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In an Uncertain Array Patent Landscape, Affy and Illumina Renew Battle Over IP

Over the past two weeks, Affymetrix and Illumina each took steps to intensify an ongoing patent litigation dispute that began in 2004 and is unlikely to be resolved for at least three more years.  
On Oct. 19, Illumina filed patent re-examination requests with the US Patent and Trademark Office for five patents at issue in a case Affy filed against Illumina in 2004. If those requests are accepted, the next phase in the 2004 litigation, scheduled to begin in February, could be postponed until the re-examination is completed.
Five days later Affymetrix filed a second round of suits against Illumina in the US, the UK, and Germany, alleging that the firm’s array and sequencing products infringe on eight of its patents.
The latest IP litigation between Affy and Illumina comes at a time when foundational array IP is under intense scrutiny both in the US and in Europe. In the US, Fliesler Meyer, a San Francisco law firm representing an undisclosed client, has filed ex parte requests to re-examine patents belonging to both Affymetrix and Oxford Gene Technology (see BAN 2/13/2007, BAN 6/19/2007). In the European Patent Office, oppositions to Affy patents are ongoing and have already resulted in the revocation or narrowing of some of the disputed patents (see BAN 7/24/2007).
All cases though appear to be headed towards resolution within the next three years, when the series of oppositions, re-examination requests, and lawsuits terminate with rulings that could uphold Affy’s IP, narrow its scope, or toss out parts of it altogether.
Axel Stellbrink, an attorney at Munich-based Vossius and Partners who is representing Protogene in an opposition against an Affymetrix patent in Europe, said there is a strong possibility that the oppositions and patent re-examination requests could pay off for those challenging Affy’s IP domination. Stellbrink and other firms scored a victory in June when the EPO decided to revoke an Affy patent, EP0619321 (see BAN 7/24/2007).
“The chances for seeing a shift in the IP landscape are rather high as I understand that many Affy patents may likely be restricted or even revoked, as in our case,” Stellbrink told BioArray News in an e-mail exchange this week.
“Affy was one of the very early birds in this particular array business. They did a good job; they filed quickly for everything they could get a patent for, but ... I have heard from competitors of Affy that they feel stronger and stronger to oppose [Affy] and feel more confident to request re-examination of that IP,” he wrote.
According to Stellbrink, Affy’s aggressive IP stance is a reaction to an increasingly competitive market. The company is “trying to protect market share because competitive products are getting better,” he said.
Re-examination Requests and New Suits
Stellbrink’s comments seem to echo the sentiments of Illumina CEO Jay Flatley. In response to the new litigation filed by Affymetrix, he called Affy’s approach to patent enforcement “overly broad” and said that Illumina is "disappointed to see that Affymetrix continues to choose to compete with Illumina in the courtroom rather than in the marketplace.”
Since Affy accused Illumina in July 2004 of infringing six of its patents — Affy eventually dropped one from the suit — Flatley’s firm has stuck to its position that it does not infringe any of the claims in the IP at issue. A jury in the US District Court for the District of Delaware, however, decided otherwise this past March, ruling that Illumina had infringed all five of Affy’s patents and awarding Affy $16.7 million, which amounted to a 15-percent royalty rate on sales ending in 2005 (see BAN 3/20/2007).
The structure of Affy’s July 2004 suit, however, requires additional trials to evaluate made by Illumina that Affy’s IP is too broad and unenforceable, and that Affy, by suing Illumina, has violated US anti-trust regulations. The second phase of the 2004 litigation is currently scheduled to begin next February (see BAN 8/14/2007).
Illumina intensified the battle on Oct. 19 by asking the USPTO to re-examine the five Affy patents in question: US Patent Nos. 5,535,531, 5,795,716, 6,355,432, 6,399,365, and 6,646,243. Affy struck back five days later by filing what it calls a “second wave” of litigation against Illumina that accuses the firm of infringing US Patent Nos. 5,902,723, 6,403,320, 6,420,169, 6,576,424, and 7,056,666, as well as European Patent Nos. 0834575, 0853679, and 0799897.
The US suit was filed in the US District Court for the District of Delaware, where both firms are incorporated, while the European suits will be contested in the UK High Court of Justice and in Germany’s Dusseldorf Regional Court. The European suits allege that Illumina’s array products infringe its IP, while the US suit alleges that, in addition to its arrays, Illumina’s next-gen sequencer also infringes Affy’s IP.
Illumina’s strategy seems to be two-fold. On one hand the company is joining other actors like Innogenetics, PamGene, and Abbott Labs in trying to invalidate Affymetrix’s IP in the US and Europe. But beyond that, the company’s legal strategies and re-examination requests may also buy it time.
All of the patents included in Affy’s latest suit “expire on or before 2010, except for two European patents,” Flatley pointed out in a statement. These patents, except European Patent No. 0799897, “belong to the same family and are related to some of the patents” in the original 2004 suit, he said. “We will continue to defend and support our customers against Affymetrix' unfounded claims.”
Affymetrix, for its part, sees itself as the injured party whose former scientists have been using techniques learned in its labs to create derivative products at Illumina. According to court documents obtained by BioArray News, Affy US suit alleges that Marc Chee, the company’s former director of genetics research, had no previous experience with microarray technology before working at Affy from 1993 to 1997. Chee left the firm to found Illumina in 1998.
Affy also alleges in its suit that technologies developed by Illumina scientists Kevin Gunderson and Jian-Bing Fan — both formerly Affymetrix employees — were first created while the scientists were under Affymetrix CEO Stephen Fodor’s tutelage. Finally, Affy states in the suit that it approached Illumina in 2002 and in 2004 about taking a license to its technology, but that Illumina “chose to disregard” its advances, triggering the July 2004 lawsuit.
During Affy’s third-quarter earnings call last week, Fodor maintained that Affy is open to negotiating a license with Illumina if it decides to seek one. “A number of years ago we made the decision to promote growth in the marketplace, by broadly licensing our intellectual property portfolio under reasonable business terms,” Fodor said.

“The chances for seeing a shift in the IP landscape are rather high as I understand that many Affy patents may likely be restricted or even revoked.”

“As we have done with many of our other licensees, we are open to all reasonable licensing discussions,” he said. “We have an obligation to shareholders and employees to defend and bring value out of the hundreds of millions of dollars that have been invested in this enterprise.”
It is unclear when Affy’s latest suit against Illumina will move to the courtroom. Fodor said last week that Affy expects the trials to start in late 2008 or early 2009 in both the UK and Germany. Vossius and Partners’ Stellbrink agreed that it will most likely take a year for the case to proceed in European court, though it depends on the number of patents involved and the court’s backlog.
Between the original 2004 infringement suit, the new cases in the US and Europe, and Illumina’s re-examination requests, it’s likely that the dispute between Illumina and Affy may not end until 2009 or later, according to Stellbrink. On top of that, Affy still faces ongoing opposition proceedings by companies such as PamGene and CombiMatrix in Europe, as well as the patent-re-examination request filed in the US by Fliesler Meyer.
Stellbrink suggested that Illumina may feel compelled to join existing opposition proceedings against Affymetrix in Europe. The firm already is opposing one Affy patent with Innogenetics in Europe, EP0799897, entitled “Kits and methods for the detection of target nucleic acids with help of tag nucleic acids,” which is now at the center of Affy’s suits against Illumina in Germany and the UK. Illumina filed its opposition to EP0799897 last December.

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