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Incyte Cracks Affy s Patent Fortress, But Doesn t Stop Infringement Claims


Affymetrix may have a dominant patent position in the microarray field, but as a recent US District Court ruling shows, the company’s IP fortress can be penetrated.

This October 3 summary judgment ruling, which the US District Court for the Northern District of California issued as part of the ongoing patent infringement battle between Affymetrix and Incyte, held that Affymetrix’s “two color patent,” US Patent Number 5,800,992, is invalid and that Incyte’s microarray platform therefore does not infringe upon this patent. The reason the patent was invalidated is that it failed to provide an adequate written description of the invention that a skilled practitioner in the art of microarraying could follow.

This so-called ë992 patent’s claims describe the use of two-color fluorescent labels to conduct microarray experiments of various kinds, including comparative gene expression analysis. In other words, if this patent were valid, it could potentially prevent other companies from making microarrays that can be labeled with the virtually ubiquitous Cy3 and Cy5 labels.

“The Court’s ruling is a victory, not only for Incyte, but for the entire medical research community,” stated Lee Bendekgey, Incyte’s General Counsel. “Affymetrix has continually asserted that it owns the field of DNA arrays regardless of the method of manufacture and regardless of the uses to which those arrays are put. These rulings significantly scale back the scope of the Affymetrix patent estate.”

Incyte’s trumpeting of victory, however, may be somewhat overblown. The District Court Judge rejected Incyte’s arguments that Affymetrix’s other microarray patents, numbers 5,744,305 and 5,445,934, were also invalid. This allowed Affymetrix to proceed in its case against Incyte for infringement of these patents in all of its microarray products, including its cDNA arrays.

“There were three patents asserted against Incyte in this litigation,” explained Affymetrix director of investor relations Anne Bowdidge. “We have gone through a number of different hearings, and are not going forward with the ë992. The other two patents have been tested, and the litigation moves to the next area.”

Tuesday, the court began hearing arguments in this infringement case. Incyte has filed a motion for summary judgment, asserting that its cDNA arrays do not infringe the patents, which cover oligonucleotide and polynucleotide arrays. The court has also previously found that Incyte does not infringe upon the oligonucleotide-related claims of the patents because it only manufactures cDNA arrays. What remains to be answered is whether Incyte’s cDNA arrays in fact fall into the “polynucleotide” definition in the Affymetrix patents.

The judge is expected to issue an initial ruling on this matter within two or three weeks, according to Affymetrix. Unless the judge grants Incyte’s motion for summary judgment on all claims, the case will head to trial in April of next year.

James Reddoch, an analyst who covers Affymetrix for Banc of America Securities, said in a note that Affymetrix has a good chance of forcing Incyte to take a license to its technology in the end, based on its polynucleotide-related claims in the two remaining patents at issue. “Affymetrix wins if even one claim is upheld,” he wrote.

The larger outcome of this case could in fact be tied to a separate suit — the original suit in which Incyte is claiming that Affymetrix infringed its patents. Although Incyte filed this suit before Affymetrix countersued, Incyte’s claims against Affymetrix remain to be litigated. When these claims are litigated, they could have a significant impact on the outcome of Affymetrix’s case against Incyte. Just as Nanogen had to pay Motorola $5 million, and forced Motorola to license its technology, after the two decided to bury the hatchet, this tangle of litigation could be resolved by cross-licensing deals, or some combination of cross-licensing and cash.

The final disposition of this litigation could also have a wide ripple effect on the whole microarray industry. Not only is Incyte the provider of arraying content to Motorola, Agilent, and Corning; these companies also manufacture oligonucleotide and cDNA arrays that are similar to Incyte’s in format, differing only in manufacturing details, choice of content, price, and quality.

Additionally, even if Affymetrix doesn’t win against Incyte on the two remaining patents at issue, it has a rich trove of more than 130 issued patents which it claims can adequately cover its microarray technology.


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