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Court Constructs Claims in Illumina vs. Affymetrix IP Suit; Trial Date Moved to 2011


By Justin Petrone

An ongoing IP dispute between array vendors Illumina and Affymetrix inched closer to resolution last week, as a US District Court ruled on the meanings of patent claims central to the case.

Judge Barbara Crabb of the US District Court for the Western District of Wisconsin handed down her claims construction ruling July 14, tacking closer to defendant Affymetrix's proposed definitions of certain claims, without full adoption of Affy's proposed language.

San Diego chip maker Illumina first sued Affy in May 2009, alleging that some of its microarray products infringe one of its patents (BAN 5/5/2010). In November of the same year, Illumina filed a second suit, similarly accusing its rival of infringing a second patent (BAN 11/10/2009). The court subsequently consolidated the cases in December 2009, pushing an earlier planned trial date of October 2010 to March 2011.

Among the Affymetrix products that Illumina claims violates its patents 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 suit and is seeking treble damages because it claims the infringement is "willful and deliberate."

The two patents central to the case were both awarded to Illumina last year. The first, US Patent No. 7,510,841, is entitled, "Methods of Making and Using Composite Arrays for the Detection of a Plurality of Target Analytes," and relates to "sensor compositions comprising a composite array of individual arrays to allow for simultaneous processing of a number of samples."

The second, US Patent No. 7,612,020, is entitled titled "Composite Arrays Utilizing Microspheres with a Hybridization Chamber," and describes 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."

In the claim-construction hearing last month, Illumina and Affy disagreed about how to define several terms common to both patents: "second substrate," "bioactive agent," and "discrete sites."

Illumina constructed "second substrate" to mean "a support," while Affy proposed "a material that is modified to contain discrete individual sites appropriate for the attachment or association of beads (small discrete particles) and is amenable to at least one detection method." The court's construction was closer to Affy's language, but differed slightly: "a material that can be modified to contain discrete individual sites appropriate for the attachment or association of beads and is amenable to at least one detection method."

Illumina constructed "bioactive agent" to be a "part that juts out from a portion of a substrate, for example like a finger," while Affy defined it as a "molecule (e.g., protein, oligopeptide, small organic molecule, coordination complex, polysaccharide, polynucleotide, etc.) attached to an array location that is also attached to a microsphere." The court constructed "bioactive agent" to mean "any molecule that can be attached to a microsphere."

Finally, Illumina constructed "discrete sites" to mean "sites that are sufficiently distinct to permit individual detection." Affy defined "discrete sites" as "sites that are non-contiguous with other sites." The court constructed the claim as "sites that do not touch another site."

Under the schedule set by the court in December 2009, Illumina and Affymetrix will now embark on a period of discovery in the case that is scheduled to end in December 2010. Possible settlement letters are expected by the court by February 2011, and both a pretrial conference and a trial hearing have been set for March 2011.

Both companies have been in and out of court for years. 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 through 2005 based on a royalty of 15 percent (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).

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