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Law Firm Asks USPTO to Re-Examine Foundational Array Patent Held by Affy

Fliesler Meyer, the San Francisco patent law firm that filed requests for ex parte re-examinations of two Oxford Gene Technology patents with the US Patent and Trademark Office earlier this year, has filed a similar request on behalf of an undisclosed client to re-examine a foundational Affymetrix patent, according to the lawfirm.
Additionally, a Fliesler Meyer attorney said this week that there is “a rationale behind” the firm’s attempts to have foundational array IP re-examined, hinting that the Affymax request could be followed by similar requests to re-examine other Affymetrix IP.
In a May 31 letter to BioArray News, Fliesler Meyer said that it has filed an ex parte re-examination request for US Patent No. 5,445,934, “Array of oligonucleotides on a solid substrate,” which was received by Affymax Technologies, a predecessor firm to Affymetrix, on Aug. 29, 1995. The lead inventor listed on the IP is current Affy CEO Stephen Fodor.
The patent describes a substrate with a surface comprising 1,000 or more oligos with different known sequences covalently attached to the surface in discrete regions of less than 1 cm square, an array made up of the substrate, and the process of producing such an array using photo-removable groups on nucleic acid building materials and the exposure of areas on the array to wavelength light. Detection methods are also described.
The patent in question was at the heart of litigation between Affymetrix and Incyte, which was settled in January 2002 (see BAN 1/4/2002).
Fliesler Meyer attorney Anthony Craig told BioArray News this week that earlier settlements between OGT and Affymetrix and Affymetrix and Incyte may have thwarted attempts to invalidate each other’s IP, but they never resolved the issues over the validity of the patents at the heart of those lawsuits.
“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.”
If neither patent is valid, and if both parties choose to settle rather than proceed with a suit, a court “can endorse that settlement and in a de facto way be endorsing something that is bad for society,” Craig said. “Neither patent should be able to generate revenue, but because the parties have brought the suits against the patents and then settled, it’s a way of endorsing each patent. And that is the story of OGT and Affymetrix in the ‘90s,” he added.
Craig said that in earlier lawsuits, it was “beneficial for both of them to settle and the circumstances may be that neither patent is valid. So what our client is concerned with is the situation where there is a settlement and they’ve used the re-examination process first to address OGT and now to address this Affymetrix patent.”
Craig said that with the Affymax patent, Affy’s original patent application addressed arrays of peptides, not oligonucleotides, which were added later, and that in his client’s opinion the IP “didn’t have sufficient written description in order to practice the invention.”
“You typically can’t use a reexamination as a forum to look into that kind of issue, but … if the patent office agrees with us that the written description was lacking, Affymetrix shouldn’t be entitled to the date of the first patent filing, and as a result, additional prior art documents are available to re-examine the patent,” Craig said.
In its May 31 letter to to BioArray News, Fliesler Meyer said that if its request is “granted and results in the narrowing or cancellation of claims in the patent, the intellectual property landscape in the DNA array field may be significantly affected.”
This week, Craig said that the repercussions of having claims amended or removed from the patent could have an affect on licensing relationships Affymetrix has with various companies, and might also create a more lenient IP environment for other firms that are developing array-related technology but are intimidated by what is often thought of as a litigious marketplace.

“Because the parties have brought the suits against the patents and then settled; it’s a way of endorsing each patent. And that is the story of OGT and Affymetrix in the 90s.”

Also, Craig said it is possible that the USPTO could leave the patents as they are, or accept that Affy does have prior art to support the patent.
“If the US Patent office actually does find that the patent does meet the written description requirement, that’s ok too because what they’ll be doing is they’ll be saying that a person that is skilled in the art is actually very skilled, and they can take up on the suggestion Affy makes and actually fill in all the blanks,” Craig said.
Craig said that there is “a rationale behind” the firm’s attempts to have foundational array IP re-examined, hinting that the Affymax request could be followed by similar requests to re-examine other Affymetrix IP.
Fliesler Meyer’s request follows two similar petitions it filed in February to re-examine two foundational Oxford Gene Technology patents. In that case, the law firm asked the USPTO to re-examine US Patent No. 5,700,637, “Apparatus and Method for Analyzing Polynucleotide Sequences and Method of Generating Oligonucleotide Arrays,” and US Patent No. 6,054,270, “Analyzing Polynucleotide Sequences."
The USPTO eventually granted the request, and the burden is now on OGT to provide the body with all information relevant to the IP. Fliesler Meyer has not disclosed its client’s identity, which is likely to remain anonymous throughout the reexamination process.
The fact that the requests regarding OGT’s IP were granted only weeks after the petitions were filed means it is likely that the USPTO could determine whether or not to proceed with the re-examination in a matter of days.
The likelihood of the USPTO granting the request is fairly high, according to a 2006 study in the North Carolina Journal of Law & Technology that found that the agency granted 98 percent of such requests filed in 2004.
Of all patents that were re-examined through 2003, the study found that 10 percent had all claims cancelled and 64 percent had some claims cancelled or limited.

Affymetrix and OGT declined to comment.

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