Ex Parte Nelson et alDownload PDFPatent Trial and Appeal BoardMay 3, 201713729566 (P.T.A.B. May. 3, 2017) 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. 13/729,566 12/28/2012 John Richard Nelson 221574-6 7908 6147 7590 05/05/2017 GENERAL ELECTRIC COMPANY GPO/GLOBAL RESEARCH 901 Main Avenue 3rd Floor Norwalk, CT 06851 EXAMINER THOMAS, DAVID C ART UNIT PAPER NUMBER 1637 NOTIFICATION DATE DELIVERY MODE 05/05/2017 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): haeckl@ge.com gpo.mail@ge.com Lori.e.rooney @ ge.com PTOL-90A (Rev. 04/07) UNITED STATES PATENT AND TRADEMARK OFFICE BEFORE THE PATENT TRIAL AND APPEAL BOARD Ex parte JOHN RICHARD NELSON, ROBERT SCOTT DUTHIE, and GREGORY ANDREW GROSSMAN Appeal 2016-002848 Application 13/729,566 Technology Center 1600 Before JEFFREY N. FREDMAN, JOHN E. SCHNEIDER, and RYAN H. FLAX, Administrative Patent Judges. FREDMAN, Administrative Patent Judge. DECISION ON APPEAL This is an appeal1 under 35 U.S.C. § 134 involving claims to a kit for DNA amplification. The Examiner rejected the claims as obvious. We have jurisdiction under 35 U.S.C. § 6(b). We affirm. Statement of the Case Background “A variety of techniques are currently available for efficient amplification of nucleic acids . . . even the slightest contamination of the 1 Appellants identify the Real Party in Interest as General Electric Company (see App. Br. 2). Appeal 2016-002848 Application 13/729,566 reagents/reagent solutions employed in such amplification reactions with an undesired nucleic acid molecule may result in a huge amount of false amplification products” (Spec. 12). “The present invention relates generally to methods and kits for removing contaminating nucleic acids from reagents or reagent solutions used in nucleic acid amplification reactions” (Spec. 1 8). The Claims Claims 6, 7, 9, 10, and 12—18 are on appeal.2 Claim 6 is representative and reads as follows: 6. A kit for DNA amplification comprising: (a) a decontaminated proofreading DNA polymerase; (b) a decontaminated exonuclease- resistant thioated primer, wherein the exonuclease-resistant thioated primer has at least one phosphorothioate linkages at 3’-terminal end of the primer sequence; and (c) an exonuclease, wherein the decontaminated proofreading DNA polymerase is generated by a method comprising the steps of: (a) providing a polymerase solution consisting essentially of a proofreading DNA polymerase that is contaminated with a contaminating nucleic acid; (b) contacting the polymerase solution with a divalent cation to form a polymerase-cation mixture; and (c) incubating the polymerase-cation mixture whereby the contaminating nucleic acid is rendered inert by the proofreading DNA polymerase to generate the decontaminated proofreading DNA polymerase, wherein the contacting and the incubating steps are performed in the absence of any substantial amount of free 2 Appellants state in the Appeal Brief that they “currently cancel claims 14 and 15” (App. Br. 5). However, 37 C.F.R. § 41.37(c)(2) states “A brief shall not include any new or non-admitted amendment.” We therefore treat these claims as pending and rejected. 2 Appeal 2016-002848 Application 13/729,566 nucleotides (dNTPs), and wherein the decontamination is performed in absence of an exonuclease or DNAse. The Issues A. The Examiner rejected claims 6, 7, 9, 10, and 12—17 under 35 U.S.C. § 103(a) as obvious over Jones,3 Tabor,4 and Lasken5 (Final Act. 4—8). B. The Examiner rejected claim 18 under 35 U.S.C. § 103(a) as obvious over Jones, Tabor, Lasken, and Steinman6 (Final Act. 8—10). Because the same issues and same prior art are dispositive for both of these rejections and because Appellants do not separately argue the limitations of claim 18, we will consider these rejections together. The Examiner finds “the methods of generating or manufacturing the components will not be considered during examination of the prior art. Therefore, the kits and compositions will only be examined based on the components themselves” (Ans. 4). The Examiner finds Jones teaches “a proofreading DNA polymerase, wherein the proofreading DNA polymerase comprises a Phi29 DNA polymerase”; “exonuclease-protected random hexamer primers”; and “a 5’ to 3 ’ exonuclease” (Ans. 4). The Examiner acknowledges that Jones “does not teach a kit comprising a decontaminated proofreading DNA polymerase, a decontaminated exonuclease-resistant thioated primer” {id. at 6). 3 Jones et al., US 2006/0073511 Al, published Apr. 6, 2006. 4 Tabor et al., US 2002/0172972 Al, published Nov. 21, 2002. 5 Lasken et al., US 2003/0207267 Al, published Nov. 6, 2003. 6 Steinman, C., US 5,516,292, issued May 14, 1996. 3 Appeal 2016-002848 Application 13/729,566 The Examiner finds Tabor teaches “a kit wherein the proofreading DNA polymerase and primers are a decontaminated proofreading DNA polymerase and primers” (id.). The Examiner finds Lasken teaches “modified primers that are resistant to degradation by exonuclease activity” where “the modified primers may comprise one or more phosphorothioate linkages between nucleotides at the 3 ’ end of the primer, including the 3’-terminal nucleotide” (id. at 7). The Examiner finds it obvious to “include reaction mixtures, reagents or solutions comprising the exonuclease-resistant primers in the methods for decontamination as taught by Tabor to remove any carry-over or contaminating nucleic acids without degrading the primers” (id. at 9). The issue with respect to this rejection is: Does the evidence of record support the Examiner’s conclusion that the prior art renders claim 6 obvious? Findings of Fact 1. Jones teaches “amplification of a collection of target sequences using two or more target specific primers and a DNA polymerase with a high processivity rate” (Jones 14). 2. Jones teaches in “one embodiment of the methods, the selected target sequences are then subjected to multiple strand displacement assay using a phi29 polymerase and exonuclease-protected random hexamer primers” (Jones 194). 3. The Specification teaches “the 3’—>5’ exonuclease activity of the Phi29 DNA polymerase” (Spec. 131). 4 Appeal 2016-002848 Application 13/729,566 4. Jones teaches “the primer is resistant to nuclease digestion because it contains phosphorothioate linkages” (Jones 19). 5. Jones teaches an “exonuclease that cleaves 5 ’ to 3 ’ but not 3 ’ to 5’” (Jones 193). 6. Tabor teaches “a method of amplifying DNA comprising (a) treating one or more reagent solutions with an enzyme in a manner to digest contaminating nucleic acids” (Tabor 116). 7. Tabor teaches treating one or more reagent solutions with an effective amount of a selectively activatable and/or inactivatable enzyme that is capable of digesting any contaminating nucleic acids, e.g. digesting any contaminating DNA and/or RNA. Preferably the reagent solutions are those commonly used to perform PCR including solutions comprising a DNA polymerase, one or more buffer solutions, one or more salt solutions, free nucleotides (dNTPs), primers, etc. (Tabor 1 62). 8. Tabor teaches “the use of 029 DNA polymerase and random hexamers to amplify small amounts of plasmid DNA. In a preferred embodiment, the methods described in this application would be used with these amplification procedures to remove contaminating DNA from the reaction mixture before adding the DNA to be amplified” (Tabor | 61). 9. Lasken teaches one can provide a premix, such as in the form of a kit, comprising a polymerase, even including more than one polymerase, a protected oligonucleotide primer, such as a hexamer, the required nucleoside triphosphates, an appropriate buffer, a pyrophosphatase, and other potentially desirable components, either with each such component in a separate vial 5 Appeal 2016-002848 Application 13/729,566 or mixed together in different combinations so as to form a total of one, two, three, or more separate vials (Lasken 126). 10. Lasken teaches “a kit for amplifying DNA sequences comprising nuclease-resistant random primers, a DNA polymerase and one or more dexoyribonucleoside triphosphates .... In a separate embodiment, said DNA polymerase has 3’-5’ exonuclease activity. In a preferred embodiment, said DNA polymerase is ^29 DNA polymerase” (Lasken 126). 11. Lasken teaches the primers contain at least one nucleotide that makes the primer resistant to degradation, commonly by an enzyme, especially by an exonuclease and most especially by 3 ’-5’- exonuclease activity. In such an embodiment, at least one nucleotide may be a phosphorothioate nucleotide or some modified nucleotide. Such nucleotide is commonly a 3 ’- terminal nucleotide (Lasken | 62). Principles of Law “The combination of familiar elements according to known methods is likely to be obvious when it does no more than yield predictable results.” KSRInt’l Co. v. Teleflex Inc., 550 U.S. 398, 416 (2007). “If aperson of ordinary skill can implement a predictable variation, § 103 likely bars its patentability.” Mat417. Analysis We adopt the Examiner’s findings of fact and reasoning regarding the scope and content of the prior art (Final Act. 4—10; FF 1—11) and agree that 6 Appeal 2016-002848 Application 13/729,566 claim 6 is rendered obvious by Jones, Tabor, and Lasken. We address Appellants’ arguments below. Appellants contend the Examiner’s rejection is improper because none of the references disclose, suggest or teach at least one of the structural elements of claims 6 and 7. None of them disclose or suggest a decontaminated exonuclease-resistant thioated primer having at least one phosphorothioate linkages at the 3’-terminal end of the primer sequence. (App. Br. 10). We find this argument unpersuasive because it fails to address the combination of Jones, Tabor, and Lasken. “Non-obviousness cannot be established by attacking references individually where the rejection is based upon the teachings of a combination of references.” In re Merck & Co., 800 F.2d 1091, 1097 (Fed. Cir. 1986). Here, Jones teaches an amplification process (FF 1) using three components: a proofreading phi29 DNA polymerase (FF 2) that inherently has 3’—>5’ exonuclease activity (FF 3); random hexamer primers that are exonuclease resistant (FF 2) and may include phosphorothioates (FF 4); and an exonuclease (FF 5). Tabor teaches decontamination of amplification reagents to eliminate background signals from contaminating nucleic acids (FF 6—7). Tabor specifically suggests decontamination of amplification reactions using phi29 polymerase and random hexamer primers (FF 8). Lasken teaches premix kits with amplification reagents including phi29 polymerases with 3’-5’ exonuclease activity, exonuclease resistant hexamer primers, and other components (FF 9—11). 7 Appeal 2016-002848 Application 13/729,566 We agree with the Examiner that the ordinary artisan, interested in performing the assay of Jones, would have formed a kit with the components used in Jones (FF 1—5) as suggested by Fasken (FF 9) and would have had good reason to decontaminate that kit as suggested by Tabor in order to reduce the impact of contaminating nucleic acids (FF 7; see Ans. 8). All three references suggest the use of the phi29 polymerase, with its 3’-5’ exonuclease activity (FF 2, 3, 8, 10), and we agree with the Examiner that because of the 3’-5’ exonuclease activity of phi29 polymerase, the ordinary artisan would follow Fasken’s suggestion to protect the primers from degradation because “primers comprising 3’-thioated linkages are resistant to exonuclease activity associated with a DNA polymerase having 3’-5’ exonuclease activity” (Ans. 17). Further, the ordinary artisan would follow Fasken’s suggestion that the location of the phosphorothioate “is commonly a 3 ’-terminal nucleotide (FF 11). That is, the ordinary artisan would have had reason to incorporate a 3 ’ terminal phosphorothioate into the hexamer primers taught by Jones, Tabor, and Fasken to protect the hexamer primers from the 3’-5’ exonuclease activity of the phi29 polymerase itself (see FF 10-11). Therefore, it is the combination of references that suggests a decontaminated exonuclease-resistant thioated primer having at least one phosphorothioate linkages at the 3’-terminal end of the primer sequence. Appellants contend “that Jones teaches away from the kits recited in claims 6 and 7. Jones discloses the use of primer sequences having phosphorothioate linkages at the 5’ end of the primer sequence. The objective of Jones’ methods is to remove the template DNA after the first 8 Appeal 2016-002848 Application 13/729,566 round of its amplification, without destroying the primer itself’ (App. Br. 10). While we agree that Jones does not wish to destroy the primer, we are not persuaded that Jones teaches away. Because Jones teaches the use of the phi29 polymerase that has a 3’-5’ exonuclease activity (FF 2), the ordinary artisan would have recognized that in order to prevent degradation of primers by the polymerase itself, exonuclease resistant nucleotides would need to be placed at the 3 ’ terminus (see FF 11). Thus, rather than teach away from the use of primers with a 3 ’ phosphorothioate, the use of the phi29 polymerase in Jones (FF 2), Tabor (FF 8), and Lasken (FF 10) provide a strong reason to incorporate a 3 ’ phosphorothioate into the hexamer primers in order that the primer is not digested by the 3 ’ to 5 ’ exonuclease activity of the phi29 polymerase {see FF 10—11). Appellants contend: A hypothetical combination of Jones with Tabor and Lasken, using decontaminated primers having phosphorothioate linkages at the 3’ terminal end would cause Jones’ methods to be inoperable. Upon employing a primer having a phosphorothioate linkage at the 3 ’ terminal end, along with an exonuclease that digests a nucleic acid sequence in 5 ’ to 3 ’ direction, would cause digestion of the primer itself. (App. Br. 10-11). We do not find this argument persuasive for the reasons already given. That is, to the extent that there is a concern over a 5 ’ to 3 ’ exonuclease in the process, there remains the same concern with the 3 ’ to 5 ’ exonuclease of the preferred phi29 polymerase. The obvious solution in that instance would be that the primers may include exonuclease resistant nucleotides at both the 5 ’ 9 Appeal 2016-002848 Application 13/729,566 and 3’ ends (see Ans. 19, “primers that may be modified at either the 5’- or 3’-terminus, or possibly both locations, depending on what the particular targets of choice may be as well as any post-amplification processing or downstream uses”). Appellants newly contend in the Reply Brief that “[i]t is a long felt need to amplify target DNA template at pictogram level without any artifacts, which is being addressed by the kits of independent claims 6 and 7 comprising, inter alia, the decontaminated exonuclease-resistant, thioated primer” (Reply Br. 2). We do not find this argument persuasive. Appellants’ argument of long felt need represents attorney argument without evidentiary basis. However, “attorney argument [is] not the kind of factual evidence that is required to rebut a prima facie case of obviousness.” In re Geisler, 116 F.3d 1465, 1470 (Fed. Cir. 1997). Moreover, Appellants do not establish the three elements necessary for long felt need: (i) the need must have been a persistent one that was recognized by ordinarily skilled artisans (ii) the long- felt need must not have been satisfied by another before Appellants’ invention; and (iii) the invention must, in fact, satisfy the long-felt need. In re Gershon, 372 F.2d 535, 538 (CCPA 1967); Newell Companies, Inc. v. Kenney Mfg. Co., 864 F.2d 757, 768 (Fed. Cir. 1988); In re Cavanagh, 436 F.2d 491,496 (CCPA 1971). Conclusion of Law The evidence of record supports the Examiner’s conclusion that the prior art renders claim 6 obvious. 10 Appeal 2016-002848 Application 13/729,566 SUMMARY In summary, we affirm the rejection of claim 6 under 35 U.S.C. § 103(a) as obvious over Jones, Tabor, and Lasken. Claims 7, 9, 10, and 12— 17 fall with claim 6. We affirm the rejection of claim 18 under 35 U.S.C. § 103(a) as obvious over Jones, Tabor, Lasken, and Steinman. 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 11 Copy with citationCopy as parenthetical citation