Ex Parte Pont-Kingdon et alDownload PDFPatent Trial and Appeal BoardNov 28, 201211268433 (P.T.A.B. Nov. 28, 2012) Copy Citation 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. 11/268,433 11/07/2005 Genevieve Pont-Kingdon 50407-5 1912 28441 7590 11/29/2012 BRINKS HOFER GILSON & LIONE/UTAH UTAH OFFICE 222 South Main Street Suite 1930 SALT LAKE CITY, UT 84101 EXAMINER SALMON, KATHERINE D ART UNIT PAPER NUMBER 1634 MAIL DATE DELIVERY MODE 11/29/2012 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 GENEVIEVE PONT-KINGDON, ELAINE LYON, and JOHN G. WARD __________ Appeal 2011-013029 Application 11/268,433 Technology Center 1600 __________ Before MELANIE L. McCOLLUM, FRANCISCO C. PRATS, and STEPHEN WALSH, Administrative Patent Judges. WALSH, Administrative Patent Judge. DECISION ON APPEAL This is an appeal under 35 U.S.C. § 134(a) from the rejection of claims directed to a chimeric nucleic acid probe and a nucleic acid complex. The Patent Examiner rejected the claims for obviousness. We have jurisdiction under 35 U.S.C. § 6(b). We affirm. Appeal 2011-013029 Application 11/268,433 2 STATEMENT OF THE CASE “[T]he invention relates to hybridization probes and methods of using such probes to determine haplotypes and genotypes.” (Spec. 2, [0002].) The Specification explains that “[t]he genetic sequence at a particular genetic locus is referred to as the ‘genotype,’ while the particular combination of genetic sequences or polymorphisms at multiple loci is referred to as the ‘haplotype.’” (Id., [0003].) According to the Specification, “[i]dentification and characterization of genotypes and haplotypes has become a primary focus of genetic research.” (Id.) Claims 1-16, 28, and 31-35 are on appeal. Appellants state that the claims stand or fall together. (App. Br. 17.) We select claim 1 as representative, and claims 2-16, 28, and 31-35 will stand or fall with claim 1. 37 C.F.R. § 41.37(c)(1)(vii). Claim 1 reads: 1. A chimeric nucleic acid probe comprising: a first binding region substantially complementary to a first polymorphic site of a polynucleotide template, and a second binding region substantially complementary to a second polymorphic site of a polynucleotide template, wherein the first polymorphic site and the second polymorphic site are noncontiguous and wherein the first polymorphic site and the second polymorphic site of the polynucleotide template are separated by a region of polynucleotides not complementary to nucleotides in the nucleic acid probe. The Examiner rejected all the claims under 35 U.S.C. § 103(a) as unpatentable over Neri1 and Guo.2 1 Bruce Neri et al., US 6,194,149 B1, issued Feb. 27, 2001. Appeal 2011-013029 Application 11/268,433 3 OBVIOUSNESS The Issues The Examiner’s position is that Neri taught (i) a chimeric bridging probe having binding regions complementary to two or more non-contiguous sites of a target template (Ans. 6); (ii) a target template having polymorphisms in a second template region (id., citing Neri at col. 13, ll. 10- 20); and (iii) the first and second sites on Neri’s target template were separated by at least five nucleotides not complementary to the probe (id.). The Examiner found the difference between Neri’s probe and Appellants’ probe is that Neri described only one of the sites on the target template as polymorphic. (Id.) The Examiner found, however, that “it is well known in the art that probes can be designed to detect multiple polymorphic sites,” and cited Guo as teaching probes complementary to multiple polymorphic sites on a template of interest. (Id. at 10, citing Guo’s Table 1.) The Examiner further found that Guo (i) taught two or more alleles are needed to define particular phenotypes, such as HLA, and (ii) motivated the ordinary artisan to design probes and probe/template complexes to detect multiple polymorphic sites on a template in order to determine if the sample has a particular phenotype. (Id. at 11.) The Examiner concluded it would have been “obvious to the ordinary artisan to modify the probes and complex of Neri et al. to detect any number of polymorphic sites on templates including a first polymorphic 2 Zhen Guo et al., Oligonucleotide Arrays for High-Throughput SNPs Detection in the MHC Class I Genes: HLA-8 as a Model System, 12 GENOME RES. 447-457 (2002). Appeal 2011-013029 Application 11/268,433 4 and second polymorphic site on a polynucleotide temple which is separated by a noncontiguous region with the reasonable expectation of designing a probe which detects multiple polymorphic sites associated with a particular phenotype.” (Id.) Appellants contend the Examiner erred “because the combination of Neri and Guo is improper,” and “[o]ne would not be inclined to modify the probe disclosed by Neri to be complementary to a second polymorphic site separated from a first polymorphic site by a region of polynucleotides not complementary to nucleotides in the nucleic acid probe.” (App. Br. 18.) More specifically, Appellants contend: (1) “[n]either Neri nor Guo teach or suggest using probes for haplotyping over distances that would require a loop-out region in a template with a second polymorphic site;” (2) “neither reference provid[ed] a reason for the asserted combination;” (3) “neither reference provid[ed] a reasonable expectation that the combination would lead to successful haplotyping.” (Id. at 18-19.) Findings of Fact 1. We adopt the Examiner’s findings concerning the scope and content of the prior art. 2. Regarding claim 1’s “template . . . region of polynucleotides not complementary to nucleotides in the nucleic acid probe,” the Specification provides: Appeal 2011-013029 Application 11/268,433 5 The first and second regions of the template are not contiguous, and are either separated by a region of polynucleotides with respect to which there are no complementary nucleotides in the nucleic acid probe, or . . . . The hybridization probe (with its adjacent first and second regions in close proximity) binds to the first and second regions of the template, which are brought together in close proximity to form a probe/template complex, thereby forcing the region of the template with respect to which there are no complementary nucleotides in the nucleic acid probe to “loopout”. The single hybridization probe is used to determine the identity and phase of the two alleles present on the template, using melting curve analysis of the hybridization probe. (Spec. 18, [0064].) 3. The Specification further provides: The DNA region of interest, and the DNA template corresponding to the DNA region, which encompass more than one multi-allelic loci, also includes a region of polynucleotides that separate the loci. The region of polynucleotides separating the first and second locus may be a length of nucleotide sequence comprising one or more nucleotides of any length. The number of nucleotides separating the first and second locus may be 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14 or greater. In particular embodiments, the number of nucleotides separating the first and second locus may be greater than 15 nucleotides, greater than 20 nucleotides, greater than 25 nucleotides, greater than 50 nucleotides, greater than 100 nucleotides, or greater than 200 nucleotides. (Id. at 27, [0091].) Principles of Law “During patent examination the pending claims must be interpreted as broadly as their terms reasonably allow,” and limitations are not to be read into the claims from the Specification. In re Zletz, 893 F.2d 319, 321 (Fed. Cir. 1989) (citations omitted). Appeal 2011-013029 Application 11/268,433 6 “A reference may be read for all that it teaches, including uses beyond its primary purpose.” In re Mouttet, 686 F.3d 1322, 1331 (Fed. Cir. 2012). In determining whether the subject matter of a patent claim is obvious, neither the particular motivation nor the avowed purpose of the patentee controls. What matters is the objective reach of the claim. If the claim extends to what is obvious, it is invalid under § 103. 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); In re Beattie, 974 F.2d 1309, 1312 (Fed. Cir. 1992) (“the law does not require that the references be combined for the reasons contemplated by the inventor”). “A reference is reasonably pertinent if, even though it may be in a different field from that of the inventor’s endeavor, it is one which, because of the matter with which it deals, logically would have commended itself to an inventor’s attention in considering his problem.” In re Clay, 966 F.2d 656, 659 (Fed. Cir. 1992). In other words, “familiar items may have obvious uses beyond their primary purposes.” KSR Int’l Co. v. Teleflex, Inc., 550 U.S. 398, [402], 127 S.Ct. 1727, 1742 (2007). In re Icon Health and Fitness, Inc., 496 F.3d 1374, 1379-80 (Fed. Cir. 2007). “Obviousness does not require absolute predictability of success. . . . [A]ll that is required is a reasonable expectation of success.” In re O'Farrell, 853 F.2d 894, 903-04 (Fed. Cir. 1988). The presence of a reasonable expectation of success is measured from the perspective of a person of ordinary skill in the art at the time the invention was made. Life Techs., Inc. v. Clontech Labs., Inc., 224 F.3d 1320, 1326 (Fed. Cir. 2000). Appeal 2011-013029 Application 11/268,433 7 Discussion After considering the evidence and the arguments, we conclude the evidence favors the Examiner’s conclusion of obviousness. Accordingly, we adopt the Examiner’s reasoning (see Grounds of Rejection, Ans. 5-11), and agree that the Examiner properly found Appellants’ arguments unpersuasive (see Response to Argument, Ans. 12-24). We provide the following points for emphasis. Issue (1) The Examiner properly found Appellants’ “loopout” argument unpersuasive because the claims do not contain a loopout limitation. (Ans. 14.) The Specification describes templates that would loopout on hybridization with the claimed probe. (FF 2.) The Specification also describes templates that contain only one nucleotide separating the polymorphic sites. (FF 3.) The Examiner rebuts Appellants’ loopout contention by pointing to the Specification’s disclosure that as few as one nucleotide could be the separation in the template (Ans. 14, citing Spec. 27, [0091].) According to the Examiner, one nucleotide is not enough to form a loop, and we find the Examiner’s technical reasoning persuasive. Appellants have not established that the appealed claims must be interpreted as requiring a loopout region in the template. See Zletz, 893 F.2d at 321. Issue (2) Appellants contend that “Neri and Guo relate to different problems than the claimed invention.” (App. Br. 19.) Even if Appellants’ characterizations are accepted as correct, that alone does not establish a Appeal 2011-013029 Application 11/268,433 8 reason to disregard other reasons for obviousness. See KSR, 550 U.S. 419- 20. Both Neri and Guo taught probes for analyzing nucleic acids. Neri explained that its probes permitted the detection and/or identification of genetic polymorphisms. (Neri, Abstract.) Guo explained that its probes permitted identifying SNPs in polymorphic targets. (Guo, Abstract.) According to the Examiner, Guo identified haplotyping as a problem that could be addressed by using probes complementary to multiple polymorphic regions on a template. The Examiner explained that changing Neri’s probe to include regions complementary to two polymorphic regions, as in Guo, rather than only one, would have provided another way to address Guo’s haplotyping. Appellants have not produced evidence that the Examiner was wrong in so reasoning. Any need or problem known in the field may provide a reason for combining elements in the manner claimed. KSR, 550 U.S. at 420. Appellants have also argued that a person of ordinary skill in the art would not have combined the Neri and Guo teachings, as Neri’s purpose was to assay formation of a secondary structure, and its probes were not designed for genotyping or haplotyping. (App. Br. 20.) This argument is unpersuasive because, as the Examiner found, Neri’s disclosure concerned probes for the detection and identification of polymorphisms (Ans. 6), and Guo’s disclosure concerned probes for detecting multiple polymorphic sites (id. at 10). The two references were therefore reasonably pertinent to each other. See Icon Health, 496 F.3d at 1379-80. Appellants argue that because the methods Neri and Guo taught were different, modifying Neri’s probe would change principle of operation of Neri. This argument is unpersuasive because Neri’s probes operated by Appeal 2011-013029 Application 11/268,433 9 hybridization, the same mechanism by which Guo’s probes operated. The two may have extracted different information from their data, but the principle of operation, hybridization, was not different. If Neri’s probe having non-contiguous binding sites were modified from being complementary to one polymorphic site and one non-polymorphic site to being complemetary to two polymorphic sites, the modified probe would still operate by hybridization to non-contiguous sites. See Mouttet, 686 F.3d at 1332 (arguments about changing operational principles inapplicable where the modified apparatus will operate “on the same principles as before”). Claim 1 defines a probe, not a method. We agree with the Examiner that because the claims on appeal define probes, the probes may have been obvious even if not used to obtain the information Appellants wish to collect. Issue (3) Appellants contend there would have been no “reasonable expectation that modifying the probe and complex of Neri would result in the successful identification of a haplotype or genotype of a template which has at least one genetic locus characterized by multiple alleles.” (App. Br. 25.) The Examiner responds that Neri allowed mismatches and Guo taught detecting multiple mismatches, and both references taught extensive template variations. (Ans. 21-24.) We find the Examiner’s thorough fact-based analysis persuasive that, from the perspective of a person of ordinary skill in the art, Neri’s probes, if modified as the rejection proposed, would reasonably have been expected to identify multiple polymorphic sites on a template. See Life Techs., 224 F.3d at 1326. Appeal 2011-013029 Application 11/268,433 10 CONCLUSIONS The claims do not require template loopout. Neri and Guo were reasonably pertinent to each other, and properly combined. Guo would have motivated the ordinary artisan to design probes and probe/template complexes to detect multiple polymorphic sites on a template in order to determine if a sample had a particular phenotype. Modifying Neri’s probes to detect multiple polymorphic sites on a template would have been obvious in view of Guo’s suggestion. The record evidence supports concluding that there would have been a reasonable expectation that Neri’s probes, if modified as the rejection proposed, would detect multiple polymorphic sites. SUMMARY We affirm the rejection of claims 1-16, 28, and 31-35 under 35 U.S.C. § 103(a) as unpatentable over Neri and Guo. No time period for taking any subsequent action in connection with this appeal may be extended under 37 C.F.R. § 1.136(a). AFFIRMED lp Copy with citationCopy as parenthetical citation