I use Nested PCR with MY09/11 followed by GP5+/6+ primers, but if anyone has a better set than these please let me know as prevalence of HPV in gingivobuccal cancer is very low, so I don't want to miss HPV present even at low copy.
Taht highly depends on the tissue! GP5+/6+ is a good choice for FFPE, but you can also test A5-A10 / A6-A8 (Wieland et al., J Invest Dermatol 2000). With good controls (b-globin, dilution series of HPV reference) you con detect with both methods up to 5 copies in your setup. In addition with p16 immunohistochemistry or FISH you should see if there is anything related.
I think that GP5+/6+ are good primers, although, the use PGMY09/11 could be good for the identification of different types! The major problem is the dna quality of samples and the "contamination" with several other DNAs for different microorganisms... We are still using the MY09/11 and if there is any doubt we use the GP5+/6+... For integrated cases, the use of good E6 primers is usefull... but it will depend on the types of HPV!
If you really don't want to have false negative, SPF10 primer system is the best one. It renders a 65 bp amplicon, very useful in FFPE samples.
If you work with fresh material, I would use PGMY09/11, and in a second round, I would retest negative samples with GP5+/6+. With this, you will be pretty sure of HPV negativity.
As pointed in previous comments, those are all L1-based set primers, be careful with integrations.
I would use primers for E6&E7 for a nested PCR because they are more likely to integrate as early genes and oncogenic factors.
- Badges
- Science topic
- Similar topics
- Medicine
- Oncology
- Cancer Research
- Cancer Biology