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Fall 2010 Trial Date Set for Illumina v. Affymetrix Array IP Infringement Suit

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By Justin Petrone

An IP infringement suit that Illumina filed against Affymetrix in May will likely go to trial in the third quarter of 2010, according to court documents obtained by BioArray News.

In a July 9 order, Magistrate Judge Stephen Crocker of the US District Court for the Western District of Wisconsin said that Illumina and Affymetrix have agreed to a case schedule that includes 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 two months ago, alleging that Affy's new 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 is arguing 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.

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 year, and a new lower-throughput instrument called GeneAtlas in 2010 (see BAN 6/9/2009).

Illumina said in the suit, filed May 4, 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.

Last month, Affy answered Illumina's complaint by denying that it had infringed the '841 patent, which it argued is invalid and unenforceable. In its June 9 answer, 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."

Affy has also filed a motion with the court to transfer the case from the Western District of Wisconsin to the Northern District of California on the basis that the suit involves "two California-based companies, concerning products developed in California" and that "witnesses to the alleged infringement reside in California."

In a June 30 response, Illumina's attorneys 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 contrast, the median time to trial in [the Western District of Wisconsin] is currently 12.3 months."

They also noted that Affy in the past has chosen to bring cases against Illumina in the District of Delaware as opposed to the Northern District of California. Those cases, filed in 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 between 2004 and 2007 (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. It 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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