Functional CDKN2A assay identifies frequent deleterious alleles misclassified as variants of uncertain significance.

Abstract

Pathogenic germline <i>CDKN2A</i> variants are associated with an increased risk of pancreatic ductal adenocarcinoma (PDAC). <i>CDKN2A</i> variants of uncertain significance (VUSs) are reported in up to 4.3% of patients with PDAC and result in significant uncertainty for patients and their family members as an unknown fraction are functionally deleterious, and therefore, likely pathogenic. Functional characterization of <i>CDKN2A</i> VUSs is needed to reclassify variants and inform clinical management. Twenty-nine germline <i>CDKN2A</i> VUSs previously reported in patients with PDAC or in ClinVar were evaluated using a validated in vitro cell proliferation assay. Twelve of the 29 <i>CDKN2A</i> VUSs were functionally deleterious (11 VUSs) or potentially functionally deleterious (1 VUS) and were reclassified as likely pathogenic variants. Thus, over 40% of <i>CDKN2A</i> VUSs identified in patients with PDAC are functionally deleterious and likely pathogenic. When incorporating VUSs found to be functionally deleterious, and reclassified as likely pathogenic, the prevalence of pathogenic/likely pathogenic <i>CDKN2A</i> in patients with PDAC reported in the published literature is increased to up to 4.1% of patients, depending on family history. Therefore, <i>CDKN2A</i> VUSs may play a significant, unappreciated role in risk of pancreatic cancer. These findings have significant implications for the counselling and care of patients and their relatives.