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Genotyping Perfect Timing: Illumina asks USPTO to Investigate Affy IP


Illumina and Affymetrix are at it again. Last October, Illumina asked the US Patent and Trademark Office to investigate the ownership of a patent Affymetrix now holds thanks to its $121 million acquisition of ParAllele Biosciences. Illumina announced its filing on the very day Affymetrix closed its deal.

Coincidence? Hardly. “It clearly is a much different situation when that technology is in the hands of Affymetrix than when it was in the hands of ParAllele,” says Illumina CEO Jay Flatley. Illumina requested that the USPTO declare an “interference” with the patent, a move that may initiate proceedings to determine who has priority in inventing the technology.

The patent in question is US Patent
No. 6,858,412, “Direct multiplex characterization of genomic DNA,” which covers methods of multiplexing nucleic acid reactions using molecular inversion probe genotyping technology. The USPTO granted the patent in February 2005 to Stanford University, which in turn licensed it to ParAllele.

Flatley notes that it is not difficult to “extrapolate ... what our motivation was for filing the interference once [the patent] was owned by Affymetrix.”

Illumina claims that the technology was first invented “during the course of early research and development at the company,” according to a statement. The technology is not currently used at Illumina, says Flatley, who adds that “the risk is quite high for [Affymetrix]” if his company is found to be the rightful patent owner. A spokesperson for Affymetrix declined to comment on this story.

Affy paid out $11.7 million in cash and approximately 2.29 million shares of common stock to acquire ParAllele in October. At the time, Stephen Fodor, founder and CEO of Affymetrix, said in a conference call that he expected the “quick and successful integration of companies” after the acquisition.

This isn’t the first time Illumina and Affymetrix have locked horns over IP. The companies have been embroiled in patent disputes since July 2004, when Affymetrix brought suit against Illumina for allegedly infringing on six patents. Illumina denies this claim, holding that Affy’s patents are so broad as to be invalid. The companies are set to meet in court in October 2006.

Incidentally, the lead inventor on the contested ’412 patent, Thomas Willis, former president of ParAllele, filed the application on October 24, 2001 — exactly four years to the day before Illumina announced its petition to the USPTO. And that, probably, is a coincidence.

— Jen Crebs

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