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EPO Revokes Affy Patent After Rivals Dispute IP; More Challenges May Ensue

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A small band of companies, including rivals and collaborators, has convinced the European Patent Office to revoke an Affymetrix patent, BioArray News has learned.

The opposition division of the EPO rendered its decision on Feb. 23, giving Affy two months to file an appeal before the decision becomes final.

While the revocation is unlikely to impact Affymetrix’ revenue — companies have freely used the method described in the patent since it was awarded in 2001 — opponents of the patent said the EPO’s decision is a strategic victory over the microarray giant that may embolden rivals to oppose additional Affy patents in Europe.

The European patent system permits corporations or individuals to formally challenge a patent through the EPO. Amit Kumar, CEO of CombiMatrix, one of six companies and individuals that opposed the patent, said the revocation is significant because smaller firms or individuals that question the intellectual property rights of dominant players like Affymetrix can go through the opposition division of the EPO and win.

“I think it’s [significant] because the patent has been revoked,” Kumar said.

Kumar said his company has used the method described in Affy’s patent despite the IP because the method is widely used in the industry, but added that the decision will benefit other competitors that are trying to break into the microarray market.

“Now other customers that are leery about using anyone else’s products don’t have that issue anymore,” Kumar said. “This will expand competition in Europe and will be beneficial to the customers [and] companies in the microarray space.”

The patent in question, “Methods using nucleic acid hybridization patterns on a matrix of oligonucleotides” (EP0834576) was initially granted to Affymetrix on Nov. 28, 2001, and published in the European Register the following month. The patent describes a method of detecting nucleic acid sequences on an array comprising more than 100 probes on which two fluorescent labels are used to differentiate between different collections of nucleic acids. Affy does not hold similar IP in the United States. (see Sidebar)

Challenges to the patent were filed 11 months later, in October 2002, by several corporations and individuals including CombiMatrix, Abbott Laboratories, PamGene, Roche Diagnostics CmbH, Applera, and others. Roche, an Affy collaborator on the pioneering AmpliChip in vitro diagnostic, withdrew its opposition in December 2003.

Kumar said his firm objected to the patent in order “to assist customers by removing what we felt were overreaching claims.” He said the other opposing parties made similar arguments.

In a notice of opposition, a representative for Abbott Labs said that Affy’s method was “commonplace in the art,” while an attorney representing Peter Schneider, a German researcher, dismissed Affy’s technique as “neither innovative nor unique.”

Now that the patent has been revoked, companies like CombiMatrix, Applera, PamGene, and Abbott Labs, each of which are opposing a number of other European patents held by Affy, may be feeling more confident about their chances.

Oppositions have also been filed by CombiMatrix, Abbott and others for “Expression monitoring by hybridization to high density oligonucleotide arrays” (EP0853679), “Identification of nucleic acids in samples” (EP0834575), and “Method and apparatus for packaging a chip” (EP0695941), according to the EPO’s database.

“We oppose a number of Affy patents,” explained Kumar. “We don’t think that Affy, or anyone for that matter, should dominate a product that it does not teach or describe.”

Representatives for Affymetrix did not return several phone calls and e-mails to comment on the EPO’s decision. A receptionist for Hepworth Lawrence Bryer & Bizley, an Epping, UK-based law firm that has been representing Affymetrix in the process, said that its patent attorneys would “not disclose details [of the case] to third parties, including journalists.”

Affy Likely to Appeal

While opponents of Affy’s patents are feeling good about the Feb. 23 ruling, most expect the company will appeal the decision.

“I expect that Affymetrix will be filing an appeal,” said attorney Christoph Schreiber, who represented Peter Schneider during his more than two years of opposition to the patent.

“They will undoubtedly appeal,” agreed Stephen Ritter, the attorney that represented Abbott Labs. “It’s a no-brainer. You pay some money, you file a statement, and it gives you a chance of getting a patent back.”

Tony Maschio, a patent attorney that works out of the Southampton, UK office of D. Young and Associates, said that the appeal was significant for the opposition, but said that the EPO’s Feb. 23 decision was far from final. Maschio said that Affy now has two months to appeal, and that its patent will still be enforceable during that time (Ritter, the Abbott attorney, claimed that the patent is not enforceable). Should Affymetrix appeal, Maschio said, the patent will remain in effect until a final decision is made by the EPO.

“It is significant in that it shows that a decision has been taken which is adverse to Affymetrix, but it is not unusual, and it is not the end for Affymetrix, although their struggle is now uphill,” Maschio said.

Maschio said that it was quite normal for a patent to be revoked through the EPO’s opposition process, but that the chances for opposing biotech patents are slimmer than in other industries.

“If you are looking at biotechnology, about 8 percent of patents are opposed annually and of those 8 percent in biotechnology about 26 percent are revoked,” Maschio said.

However, a benefit to opposition parties, Maschio said, was that European courts are unlikely to touch any lawsuits Affymetrix could bring forth related to the patent until the EPO settled the matter.

“Its enforceability in a court will be quite suspect,” Maschio said. “[For example], if Affymetrix decided to bring a suit in Germany, the German court could say, ‘Well, the EPO is still dealing with this, so we’ll park this case,’ and they’ll let it sit on the sidelines until it is resolved.”

— JP

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