While some CNVs are shared across HNSCC (e.g., focal amplification of 3q26/28 encompassing TP63, SOX2 and PIK3CA, or amplification of 11q13 regions encompassing FADD and PPFIA1), distinct CNV patterns reflect the HPV-associated dichotomization of HNSCC entities (Figure 1) [20,22,23]. Here, SOX2 is linked to head and neck squamous cell carcinoma.