Somatic mutations in HPV-positive OSCCs. (A) Somatic mutation rates in exons of 149 HPV-positive OSCC samples were determined from WGS and WES data. Mutation rates were calculated as the number of single nucleotide variants (SNVs) per megabase pair (Mbp) sequenced. Individual tumor samples were ranked by these rates (vertical alignments, left to right). (B) Heat map of log₁₀-transformed counts of APOBEC-associated mutations in 5′-TCW-3′ sequence context in each cancer. (C) HPV viral types in cancers: key, right: dark red, HPV-16; lavender, 18; green, 33; yellow, 35; orange, 59; dark blue, 69. (D) Cigarette smoking history for each patient: black, ≥10 pack-years; gray, <10 pack-years; white, never smoker; X, no data. (E) Heat map of variants in 24 significantly mutated genes (left) identified by MutSig (adjusted P-value < 0.2) (Lawrence et al. 2013) in samples ordered as in A (x-axis). Key: red, copy number gain involving gene; blue, copy number loss; black dots, somatic variants including missense, nonsense, and splicing site SNVs, and frameshift or in-frame insertions or deletions (indels). Bold font (gene names): adjusted P-value < 0.1. Table at right: percentages of samples that have single nucleotide mutations and short indels; copy number variants (CNVs) (gains or losses); and total (combined). Individual genes were ranked by these combined frequencies (top to bottom). See also Supplemental Figure S1 and Supplemental Table S1.