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.