Focal structural variations are associated with HPV integrants in primary tumors. Schematics depict HPV-associated genomic structural variation in primary tumors of the (A–C) tongue (i.e., Tumor A) and (D–F) tonsil (i.e., Tumor B). (A,D) WGS coverage histogram features are as described in Figure 3 legend. (B,D,E) Target gene schematic and connectivity map features are as described in Figure 4 legend. (C) Looping model for HPV-associated structural variation in Tumor A. See Figure 4 legend. (E) Chromosomal translocation structure depicting multiple connections between segments on chromosomes 11 and 8, associated with HPV integrants (red arrows). (F) Scatterplots showing WGS coverage in 50-kb blocks on chromosomes 11 and 8, to estimate (y-axis, left) chromosomal ploidy and (right) ratios of observed local coverage versus mean autosomal coverage. (Gray vertical dots) Centromere; (red arrows) HPV insertion sites.
