*3.6. Integration*

Although it was not the main aim of the study, the absence of part of the HPV 16 genome was identified in 13/119 (10.92%) of the anal cancer samples. This absence indicates the potential integration of the HPV16 in the human genome. The E2 gene was the most frequently missing region, followed by E4, E5 and L2 E1 and L1 (see Table 5 for details). Notably, all cases retained E6 and E7 oncogenes. Due to the small number of cases in which integration was detected, no further analysis was performed. No integration was detected in the asymptomatic cohort.

**Table 5.** HPV integration identified in the anal cancer cohort.

