The genetic diagnosis of brain tumors necessitates the direct collection of tumor tissue. Recently, genetic diagnosis using cell-free DNA (cfDNA) from plasma has been clinically applied to some somatic cancers, but it has not been established for brain tumors. This study conducted a genetic diagnosis via liquid biopsy (LB) using cfDNA extracted from the plasma and cerebrospinal fluid (CSF) of pediatric brain tumor patients. METHODS: The study included children who underwent surgical resection or biopsy for brain tumors between January 2019 and December 2020. Tumor-specific variants were identified using whole-exome sequencing of genomic DNA from tumor samples and normal blood cells. Subsequently, CSF and plasma collected during surgery were analyzed for these specific variants using droplet digital PCR. RESULTS: Tumor-specific variants were detected in six of 13 (46.2%) CSF samples. In contrast, no tumor-specific variants were detected in plasma in any patient. Among the six CSF-positive cases, two had negative or inconclusive CSF cytology (Class I or II), and one was a case of low-grade pilocytic astrocytoma. The median variant allele frequency in the positive CSF samples was 16.0% (range: 0.6%-86.1%). CONCLUSION: In certain pediatric brain tumors, genetic diagnosis using cfDNA from CSF demonstrated promising potential. This approach has the potential for diagnosis in cases with negative cytology or low-grade tumors. However, several issues must be addressed before this method can achieve clinical utility, including its low sensitivity and the extended turnaround time for analysis.