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Affymetrix Appeals EPO s Patent Amendment Following Opposition

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Unsatisfied with a decision from the European Patent Office that forced Affymetrix to abandon several claims on a 2001 European patent, Affy and four rival companies that disputed the IP in January appealed the decision last month for a hearing, BioArray News has learned.

In March, Affymetrix requested that the EPO's appeals division reinstate the portions of the patent that were removed during opposition proceedings (the patent was left intact in amended form). The rival companies, which include CombiMatrix, Applera, Clondiag, and Abbott Laboratories, are seeking to have the patent revoked in its entirety.

The patent describes a method for identifying a target nucleic acid in a sample by running the sample on a standard microarray platform and comparing the hybridization pattern to a reference pattern to distinguish the target nucleic acid. The amended patent omits much of the protection for Affy's hybridization process.

According to Mary Ann Hartman, a formalities clerk at the EPO's headquarters in Munich, Germany, parties in an opposition case have two months to file an appeal of a decision rendered by the EPO, and Affy and its rivals must wait until June to learn whether the appeals division will hear the case.

If the appeals division agrees to hear arguments, it will make a final ruling that will affect whether Affy loses another patent to aggressive opposition in Europe, will win back all of its claims, or will live with the amended patent.

The time frame for a final decision, according to Hartman, varies from case to case.

Clondiag, a Jena, Germany-based microarray vendor, was the first to appeal the original decision on March 24, requesting that the EPO "set the decision aside and revoke the patent in its entirety." Similar appeals were made by CombiMatrix and Abbott Labs, which are both being represented by the London firm of Mathys & Squire. Applera appealed the following week.

Kathryn Taylor, the attorney for CombiMatrix and Abbott, requested that the decision be cancelled and requested "revocation of the opposed patent in its entirety."

In response to the decision, Affy's patent attorney Richard Bizley of the Epping, UK-based office of Hepworth Lawrence Bryer & Bizley, filed an appeal on March 30 informing the EPO that the decision "was adverse to Affymetrix."

Both camps have requested oral proceedings. When the appeals division hands down its decision, which is final according to European patent law, the second of several opposition proceedings to Affy patents in the UK will come to an end.

Affy had its first European patent revoked in late February after similar opposition from Applera, Abbott Labs, CombiMatrix, Clondiag, and others, and opposition parties have seen an opening in Europe to strike down patents they feel are stifling the competitive microarray space (see BAN 3/9/2005).

"We feel that our industry, our specific market segment, has certain patents that we think are limiting competition, and are limiting the ability of companies to innovate," CombiMatrix' CEO Amit Kumar told BioArray News this week (see Q&A). "As a result, we are interested in rectifying that situation," Kumar said.

The patent in question, European Patent No. 0 834 575, "Methods for Detecting Nucleic Acids in Samples," was first published in the European Register in November 2001. Oppositions to the patent were filed in August 2002 by Combimatrix, Applera, Abbott Laboratories, Clondiag, and Roche Diagnostics CmbH.

Roche withdrew its opposition in December 2003, and soon after invited Affy to help it develop its CYP450 Amplichip, which became the first array-based in vitro diagnostic to receive European and American regulatory approval (see BAN1/5/2005).

CombiMatrix and Abbott argued in 2002 that the patented methods lacked novelty and that the patent was too vague. Stephen Ritter of Mathys & Squire, who represented the companies at the time, argued that Affy's patent did not proscribe a method for doing the hybridization, nor a method for creating the arrays. "The patentee's claims are founded on essentially absent technical content," Ritter wrote in opposition.

Affy defended its patent in the opposition process, saying the array it had described, with densities of probes no less than 1,000 probes per square centimeter, was indeed novel.

Two years later, during the opposition hearings, the EPO cut away at Affy's claims, deleting many of the provisions that dealt with comparing the hybridized sample with a reference pattern for distinguishing a target nucleic acid and making the company's patented probe densities more specific.

While Affy was allowed to retain its European patent, it was left with a patent that appeared to only cover a high-density array. In return, most of the opposition's chief critiques of the patent were not rectified by the amended patent.

While both sides could claim victory in the proceedings, they didn't shy away from paying the €1,020 (around $1,314) appeals fee and additional attorneys' fees to make sure that their IP strategies played out to the fullest extent under European Patent Law. In comparison, it only costs €610 to file an opposition fee.

Mathys & Squire's Stephen Ritter, who represented Abbott in the opposition proceedings that resulted in a separate Affy patent revocation in February, called the appeals process a "no-brainer" for companies wishing to defend or extend their IP position in Europe.

Affymetrix has yet to appeal the February ruling that struck down the separate patent for "Methods using nucleic acid hybridization patterns on a matrix of oligonucleotides."

Richard Bizley, the Affy attorney, was not available to comment on proceedings in either case.

— JP