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Does disclosure of laundry list of protein variants provide adequate written description for later claim to specific protein

The traditional written description requirement prevents patent applicants from amending their claims during patent prosecution to encompass subject matter not disclosed in the patent specification as filed. Clearly, a patent specification that specifically discloses (without claiming) a small number of protein sequences provides adequate written description to support adding a claim later that recites one of those protein sequences. But what if a patent specification effectively discloses all protein sequences, for example, by generically describing "a protein comprising between 10 and 1000 amino acids, wherein at each position in the sequence the amino acid can be any of the 20 genetically coded amino acids.” It defies common sense to think that such a broad, generic disclosure would be sufficient to satisfy the written description requirement with respect to a claim introduced by amendment specifically reciting any protein of this size, even though the disclosure does literally describe any possible protein of 10 to 1000 amino acids in length.

The question then becomes, at what point do we draw the line? In other words, to what extent is it possible for a patent applicant to satisfy the written description requirement with respect to a later added claim directed towards a specific protein sequence by simply disclosing in the specification as filed an astronomical "laundry list" of protein sequence variants that happens to include the later claimed proteinsequence? This is the question that was presented to a district court recently in the lawsuit brought by Novozymes against Danisco/Genencor, alleging infringement of a patent claiming certain alpha-amylase variants genetically engineered for improved thermostability. (Last September I reported on the district courts denial of a motion for preliminary injunction by Novozymes, available here).

The Federal Circuit (and its predecessor court the CCPA) has addressed this question in the context of traditional small molecules. A seminal case is In re Ruschig, a 1967 CCPA decision that held that the mere disclosure of a large genus of molecules is not necessarily sufficient to satisfy the written description requirement with respect to a later claim directed to some species falling within the genus. Under such circumstances, the Ruschig court held that in order to satisfy the written description requirement, the specification must provide "blaze marks" specifically pointing towards the later claimed species.

In 1996, the Federal Circuit applied the Ruschig "blaze mark standard” in Fujikawa v. Wattanasin, and held that the disclosure of a genus did not provide adequate written description of a later claimed sub-genus, pointing out that "just because a moiety is listed as one possible choice for one position does not mean there is [adequate] support for every species or sub-genus that chooses that moiety. Were this the case, a laundry list disclosure of every possible moiety for every possible position would constitute a written description of every species in the genus. This cannot be because such a disclosure would not reasonably lead those skilled in the art of any particular species."

In the Novozymes v. Danisco, the issue was raised in a motion for summary judgment filed by Danisco, arguing that a disclosure in Novozymes specification of a laundry list comprising an astronomical number of protein variants does not provide adequate written description support for a claim added later directed toward a small subset of those variants. The Novozymes patent specification, filed in 2000, disclosed variants of a specific alpha-amylase (the sequence of which was disclosed in the application) comprising an alteration at one or more positions selected from a list of 33 possible positions. The specification went on to define an alteration as either an insertion downstream of the amino acids which occupies position, a deletion of the amino acid which occupies a position, or a substitution of the amino acid which occupies the position with a different amino acid. So there are multiple variable parameters.

The 33 positions can be independently altered in three different ways. Any number of the 33 positions can be altered independently, and there are 20 different amino acids from which to choose in deletions or substitutions. Genencor did the math, and concluded that this amounted to a “staggering” 8.598 x 1042 different possibilities, a long laundry list indeed. Novozymes did not dispute this calculation. Furthermore, the specification does not specify what effect a specific mutation would have on thermostability, although one passage in the specification discusses "achieving altered stability, in particular improved stability (i.e., higher or lower), at especially high temperatures."

In 2009, nine years after the specification was filed, Novozymes added the claims at issue in the case, directed specifically toward a subset of the proteins on the laundry list that have a substitution at position 239 in amino acid sequence, resulting in increased thermostability. That is, the claim is limited to one of the 33 amino acid positions identified in the specification as filed (position 239), one of the three alterations (substitution), and one of the possible alterations in stability (increased thermostability).

The court discussed applicable precedents such as Ruschig and Fujikawa, but did not really seem to demonstrate a thorough understanding of the principles behind those decisions. Perhaps this is because, as the judge complained in her decision, "a general difficulty in this case has been the partys tendency to argue past each other." Nonetheless, she ultimately concluded that although "I still have doubts that the specification . . provides an adequate written description for the claims, I conclude that the defendants have not met their burden to prove by clear and convincing evidence that the [patent] is invalid as a matter of law." The decision was largely dictated by the cases procedural posture, which imposed a substantial burden of proof on Danisco in attempting to invalidate an issued patent on summary judgment as a matter of law.

The judge explicitly noted that "it is not without hesitation that Im denying defendants motion.” It seems clear that she was bothered by the fact that the originally filed specification discloses such an astronomical number of "possible inventions" without seeming to provide any "blaze marks" directing one towards the later claimed variants. But she went on to point out that even if the claims comply with the written description requirement, "to the extent the specification would require undue experimentation before a person of ordinary skill in the art could discover the claimed invention, that may suggest a lack of enablement rather than a problem with the written description." I think she might have a point there.

A copy of the decision is provided here. Thanks to Docket Navigator (www.docketnavigator.com) for making me aware of this case.

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