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With Two Agreements, Ingenuity s IPA 3.0 Extends into Several New Application Areas

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Ingenuity Systems last week announced two licensing agreements for its Ingenuity Pathway Analysis 3.0 platform that indicate the software is finding use in applications well beyond its common role in gene-expression analysis for target discovery.

In one agreement, with Wyeth, the companies extended a licensing agreement originally announced early last year. [BioInform 02-02-04]. In the second agreement, Genizon BioSciences signed a licensing agreement for IPA 3.0, which it plans to integrate with its in-house bioinformatics platform called Target Express.

Both companies are extending the reach of the technology.

Steve Howes, senior director of bioinformatics at Wyeth Research, said that Wyeth researchers use IPA primarily for analyzing gene-expression and proteomic data, but since these technologies cross a number of boundaries within drug development, "we use Ingenuity at different stages, so both our early-stage projects having to do with target ID and validation and also more downstream ones."

Currently, Howes said, "we are looking at [using] it specifically in translational medicine initiatives" — a move that is already bearing fruit in the form of a study that Wyeth researchers published in the October issue of the Archives of Neurology, in which IPA was used to help identify two sets of biomarkers in a pharmacogenomics study related to Alzheimer's disease. The software identified one set of biomarkers associated with the risk of developing meningoencephalitis during beta-amyloid immunotherapy for Alzheimer's, and a separate set of biomarkers that predicted a favorable response to therapy.

Howes cited the study as one example of how Ingenuity is being used "in a novel context" at Wyeth.

While he was unable to disclose the specific terms of the extended agreement with Ingenuity, Howes said the company has "made arrangements to continue to use the IPA application over longer periods of time, and Ingenuity has given us terms to make that available to a wider set of scientists."


"The market is changing, there are lots of different tools that are out there, and any industry or business customer needs to keep their eyes open, so we're always doing that. But thus far, we've been pleased with Ingenuity and hope things keep going well."

Howes said that his group evaluated several other pathway informatics platforms, but chose Ingenuity for several reasons, including "the ability to do batch-style analysis, which is very important." He also mentioned that the collaborative capability that Ingenuity introduced with IPA 3.0 "starts to put it in the context of being something a general user — not necessarily someone generating expression profiling data or generating proteomic data — would use."

Howes said that Wyeth has a number of internally developed pathway tools, and added that he wouldn't rule out other third-party tools. "The market is changing, there are lots of different tools that are out there, and any industry or business customer needs to keep their eyes open, so we're always doing that," he said. "But thus far, we've been pleased with Ingenuity and hope things keep going well."

Genizon, meanwhile, just began using IPA 3.0 about a month ago, according to Randall Little, executive director of computational biology. The firm is also stretching the capabilities of the software, into the realm of genetics.

"Most people who license [IPA] have a lot of microarray data that they use to input hundreds of genes and try to see if there are some trends in terms of networks and pathways that emerge," Little said. "We're doing genetics, which is a little bit different."

Little said that Genizon identifies genes of interest based on genome-wide association studies, resulting in lists of susceptibility genes for specific diseases. He said the company's researchers use IPA for "its extensive curation of the literature to understand individual genes, but also to use its information about protein interactions to understand if there are inter-relationships between genes that we've identified."

The company uses these interactions to create a genetic network, which it calls a GeneMap, that it uses to validate drug targets.

Little said that Genizon also evaluated other tools before licensing IPA, "but they have many PhD scientists that curate the public literature, so it saves us a lot of time."

He added that Genizon is currently "building capabilities" to integrate information about novel genes that it has discovered with the data in IPA.

"I think they understand the need to expand their system to accommodate genetic studies," Little said, adding that he'd like to see Ingenuity "incorporate various aspects of genetic studies in future releases."

— Bernadette Toner ([email protected])

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