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Affymetrix Disagrees with Incyte, Hyseq on Patent Ruling

NEW YORK, Jan 26 – Just hours after Incyte and Hyseq proclaimed that a ruling in their patent infringement cases with Affymetrix favored them, Affymetrix issued a conflicting statement, saying the ruling actually protects its patent position.

Jeremy Fogel, a judge in the US District Court for the Northern District of California issued this so-called Markman ruling, a determination on the scope and meaning of four Affymetrix patent claims, in order to define the terms of the claims for future legal proceedings.

Thursday, Incyte’s general counsel, Lee Bendekgy, called Judge Fogel's ruling “a victory, not only for Incyte, but for the entire medical research community." An Incyte spokesperson also said the ruling gave Incyte hope that the matter could be resolved without going to trial.

But Affymetrix fired off its own statement late Thursday countering this view.

" Today's Markman ruling strengthens these patents and solidifies our intellectual property portfolio,” Affymetrix senior vice president and general counsel Vern Norviel said in a statement. " The ruling reinforces our cases against Incyte and Hyseq and we will move expeditiously to prove their infringement."

This response seems to ensure that these cases, the first of which Affymetrix filed in January 1998, will proceed to trial.

At issue are four microarray-related patents which Affymetrix has asserted in separate suits against Incyte and Hyseq. Incyte and Hyseq both said the ruling limits these patents to arrays made using exposure to an energy source. Affymetrix activates its arrays by exposing the microwells to light, in a process known as photolithography, whereas Incyte uses spotted arrays where the cDNA is printed on the chip.  

Given this difference, Incyte said its microarray process is not covered under the patents at issue. HySeq has not yet produced arrays, but said its array process also would not fall under the rubric of the patent language.

But Affymetrix argued in its response to the ruling that Incyte does activate its arrays through exposure to an energy source. It also pointed out that this ruling does not limit the scope of patent number 5,795,716, which refers to " c omputer-aided visualization and analysis system for sequence evaluation,” a patent Affymetrix said Hyseq also infringes.

Furthermore, it noted that the patents at issue in this case are part of a broader family of patents that detail with methods for making spotted arrays. Affymetrix said this ruling does not address its assertion that Incyte infringed on its patent 6,040,193, which covers array spotting.

" The court's interpretation combined with the recent notices of allowance establish that Affymetrix' family of array patents covers arrays made by a wide variety of techniques for in situ synthesis and deposition of pre-formed polynucleotides,” Affymetrix noted in its statement.

Affymetrix was not immediately available for further comment.

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