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Judge in Illumina vs. Affy IP Infringement Suit Denies Motion to Transfer Case to California

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By Justin Petrone

The IP infringement suit that Illumina filed against Affymetrix in May will stay in Wisconsin and follow a schedule that calls for a court trial next fall, according to court documents obtained by BioArray News.

In a Sept. 18 order, Magistrate Judge Barbara Crabb of the US District Court for the Western District of Wisconsin denied a motion from Affy's attorneys to transfer the case to the US District Court for the Northern District of California.

Affy had argued in favor of transferring the suit on the basis that it involves "two California-based companies, concerning products developed in California" and that the "witnesses to the alleged infringement reside in California." Illumina's attorneys meantime maintained their desire to pursue the case in Wisconsin, citing the speed with which the case could be heard there.

"The most recent available statistics for civil cases in the Northern District of California show that the median time from filing to trial has lengthened to a glacial 30.0 months," Illumina's attorneys said in a June 30 filing. "In contrast, the median time to trial in [the Western District of Wisconsin] is currently 12.3 months."

The decision to keep the case in Wisconsin rather than transfer it to California affects the timing of when the two array makers will go to trial. A trial date has already been set for October 2010 in Wisconsin. Had the case been transferred to California, the time from filing to trial could have taken two and a half years (see BAN 7/21/2009).

Judge Crabb wrote in the Sept. 18 order that Illumina's interest in the "speedy resolution" of the suit was an "important consideration" in her decision, and that Affy's argument that it would be more convenient and less costly to transfer the case to California was "not particularly compelling."

Crabb wrote that there is "no evidence that the greater travel or transfer costs would not be canceled out by the money saved by reaching the end of the litigation 18 months sooner than if this case were litigated in the Northern District of California."

According to a case schedule set in June, the case will proceed with a claim construction hearing in January 2010, a discovery cutoff of September 2010, a pretrial conference date of Sept. 23, 2010, and a trial date of Oct. 4, 2010.

Illumina sued Affymetrix in May, alleging that Affy's GeneTitan automated platform, as well as several of the system's components and related products, infringe Illumina's array technology (see BAN 5/5/2009).

Specifically, Illumina argues that Affy's products infringe US Patent No. 7,510,841, entitled, "Methods of Making and Using Composite Arrays for the Detection of a Plurality of Target Analytes." The US Patent and Trademark Office awarded the patent to Illumina on March 31.

The Affy products named in the suit include the GeneChip HT RG-230 PM Array Plate, the GeneChip HT Array Plate Scanner, the GeneChip HT 3' IVT Express Kit, the GeneChip Array Station, and the GeneTitan instrument. Illumina filed an amended complaint in August that also named the GeneAtlas instrument as an infringing product.

Affy launched gene expression products on its automated, next-generation GeneTitan last September. The company is also preparing to launch genotyping assays on GeneTitan later this quarter, and the new lower-throughput GeneAtlas next year (see BAN 6/9/2009).

Illumina said in the suit that it is seeking a judgment from the court that Affy has indirectly and directly infringed one or more of the claims of the '841 patent and that each of the claims of the patent is valid and enforceable. It also seeks a permanent injunction barring Affy from making and selling the named products, as well as a judgment that Affy has willfully infringed the '841 patent and should pay triple damages as a result.

In August, Affy answered Illumina's amended complaint by denying that it had infringed the '841 patent, which it argued is invalid and unenforceable. In its answer, filed on Aug. 28, Affy called on the court to dismiss Illumina's suit with prejudice, declare the '841 patent invalid, cover its litigation fees, and award Affy "other and further relief as the Court may deem proper." In a Sept. 14 response, Illumina asked the court to uphold the validity of the '841 patent.

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This is not the first time Illumina and Affymetrix have met in the courtroom. Previous IP infringement cases, filed between July 2004 and October 2007, were settled in January 2008 when Illumina paid Affy a one-time $90 million payment to settle multiple suits that Affy had filed in the US, Germany, and UK (see BAN 1/15/2008). Illumina did not admit liability as part of the settlement.

Illumina's case is based on its ownership of the technology described in the '841 patent. The patent was originally filed on January 28, 2004, with a parent case text that stretched back to patents originally filed in 1998, 1999, and 2000. John Steulpnagel, Mark Chee, and Steven Auger are named as its inventors.

A co-founder of Illumina, Stuelpnagel was Illumina's chief operations officer until April 2008. Chee, another co-founder of Illumina, currently is CEO of La Jolla, Calif.-based Prognosys Biosciences. Prior to co-founding Illumina in 1998, he was director of genetics research at Affymetrix. Auger, also an Illumina co-founder, is now the principal consultant for Cohasset, Mass.-based consultancy BioDevice Partners. All three are inventors on a number of Illumina patents.

The '841 patent relates to "sensor compositions comprising a composite array of individual arrays to allow for simultaneous processing of a number of samples." It describes a method of detecting the presence or absence of a plurality of different target analytes by: a) providing a first substrate with a surface of assay wells, where the assay wells contain sample solutions, each with different target analytes; b) providing a second substrate of array locations, where the discrete sites in each location are different bioactive agents; c) dipping in parallel the projections of the second substrate into the assay wells so that each array location on the second substrate contacts sample solution in a different well of the first substrate; and d) detecting the presence or absence of the target analytes.

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