Hi...
If you had a budget of 500,000 dollars and had to propose the core requirements of a small/medium genotyping center, what instruments would you recommend to purchase (applied biosystems preferably) such as real-time pcr or capillary electrophoresis...etc..
Your help is greatly appreciated..

From my experience i like the SNPstream Genotyping system. It is a Beckman product which means it has full automation capabilities. it uses a 12 or 48 plex microarray that you can customize to any snp you wish to look at. when you break down a cost per genotype it is only 5-10 cents because it is a H-T system. there are drawbacks of course like any system, the micro array plates are expensive and the software is not that intuitive.

I like ABI taqman because it is fool proof but it is very expensive, if you want to look at only a few snps i think taqman is the best, but for more than that it will get very expensive quickly.

Anyone out there with experience (either good or bad) using the Illumina BeadArray? I am looking into it and it is looking quite attractive for my purposes. Is there anything out there that is comparable? In other words, if you want to genotype SNPs that are not on the Affy 500k array or in dbSNP, is there any other high-throughput option?

thanks,

Ryan

With regards to the BeadArray (Golden Gate Assay), I have been informed that it cannot be applied to mitochondrial genes. Also, there appears to be a fairly high 'dropout' rate for identifying assayable novel SNPs/mutations not in HapMap.