CMET-29. DETECTING TUMOR MUTATIONS IN CEREBROSPINAL FLUID: LIQUID BIOPSY FOR THE DIAGNOSIS OF CENTRAL NERVOUS SYSTEM METASTASES

Abstract There is a critical need for better methodologies to diagnose and monitor patients with central nervous system (CNS) tumors. Recent advancements in the use of circulating tumor DNA (ctDNA) show that it is a promising tool for the evaluation of patients with primary or metastatic CNS tumors. Cerebrospinal fluid (CSF) is a more suitable sample type to evaluate metastatic CNS cancers than plasma. The current techniques for diagnosing metastatic CNS tumors include imaging (e.g., MRI), examination of tumor cells in CSF (CSF-cytology) and biopsies. However, MRI and CSF-cytology have poor specificity and sensitivity, respectively, and brain biopsies are invasive. The objective of this study is to optimize and validate a next generation sequencing (NGS) assay to detect ctDNA in the CSF of patients with metastatic CNS tumors. We have compared several methods to isolate ctDNA from CSF and identified the optimal method based on the quantity and quality of ctDNA obtained. CSF-ctDNA was extracted using QIAamp Circulating Nucleic Acid kit from CSF patient samples (CNS tumor= 10, Breast cancer=17, Lung cancer=8, Ovarian cancer=1, Melanoma=1, B-cell lymphoma=2, and Uterine cancer=1). We analyzed CSF-ctDNA mutations with the OncomineTM Pan-Cancer cell-free assay and found mutations in 19/40 (47.5%) CSF samples. The targeted panel detected 22 single nucleotide variations involving 11 genes and TP53 was the most commonly mutated gene. Copy number variations were detected in FGFR3, MYC, CCND1, CCND3, FGFR1, and CDK4 genes. We compared the sensitivity of the NGS assay to detect ctDNA with CSF-cytology and found that 7/22 (31.8%) CSF-cytology negative patients were positive for CSF-ctDNA. In conclusion, CSF-ctDNA targeted sequencing is more sensitive than CSF-cytology in the evaluation of patients with CNS metastasis. This approach will improve the diagnosis and management of primary and metastatic CNS tumors.