Variant Allelic Frequency to Track Therapy Response and Evaluate Leptomeningeal Disease in Metastatic Central Nervous System Cancers

<b>Background</b>: Diagnosis of leptomeningeal disease (LMD) remains a clinical challenge due to nonspecific neurological symptoms, limitations of imaging, and the low sensitivity of cerebrospinal fluid (CSF) cytology. Molecular biomarkers, such as circulating tumor DNA (ctDNA) variant allele frequencies (VAFs), offer potential for improved detection and disease monitoring. <b>Methods</b>: Gene-level VAFs were analyzed from 118 Summit™ positive CSF specimens and evaluated in the context of clinical diagnosis, neurological presentation, neuroimaging, and CSF cytology. Longitudinal analyses were performed on serial CSF samples to assess VAF dynamics following therapy. <b>Results</b>: Longitudinal assessment demonstrated that decreases in VAF post-treatment aligned with clinical stabilization, whereas rising or persistent VAFs reflected disease progression, therapeutic resistance, or evolving clonal mutations. Elevated VAFs correlated strongly with clinically confirmed LMD and were concordant with radiographic and clinical indicators of disease. <b>Conclusions</b>: VAF analysis in CSF provides a quantitative biomarker for the detection and monitoring of metastatic CNS disease. These findings support its utility as a complementary tool to conventional diagnostics, offering real-time insights into disease burden, therapeutic response, and clonal evolution in LMD.