PRINCETON, NJ--The SNP Consortium has selected pharmacogenetics company Orchid Biocomputer here to perform independent confirmation and quality-control testing on a sample of the several thousand single-nucleotide polymorphisms identified so far by the four laboratories participating in its initiative. Lincoln Stein of the Cold Spring Harbor Laboratory, who is directing bioinformatics tasks for the consortium, noted, "This is a step being performed before the initial release so we can tell the community with confidence that we are publishing the correct SNPs."
Ten major pharmaceutical companies and the Wellcome Trust formed the consortium in April to fund a $45 million, two-year project aimed at identifying and releasing to the public 300,000 SNPs on the human genome. The Whitehead Institute for Biomedical Research, Washington University School of Medicine, and the Sanger Centre have been retained by the consortium to carry out SNP discovery using Perkin-Elmer ABI sequencing machines. The Stanford Human Genome Center and the Sanger Centre will then map at least 150,000 SNPs.
While participating labs are validating their discoveries by resequencing, Orchid will employ a more efficient technique involving polymerase extension technology to assay and confirm, or "score," the SNPs. Based on preliminary studies, Stein said the labs expect 95 percent of their SNPs to be validated.
"A lot of work in pharmacogenetics is done using sequencers, not only for discovery, but then for confirmation," remarked Dale Pfost, president and CEO of Orchid. "Our technique takes over after discovery, and is about 100 times more efficient on a per-run basis." He added, "It's like a high-throughput screening process where we're only focusing on the bases that are known or thought to be SNPs." Orchid intends next week to introduce a commercial SNP-scoring instrument called SNPstream. The product employs the patented polymerase extension Genetic Bit Analysis technology that Orchid is applying to the consortium's data.
Involvement with the consortium project is something of a coup for Orchid, which is positioning itself to be the leading supplier of SNP-scoring technology and products--a strategy that hinges on the discovery and dissemination of large numbers SNPs.
Russ Granzow, Orchid's senior director of business development and marketing, remarked, "SNPs are the raw material for a lot of the research that will go on in the genetic variation field. Once they're out there people will adopt them and start to run hundreds of their own experiments using, we hope, our products."
Pfost said Orchid is also benefiting from helping the SNP Consortium by establishing Genetic Bit Analysis as a standard for validation, but added, "we really think the high ground is going to be in finding the utility of SNPs by scoring them on large populations."
Several steps are required for SNPs to be useful in drug discovery, he explained: "You first discover the early potential SNP; then you confirm its presence or absence; third, you look for the utility of that SNP. The technologies we're providing are geared toward finding the utility in SNPs." And of course, Pfost added, Orchid is in separate discussions now with each of the SNP Consortium members about helping them do just that.