I'm interested in the genetic polymorphism within genes coding variable parts of T-cell receptors in rodents (vole). I'm looking for best genotyping method. I figured out there are separate sets of primers for each TCR subfamily but are there any primers that would amplify all TCR-V genes? What do you recommend?
Dear Agnieszka, to my knowledge, there are no such primers. We encountered problems even in typing of different Valpha and Vbeta due to allelic differences between B6 and 129 mouse strains. In addition, there is big similarity between homologs in different clasters of TCR V-genes. Therefore, it is difficult to design primers possessing sufficient specificity. Introns in mouse V-genes show more individuality. In any case you will need to perform sequencing of every amplified product to identify one exactly. It may be, the problem will be easier resolved after full sequencing of vole chromosomes encoding Valpha and V beta genes.
Dear Agnieszka,
There are no primers that could amplify all V regions. You could get a couple for the C (specific for each mouse strain), but not for the V. You can design several, I tried myself and design almost 30. The problem is you run out of your sample pretty fast if it is a tiny population. Another option is to extract RNA and perform a 3' RACE using C primers. It is a technique that allows amplification of sequences when 3' region is unknown. You can clone and sequence the product you get. I hope this helps. Good luck!
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