NEW YORK (GenomeWeb) – During the annual Plant and Animal Genome Conference last week, Affymetrix announced the launch of a new Eureka genotyping-by-sequencing kit, as well as two updates in its Axiom line of array products for agricultural genomics.
Overshadowed somewhat by news of Affy's acquisition by Thermo Fisher Scientific, the new kit version of Affy's Eureka genotyping solution is something that the market has anticipated since the company bought Eureka Genomics for $15 million in the spring of 2015.
Shantanu Kaushikkar, director of product marketing for Affymetrix's genetic analysis business unit, told GenomeWeb that some customers including those inherited from Eureka have already been able to access the low-cost, low-plex genotyping solution as a service since the acquisition.
But the plan at that time was also to develop a kit version of the product for Affymetrix customers to run in their own facilities.
Eureka is a targeted genotyping-by-sequencing (GBS) solution that delivers high-throughput sample processing with low cost per sample to enable analysis of between about 300 and 3,000 target SNPs.
According to Kaushikkar, Eureka overcomes several challenges associated with other available GBS technologies, including variability in genomic reads, missing SNP information, a need for high-quality DNA, potentially complicated informatics, and relatively high cost. As such, it addresses a more niche need in the ag-bio sector: cheap and reliable interrogation of a set of known target markers in a large number of samples.
While other GBS technologies sequence larger regions of the genome, Eureka pulls out specific target SNPs using a process of triplicate barcoding.
"There is no other platform right now that can look at 300 to 3,000 markers in this type of affordable way," he said. "There are lots of GBS methods, but they rely on capturing and sequencing a whole region of the genome [rather than a single SNP of interest] so you are at the mercy of the samples and the sequencing. You don’t have as much control. We saw that Eureka addressed some of the problems with those technologies."
Importantly, the technology also extends Affy's reach in the agrigenomics space beyond the high-throughput applications addressed by its Axiom arrays.
"In many agricultural applications, customers are at a place where they only need 1,000 or 1,500 markers, not 50,000," Kaushikkar explained. "They’ve characterized their population of animals or plants or whatever if it may be, and they have 1,000 or 1,500 markers that they know now are critical to their breeding program."
Affymetrix's overall ag-bio revenues have increased to account for roughly 25 percent of its total genotyping revenue as of the company's most recent financial results. Kaushikkar said he couldn't quantify what effect the new kit version of Eureka, along with the company's existing service-based Eureka genotyping, may have on the firm's overall agricultural business going forward, but he explained that Affymetrix does see the platform allowing it to reach more customers who have had an otherwise unmet need.
At the same time as it announced the launch of a new kit version of Eureka, Affy also said it is making available two new array configurations for its Axiom genotyping platform, which widen throughput choices for the company's customers.
The new 24-sample configuration on the high-density Axiom 96 platform can interrogate upward of 800,000 markers while the new 96-sample configuration on the Axiom 384 HT platform can assay about 50,000 genetic variants, the company said.
Overall, the two new product announcements serve to broaden the options Affymetrix can offer its agrigenomics users in terms of flexibility of throughput and multiplexing.
Some customers may find themselves requiring two different technologies, while others who haven't worked with Affy before on the arrays side could be drawn to the company for the first time by the new Eureka platform for applications where they have a limited a set of target markers, but a need to genotype large numbers of samples cheaply, Kaushikkar said.
The company's Axiom HD system is mainly used for GWAS-type studies and marker-trait association research, he explained. Then the 384 HT platform comes in farther downstream in the breeding environment.
For many aspects of the ag-bio space, arrays are the most appropriate tools, and customers for these technologies remain a central part of Affymetrix's business, Kaushikkar said.
For example, the company also announced a deal last week with UK-based Bio-Genesys Diagnostics, under which all of Bio-Genesys' genetic testing services for cattle, pigs, goats, sheep, and camelids will be run exclusively on the Axiom 384 HT.
Meanwhile, for other customers the genotyping focus may be on a breeding population that comes out every year, which is in the millions," Kaushikkar explained. "In that case, the Eureka solution allows them to genotype many more samples a week in an affordable manner."
When Eureka was acquired by Affy, it offered a barley panel to screen for over 400 SNPs and a bovine parentage assay focused on 122 SNPs. In addition to developing custom assays for customers, which takes about six to eight weeks, Kaushikkar said Affy still plans to release its own additional Eureka panels, but has not yet disclosed what these will be.