Laboratory assays for HPV

Following previously established protocols, anogenital specimens were collected at the baseline visit using prewetted Dacron swabs from the coronal sulcus or glans penis, penile shaft, anus, and scrotum, combined into one sample per participant, and stored at -80°C [20]. DNA was extracted at the Moffitt Cancer Center (in Tampa, FL) using the QIAamp Media MDx Kit, followed by polymerase chain reaction and HPV genotyping. Samples positive for β-globin or at least one HPV genotype were considered adequate and included in the analysis (overall β-globin positivity = 98%). The Roche Linear Array assay was used to detect 37 HPV genotypes classified as high risk (oncogenic; HPV 16, 18, 31, 33, 35, 39, 45, 51, 52, 56, 58, 59, and 68) or low risk (nononcogenic; HPV 6, 11, 26, 40, 42, 53, 54, 55, 61, 62, 64, 66, 67, 69, 70, 71, 72, 73, 81, 82, 82 subtype IS39, 83, 84, and 89 [formerly CP6108]) [21]. The genotypes were further classified into HPV9 vaccine genotypes (i.e., 6, 11, 16, 18, 31, 33, 45, 52, and 58).