Analytical validation of the Belay Vantage™ assay for evaluation of MGMT promoter methylation using enzymatically converted tumorDNA from cerebrospinal fluid
Kala F. Schilter, Qian Nie, Jennifer N Adams, Rakshitha Jagadish, Anthony Acevedo, Alexandra Larson, Samantha A Vo, Brett A Domagala, Kyle M. Hernandez, Christopher Douville, Yuxuan Wang, Brian Coe, Chetan Bettegowda, Honey V. Reddi
Abstract
• Novel application - The Belay Vantage™ assay evaluates MGMT promoter methylation status in cerebrospinal fluid (CSF) of individuals with known or suspected central nervous system tumors using low input DNA (current methods are limited to tumor tissue). • Improved methodology – The test uses enzymatic conversion of DNA which does not affect the integrity of the DNA, minimizing damage, increasing ability to process converted DNA downstream (current commercial tests use bisulfite conversation which causes DNA damage). • Additional Content – Vantage™ evaluates 12 CpG sites in the MGMT promoter compared to only 4-8 sites that other commercial tests do. MGMT promoter methylation status (hypermethylation) is one of the strongest prognostic and predictive biomarkers in glioblastoma (GBM) and is associated with a more favorable response to alkylating chemotherapies such as Temozolomide (TMZ). Additionally, it is associated with pseudo progression in GBM, a phenomenon in which early radiographic changes after treatment are indicative of possible tumor recurrence though on histological examination it is consistent with treatment effect. Current methods for evaluation of MGMT promoter methylation status are limited to tumor tissue, requiring invasive biopsy or surgery, prompting the need for a liquid biopsy-based assay to expand and manage therapeutic interventions. The Belay Vantage™ assay evaluates MGMT promoter methylation status in cerebrospinal fluid (CSF) of individuals with known or suspected central nervous system tumors using low input DNA. The assay uses quantitative polymerase chain reaction (qPCR) on DNA extracted from CSF after enzymatic conversion and has an analytical sensitivity of 95.5 % and specificity of 100 %.