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EPO Upholds Revocation of 'Important' Affy Patent in Europe, Despite Appeal

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By Justin Petrone

The board of appeals of the European Patent Office recently upheld the revocation of an Affymetrix patent that covers the making of high-density arrays, BioArray News has learned.

Pierre Cremona, a formalities officer for the appeals board, confirmed this week that the board, after hearing oral proceedings in the case, decided to uphold the revocation of European Patent 0619321, "Method and apparatus for investigating polynucleotide or amino acid sequences."

The EPO's opposition division initially revoked the patent in November 2007, and Affy laid ground for an appeal with the appeals board earlier this year (see BAN 7/27/2007).

Cremona told BioArray News that following the June 26th oral proceedings in the appeal, the board agreed with the November 2007 decision of the opposition division. According to Cremona, the decision on the revocation of the '321 patent is "final." He said that technically Affy's representatives in Europe could ask an enlarged appeals board to review the decision. Unless they choose to do so, the revocation will remain in force.

An Affy spokesperson this week said the company does not comment on litigation strategy.

According to an attorney familiar with the case, the revoked patent was "important" and the EPO's decision could have ramifications for the "entire scientific community in Europe" and lead to potential losses in licensing fees for Affy.

"Not only for us, but for the entire scientific community in Europe, the patent is dead," said Axel Stellbrink of Munich, Germany-based Vossius and Partner. The firm has represented first Protogene and then its successor company Metrigen in opposing the '321 patent in the EPO since 1999. Other opponents of the patent include Multilyte, Oxford Gene Technology, and Incyte Pharmaceuticals.

The patent describes a “method of preparing pre-selected chemical sequences at known locations on a single substrate surface,” as well as an apparatus for creating such an array and a fluorescence-based detection system for reading the results of an experiment using the invention.

The patent was originally published by the EPO in 1994 and assigned to Affymetrix’s predecessor firm, Affymax Technologies. It is at the center of a family of hundreds of additional patents that have been granted to Affymetrix worldwide.

Opponents of the patent argued that its claims were too broad and hindered their ability to operate in the European microarray market.

"This patent had a broadened scope of protection," said Stellbrink. "It was more dangerous for people in the scientific area who wanted to use this technology."

Stellbrink added that the patent was "very important" because it claimed density of more than 1,000 spots on an array. "All other arrays with more than 1,000 would be affected," he said.

Beyond being unenforceable, the impact of the demise of the '321 patent on Affy's business is unclear. Stellbrink said he is aware of "numerous parties" that have paid Affy license fees at least partially based on the patent. "If they were clever enough to include the stipulation in their contract, they can ask license fees to be paid back in terms of revocation," Stellbrink said of such firms."If not, then Affy would keep the license fee," he said.

"These license contracts are seen as very risky, but, still, the basis for some agreements has been killed," he noted.

Still, though the patent has been revoked in Europe, it may have a limited effect on Affy's business as the company sells its chips worldwide, according to others familiar with the array IP landscape

"It is not uncommon for licensing agreements to carry on while there is a patent somewhere in the world still in force," Tony Maschio, a patent attorney at London-based Edwards Angel Palmer and Dodge, told BioArray News earlier this year. "Unless these agreements are tied to specific European patents, it's not something about which to be concerned" (see BAN 1/20/2009).

If licensing agreements are tied to specific European patents, though, the agreements could be terminated, Maschio said. He also noted that firms like Affy have "built up such a reputation in the field" that, even without certain IP, their business will continue to function.

"Even if the patents were knocked out, it won't seriously affect the company. It could affect share price and perhaps more competitors will spring up, but patents filed in the 1990s will expire within less than 10 years," Maschio said.

"In the beginning, IP is important when a company has nothing else," Maschio said. "But now they have facilities and know-how. If you are a user who wants to work with array technology, you are probably better off going with Affy than a new competitor anyway."

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