In the present study, the mean sequence coverage of targeted CAGE reached 3099-fold, and the frequency of mutations was quite similar to that reported in the TCGA HNSCC database, with the only exception being the NOTCH1 gene, which had a significantly higher mutation frequency in our cohort than that in the TCGA HNSCC database. This evidence concerns the gene NOTCH1 and head and neck squamous cell carcinoma.