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Illumina Developing Cross-Mapping Tool To Help CodeLink Users Adopt its Platform

Illumina has been developing a bioinformatic tool that will help users of GE Healthcare’s CodeLink bioarrays switch to the Illumina platform once GE stops manufacturing CodeLink this coming spring.
GE last month decided to abandon its CodeLink business, informing customers that it would put out its final shipment in April. GE also said it would help customers switch to rival platforms in order to continue their research projects (see BAN 12/19/2006).
Illumina joins Agilent Technologies and NimbleGen Systems in disclosing its strategy to woo CodeLink users (see BAN 1/2/2007).
According to Todd Dickinson, Illumina’s associate director of product marketing, the company has obtained probe sequence data for GE’s arrays and is currently preparing a cross-mapping file that the company believes will entice CodeLink customers to switch to Illumina.
“The transition from GE’s CodeLink platform to the Illumina platform should be relatively easy as the assays are so similar,” Dickinson wrote BioArray News in an e-mail. “In addition to both being one-color, single probe assays, the labeling systems are both based on Ambion’s MessageAmp II technology,” he wrote.
Moreover, to simplify the transition to its platform “Illumina has worked closely with [its] colleagues at GE Healthcare to obtain the probe sequences for their whole-genome products,” Dickinson wrote. “Using this list, Illumina bioinformatics scientists are actively developing a cross-mapping file, which will aid GE Healthcare customers in translating their results to the Illumina platform.” He added that the tool will be available through Illumina’s website “very soon.”
In a follow-up e-mail, Maurissa Bornstein, Illumina’s PR manager, wrote that a cross mapping file is “a simple mapping of probes or probe sets between two gene expression platforms” that lets researchers know “which probes across the two platforms should be functionally equivalent, or designed to measure the same transcript.” 
According to Bornstein, Illumina has chosen a “rigorous approach” to creating the tool that involves “comparing the sequences of all of the probes to a common reference source” — in Illumina’s case, the National Center for Biotechnology Information’s Reference Sequence database. 
“This allows us to take advantage of the absolute latest information from a very trusted source,” Bornstein wrote.  “We’ve already created individual files for mapping our probes to Affy’s probe sets and we’re in the process of doing the same for the CodeLink arrays,” she added.
Divulging Strategies
GE Healthcare could not be reached to confirm that it has shared probe sequence information with Illumina, or to answer whether it has shared the information with any other former rival companies that it will now work with to transition its customers to new platforms.
Though Illumina may be the first company to create a cross-mapping tool for transitioning CodeLink users, it doesn’t mean that other companies haven’t been positioning themselves to pick up where GE left off.

“Illumina bioinformatics scientists are actively developing a cross-mapping file which will aid GE Healthcare customers in translating their results to the Illumina platform.”

Last week both Agilent Technologies and NimbleGen Systems discussed their plans to win over CodeLink users by building stronger customer support systems, diversifying array formats, expanding custom array resources, and introducing newer catalog arrays.
Specifically, Agilent is planning new multi-pack formats and is mulling launching microRNA arrays to complement its expression line. Meantime, NimbleGen is planning to upgrade its density to 2.2 million features per slide and to implement a new multiplex hybridization gasket to enable the production of sub-arrays on its slides (see BAN 1/2/2007 and related article, this issue).
According to Dickinson, Illumina is planning similar overtures to the marketplace this year. Dickinson wrote in an e-mail that the company is considering new additions to its expression product line, which includes whole-genome arrays for rat, human, and mouse. He also wrote that Illumina has “recently implemented a system for supplying annotation updates for our gene expression arrays [that] will allow [its] customers to have access to the latest information available.” 
Illumina will also continue to capitalize on the results of the Microarray Quality Control project, which were published in a special issue of Nature Biotechnology in September (see BAN 10/3/2006). The company has been marketing itself to researchers as a more affordable partner.
“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.
In his e-mail, Dickinson similarly stressed that “the MAQC clearly demonstrated that Illumina’s arrays perform extremely well” and that the method the company is using to correlate probes from CodeLink to its own was “the exact same approach that we and others recommended for the MAQC project.”

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