SAN DIEGO – GeneSeek, an Lincoln, Neb.-based company that provides genomic services to agricultural researchers and breeding companies, recently introduced a new, high-density porcine array.
Jeremy Walker, a marketing director at the firm, said that the chip, called Genomic Profiler Porcine, is based on the catalog 60,000-marker Illumina chip but contains different content as well as 10,000 additional SNPs.
He discussed the new array during a workshop at the Plant and Animal Genome conference, held here this week.
"A lot of our customers that run these chips heavily will begin by using catalog Illumina products," Walker told BioArray News at the conference. "GeneSeek goes one step further and improves on it, remov[ing] the SNPs that are not as informative, as well as adding causative SNPs that have known impact on specific traits — so there might be a trait that improves feed efficiency [or] one that increases resistance to a particular disorder," Walker said.
In the case of the new chip, the array contains a SNP known to be related to tolerance of porcine reproductive and respiratory syndrome, or PRRS.
"An animal may be infected by the virus, but has no symptoms, and so it thrives in the population," said Walker, "whereas in other animals that are susceptible, they don't gain weight, they don't thrive, and it costs the breeder a lot of money."
By including such markers on the expanded porcine array, customers "get the best of both worlds," he said. "You get a tool that is used for genomic selection, but you also have the ability to collect information for no additional cost for causative SNPs."
GeneSeek also offers high-density Genomic Profiler tools for dairy and beef cattle. The arrays are manufactured on Illumina's 24-sample iSelect platform. Walker said that the company often includes private content from multiple partners on its custom arrays, but runs the chips in house, and masks the data it returns to clients. In that way, it is able to reduce costs passed on to customers, rather than making individual arrays for each client.
"GeneSeek is kind of like the Switzerland of the market," said Walker. "Everybody comes to us, but we are neutral and we run the projects and report back the data," he said. Walker noted that by offering such a fine-tuned service, Illumina does not need to "get down to that micro-level" to serve breeding companies.
As an example, he noted that GeneSeek has built out content on Illumina's 7,000-SNP chip for genomic selection in dairy cattle, and said that GeneSeek will by April make a newer version available that contains about 23,000 SNPs.
"We make content better, but cost stays the same, because volumes are higher, so we can keep costs low," he said.
In addition to high-density arrays for porcine and dairy and beef cattle, and the lower-density bovine array, GeneSeek continues to offer a 10,000-SNP chip for porcine studies, as well as services on catalog Illumina arrays for studying ovine, equine, and canine researchers. The company also offers a Mouse Universal Genotyping Array that contains 76,000 markers.
Implementing GBS
While researchers and breeding companies have an ever-expanding number of tools available to them, GeneSeek is aware that genotyping-by-sequencing (GBS) is becoming a popular approach in the agricultural research community. He said that GeneSeek is currently establishing next-generation sequencing in house, that GBS is in a beta testing phase, and that the company hopes to be able to offer GBS as a service to its customers by the middle of the year.
"In contrast to popular belief, the cost of whole-genome sequencing is not as cheap as the volumes we operate in," Walker said. "I think it will be cheaper fairly soon, so we are investing in our next-generation sequencing resources, once it becomes cheap enough to offer commercially," he said.
The company also continues to expand the number of lower-density arrays it offers to its clients. Walker said that such chips will "work synergistically" with its higher-density arrays.
"The idea is that you can offer a lower cost chip for maybe half the price and then impute step wise up to each of those higher densities," said Walker. "The power of imputation is getting better and better, so if you can spend $20 on a 3,000-SNP chip and have 95 percent accuracy up to 40,000 SNPs, it makes sense," he said. "You will lose out on a little bit of accuracy, but depending on the focus of the breeding program, if it costs half as much you can get a lot more information out of it."