Human papillomavirus and gastrointestinal cancer: A review

Table 2 Comparison of human papillomavirus detection methods

Methods	Specimens	Advantages	Disadvantages
Southern blotting assay	Fresh/frozen samples	High specificity, ability to differentiate between episomal and integrated DNA	Not easily applied to FFPE samples
ISH	FFPE, fresh samples	High specificity, ability to differentiate between episomal and integrated DNA	Low sensitivity, technically difficult
HPV PCR	Fresh/frozen samples brushing washing any body fluid	High sensitivity, cost effective	Low specificity, provides no quantitative measure of viral load, no confirmation of transcriptionally active virus
Real-time PCR	Fresh/frozen samples, FFPE brushing washing any body fluid	High sensitivity and specificity, ability to differentiate between episomal and integrated DNA	Labour-intensive
Reverse Transcriptase PCR	Fresh/frozen samples, FFPE	High sensitivity	Time consuming, technically difficult
p16 immunostaining	Fresh/frozen samples FFPE brushing washing	High sensitivity, easy and accessible to most laboratories, marker of transcriptionally active virus	Low specificity
Signal amplification methods	Fresh/frozen samples FFPE brushing washing	Easy to perform	False positive products, no typing

FFPE: Formalin-fixed, paraffin-embedded tissues; HPV: Human papillomaviruse; PCR: Polymerase chain reaction; ISH: In situ hybridization.