NIH Funds First National SNP Genotyping Center
at Broad Institute
Bethesda, Maryland — The National Center for Research
Resources (NCRR), a component of the National Institutes of Health
(NIH), announced today it will fund the first national center for
high-throughput genotyping dedicated solely to large-scale SNP (single
nucleotide polymorphism) analysis at the Eli and Edythe L. Broad Institute
of MIT and Harvard University in Cambridge, Mass. A five-year cooperative
agreement will provide over $14 million to create a high-capacity
resource so that U.S. researchers can quickly and cost-effectively
carry out large-scale studies of genetic variation in humans and animals
to advance disease gene identification.
Research on genetic variation is aimed at improving the diagnosis
and treatment of numerous diseases of humans that may have significant
genetic components — such as Type 1 diabetes, schizophrenia,
and some types of cancer — by identifying specific genetic markers,
or genotypes, that are associated with particular diseases or responses
to drug therapies. Studies examining genetic variation in animals
such as mice and rats can identify genetic regions that, in humans,
may contribute to complex diseases such as diabetes and hypertension.
“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 NCRR Division for Clinical Research Resources Director Anthony
Hayward, M.D., Ph.D. “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.”
Many diseases can be traced to inherited differences in each individual’s
genes. The most common type of variation in the human genome is the
single nucleotide polymorphism, or SNP (pronounced “snip”).
A SNP 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, although no
two individuals will vary at every such position. 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, well-characterized collections
of patient data and design experiments using secure informatics tools
for sample management.
An integrated SNP selection tool will be provided 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. Two decades ago, the cost was $10 per genotype, and
prices are expected to drop further as technology improves. A portion
of the center’s annual budget will be used to partially support
compelling genotyping research projects, to be selected by a steering
committee.
The first genotyping studies within the NCRR-funded Broad Institute
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 ncrr_gc@broad.mit.edu
or refer to the Broad Institute Web site, www.broad.mit.edu,
which will contain details on the application process later this fall.
Stacey Gabriel, Ph.D., the new center’s principal investigator
and director, currently oversees the Broad’s Genetic Analysis
platform where she manages all of the genotyping, SNP discovery, and
production activities related to human genetics. She also serves as
scientific director of 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
(www.hapmap.org).
“We are thrilled that the NCRR has selected the Broad Institute
for this important responsibility. 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,” said
Eric Lander, Ph.D., founding director of the Broad Institute.
High-resolution images of SNP technologies used by the Genotyping
Center are available at http://www.ncrr.nih.gov/genotyping.asp.
NCRR is part of the National Institutes of Health, an agency
of the Department of Health and Human Services. NCRR is the nation’s
leading federal sponsor of resources that enable advances in many
areas of biomedical research. NCRR support provides the scientific
research community with access to a diverse array of biomedical research
technologies, instrumentation, specialized basic and clinical research
facilities, animal models, genetic stocks, and such biomaterials as
cell lines, tissues, and organs. Additional information about NCRR
can be found at www.ncrr.nih.gov.
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