INNV-08. Using cell free DNA (cfDNA) and RNA (cfRNA) in the diagnosis and monitoring of primary and metastatic CNS tumors

Abstract CSF is relatively accessible and current molecular approaches using next generation sequencing provide information on the genomic abnormalities that can guide clinical decisions and therapy. We present the results of testing 970 CSF samples submitted for routine clinical testing using cfDNA and cfRNA. cfDNA and cfRNA were extracted from 970 CSF samples and sequenced using targeted DNA panel of 302 genes and targeted RNA panel of 1600 genes. We used hybrid capture procedure based on KAPA HyperPrep kit. Minimal depth of 20,000X is required for DNA. Six of the 970 samples (0.6%) were considered QNS. Of the 641 informative cases submitted for metastatic tumor testing, 507 (79%) showed abnormalities associated with neoplastic process. Of these 28 (4%) deemed CHIP (clonal hematopoiesis of indeterminate potential) only. Four cases showed only chromosomal gain or loss without specific gene mutations. Between the 153 informative primary CNS cases, 109 (71%) showed abnormalities associated with neoplasm, 6 of which considered CHIP and one case showed only EGFR gene amplification without mutations. Of the 170 hematologic cases, 127(75%) showed mutations, seven of which were classified as CHIP. In addition to confirming presence or absence of cancer, the testing provided therapy-related information including detecting ESR1 mutation in 31 of 140 (22%) breast cancers, EGFR mutation in 96 (57%) of the 168 lung cancer cases. Chromosomal structural abnormalities were detected in 303 cases of the 811 metastatic and hematologic cases (37%), including ERBB2 amplification and ALK rearrangement. Germline mutations were detected in BRCA1/2 (8%), CHECK2 (2%), ATM (1%), and in Fanconi genes (3%). RNA levels using cfRNA were extremely low in majority of cases with expression level around zero in significant number genes but allowed cancer classification in some cases. This data suggests that this approach is reliable and provides information that potentially practice changing.