Tips for tackling medium-throughput analysis

Often, companies will tell you you're paying $0.10 per sample, but "you can't just go off their numbers. You have to really cost it out," says Jeanette Papp, director of the UCLA Genotyping and Sequencing Core Facility. Some companies will sell enough primer for 4,000 samples even if you don't need it. Anticipate the sample quality and whether you need to rerun the samples, a factor that companies don't account for.

The decision on how you're going to genotype SNPs will change based on how many you have. The window between 30 SNPs and 300 can be tricky because it's not entirely clear what platform you should be using, says Peter Zandi. Sequenom instruments can work in that range, but users must do the cost comparison, he adds.

"You need to make sure you have the power to be able to answer your question before you ask it," says Seth Crosby, director of translational research at Washington University in St. Louis. The number of cases and controls you might need for an association study will vary depending on several factors, such as the number of SNPs you're looking at, how many cases you have, and whether in a human study your cases and controls are from the same families.

Even though most multiplexing platforms nowadays can handle different concentrations of DNA, keep the samples consistent, even if they're consistently low quality, Papp says. This isn't always obvious to new users who are multiplexing.

If you're thinking of using a newer high throughput platform, be sure to check the minimum amount of DNA required for the platforms on the market today. Hayes' group just started working with Illumina's Bead Xpress and Beadstation. These require 100-200 ng of DNA, more than five times the DNA requirement using a Sequenom instrument, says Hayes. "This is a major problem for our research," Hayes says. "That's quite a lot of DNA when resources are at a premium, yet the number of markers one can screen are large," she says.