Analytical validation of the Belay Vantage™ assay for evaluation of MGMT promoter methylation using enzymatically converted tumorDNA from cerebrospinal fluid (CSF)
Authors:
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
Journal:
Cancer Genetics. Volumes 294–295, June 2025, Pages 94-98
Abstract:
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 %.
Molecular Analysis of Cerebrospinal Fluid Tumor-Derived DNA to Aid in the Diagnosis and Targeted Treatment of Breast Cancer Brain Metastasis
Authors:
Michael Youssef, Alexandra Larson, Vindhya Udhane, Viriya Keo, Kala F. Schilter, Qian Nie, Honey V. Reddi
Journal:
Diseases, 2025, 13(10), 336.
Abstract:
A woman in her 40s with a history of ER/PR+, HER2-negative breast cancer presented with a seizure three years after mastectomy. Magnetic resonance imaging (MRI) revealed a right caudate head mass, which was concerning for either high-grade glioma or metastatic disease, but biopsy was deemed too high risk. Cerebrospinal fluid (CSF) tumor-derived DNA (tDNA) analysis by next-generation sequencing (NGS) was ordered, revealing a gain-of-function variant in PIK3CA, ERBB2 copy number gain, and high aneuploidy, findings consistent with breast cancer brain metastasis. Based on these results, the patient was treated with stereotactic radiosurgery (SRS) followed by trastuzumab deruxtecan, a HER2-targeted therapy. This case highlights the diagnostic and therapeutic value of CSF tDNA analysis in central nervous system (CNS) lesions when biopsy is not feasible. The report also illustrates how clonal evolution, such as acquired ERBB2 amplification, can occur in metastatic disease and influence treatment decisions.