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USDA-Hosted Consortium Aims to Deliver Pig SNP Chips to Market by Next Summer

The US Department of Agriculture, the University of Illinois, Iowa State University, and the National Pork Board are pooling their resources and reaching out to the international porcine community to aid in developing a high-density SNP chip for pigs that could ultimately aid in biomarker discovery.
ISU’s Max Rothschild, who also serves as the USDA’s pig genome coordinator, told BioArray News this week that the consortium is amassing SNPs from public databases and individual labs around the world and that an “affordable” 50,000-feature SNP chip could be available to the public through the consortium as soon as next summer.
Rothschild said that the consortium has not yet determined which array vendor will manufacture the chip.
According to Rothschild, the main objective of the consortium is to enable more genetic discoveries in the pig that could benefit both the agricultural community by allowing them to breed better animals, and researchers that use pig as a model organism for studying human diseases like diabetes and obesity.
“We are trying to find genes of interest that effect liver size, growth rate, feed efficiency, and things of that nature,” he said. In terms of benefit to human healthcare, Rothschild said that the “pig is more closely aligned physiologically to what a human is in terms of heart and lung issues related to obesity and diabetes.
“If you could determine genes that [are] associated with diabetes in the pig or genes associated with other disorders affecting lungs or heart, the pig could be used as a model in human work,” he added.
Unlike other agricultural species like the horse, cow, or chicken, the pig has not yet been fully sequenced and whole-genome information is not expected to become available until 2009 when a consortium led by the Wellcome Trust Sanger Institute completes the project.
In light of that lack of sequence information, Rothschild said it made the most sense to generate SNP arrays for the community that would be available at an affordable price for academic researchers for use in whole-genome analysis studies.
“These SNP chips are very expensive and we derive a discount when we have more bodies buying the products,” he said. “There is an enormous desire to find genes that are associated with economic traits of interest and a SNP chip would allow a much faster way to do association studies.”
Interest from Industry
While the main actors in the consortium to develop a pig SNP chip are in government and academia, Rothschild said there is a clear link between the discovery work that could be done on the 50K chips and the animal testing market.
For example, ISU recently licensed the rights to five genetic markers to Lincoln, Neb.-based GeneSeek, which sells genetic tests to the pork industry. The five markers, discovered in Rothschild’s lab at Iowa State, enable breeders to test for traits related to feed intake and conversion, weight gain, lean growth, fat content, and meat quality in pigs.

“It could be used by anybody from Farmer Ted, your individual breeder, all the way up to the biggest industry breeders.”

Jeremy Walker, director of customer solutions and marketing at GeneSeek, told BioArray News this week that the company rolled out the markers last month through its Seek-Gain Swine Performance Trait Testing Program, with an initial offer of all five tests for $22 per sample. GeneSeek uses a variety of platforms in its services, including a Sequenom MassArray platform.
He said that GeneSeek expects strong demand for the program.
“Historically we have been doing similar types of tests within the pig industry for several years and tests related to performance traits have been very well received,” he said. “So based on the history, I anticipate that these newer tests will be well received.”
In terms of the market, Walker said that the low cost of the genetic tests should enable a broad reach. “It could be used by anybody from Farmer Ted, your individual breeder, all the way up to the biggest industry breeders. So there’s really an unlimited market size,” said Walker.
According to Rothschild, the deal with GeneSeek is indicative of how biodiscovery fueled by array technology can have a direct impact on agricultural markets. “Breeding companies take DNA samples from animals and select pigs based on their genetic markers,” he said. “So we are moving towards something we hope eventually that will be called genomic selection,” said Rothschild. “Basically you would be selecting animals for breeding [based] on thousands of genes. You would then develop a breeding value estimate based on genomic effects.”
Looking for a Platform Provider
Through his role as the USDA’s pig genome coordinator, Rothschild previously helped create a line of pig expression arrays for researchers. For example, Rothschild and fellow porcine researchers teamed up to create a swine protein annotated oligonucleotide microarray manufactured by Qiagen and Operon in 2006 that is presently being used by approximately 30 labs worldwide.
Also, over the past year, Illumina helped produce a 7,500-feature porcine SNP chip for use by a smaller group of porcine scientists. Rothschild said the consortium might turn again to Illumina for the 50K chips in development, though he stressed that the group had not yet determined which provider it would work with.
“Illumina is certainly one of the possibilities that could be the provider,” he said. “There are only three or so companies out there that can do this and we will go with the best provider with the best cost,” he said.
Right now, however, the consortium is focused on getting enough interested parties so that it can negotiate an affordable price with whomever it chooses to be the array manufacturer. “We are getting a lot of interest and I am collecting names from commercial and research groups throughout the world,” said Rothschild. “The question is will we have enough people who want to buy.”

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