TBIO-06. Study of cell free DNA extracted from CSF enables molecular classification of embryonal brain tumors

Abstract

Abstract Liquid biopsies are revolutionary tools to detect tumour-specific genetic alterations in body fluids. Here, we assess whether the circulating tumor DNA (ctDNA) in Cerebral Spinal Fluid (CSF) could be used for the tumor genetic profiling of pediatric embryonal brain tumors (EBT). Cell free DNA extracted from CSF from 4-5 lumbar puncture droplets from patients with Medulloblastoma (n=18), ATRT (n=3), ETMR(n=1), FOXR2 EBT (n=2) or other pediatric EBT (n=1) (cfDNA mean quantity 48 ng/ml ; range 5.6 - 442 ng/ml) and matched genomic DNA from primary tumors were sequenced by WES (Illumina 100PE) using Nimblegen Medexome Capture. SNVs/mutations were called using GATK-UnifiedGenotyper, GATK-HaplotypeCaller and Samtools. Copy Number profiles were generated with CNVkits. 10/13 cfDNA WES yielded satisfactory depth (>10x). A mean of 466 (range 93-945) SNVs were detected in the primary tumor and 474 (range 18-922) in the CSF. A mean of 416 (range 18-872) commons SNVs were observed between the cfDNA and the primary tumor, comprising classical medulloblastoma genes such as SMO or MLL2. Interestingly, several SNVs were observed either in the tumor only (mean 50 ; range 3-115) or in CSF only (mean 58 ; range 0-148) suggesting a clonal heterogeneity. For 5 cases, Copy Number profiles were also available, allowing the detection of MYCN amplification or 19q13 miRNA cluster amplification. Altogether, we demonstrate the feasibility of WES on CSF with a low input of ctDNA. These results may pave the way for new tumor monitoring tools.