Droplet digital PCR assay for detecting TERT promoter mutations in patients with glioma

Two hot spot mutations (C228T, C250T) in the telomerase reverse transcriptase (TERT) gene are frequently identified in glioblastoma and oligodendroglioma. TERT mutations predicts an aggressive clinical course in isocitrate dehydrogenase (IDH) wild-type astrocytic tumors. Therefore, it is important to accurately detect TERT promoter mutations in glioma. Sanger DNA sequencing is the currently standard method for analyzing TERT mutations. However, PCR amplification in the first step of the sequencing has proven technically difficult because of the high GC content around the TERT mutation. In this report, we described a novel droplet digital PCR (ddPCR) assay to evaluate TERT hot spot mutations in fresh frozen and formalin-fixed paraffin-embedded (FFPE) specimens of glioma and verified the difference in results from the Sanger DNA sequencing results. We obtained the mutant allele fraction for TERT mutations of in a single ddPCR run in all cases, including the micro-dissected FFPE sections. On the contrary, up to twice the DNA sequences were required from fresh frozen tissue to obtain the results, consistent with ddPCR assay. When FFPE specimens were used, more time was required to evaluate TERT mutations through DNA sequencing. DdPCR is an effective and sensitive assay compared to the conventional standard Sanger DNA sequencing.