10194359 (B.P.A.I. Sep. 24, 2010)

Ex Parte Baker et al

Board of Patent Appeals and InterferencesSep 24, 2010

10194359 (B.P.A.I. Sep. 24, 2010)

UNITED STATES PATENT AND TRADEMARK OFFICE ____________________ BEFORE THE BOARD OF PATENT APPEALS AND INTERFERENCES ____________________ Ex parte KEVIN P. BAKER, JIAN CHEN, LUC DESNOYERS, AUDREY GODDARD, PAUL J. GODOWSKI, AUSTIN L. GURNEY, JAMES PAN, VICTORIA SMITH, COLIN K. WATANABE, WILLIAM I. WOOD, and ZEMIN ZHANG, Appellants1 ____________________ Appeal 2010-002096 Application 10/194,359 Technology Center 1600 ____________________ Before CHUNG K. PAK, CAROL A. SPIEGEL, and JEFFREY T. SMITH, Administrative Patent Judges. SPIEGEL, Administrative Patent Judge. DECISION ON APPEAL2 1 The real party in interest is GENENTECH, INC. (Appellants' Brief filed 9 March 2009 ("Br.") at 2, as supplemented with a Response to Notice of Non- Compliant Brief filed 11 June 2009). This decision also cites the Examiner's Answer mailed 25 August 2009 ("Ans.") and the Specification ("Spec.") of Application 10/194,359 ("the 359 Application"). 2 The two-month period for filing an appeal or commencing a civil action, as recited in 37 C.F.R. Â§ 41.52, begins to run from the "MAIL DATE" (paper delivery mode) or the "NOTIFICATION DATE" (electronic delivery mode) shown on the PTOL-90A cover letter attached to this decision. Appeal 2010-002096 Application 10/194,359 2 Appellants appeal under 35 U.S.C. Â§ 134(a) from an Examiner's final rejection of all pending claims, claims 25-29 (Br. 2; Ans. 2). We have jurisdiction under 35 U.S.C. Â§ 134. We REVERSE. I. Statement of the Case The subject matter on appeal is directed to antibodies that specifically bind to a polypeptide defined by SEQ ID NO:548 of the 359 Application. Claim 25, the only independent claim on appeal, is illustrative and reads (Br. 16): 25. An isolated antibody that binds specifically to the polypeptide of SEQ ID NO:548. The Examiner rejected claims 25-29 under 35 U.S.C. Â§ 102(e) as anticipated by Shimkets3 (Ans. 3-4). The Examiner found that Shimkets teaches an isolated polypeptide of SEQ ID NO:42 ("the Shimkets polypeptide") consisting of 126 amino acids, wherein amino acid residues 57-116 were identical to amino acid residues 174-233 of polypeptide SEQ ID NO:548 recited in the claims ("the claimed polypeptide") (Ans. 3-4). The Examiner further found that Shimkets teaches an antibody that binds to the Shimkets polypeptide (id. at 3). According to the Examiner, given the stretch of consecutive and identical amino acid residues shared by the Shimkets polypeptide and the claimed polypeptide, 3 US Patent Application Publication 2002/0076700 A1, Novel Polypeptides and Nucleic Acids Encoding Same, published 20 June 2002, based on Application 09/740,668, filed 18 December 2000, by Richard A. Shimkets ("Shimkets"). Application 09/740,668 is a continuation-in-part of Application PCT/US99/29845, filed 17 December 1999, which is a continuation-in-part of Application 09/465,512, filed 16 December 1999, which claims benefit of provisional Applications 60/113,485 and 60/112,837, filed 21 December 1998 and 18 December 1998, respectively. Appellants did not challenge Shimkets as prior art qualifying under 35 U.S.C. Â§ 102(e). Appeal 2010-002096 Application 10/194,359 3 "one would expect that epitopes exist within the common region" and "[a]n antibody â€¦ which specifically binds to one of those shared epitopes â€¦ would also be expected to bind to the [claimed] polypeptide â€¦" (id. at 4). Appellants essentially argue that the claims require an antibody that "binds specifically to" the claimed polypeptide, not a cross-reactive antibody that binds to a common epitope present on both the Shimkets polypeptide and the claimed polypeptide (Br. 6-14). According to Appellants, a cross- reactive antibody that binds to both the Shimkets polypeptide and the claimed polypeptide is not within the scope of claims 25-29 (id. at 5). Appellants emphasize that the Shimkets polypeptide and the claimed polypeptide do not have 100% identical amino acid sequences (id. at 6). In addition of Shimkets, Appellants rely on the following evidence in support of their position: Predicted Antigenic Peptides printout,4 Frank,5 Janeway,6 and NCBI7 (Br. 12-13). At issue is whether Shimkets describes an antibody which "binds specifically to" the polypeptide defined by SEQ ID NO:548. II. Findings of Fact ("FF") 4 MIF Bioinformatics partial printout of predicted antigenic peptides within a 300 amino acid residue polypeptide said to be the claimed polypeptide obtained 5 December 2007 using http:bio.dfci.harvard.edu./Tools/antigenic.pl. ("Predicted Antigenic Peptides"). 5 Chapter 4, Specificity and Cross-Reactivity, in IMMUNOLOGY AND EVOLUTION OF INFECTIOUS DISEASE by Steven Frank, Princeton University Press (2002), page 33 only ("Frank"). 6 IMMUNOBIOLOGY, 5th ed., by Janeway et al., Garland Publishing (2001), page 614 only ("Janeway"). 7 Protein-protein search said to be from "Database NCBI PubMed Services [Online] October 3, 2007" (Br. 17) ("NCBI"). Appeal 2010-002096 Application 10/194,359 4 [1] According to the Specification of the 359 Application, "[a]n antibody that 'specifically binds to' or is 'specific for' a particular polypeptide â€¦ is one that binds to that particular polypeptide â€¦ without substantially binding to any other polypeptideâ€¦" (Spec. 49:19-21, emphasis added). [2] Figure 548 of the 359 Application provides the amino acid sequence of the claimed polypeptide. According to Figure 548, the polypeptide defined by SEQ ID NO:548 consists of 300 amino acid residues, wherein residues 1-32 define a signal peptide. (Id. at 35:12-13.) [3] Figure 21 of Shimkets provides the amino acid sequence of the Shimkets polypeptide. According to Figure 21, the polypeptide defined by SEQ ID NO:42 of Shimkets consists of 126 amino acid residues, wherein residues 1-66 define a signal peptide (Shimkets 3, Â¶ 47; 7, Â¶Â¶ 142-145.) [4] The Examiner found that the Shimkets polypeptide and the claimed polypeptide contained a region of identical amino acid residues (i.e., a shared subsequence): amino acid residues 57-116 and 174-233, respectively (Ans. 4). [5] According to Predicted Antigenic Peptides printout, the claimed polypeptide contains eleven putative antigenic regions, including three regions defined by amino acid residues 147-182, 189-195, and 200- 216 (Predicted Antigenic Peptides printout 3). III. Discussion A. Legal principles Claims are interpreted as they reasonably would have been interpreted by persons having ordinary skill in the art. Phillips v. AWH Corp., 415 F.3d Appeal 2010-002096 Application 10/194,359 5 1303, 1315-16 (Fed. Cir. 2005). The specification is the primary aid in deciphering claim language. Id. at 1315. Anticipation is a question of fact. In re Graves, 69 F.3d 1147, 1151 (Fed. Cir. 1995). Anticipation requires that a prior art reference describe every limitation in a claim either explicitly or inherently. In re Schreiber, 128 F.3d 1473, 1477 (Fed. Cir. 1997). "Inherency, however, may not be established by probabilities or possibilities. The mere fact that a certain thing may result from a given set of circumstances is not sufficient." In re Oelrich, 666 F.2d 578, 581 (CCPA 1981). B. Analysis The claims on appeal recite an antibody that "binds specifically" to the claimed polypeptide. The Specification defines an antibody that "specifically binds" to a particular polypeptide as one that binds to that particular polypeptide without substantially binding to any other polypeptide (FF 1). If the Shimkets polypeptide and the claimed polypeptide were the same or substantially the same polypeptides, then one of ordinary skill in the art would have reasonably expected that an antibody that "binds specifically" to the claimed polypeptide would also "bind specifically" to the Shimkets polypeptide. However, there is no factual basis for finding that the Shimkets polypeptide and the claimed polypeptide are the same or substantially the same polypeptide. To the contrary, the former is a 126 amino acid polypeptide where amino acid residues 1-66 define a signal peptide (FF 3), while the latter is a 300 amino acid polypeptide wherein amino acid residues 1-66 define a signal peptide (FF 2). The Examiner "understands that Appellant is attempting to claim an antibody that binds epitopes that are unique" to the claimed peptide (Ans. 7). Appeal 2010-002096 Application 10/194,359 6 Yet, the Examiner evidently misunderstands the meaning of an antibody that "specifically binds" to a particular polypeptide as expressly defined in the Specification (FF 1). The Examiner's position is premised on the existence of common antibody binding sites within the amino acid subsequence shared by the Shimkets polypeptide and the claimed polypeptide (FF 4; Ans. 4). Assuming arguendo that there were three common antibody binding sites (putative antigenic peptides or epitopes) in the shared amino acid subsequence, antibodies which bind to these common binding sites are "cross-reactive," not "specific binding," antibodies (FF 1) (see also Frank ("Specificity measures the degree to which the immune system differentiates between different antigens. Cross-reactivity measures the extent to which different antigens appear similar to the immune system.")). Thus, we are in agreement with Appellants' arguments. C. Conclusion Therefore, we reverse the rejection of claims 25-29 under Â§ 102(e) as anticipated by Shimkets. Contrary to the Examiner's findings, Shimkets does not describe an antibody which "binds specifically to" the polypeptide defined by SEQ ID NO:548. Appeal 2010-002096 Application 10/194,359 7 IV. Order Upon consideration of the record, and for the reasons given, it is ORDERED that the decision of the Examiner to reject claims 25-29 under 35 U.S.C. Â§ 102(e) as anticipated by Shimkets is REVERSED. REVERSED alw ARNOLD & PORTER LLP (24126) Attn: SV Docketing Dept. 1400 Page Mill Road Palo Alto, CA 94304