In this study, we have conducted a focused analysis of the genome and immune microenvironment from multiple, matched normal squamous tissues, premalignant lesions, primary, and recurrent tumors from seven patients with p16-negative HNSCC with the aim to identify novel molecular mechanisms that could drive tumor evolution in the upper aerodigestive tract. This evidence concerns the gene CDKN2A and head and neck squamous cell carcinoma.