BIOM-68. TAPS LIQUID BIOPSY: AN ULTRASENSITIVE, INTEGRATED GENOMIC-EPIGENETIC CSF ASSAY FOR CNS TUMORS

Abstract Liquid biopsy of cerebrospinal fluid (CSF)-derived circulating tumor DNA (ctDNA) has been shown to be a feasible and low-risk alternative to tissue sampling for patients with central nervous system (CNS) tumors. The implementation of CSF ctDNA liquid biopsy has proven challenging due to the molecular diversity of CNS diseases. We report the development of a liquid biopsy assay that integrates epigenomic and genomic analysis of CSF-derived ctDNA, enabling simultaneous DNA methylation classification and mutational, copy number, and gene fusion analysis. TAPS (TET-assisted pyridine borane sequencing) chemistry enables high-throughput epigenomic and genomic analysis without DNA destruction. We analyzed ctDNA from 62 CSF samples from primary and metastatic CNS tumors. Library preparation was performed using TAPS chemistry (Watchmakers Genomics). Libraries were sequenced on NOVASeq 2000, fastq files processed using an NF-CaseReports pipeline, coverage bias corrected using fragCounter, and rPCA denoising with Dryclean. Methylation signals were extracted using Rastair, then integrated with the Infinium MethylationEPIC v2.0 array probe set. Copy number analysis was performed with CBS and structural variants called using GRIDSS with visualizations from the skitools suite. With TAPS, we detected SNVs, CNAs, and fusions including alterations such as 1p19q loss in oligodendroglioma (N=3), chromosome 7 trisomy (N=9), chromosome 10 loss (N=8), high-level amplifications of EGFR and MET in GBM (N=11), and ERBB2 (Her2) in metastatic breast cancer. Mutational analysis enabled differentiation of IDH-mutant (N=17) and wildtype (N=28) gliomas based on mutations in IDH1/2, ATRX, TP53 and TERT promoter, amplifications, and CDKN2A/B, PTEN loss. We detected gene fusions including MN1::CXXC5 and EGFRvIII. TAPS enabled targeted analysis of MGMT promoter methylation status in GBM (N=10), consistent with methylation array findings. Our pan-CNS cancer liquid biopsy assay utilizing TAPS chemistry provides comprehensive genomic landscape analysis from CSF samples with high fidelity to tumor tissue-derived data, demonstrating its potential for non-invasive CNS tumor profiling.