Mutation signatures and molecular risk factors in OSCC. (A,B) Dot plots show (y-axis) fraction of (x-axis) SNVs in all 96 possible mutation 3-nt sequence contexts identified in each (A) HPV-positive (n = 149) and (B) HPV-negative (n = 50) OSCC studied by WGS. Key: Colors indicate the somatic SNVs located in (asterisk, x-axis labels, mutation sequences) the central mutation position in each 3-nt sequence. (C) Bar graph depicting the (y-axis) mean fraction of mutations in (x-axis) 30 mutation signatures across the collection of (yellow) HPV-positive and (purple) HPV-negative OSCCs with available WGS data. Similar results were obtained using WES and exonized WGS data. Signatures showing significant differences between HPV-positive and HPV-negative cancers included signature 2 and 16. (*) adjusted P < 0.01. (D) SNVs in signature 2, linked to APOBEC cytidine deaminase genome editing, were strongly associated with overall mutation burden in individual HPV-positive OSCCs (red dots; r = 0.91; adj. P = 8.25 × 10⁻³⁹). A similar association was observed for signature 13, also linked to APOBEC activity (see Supplemental Fig. S2). (E) Box and whisker plot showing significant relative increase in SNVs in signature 16 in HPV-negative OSCC patients associated with heavy cigarette smoking (adj. P = 5.23 × 10⁻³). (F) Pack-years of cigarette smoking directly correlated with number of signature 16 mutations in HPV-negative OSCCs (red dots; r = 0.62; adj. P = 1.91 × 10⁻⁴). See also Supplemental Figure S2 and Supplemental Table S2.