ID #866 Liquid biopsy using multiple functional genomic tools reveals clinical and biological insights into replication repair deficient gliomas

Background Analysis of cerebrospinal fluid (CSF) circulating tumor DNA (ctDNA) has shown promise in multiple brain tumor types. The role of CSF-based liquid biopsy in early detection, surveillance, monitoring response and predicting relapse in patients with cancer predisposition syndromes has not been described. Methods We established a protocol for CSF-ctDNA collection from patients with hereditary replication repair deficiency (RRD) for surveillance, response assessment, and monitoring of gliomas post-therapy. ctDNA was assessed for single-nucleotide variants (SNVs), copy number variants(CNVs) and MMRD signatures (MMRDness score) using a combination of hybrid capture and low-pass whole-genome sequencing. Results A total of 84 CSF samples from 48 patients (CMMRD(32), Lynch (15), POLE(1)) were analyzed. Diagnostic sensitivity for high-grade glioma was 93% with 100% specificity. Three tumors were diagnosed >6 months prior to tumor evidence by diagnostic procedure. CSF-ctDNA status was significantly associated with survival - 58 samples were taken during RRD-glioma immunotherapy, overall survival was 91% and 15% for patients with negative versus positive CSF-ctDNA, respectively (p = 0.005). MMRDness scores were elevated at diagnosis and became negative in association with treatment response. These patients eventually had repeated negative CSF-ctDNA and are being monitored post therapy cessation. Ongoing monitoring of 12 patients post immunotherapy revealed 2 positive samples which were confirmed by biopsy upon positive imaging. One is alive upon changing immunotherapy. Comparative tumor and repeated CSF mutation analysis revealed unique patterns of spatial and temporal clonal evolution shaped by common drivers, new drivers and loss of antigens suggesting immune editing. Conclusions This is the first report of RRD patients benefiting from CSF-ctDNA for early detection, monitoring response and MRD with immunotherapy. In addition to CNV and SNV detection, MMRDness score is a unique quantitative tool to assess tumor burden during therapy. These data can be expanded to other cancer syndromes and malignant glioma management.