Are there big DNA difference of HPV 16/18/31/32 and other HPVs?

Question

[chen]

I am designing a panel to capture HPV, I wonder if there are big DNA difference of HPV 16/18/31/32 and other HPVs? Do I need to design a panel for each one, or just one panel is enough?

[pld]

At face value, this isn't really a question for this website.

I'm sure you could do a little digging in pubmed about HPV detection methods and see what is currently available.

If there are no commercial products that specifically include your targets, tou should align the genomes of the one's you're interested in against HPV isolates/strains for which commercial panels are available. From there you can look at regions those panels target and see if they're conserved in your target strains.

If there are no conserved regions targeted by any commercial products, then yes, you will have to design your own.

Answer 1

[agata88]

First check if anybody already create primers for all HPV types. I know there are some publications that identify most of HPV types. Second, the differences between HPV references are small so you can design degenerative primers for your regions of interest. After designing check in e.g. PrimerMap that primers cover all HPV references you want to amplify.

http://www.bioinformatics.org/sms2/primer_map.html

Best, Agata