Ex Parte Mullins et al

Patent Trial and Appeal BoardSep 18, 2012

11713474 (P.T.A.B. Sep. 18, 2012)

UNITED STATES PATENT AND TRADEMARK OFFICE UNITED STATES DEPARTMENT OF COMMERCE United States Patent and Trademark Office Address: COMMISSIONER FOR PATENTS P.O. Box 1450 Alexandria, Virginia 22313-1450 www.uspto.gov APPLICATION NO. FILING DATE FIRST NAMED INVENTOR ATTORNEY DOCKET NO. CONFIRMATION NO. 11/713,474 03/02/2007 James Mullins 4075-INV-0002P.1US 8386 92855 7590 09/19/2012 McDonnell Boehnen Hubert & Berghoff LLP/UW 300 S. Wacker Drive Suite 3100 Chicago, IL 60606 EXAMINER JANSSEN, SHANNON L ART UNIT PAPER NUMBER 1653 MAIL DATE DELIVERY MODE 09/19/2012 PAPER Please find below and/or attached an Office communication concerning this application or proceeding. The time period for reply, if any, is set in the attached communication. PTOL-90A (Rev. 04/07) UNITED STATES PATENT AND TRADEMARK OFFICE ____________ BEFORE THE PATENT TRIAL and APPEAL BOARD ____________ Ex parte JAMES MULLINS, DAVID NICKLE, and MORGANE ROLLAND ____________ Appeal 2011-009552 Application 11/713,474 Technology Center 1600 ____________ Before TONI R. SCHEINER, DONALD E. ADAMS, and STEPHEN WALSH, Administrative Patent Judges. ADAMS, Administrative Patent Judge. DECISION ON APPEAL This appeal under 35 U.S.C. § 134 involves claims 1-10 (App. Br. 2; Ans. 2). We have jurisdiction under 35 U.S.C. § 6(b). STATEMENT OF THE CASE The claims are directed to a computational method for identifying conserved elements in a set of biopolymer sequences for incorporation into a vaccine. Claim 1 is representative and is reproduced in the Claims Appendix of Appellants’ Brief. Appeal 2011-009552 Application 11/713,474 2 Claims 1-5 and 7-10 stand rejected under 35 U.S.C. § 102(b) as being anticipated by Baker. 1 Claims 1-10 stand rejected under 35 U.S.C. § 103(a) as unpatentable over the combination of Baker and De Groot. 2 We reverse. Anticipation: ISSUE Does the preponderance of evidence on this record support Examiner’s finding that Baker teaches Appellants’ claimed invention? FACTUAL FINDINGS (FF) FF 1. Examiner finds, inter alia, that Baker teaches a method wherein “each position within the biopolymer sequence [(i.e. candidate peptide epitope) is classified via a computer program] as conserved, semi-conserved (i.e.: variable), or non-conserved (i.e.: unconserved) ([00112], Table 5 3 )” (Ans. 4). FF 2. Baker teaches “a method for identifying a candidate peptide epitope which induces a HLA class I CTL response against variants of … [the] peptide epitope” (Baker 31: ¶ [0112]). 1 Baker et al., WO 2005/012502 A2, published February 10, 2005. 2 De Groot et. al., From genome to vaccine – new immunoinformatics tools for vaccine design, 34 Methods 425-428 (2004). 3 Examiner finds that Baker’s “Table 5 is merely a representation of what the different classifications are, not a description of the step of classifying” (Ans. 13). Appeal 2011-009552 Application 11/713,474 3 FF 3. Baker’s method comprises: a) identifying, from a particular antigen of an infectious agent, variants of a peptide epitope 8-11 amino acids in length, each variant comprising primary anchor residues of the same HLA class I binding motif; b) determining whether each of said variants comprises conserved, semi-conserved or non-conserved non-anchor residues in comparison to each of the remaining variants; and c) identifying a variant which comprises only conserved non- anchor residues in comparison to at least one remaining variant. (Id.) FF 4. Baker teaches that the “primary anchor residues” may be, for example, preferred for the “motif and which occur[] with high frequency within … [a] population” or different as illustrated in Baker’s Tables 1-2 (Baker 33: ¶ [00122]; id. at 34: ¶ [00133]). FF 5. Baker’s Table 1 is reproduced below for clarity: Appeal 2011-009552 Application 11/713,474 4 Table 1 summarizes some of Baker’s “primary anchor residues of the HLA class I peptide epitope supermotifs and motifs…. Preferred primary anchors are shown in bold, while tolerated primary anchors are shown in italics” (Baker 35: ¶ [00143]). FF 6. Examiner finds that Baker’s “anchor positions are the same binding motif (i.e.: conserved)” (Ans. 12). ANALYSIS Appellants contend that Baker’s method identifies “variants of a particular epitope … in a particular antigen of an infectious agent. Within these variants … only the non-anchor residues of the variant are determined to be conserved, semi-conserved, or non-conserved” (App. Br. 9 (emphasis added)). We agree (FF 1-3). Appellants contend that Baker fails to teach Appellants’ claimed invention because Baker teaches that “only a portion of the residues of the identified variants … are subjected to the determination step (b) in paragraph [00112]” (App. Br. 9). We agree (FF 3 (Baker’s step “b) determin[es] whether each of said variants comprises conserved, semi- conserved or non-conserved non-anchor residues”) (emphasis added)). Examiner asserts that Baker’s “anchor positions are the same binding motif (i.e.: conserved)” (FF 6). Examiner’s position appears to be that Baker implicitly determines the identity of the anchor points because they are conserved residues. Examiner does not, however, identify a portion of Baker that supports this assertion. In contrast, Baker teaches that the anchor positions may be variable (FF 4-5). In the absence of an evidentiary basis on this record to support a finding that Baker teaches the classification of “each position within the biopolymer sequences as conserved, variable, or Appeal 2011-009552 Application 11/713,474 5 unconserved,” are required by Appellants’ claim 1, we are compelled to find that Examiner failed to establish an evidentiary basis on this record to support a prima facie case of anticipation (see Claim 1; Cf. FF 3). CONCLUSION OF LAW The preponderance of evidence on this record fails to support Examiner’s finding that Baker teaches Appellants’ claimed invention. The rejection of claims 1-5 and 7-10 under 35 U.S.C. § 102(b) as being anticipated by Baker is reversed. Obviousness: ISSUE Does the preponderance of evidence on this record support a conclusion of obviousness? FACTUAL FINDINGS (FF) FF 7. Examiner relies on Baker as set forth above. FF 8. Examiner finds that De Groot teaches a method “comprising classifying potential peptide epitopes relative to known epitopes, ranking binding probability, and selecting epitopes with highest conservation and binding potential” (Ans. 8). In this regard, Examiner directs attention to the “entire document, particular pp 4388-4389” and page “4393, col 1, para 2” of De Groot (Ans. 8 and 15, respectively). ANALYSIS Initially, we note that the De Groot reference cited in the “Evidence Relied Upon” section of Examiner’s Answer contains pages 425-428. Accordingly, it is unclear if Examiner’s citation of pages 4388-4389 and Appeal 2011-009552 Application 11/713,474 6 4393 represent a typographical error or whether Examiner intended to rely on a different De Groot reference. Nevertheless, based on the combination of Baker and De Groot, Examiner finds that, at the time of Appellants’ claimed invention, it would have been prima facie obvious to a person of ordinary skill in this art [T]o avoid sequences with similarity to self as taught by De Groot et al. in the vaccine design taught by Baker et al. because all the claimed elements were known in the prior art and one skilled in the art could have combined the elements as claimed by known methods (such as the methods taught by Baker et al. or De Groot et al. regarding computer algorithms to select or eliminate sequences) with no change in their respective functions, and the combination would have yielded predictable results (sequences that do not cross-react with self) to one of ordinary skill in the art at the time of the invention. (Ans. 8-9.) Having reviewed the evidence relied upon by Examiner, we find that Examiner failed to establish that De Groot makes up for the deficiencies in Baker (see generally App. Br. 11-12). CONCLUSION OF LAW The preponderance of evidence on this record fails to support a conclusion of obviousness. The rejection of claims 1-10 under 35 U.S.C. § 103(a) as unpatentable over the combination of Baker and De Groot is reversed. Appeal 2011-009552 Application 11/713,474 7 REVERSED alw