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Agilent Takes a Step Closer to Systems Biology Goal With Silicon Genetics Buy

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Taking aim at the top of the life sciences informatics market, Agilent has signed an agreement to acquire Silicon Genetics, the Redwood City, Calif.-based maker of the GeneSpring gene expression data analysis and management software. Meanwhile, the company also said that it has reaffirmed its commitment to developing and distributing Rosetta’s gene expression data analysis platforms.

The acquisition of Silicon Genetics enables the company to add another crucial piece to its life sciences business and significantly bolster its systems biology offerings. The company signaled its intention to become a full-fledged systems biology entity in March, merging its gene expression, proteomics, and reagents business into a new unit called Integrated Biology Solutions.

“It is our intention to create full end-to-end solutions for our customers studying life sciences, and informatics is a critical aspect of being able to provide complete solutions to our customers who are challenged with not only the development of data but the translation of that data,” Fran DiNuzzo, vice president and general manager of the Integrated Biology Solutions unit, told BioArray News.

He added, “Silicon Genetics provides us with not only great products in the gene expression space for doing informatics work but also a strong set of both development and commercial capabilities. What they bring in terms of talent, resources, and knowledge — the combination of that and the portfolio fit really well with where we’re trying to go in life sciences.”

In addition to GeneSpring, Silicon Genetics’ key products include its Varia line of genetic analysis software and its GeNet scalable repository for expression data.

GeneSpring was launched in 1998 and remains a favorite of researchers, with over 4,000 users worldwide, despite an explosion of competing products and companies since its launch. DiNuzzo said the GeneSpring “software package is being used by many of our customers today. It’s being used broadly within the industry by people doing gene expression analysis, whether they’re doing it on our platform, a competitor’s platform, or home-brew arrays.

“The fit is very simple. They have an informatics package that’s really critical and necessary for people trying to do desktop work relative to understanding and translating expressed array data into useful informatics.”

In March, Silicon Genetics introduced the Varia software package for whole-genome genotyping experiments, and it is counting on a similar effect with the Varia product. In fact, the company predicted that the market potential for genotyping technology — and, subsequently, genotyping software — could outstrip that of gene expression.

In a March interview with BioArray News’ sister publication BioInform, Silicon Genetics CEO Saeid Akhtari said, “I personally believe the genotyping market is where the gene expression market was in 1998, except I don’t believe it’s going to take as many years to get to where the gene expression market is today, in terms of size and usage.”

Many of the “technical issues” that plagued microarray technology in the early days have since been worked out, the price of genotyping microarrays is much lower than that of gene expression chips several years ago, and many labs have already invested in the infrastructure to run expression arrays, he pointed out. So the barrier to entry for running genotyping chips is far lower.

But DiNuzzo believes it is hard to predict whether genotyping will be bigger than gene expression in terms of revenue opportunity.

“The gene expression marketplace, while it’s not nascent, it’s still a very early-stage market, and the rate of discovery of applications of gene expression platforms is fairly high still,” DiNuzzo said. “Genotyping certainly seems to be an opportunity and is being pursued by many people, and I think that’s what led Silicon Genetics to create a new product for the genotyping area.”

DiNuzzo said that Agilent does not share data on sales of its gene expression systems and he declined to comment on whether the firm has been gaining ground on competitors in the field. However, he said, “We continue to be pleased with the progress of our gene expression business and the addition of customers.”

According to Silicon Genetics, its customers include more than 600 pharmaceutical companies, academic institutions, and major research organizations worldwide. The privately held firm employs approximately 50 people, most of whom are expected to join Agilent.

DiNuzzo said he could not confirm whether members of Silicon Genetics’ management would join Agilent. He also declined to comment on when Agilent expects to complete the deal or the price of the acquisition.

“We don’t want to talk about the details,” he said. “I will say that it will not be a wholly owned subsidiary. It will become part of the Integrative Biology Solutions bus-iness.”

It is likely that Agilent is not done exploring opportunities to further its offerings in the life sciences arena. Although DiNuzzo declined to say what types of businesses or partnerships the firm might be looking at, he said, “We’ll always pursue things that are valuable to [making Agilent stronger in the life sciences] both in terms of bringing technology to the table ourselves as well as to a variety of partnerships.”

One interesting sidebar to Agilent’s purchase is Silicon Genetics’ ongoing collaboration with Agilent competitor Affymetrix.

Silicon Genetics and Affy have a relationship dating back to July 2003, when the firms signed a pact enabling Silicon Genetics to redistribute GeneChip probe-level data directly within its GeneSpring software. The firms signed another agreement in February intended to further integrate their respective technologies.

But DiNuzzo sees no conflict of interest for Agilent. “One of the strengths of Silicon Genetics’ products — and if you look at the products we distribute from Rosetta as well — is those products have the ability to import data from all of the major microarray platforms.

“Agilent has always been committed to open platforms,” DiNuzzo said. “Our goal would be to make data migration and data exchange between multiple platforms easier than it is today. We think this is a benefit to the customer.”

ReAffirming Commitment to Rosetta

In addition to the Silicon Genetics deal, Agilent said that it had increased its commitment to the continued development and enhancement of Rosetta Biosoftware’s platforms. Agilent has been the exclusive distributor of Seattle-based Rosetta’s Resolver and Luminator gene expression data analysis systems for several years.

The firms were vague on the details of the updated relationship and exactly what is different from the initial agreement between the partners. DiNuzzo also declined to give any further information about the new pact.

“We have had a wonderful relationship with Rosetta in collaboration both in software as well as in the gene expression area. We expect that to continue,” DiNuzzo said.

“What we announced was really the fact that we have reaffirmed our relationship with each other. We have reaffirmed our continued investment in development of the Rosetta Biosoftware platform, and we see it as a critical element of our overall business strategy, and specifically the informatics portion of that.”

Although the timing of the announcement seems curious — coming on the same day as the announcement of the Silicon Genetics purchase — DiNuzzo insists the timing was coincidental and was not done to allay customers’ or Rosetta’s fears about Agilent’s commitment to selling the Rosetta products.

But, he said, “We need our customers to be assured that these are not competing elements of our strategy, they are actually complementary. For those who are committed to one or the other platform or thinking about utilizing both of them in tandem, we are committed completely to the entire informatics portfolio.”.

He added, “While in any informatics portfolio, you not only will have some overlap, you actually desire to have some overlap between various levels of software.

“These products will effectively co-exist within our portfolio,” DiNuzzo said.

Launch of Whole-Mouse-Genome Microarray

Capping a busy week, Agilent also launched its new whole mouse genome microarray, which incorporates the most current mouse genome data from RefSeq, Ensembl, USCS Golden Path, RIKEN, NIA, MGI, GenBank, and UniGene.

The newest array is the third whole-genome microarray to be released by Agilent this year. It introduced a whole human genome chip early this year and followed that with the release of its whole genome microarray for Arabidopsis thaliana.

— EW

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