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Affymetrix Files Complaint Against Illumina to Update BeadArray Patent Ownership

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This story was first posted on March 17.

By Justin Petrone

Affymetrix and an independent inventor have filed a complaint against Illumina, arguing that the inventor, Gregory Kirk, aided Illumina in the development of its BeadArray platform and should be listed as a co-inventor on two of the San Diego life science tool vendor's patents.

Affy and Kirk filed the complaint on March 14 in the US District Court for the Western Court in Wisconsin. In it, they argue that Kirk should be added as an inventor on US patent numbers 7,510,841, and 7,612,020. Both patents were central to Illumina's patent infringement cases against Affy, which the same court dismissed last December (BAN 12/21/2010).

If the action is successful, it will give Affymetrix and co-defendant Gregory Kirk rights in the two Illumina patents. According to the complaint, Affy is a licensee of Kirk's alleged rights under the '841 and '020 patents, and also holds an "undivided, one-half interest" in Kirk’s rights in the IP. The background of the relationship between Kirk, a Princeton University-educated physicist with experience in the biotech industry, and Affy is unclear.

The complaint alleges that Kirk provided assistance to Illumina at the time the BeadArray technology was developed but was not credited as an inventor on either of the patents in question.

The '841 patent is entitled "Methods of making and using composite arrays for the detection of a plurality of target analytes" and was issued on March 31, 2009. The patent identifies John Stuelpnagel, Mark Chee, and Steven Auger as inventors. All three have assigned their rights in the '841 patent to Illumina, according to the complaint.

The ‘020 patent is entitled “Composite arrays utilizing microspheres with a hybridization chamber” and was issued on Nov. 3, 2009. Stuelpnagel, Chee, and Auger are also listed on the '020 patent, and have similarly assigned their rights to Illumina.

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 Affy. Auger, also an Illumina co-founder, is now the principal consultant for Cohasset, Mass.-based consultancy BioDevice Partners.

According to the complaint, Stuelpnagel in 1998 approached Kirk, along with Chee and Auger, to develop an optical sensor array technology pioneered in the lab of Tufts University professor David Walt that would become the basis for Illumina's microarray platform. BioArray News spoke with Walt about the evolution of the BeadArray technology in 2009 (BAN 9/8/2009).

While Kirk contributed to the development of the platform, he later decided against joining the firm, Affy and Kirk maintain, while Chee and Auger joined Illumina and assigned their patent rights to the company. As Kirk was not affiliated with Illumina, Affy and Kirk allege that Kirk was intentionally not listed as an inventor on the patents in question because it would have meant that Illumina did not hold exclusive rights to those patents.

"Had Kirk been named as an inventor, Illumina would have to acknowledge Kirk’s ownership interest" in the IP and Illumina "would not have been able to claim exclusive control of the application," Affy and Kirk state in the complaint. "Upon information and belief, at least Stuelpnagel deliberately excluded Kirk as a named inventor of the [patent] application in an attempt to secure for Illumina exclusive ownership rights to that application and any patents that may issue from that application," they alleged.

Affy and Kirk aim to move the US Patent and Trademark Office to reissue certificates for the '841 and '020 patents that name Kirk as an inventor. They also argue that Illumina should bear their attorneys’ fees and costs and are seeking "other and further relief as the court may deem proper."

The new complaint has its origins in the infringement suit that was dismissed in December. Affy and Kirk claim that in that prior action, the court concluded that Affy "made a prima facie showing that Kirk is a joint inventor of the patents."

A hearing to determine whether the patents should be corrected was never held, as the case was dismissed on the grounds on noninfringement.

Affy and Illumina have been in and out of courtrooms for years. The December dismissal came nearly two years 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 (BAN 1/15/2008). Illumina did not admit liability as part of that settlement.


Have topics you'd like to see covered in BioArray News? Contact the editor at jpetrone [at] genomeweb [.] com.

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