Differential sensitivities of E6 type-specific and L1 consensus primers in the detection of human papillomavirus in anal carcinoma.

Anogenital malignancy has been increasing in incidence in recent decades. There is strong evidence in the literature suggesting that human papillomavirus (HPV) plays a role in the genesis of anogenital neoplasia. In addition, identification of oncogenic HPV types in anogenital carcinomas may have prognostic significance. The method used to detect HPV infection, however, affects the frequency with which viral DNA is identified. We examined tissues from 56 patients with anal squamous cell carcinoma for the presence of HPV DNA by in situ hybridization and polymerase chain reaction using both consensus and type-specific primers to determine if HPV detection varies when different methods are used. In situ hybridization identified the presence of HPV DNA in 41.1% of patients. Polymerase chain reaction using type-specific probes for the HPV E6 gene demonstrated HPV DNA in 46% of anal carcinomas, whereas polymerase chain reaction with consensus primers detected HPV DNA in only 16.3% of cases. All cases containing HPV type 6 were identified with L1 primers, whereas only three of 23 cases containing HPV type 16 were identified. The differences in the rate of HPV detection by the two polymerase chain reactions methods are most likely related to L1 gene loss in cells containing integrated HPV type 16.