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EPO Could Revoke Key Affy Patent as the Validity of Core Microarray IP Is Questioned

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The European Patent Office has taken steps to revoke a 13-year-old, foundational Affymetrix patent in Europe after eight years of opposition from firms including Multilyte, Oxford Gene Technology, and Incyte Pharmaceuticals, BioArray News has learned.
 
According to EPO documents, the opposition division of the EPO decided to revoke European Patent No. 0619321, “Method and apparatus for investigating polynucleotide or amino acid sequences,” on June 20.
 
According to an attorney familiar with the case, the decision is preliminary, and Affy has about four months to lay the groundwork for retaking the rights to at least part of the patent.
 
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. Moreover, it is at the center of a family of hundreds of additional patents that have been granted to Affymetrix worldwide.
 
Opponents of the patent have argued that its claims are too broad and hinder their ability to operate in the European microarray market.
 
Axel Stellbrink, an attorney with the Munich, Germany-based patent law firm Vossius and Partner who represents opposition to patent, told BioArray News this week that the the EPO’s June 20 decision is preliminary following opposition hearings last month, but that it is highly likely that the opposition division will officially revoke Affy’s rights to EP0619321 in coming weeks, which would prompt Affy to appeal.
 
“They have not yet received an official decision,” Stellbrink said. “I do believe that [once the EPO renders its final decision] Affy will probably appeal. Affy then has two months to file for appeal and another two months to file the grounds for the appeal,” he said.
 
Vossius and Partners has represented Protogene, a Menlo Park, Calif.-based array start-up, since it filed its opposition to the Affy patent in 1999. Protogene shuttered its business in 2004, but Vossius continued to represent the firm because it saw a revocation of the patent as being in the interest of the European chip market, Stellbrink said.
 
“This case has a little bit of a history because ... we knew from investors and every company in the field that this patent has made it very difficult to operate,” Stellbrink said. The general theme of the opposition to the patent was that it was so broad as to prohibit other array vendors to freely operate, Stellbrink explained.
 
“What they claim is what is known as high-density microarrays, which affects everybody that is working in this area,” he said. “Another technology claimed is how to create lab-on-a-chip. This patent has the largest family I have ever seen. They have pages and pages of documents corresponding to this patent and its family so it is very important patent to Affymetrix,” he added.
 
A Shift in IP Landscape?
 
This is not the first time that an Affymetrix patent has been revoked by the EPO’s opposition division. In February 2005 the EPO revoked EP0834576, “Methods using nucleic acid hybridization patterns on a matrix of oligonucleotides” (see BAN 3/9/2005).
 
Opponents in that case again took aim at the alleged broadness of the patent’s claims. Affymetrix subsequently filed an appeal, which is still pending before the appellate division of the EPO. Two former opponents, Applera and Abbott, withdrew their opposition after signing licensing agreements with Affymetrix in 2006, leaving PamGene and CombiMatrix to oppose the patent during the appeal (see BAN 5/30/2006).
 
Stellbrink this week said that it is unusual for the EPO to revoke patents. “In my experience, about 5 percent of these cases end in a revocation,” he said. He added that even if the appellate division doesn’t decide to uphold the opposition division’s revocation of  EP0619321, Vossius still has other vehicles to invalidate at least parts of the company’s patent.
 
“Even if the second instance will come to a different conclusion, we have plenty of arguments to make against it. So at the very end I think it is quite likely that the patent will not continue in its present form,” he said.
 
The challenge to Affy’s core IP in Europe is mirrored by a similar situation in the United States, where San Francisco law firm Fliesler Meyer recently made an ex parte request of the US Patent and Trademark Office to reexamine an Affymetrix patent (see BAN 6/19/2007).
 

“This patent has the largest family I have ever seen. They have pages and pages of documents corresponding to this patent and its family so it is a very important patent to Affymetrix.”

Anthony Craig, a Fliesler Meyer attorney who is handling the reexamination request on behalf of an undisclosed client, told BioArray News last month that challenges to foundational IP such as Affy’s have often been settled behind closed doors, leaving unanswered questions over the validity of the patents.
 
“Litigation has its role in our society for being able to weed out bad patents,” he said. “But when two parties each have a patent that doesn’t meet those requirements for whatever reason and they are in litigation, they can actually agree to endorse each others’ patents and what happens is that society is the loser,” he said.
 
According to Kazunori Hashimoto, a patent attorney and associate professor in the intellectual property division of Tokyo Medical and DentalUniversity, challenges to foundational Affy IP in Europe and the US are a systemic issue associated with examination processes that have been too lenient in the past.
 
Hashimoto told BioArray News via e-mail this week that “examinations in Europe and the US are not [as] strict for biotech pioneer patent applications compared with those in Japan.” He recently co-authored an article arguing that a more stringent IP environment in Japan has limited the lifespan of some of the microarray industry’s foundational IP in that country [Aida T, et al. Shortened life spans of biotech pioneer patents in Japan: a lesson from the DNA chip. Nature Biotechnology. 2007 May;25(5):533-5]. 
 
“I think that this situation leads to instability of the issued patents in Europe and the US,” he said. “In order to stabilize and facilitate international business processes of both patent holders and third parties — businesses that are constrained by the patents — harmonizing the examination policy toward biotech pioneer inventions among the patent offices, especially among EPO, USPTO, and the Japanese Patent Organization, would be needed,” Hashimoto wrote.

If the world’s larger patent organizations are unable to cooperate more in the future, Hashimoto warned, similar challenges to pioneer bioarray IP should be expected.