This prospective, single-center study will evaluate whether cerebrospinal fluid (CSF) circulating tumor DNA (ctDNA) testing using the Belay Summit assay can improve the clinical management of patients with malignant gliomas or brain metastases from non-small cell lung cancer (NSCLC) or breast cancer who are suspected of having central nervous system (CNS) disease. Patients undergoing clinically indicated CSF evaluation will receive standard clinical testing, including CSF cytology and the Belay Summit ctDNA assay. Treatment decisions will remain at the discretion of the treating multidisciplinary neuro-oncology team. The primary objective is to evaluate 6-month clinical CNS progression-free survival (cCNS-PFS), with secondary objectives assessing safety and the association between CSF ctDNA dynamics and clinical outcomes. Exploratory proteogenomic analyses will be performed on residual CSF specimens when sufficient sample is available.

Leptomeningeal disease (LMD) and other advanced CNS malignancies remain associated with poor prognosis and limited tools for monitoring disease activity and treatment response. Conventional CSF cytology has limited sensitivity, particularly in the early stages of disease. Circulating tumor DNA (ctDNA) analysis of cerebrospinal fluid has emerged as a promising liquid biopsy approach for detecting molecular evidence of CNS disease and monitoring treatment response.

This prospective, single-center investigator-initiated study will evaluate the clinical utility of the Belay Summit CSF ctDNA assay in patients with malignant gliomas or brain metastases from NSCLC or breast cancer undergoing clinically indicated CSF evaluation. Patients may be enrolled either before or after clinically indicated lumbar puncture, provided eligibility criteria are met. Clinical management, including consideration of Ommaya reservoir placement, intraventricular therapy, systemic therapy modification, radiation therapy, or other CNS-directed interventions, will remain at the discretion of the treating multidisciplinary neuro-oncology team. The study does not mandate treatment assignment based on ctDNA results.

Inclusion Criteria:

• Age ≥ 18 years.
• Diagnosis of histologically or cytologically confirmed HER2+ breast cancer, or triple negative breast cancer, or Stage IV non-small cell lung cancer, or recurrent high-grade glioma).
• Undergoing clinically indicated cerebrospinal fluid (CSF) collection as part of routine clinical care: CSF may be obtained via lumbar puncture or existing CSF access device. Decision for CSF collection must be made independently by the treating clinical team and not solely for research purposes.
• Detectable CSF ctDNA and/or positive CSF cytology, with consideration for CNS-directed management by the treating neuro-oncology team.
• Ability to provide informed consent, or availability of a legally authorized representative (LAR).

Exclusion Criteria:

• Age <18 years.
• Inability to provide informed consent and no legally authorized representative (LAR) available.
• Not undergoing clinically indicated CSF collection as part of standard clinical care.
• Absence of detectable CSF ctDNA and absence of positive CSF cytology.
• Not being considered for CNS-directed management by the treating neuro-oncology team.
• Clinical contraindications to CSF collection, including but not limited to: Significant intracranial mass effect; (e.g., midline shift >5 mm or effacement of basal cisterns); Obstructive hydrocephalus or posterior fossa mass effect; Coagulopathy or bleeding risk precluding lumbar puncture or CSF access; Inability to safely obtain CSF access.