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In Bid to Attract CodeLink Users, Agilent, NimbleGen Look to Build On Strong Suits

Though GE Healthcare’s CodeLink bioarray unit was never as competitive in the gene expression market as rivals like Affymetrix and Agilent Technologies, it had its share of true believers that invested heavily in the platform. Now that GE has announced its intentions to shutter CodeLink by April, some array manufacturers are planning product upgrades and launches to attract CodeLink customers to their expression array platforms.
It’s clear that CodeLink’s demise will spark a flurry of interest from its former competitors looking to woo the firm’s microarray leftovers. Additionally, GE has said that it will help its customers move to rival platforms once the business closes down this year (see BAN 12/19/2006).
Two companies have already disclosed their plans to take advantage of this market opportunity. According to officials from Agilent and NimbleGen, both firms are looking to capitalize on GE’s decision by offering customers higher-density chips, more versatile array formats, new products, and more wide-scale availability. The efforts herald a renewed competitive intensity in the gene expression market, which has recently been overshadowed by genotyping and emerging applications such as array comparative hybridization.
“The gene expression market has been around for many years for microarrays and we’ve really been focused on getting the line toward a very mature customer profile,” said Erik Bjeldanes, marketing manager of gene expression at Agilent Technologies.
Bjeldanes told BioArray News last month that customers can expect Agilent to offer a gene expression product line that is “really focused on … high stable performance as well as lowering the cost per sample.”
Gene expression analysis is “not any longer the sexy, new application space, but more of a product line that is directed towards stability, cost per sample, throughput, and the more mature product line attributes,” he said.
Part of creating that face for the expression line has been a series of density upgrades that took Agilent from 44,000-feature arrays to 244,000-feature arrays in 2006 (see BAN 7/11/2006).
The density upgrades coincided with Agilent’s launch of methylation arrays, and according to Bjeldanes, the 2007 component of Agilent’s upgrade is likely to include more flexible array formats as well as new chips for miRNA research.
“What you can expect to see in 2007 is a continuing strategy to deliver new multipack formats that drive [down] further the cost per sample for gene expression,” he said. The company is seeking to provide multiple arrays per slide in order to reduce costs for customers.
Yvonne Linney, general manager of Agilent’s genomics business, said that the company has also submitted proof-of-principle studies to scientific journals related to microRNA and it’s “that area that we are thinking of productizing.”
Both Linney and Bjeldanes said that Agilent’s similarity to CodeLink would make it an easy switch for CodeLink users.
“Right now because we are an open 1X3-inch format, similar to the CodeLink 1X3-inch format, there is a very low switching cost for customers from homebrew or from CodeLink to come over to the Agilent platform,” Bjeldanes said.
Linney added that the company has a “very flexible manufacturing process” that enables it to easily develop custom products for its customers, a characteristic it considers key to building its expression line this year.
For some CodeLink users that are contemplating a switch, Agilent is definitely on their lips. Anticipating the demise of CodeLink, Naftali Kaminski, director of the Simmons Center and the Functional Genomic Resource Center at the University of Pittsburgh’s Medical Center, said that his center began looking for an alternative last spring, eventually settling on Agilent Technologies (see BAN 12/19/2006).
But other CodeLink users, such as Vladimir Benes, head of the genomics core facility at the European Molecular Biology Laboratory in Heidelberg, Germany, are eying other platforms. Benes told BioArray News last month that the core facility will most likely assess arrays from Agilent and NimbleGen Systems for projects supported in the lab. EMBL has offered Affymetrix GeneChips, as well as CodeLink, to its customers in the past.
Other CodeLink users, like Roderick Jensen, director of the BiotechnologyCenter at the University of Massachusetts in Boston, also mentioned Illumina as a platform they were considering to replace CodeLink.
Of the array companies positioned to lure CodeLink customers to their technology, one wild card is NimbleGen Systems. The company traditionally followed a services model, by delivering data to customers after running experiments in its labs in Reykjavik, Iceland. However, in October the company concluded a licensing deal with Affymetrix that will allow it to deliver its arrays directly to labs worldwide (see BAN 10/10/2006).
So, for the first time, NimbleGen will be on equal footing when competing against companies like Agilent Technologies and Illumina that have traditionally sold directly to customers.

“This is not any longer the sexy, new application space, but more of a product line that is directed towards stability, cost per sample, throughput, and the more mature product line attributes.”

The Affymetrix “agreement is part of a strategy to expand access to our technology to include direct array delivery to all laboratories worldwide, as well as to continue to expand and improve our service laboratory,” Tsetska Takova, manager of NimbleGen’s gene expression business unit, wrote in an e-mail to BioArray News last month.
Takova said that this year NimbleGen expression array customers can also expect a sizeable density upgrade as well as wider multi-pack formats for its arrays.
“We will launch our [second high-density] format” this quarter, she wrote. “This array format contains 2.2 million probes per slide [and] will further enable new applications of arrays like gene expression tiling and whole-genome spliceosome analysis that require millions of probes,” she said. NimbleGen will also enable customers to segment its arrays into smaller subarrays using a new multiplex hybridization gasket. 
“Several different multiplex formats will be available over the coming year,” she wrote. “We already offer a four-plex with 70,000 features per sub-array, and will be offering new products with more sub-arrays and more features per sub-array on each slide,” Takova explained.
According to Takova, NimbleGen will also be expanding its whole-genome chip portfolio, adding sea urchin and honeybee genome arrays to its menu this quarter.
By continuing to add to its array portfolio, NimbleGen will be competing more directly with Affymetrix, which similarly offers a sizeable number of genomes, whereas companies like Agilent Technologies, Applied Biosystems, and Illumina have focused their expression array businesses on human, mouse, and rat arrays — the same organisms offered by GE.
Illumina is similarly putting energy into its gene expression product line. The company recently paired the results of the Microarray Quality Control project in September with an attractive pricing scheme to urge customers to switch to its platform.
“The results of the MAQC basically say that there is good correlation across all platforms,” Shawn Baker, Illumina’s gene expression scientific product manager, told BioArray News in September.  “So all things being equal, we think that the key factor is actually going to be value,” he said (see BAN 10/3/2006).
Over the past year Affymetrix and Applied Biosystems have also made investments in gene expression, with Affy launching new arrays for the cotton and citrus genomes and Applied Biosystems launching a service provider labs program (see BAN 2/14/2006).

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