Ex Parte Kido et alDownload PDFPatent Trial and Appeal BoardMay 18, 201610556679 (P.T.A.B. May. 18, 2016) Copy Citation UNITED STA TES p A TENT AND TRADEMARK OFFICE APPLICATION NO. FILING DATE 10/556,679 0612912007 23373 7590 05/20/2016 SUGHRUE MION, PLLC 2100 PENNSYLVANIA A VENUE, N.W. SUITE 800 WASHINGTON, DC 20037 FIRST NAMED INVENTOR Hiroshi Kido 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 ATTORNEY DOCKET NO. CONFIRMATION NO. Q91487 4266 EXAMINER BOESEN, CHRISTIAN C ART UNIT PAPER NUMBER 1639 NOTIFICATION DATE DELIVERY MODE 05/20/2016 ELECTRONIC 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. Notice of the Office communication was sent electronically on above-indicated "Notification Date" to the following e-mail address( es): PPROCESSING@SUGHRUE.COM sughrue@sughrue.com USPTO@sughrue.com PTOL-90A (Rev. 04/07) UNITED STATES PATENT AND TRADEMARK OFFICE BEFORE THE PATENT TRIAL AND APPEAL BOARD Ex parte HIROSHI KIDO, MINEYOSHI HIYOSHI, MIW A BANDO, MORITOSHI KINOSHITA, YOJI FUKUDA, and HIROSHI MIZUGUCHI Appeal2013-004404 1 Application 10/556,679 Technology Center 1600 Before FRANCISCO C. PRATS, MELANIE L. McCOLL UM, and RICHARD J. SMITH, Administrative Patent Judges. PRATS, Administrative Patent Judge. DECISION ON APPEAL This appeal under 35 U.S.C. § 134(a) involves claims to a transcription chip to which a polynucleotide is bound. The Examiner rejected the claims for anticipation and obviousness. We have jurisdiction under 35 U.S.C. § 6(b). We affirm. 1 Otsuka Pharmaceutical Co., Ltd., is the real party in interest. App. Br. 2. Appeal2013-004404 Application 10/556,679 STATEMENT OF THE CASE The Specification discloses a "transcription chip where single or double-stranded DNA comprising one or more element sequences of transcription factors are immobilized on a substrate." Spec. 2. The Specification discloses that expression levels of a "transcription factor or a substance which interacts with the factor can be profiled by the chip based on a biological function such as DNA binding capacity." Id. The Specification explains that, using the disclosed chips, binding to DNA of a number of transcription factors, such as NFKB, can be evaluated. Id. at 5. The Specification explains further: The [bound] transcription factor can be quantified by immunologically measuring using an antibody against the transcription factor and a publicly known method such as ELISA or measuring using mass spectrometer. For example, the transcription factor may be directly measured by mass spectrometer, but it is preferable to identify and quantify the bound transcription factor by digesting the transcription factor bound to the chip with an appropriate protease such as trypsin, analyzing the resulting peptide fragments by mass spectrometer and comparing with a mass spectrum pattern (mass fingerprint) of the protease-digested transcription factor. As the mass spectrometer, MALDI-TOF is preferably exemplified. Id. at 8. Claim 1 is representative and reads as follows (App. Br. 20): 1. A transcription chip wherein at least one polynucleotide comprising one or more element sequences to which a transcription factor can be bound is immobilized on a substrate, wherein the transcription factor bound to one or more element sequences of the polynucleotide is detected by a peptide mass fingerprint method. 2 Appeal2013-004404 Application 10/556,679 The following rejections are before us for review: (1) Claims 1-3 and 10-20, under 35 U.S.C. § 102(b), for anticipation by Remacle2 (Final Action 4-6); (2) Claims 1-3 and 10-20, under 35 U.S.C. § 102(b), for anticipation by Smith3 (Final Action 6-7); (3) Claims 1-5 and 10-20, under 35 U.S.C. § 103(a), for obviousness over Remade and Kido4 (Final Action 7-1 O); and (4) Claims 1-5 and 10-20, under 35 U.S.C. § 103(a), for obviousness over Smith and Kido (Final Action 10-11 ). ANTICIPATION Appellants argue the merits of the two anticipation rejections together. See App. Br. 11. Accordingly, we consider those two rejections together. We select claim 1 as representative of the rejected claims. 37 C.F.R. § 41.37(c)(l)(iv). As stated in In re Oetiker, 977 F.2d 1443, 1445 (Fed. Cir. 1992): [T]he examiner bears the initial burden ... of presenting a primafacie case ofunpatentability .... After evidence or argument is submitted by the applicant in response, patentability is determined on the totality of the record, by a preponderance of evidence with due consideration to persuasiveness of argument. 2 WO 01/73115 Al (published Oct. 4, 2001 ). 3 Emily A. Smith et al., Surface Plasmon Resonance Imaging of Transcription Factor Proteins: Interactions of Bacterial Response Regulators with DNA Arrays on Gold Films, 19 Langmuir 1486-92 (2003) ("Smith"). 4 Hiroshi Kido et al., Application of the "Gene-Dia®" Diamond DNA Chip and Development of a Protein Chip, 85 J. Inst. Electronics Information and Communication Engineers 725-27 (2002) (as translated) ("Kido"). 3 Appeal2013-004404 Application 10/556,679 Appellants' arguments do not persuade us that a preponderance of the evidence fails to support the Examiner's prima facie case of anticipation as to claim 1. Claim 1 recites a transcription chip that is composed of at least one polynucleotide which is immobilized on a substrate. App. Br. 20. The immobilized polynucleotide must include one or more element sequences to which a transcription factor "can be bound." Id. As the Examiner found (Final Action 5-7), both Remade and Smith describe substrate-immobilized polynucleotides to which transcription factors may be bound. See Remade, abstract ("[P]utting into contact the transcriptional factor (1) with a double-stranded DNA sequence (2) bound to an insoluble solid support (3), and detecting and/or quantifying said fixed transcriptional factor (1 ), said double-stranded DNA sequence having a specific sequence able to be fixed by the transcriptional factor."); see also Smith 1486 (abstract) ("DNA arrays were fabricated from oligonucleotide sequences of known DNA binding regions for two response regulators .... The proteins exhibited specificity for the known binding sequences compared to control sequences on the DNA array."). As the Examiner found (Final Action 5), Remade, like Smith, discloses that the transcription factors are proteins. Remade iJ 18 ("The transcriptional factors ... can be part of a large protein complex .... "). Thus, both Remade and Smith describe products that have the structural elements expressly recited in claim 1, and which are capable of the intended use of binding a transcription factor. 4 Appeal2013-004404 Application 10/556,679 Claim 1 also recites "wherein the transcription factor bound to one or more element sequences of the polynucleotide is detected by a peptide mass fingerprint method." App. Br. 20. The Examiner concluded that this recitation is "at best either a characteristic or an intended use limitation." Final Action 4, 6. The Examiner found that the polypeptide transcription factors that bound the immobilized polynucleotides in Smith and Remade met that intended use. Id. at 5-7. The Examiner concluded that, because there was a reasonable basis to find that the chips of Remade and Smith met this intended use, and were therefore identical to the chip recited in claim 1, the burden had shifted to Appellants to show that the chips of Remade and Smith did not meet all of the claimed limitations. Id. at 4, 6 (citing In re Best, 562 F.2d 1252, 1255 (CCPA 1977); In re Fitzgerald, 619 F.2d 67 (CCPA 1980)). Appellants contend that, to show that a prior art reference inherently meets a claimed feature, and to shift the burden under Best or Fitzgerald, it is imperative that the Examiner provide a basis in fact or technical reasoning to show that the allegedly inherent property is necessarily present in the cited prior art, as opposed to merely being a possibility. App. Br. 12-15. Appellants contend that the Examiner did not adequately establish, through such reasoning, that the polypeptide transcription factors of Remade and Smith inherently meet the requirements of the final "wherein" clause of claim 1. Id. at 13; see also Reply Br. 5-6 (arguing that the Examiner did not show that one or more of the polypeptide transcription factors of Remade and Smith "is detected by a peptide mass fingerprint method")( emphasis in original); Reply Br. 7 (arguing that claim 1 recites that the transcription factor is bound to the polynucleotide ). Appellants contend that 5 Appeal2013-004404 Application 10/556,679 "[a ]tlinnance of rejections such as this would overburden and or incapacitate every Appellant facing a conclusory allegation of inherent anticipation and is contrary to law because, as courts have held, proof that the alleged inherent characteristic necessarily flows from the teachings of the applied prior art is unequivocally required." App. Br. 14-15. Appellants' arguments do not persuade us that the Examiner erred in maintaining these rejections. As an initial matter, as to claim interpretation, we conclude that the Examiner's interpretation of claim 1 is consistent with the broadest reasonable interpretation in light of the Specification. Adopting Appellants' interpretation, that claim 1 actually requires a step of detecting the transcription factor by a peptide mass fingerprint method, would place claim 1 in violation of the prohibition against claims simultaneously directed to both an apparatus and a process. See MPEP § 2173.05(p)(II) ("A single claim which claims both an apparatus and the method steps of using the apparatus is indefinite under 35 U.S.C. 112 ... , second paragraph."). As the Examiner pointed out, moreover, claim 1 does not require the transcription factor to be actually bound to the immobilized polynucleotide, only that the factor "can be bound." App. Br. 20. As to the issue of whether the Examiner provided a reasonable basis for finding that the chips of Remade and Smith meet the intended use that a bound transcription factor be detectable by a peptide mass fingerprint method, as noted above, and as the Examiner found (Final Action 5, 7), both references disclose that their immobilized polynucleotides can bind protein, i.e., polypeptide, transcription factors. See Remade ,-i 18; Smith 1486 (abstract). Thus, while the Examiner might not have been as articulate as he could have been, the Examiner's evident position is that, because the 6 Appeal2013-004404 Application 10/556,679 transcription factors that may become bound to the substrate-immobilized polynucleotides of Remade and Smith are polypeptides, they would be detectable by a peptide mass fingerprint method. We detect no error in this reasonmg. As noted above, the Specification discloses that bound transcription factors may be quantified by a "publicly known method such as ... using mass spectrometer." Spec. 8. As a preferred example of such methods, the Specification discloses "digesting the transcription factor bound to the chip with an appropriate protease such as trypsin, analyzing the resulting peptide fragments by mass spectrometer and comparing with a mass spectrum pattern (mass fingerprint) of the protease-digested transcription factor." Id. We agree with the Examiner that, because the transcription factors of Remade and Smith are polypeptides, it was reasonable to find that those transcription factors would be detectable by known polypeptide analytical methods, including the peptide mass fingerprint method described in the Specification. Accordingly, in addition to establishing that Remade and Smith describe products having all of the structural elements required by claim 1, the Examiner had a reasonable basis for finding that those products would be capable of the intended uses recited in claim 1. We, therefore, find also that the Examiner had a reasonable basis for shifting to Appellants, under In re Best, the burden of explaining why the products in Remade and Smith would not meet the intended uses recited in claim 1. As our reviewing court's predecessor explained in In re Best, 562 F.2d at 1254-1255 (quoting In re Swinehart, 439 F.2d 210, 212-13 (CCPA 1971)): 7 Appeal2013-004404 Application 10/556,679 [W]here the Patent Office has reason to believe that a functional limitation asserted to be critical for establishing novelty in the claimed subject matter may, in fact, be an inherent characteristic of the prior art, it possesses the authority to require the applicant to prove that the subject matter shown to be in the prior art does not possess the characteristic relied on. In the instant case, Appellants do not identify any clear or specific evidence showing, nor do Appellants explain specifically why, the Examiner erred in finding that the polypeptide transcription factors disclosed in Remade and Smith would be incapable of the intended use recited in the final "wherein" clause recited in claim 1. As to Appellants' argument that the Examiner improperly examined the Specification rather than the appealed claims (Reply Br. 7), we are not persuaded that it was unreasonable for the Examiner to consult the Specification (see Ans. 2) to determine whether the Specification disclosed any features that might be critical to the intended use recitation at issue. In sum, for the reasons discussed, Appellants' arguments do not persuade us that the Examiner erred in finding that Remade and Smith describe products that have all of the features required by claim 1. Accordingly, we affirm the Examiner's rejections of claim 1 as anticipated by those references. Because they were not argued separately, claims 2, 3, and 10-20 fall with claim 1. 37 C.F.R. § 41.37(c)(l)(iv). As to Appellants' argument that the Examiner's Answer failed to include a number of required sections (Reply Br. 8-10), MPEP § 1201 explains that, in relation to appeals in which the notice of appeal was filed after January 23, 2012, the appeal rules are significantly different than they were previously. Current MPEP § 1207.02, applicable here, does not require 8 Appeal2013-004404 Application 10/556,679 the content Appellants assert is mandatory in the Examiner's Answer. As to Appellants' argument that the Examiner's Answer included an unreviewed new interpretation of law (Reply Br. 10), as evidenced by the discussion above, we are not persuaded that that Examiner's interpretation is inconsistent with precedent. OBVIOUSNESS In rejecting claims 1-5 and 10-20 for obviousness over Remade and Kido, the Examiner relied on the teachings of Remade discussed above, and cited Kido as evidence that an ordinary artisan would have considered it obvious to use the diamond thin film support and spacer recited in claims 4 and 5 on Remacle's transcription factor-analyzing chip. Final Action 9-10. Appellants argue that Kido fails to "remedy the deficiencies of Remade, et al. therefore, it is impossible to combine the information in Remade, et al. and Kido, et al. and arrive at Appellant's invention. One having ordinary skill in the art could not possibly have been motivated to combine information that is missing from references." App. Br. 16. As discussed above, Appellants do not persuade us that Remade is deficient as to any of the limitations of claim 1. Accordingly, because Appellants' arguments do not identify any deficiency in the Examiner's obviousness rejection of claims 1-5 and 10-20 over Remade and Kido, we affirm that rejection. In rejecting claims 1-5 and 10-20 for obviousness over Smith and Kido, the Examiner relied on the teachings of Smith discussed above, and cited Kido as evidence that an ordinary artisan would have considered it obvious to use the diamond thin film support and spacer recited in claims 4 and 5 on Smith's transcription factor-analyzing chip. Final Action 10-11. 9 Appeal2013-004404 Application 10/556,679 Appellants argue that Kido fails to "remedy the deficiencies of Smith, et al. therefore, it is impossible to combine the information in Smith, et al. and Kido, et al. and arrive at Appellant's invention. One having ordinary skill in the art could not possibly have been motivated to combine information that is missing from references." App. Br. 16. As discussed above, Appellants do not persuade us that Smith is deficient as to any of the limitations of claim 1. Accordingly, because Appellants' arguments do not identify any deficiency in the Examiner's obviousness rejection of claims 1-5 and 10-20 over Smith and Kido, we affirm that rejection. SUMMARY For the reasons discussed, we affirm the Examiner's rejection of claims 1-3 and 10-20, under 35 U.S.C. § 102(b), for anticipation by Remade. For the reasons discussed, we affirm the Examiner's rejection of claims 1-3 and 10-20, under 35 U.S.C. § 102(b), for anticipation by Smith. For the reasons discussed, we affirm the Examiner's rejection of claims 1-5 and 10-20, under 35 U.S.C. § 103(a), for obviousness over Remade and Kido. For the reasons discussed, we affirm the Examiner's rejection of claims 1-5 and 10-20, under 35 U.S.C. § 103(a), for obviousness over Smith and Kido. No time period for taking any subsequent action in connection with this appeal may be extended under 37 C.F.R. § l.136(a). AFFIRMED 10 Copy with citationCopy as parenthetical citation