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USDA Will Use Sequenom s MassArray System to Beef Up Livestock Database

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CLAY CENTER, Neb.--With newly installed, high-speed, mass-spectrometry-based, genotyping technology from the San Diego-based company Sequenom, the US Department of Agriculture's Meat Animal Research Center here will be able to expand upon what already may be the most extensive public livestock genomics database available.

Researchers at the center will use Sequenom's MassArray System to discover and score single-nucleotide-polymorphism markers in cattle, sheep, and swine as part of a livestock genomics project launched eight years ago. Finding and scoring SNPs in livestock will enable them to understand the causes of diseases in animals, develop therapies and prevention techniques for them, and carry out genetic-marker-assisted breeding.

Dan Laster, the research center's director, told BioInform that SNPs will be employed in livestock genomics to improve the efficiency, effectiveness, and safety of meat production. For instance, he said, SNPs could provide "some means of determining what genes control or effect the relevant tolerance to E. coli 15787, for which we have a major program here."

The facility, Laster added, is the world's largest livestock genomics resource, with a multimillion-dollar budget. About 15 scientists here work strictly in genomics research, and another dozen contribute to livestock genomics. Laster noted that, with only two PE ABI 377 machines for SNP discovery and a single PE ABI 3700 for sequencing expressed-sequence tags, the center is more a research than a sequencing facility.

Even so, scientists here expect to have compiled a major share of pig and cattle libraries in the next 14 months. They have already produced and stored in an interactive database on the internet (http://www.sol.marc.usda.gov) the most extensive livestock linkage maps available, Laster claimed. Data generated by the MassArray System will be integrated with those databases as well as with other farm animal genomics databases and with human databases, Laster said. Human genomic data, he explained, will be of great value to livestock research. Because animal genomics projects cannot yet afford to sequence entire genomes, livestock researchers look at ESTs, relate those to similar genes in humans, and then observe expression of those genes in livestock, he said.

Biomedical technology applied to animals

USDA's relationship with Sequenom was initiated two years ago. "We'd done genotyping with gels and we were interested in a rapid method as well as a mass-spectrometry-based one that did not require so much manual interpretation," Laster said. "Previously, we viewed the rapid collection of genotypic data as a rate-limiting step in our genome program." Sequenom's technology will remove that constraint, he said.

Toni Schuh, Sequenom's executive vice-president of business development, observed that the ARS center now possesses "a technology so accurate that they can deal with reasonable sample sizes, and a technology so powerful and fast that they can handle these sample sizes. That's really new and that's why they share our excitement about the technology."

Samples for the MassArray System are prepared using standard enzymatic technologies, Schuh said. Then the mass spectrometer separates nucleic acid fragments and determines their identity by molecular weight. He explained, "The advantages are that we do not need any label to see a molecule because we see a property that is intrinsic to the molecule--it's weight, and we are dealing with a method that is physically accurate and therefore far more accurate than anything else that is out there."

Laster said Sequenom's technology "is something that is needed very much" to process large numbers of samples. There's no question that the research center will use SNPs in research and development, he said, "So the more we get, the greater need we have for high-speed genotyping."

Schuh called the use of the mass-spectrometry technology in SNP discovery a paradigm shift. "For the first time you get an analysis signal that is coming from the molecule itself with a precision and accuracy that is as much as 300 times higher than conventional separation methods."

Although the MicroArray System is being tested elsewhere in pharmaceutical and human health care uses, Schuh sees vast opportunities for the technology in agriculture. For instance, he explained, "USDA is probably the most renowned animal genetics research institution in the world. If it comes up with a set of genetic markers that have been proven useful in animal breeding, then immediately there are quite a number of potential customers for Sequenom systems. All people involved in large-scale or commercial animal breeding will want to use these markers and will want to use our system to run these markers of the animals they are breeding." Major ag biotech companies such as Monsanto, Novartis, and DeKalb are looking to marker-assisted breeding as a key strategy for producing seeds, he noted. "They will follow exactly the same strategy that the USDA is applying now to cattle, and will need the same tools in much larger orders of magnitude." Sequenom will launch the MassArray product commercially later this year.

--Adrienne Burke

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