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Agilent, Hoping to Play in Growing Agbio Sector, Will Debut 30 New Expression Chips

Agilent Technologies will debut approximately 30 new organism-specific, gene-expression array products by the end of the year in a bid to capture more business from the burgeoning agricultural biotechnology community, according to a company official.
The product launches come at a time when array platform vendors have become increasingly interested in the agbio sector, which some predict will become a growth area for applications as diverse as gene expression, genotyping, and comparative genomic hybridization.
Agilent in the past has worked alone and with partners to develop chips for agbio customers, such as a whole-genome rice array launched in February, which was the end result of a collaboration with Japan’s National Institute of Agrobiological Sciences (see BAN 2/5/2008).
But due to increasing demand from this sector, Agilent has decided to sell as catalog array products chips it would normally manufacture on a custom-order basis. While a full list of the arrays is not yet available, Agilent spokesperson Stuart Matlow told BioArray News via e-mail that the new chips will likely include whole-genome expression arrays for pig, sheep, Arabidopsis, rabbit, tomato, soybean, Brassica, tobacco, cotton, and wheat.
Irina Sini, Agilent’s genomics model organism product manager, told BioArray News recently that the company expects to release “about 30 different key products” for the agbio market by the end of the year. “The list [of new products] comes from the interest that we see in our customer base,” she said.
Sini said that the new chips will be made available in Agilent’s multiplex array formats, either four distinct 44,000-feature arrays on a slide, or, in some cases, eight separate 15,000-feature arrays per slide. The company will stagger the launches: It expects to debut around five this month, 10 in September, and 10 by year-end.
According to Sini, Agilent is now looking for collaborations similar to its effort with Japan’s NIA in order to produce higher quality products. The company will also draw sequence information from a number of different public databases to select content for the chips.
“This data pipeline increases our flexibility and decreases the turnaround time of products,” she said. Sini particularly credited Agilent’s inkjet array printing method for giving the company the ability to launch all of the planned arrays in one year.
“I think what basically we are doing is taking specific organisms that have been ordered from custom work, and just putting them on the shelf,” said Chris Grimly, Agilent’s genomics applications manager. “The goal is that the customers will get the array quickly by just buying it off the shelf.”
Sini said that there are a number of factors fueling demand for the agbio-oriented arrays. She pointed out that the collaboration with NIA had allowed the firm to produce a rice product that has become widely used by biotech and academics customers.
“These are customers that are studying genes associated with different biological functions — growth strategies, threat responses, et cetera,” Sini said.
She also said that an increase in available sequence information for organisms as diverse as rabbit and cotton made it possible to design arrays that would, in turn, drive interest in microarray organism products.
In terms of customer demand, Sini said that most of Agilent’s agbio customers are interested in using gene-expression arrays. Agilent also offers arrays for ChIP-on-chip, DNA methylation profiling, and comparative genomic hybridization.
Of its other application areas, Sini said the company is most likely to see an increase in the use of CGH in the agbio sector. She referred to a recent collaboration with an partner in the Netherlands that led to the launch last month of the Chicken CGH Microarray Kit 244A.
“We are seeing an interest in mostly gene expression and some CGH, though there is the potential to do other applications as well,” Sini said.
Whole-Genome Demand
Agilent’s experience with the growing agbio market seems to reflect that of rivals like Affymetrix, NimbleGen, and Illumina. For instance, speaking during their respective first-quarter earnings calls last month, Affy CEO Stephen Fodor and Illumina CEO Jay Flatley both called the agricultural sector a business opportunity for arrays.

“We had been using microsatellite for 15 years and this technology came along and hit everyone between the eyes like a baseball bat and we are going full out with it.”

While no company has put forward an estimate of how large the market for agbio-oriented arrays actually is, most agree that it is growing and that whole-genome gene expression is still the application of choice, though genotyping demand is also growing.
According to Ricardo Mancebo, product manager of academic product marketing at Affymetrix, the company launched its MyGeneChip Program in January specifically to meet the needs of this market. Under the new program, Affymetrix works with agbio researchers to design and create custom gene-expression and genotyping arrays.
In an e-mail to BioArray News, Mancebo credited Affy with developing the market. “Prior to the availability of Affymetrix technology, researchers in various agbio communities did not have a commercial microarray option to monitor the genetic mechanisms regulating traits that are inherent to their organisms of interest, such as disease resistance and stress tolerance,” he said. 
Mancebo said that to date, Affy’s top six agbio-related expression products are porcine, bovine, chicken, wheat, rice, and soybean. However he said that the firm’s genotyping products have received increased over the past year. The company expects revenues from the sector to “increase due to the increased demand for these genotyping applications,” Mancebo said.  
Genotyping and Beyond
In the case of Illumina, genotyping may turn out to be the firm’s gateway to the agbio sector. In January, the company launched the Infinium BovineSNP50 BeadChip, a 12-sample genotyping product for detecting genetic variation in any breed of cattle.
The BovineSNP50 features more than 54,000 SNPs spaced across the entire bovine genome. Illumina developed the BovineSNP50 with researchers from the US Department of Agriculture-Agricultural Research Service, the University of Missouri-Columbia, the University of Alberta, and other industry partners. The company also recently released the Infinium CanineSNP20 BeadChip, and plans to release an equine chip this spring.
According to Curt Van Tassell, a research geneticist at ARS-USDA, the use of array technology will “irrevocably change the way genetic improvement is done in the dairy industry.”
ARS-USDA has been offering genetic predictions to the dairy industry for six weeks using the BovineSNP50, Van Tassell said. “Our primary customers have traditionally been a group of eight or so companies that are in the business of identifying elite animals and contract breeding elite cows to make elite bulls,” he said. “They send out semen across the country and generate a fair number of daughters. Those were the companies that we started into this project.”
Previously, ARS-USDA had been using microsatellite genotyping to supply the industry with genetic predictions, but Van Tassell said that the array throughput is “phenomenally higher, [and] the fidelity and quality of the data are not even on the same orders of magnitude.
“We had been using microsatellite for 15 years and this technology came along and hit everyone between the eyes like a baseball bat and we are going full out with it,” he said. Van Tassell added that he first learned about the array technology at a conference in 2005.
Mark McCormick, senior manager of global e-marketing at Roche NimbleGen, told BioArray News this week that the firm has experienced increasing demand from the agbio sector across all application areas. For example, he said the firm’s 2.1-million feature high-density arrays are attractive to customers studying large plant genomes.
“The increase in agbio research activity is evidenced by the growing number of scientific publications as well as rising attendance at key conferences,” McCormick said. “We are also receiving increasing requests for microarray analysis of newly and partially sequenced plant and animal genomes.”
In particular, McCormick said that NimbleGen’s agbio customers are interested in using the company’s sequence-capture technology, which uses high-density, long-oligo NimbleGen arrays for the targeted hybridization and sequencing of targeted genome regions.
“We are receiving many requests from customers and prospects interested in using NimbleGen Sequence Capture in the agricultural biotechnology market,“ said McCormick. “They are either interested in sequencing quantitative trait loci, or sequencing many exons in the genome to provide SNP markers for association and linkage studies.”

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