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Bioinformatics, Genomics Collaborations Blur Industry And Academia Relationships

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CAMBRIDGE, Mass.--A dearth of adequate bioinformatics tools and personnel, combined with a rapid stream of DNA data, is driving publicly funded research laboratories to collaborate with corporate entities. Traditionally viewed as separate camps, companies and universities involved in genomic research frequently share talent and technology nowadays.

David Fischoff, president of Cereon Genomics in Cambridge, Mass., told BioInform, "From the points of view of both industry and academia, high-throughput sequencing can generate vast amounts of raw data and create whole new opportunities." He added, "That makes collaboration more attractive. A single organization can't deal with it all."

The trend, which some say heralds a new era for academic-industry collaboration, is raising some complicated questions for universities about intellectual property rights and the integrity of corporate-sponsored training.

Certain aspects of research are bound to remain strictly in the academic domain. David Searls, vice-president and director of bioinformatics at SmithKline Beecham Pharmaceuticals in King of Prussia, Pa., contended that universities have been known for conducting research that looks "further out" and "pushes the envelope." Industry, he said, has its "eyes on applications." For that reason, deeper, more time-consuming or labor-intensive analysis is likely to remain in the academic sector, added Fischoff.

But in other areas of genomics-related research, product development, and student training, the separation between academia and industry is blurring.

An example of the trend is a recent agreement between the University of California, Berkeley, and Celera Genomics of Rockville, Md. The two will collaborate to complete the sequence of the Drosophila genome, which the university has been pursuing with funding from the US National Institutes of Health.

Berkeley's Department of Plant and Microbial Biology also recently teamed up with the Novartis Agricultural Discovery Institute. The institute was established in LaJolla, Calif., last year with a strategy to fund academic genomic research that could ultimately be of use in product development by its corporate parent.

Property rights

Intellectual property ownership can be a point at which academic and industry cultures clash. Responsibility owed to shareholders by for-profit research endeavors may not mesh with the mandate government-funded researchers have to put results into the public domain. The conflict boils down to the "fundamental dilemma of investment for the well-being of shareholders, a narrow group, versus the well-being of taxpayers, a broad group," said Steven Briggs, president of the Novartis institute.

Briggs said when goals clash, he keeps in mind that "our partner needs to be strong to be a good partner." Negotiating deals that leave both parties at a long-term advantage is the best approach, Briggs asserted.

Hans Bohnert, professor of biochemistry at the University of Arizona and a member of the US National Science Foundation-funded Plant Genome Initiative, said he sees no barriers to bringing sequence data into the public domain. When private and public sector researchers collaborate to decode a sequence, results would most likely be covered under a materials patent. Instead, corporate entities would be interested in the more valuable process patents that would secure their rights to sequence function. Celera has said it will publicize Drosophila sequence data as it becomes available.

Frank Hartdegen, senior licensing associate for biological sciences at University of Arizona's office of technology transfer, said he finds companies becoming "more and more aggressive" about extending the time period for prepublication review and "more demanding on secrecy." Hartdegen said his office allows industry partners to keep "reasonable" proprietary information confidential, but will not allow the university's intellectual property to be withheld from a publication or from the public domain.

The California Institute of Technology will not sign a contract that gives a sponsor an opportunity to review a paper before publication. Steven Koonin, Caltech's provost and vice-president, said his office insists "on full and open exchange of information" and plans to maintain this policy as it proceeds with a $100 million Biological Sciences Initiative.

A similar approach will be used by the new Harvard University Center for Genomic and Proteomic Research in Cambridge, Mass. Douglas Melton, professor of cellular and molecular biology and codirector of the center, said it "will not enter into agreements that restrict academic freedom or fail to allow an open exchange." In some instances, he acknowledged, "companies are not able or interested in open and full exchange because of concerns for confidentiality and exclusivity."

Companies require a certain amount of privacy and "at some level it is beyond their self-interest to be full collaborators," added George Michaels, head of the bioinformatics PhD program at George Mason University in Fairfax, Va. "As long as there's a profit motive, companies need to have their competitive edge," he said.

Academics also need a competitive edge. Tony Cavalieri, vice-president of trait and technology development at Pioneer Hi-Bred, which has several genomics research collaborations with academic laboratories, said academics want to see their research applied. Teaming up with industry is a way to do that. "The line within either genomics or biotechnology between what's basic and what's applied is really blurred because it's pretty easy to apply and use a lot of the outcomes of what looks like basic research," Cavalieri said. "I think academics are much more open to collaborating with industry," he added. "They see industry as having some technologies and capabilities that they don't have internally."

As Hartdegen pointed out, there was a time when faculty would be denied tenure for having a patent on their résumé and "nowadays that is seen as something very positive." Observed Searls: "Academics are becoming a lot more like industry."

Pharmaceutical universities

That's not surprising considering that, at least in bioinformatics, some academics have been trained by industry. "There is a strain on bioinformatics training resources," admitted Michaels, who counts George Mason's as the only full-fledged bioinformatics PhD program in the US, and one of only six worldwide. Pharmaceutical companies, which have lured resources away from many universities, have responded to the problem by offering academic instruction by their own staff.

Having attracted the "top people" in bioinformatics, Searls said industry can contribute to training PhD-level computer scientists and biologists in collaboration with academic institutions. SmithKline is "very active in sending people to do course work in academic settings," he added. For example, James Fickett, director of bioinformatics research at SmithKline, also serves as adjunct faculty in the department of genetics at the University of Pennsylvania. Novartis hopes to initiate a summer bioinformatics school for undergraduates next year, according to Briggs.

Such interaction can make the flow of knowledge between academia and industry almost seamless.

--Mona Mort

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