Table 3: A Summary of the Most Common DNA and RNA Based HR-HPV Integration Detection Methods

Method Description Strengths Limitations
RS-PCR Host/viral genomic regions are amplified by PCR using HPV specific primers and a primer designed to bind to restriction enzyme sites. Can obtain DNA sequence of host/viral junctions. Large concentrations of DNA required and labour intensive.
APOT RT-PCR followed by PCR using HPV specific primer discriminates HPV mRNAs derived from integrated and episomal viral genomes. Can obtain DNA sequence of host/viral junctions. Labour intensive and expensive.
DIPS Single-side-specific ligation-mediated PCR. Involves vectorette PCR and suppression PCR to detect integrated HPV DNA. Can obtain DNA sequence of host/viral junctions. Labour intensive.
Southern blot Cellular DNA digestion and electrophoresis followed by hybridisation of labelled HPV DNA probes to determine the physical state (integrated or episomal) of HPV. Can reliably distinguish episomal from integrated HPV DNA. Uses large concentrations of DNA and labour intensive. The use of radio-labelled probes has health and safety implications.
Real-time PCR Physical state of HPV is estimated by calculating HPV E2:E6/E7 ratio by real-time PCR amplification of HPV E2 and E6/E7. Uses small concentrations of DNA and is less labour intensive. HPV E2:E6/E7 ratio may not reliably distinguish integrated DNA in a background of episomal DNA. Consumables expensive.

Abbreviations: RS-PCR= Restriction Site PCR; APOT=Amplification of Oncogene Transcripts; DIPS=Detection of Integrated Papillomavirus.