132 Optimizing Success Rates of CSF Liquid Biopsy Examined With Next Generation Sequencing in Pediatric Central Nervous System Tumors

Abstract

INTRODUCTION: Cerebrospinal fluid (CSF) liquid biopsy presents an attractive option for minimally invasive diagnosis and follow up for pediatric brain tumors. Best practice for obtaining appropriate cfDNA for next generation sequencing (NGS) is not currently known. METHODS: CSF was collected from patients under a prospective study to evaluate diagnostic utility of NGS. Samples were collected from control (non-tumor) and CNS tumor patients. CSF was collected at the dura opening, immediate ventricular catheter (IVC) from CSF divergent procedures, or ventricular shunt taps. Data was gathered on demographics, pathological diagnosis, tumor location, volume of CSF extraction, and DNA yield. RESULTS: CSF was extracted from 72 CNS tumor patients and 20 controls (48 female, 44 male). Of the CNS tumors, there were forty low-grade tumors (40/72) and thirty-two high-grade tumors (32/72). CSF collection location included dura opening (57), ventricular catheter (23), and shunt taps (12). cfDNA yield (ng) for CNS tumors displayed a mean of 135.5 ng (±353.4) and controls displayed a mean of 95.6 ng (±241.0). CNS tumor patients generated a significantly higher (p < 0.0001) DNA concentration (ng/cc) with a mean of 18.9 ng/cc (±82.7) compared to 0.5 ng/cc (±0.7) mean for controls. High grade tumors demonstrated a significantly greater amount of cfDNA concentration with a mean of 33.6 ng/cc (±116.6) whereas low grade tumors had a mean of 4.2 ng/cc (±5.0). CSF acquisition was 90.2% successful for NGS with a mean volume of 4.9 cc. In addition, infratentorial tumors revealed a 96% success rate with a mean volume of 5 cc. CONCLUSIONS: Extracting 4.9 cc of CSF had an 90.2% success rate for NGS. CSF may be acquired from either ventricular catheter or dura opening. High grade tumors had significantly higher cfDNA yield and concentration in CSF compared to low grade.