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Illumina Debuts New BeadChips to Meet 'Continued Interest' from GWAS, Agbio Markets


By Justin Petrone

Illumina this week rolled out two new microarrays targeted at researchers conducting genome-wide association and agricultural biotechnology studies.

The San Diego firm views both the GWAS and agbio market segments as opportunities for its arrays, and plans additional product launches this year, according to a company official.

Illumina's latest offering for users conducting GWA studies is its HumanOmniExpress BeadChip. Designed as a 12-sample BeadChip, OmniExpress enables researchers to interrogate over 700,000 variants per sample, according to the firm. Using Illumina's iScan System, customers that run OmniExpress chips can process around 1,400 samples per week, it added.

OmniExpress is the latest addition to Illumina's Omni family of BeadChips. Last May, the array vendor launched its first Omni chip, the 4-million-feature HumanOmni1-Quad (see BAN 5/19/2009). In October, it announced a roadmap to debut first a 2.5-million-variant and then a 5-million-variant BeadChip during 2010. All chips contain rare variant content selected from the 1000 Genomes Project and other sources (see BAN 11/3/2009).

Illumina said that the markers on the OmniExpress are a subset of the content on the HumanOmni1-Quad, and incorporate an "optimized" set of SNPs chosen from all three phases of the International HapMap Project. Researchers starting with OmniExpress can also include supplemental Omni BeadChips containing new content derived from the 1000 Genomes Project in future studies, the firm said. OmniExpress chips are priced at $250 per sample, or around $3,000 per array.

Carsten Rosenow, associate director of product marketing for Illumina's DNA arrays and instrumentation, told BioArray News that although Illumina has seen a slowdown in demand for its genotyping arrays in recent quarters as customers wait for more rare content to become available, "there is continued interest and we don't see a downtrend."

He also said that Illumina is planning other releases this year that will target GWAS customers, including an iScan sequencing module designed to enable researchers to perform targeted resequencing of genome regions. Also in the pipeline are products for mRNA sequencing, ChIP sequencing, small RNA sequencing, and bacterial genome sequencing.

The sequencing module, which is expected to launch by the end of the second quarter, uses the same cluster station, flow cells, and sequencing chemistry as Illumina's Genome Analyzer sequencing instrument. However, image acquisition occurs inside the iScan Reader, which is the array-scanner portion of the iScan system.

"We have seen a lot of interest, mainly from array users, but even sequencing people are getting interested to run arrays now or in the future," Rosenow said of the module.

He added that Illumina continues to invest in both its array and sequencing platforms, but did not elaborate.


Illumina also hopes to expand its presence in the agbio market. The company is now selling its High-Density Bovine BeadChip, which contains data from more than 20 diverse breeds that was generated from recent sequencing largely done with the GA, Illumina said.

The BovineHD enables users to interrogate more than 500,000 loci — 10 times more genetic markers than the BovineSNP50 BeadChip, the current Illumina array for cattle researchers.

The company also sells focused whole-genome genotyping chips for human, bovine, canine, porcine, and ovine researchers, as well as its iSelect HD Custom Genotyping product for researchers studying other organisms.

Illumina said the new Bovine HD product is the result of an international collaboration involving the company and several agricultural research organizations, including the US Department of Agriculture's Agricultural Research Service, Pfizer Animal Genetics, the University of Missouri, the National Association of Livestock and Artificial Insemination Cooperatives in France, and the French National Institute for Agricultural Research. The team performing the SNP discovery and selection was led by Curt Van Tassell, a research geneticist at USDA-ARS, Illumina said.

Maurice Barbezant, director of the UNCEIA in France, and Didier Boichard, chief of Animal Genetics at INRA, said in a statement that Bovine HD will be used for the "identification of agriculturally important genes and for a deeper implementation of genomic selection in cattle." Bovine HD is available now for advance orders. Collaborators will receive the chip later this quarter, while other customers must wait until the second quarter for a commercial release.

Rosenow said that Illumina plans to add more focused whole-genome genotyping chips like the Bovine HD to its agbio menu in coming quarters. "We haven't decided which organisms we will do, but we will definitely do additional ones," Rosenow said. "There is a lot of interest from various new organisms like rice, salmon, certain trees — there is a whole slough coming in."

Rosenow added that the company is looking to make its offering "more flexible," but did not elaborate.

Of all animal- and plant-focused research groups, Rosenow said that "clearly bovine was the leading group that used arrays in the ag market to large scale." He said other groups have followed the bovine community's examples. "They have talked about their experience to a lot of other organizations," he said. "These groups all plan to do future studies. There is an opportunity here."