I want to genotype 12 single nucleotide polymorphisms. I know the exact sites of these polymorphisms. I want to know the best and most cost-effective system (ABI/Sequenom etc...) to do genotyping of 100 Samples. Secondly, for longer run if I have to the same thing but with the volume of about 40 samples per week for about more than 6 months is there any other better system?

I've had a lot of experience with SNaPshot and have had success multiplexing assays for several SNPs. I'd say that 12 is easily done within one tube, but for 100 samples you might want to put them in more tubes to save on development costs.

Taqman is also good for small numbers of SNPs.

I would say for the numbers you're looking at, the deciding factors wouldn't be what is the best assay, but what equipment do you already have access to.

SNaPshot requires capillary electrophoresis equipment, and pcr, and Taqman just uses pcr.

Also, snapshot requires you to design your own primers, whereas Taqman is designed for you. Benefits to both, but it depends whether you want more control, or more manufacturer support.

I don't know much about prices I'm afraid because I don't get involved in all of that.