October 17th, 2007

so confused

A Genotyping Question..

Sort of an idle question, but I can't wrap my head about this in a meaningful way, so maybe one of you can lend some insight.. I maintain our mouse colony, so I'm used to asking other labs for their genotyping protocols when we import mice from them. The last two labs we've done this with have given me... what I think are sort of strange protocols. One seems to use Taqman to genotype, and the other gave me a protocol for Southern blotting. I know I can adapt the Taqman protocol to work with normal PCR, although I generally don't like running out such small products. But aren't Taqman probes pretty expensive? Why would you do that? The tech I talked to said they genotype a lot of their lines that way. Maybe they, like I plan to do, omit the probes when they're just genotyping, but the e-mail didn't sound like that was what they do. The Southern totally baffles me, it (seems like it) would be so much less work to just figure out some normal PCR primers to amplify a band from the region in question rather than probing for it. Anything thing I'm missing here, reasons why these approaches may be "better"? Or is this just a case of a lab set in their ways, or a lab being too lazy to design multiple protocols? In both cases, we're talking about animals with floxed genes. I have SEVERAL other floxed lines in my bag, all of which came with regular old PCR protocols to distinguish between the floxed alleles and the wt alleles, easily! Never had any problems with them beyond optimizing the primer concentrations and PCR programs to work with our DNA extraction/PCR kit.