Copy number profiling of tumor suppressor genes in head and neck cancer

Background Sensitive and reliable new biomarkers are needed in head and neck cancer to predict the outcome and for therapy that is more effective. Copy number alterations are frequent and play a critical role in cancer. Methods Copy number alterations of 24 tumor suppressor genes in head and neck cancer were analyzed simultaneously in matched tumor and normal samples from 93 patients using multiplex ligation-dependent probe amplification (MLPA). Results Chromosomes 3p and 9p displayed the most common alterations. The gene displaying most frequent losses was the mutL homolog 1 (MLH1) gene, followed by the cyclin-dependent kinase inhibitor 2A (CDKN2A) and CDKN2B genes. A significant correlation was observed between the CDKN2A and CDKN2B genes. The tissue inhibitor of metalloproteinase (TIMP)3 gene alterations were observed in 8 tumors. Conclusion Our data confirm previous observations and suggest that losses of the MLH1 and CDKN2 genes and alterations of the TIMP3 gene play an important role in head and neck carcinogenesis. © 2016 Wiley Periodicals, Inc. Head Neck 39: 341–346, 2017