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Delta Genomics Plans to Develop Genotyping-by-Sequencing Assays for Livestock

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About a year after opening, the Edmonton, Alberta-based Delta Genomics Center's primary focus is SNP-based analysis of cattle, including developing genotyping-by-sequencing assays for cattle and other livestock.

The center is the service arm of Livestock Gentec, a research center supported by the Alberta government and by the Alberta Livestock and Meat Agency.

Delta Genomics is equipped with Life Technologies' SOLiD 5500 and an Illumina HiScan SQ, as well as genotyping arrays, and recently received a C$575,000 (US$583,000) grant to facilitate SNP testing of cattle to determine parentage.

Colin Coros, the center's vice president of operations, said that the center provides three main services: biobanking, genotyping, and next-generation sequencing.

The biobank serves as a way for customers to "retest historical samples with the latest technology or for the latest markers," Coros told In Sequence.

Genotyping is currently the center's most common service and as such it is equipped with all "major genotyping platforms that are available," Coros said. However, it also offers next-gen sequencing including whole-genome sequencing, targeted sequencing, and RNA-seq.

Coros said that moving forward, the center will likely transition from array-based genotyping to sequencing-based, and one project the center is focused on is in developing genotyping-by-sequencing assays.

"It's the genotypes that our customers want," he said. "But they don't care how they get it, and it's looking like genotyping-by-sequencing might be the cheapest way."

While the center currently has the 5500 and HiScan SQ, Coros said he is always evaluating new sequencing technology. For livestock applications, "the number one driver for new technology will be cost," he said. "So when I'm evaluating platforms, the bottom line is, 'How much cheaper can I do it?' The industry is very price sensitive."

Currently, of its next-gen sequencing customers, about half request whole-genome sequencing and half order RNA-seq. Depending on the number of samples, the transcriptome sequencing can often be done on the HiScan SQ, Coros said.

The center originally purchased the HiScan for its array capabilities, but as sequencing became more widespread, it added on the sequencing capability, Coros said. "For a lot of our RNA-seq work, we don't really need that high of capacity, so it made sense to add that on."

The 5500 machine helped boost the center's capacity and also gave it "access to two competing technologies," he said. Additionally, they previously had a SOLiD 4, so "had some expertise and familiarity with the chemistry."

Aside from working to develop genotype-by-sequencing assays, Coros said the center is involved with larger sequencing projects with Genome Canada. One project, which is being led by its parent organization, Livestock Gentec, involves sequencing 30 animals from each of the 10 major bovine breeds in Canada and genotyping 10,000 of the "key ancestral bulls in Canada," Coros said.

The center is doing some of the sequencing itself and contracting some out, Coros said.

Additionally, it is involved in a project studying pig viruses and is genotyping and doing RNA-seq of pigs to help identify animals that are genetically more resistant to disease and to try and understand virus/host responses to eventually eliminate the viruses from the population.

Aside from the government-funded projects, Coros said the majority of Delta Genomics' customers are academic customers, with a few commercial customers. "But we've been growing our industry customers over time and as more and more of these genomic tools come on the market, we see a real growth potential in industry."

The center seeks to distinguish itself as a service provider by offering expertise in the livestock industry, Coros said. Because the center is small, it cannot compete with sequencing service providers like BGI on cost. "BGI is setting the bar for sequencing," he said. "They've got access to hundreds of next-gen sequencers, so it's hard to compete on [cost], unless you have some added value."

In the near term, Coros said that the center's main focus would be developing the genotyping-by-sequencing assays and determining which sequencing platform to run those assays on. Because cost is the primary driver, he said he would be evaluating all the recently launched and upcoming platforms to determine which would best suit the center's needs.

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