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At Your Service Next Year: National SNP Genotyping Center at Broad Institute

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The first national SNP genotyping center is slated to open its doors in January at the Broad Institute of MIT and Harvard University.

Equipped with $14 million over five years from the National Center for Research Resources, the new National Center for Genotyping and Analysis will offer large-scale SNP-genotyping services to public and private researchers, according to Director Stacey Gabriel.

Gabriel currently manages all genotyping at the Broad Institute and serves as scientific director of Broad’s portion of the International HapMap Project. The new center will employ three SNP-genotyping platforms already installed at the Broad: Illumina’s BeadLab station, Affymetrix’s GeneChip platform, and Sequenom’s MassArray system.

Gabriel only plans to acquire small pieces of equipment for the new center to complement the existing systems. But she is looking to ramp up personnel, bringing in two new project managers, a handful of technical staff, and a few programmers or software engineers.

A portion of the funding — about $1 million per year — will go towards subsidizing academic genotyping research projects. These will be chosen by a steering committee, Gabriel said, and will have to have undergone some form of peer review — for example, by winning an NIH grant. Successful applicants will receive a 50 percent discount on the cost of genotyping for their project.

At present, Gabriel charges between about 5 cents and 20 cents per genotype, depending on the platform. But the price could come down in the future when new technologies arrive, she said, allowing researchers to conduct whole-genome association studies that are currently cost-prohibitive.

Higher-density chip technology might be the first new technology to be adopted by the center: “Affymetrix has a good chance of greatly increasing the SNP density to a point that we could do whole-genome association studies for a reasonable cost,” Gabriel said.

Indeed, Affymetrix said last month that it will provide the Broad Institute with next-generation SNP genotyping arrays, based on the same technology that underlies its current Mapping 10K and 100K arrays, and that it plans to make these arrays broadly available in the future.

But other technologies, based, for example, on single-molecule sequencing, are also on Gabriel’s radar. “We will wait to see until they are proven,” she said. “They are close right now to doing genotyping with those technologies, that’s something to think about.”

The NCRR has been funding two other genotyping centers, the Johns Hopkins Center for Inherited Disease Research and the Marshfield Center for Medical Genetics, according to an NCRR spokeswoman. However, the Broad Institute’s will be the first center to focus solely on SNP analysis. “As I understand it, SNP is becoming the emerging preferred technology,” the spokeswoman said.

— JK

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