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Trial Date for Illumina’s IP-Infringement Suit Against Affymetrix Moved to Spring 2011

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By Justin Petrone

Two separate IP-infringement suits Illumina filed against Affymetrix this year have been consolidated into a single case, and the court has set a new trial date, delaying it by at least five months, according to court documents obtained by BioArray News.

In a Dec. 10 order, Magistrate Judge Stephen Crocker of the US District Court for the Western District of Wisconsin agreed on a new schedule for the case, which would schedule a claim-construction hearing for June 2010 and set pretrial conference and trial dates for March 2011.

Illumina filed its suits in May and November and has argued in favor of the consolidation.

The first case claims that Affy’s GeneTitan automated platform and several of the system's components and related products infringe Illumina's array technology (see BAN 5/5/2009).

Illumina alleges 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.

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's benchtop GeneAtlas, scheduled to launch next year, was added to the complaint in August.

In July, the court set a case schedule that included holding a claim-construction hearing in January 2010, a discovery cutoff of September 2010, a pretrial conference on Sept. 23, 2010, and a trial on Oct. 4, 2010 (see BAN 7/21/2009). Shortly after, Affy asked the court to move the case to California from Wisconsin, but the motion was denied (see BAN 10/6/2009).

Illumina sued Affy a second time last month. In this second suit, also filed in the US District Court for the Western District of Wisconsin, Illumina alleges that several Affy products infringe US Patent No. 7,612,020, entitled "Composite Arrays Utilizing Microspheres with a Hybridization Chamber."

Among the Affymetrix products that Illumina claims violate its '020 patent are the GeneTitan, GeneAtlas, and ArrayStation instruments, along with related array plate sets and kits. Illumina has asked the court to permanently bar Affy from selling products listed in the suits and is seeking treble damages because it claims the infringement is "willful and deliberate".

After filing the second suit, Illumina requested the cases be consolidated and a new schedule be set by the court. On Nov. 12, the court agreed to consolidate the suits so that the new combined suit concerns the alleged infringement of both the '020 and the '841 patents.

Illumina had argued in favor of the consolidation, stating that "both the ’841 and ’020 patents issued from patent applications filed on the same date, by the same inventors, and prosecuted by the same patent attorneys." According to Illumina, "nearly all of the prior art references cited in the ‘020 patent were also cited in the ‘841 patent" and "both patents are drawn to the same general subject matter of composite arrays."

Affymetrix has denied infringing either patent and has argued that they are both invalid and unenforceable. In documents filed with the court on June 9 and Nov. 24, Affy called on the court to dismiss Illumina's suit with prejudice, declare the patents invalid, cover its litigation fees, and award Affy "other and further relief as the Court may deem proper."

Affy and Illumina are the two main players in the whole-genome genotyping microarray market. The two have battled in the courtroom before. Earlier suits, filed by Affy in July 2004 and October 2007, were settled in January 2008 when Illumina paid Affy a one-time $90 million payment (see BAN 1/15/2008). Illumina did not admit liability as part of the settlement.

Illumina's current case is based on its ownership of the technology described in the '841 and '020 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 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.

The USPTO awarded Illumina the '020 patent on Nov. 3, the same day it filed its suit. The patent claims an "array of arrays" composing a first substrate with a surface that includes assay wells containing samples; and a second substrate composed of projections in which each projection includes an array location composed of discrete sites containing different bioactive agents. The patent also claims an "array of arrays" composed of a "plate having wells."

The inventors of both patents are John Stuelpnagel, Mark Chee, and Steven Auger. 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 helping to found 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.

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