Utility of digital PCR for detecting TERT promoter mutations and CDKN2A homozygous deletion in meningioma.

Telomerase reverse transcriptase (TERT) promoter mutations and cyclin-dependent kinase inhibitor 2A/2B (CDKN2A/B) homozygous deletion (HD) are strongly associated with meningioma recurrence. Therefore, it is important to accurately detect TERT promoter mutations and CDKN2A/B HD in meningiomas. Sanger sequencing and pyrosequencing are conventional methods used to analyze TERT promoter mutations. However, due to the high GC content around the TERT promoter mutation, PCR amplification by sequencing has proven to be technically difficult. In this report, we describe a novel digital PCR (dPCR) assay to evaluate TERT promoter mutations and CDKN2A HD in freshly frozen and formalin-fixed paraffin-embedded (FFPE) meningioma specimens and verify the difference in results from conventional methods. Of the 76 meningioma specimens, 10 and 17 specimens were detected by pyrosequencing and dPCR assays, respectively, to harbor TERT promoter mutations. And when using dPCR assay to detect CDKN2A HD, a cut-off value was set at 0.73, which gave a detection rate comparable to qPCR. Using a dPCR assay, TERT promoter mutations and CDKN2A HD can be detected approximately 2 h after tumor resection. Therefore, the dPCR assay is fast and sensitive compared to conventional methods, which can be of great help in treatment-strategy decision making.