Tumors with different HPV16 DNA and RNA (E6*I) status from 290 consecutively recruited HNSCC patients was compared by gene expression profiling and targeted sequencing of 50 genes. The study confirmed that the HPV16 DNA+ RNA+ tumors are HPV-negative (DNA-) HNSCC and have elevated expression of cell cycle genes and rare TP53 mutations. This evidence concerns the gene TP53 and head and neck squamous cell carcinoma.