Middling Measures

© John McLean / Photo Researchers, Inc.

As researchers busily catalog the sequence variations across human populations in the HapMap Project, instrument developers are ramping up the throughput on platforms assessing single nucleotide polymorphisms (SNPs). New technologies can sequence millions of reactions on a single chip. With platforms becoming ever more powerful, sequencing experiments that used to be considered high-throughput - in the hundreds of SNPs - are starting to fall into a vast middle ground where the technology falls short.

Medium-range studies, broadly defined as ranging from 10s of SNPs to 3,000, are crucial for follow-up studies verifying results of genome-wide association studies, fine mapping, and candidate gene mapping, says Jeanette Papp, director of a core genotyping facility at the University of California, Los Angeles. Because medium scale projects aren't cost-effective, researchers don't always have a core facility at their disposal that will conduct them, and they face challenges at every turn, from the incompatibility of platforms for certain tissue types, to SNP selection, to how to save money on sample prep. "Outsourcing can be quite expensive," says University of Kansas geneticist Stuart Macdonald, "and companies generally offer technologies that are only cost-effective and efficient when applied to hundreds of samples for thousands of SNPs."

The Scientist asked researchers working on SNPs to share their insight on addressing the challenges of medium-throughput studies. Read what they said by clicking on the User Profiles in the yellow box to the right.