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New Illumina Suit Alleges Affy's GeneTitan, GeneAtlas, ArrayStation Infringe IP

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This story was first published on Nov. 4.

By Justin Petrone

Illumina has filed a lawsuit against Affymetrix — its second in six months — alleging that a variety of its GeneChip products infringe a patent that was issued to Illumina last week.

The suit, filed in the US District Court for the Western District of Wisconsin, alleges that several Affymetrix products infringe US Patent No. 7,612,020, titled "Composite Arrays Utilizing Microspheres with a Hybridization Chamber."

Among the Affymetrix products that Illumina claims violates its patent are the GeneTitan, GeneAtlas, and ArrayStation instruments, along with related array plate sets and kits.

This is the second suit Illumina has filed against Affy in the US District Court for the Western District of Wisconsin this year. A suit filed in May claims Affy’s GeneTitan instrument and related products infringe a patent granted to Illumina in March. A trial date for that case has been set for October 2010 (see BAN 5/5/2009, BAN 10/6/2009).

In the suit filed last week, Illumina asked the court to permanently bar Affy from selling products listed in the suit. Illumina is seeking treble damages because it claims the infringement is "willful and deliberate."

The USPTO awarded Illumina the '020 patent on Nov. 3. 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 the patent are John Stuelpnagel, Mark Chee, and Steven Auger.

The suit is the latest in a string of legal battles between the two West Coast array firms. Affymetrix first sued Illumina in July 2004 for allegedly infringing six of its patents. One patent was later dropped from the suit, and Illumina fired back with counterclaims alleging unfair competition and accusing Affy of violating US anti-trust legislation.

In March 2007, a jury sided with Affy in the first phase of the litigation, finding that Illumina's products infringed "one or more claims" of Affy’s patents and awarding Affy damages of more than $16.7 million for the period of 2002-2005 based on a royalty of 15 percent (see BAN 3/20/2007).

In October 2007, Affy filed more suits against Illumina, alleging that its array products as well as its next-generation sequencing technology were in violation of five US patents awarded to Affy, as well as three European patents. Affy agreed to drop the suits in return for a $90 million settlement in January 2008 (see BAN 1/15/2008).

In the suit filed in May, Illumina alleges that a variety of Affymetrix products infringe Illumina's 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 Illumina the patent on March 31.

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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