Ex Parte Espy et alDownload PDFBoard of Patent Appeals and InterferencesAug 6, 201011459789 (B.P.A.I. Aug. 6, 2010) Copy Citation UNITED STATES PATENT AND TRADEMARK OFFICE ____________________ BEFORE THE BOARD OF PATENT APPEALS AND INTERFERENCES ____________________ Ex parte MARK J. ESPY and THOMAS F. SMITH, Appellants1 ____________________ Appeal 2010-003551 Application 11/459,789 Technology Center 1600 ____________________ Before CAROL A. SPIEGEL, FRANCISCO C. PRATS, and JEFFREY N. FREDMAN, Administrative Patent Judges. SPIEGEL, Administrative Patent Judge. DECISION ON APPEAL2 Appellants appeal under 35 U.S.C. § 134(a) from an Examiner's final rejection of all pending claims, claims 23, 26, and 27 (Br. 4; Ans.3 2). We have jurisdiction under 35 U.S.C. § 134. We AFFIRM. 1 The real parties in interest are MAYO FOUNDATION FOR MEDICAL EDUCATION AND RESEARCH and ROCHE MOLECULAR SYSTEMS, INC. (Brief On Appeal filed 6 July 2009 ("Br.") at 2). 2 The two-month period for filing an appeal or commencing a civil action, as recited in 37 C.F.R. § 1.304, or for filing a request for rehearing, as recited in 37 C.F.R. § 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. 3 Examiner's Answer mailed 19 October 2009 ("Ans."). Appeal 2010-003551 Application 11/459,789 2 The subject matter on appeal is directed to articles of manufacture containing specified pairs of probes and primers suitable for use in a real- time polymerase chain reaction ("PCR") for detecting influenza A virus. Claim 23 is illustrative and reads (Br. 15): An article of manufacture, comprising: a pair of influenza A primers, wherein said pair of influenza A primers comprise a first influenza A primer and a second influenza A primer, wherein said first influenza A primer consists of the sequence 5'-TAA CCG AGG TCG AAA CGT ATG TTC T-3' (SEQ ID NO:1) and wherein said second influenza A primer consists of the sequence 5'-GGC ATT TTG GAC AAA GCG TCT A-3' (SEQ ID NO:2); a pair of influenza A probes, wherein said pair of influenza A probes comprises a first influenza A probe and a second influenza A probe, wherein said first influenza A probe consists of the sequence 5'-CGA AAT CGC GCA GAG ACT TGA AGA TGT-3' (SEQ ID NO:3) and wherein said second influenza A probe consists of the sequence 5'-TTG CTG GGA AAA ACA CAG ATC TTG AGG C-3' (SEQ ID NO:4); and a donor fluorescent moiety and a corresponding acceptor fluorescent moiety. The Examiner rejected claims 23, 26, and 27 as unpatentable under 35 U.S.C. § 103(a) over Smith4 in view of Hall,5 Boivin,6 and Buck7 (Ans. 4-8). 4 Smith et al., Rapid detection of influenza A and B viruses in clinical specimens by Light Cycler real time RT-PCR, 28 JOURNAL OF CLINICAL VIROLOGY 51-58 (2003) ("Smith"). 5 Hall et al., Variation in Nucleotide Sequences Coding for the N-Terminal Regions of the Matrix and Nonstructural Proteins of Influenza A Viruses, 38 JOURNAL OF VIROLOGY 1-7 (April 1981) ("Hall"). 6 WO 2004/057021 A2, Molecular Methods and Compositions for Detecting and Quantifying Respiratory Viruses, published 8 July 2004, for Guy Boivin ("Boivin"). 7 Buck et al., Design Strategies and Performance of Custom DNA Sequencing Primers, 27 BIOTECHNIQUES 528-536 (1999) ("Buck"). Appeal 2010-003551 Application 11/459,789 3 The Examiner found that Smith teaches a pair of primers and a pair of probes, each probe labeled with either a donor or an acceptor fluorescent moiety, for detecting influenza A virus by real time PCR, albeit not the specifically claimed pairs of probes defined by SEQ ID NOs: 1 and 2 and primers defined by SEQ ID NOs: 3 and 4 (Ans. 4). The Examiner relies on Hall and Boivin for teaching sequences similar (88%) or substantially identical to the sequences of the claimed primers and probes (id. 4-5). The Examiner also relies on Buck as evidence of a reasonable expectation of success when using primers selected according to ordinary criteria (id. 7-8). The Examiner concluded that the claimed primers and probes would have been prima facie obvious over the cited references in the absence of secondary considerations of patentability (id. 6). Appellants argue that primer and probe design for real-time PCR amplification is not always predictable, citing Guidelines,8 Csordas,9 Elnifro,10 Tichopad,11 and Abd-Elsalam12 in support of their position (Br. 9- 10). According to Appellants, DNA sequencing requires only forward 8 University of Chicago Cancer Research Center DNA Sequencing Facility, Choosing Primers for Sequencing, downloaded from http://cancer- seqbase.uchicago.edu/primers.html ("Guidelines"). 9 Csordas et al., Comparison of primers for the detection of Salmonella enterica serovars using real-time PCR, 39 LETTERS IN APPLIED MICROBIOLOGY 187-193 (2004) ("Csordas"). 10 Elnifro et al., Multiplex PCR: Optimization and Application in Diagnostic Virology, 13 CLINICAL MICROBIOLOGY REVIEWS 559-570 (2000). 11 Tichopad et al., Inhibition of real-time RT-PCR quantification due to tissue-specific contaminants, 18 MOLECULAR AND CELLULAR PROBES 45-50 (2004) ("Tichopad"). 12 Kamel A. Abd-Elsalam, Minireview: Bioinformatic tools and guideline for PCR primer design, 2 AFRICAN JOURNAL OF BIOTECHNOLOGY 91-95 (2003) ("Abd-Elsalam"). Appeal 2010-003551 Application 11/459,789 4 primers, whereas PCR amplification requires both forward and reverse primers. Thus, insofar as Buck relates to DNA sequencing, Buck is not representative of primers for PCR amplification (id. 9). Appellants further argue that the claimed sequences provide "an extremely high sensitivity and specificity toward their targets" and that the probes can be used to further increase the accuracy of detecting influenza A as shown by Examples 2 and 4 of their specification (id. 12). Further according to Appellants, there is no motivation to select the particularly claimed primer and probe pairings from a very large genus of oligonucleotides complementary to the full-length gene sequence of influenza A (id. 10-13). In particular, Appellants maintain that there is no case law holding that "a longer sequence makes per se obvious specific primer and probe sequences from within that longer sequence", i.e., "that two oligonucleotides that have different sequences but are complementary to the same target sequence are 'structural homologs'" (id. 11). According to Appellants, claims 23, 26, and 27 stand or fall together (Br. 9). Therefore, we decide this appeal on the basis of claim 23. 37 C.F.R. § 41.37(c)(1)(vii). At issue is whether the claimed primers and probes defined by SEQ ID NOs: 1-4 would have been obvious based on standard criteria used to design primers for real-time PCR use and, if so, whether Appellants have provided objective evidence of nonobviousness. II. Findings of Fact The following findings of fact ("FF") are supported by a preponderance of the evidence of record. Appeal 2010-003551 Application 11/459,789 5 [1] Respiratory tract infection caused by influenza viruses is a significant cause of morbidity and mortality and, thus, there is a need for rapid detection and diagnosis of influenza (Spec.13 1:13-30; Smith abstract; Boivin 1:17-24 and 9:25-28). [2] Smith teaches detecting influenza A virus by real-time PCR analysis with primer/probe sets designed to recognize an N-terminal 300 bp region of the matrix gene (M1) as the viral target sequence based on criteria of Roche Light Cycler probe design software, version 1.0, available from Roche Diagnostics (Smith abstract; p. 53, col. 2, ¶ 2; p. 54, col. 1, ¶ 1). [3] Smith does not disclose the consensus sequence of the M1 gene region used to design its probes and primers for the real-time PCR (Smith p. 53, col. 2, ¶ 2). [4] Hall discloses the N-terminal sequence of a human influenza virus A M1 (Hall Figure 1). [5] Smith does disclose the sequences of its probes and primers, which are not identical to SEQ ID NOs: 1-4 of the claimed probes and primers. [6] Boivin describes known PCR primer sequences for amplifying influenza A virus useful in a multiplex PCR for detecting respiratory viruses, i.e., SEQ. ID. Nos. 139 and 140 (hereinafter "primers 139 and 140") (Boivin abstract; 24:23-24; 35:29-30). [7] According to Tables 10 and 12 of Boivin, forward and reverse primers 139 and 140 were used to amplify a 245 bp region of the matrix gene of influenza A virus (Boivin 72, 74). 13 Specification of Application 11/459,789 ("Spec."). Appeal 2010-003551 Application 11/459,789 6 [8] The Examiner found that Boivin primer 140 was substantially identical to the claimed primer defined by SEQ ID NO:2 (Ans. 4-5). [9] Boivin also provides DNA sequences of human influenza virus A strains Hong Kong and Charlottesville, i.e., SEQ. ID. NOs. 130 and 131 (Boivin Figures 42-43/52), and viral probe SEQ. ID. NO. 162 (id. Table 11, p. 73). [10] The Examiner found that the claimed probes defined by SEQ ID NOs: 3 and 4 were substantially identical to nucleotides 9-117 [sic, 9-17] and 120-147, respectively, within Boivin SEQ ID NO. 130, while the claimed primer defined by SEQ ID NO:1 was 88% identical to nucleotides 39-60 within Boivin SEQ ID NO. 130 (Ans. 4-5). [11] Table 1 of Buck enumerates optimal and observed characteristics of primers for DNA sequencing or PCR, i.e., Appeal 2010-003551 Application 11/459,789 7 [12] According to the Guidelines, DNA sequencing primers should have a melting temperature in the range of 50o-60oC; lack dimerization capability, hairpin formation capability, and secondary priming sites; will be about 18 to 30 nucleotides long; and, have a GC content of 40 to 60% (Guidelines 1-2). [13] The Guidelines "strongly recommend the use of computer software to design primers with these characteristics", e.g., LaserGene, Oligo, MacVector, and the GCG suite, but note that "no set of guidelines will always accurately predict the success of a primer" (Guidelines 2). [14] Csordas teaches that primers originally designed for end-point PCR may yield poor sensitivity in real-time PCR because of their tendency to form primer dimers (Csordas p. 187, col. 1, ¶ 1; p. 191, col. 2, ¶ 5). [15] Csordas uses software (Primer Premier 5.0) to design a primer set for real-time PCR which, given a particular target sequence and primer set, searches for potential primer dimers as well as for locations outside the target sequence where primers have a tendency to anneal, leading to nonspecific product formation (Csordas p. 189, ¶ bridging cols. 1-2). [16] Csordas uses software (Primer Premier 5.0, PREMIER Biosoft International) to design a primer set given a particular target sequence (Csordas p. 189, col. 1, ¶ 4). [17] Elnifro explains that in multiplex PCR more than one target sequence can be amplified by using more than one pair of primers in the reaction (Elnifro, p. 559, col. 1, ¶ 1), however the presence of Appeal 2010-003551 Application 11/459,789 8 more than one primer pair increases the chances of nonspecific amplification products, primarily because of primer dimer formation (id., col. 2, ¶ 4). [18] Elnifro states that [e]mpirical testing and a trial-and-error approach may have to be used when testing several primer pairs, because there are no means to predict the performance characteristics of a selected primer pair even among those that satisfy the general parameters of primer design. However, special attention to primer design parameters such as homology of primers with their target nucleic acid sequences, their length, the GC content, and their concentration have to be considered. Ideally, all the primer pairs in a multiplex PCR should enable similar amplification efficiencies for their respective target. This may be achieved through the utilization of primers with nearly identical optimum annealing temperatures (primer length of 18 to 30 bp or more and a GC content of 35 to 60% may prove satisfactory) and should not display significant homology either internally or to one another. [Elnifro p. 560, col. 1, ¶ 1, endnotes omitted.] [19] Tichopad discusses inhibition of real-time reverse transcription-PCR due to tissue-specific contaminants, observing that this affect can be ameliorated in part by appropriate primer selection (Tichopad abstract). [20] According to Abd-Elsalam, "[m]aybe the most critical parameter for successful PCR is the design of Primers" (Abd-Elsalam p. 94, col. 1, ¶ 2). [21] Abd-Elsalam Appeal 2010-003551 Application 11/459,789 9 provide[s] a guide to choosing the most efficient way to design a new specific-primer by applying current publicly available links and Web services. Also … general recommendations for the design and use of PCR primers. [Abd-Elsalam abstract.] [22] Tables 1, 2, and 3 of Abd-Elsalam describe twenty online primer design sites, six PCR oligonucleotide resources for predicting primer parameters such as melting temperature, and eighteen PCR primer design software programs for personal computers, respectively (Abd- Elsalam pp. 92-93). [23] Abd-Elsalam provides express guidelines for choosing two PCR amplification primers, including primer length, melting temperature, GC content, 3'-end sequence, avoidance of primer sequences leading to self-dimerization or primer-dimer formation (Abd-Elsalam pp. 94- 95). [24] According to the Specification, primers that amplify an influenza A molecule can be designed using a computer program, e.g.,. OLIGO, taking into account important features including similar melting temperatures for the members of each pair of primers and primer length, typically 15 to 30 nucleotides (Spec. 7:23-8:2). [25] Further according to the Specification, probes can be designed in a manner similar to primers, e.g., with similar melting temperatures and lengths also generally from 15 to 30 nucleotides (Spec. 8:3-21). [26] The Specification states that "the PCR test method compared with standard cell culture [resulted in]: sensitivity, 96%, specificity, 92%; positive predictive value, 53%; and negative predictive value, 100%" based on the results of Example 2 (Spec. 24:23-25:2). Appeal 2010-003551 Application 11/459,789 10 [27] According to Example 2 of the Specification, of 557 tested clinical samples, 49 were positive by both PCR and cell culture methods, 463 were negative by both PCR and cell culture methods, 43 were positive by PCR but not cell culture, and 2 were positive by cell culture but not PCR (Spec. 24:19-22). [28] According to Example 4 of the Specification, [i]nfluenza A virus infections were detected by sensitive real-time PCR technology in 10 of 50 (20%) study patients after 7 days of hospitalization (Table 3). In contrast, only 5 of 50 (10%) patients were positive by the shell-vial [cell culture] assay after 7 days and none [were] positive using conventional tube cell culture methods (Table 3). These data suggest that patients can shed influenza A virus beyond the CDC recommended 5 day droplet isolation period. Importantly, PCR results may not equate with active virus; however, a positive molecular result may indeed indirectly indicate infectious or active virus since cell culture techniques have reduced sensitivity compared to PCR. [Spec. 26:9-16.] III. Discussion A. Legal principles "One of the ways in which a patent's subject matter can be proved obvious is by noting that there existed at the time of invention a known problem for which there was an obvious solution encompassed by the patent's claims." KSR Int’l Co. v. Teleflex Inc., 550 U.S. 398, 419-20 (2007). "When there is a design need or market pressure to solve a problem and there are a finite number of identified, predictable solutions, a person of ordinary skill has good reason to pursue the known options within his or her Appeal 2010-003551 Application 11/459,789 11 technical grasp." Id. Furthermore, "[o]bviousness does not require absolute predictability of success.… For obviousness under § 103, all that is required is a reasonable expectation of success." In re O’Farrell, 853 F.2d 894, 903- 04 (Fed. Cir. 1988). B. Analysis There is a recognized need to detect and diagnose respiratory tract infection caused by influenza A virus (FF 1). Smith teaches detecting influenza A virus by real-time PCR analysis using primer/probe sets designed to target the M1 (matrix) gene region of influenza A virus (FF 2). The DNA sequence of the M1 gene is known (FF 4). It is not only conventional, but also strongly recommended (FF 13), in the art to use primer design software to design primers for use in real-time PCR based on defined criteria, such as nucleotide length, melting temperature in the range of about 50o-60oC, about 40-60% GC content, and avoiding significant homology within a primer or between primers (FF 3, 11, 12, 15, 16, 18, 21- 23). Indeed, as noted by the Examiner (Ans. 10-11), the instant Specification describes using primer design software, taking into account nucleotide length and melting temperatures, etc. to obtain primers and probes (FF 24-25). Thus, given a known influenza A detection target sequence in the prior art (the M1 gene), we agree with the Examiner that one of ordinary skill in the art would have had every motivation to use conventional primer design software and every reasonable expectation of success in obtaining the primers and probes of claim 23. Notably, the Guidelines state that no set of guidelines for primer design will always accurately predict the success of a primer (FF 13), but obviousness does not require absolute predictability of success, only a Appeal 2010-003551 Application 11/459,789 12 reasonable expectation of success. In re O’Farrell, 853 F.2d at 903-04. Here, the prior art cited by the Examiner, particularly Buck, as well as the rebuttal prior art cited by Appellants consistently teach using the same or substantially the same criteria to design primers and provide a reasonable expectation of success of detecting a target DNA sequence (FF 3, 11, 12, 15, 16, 18, 21-23). Unlike in In re Deuel, 51 F.3d 1552 (Fed. Cir. 1995), one of ordinary skill in the art is not selecting a particular DNA sequence from among a large number of degenerate variants, but rather selecting particular DNA sequences (primers and probes) having particular art-recognized parameters, e.g., nucleotide length, GC content, melting temperature, and homology both within and without the particular DNA sequence. Similarly, unlike in In re Bell, 991 F.2d 781, 784 (Fed. Cir. 1993), here the prior art is not suggesting a nearly infinite number of primer and/or probe possibilities without any suggestion of which of those possibilities to select. Therefore, we agree with the Examiner that the subject matter of claim 23 is prima facie obvious over the applied prior art. Appellants argue that Examples 2 and 4 of their Specification demonstrate that the claimed probes and primers exhibit "extremely high sensitivity and specificity toward their targets" (Br. 12). However, Examples 2 and 4 compare the results of a real-time PCR method to the results of cell culture methods (FF 26-29), not to the closes prior art, the real-time PCR method of Smith. However, to establish that claimed subject matter yields an unexpected result, the claimed subject matter must be compared to the closest prior art. In re Baxter-Travenol Labs., 952 F.2d 388, 392 (Fed. Cir. 1991) ("[W]hen unexpected results are used as evidence Appeal 2010-003551 Application 11/459,789 13 of nonobviousness, the results must be shown to be unexpected compared with the closest prior art."). This Examples 2 and 4 fail to do. C. Conclusion Therefore, we will sustain the rejection of claims 23, 27, and 28 under 35 U.S.C. § 103(a) over Smith in view of Hall, Boivin, and Buck. Based on the evidence of record, the claimed primers and probes defined by SEQ ID NOs: 1-4 would have been obvious based on standard criteria used to design primers for real-time PCR use and Appellants have not provide evidence secondary considerations of patentability sufficient to overcome that conclusion of obviousness. IV. Order Upon consideration of the record, and for the reasons given, it is ORDERED that the decision of the Examiner to reject claims 23, 27, and 28 as unpatentable under 35 U.S.C. § 103(a) over Smith in view of Hall, Boivin, and Buck is AFFIRMED; and, FURTHER ORDERED that no period for taking any subsequent action in connection with this appeal may be extended under 37 C.F.R. § 1.136(a)(1)(iv). AFFIRMED dm FISH & RICHARDSON P.C. P.O. Box 1022 Minneapolis, MN 55440-1022 Copy with citationCopy as parenthetical citation