We can run bazillions (well, up to 40-plex SNPs per individual reaction and about 150,000 per day) of SNPs on our
Sequenom MassARRAY:
I could never have this sort of throughput on the Applied Biosystems 3130 I use for small batch genotyping:
It'll take two 96 well plates, but it samples sixteen wells at a time. Even running 7-plex per well, that's only 672 every three hours or so. With the Applied Biosystems 3730, we can run 384-well plates, but with two of these machines we're already at capacity with normal sequencing runs, so we added the Sequenom MassARRAY to our arsenal.