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In New Suit, Illumina Alleges Affy's GeneTitan System, Associated Products Infringe its IP

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Illumina this week filed a lawsuit against Affymetrix that alleges the company's new GeneTitan automated platform, as well as several of the system's components and related products, infringe Illumina's array technology.

The new litigation commenced nearly a year and a half after 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.

The new suit, filed May 4 in the US District Court for the Western District of Wisconsin, 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 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.

In a research note published this week, Leerink Swan analyst Isaac Ro described the new suit as "Round 2" of litigation between the companies. Ro predicted that the suit would have "no material impact" on Illumina, which he described as "actively seeking to protect its IP," and described it as "marginally negative" for Affy.

"We think this news could pressure [Affy's] existing burn rate and note that the new line of peg arrays [named in the suit] is key to reducing [Affy's] manufacturing costs and cost per data point," Ro said.

Affy launched the products named in the suit last September as part of the rollout of its new upgraded microarray platform. The system, priced at roughly $300,000, includes Affy’s ArrayStation, launched in 2005, which fulfills automated sample-preparation and liquid-handling duties, while the GeneTitan provides all other array-processing steps.

GeneTitan is also designed to handle Affy's new "peg array" format — strips of arrays produced to work with existing 96-well microtiter plates, allowing higher-throughput processing of the arrays. Affy launched legacy gene-expression assays in the new format when it debuted GeneTitan last year. Alternative splicing arrays and whole-transcriptome profiling arrays in the peg format are set to debut this quarter, while new genotyping assays should become available in the second half of the year (see BAN 4/28/2009).

Affy CEO and President Keving King noted during the firm's first quarter earnings call last month that the new peg array format "costs less" to produce and will also "sell for less to the end user." King said the new platform is a "win for both customers as well as to ourselves in terms of gross margins."

Illumina 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 a filing with US Securities and Exchange Commission on Monday, Affy said that it believes Illumina's claims are without merit and that it will "vigorously defend against them."

Illumina acknowledged the suit in a statement this week and said it is "asking the federal court to enjoin Affymetrix from continuing to make and sell its HT Array Plate and Scanner products, as well as for unspecified monetary damages."

According to documents obtained by BioArray News, Affy now has 20 days to answer the claims of infringement in Illumina's complaint.

'Perpetual Covenant'

This is not the first time the two companies have sparred over IP in the courtroom. 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 (see BAN 10/30/2007). Affy agreed to drop the suits in return for a $90 million settlement in January 2008.

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As part of that settlement, Affy granted Illumina, its affiliates, and its customers a perpetual covenant not to sue them for making, using, or selling any of Illumina's current products, evolutions of those products, and services related to those products. Affymetrix also extended the covenant not to sue for four years for making, using, or selling Illumina products or services that are based on future technology developments.

Illumina noted at the time that the covenant would not prevent Illumina from suing Affymetrix for using or selling future products in that same window of time. The covenant “only says that Affy cannot sue Illumina for any future products for the next four years,” Illumina spokesperson Maurissa Bornstein told BioArray News last year. “It does not say that Illumina cannot initiate litigation against Affy” (see BAN 1/15/2008).

The '841 Patent

Central to Illumina's case against Affy is its latest patent, No. 7,510,841, which was granted to the company on March 31. Originally filed on January 28, 2004, with a parent case text that stretched back to patents originally filed in 1998, 1999, and 2000, the '841 patent names John Steulpnagel, Mark Chee, and Steven Auger 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 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. 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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