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A federal judge in San Francisco took away Hoffman LaRoche’s rights to a valuable enzyme on May 18, but other aspects of the judge’s decision keep alive a 12-year-long dispute — which recently has spread to other courtrooms. In 1993 Roche accused Promega Corp. of infringing its patent on Taq polymerase, an enzyme that is the crucial ingredient in polymerase chain reaction (PCR), a Nobel Prize-winning procedure that makes biological copies of DNA [see " Going, Going ..."]. Crime detectives and laboratory scientists widely rely on the PCR process. Royalties on sales of the enzyme alone has brought the private Swiss company roughly $250 million since 1991. Overall, observers estimate that Roche has gained $2 billion from its control of the PCR process. But Roche’s licensing triumph could unravel just as the patents expire in 2005. The company may have to disgorge its royalties on enzyme patents, unless it sways appeals courts that have rebuffed it before. Roche’s trouble began in 1999, when district court Judge Vaughn Walker first deemed the patent invalid because the inventors behind Roche’s polymerase patent misled the Patent and Trademark Office. Appellate judges subsequently said Walker needed to better explain his conclusion. In his May ruling, Walker elaborated on the scientists’ misstatements about prior art and about their experiments. The court skirmishes are not over. Three courts — two in California, and one in Virginia — are examining Roche’s right to PCR profits. Roche isn’t entirely on the defensive. In Walker’s court, it continues to seek damages from Promega, a biological supply company based in Madison, Wis. Roche accuses Promega of inducing customers to break licensing agreements with it. Walker concluded that Roche can still pursue those old claims. Promega attorney Jim Troupis, of Michael, Best & Friedrich in Madison, contends that the judge declined to dismiss the tortious interference claims to allow arguments from Applera Corp. as a so-called “necessary party.” Applera gained that status because it recently sued Roche over PCR profits, too. In October 2003 Applera, which licenses some Roche-owned patents and grants Roche the use of other PCR patents, told a California state court that Roche has shortchanged it on its contractual share of royalties from the breakthrough biotechnology. Meanwhile, Promega has launched a second attack on Roche’s PCR franchise in federal court in Alexandria, Va. The company filed a lawsuit under the False Claims Act, saying that Roche caused the U.S. government to unfairly pay a royalty on the PCR supplies it bought from Promega. According to the recently unsealed complaint, during the 1990s the National Institutes of Health spent more on licensing PCR than any other technology. The Department of Justice has declined to join the suit, an option it has on whistleblower suits. Still, in April its lawyers complained to the court that Roche had distorted the law in one of its defenses. And Roche may start yet another lawsuit against Promega. The company says that it will not only appeal Walker’s main finding that the Taq enzyme patent is unenforceable, but will press claims that Promega infringed the core PCR patents — a $2 billion gamble, as Promega has long contended that the fraud on the enzyme patent also invalidates the main patents. “We intend to hold Promega accountable for this irresponsible misuse of Roche’s intellectual property,” says Heino von Prondzynski, head of Roche’s diagnostics unit, in a statement. Of course, tough talk is essential: Roche doesn’t want to field demands from other PCR licensees emboldened by Promega’s victories. Roche says that, so far, none have asked to renegotiate. The company intends to keep it that way.

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