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UPDATE: Both Sides See Upside of Applied Biosystems-AP Biotech Patent Ruling

NEW YORK, Dec 28 – Applied Biosystems and AP Biotech have both claimed partial victory after a judge issued a pretrial ruling December 22 on whether the companies had infringed each other’s patents for key sequencing technologies.

The patent litigation, filed in U.S. District Court for the Northern District of California, covers patents for energy-transfer fluorescent labeling dye technology and DNA sequencing instrumentation.

In the ruling, US District Court Judge Charles Breyer held that Applied Biosystems’ BigDye DNA sequencing chemistries infringe upon AP Biotech’s energy-transfer fluorescent labeling patent, which it uses for labeling in its DYEnamic ET Terminator Kits, but allowed the trial to go forward on the issue of whether AP Biotech’s patent is valid and enforceable.

This decision “impacts all of Applied Biosystems' Big Dye products currently sold by Applied Biosystems and used by Celera Genomics,” AP Biotech said in an official company statement. “The decision is a significant step forward for Amersham Pharmacia Biotech in successfully concluding the case.”

But Applied Biosystems has taken a different view of the matter.

" With respect to the dye-related case, we continue to believe that we will prevail, primarily because of our position that the claims of [AP Biotech’s] patent are invalid and unenforceable due to prior technical work published by others,” Applied Biosystems president Michael Hunkapiller said in a statement.

Sheryl Zimmer, an analyst at DeutscheBank who covers Applied Biosystems, issued a report Wednesday in which she called one of the rulings in the dye case “a coup” for Applied Biosystems. “We are not terribly concerned by the ruling of infringement since the patent still needs to be determined to be valid for infringement to be relevant to the trial on validity,” Zimmer added in the report. “Nevertheless, we also note that we believe that ABI has other dye chemistries that could be used should the patents be found to be enforceable.”

Judge Breyer also rejected one of AP Biotech’s claims that Applied Biosystems is infringing on one of AP Biotech’s instrument patents through selling its ABI Prism 377 DNA sequencing system, but allowed another claim on this type of infringement to go forward. A separate claim by Applied Biosystems that AP Biotech is infringing on its patent through selling its MegaBACE DNA sequencing instrument will also go to trial.

This trial on the instrument claims will be conducted separately from the trial in the dye case, and a trial date has not yet been set.

On the instrument claims, Hunkapiller said Applied Biosystems was “pleased with the court's rulings that Applied Biosystems does not infringe [AP Biotech’s] patents and believe them to be a substantial step forward toward the successful resolution of this portion of the litigation.”

AP Biotech has not yet issued a formal comment on the instrument patent portion of the litigation, but is expected to comment formally on the matter next week.

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