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Agendia to Use Rosetta Resolver for Biomarker Discovery, Sees Promise in Downstream Utility

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Rosetta Biosoftware has dipped a toe in the microarray-based diagnostics market in an agreement with Agendia that it announced last week.

Agendia, based in Amsterdam, is the developer of MammaPrint, a gene expression-profiling service that assesses the risk of breast cancer recurrence. Initially, Agendia plans to use Rosetta Resolver in its R&D pipeline to discover new gene expression signatures for future diagnostics, but the diagnostics company is hoping to eventually move the software downstream into clinical use.

Rene Bernards, CSO of Agendia, said that the "ultimate goal" of the collaboration is to make Rosetta Resolver "suitable" for what he described as the "diagnostic utility" — the software application that analyzes gene-expression data in a clinical diagnostic setting. The company is currently using its own software to analyze the output from MammaPrint, but Bernards said that if the collaboration with Rosetta proves successful, "we of course expect that we will shift our diagnostic utilities to Resolver as well."

The companies have an indirect history. The 70-gene signature that underlies the MammaPrint test was discovered through a collaboration between Bernards and colleagues at the Netherlands Cancer Institute and Rosetta Inpharmatics — a wholly owned Merck subsidiary and the parent company of Rosetta Biosoftware, which operates as a separate business unit. The team published the results of the study in the New England Journal of Medicine in 2002.


"Nobody has standardized software to allow you to do data analysis on these diagnostic chips under quality-controlled conditions."

Now that Agendia has commercialized MammaPrint and is seeking to develop new diagnostics, "we have an absolute need for reliable software," Bernards said. "Therefore, since we need this type of utility, and they are in a position to further incorporate new utilities into their Resolver package, it would seem logical for them to work with us and for us to work with them to further enhance Resolver into a tool that also has diagnostic utilities and to ensure those diagnostic utilities meet all the requirements for clinical diagnostic use."

Rosetta downplayed any plans it may have to drive its software into the clinical diagnostic arena, however. Yelena Shevelenko, vice president and general manager of Rosetta Biosoftware, stressed that the primary goal of the agreement with Agendia is biomarker discovery. "We are enabling the research and development of diagnostic methods, and this is the key in our relationship with Agendia right now," she said. "Agendia will use Rosetta Resolver to develop their diagnostic methods and services."

Shevelenko noted that any aspects of the collaboration aimed at longer-term possibilities are exploratory. "The relationship will help us understand how Agendia is developing methods for diagnostics, and just get a better understanding of the needs of this market," she said.

Diagnostics could represent a growth opportunity for Rosetta's business — whether its software is used in the discovery stage or the clinic. Shevelenko said that a number of its pharmaceutical customers are already using Resolver to identify potential biomarkers "concurrently" with therapeutics.

"We cannot speak for pharmaceutical companies, but we do understand that when they're planning their experiments, they're thinking not only about efficacy and safety in parallel, but also they are thinking about diagnostics," she said.

Under the terms of the agreement with Agendia, Rosetta will integrate the company's large database of clinical information with the Resolver system — a service that the firm has already provided for a number of its customers in industry and academia, Shevelenko said. "It's an important capability of our system to integrate with external data sources, and clinical information is one of them," she said.

Rosetta's reticence about a potential role for its software in the clinic is understandable. The field of microarray-based diagnostics is in its infancy, the regulatory landscape for genomic tools is evolving rapidly, and many of the potential risks are still unknown.

"There are totally different requirements for bioinformatics in a clinical diagnostic setting than you have in a research setting," Bernards said. "If you're taking a research test into the clinic, there are a lot of issues in terms of quality assurance and quality control that you really don't consider in the discovery stage."

So far, "nobody has standardized software to allow you to do data analysis on these diagnostic chips under quality-controlled conditions," he said — a fact that could give Rosetta a considerable advantage over its competitors in the gene-expression analysis market if it is able to navigate the nuances of the clinical diagnostics landscape.

But for now, the company is focused on the short term. The deal with Agendia "represents the first time Rosetta Biosoftware has signed an agreement with a company engaged in using gene expression to diagnose disease," Shevelenko said in a statement.

Shevelenko said that there is "no exclusivity" in the agreement with Agendia, and that Rosetta will approach other developers of molecular diagnostics about similar collaborations.

— Bernadette Toner ([email protected])

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