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Two decades ago, Yale patented technology that helped unlock the secrets of the human genome, but some representing the University in its ongoing legal battle for licensing fees and damages have accused a biochemical company of unlawfully using this technology without Yale’s permission.

Yale and licensee Enzo Biochem of Manhattan have successfully extended the discovery phase of a patent infringement lawsuit against the Applera Corp. and Tropix, Inc. — biochemical companies principally located in Norwalk and Bedford, Mass., respectively — to Dec. 16. In their complaint, the University and Enzo Biochem have accused Applera of appropriating without permission seven patents, including four DNA sequencing aids and systems developed by professor David Ward at Yale during the 1980s and fully licensed to Enzo since 1986. Attorneys for the plaintiffs said they seek an injunction to bar Applera and Tropix from unauthorized use of the technology and damages, but attorneys for the defendants said the case is without merit.

The technology at the center of the lawsuit consists of luminescent molecules called fluoroflores, which, when attached to the amino acids in a DNA sequence, can identify through specific colors each of the four bases: adenine, cytosine, guanine and thiamine. The sequence of the DNA chain can be determined from the colors.

Scott Robertson, an attorney representing Yale and Enzo, said Ward’s fluoroflores revolutionized genomics, and he said Applera’s products conspicuously use the inventions.

“That is the dominant technology used today in just about any kind of DNA sequencing, from tracking a rapist to mapping the human genome,” Robertson said. “Applera makes methods and kits for performing gene sequencing, and we believe they’re infringing.”

Although the aims of Applera’s products are the same as those of the plaintiffs, their means are different and therefore there is no claim for patent infringement, defense attorney Nicholas Groombridge said.

“We’re just not using the same chemical processes,” Groombridge said. “What Professor Ward invented was a chemical system, and there’s not just one set of chemicals that would work.”

Both Robertson and Groombridge said Enzo and Applera each offer several similar products and representatives of the two companies had discussed a sublicense for the defendant, but each said his clients offered differing accounts of the negotiations. The plaintiff’s attorney said the negotiations had just recently broken down, but the defendant’s attorney said communications had broken down more than six years before the suit was brought in June.

“We were very surprised that this case was brought, because it had taken place many years ago and Applera thought there was no issue here,” Groombridge said.

Some of the Ward patents are about to expire later this month, when the inventions will pass into the public domain, but Robertson said timing was not the primary factor behind the complaint against Applera.

“That doesn’t make it any less a great invention, and it doesn’t mean they escape free from six and a half years of infringement,” he said.

The determining factor in the case will likely be the degree of similarity between the parties’ chemical processes, since a product must make, use, sell, offer for sale or import every element of the invention detailed in the patent claim, according to Dan Burk, a professor of intellectual property law at the University of Minnesota who specializes in cyberlaw and biotechnology.

Burk said a credible defense would rest on proof that Applera’s products’ use falls outside the patent claims or evidence that the patent was defective or issued erroneously.

Neither party is actively pursuing a settlement, but both Robertson and Groombridge said they would not rule out such a possibility before the projected April 2006 trial date.

Ward, now the deputy director of the Nevada Cancer Institute, could not be reached for comment.