Extended Data Fig. 2: HPV-related features and genetic associations with outcomes.
a. Volcano plot showing mutations associated with HPV positive vs HPV negative cancers (Fisher’s Exact Test; dotted line represents p-value adjusted for false discovery). Recurrently mutated genes in SCCHN occur at markedly different frequencies between HPV+ (N=149) and HPV- (N=272) tumors. b. Oncoplot of patients identified as HPV-positive (N=149) by p16 status reveals that cases of low coverage by NGS of viral genomes (left side of oncoplot) are more likely to have mutations or copy number changes in TP53 and CDKN2A, suggesting these cases may not be driven by HPV.
