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New National Agricultural Genotyping Center to Rely on Luminex-based SNP Genotyping Platform

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NEW YORK (GenomeWeb) – A Luminex-based SNP genotyping assay will serve as the main workhorse for a major new facility that intends to serve the US agricultural sector.

Rick Vierling, director of research and new uses at the National Corn Growers Association, told BioArray News this week that the NCGA's planned National Agricultural Genotyping Center will rely mainly on the assay for its fee-for-genotyping services, contract research, and business development needs.

NCGA, a Chesterfield, Mo.-based organization that represents the American corn industry, partnered with Los Alamos National Laboratory and the Donald Danforth Plant Science Center in 2011 to create the center. Last week, the NCGA announced that it had selected Fargo, ND, to host the facility, which Vierling said will cost $2.5 million to set up, employ about 10 personnel, and likely be operational by the spring of 2015.

"The growers need and want new traits and improved genetics if they are going to continue to provide the world's safest and inexpensive food supply," said Vierling of the new center. He noted that the facility will not only serve the corn industry, but will partner with researchers "working in all crops, livestock, and microbiologists."

In addition, the new center will serve both private and public researchers. "This center is set up to be a development center," said Vierling. "Yes, it will do research, but a major function will be in business development," he said. "The goal is to bridge the gap between public research and commercialization."

The planned National Agricultural Genotyping Center will operate as a nonprofit with the goal of helping private industry, vetting technologies, and collaborating in joint ventures or spinning out for-profit companies. Given its various objectives, Vierling said that the center will serve a need not yet met by academic centers or for-profit CROs.

"By helping with product development and getting more traits and genetics to market, the farmers will benefit from increased competition in the marketplace," Vierling said. "Also farmers will have access to genotyping, which will be as commonplace in their production as data-driven technology is now," he added.

On the center’s website, organizers list potential clients from the government, academic, and private sectors, including the US Department of Agriculture, the Environmental Protection Agency, various colleges, universities, agriculture-focused companies, veterinarians, and farmers. Suggested services include food testing, environmental monitoring, genomic selection, pathogen detection, and confirmation of parentage in livestock.

The core genotyping platform within the new facility will be an assay called multiplex oligonucleotide ligation-PCR that was developed at Los Alamos National Laboratory.

Researchers at Los Alamos first described the approach in two papers that appeared in Advances in Experimental Medicine and Biology and the Journal of Microbiological Methods in 2010.

According to the studies, MOL-PCR is a four-hour multiplex nucleic acid assay. It consists of a single-tube reaction, followed by hybridization to a Luminex bead array for detection and uses flow cytometry for detection and readout. The authors described the assay as versatile, and capable of interrogating insertions/deletions, SNPs, and the presence or absence of various signatures through the use of specific probe sets.

In the JMM paper, they argued that the approach could “accomplish a higher level of multiplexing more easily than RT-PCR” because it employs a pre-PCR ligation step that accomplishes the target detection. Following amplification and labeling, the PCR products are hybridized to Luminex’s xTAG microsphere array.

According to the paper, up to 100 genetic markers can be analyzed in each assay, and, because it uses 96-well plates, an equivalent of 9,600 assays can be obtained in a single run. Parallel processing and the use of 384-well plates can drive the throughput even higher.

It is this high throughput — and associated low cost — that led the organizers of the new center to favor MOL-PCR over other approaches. In a white paper describing the project, they cited the technique as cost effective and customizable. They also stated that a single assay can provide information on up to 125 times more traits at a 25-fold lower cost than competitive technologies, without naming them. The organizers also claimed that MOL-PCR can generate 15 million data points in a single week using two Luminex instruments.

According to the paper, the technique was initially developed for the US Department of Homeland Security for pathogen detection, but has been licensed to the new center for agricultural purposes. Given its role in developing the platform, Los Alamos retains special bioinformatics capabilities that also support the use of MOL-PCR by the new center, the organizers stated in the paper.

However, Vierling noted that the new center will not be “technology-centric” and stressed that it is “not picking one platform over another,” a fact supported by the white paper, which stated that Taqman PCR, quantitative PCR, microarrays, Sanger sequencing, and enzyme-linked immunosorbent assays will all be in use at the new center in Fargo. Investigators who partner with the center will also have access to next-generation sequencing for discovery projects through cooperation with Los Alamos' facilities.

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