Ranked variant allele fractions in HPV-positive OSCCs. VAFs for somatic variants located inside exons were ranked in each tumor. Shown are genes with ranked VAFs that were significantly enriched in the top fifth percentile across all HPV-positive OSCCs. Distributions of ranked VAFs of somatic variants in (A) ZNF750 in 19 cases; (B) PIK3CA in 41 cases; (C) EP300 in 18 cases; (D) NSD1 in 12 cases; (E) CYLD in 12 cases; and (F) all highly mutated MutSig genes in 145 HPV-positive cases. Of these 247 somatic variants, 54 (22%) were identified within the top fifth percentile of VAFs (P = 2.2 × 10−23). (G) Heat map showing ranked VAF percentiles of mutations disrupting five highly mutated genes (left) in individual HPV-positive OSCCs, ordered by overall mutation frequency (vertical columns; see Fig. 1). Key, right: percentiles of ranked VAFs. See also Supplemental Figure S6 and Supplemental Table S6.
