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GeneSeek to Expand Menu of Ag Chips in Bid to Bring 'Genomics to the Masses'


By Justin Petrone

Agrigenomics service provider GeneSeek will this year add several new agriculture-related SNP genotyping arrays to round out its offering to livestock researchers and breeders.

GeneSeek's new products will include low-density arrays for beef and dairy cattle, as well as a medium-density option for bovine research, and low-density arrays for association studies and genomic selection in pigs and chickens.

Daniel Pomp, GeneSeek’s co-founder, discussed the pending availability of the arrays at the Plant and Animal Genome Conference, held last week in San Diego. Pomp currently serves as a consultant for GeneSeek's parent company Neogen.

Illumina will manufacture all of the new arrays in its Infinium iSelect custom genotyping format. GeneSeek has branded the new bovine chips as the Genomic Profiler Low Density for Beef Cattle, the Genomic Profiler Low Density for Dairy Cattle, and the Genomic Profiler 90K for Bovine.

Pomp said that the company partially selected content for the new chips from arrays already on the market. The Genomic Profiler Low Density arrays for dairy and beef cattle, currently in the process of being introduced, are based on the existing Illumina BovineLD, but add disease tests for beef and dairy cattle. The arrays also include SNPs from Illumina’s 3K bovine array that were not included on the BovineLD chip Illumina launched last year. According to Pomp, the inclusion of these SNPs will help with "continuity and comparability" for GeneSeek customers who have used the 3K in their previous studies.

In three months, GeneSeek will also debut the Genomic Profiler 90K, a "merger" of Illumina’s BovineHD, BovineSNP50, and BovineLD arrays. It includes all the SNPs on the BovineLD, 24,000 of the "best and most informative" SNPs from the BovineSNP50, and 53,000 SNPs from the BovineHD that were selected "based on impact on dairy net merit."

In addition, GeneSeek has added to the Genomic Profiler 90K array 10,000 new SNPs from different varieties of beef and dairy cattle breeds, with the idea that the SNPs might detect genetic variation that occurred after the content for the older bovine arrays was selected.

According to Pomp, GeneSeek worked with US Department of Agriculture-Agricultural Research Service geneticists Curt Van Tassel, George Wiggans, Paul VanRaden, and Matthew McClure to develop the new suite of bovine-related chips.

In addition to planning new arrays for chicken and pig studies, GeneSeek is looking to develop a high-density genotyping array for mouse studies. The company last year launched a 9,000-marker mouse chip, and is creating an 80,000-marker chip for that community.

Neogen spokesperson Rod Poland said that the company is eager to create new lower-density arrays to enable "imputation in pig, chicken, and any species where training sets are available on higher-density chips." He did not provide further comment on the new arrays.

According to Poland, GeneSeek already offers the Illumina BovineHD, BovineLD, and BovineSNP50 Beadchips to its clients, as well as the Affymetrix Bos-1 High Density array. The company also offers the CanineSNP50, PorcineSNP60, and OvineSNP50 arrays from Illumina’s catalog; as well as custom EquineSNP70 and GoatSNP50 arrays.

Poland said that the company sees "growing demand" for new genotyping arrays, hence the product introductions.

"The market is growing – this year we are experiencing a greater than 10 percent increase in sample volume in cattle and porcine genotyping – and globally for various commercial genotyping arrays we see a growing demand for additional tools," he said.

He attributed the demand to dropping costs for genotyping arrays. "As Illumina and Affymetrix technologies have become more affordable, a greater number of species can now be genotyped on these platforms, essentially bringing genomics to the masses," he said.

Founded in Lincoln, Neb., in 1998, GeneSeek was acquired by Lansing, Mich.-based Neogen for $13.5 million in stock in 2010 (BAN 4/6/2011). According to Poland, the acquisition has allowed GeneSeek to "expand and grow faster due to additional resources and investment."

At PAG, Pomp noted that GeneSeek recently hired managers to cover the European and Latin American markets (see related story, this issue). Neogen has provided GeneSeek with a larger global presence: While GeneSeek has maintained a European presence with an office in Nottingham, UK, since 2007, Neogen maintains offices in the UK, Mexico, Brazil, and China.

Have topics you'd like to see covered in BioArray News? Contact the editor at jpetrone [at] genomeweb [.] com