The data gained from this study provided great insight into the biological difference between HPV+ and HPV− cancers at similar anatomical sites, identifying differential integration patterns observed between different HPV types in cervical cancer, and novel deletions in the TRAF3 gene in HPV+ HNSCC, suggesting aberrant activation of NFκB signaling in this subset of HNSCC. Here, TRAF3 is linked to head and neck squamous cell carcinoma.