Quantitative evaluation of MGMT promoter methylation in FFPE and fresh frozen brain tumor samples by EpiDirect MGMT Methylation qPCR Assay compared to pyrosequencing: correlation and corresponding cutoffs

MGMT promoter (MGMTp) methylation is a clinically important epigenetic biomarker that guides therapeutic decision-making in patients with glioblastoma and related brain malignancies. Pyrosequencing is a widely used method for analysis of MGMTp methylation in molecular pathology laboratories which relies on chemical conversion of DNA prior to amplification by polymerase chain reaction (PCR) and subsequent sequencing. The EpiDirect technology represents a novel analytical approach that enables direct, quantitative assessment of DNA methylation by qPCR using native, unmodified DNA. Here we compared the EpiDirect MGMT Methylation qPCR Assay to MGMTp pyrosequencing using brain tumor samples to evaluate the correlation between the two methods. We show that there is a clear correlation across two different clinical cohorts involving both formalin-fixed paraffin-embedded (FFPE) and fresh frozen samples and show that the EpiDirect MGMT Methylation qPCR Assay is a valid alternative to pyrosequencing for quantitative assessment of MGMTp methylation in brain cancer samples.