Targeted next-generation sequencing-based sequencing of cell-free DNA in cerebrospinal fluid uncovers cancer-specific mutations in patients with brain cancer using a widely available panel

Background: The gold standard for the diagnosis of brain tumors comprises neurosurgical biopsies or resections for tissue acquisition. Depending on the anatomical location of the tumor, this might not always be feasible. The aim of this study was to assess whether targeted sequencing of cell-free DNA (cfDNA) could be applied in a clinical setting for the detection of cancer-specific mutations in cerebrospinal fluid (CSF) and blood using a widely available panel, investigating if this approach would facilitate brain tumor diagnosis. Methods: Patients with newly suspected or confirmed CNS tumors or suspected leptomeningeal metastasis were included. CSF and blood were sampled for each patient. Using next-generation sequencing (NGS), targeted sequencing was performed on cfDNA. If available, matched tissue samples were also sequenced using the same gene panel. Results: We investigated 58 samples from 29 patients. Sequencing was successful in 16 CSF samples (55%) and 29 blood samples (100%). On average, more tumor-specific mutations were found in CSF compared to blood. Patients in whom cfDNA sequencing in CSF was successful had tumors with a significantly shorter distance to the CSF space and were larger in size. In 2 cases, where surgeries were not considered because of high surgical risk due to the anatomical locations of the lesions, the diagnosis was aided by CSF sequencing results. One primary CNS lymphoma and 1 H3 K27M diffuse midline glioma were identified, respectively. Conclusions: NGS-based targeted sequencing in CSF has the potential to facilitate brain tumor diagnosis in patients presenting with new cerebral lesions.