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Incyte, Hyseq Claim Victory in Affymetrix Patent Ruling

NEW YORK, Jan 25 – Claiming victory in their DNA microarray patent disputes with Affymetrix, both Incyte and Hyseq said Thursday the US District Court for the Northern District of California narrowly interpreted Affymetrix’s patents to exclude their microarray manufacturing processes this week.

A District Court judge in San Jose issued a so-called Markman ruling covering both cases, which describes how the patents will be interpreted for the purposes of the litigation.

In both cases, Affymetrix asserted that its patents cover the entire field of DNA arrays, b ut the Markman ruling held instead that the claim on two of Affymetrix' patents cover microarrays in which activation of a DNA polymer ”is accomplished through exposure of the localized area to an energy source,” Incyte said in a statement.

Affymetrix, which can now either appeal the Markman ruling, proceed with the case under the ruling, or settle, did not return calls seeking comment.

Since Affymetrix uses photolithography, where the polymers on the chip are activated through exposure to a light source, and Incyte uses arrays where cDNA is printed onto a chip and not activated through exposure to an energy source, Incyte claimed the ruling favors its case. Hyseq also has plans to commercialize its HyChip that does not use photolithography, but has not yet done so partially due to the litigation with Affymetrix.

" The court's ruling is a victory, not only for Incyte, but for the entire medical research community," Lee Bendekgey, Incyte’s general counsel, said in a statement. “We have maintained from the start that these claims have no merit,” and we are confident that the District Court ruling will help to bring these matters to a successful conclusion for Incyte."

Incyte is optimistic that it will be able to resolve the litigation without going to trial, an Incyte spokesman said.

Separately, Hyseq said the ruling provided support to its position of non-infringement, and gave new energy to its ongoing efforts to resolve the litigation out of court.

Hyseq CEO George Rathmann also indicated the definition of Affymetrix’s claims might have larger implications for the whole microarray industry.

“What is at issue is more far reaching than one construction [of a patent claim]," Rathmann told GenomeWeb. “It’s to establish the ground rules and the scope by which Affymetrix can maintain its position as the exclusive provider of these arrays. The Markman interpretation will help people decide whether their particular array looks like it is of the nature that will be viewed as infringing.”

Rathmann noted that the Markman ruling is not final and is subject to different interpretations.    

Affymetrix first filed a patent infringement suit against Incyte in January 1998, alleging that Incyte was infringing on its patent number 5,445,934, which covers an “ array of oligonucleotides on a solid substrate .” Then in September 1998 Affymetrix added patent infringement claims for numbers 5,800,992, which outlines a “ method of detecting nucleic acids,” and 5,744,305, which refers to “ arrays of materials attached to a substrate.”

Affymetrix’ patent infringement suit against Hyseq, which it filed as a countersuit after Hyseq sued it for patent infringement in 1997, covers patent numbers 5,744,305. 5,800,992, as well as patent number 5,795,716, which refers to “c omputer-aided visualization and analysis system for sequence evaluation”.

The Markman ruling covers the ‘934 patent and the ‘305 patent.

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