A comparison of CDKN2A status in gliomas using different techniques: The loss of p16 as a surrogate marker

The presence of a CDKN2A homozygous deletion (HD) plays an important role in the diagnostic approach for neuropathologists and the clinical prognostic stratification of several CNS tumors. CDKN2A is located on chromosome 9p21 next to CDKN2B and MTAP and encodes for the protein p16. Various molecular diagnostics are routinely used for assessing the deletion. In this context, we studied a cohort of 40 adult-type gliomas to analyze the concordance of three different molecular techniques, ie, FISH, NGS, and SNP array, for determining CDKN2A status and compared the results to p16 and MTAP immunostainings. The results showed that SNP array is the most reliable technique for the detection of CDKN2A HD and that p16 IHC constitutes a surrogate for the detection of biallelic inactivation of CDKN2A. p16 IHC was more accurate than MTAP IHC in detecting CDKN2A HD because a subset of CDKN2A HD gliomas did not present a deletion of the MTAP gene. IHC also allowed the detection of tumors with a hemizygous deletion of CDKN2A harboring a concomitant second molecular event on the remaining allele, ie, hypermethylation of CDKN2A promoter. We conclude that p16 immunostaining is an accurate biomarker for detecting CDKN2A HD.