2.1.2. Residual Rectal Swabs from Asymptomatic Men

To contextualize the sequences observed in the anal cancers, a disease-free control group of anonymized residual rectal swabs obtained from asymptomatic men attending sexual health clinics were collated for downstream WGS. These samples had previously been genotyped as a consequence of immunization surveillance in Scotland [17]. DNA was extracted from the residual rectal swabs by Qiagen MDx (Hilden, Germany) or Seegene Universal Extraction System, obtaining an eluate volume of 100 µL. HPV genotyping was performed using the Seegene Anyplex II and the Optiplex HPV Genotyping Kit (Heildelberg, Germany), detecting 28 and 24 different HPV types, respectively.

A total of 182 anonymized DNA extracts from residual rectal swabs were collated. Samples had originally been collected in the years 2016–2017 and were included if positive for HPV 16.
