SALT LAKE CITY— Agilent Technologies, as part of its array-technology overhaul, will roll out a new protocol that will enable researchers to run both one-and two-color assays on the company's platform, company representatives told BioArray News at the American Society of Human Genetics conference, held here last week.
The decision to expand assay capabilities comes just two week's after the Palo Alto, Calif.-based company pledged to possibly quadruple feature density on its arrays by mid-2006 (see BAN 10/12/2005).
According to company officials, this expansion of experimental capabilities will complement its decision to provide higher density arrays. No further upgrades are expected in the near future.
Agilent is taking the step at a time when array companies in general are expanding their offerings. Affymetrix, for example, is trying to establish itself as a leader in SNP analysis, while Illumina is playing in the expression market.
Until now, Agilent has only offered two-color microarray experiments. And, like its recent investment in density, the company said the upgrades should make its arrays more competitive against rivals Affymetrix and GE Healthcare.
"We saw in our customer base and in the general market a need for our customers to have a platform that can accommodate more open experimental design," Erik Bjeldanes, Agilent's product manager, told BioArray News.
According to Bjeldanes, the new one-color capabilities will now enable users to make "less-specific gene-expression comparisons."
"The impetus for two-color assays has been limitations in creating arrays. You use two colors to normalize for the difference in spots. We feel we can get satisfactory data with one color."
"You can imagine our previous single capability was two color, where you have a control, a treated RNA sample hybridized on an array, and you get a direct comparison very accurately. However, if you have an experiment where you are making multiple comparisons or you don't know which comparison you want to make, then that can be problematic because if you don't run those two samples on one array then you can't extract that data easily," he said.
The new one-color assays will allow users to run as many arrays as they want with as many samples as they want — removing the limitations created by the two-color format. Also, Agilent customers will not be required to go out and invest in new hardware to take advantage of the technology upgrade, Bjeldanes said.
"We've adapted our protocols and methods with some forethought of launching our product into the market, capturing the capability that we would need for the last 18 months of product so that we can roll this out when all the pieces are in place," he said last week.
"Our current installed base already has this. We just need to provide them with the protocols and take the final steps to make this happen."
Part of that upgrade will be new software, Bjeldanes said. He said that a general upgrade will be distributed to customers and that the "feature extraction software that goes with our scanner will know whether it's a one-color experiment or two-color experiment." The new informatics capabilities will integrate tools from GeneSpring, the bioinformatics package that Agilent acquired last year with its purchase of Silicon Genetics (see BAN 9/1/2004).
Scott Cole, Agilent's microarray manager, told BioArray News earlier this month that the company has various designs for its new software, which should launch next year.
"Next year GeneSpring is going to be called GeneSpring GX, for gene expression," Cole said. The company will also launch GeneSpring CGH, for array CGH, GeneSpring LA for location analysis, and it is "building out a GeneSpring MS, for mass spectrometry data."
"SG isn't just here to create next-generation gene-expression software," Cole said. "They are creating a completely integrated informatics package that will deliver multi-application integrated microarray analysis going forward."
Customers and Competitors
According to Bjeldanes, the company is specifically targeting core labs and service providers with its latest technology upgrade.
"[For] core labs and service providers that run multiple platforms, the distinguishing factor of whether or not they send their customers to the Affymetrix platform or another platform is the capability of the one-color or two-color processing," Bjeldanes said. "Now with this combined capability we can provide both to our end users."
Calvin Lin, director of gene expression at Regeneron Pharmaceuticals concurred in a statement.
When you compare "two RNA samples, two-color microarrays usually give the most accurate results," Lin said. "However, for experiments involving large numbers of samples … experimental design for one-color microarrays is more straightforward and efficient."
Still, just because the company is adding a one-color feature, doesn't mean that competing single capability platforms will be making similar overtures in the market.
Randall Lockner, a senior scientist at GE Healthcare that works in its CodeLink Bioarray unit, told ASHG attendees last week that his company has no plans to introduce two-color experimental capabilities.
"One color is sufficient for [our] arrays," Lockner said. "There is no need for dual color normalization. The impetus for two-color assays has been limitations in creating arrays. You use two colors to normalize for the difference in spots. We feel we can get satisfactory data with one color," he said.
— Justin Petrone ([email protected])