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Startup Compendia Bets Popularity of Oncomine Database Will Help It Sell In the Private Sector

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In 2003, Arul Chinnaiyan, a professor of pathology at the University of Michigan, began compiling a database of cancer gene-expression data dubbed Oncomine to support his own research. Three years later, the resource has more than 7,500 users and has spurred the launch of a new bioinformatics company called Compendia Bioscience.

This week, Compendia obtained exclusive rights from the university to begin selling to the private sector a commercial version of Oncomine and another bioinformatics tool from Chinnaiyan's group called HiMap, which helps researchers navigate protein-protein interaction networks.

Chinnaiyan, who co-founded Compendia and serves as scientific advisor to the three-person firm, told BioInform that the university's technology-transfer office had been managing commercial licenses to Oncomine to pharma and biotech firms. The software is freely available to non-profit researchers.

Approximately 10 companies had licensed the database from the tech-transfer office, Chinnaiyan said — enough for him and his colleagues to start thinking seriously about commercial models for supporting the continued development of Oncomine.

"We felt that we were getting a lot of interest [from industry], but it was sort of passive interest. They were looking at our publications and getting onto the website and so forth, but we felt that it could actually go better if it was more active in a commercial setting," Chinnaiyan said. "In the commercial setting, we would have sales and marketing individuals that would go out to the different biotechs and pharmaceuticals and try to sell the product in addition to the passive customers."


"We felt that we were getting a lot of interest, but it was sort of passive interest. They were looking at our publications and getting onto the website and so forth, but we felt that it could actually go better if it was more active in a commercial setting."

Compendia has not disclosed the financial terms of its licensing agreement with the university, and officials from the tech-transfer office could not be reached for comment in time for publication. Company officials also declined to provide pricing information for Oncomine.

Prior to the launch of Compendia, commercial firms who paid for an Oncomine license had access to the same version of the database that academic users could access for free. Now, the company is developing a separate version of the database for commercialization (www.oncomine.com) that is markedly different from the free version, which is still available at www.oncomine.org. (See chart for a comparison of the free and commercial versions of Oncomine.)

In addition to published cancer transcriptome data, Oncomine includes a number of data-mining tools as well as pre-computed gene-expression profiles for particular cancers.

Chinnaiyan said that these analysis tools help distinguish Oncomine from publicly available gene expression repositories like GEO or ArrayExpress. Oncomine's focus on cancer also sets it apart from would-be competitors, he said, noting that the database is "the largest compendium of human tumor profiling studies in one place."

The commercial version of Oncomine database is also integrated with the company's HiMap software so that users can use gene-expression data to model predicted protein-protein interaction networks.

In addition to sales of the database, Compendia plans to supplement its revenues through bioinformatics service agreements based on the data and tools in Oncomine. The company has a version of the database called MyOncomine that companies can install behind their firewalls and use to store and mine their own microarray data in the context of publicly available information.

Added Value: Oncomine.org vs. Oncomine.com
Oncomine.org Oncomine.com
Studies (catalog)
334
439
Studies (analyzed)
118
144
Microarrays
9,930
12,213
Data points
167,962,352
221,871,727
Cancer types
31
36
*Statistics as of March 15, 2006.

So far, the firm has some initial funding from Spark, a business accelerator in the Ann Arbor region, but Chinnaiyan said that the bulk of the company's startup costs were covered by early licensing fees.

Short-term goals include ramping up the sales force, which Chinnaiyan described as "the major area that we're planning to expand." Compendia has applied for funding through Michigan's 21st Century Jobs Fund — an initiative of the state's Economic Development Board — to support this effort.

In the longer term, Chinnaiyan said that Compendia will eventually move beyond its current focus on cancer into other disease areas, such as cardiovascular and neurodegenerative disease.

— Bernadette Toner ([email protected])

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