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Moving GeneSpring from Product to Platform, Agilent Plans to Launch MS Biomarker Software

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Agilent Technologies is consolidating its life science informatics business around the GeneSpring software product that it picked up in its acquisition of Silicon Genetics in late 2004.

Following the acquisition, "We looked at the assets that we had between the technology that's being brewed by Agilent Labs, the technology that Silicon Genetics brought to the table, the technologies that we have from our partners, and we rapidly consolidated this around the GeneSpring platform," François Mandeville, manager of informatics solutions at Agilent, told BioInform.

"We've taken the product, and transformed it into a platform, and a platform that actually spans all disciplines in the marketplace," he said. In late 2005, the company released GeneSpring GT 2, a version of the software designed for genotyping analysis that was originally called Varia under Silicon Genetics. Last month, Agilent released version 7.3 of the GeneSpring gene expression-analysis package, now called GeneSpring GX, and in a few months, the company expects to release a version of the software for mass spec biomarker analysis called GeneSpring MS.

All of these products, as well as Agilent's software for comparative genomic hybridization and ChIP-on-chip analysis, have "the same look and feel, the same backbone, as GeneSpring for gene expression," Mandeville said.


"That was an engineering decision, and effectively a bonding vision about enabling systems biology."

"That was an engineering decision, and effectively a bonding vision about enabling systems biology," he added. "What we did is, both from a marketing standpoint and an engineering standpoint, ensure that every project that was launched to address new applicative markets, were all done in a manner that was consistent — so the experience was consistent, so that the information could effectively flow between the different products."

Agilent is currently in the "final stage" of this, plan, Mandeville said, which entails branding its software products with the GeneSpring moniker. "Literally, from a branding standpoint you can expect that all these things are going to be called GeneSpring 'XX,' so for example in gene expression it's GeneSpring GX, in genotyping it's GeneSpring GT, in mass spec it's GeneSpring MS," he said.

Mandeville acknowledged that the company has been "quiet" about its informatics activities in the year since it acquired Silicon Genetics. Indeed, Agilent has not issued any press releases for new software product launches or customer deals in that time. Nevertheless, he said, "the business is doing well, we've released several products, we've expanded our user base, we've grown the business, we've improved the profitability."

There are currently "several thousand" GeneSpring users, Mandeville estimated, noting that the company has seen "double-digit" growth in its customer base since the acquisition.

Now, the company hopes to exploit this rich user base to expand its reach into new application areas. "We expect for our community of users, as they expand the spectrum of applications, to continue to use these derivatives of the core GeneSpring technology," Mandeville said. "We've seen this over the last year, we're seeing it, and I think in order to be able to enable this, we've had to take the conscious action of moving to a platform view and really look at how people consume the information."

One key element of this "platform view" involves the company's Synapsia data-integration technology. Mandeville said that in addition to marketing Synapsia as a standalone system, Agilent has embedded components of the technology into the GeneSpring product line to enable customers to share information across application areas using a "project-relevant" approach to storing and managing data.

Features from Synapsia have also been added to the server-side version of GeneSpring GX, which was formerly called GeNet, and later SigNet, and is now called GeneSpring GX Workgroup.

Mandeville stressed that Synapsia is "still very much alive" as a standalone product, "and used by key pharmas to manage their data, manage their projects, and make decisions." The company's recent decision to pull out of a joint $11.7 million ATP grant with Icoria [BioInform 01-27-06] that was supposed to use the Synapsia technology "was actually quite independent from the technology itself," he said.

"If there's a good alignment between the tasks that you're performing and what your commercial aspirations are, then [a government grant] is a good way to actually get where you want to go," Mandeville said. "But if one day you realize that the specific intentions and conditions of the grant actually call for a detour, you have to ask yourself, 'Is that the best way for me to get my technology out there?' And that's what prompted our request to actually end the project."

Mandeville added, "The market moves in a quite fluid manner, so what looked to us like a good commercial venue in the 2003 timeframe when we started dialogue with Icoria and the government — our assessment of [whether] that is the best path for us now is no longer in alignment [with our goals]."

One area that Agilent has identified as a good commercial venue, however, is the field of biomarker analysis, which is already attracting a fair bit of attention from other mass spectrometry vendors, such as PerkinElmer, Bruker Daltonics, and Applied Biosystems [BioInform 06-13-05]. In addition, Nonlinear Dynamics recently launched a biomarker analysis product called Progenesis PG600, and Rosetta Biosoftware, whose Rosetta Resolver software is exclusively distributed by Agilent, also sells a biomarker analysis platform called Rosetta Elucidator.

One way that GeneSpring MS will compete in the market is via the user-friendly interface and workflows borrowed from GeneSpring GX — not to mention GeneSpring's installed customer base. In addition, Mandeville said, the software will be fully integrated with the company's Spectrum Mill software for protein characterization.

The development team that came from Silicon Genetics "has this really good intuition for what is the optimal solution to solve an informatics problem, but didn't necessarily bring in the domain expertise specific to different new techniques," Mandeville said. "We had in Agilent Labs some major research on the use of mass spec — both LC/MS and GC/MS — to discover biomarkers, and when you put all these people in one room, you get a pretty interesting combination and a very interesting solution."

Mandeville said that the release of GeneSpring MS is "imminent." Customers are currently evaluating the product, and it's expected to be broadly available "in a manner of just a few months," he said.

While Agilent has a clear interest in supporting its mass spec customers with user-friendly analytical software, Mandeville stressed that the company intends to keep its GeneSpring products platform-agnostic. He cited GeneSpring GT as the "ultimate example" of this strategy because the software supports genotyping platforms from Affymetrix, Illumina, and other competitors in the microarray market.

Mandeville declined to comment, however, on whether the company plans to develop a version of GeneSpring that will analyze Affy's new exon arrays. "We follow the marketplace, we follow the needs of our customers, and our goal is to support the experiments that our customers are conducting," he said. "As we see needs emerging, we take action.

— Bernadette Toner ([email protected])

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