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Agilent Wins Appeal in Dispute with Affymetrix over Microarray Hybridization IP

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By Justin Petrone

A five-year-old IP dispute between Agilent Technologies and Affymetrix is headed back to the US Patent Trademark Office following a successful appeal from Agilent, according to court documents obtained by BioArray News.

The US District Court for the District of Northern California on Jan. 28 reversed a 2008 decision by the USPTO's Board of Appeals and Interferences that had reaffirmed a ruling supporting Affymetrix in a patent interference proceeding between the two firms.

Last month's appeal decision, handed down by Judge James Ware, follows a June 2009 judgment by the US Court of Appeals for the Federal Circuit that also decided in Agilent's favor.

The Jan. 28 decision redirects the case to the USPTO as guidance on how to interpret the IP in question. Agilent and Affy are expected to cover their own court costs.

"The federal court ruling was only guidance on how to interpret the patent. This guidance was in Agilent's favor," an Agilent spokesperson told BioArray News this week. "Now armed with this guidance, the ball is back in the USPTO's court to make another ruling on the patent."

The dispute between Agilent and Affy concerns US Patent No. 6,513,968, "Apparatus and method for mixing a film of fluid," which was issued to Agilent on Feb. 4, 2003. It covers a method for mixing a film of chemical, biochemical, or biological fluids undergoing a reaction. The patent is relevant to microarray hybridization processes.

According to court documents, Affy copied the claims into its US Patent Application No. 10/619,244, which it filed in July 2003. The move prompted the USPTO to initiate an interference proceeding seeking to determine whether the subject matter of the '968 patent was patentable, and to establish which party had discovered the invention first.

In June 2006, the USPTO's Board of Appeals determined that Affy had priority in the dispute and canceled parts of the '968 patent. Agilent appealed the decision in the US District Court for the District of Northern California that year.

In June 2008, the court reaffirmed the USPTO's decision, prompting Agilent to appeal it the same month with the Court of Appeals. That court reversed the lower court's decision, arguing that the lower court had "erred" in claim construction and "improperly" dismissed an Agilent motion for summary judgment. Affy request for a rehearing before the USCA was denied in September.

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