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SNP Analysis Determines Origin of Mad Cow Case 1/15/04

Fri, 01/16/2004 - 4:49am
The origin of the recent case of bovine spongiform encephalopathy (BSE), or mad cow disease, in the United States was determined using MassArray technology from ">Sequenom Inc. , San Diego. Genaissance Pharmaceuticals Inc., New Haven, Conn., and GeneSeek Inc., Lincoln, Neb., were chosen by the US Department of Agriculture (USDA) to use the platform to independently screen samples of DNA from suspected animals.

"We used the MassArray to trace the lineage of the cow that was found to have BSE," says Daniel Pomp, PhD, vice president and chief scientific officer of GeneSeek. "The screen is very similar to parentage analysis."

With the limited paperwork they had, the USDA suspected that the cow originated in Canada, says Pomp. "We needed to definitively place the cow's origin in Canada and find the sire (father) that it came from. This needed to be done very quickly and accurately. There were huge implications for world cattle markets," he says.

GeneSeek used the MassArray to confirm the results they obtained with more traditional DNA analysis based on microsatellites. "Analyzing SNPs (single-nucleotide polymorphisms) is a new way of doing parentage analysis, but it was important for validating our information," says Pomp."The assays were developed in 2000 with the purpose to perform cattle identification whenever the need arose. And the need arose," says Charles Cantor, PhD, chief scientific officer at Sequenom. "The USDA was our first commercial customer in the United States. They developed the assays on the Sequenom platform, which now includes 45 SNPs. The test was made available to Genaissance and GeneSeek [so the companies could] run them independently. The tests were done at a very intense pace over New Year's weekend and showed unequivocally that the infected cow was of Canadian descent," says Cantor."Our technology is based on mass spectronomy," says Cantor. "This is state-of-the-art technology for cattle identification. It uses a set of markers that are so dense it's essentially foolproof. Microsatellites are more error prone, manual and expensive."

The disease scare has grave implications to the US food supply, but it provided a valuable proving ground for Sequenom's MassArray. "This case, while unfortunate, called attention to the technology," says Cantor. "We're pleased that this new application has emerged. I think it will do a lot of good."
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