Simple HPV69 integrants induce high expression of an imprinted oncogene, RTL1, and of C15orf65. (A–C) Box and whisker plots depict log₁₀-transformed counts of (A) SNVs or small indels per megabase pair, (B) copy number step-changes (±0.5 n), and (C) SV breakpoints in 105 OPSCC (circles): red, tumor with HPV69 integrants; no fill, all others. (D,E) Sashimi plots of (top) chimeric transcripts initiated in HPV69, spliced to exons of (D) RTL1 and (E) C15orf65, leading to extremely high expression relative to controls. Black line, numbers, read counts connecting spliced exons; bottom, read counts of conventional transcripts in control tumor. Some RTL1 fusion transcripts extend past the 3′ transcription termination signal. (F,G) Box and whiskers plots of expression levels of (F) RTL1 and (G) C15orf65 in 103 HPV-positive OPSCC. Red, HPV69-positive tumor; gray, all others. See also Supplemental Table S7.