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National center based at MIT to study genotyping

Stacey Gabriel, principal investigator and director of the new National Genotyping Center at the Broad Institute.
Stacey Gabriel, principal investigator and director of the new National Genotyping Center at the Broad Institute.
Photo courtesy / Broad Institute

A $14 million grant to the the Eli and Edythe L. Broad Institute of MIT and Harvard will allow U.S. researchers to quickly and cost-effectively carry out large-scale studies of genetic variation in humans and animals, work key to the identification of genes linked to disease.

The funds from the National Center for Research Resources (NCRR), a component of the National Institutes of Health (NIH), will establish the first national center for high-throughput genotyping dedicated solely to the analysis of large-scale SNP (single nucleotide polymorphism), the most common type of variation in the human genome.

"We are thrilled that the NCRR has selected the Broad Institute for this important responsibility," said Eric Lander, founding director of the Broad Institute and a professor of biology at MIT. "Human genetics is undergoing an extraordinary transformation, which is leading to the ability to take a comprehensive view of all human genetic variation and its association with disease. The National Genotyping Center at the Broad will make this capability accessible to many biomedical researchers and thereby have a direct impact on the understanding of disease."

Many diseases can be traced to inherited differences in each individual's genes. A SNP (pronounced "snip") is a single DNA base pair, or unit of DNA, the sequence of which can vary from individual to individual. It is estimated that there are at least 10 million SNPs in the human population. Scientists have found that certain SNP combinations are associated with predisposition to particular diseases or adverse drug reactions.

The new center will offer tools to aid in the selection, discovery and analysis of SNPs by providing broad access to flexible, accurate and affordable genotyping and sequencing. Integrated computational tools will help researchers manage large collections of patient data and design experiments using secure informatics tools for sample management.

"The tremendous potential of genetic research makes it critical that we develop this central resource so investigators around the country can access high-capacity genotyping with the additional benefits of economies of scale, quality assurance and data sharing," said Anthony Hayward, director of the NCRR Division for Clinical Research Resources.

"The demand for genotyping will grow exponentially as investigators prioritize potential targets for treatment and as members of afflicted families try to better estimate their risk for a particular condition."

The new center will provide an integrated SNP selection tool to automate queries and create SNP panels. A secure, web-based environment will provide access to a database linked to an in-house DNA repository and all samples will be coded to assure subject confidentiality. Results will be accessible to the investigators through a secure database integrated with a suite of data management and analytic tools for analysis of correlations among variants and with disease phenotypes.

Because investigators use different technologies based on the scales and configurations needed, a menu of services will be offered using three different technology platforms. When fully operational, the center will be able to process from 200 million to as many as billions of genotypes per year, depending on the technology platform used and the needs of outside users.

The cost for genotyping will be on the order of pennies per genotype, varying according to the technology platform used. Prices are expected to drop further as technology improves. Two decades ago, the cost was $10 per genotype. A portion of the center's annual budget will be used to partially support compelling genotyping research projects.

The first genotyping studies within the new genotyping center will be performed in early 2005. Researchers interested in access to the center or applying for subsidized genotyping should contact the Broad Institute at or refer to the Broad Institute web site for details on the application process later this fall.

Stacey Gabriel, the new center's principal investigator and director, currently oversees the Broad's genetic analysis platform; she manages all of the genotyping, SNP discovery, and production activities related to human genetics. Gabriel also serves as scientific director of the Broad Institute's portion of the International HapMap Project, a collaborative public project designed to advance genetic research and its application to disease gene discovery by determining patterns of genetic variation throughout the human genome.

The Broad Institute (rhymes with "code") is a research collaboration of MIT, Harvard University and its hospitals and the Whitehead Institute for Biomedical Research. The Broad's mission is to create comprehensive tools for genomic medicine, make them freely available to scientists worldwide and pioneer their application to understand and treat disease.

A version of this article appeared in MIT Tech Talk on October 20, 2004 (download PDF).

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