Ex Parte Nelson et al

Patent Trial and Appeal Board

Sep 15, 2017

13330745 (P.T.A.B. Sep. 15, 2017)

United States Patent and Trademark Office
UNITED STATES DEPARTMENT OF COMMERCE
United States Patent and Trademark Office
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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.
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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”).
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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.”).
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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.
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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.
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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.
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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
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