Ex Parte Nelson et alDownload PDFPatent Trial and Appeal BoardSep 15, 201713330745 (P.T.A.B. Sep. 15, 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. 13/330,745 12/20/2011 John Richard Nelson 204091-4 5969 6147 7590 09/19/2017 GENERAL ELECTRIC COMPANY GPO/GLOBAL RESEARCH 901 Main Avenue 3rd Floor Norwalk, CT 06851 EXAMINER CHUNDURU, SURYAPRABHA ART UNIT PAPER NUMBER 1637 NOTIFICATION DATE DELIVERY MODE 09/19/2017 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, CARL WILLIAMS FULLER, GREGORY ANDREW GROSSMANN, and ANURADHA SEKHER1 Appeal 2016-005977 Application 13/330,745 Technology Center 1600 Before: JEFFREY N. FREDMAN, BRIAN P. MURPHY, and DEVON ZASTROW NEWMAN, Administrative Patent Judges. NEWMAN, Administrative Patent Judge. DECISION ON APPEAL This appeal under 35 U.S.C. § 134 involves claims to methods for producing at least one amplicon based on a target DNA. The Examiner entered final rejections for obviousness. We have jurisdiction under 35 U.S.C. § 6(b). We REVERSE. 1 Appellants identify the Real Party in Interest as General Electric Company. App. Br. 2. Appeal 2016-005977 Application 13/330,745 STATEMENT OF THE CASE Background The Specification teaches regarding “the synthesis of DNA using DNA polymerase.” Spec. 1 56. DNA polymerases use nucleoside triphosphates to add nucleotides to the 3 ’ end of a primer based on a template strand of DNA in a complementary fashion, creating a new DNA strand complementary to the original. The product may be single stranded or double-stranded DNA, often extending to the end of the template strand. Endonuclease V is a nuclease that specifically nicks DNA two nucleotides 3’ of an inosine nucleotide, when the target DNA is double stranded the nick occurs in the same strand as the inosine. The endonuclease, in combination with a strand displacing DNA polymerase and a primer produces targeted DNA amplification. First, the DNA polymerase extends the primer, creating a nicking site for the nuclease. Nicking creates an initiation site for the DNA polymerase, displacing a single-stranded DNA product while it re-creates the double-stranded primer extension product. The cycle repeats, synthesizing multiple single strands of DNA complementary to the downstream portion of the template. Id. The Specification discloses: methods for synthesizing nucleic acid sequences by introducing an inosine into a specific position of a target DNA using, for example, an oligonucleotide primer, followed by application of a polymerase and an endonuclease V to nick the DNA and a polymerase to repeatedly make the compl[e]ment of the target DNA strand. Id. 155. 2 Appeal 2016-005977 Application 13/330,745 The Claims Claims 1, 2, 4-7, 9, 12, 13, 18, 19, 22, 24, 27-29, 31-36, and 39-52 are on appeal. Final Act. 2; see also App. Br. 4. Claim 1 below is illustrative and reads as follows: 1. A method of producing at least one amplicon based on a target DNA comprising: (a) providing the target DNA; (b) annealing at least one ino sine-containing primer to the target DNA to create a target DNA:primer hybrid; (c) nicking the inosine-containing primer in the target DNA:primer hybrid at a residue 3 ’ to the inosine residue using a mutant endonuclease V; and (d) extending the nicked inosine-containing primer via a nucleic acid amplification reaction to produce at least one amplicon complementary to at least one portion of the target DNA; wherein extending the nicked inosine-containing primer uses a dNTP mixture which is devoid of deoxyinosine triphosphate. App. Br. 14 (Claims Appendix). Appellants seek our review of the Examiner’s rejection of claims 1, 2, 4-7, 9, 12, 13, 18, 19, 22, 24, 27-29, 31-36, and 39-52 under 35 U.S.C. § 103(a) as obvious over Walker,2 in view of Barany.3 Final Act. 3. 2 Walker et al., US 2005/0026147 Al, published February 3, 2005 (“Walker”). 3 Barany et al., US 7,198,894 B2, issued April 3, 2007 (“Barany”). 3 Appeal 2016-005977 Application 13/330,745 DISCUSSION In rejecting the claims, the Examiner finds that Walker discloses a method meeting most of the limitations of claim 1, except that it does not “specifically teach a mutant endonuclease V or mutant endonuclease V comprising the sequence of SEQ ID No. 2 or 3 or conservative variants thereof and PCR additives such as albumin and reducing agent.” Ans. 2-4. The Examiner further finds that “Walker [Jdiscloses an endonuclease (DNA- N-glycosylase) which recognizes abasic sites (inosine containing bases) in a duplex DNA and nicks the DNA to form a nicked DNA, which is extended by a DNA polymerase.” Advisory Act. 2.4 The Examiner finds that Barany discloses a method comprising a conservative variant of endonuclease V comprising SEQ ID. 2 or 3 and its use in nicking or cleaving heteroduplex DNA and detecting sequence variations in a target nucleic acid sample. Id. The Examiner concludes that it would have been obvious to use a mutant endonuclease V as taught in Barany in the method of Walker “to achieve expected advantage of developing an improved sensitive reaction mixture for amplification of a target nucleic acid” because Barany teaches the mutant endonuclease “preferentially nicks or cleaves at least one heteroduplex DNA containing mismatched bases, better than a wild-type endonuclease V.” Final Act. 4—5. Issue The issue in this case is whether a preponderance of the evidence of record supports the Examiner’s findings that Walker and Barany suggest the 4 Advisory Action, mailed March 25, 2015 (“Advisory Act.”). 4 Appeal 2016-005977 Application 13/330,745 claimed invention. We select claim 1 as representative of the claims subject to this ground of rejection. 37 C.F.R. § 41.37(c)(l)(iv). Analysis Appellants argue, among other points, that “neither Walker nor Barany teach the step of extending the nicked inosine-containing primer recited in claim 1.” App. Br. 9. Appellants argue “Walker specifically teaches that a DNA polymerase extends a DNA strand from which an abasic site is cleaved off” which is essential to Walker’s “methods for repair and amplification of damaged DNA.” Id. at 11. Appellants argue that Walker does not disclose the claimed method in which “the inosine residue is retained in the primer even after the nicking reaction, and the DNA polymerase extends the nicked inosine-containing primer.” Id. Rather, Appellants argue, “[i]f the inosine residue is cleaved off in a manner suggested by Walker, the methods recited in independent claim[ 11 would be rendered inoperable because once the inosine residue is cleaved off at the first nicking step, the steps of extension and nicking cannot repeat.” Id. The Examiner responds that Walker teaches use of a blend of DNA repair enzyme (nicking enzyme) to nick or produce an overhang at the abasic site of target DNA:primer duplex and a DNA polymerase to extend the nicked primer (see at least page 2-3, para 0024 and 0029, page 8, para 0073-0075) as opposed to the assertions drawn to polymerase cleaving off the abasic site. [The cited portions disclose] a method comprising: forming a mixture comprising [an] effective amount of DNA, enzyme blend (DNA repair enzyme and DNA polymerase) dNTPs and a pair of primers wherein the primers are substantially complementary to segments of DNA and having thiophosphate linkages, incubating the mixture and amplifying the DNA. Ans. 5—6. 5 Appeal 2016-005977 Application 13/330,745 In reply, Appellants argue that “Walker does not teach nicking an inosine-containing primer at a residue 3 ’ to the inosine residue and extending the nicked primer as recited in independent claim[ 1].” Reply Br. 2.5 Rather, Appellants argue, “Walker employs an AP endonuclease that cleaves a DNA phosphodiester backbone at a residue 5’ to the abasic sites.” Id. We agree with Appellants that the Examiner has not shown that the claimed process would have been obvious based on Walker and Barany. Claim 1 requires “nicking the inosine-containing primer in the target DNA:primer hybrid at a residue 3 ’ to the inosine residue using a mutant endonuclease V.” Walker discloses a method for amplification of DNA that is damaged, undamaged, or suspected of being damaged comprising: a) forming a mixture comprising the DNA, an effective amount of the Enzyme Blend of the present invention, deoxynucleoside 5 ’ triphosphates, and a pair of oligonucleotide primers, wherein the pair of oligonucleotide primers is substantially complementary to segments of the DNA[.] Walker 124. Amplification is achieved through “a) forming a mixture comprising the DNA, an effective amount of a DNA polymerase, deoxynucleoside 5 ’ triphosphates, and a pair of oligonucleotide primers having thiophosphate linkages, wherein the pair of primers is substantially complementary to segments of the DNA; b) denaturing the DNA; and c) amplifying the DNA.” Id. 129. Walker discloses that “[t]he oligonucleotide primer may be ‘substantially complementary’ to the DNA template, such that the extension product synthesized from one primer, [and 5 Appellants’ Reply Brief is not paginated. Herein we refer to the Reply Brief as if numbered consecutively starting on the title page. 6 Appeal 2016-005977 Application 13/330,745 that a] person of ordinary skill in the art will appreciate that some oligonucleotide primer[s] may contain degenerate nucleotides. A non limiting example of a degenerate nucleotide is inosine.” Id. 1 53. Barany discloses: a thermostable endonuclease [that] preferentially nicks or cleaves at least one heteroduplex formed for any single base mutation or polymorphism . . . and generates ends which are suitable for ligation when nicking perfectly matched DNA [or] preferentially nicks or cleaves heteroduplexed DNA, contains one, two, and three base insertions or deletions, at a location where the base pairs are mismatched or one base beyond the unpaired bases, and generates ends which are suitable for ligation when nicking DNA at perfect matched DNA. Barany 20:5—28. Barany further discloses examples of cleavage of deoxyinosine-containing oligonucleotides using the mutant endonuclease V. See, e.g., id. at 24:25—25:38 and Figure 1, (Disclosing that Endonuclease V will “[preferentially nick DNA one base to the 3’ side of mismatches.”). We agree with the Examiner that, in light of the teachings of Barany, the skilled artisan would have known that mutant endonuclease V could be used to nick DNA containing inosine in the 3’ position of a double-stranded DNA. However, “[o]bviousness requires more than a mere showing that the prior art includes separate references covering each separate limitation in a claim under examination.” Unigene Labs., Inc. v. Apotex, Inc., 655 F.3d 1352, 1360 (Fed. Cir. 2011). “Rather, obviousness requires the additional showing that a person of ordinary skill at the time of the invention would have selected and combined those prior art elements in the normal course of research and development to yield the claimed invention.” Id. 7 Appeal 2016-005977 Application 13/330,745 We are not persuaded by the Examiner’s stated motivation for combining the references. Although Barany does teach efficient cleavage at inosine sites, Barany uses the method for the purpose of detecting mismatches in DNA, generating ends that are suitable for ligating to repair the DNA, and identifying mutant nucleic acid sequences. Barany 4:36—8:17. Barany discloses that “[a] further aspect of the present invention is directed to a mutant endonuclease V which preferentially nicks or cleaves at least one heteroduplexed DNA, containing mismatched bases, better than a wild-type endonuclease V,” (Barany 7:3—6), but Barany does not suggest use of the mutant endonuclease V for any purpose other than those discussed above. Hence, we find that the Examiner has not provided an adequate basis for concluding that the skilled artisan would have found it obvious to use the mutant endonuclease V of Barany in the method of Walker, to nick an inosine-containing primer for the purpose of amplifying DNA by DNA extension. “An examiner bears the initial burden of presenting a prima facie case of obviousness.” In re Huai-Hung Kao, 639 F.3d 1057, 1066 (Fed. Cir. 2011). Because that burden has not been carried here, we reverse the rejection of claims 1, 2, 4—7, 9, 12, 13, 18, 19, 22, 24, 27—29, 31—36, and 39-52 under 35 U.S.C. § 103(a). SUMMARY We reverse the rejection of claims 1, 2, 4—7, 9, 12, 13, 18, 19, 22, 24, 27-29, 31-36, and 39-52 under 35 U.S.C. § 103(a). REVERSED 8 Copy with citationCopy as parenthetical citation