Fig. 6.

HPV integration site in an expanded clone. In this expanded clone HPV shows evidence of “looping” integration [18, 44] whereby noncontiguous genomic sequences are brought adjacent to one another. a PCIP-seq reads mapping to a ~ 87-kb region on chr3 revealed three HPV-host breakpoints. The large number of reads suggests expansion of the clone carrying these integrations. b PCR was carried out with primer pairs matching regions α and β, as well as α and γ. Both primer pairs produced a ~ 9 kb PCR product. Nanopore sequencing of the PCR products show the HPV genome connects these breakpoints. c Schematic of the breakpoints with the integrated HPV genome. This conformation indicates that this dramatic structural rearrangement in the host genome was generated via “looping” integration of the HPV genome