By Donald Zuhn --
Last month, we reported on a presentation that Dr. George Elliott, Group 1600 Director of the U.S. Patent and Trademark Office, gave at this year's BIO International Convention (see "Docs at BIO: Representatives from JPO, EPO, SIPO, and USPTO Discuss Recent Developments in Japan, Europe, China, and the U.S." and "Docs at BIO: "Gotcha" Games Continue at USPTO"). Among the topics that Dr. Elliott addressed during his presentation were the new written description training materials -- specifically, Example 11, which concerns claims directed to a polynucleotide or polypeptide sequence that shares percent identity with another sequence.
As we noted in an earlier report, Example 11 seems to suggest that the recitation of a functional limitation can render an otherwise allowable claim unallowable (see "An Analysis of the New Written Description Training Materials - DNA Hybridization & Percent Identity"). In particular, Example 11 introduces the following exemplary claims:
Claim 1: An isolated nucleic acid that encodes a polypeptide with at least 85% amino acid sequence identity to SEQ ID NO: 2.
Claim 2: An isolated nucleic acid that encodes a polypeptide with at least 85% amino acid sequence identity to SEQ ID NO: 2; wherein the polypeptide has activity X.
Example 11 concludes that despite the specification's disclosure of only a single species encoding the polypeptide of SEQ ID NO: 2 (i.e., SEQ ID NO: 1), and the lack of any teaching in the specification regarding which amino acid residues in SEQ ID NO: 2 are tolerable to change, the specification satisfies the written description requirement with respect to claim 1 (because a skilled artisan could use a computer to identify all of the nucleic acids encoding a polypeptide sharing at least 85% sequence identity with SEQ ID NO: 2), but not claim 2 (because the specification lacks any teaching of the residues associated with the recited function).
During his BIO presentation, Dr. Elliott noted that with respect to the situation presented in Example 11, the USPTO had reversed its position, having previously asserted that claims lacking functional language failed to comply with the written description requirement and that claims possessing such language complied with the requirement. According to Dr. Elliott, claims with functional language (where the specification lacks any teaching regarding the amino acid residues that are tolerable to change) do not satisfy the written description requirement because "the minute you add function, you've limited the claim to a subset of species, and you don't know which species are in the subset and which species aren't." In other words, absent any teaching of structure/function relationships, the USPTO's (and Dr. Elliott's) position is that one cannot determine the species that share at least 85% sequence identity with the recited sequence and also possess the recited function (this explanation does not, of course, take into account case law that allows for the recitation of a genus containing some inoperative species).
Dr. Elliott also acknowledged that Example 11 may be a little disingenuous in that it appears to suggest that an applicant would be better off omitting a functional limitation from a claim. However, he pointed out that this example includes the following practice note:
Dr. Elliott informed session attendees that just because claim 1 in Example 11 satisfied the written description requirement, this does not mean that the claim would necessarily satisfy the enablement and utility requirements. For a more thorough discussion of the rationale behind the USPTO's reversal on functional limitations, Dr. Elliott recommended that attendees read the decision in Ex parte Porro. We decided to take Dr. Elliott's advice.
In Porro, which was decided last March, the Board of Patent Appeals and Interferences affirmed the Examiner's determination that claims to a method of making ascorbic acid (vitamin C) lacked an adequate written description. Claims 12-14 were at issue on appeal; representative claim 13 recites:
13. A method of generating ascorbic acid, comprising:
a) obtaining a recombinant yeast capable of converting an ascorbic acid precursor into ascorbic acid, wherein the yeast is functionally transformed with a coding region encoding L-galactose dehydrogenase (LGDH) enzyme having at least about 90% identity with SEQ ID NO: 11,
b) culturing the recombinant yeast in a medium comprising an ascorbic acid precursor, thereby forming ascorbic acid, and
c) isolating the ascorbic acid.
During prosecution of the claims at issue, the Examiner noted that the specification disclosed only a single LGDH sequence (i.e., SEQ ID NO: 11), which the inventors had obtained from Arabidopsis thaliana. The Examiner also noted that the prior art failed to disclose other LGDH enzymes sharing 90% identity to SEQ ID NO: 11. Concluding that the claims encompassed a very large genus of sequences and that the specification and prior art provided a limited description of the motifs or structures responsible for LGDH activity, the Examiner determined that the specification did not adequately describe the genus of "L-galactose dehydrogenase (LGDH) enzyme[s] having at least about 90% identity with SEQ ID NO: 11."
The Board affirmed the Examiner's determination that claims 12-14 lacked an adequate written description, citing University of California v. Eli Lilly and Co., 119 F.3d 1559 (Fed. Cir. 1997) and University of Rochester v. G.D. Searle & Co., 358 F.3d 916 (Fed. Cir. 2004) in support of its decision. With respect to Eli Lilly, the Board determined that "[t]he Eli Lilly court held that a fully described genus is one for which a person skilled in the art can 'visualize or recognize the identity of the members of the genus,'" and in the instant case, "the Specification does not provide guidance regarding what structural features are responsible for the enzymatic activity of LGDH, nor does it describe what amino acid changes can be made in the wild-type sequence without affecting the enzymatic activity of the protein." The Board concluded that "the Specification does not describe the recited genus adequately for those skilled in the art to distinguish the SEQ ID NO: 11 variants that are within the claims from other variants of SEQ ID NO: 11," and therefore, "does not adequately describe the recited genus under the standard of Eli Lilly."
With respect to University of Rochester, the Board stated that:
Just as in University of Rochester, the present application discloses a genus of chemical compounds (proteins having amino acid sequences at least 90% identical to SEQ ID NO: 11). According to Appellants’ calculations, the genus encompasses 3.4 x [ten to the power of 41] different proteins. But the claims are limited to only those compounds having a desired characteristic (having LGDH enzymatic activity). Just as in University of Rochester, the present Specification does not guide the skilled artisan to the subset of proteins within the genus of 3.4 x [ten to the power of 41] proteins that are at least 90% identical to SEQ ID NO: 11 that have the recited enzymatic activity.
In affirming the Examiner's rejection, the Board concluded that a subgenus of "functional variants" within a genus of "variants" must be described by disclosing a representative number of functional variants or by disclosing "structural features that are common to functional variants that distinguish them from the rest of the genus (i.e., structural features that correlate with enzymatic activity regardless of other variations from SEQ ID NO: 11)," and that the application at issue provided neither. Interestingly, the Board conceded that there may be other ways to describe such a subgenus, but that "the case law is a little hazy in this area."
While the Written Description Training Materials (which were published in late March) do not mention the Porro case by name, the language of Example 11 leaves little doubt that Porro (which was decided March 11) served as the basis for Example 11. For example, the Board states that:
Certainly SEQ ID NO: 11 is adequately described. We can also assume, for present purposes, that a description of SEQ ID NO: 11 is adequate to describe amino acid sequences that are 90% identical to SEQ ID NO: 11[.] Given a computer and sequence-comparison software, a skilled artisan may well be able to visualize or recognize the identity of members of that genus.
The Board's conclusion and reasoning in Porro is nearly identical to that provided by the Training Materials for exemplary claim 1 (including statements about using a computer to identify sequence variants).
Moreover, the Board's response to the applicants' argument that "[t]he skilled artisan would have a reasonable expectation that an LGDH . . . would be operable in the claimed methods" evokes Example 11's Practice Note. In particular, the Board stated that such an argument was not directed to the issue raised on appeal since the Examiner had not made an enablement rejection. In view of the decision in Porro and the new Training Materials, it will be interesting to see how the Patent Office balances the issues of operability and enablement with respect to pending claims that resemble exemplary claim 1 of Example 11 (particularly since Judge Lourie did not find these issues to present a problem for hybridization variants in Enzo Biochem, Inc. v. Gen-Probe Inc., 296 F.3d 1316 (Fed. Cir. 2002)).
Ex parte Porro (B.P.A.I. 2008)
Panel: Administrative Patent Judges Scheiner, Mills, and Grimes
Opinion by Administrative Patent Judge Grimes
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