In situ detection of human papillomavirus DNA after PCR-amplification

Human papillomavirus (HPV) is an essential cofactor for cancer at many sites, including the genital tract, oral cavity, conjunctiva, and periungual region. The in situ detection of HPV allows us to determine the cellular targets of the virus. In situ-based coexpression analyses of HPV with putative target proteins provide tremendous insight into the molecular evolution of these viral-associated cancers. HPV DNA is present in high copy number in the precancerous lesions and is, thus, readily detected by in situ hybridization. However, viral integration, typical during oncogenesis, is associated with reduced copy number of the virus, necessitating in situ polymerase chain reaction amplification for accurate in situ detection of HPV. This chapter provides the protocols that can be used to detect HPV DNA in situ as well as to correlate viral DNA with coexpression of relevant protein targets.