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INTELLECTUAL PROPERTY · Considered one of the most important patent decisions in history, the Supreme Court's Festo ruling has great significance for biotech inventions.

By Murray Spruill and Kathryn Coulter

November 19, 2004 | It has now been over two years since the Supreme Court handed down the Festo decision regarding the role of prosecution history estoppel in determining whether a device or method infringes a patent under the doctrine of equivalents (Festo Corp. v. Shoketsu Kinzoku Kogyo Kabushiki Co., 535 U.S. 722; 2002). Under the doctrine of equivalents, a patent claim may be found to be infringed even if the allegedly infringing device or process does not fall within the literal scope of the claim if it performs substantially the same function in substantially the same way to achieve the substantially the same result as the patented invention. The purpose of the doctrine of equivalents is to prevent potential infringers from avoiding liability for infringement merely by incorporating insubstantial changes in a device or process covered by a patented claim. In applying the doctrine of equivalents, the courts must to balance the patent owner's right to pursue those who have made minor changes to avoid infringement with the public's right to certainty in determining what a patent covers, and it was this balance between these competing interests that was at issue in Festo.

The specific issue before the Supreme Court in Festo was whether a patent applicant who makes a narrowing amendment to a claim during prosecution is barred from alleging infringement of the claim under the doctrine of equivalents. The Court held that "a narrowing amendment made to satisfy any requirement of the Patent Act may give rise to an estoppel." The Supreme Court refused to uphold the Federal Circuit's holding that a patentee is completely barred from claiming any equivalents when narrowing amendments have been made during prosecution of a patent application. Instead, the Supreme Court held if the patent applicant makes narrowing claim amendments during prosecution, this creates a presumption that the patentee has surrendered the subject matter that falls between the scope of the original claims and the scope of the amended claims. The patentee may rebut the presumption of surrender by "showing that the alleged equivalent could not reasonably have been described at the time the amendment was made, or that the alleged equivalent was tangential to the purpose of the amendment, or that the equivalent was not foreseeable (and thus not claimable) at the time of the amendment." The Court stated that old technology was generally likely to be foreseeable, while later-developed technology or technology that was unknown in the relevant art would not be foreseeable.


Recommendations Post-Festo 
Because of the impact of the Festo decision on claim scope, many patent practitioners have provided recommendations for drafting and prosecuting patent applications in view of this case. Such recommendations have included: filing with narrow claims that should be allowable without any need for amendments, filing continuation applications after the allowance of narrow claims in order to prosecute broader claims; explaining why amendments to the claims do not narrow their scope when amendments become necessary; and studying the prior art before drafting claims to avoid the necessity of amendments to overcome rejections based on the art.

These recommendations work best for new applications, that is, those applications that have been filed after the Festo opinion. However, these suggestions generally don't apply to patent applications that were pending when the Festo opinion was decided. Prior to Festo, patent applicants have usually been greedy in seeking claim scope and have filed applications with very broad claims with the intention of amending to overcome any rejections by the Patent and Trademark Office. However, the following cases illustrate that this approach can have adverse consequences in pharmaceutical and biotechnological patent applications.

In Ranbaxy Pharmaceuticals, Inc. v. Apotex, Inc., 350 F.3d 1235 (Fed. Cir. 2003), the Federal Circuit cited Festo in holding that a patent applicant is presumed to have surrendered equivalents by amending an existing limitation in a claim. In this case, Apotex asserted that Ranbaxy's process for producing cefuroxime axetil infringed U.S. Patent No. 5,847,118. The '118 patent, owned by Apotex, is directed to a process for preparing amorphous cefuroxime axetil using a highly polar organic solvent. Ranbaxy sought a declaratory judgment that it did not infringe the '118 claims, and Apotex filed a counterclaim for infringement. Apotex argued that while Ranbaxy's process, which used acetic acid, did not literally infringe the claimed process, it did infringe the claims under the doctrine of equivalents.

The '118 patent distinguished a prior art method as disadvantageous because it used acetone and thus required the use of elaborate procedures. The '118 invention overcame this disadvantage by using a highly polar solvent. However, during prosecution, the examiner rejected some of the original claims as indefinite for reciting the term "highly polar organic solvent." Apotex submitted new claims with the limitation, "wherein the highly polar organic solvent is selected from the group consisting of a sulfoxide, an amide and formic acid." Apotex argued that the claims had not been subjected to a narrowing amendment but rather resulted from a combination of dependent claims that had been rewritten in independent form.

In a pre-Festo ruling, the district court concluded that prosecution history estoppel precluded Apotex from relying on the doctrine of equivalents. Following the Festo case, the district court's decision was affirmed by the Federal Circuit, which concluded that the '118 claims had been amended to further define and circumscribe the existing limitation "highly polar solvent." As a result, the patentee was presumed to have surrendered the equivalents encompassed by the term "highly polar solvent" and was limited to the specified group of solvents.

To overcome the presumption that all equivalents had been surrendered, Apotex argued that it had not been foreseeable that the amendment in question would constitute surrender of acetic acid. Ranbaxy responded that acetic acid was a foreseeable equivalent to formic acid that could have been included in the original claim, and pointed out that the '118 patent described acetone, which has a similar polarity to acetic acid, as part of the prior art. Therefore, Ranbaxy concluded that Apotex had surrendered coverage for acetic acid. The Federal Circuit concluded that formic acid was a foreseeable equivalent to acetic acid and that Apotex had not overcome the presumption that it had surrendered coverage of acetic acid. Therefore, the district court had properly found that Ranbaxy's process for producing cefuroxime did not infringe the '118 patent.


Mycogen v. Monsanto 
A second example of the adverse consequences of narrowing claim amendments is found in an unpublished opinion by the Federal Circuit. In Mycogen Plant Science, Inc. v. Monsanto Co. (91 Fed. Appx. 666 (Fed. Cir. 2004; unpublished), the Federal Circuit affirmed that equivalents were not available for narrow, unamended claims when claims of broader scope were cancelled during prosecution.

In this case, Mycogen sued Monsanto for infringement of U.S. Patent No. 5,380,831, which is directed to making synthetic Bacillus thuringiensis (Bt) toxin genes for expression in plants and seeds. Mycogen alleged that Monsanto infringed claims 13 and 14 of the '831 patent, which are drawn to particular DNA sequences encoding a synthetic Bt toxin. Monsanto moved for summary judgment of non-infringement, alleging that their commercial products containing the Bt toxin gene did not literally infringe the '831 patent claims because the nucleotide sequence used in Monsanto's product was significantly different from the sequence set forth in claims 13 and 14. Monsanto further argued that because Mycogen had cancelled several broader claims during prosecution of the patent, Mycogen was barred by prosecution history estoppel from asserting the doctrine of equivalents for claims 13 and 14.

While Mycogen asserted that it did not intend to surrender any subject matter by canceling claims, the Federal Circuit affirmed the lower court's ruling that Mycogen was estopped from asserting the doctrine of equivalents against Monsanto based on claims 13 and 14 because Mycogen had narrowed the scope of its claim coverage. The Federal Circuit noted that cancellation of claims for reasons related to patentability in favor of claims with a narrower, literal scope has the same presumptive effect on claim limitations as amending the claims directly.

In this case, the Court reasoned that the cancellation of the broader claims created a rebuttable presumption that all subject matter between the limitations of the original claims and those of the final, issued claims was surrendered. Turning to the question of rebuttal of the presumption of surrender, the court found that broader coverage had been foreseeable because Mycogen originally attempted to claim all functionally equivalent genes in original independent claim 1 but was unable to obtain such coverage, and as a result, no equivalents were available.


Appeal to the Board
These cases illustrate the difficulties involved in asserting claims in an infringement action when the claims have been amended during prosecution. One solution to this problem — which should be seriously considered by patent applicants — is to appeal claim rejections to the Board of Patent Appeals and Interferences instead of narrowing the claims to gain allowance. This is particularly true if the Examiner's rejections are based on a lack of patentable utility, enabling disclosure and/or insufficient written description, because a recent decision in a case that we prosecuted illustrates that the Board will reverse unsupported rejections by the Examiners.

The claims in our case were drawn to nucleic acid molecules encoding a novel polypeptide and methods for their use. The claims encompassed nucleic acid molecules comprising the novel nucleotide sequence, a nucleotide sequence encoding the novel amino acid sequence, and a nucleotide sequence having at least 70%, 80%, or 90% sequence identity to the novel sequence, where the nucleotide sequence encoded a functional polypeptide, as well as host cells, kits, and methods of using the novel sequences. The Examiner rejected all of the claims using the rejections that are frequently seen in genomics cases. The claims were rejected under 35 U.S.C. § 101 as lacking patentable utility, and under 35 U.S.C. § 112, first paragraph, as lacking both enablement and an adequate written description of the invention. Rather than amend the claims to limit the scope to a narrower genus of sequences and risk losing the right to claim equivalents under the doctrine of equivalents, we opted to appeal the case to the Board. In a recent decision, the Board reversed the Examiner on all of the rejections in this case.

The specification of the application stated that the function of the claimed novel polypeptide was determined by comparing the amino acid sequence of the polypeptide to the Pfam database of protein families. The Examiner argued that the claims lacked patentable utility because the asserted function was simply a computer-generated hypothesis that did not establish a biological function, and because no working examples demonstrating the activity of the protein were provided in the specification. The Board reversed, finding that the Examiner had offered no evidence to show that Pfam analysis was not an art-accepted method for determining protein function. In addition, the Board stated that a working example was not a requirement for establishing patentability. As a result, the Board found that the Examiner had failed to meet his burden of challenging the Applicant's presumptively correct assertion of utility.

The Examiner also rejected the claims directed to variants having 70%, 80%, or 90% sequence identity with the novel nucleotide sequence as lacking enablement under 35 U.S.C. § 112, first paragraph, on the grounds that the specification did not teach which sequences could be added, deleted, or substituted such that the variant encoded by the resulting nucleotide sequence would retain functional activity. The Examiner argued that it was "general knowledge in the art" that even conservative amino acid substitutions can have an adverse effect on protein folding and activity. The Board reversed, finding that the Examiner's reference to "general knowledge" did not fulfill his obligation to cite evidence to support his conclusions.

The Board also rejected the Examiner's argument that the Applicant must disclose the role of the novel polypeptide in any particular disease in order to satisfy the requirement for an enabling disclosure. The Board noted that the Applicant had asserted that the novel polypeptide belonged to a class of proteins having well-established utility, and that the Examiner had not disputed this assertion.

The claims directed to host cells containing the novel nucleic acid molecules had been rejected by the Examiner on the grounds that these claims read on methods of gene therapy and methods for the production of transgenic animals, and that the specification failed to provide an enabling disclosure for these methods. The Board reversed the Examiner, noting that none of the claims on appeal were directed to gene therapy or the treatment of a disease. In addition, the Board noted that while the specification did disclose the use of the novel nucleic acid molecules for use in gene therapy or the production of transgenic animals, "the enablement requirement is met if the description enables any mode of making and using the invention." The Board found that the specification taught a number of additional uses for the claimed host cells, and that the Examiner had not explained why the specification failed to enable all of these uses. The Board stated that in the absence of such evidence, there was no reason to doubt the Applicant's presumptively enabled specification, whether or not the specification was enabling for gene therapy or the production of transgenic animals.

Finally, the Examiner argued that the claims encompassing nucleotide sequences having 70%, 80%, or 90% sequence identity with the novel nucleotide sequence failed to satisfy the requirement for written description under 35 U.S.C. § 112, first paragraph, because the specification did not disclose "any and all" variants of the novel nucleotide sequence that would be functional. However, the Board once again reversed, finding that the Examiner failed to meet his burden of providing evidence to support the rejection. The Board noted that in the recently decided case of In re Wallach (Fed. Cir. 2004), the Federal Circuit stated that "the state of the art has developed such that the complete amino acid sequence of a protein may put one in possession of the genus of DNA sequences encoding it." Therefore, the Board found that the applicants were in possession of all the DNA sequences that could encode the novel polypeptide. The Board also noted that the claims at issue were limited to nucleotide sequences meeting particular structural requirements (i.e., percent sequence identity with the disclosed nucleotide sequence) and encoding polypeptides having a defined functional activity. The Board found that in view of the Pfam data presented by the applicant, one of ordinary skill of art at the time the invention was made would recognize the relevant structural characteristics of the novel protein that were necessary to place the protein in the recited protein family.

The outcome in this case was similar to that in Ex parte Sun (Bd. Pat. App. Int. Jan. 20, 2004), another appeal involving claims directed to sequence encoding a novel polypeptide. The claims at issue in Ex parte Sun were directed to a nucleotide sequence encoding a novel maize homolog of WEE1, a protein known in the art to be involved in cell cycle regulation, and to nucleotide sequences having at least 80% identity with the coding sequence of the novel WEE1 protein. As in the case described earlier, the Examiner rejected the claims on the grounds that they failed to satisfy the enablement and written description requirements of 35 U.S.C. §112, first paragraph. To support the rejections, the Examiner cited a prior-art reference that taught that a particular region of the WEE1 protein was critical for function. Based on this art, the Examiner concluded that alterations to this critical region could affect the function of the protein, and that one of skill in the art would not be able to predict the structure and function of sequence variants of the novel protein.

In reviewing whether the claims met the written description requirement, the Board emphasized that the relevant analysis was whether the claim limitations were described so that one of skill in the art would recognize that the applicants had invented the claimed subject matter. The Board discussed the standard for written description set forth in The Regents of Univ. of Calif. v. Eli Lilly and Co. (Fed. Cir. 1997), and Enzo Biochem, Inc. v. Gen-Probe, Inc. (Fed. Cir. 2002), stating that:

[T]he written description requirement can be met by 'showing that an invention is complete by disclosure of sufficiently detailed, relevant identifying characteristics...i.e., complete or partial structure, other physical and/or chemical properties, functional characteristics when coupled with a known or disclosed correlation between function and structure, or some combination of such characteristics.

(slip op. at 6, citing Enzo, 119 F.3d at 1324; emphasis added by the Board).

The Board found that contrary to the Examiner's arguments, the fact that the specification did not disclose a functional variant having 80% sequence identity with the novel WEE1 sequence was not dispositive of whether the written description requirement was met. The Board observed that the specification provided nucleotide sequences encoding the novel WEE1 protein and examples of how to screen for WEE1 functional activity. The Board noted that those of skill in the art knew that most WEE1 variations occurred at the amino terminal end of the protein, while the central region and carboxy-terminal region contained conserved protein kinase domains and substrate recognition regions. The Board found that in view of the knowledge in the art regarding regions of the WEE1 protein that would be most likely to tolerate modification, and the assays for WEE1 activity provided in the specification, one of skill in the art would recognize that the applicants invented the claimed functional variants of the novel WEE1 protein. Accordingly, the Board concluded that the Examiner had not met his burden of establishing why one of ordinary skill in the art would be unable to recognize that the applicants had invented the claimed subject matter and reversed the written description rejection.

In reviewing the enablement rejection, the Board noted that the Examiner had the initial burden of establishing a reasonable basis for questioning the enablement provided for the claimed invention. In his arguments supporting the enablement rejection, the Examiner had focused on the fact that the specification did not teach "any specific structural or functional characteristics of any isolated nucleic acid comprising a polynucleotide having at least 80% identity to the entire coding region of SEQ ID NO:1," and on the fact that the applicants had provided no working examples showing that introducing such a polynucleotide into a plant would alter the plant's phenotype. The Examiner concluded that the art of modifying plant phenotypes using cell cycle proteins was unpredictable, and therefore the requirement for an enabling disclosure was not met.

The Board, noting that the analysis of the enablement requirement "dovetail[ed]" here with the analysis of the written description requirement, observed that the specification taught a nucleotide sequence encoding the novel WEE1 protein, assays for WEE1 activity, and regions of the protein that were most likely to be tolerant of modification. The Board also observed that the specification provided examples showing that the novel WEE1 protein could be produced in E. coli, and that the recombinantly produced protein inhibited the activity of cyclin-dependent protein kinase. The Board found that the Examiner had not established that these teachings were insufficient to enable the claimed genus of nucleotide sequences. Accordingly, the Board also reversed the rejection of the claims for lack of enablement.

These two cases demonstrate that an appeal to the Board of Patent Appeals and Interferences can be a valuable tactic for avoiding narrowing amendments during prosecution. This approach is particularly likely to succeed when the claims are rejected only on the grounds that they lack patentable utility, enabling disclosure, and/or sufficient written description. These decisions demonstrate that good scientific arguments can win on appeal and preserve the patent holder's right to prove infringement under the doctrine of equivalents.

Murray Spruill, a former federal patent examiner with a Ph.D. in genetics/molecular biology, is chair of the Biotechnology and Pharmaceutical Patent Group at Alston & Bird LLP, in Raleigh, N.C. E-mail: wspruill@alston.com. Kathryn Coulter is a patent agent with Alston & Bird. E-mail: Kcoulter@alston.com. 








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