Skip to main content
Premium Trial:

Request an Annual Quote

Agilent to Extend Silicon Genetics Tools Far Beyond Gene Expression in 2005


Less than two months after its purchase of Silicon Genetics, Agilent Technologies is hard at work identifying new application areas for the GeneSpring software platform, with the area of comparative genomic hybridization analysis on the short-term horizon, according to a company executive.

Francois Mandeville, business manager of informatics solutions at Agilent, told BioInform last week that all of Silicon Genetics’ products — GeneSpring, SigNet, and Varia — are based on “one common platform, one code stream,” and that Agilent’s goal in the wake of the acquisition “is to expand the breadth and the reach of that valuable analysis code stream.”

Silicon Genetics made its name in the microarray gene expression market with its flagship GeneSpring package, but the company’s technology platform has applications in areas “far beyond gene expression,” Mandeville said.

As Agilent “enters markets such as CGH, you can clearly expect that we will be expanding the Silicon Genetics platform to support that marketplace,” Mandeville said.

Silicon Genetics has already proven that its technology is extensible, he noted, citing the company’s launch of the Varia genotyping package in March as an example. “They added import capabilities, data models, and visualization capabilities on top of the GeneSpring capabilities to create Varia, and in the months to come, we will be taking this product development recipe and expanding on the Varia concept,” Mandeville said.

Mandeville did not disclose Agilent’s product launch timeline, or provide details on future software products under development.

Agilent began mulling the purchase of an informatics firm soon after forming its Integrated Biology Solutions business unit in early 2004, Mandeville said. “We undertook a strategic process of really looking at what were the foundations that we needed to have to be successful, and it became very obvious to us that having a strong informatics foundation — having a platform that could be used to support new workflows as we choose to offer them; having expertise in listening to scientists and quickly crafting the definition of informatics solutions …; having a commercialization platform that would allow us to bring informatics products rapidly to market effectively — were all attributes that we felt were critical to our success,” he said.

This effort, he added, “effectively led us to consider the acquisition of Silicon Genetics.”

Silicon Genetics had “a lot of talent and great technology,” but was “cash limited,” Mandeville said. “We felt that we could actually be an ideal parent, an ideal container for Silicon Genetics.”

In a 10-K report filed with the US Securities and Exchange Commission on Dec. 21, Agilent disclosed that it had issued 771,573 shares of its stock on Oct. 28 for all of Silicon Genetics’ shares. Agilent’s stock closed at $24.80 that day, giving the acquisition a value of around $19 million.

Agilent had not previously revealed the financial details of the acquisition, but the price is on par with the informatics sector’s other major acquisition during 2004: Accelrys’ purchase of SciTegic for $21.5 million. SciTegic and Silicon Genetics were around the same size, at roughly 40-50 employees, and founded at around the same time — Silicon Genetics in 1998 and SciTegic in 1999. Neither of the privately held firms provided revenue figures prior to their acquisitions, although both claimed to be profitable. Neither Agilent nor Accelrys has provided any revenue projections for the firms since they were acquired.

Since the acquisition closed, Mandeville said, Agilent has been “preaching the concept of reverse integration,” by moving its own informatics product teams into Silicon Genetics’ development pipeline. “We wanted to keep the recipe that has made them successful as an informatics vendor,” he said.

Other Informatics Efforts

Agilent’s informatics activities are not limited to the Silicon Genetics group, however. The company also markets an internally developed scientific data-management system called the Synapsia Informatics Workbench, as well as SpectrumMill, a mass spectrometry analysis software package originally developed by Millennium Pharmaceuticals.

Mandeville said that Synapsia, which was launched in 2002, “is deployed in various pharmas and biotechs.” The platform allows scientists to manage data in a “project-centric” manner — as opposed to the “file-centric” approach of other systems, Mandeville said — which makes Synapsia “the ideal companion to the analysis capabilities that you have in GeneSpring and SpectrumMill,” he said. With Silicon Genetics now under its belt, Mandeville said that “we have effectively aligned the planets to start leveraging a series of these [informatics] investments.”

It’s “likely,” Mandeville said, that customers will find features of Synapsia embedded in future releases of Agilent’s informatics products, but he declined to disclose specific integration plans.

One product with a “delayed” integration roadmap is SpectrumMill, Mandeveille noted, although he said that Agilent plans to integrate that package with the rest of its portfolio sometime in 2005. Since licensing the technology from Millennium in 2002, Agilent has invested in the package’s development “only to expand the difference between what it can do and what other packages in the same family can do,” Mandeville said. For example, he said, SpectumMill allows users to define amino acid modifications in order to automate the validation of results. Competing systems like Mascot and Sequest require scientists to validate their results following analysis, Mandeville said, but SpectrumMill has “far superior” algorithms for error detection, he said.

In addition, Mandeville said that Agilent’s recently announced collaboration with Icoria — an $11.7 million project funded by the National Institute of Standards and Technology to develop a bioinformatics platform called the Target Assessment Technologies Suite [BioInform 10-11-04] — “embodies our vision for integrated biology.”

The project, for which Icoria and Agilent will develop new databases and tools to integrate information from multiple disciplines, “is a great way for us to pioneer some of the new capabilities that we can then roll out in commercial products, such as Synapsia, in the marketplace,” he said.

As for the company’s broader informatics strategy, Mandeville said that Agilent views informatics as both a standalone revenue driver, and a way to complement its other product lines. “Fundamentally, informatics is and will continue to be the key to materializing the vast value of the various ‘omics technologies,” he said. While acknowledging the company’s motivation to develop and sell “complete solutions” built upon its range of instrumentation and informatics tools, Mandeville said that “when you have solutions that have been engineered to work with one another and to work with the platforms of various vendors ... you can actually run a decent P&L out of your informatics business.”

Mandeville said that Agilent remains “committed” to keeping its informatics tools open to third-party vendors.

“This is not the first time that Agilent has operated in an environment where it was both a supplier and a competitor at the same time,” he said. “If you look at multiple industries that have grown and have succeeded in becoming viable, it only took place when the ecosystem of partners and competitors learned to work with each other.”

The informatics industry is “maturing,” he said. “Vendors are realizing that we’re all in this together, and that unless we start to ensure that our solutions can support each other’s platforms and each other’s tools, we’re just reducing the achievable market to all of us.”

— BT

Filed under

The Scan

Steps for Quick Review

The US Food and Drug Administration is preparing for the quick review of drugs and vaccines for the Omicron variant, according to the Wall Street Journal.

Moving Away From Using Term 'Race'

A new analysis finds that geneticists are using the term "race" in their papers less than in years past, as Science reports.

Point of the Program

The Guardian writes that some scientists have called the design of a UK newborn sequencing program into question.

Science Papers Present Multi-Omic Analysis of Lung Cells, Regulation of Cardiomyocyte Proliferation

In Science this week: a multi-omic analysis of lung cells focuses on RIT1-regulated pathways, and more.