Ex Parte Duthie et al

Patent Trial and Appeal Board

Jan 26, 2018

13965696 (P.T.A.B. Jan. 26, 2018)

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.
13/965,696 08/13/2013 Robert Scott Duthie 259103-1 9415
6147 7590 01/30/2018
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
01/30/2018 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 ROBERT SCOTT DUTHIE,
JOHN RICHARD NELSON, and ANURADHA SEKHER1
Appeal 2017-000871
Application 13/965,696
Technology Center 1600
Before RICHARD M. LEBOVITZ, JOHN G. NEW, and
ROBERT A. POLLOCK, Administrative Patent Judges.
NEW, Administrative Patent Judge.
DECISION ON APPEAL
appellant states that the real party-in-interest is the General Electric
Company. App. Br. 2.
Appeal 2017-000871
Application 13/965,696
SUMMARY
Appellants file this appeal under 35 U.S.C. § 134(a) from the
Examiner’s Final Rejection of claims 1—3, 5—9, and 12—16 as unpatentable
under 35 U.S.C. § 102(b) as being anticipated by McCarthy et al. (US
2004/0067559 Al, April 8, 2004) (“McCarthy”).2’3
We have jurisdiction under 35 U.S.C. § 6(b).
We AFFIRM.
NATURE OF THE CFAIMED INVENTION
Appellants’ claimed invention is directed to methods for an
endonuclease-assisted DNA amplification reaction using decontaminated
primer solutions that are pre-treated with a nuclease. Abstract.
REPRESENTATIVE CLAIM
Claim 1 is representative of the claims on appeal and recites:
1. A method of producing at least one amplicon based on a
target DNA comprising:
providing the target DNA;
2 The Examiner’s Final Rejection was of claims 1—3 and 5—16. Final Act. 2.
The Examiner has withdrawn the rejection of claims 10 and 11 as moot.
See Adv. Action, September 24, 2015. Claims 4 and 17—22 are canceled.
See Final Act. 2.
3 Appellants state that the Examiner’s additional rejection of claims 1—16 as
unpatentable under the judicially-created doctrine of obviousness-type
double patenting over claims 1—2, 4—7, 9, 12—13, 18—19, 22, 24, 27—29,
31—36, and 39-52 of Appellants’ co-pending Application US. Ser.
No. 13/330,745 is not at issue in the present Appeal. App. Br. 4. We
consequently summarily affirm the Examiner’s rejection on this ground.
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Application 13/965,696
providing a primer solution comprising at least one
exonuclease-resistant, inosine-containing primer;
decontaminating the primer solution by treating the primer
solution with an exonuclease to remove any contaminating
nucleic acids to generate a decontaminated primer solution;
generating a DNA amplification reaction mixture by
mixing together the target DNA, the decontaminated primer
solution, at least one 5'—>3' exonuclease-deficient DNA
polymerase having a strand displacement activity, and at least
one endonuclease that is capable of nicking an inosine-
containing strand of a double stranded DNA at a residue 3' to an
inosine residue; and
incubating the DNA amplification reaction mixture to
amplify at least one portion of the target DNA using the at least
one exonuclease-resistant, inosine-containing primer to produce
the at least one amplicon.
App. Br. 12.
ISSUES AND ANALYSES
We adopt the Examiner’s findings of fact and conclusion that the
appealed claims are anticipated by the cited prior art. We address the
arguments raised by Appellants below.
Issue 1
Appellants argues that the Examiner erred because McCarthy fails to
disclose “decontaminating” the primer solution as recited in claim 1 or
“treating” the primer solution as recited in independent claim 15. App. Br.
9.
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Application 13/965,696
Analysis
The Examiner finds McCarthy discloses treating the primer with
nucleases, including exonuclease, to unblock or create a free 3' OH, which
can be extendable in a DNA amplification reaction. Final Act. 2. The
Examiner also finds McCarthy discloses cleaving the abasic4 site after each
amplification cycle to convert the displaced template to a primer for
subsequent amplification cycles. Id. The Examiner finds McCarthy
therefore discloses that the primer is treated prior to amplification by an
exonuclease, as required by Appellants’ claims on appeal. Id.
Appellants point to the limitations of claim 1 and 15 reciting,
respectively, “decontaminating the primer solution by treating the primer
solution with an exonuclease to remove any contaminating nucleic acids to
generate a decontaminated primer solution” (claim 1) and “providing a
primer solution consisting essentially of an exonuclease-resistant, inosine-
containing primer” and “treating the primer solution with an exonuclease to
remove any contaminating nucleic acids from the primer solution.” App. Br.
6. According to Appellants, their Specification discloses that such
decontamination may include removal of prior amplicons or undesired
nucleic acids, and is performed “prior to adding a target DNA.” Id. (citing
Spec. 117). In this manner, Appellants contend, unwanted nucleic acids are
prevented from serving as primers during amplification. Id.
Appellants contend that the Examiner has relied upon paragraphs
[0116]—[0131] and, specifically, paragraph [0128] of McCarthy, as
4 That is, a site in a sequence from which the nucleotide base has been
excised. See, e.g., McCarthy 122.
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Application 13/965,696
anticipating these limitations of the claims. App. Br. 6—7 (citing Final Act.
2). However, Appellants assert, insofar as McCarthy discloses treatment of
double-stranded nucleic acids with any exonucleases, such treatment is not
treating or decontaminating the primer solution, as required by the claims.
Id. at 7. Appellants contend that a person of ordinary skill in the art would
have understood that primers are single-stranded oligonucleotides that
hybridize to complementary sequences to initiate amplification reactions.
Id. According to Appellants, this definition is consistent with the
Specification, which discloses that “the term ‘primer’ refers to refers to a
short linear oligonucleotide that hybridizes to a target nucleic acid
sequence.” Id. (quoting Spec. 120). Appellants argue that, in contrast,
McCarthy discloses that the exonuclease treatment is specific for double
stranded nucleic acids that are already bound to the target and incorporated
into amplicons and are not part of a “primer solution” as recited in the
claims. Id.
Furthermore, argue Appellants, even if the reaction taught by
McCarthy could be considered as being performed on a primer solution,
McCarthy fails to disclose any treating or decontaminating “to remove any
contaminating nucleic acids.” App. Br. 7. Appellants contend that there is
no disclosure by McCarthy that the disclosed exonuclease “removes” any
contaminating nucleic acids. Id. Rather, Appellants assert, the exonuclease
treatment step results in “enabling the cleaved DNA to function as an IP
[initiating primer] in a GMA [glycosylate-mediated amplification],” i.e., the
exonuclease treatment results in the release of additional sequences formed
from downstream displaced strands. Id. Appellants argue that McCarthy
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Application 13/965,696
discloses that the exonuclease treatment creates new primers in the
amplification mix rather than deactivating or decontaminating as recited. Id.
The Examiner responds that the decontaminating step recited in the
claims require an exonuclease step and McCarthy discloses a primer
extension template comprising a modified precursor (inosine) as a primer,
and treating the primer extension template comprising inosine with an
exonuclease. Ans. 4. The Examiner finds this disclosure is within the scope
of the claims because the instant dependent claim 14 requires a primer
comprising an extender template. Id. (citing McCarthy H 51—52, 65). The
Examiner finds that McCarthy discloses incorporating the modified inosine
precursor into the target and that the primer extension product comprises that
modified precursor, which acts as a primer in the next round of
amplification. Id. Therefore, the Examiner finds, the primer extension
product containing the modified inosine precursor is interpreted to mean a
primer comprising inosine, which is decontaminated in the next cycle of
amplification by the activity of exonuclease which cleaves the primer
extension template at the modified precursor, inosine base. Id. (citing
McCarthy 11 128, 142).
The Examiner therefore finds that the recited decontamination step
requiring treatment with an exonuclease is taught by McCarthy because the
primer recited in the claims reads on the primer extension template (as
recited in dependent claim 14 and, further, McCarthy discloses treating the
primer extension template with an exonuclease or T7 gene 6 exonuclease.
Id.
We are not persuaded by Appellants’ arguments. We agree with
Appellants’ contention that the limitation of claim 1 reciting
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Application 13/965,696
“decontaminating the primer solution by treating the primer solution with an
exonuclease to remove any contaminating nucleic acids to generate a
decontaminated primer solution” and its corresponding “treating” step in
claim 15 would be understood by a person of ordinary skill in the art to
necessarily precede the step of “generating a DNA amplification reaction
mixture” because the plain language of the claims requires that the latter
mixture contain the “decontaminated primer solution” recited in the
preceding step.
Moreover, we are not persuaded by the Examiner’s finding that “the
primer extension product comprising modified precursor, inosine, was
interpreted as a primer comprising inosine, which is decontaminated in the
next cycle of amplification by the activity of exonuclease which cleaves the
primer extension template at the modified precursor, inosine base.” Ans. 4.
We think that this reflects a misreading by the Examiner of the disclosures
of McCarthy, in which the cleavage at the inosine base corresponds to step ii
of the method taught by McCarthy, which occurs after the primer has been
annealed to the corresponding target DNA. See McCarthy || 32—36.5
Furthermore, the excision of the inosine base, which is contained within the
primer sequence, would require the use of an ewJonuclease rather than an
exonuclease, as recited in the claims.
5 Paragraphs [0032]—[0036] of McCarthy disclose that the substituted base is
uracil and is excised by DNA glycosylase. See also McCarthy Fig. 1.
However, McCarthy also discloses that: “[I]t will be appreciated by those
skilled in the art that other modified nucleic acid precursors can also be
used, such as dITP [deoxyinosine triphosphate] and 8-OH dGTP. Id. at |
51. McCarthy thus discloses that inosine can be a substitute base.
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Application 13/965,696
However, McCarthy also discloses the generation of an initiating
primer (“IP”)
from a naturally occurring or amplified nucleic acid by full or
partial enzymatic or chemical cleavage with DNA or RNA
cleaving agents such as DNAses, RNAses, restriction
endonucleases, DNA glycosylases following conversion of a
normal DNA base to a glycosylase substrate base [or inosine] or
incorporation of such a base during amplification
A double stranded nucleic acid may be cleaved to expose
its free 3 'OH terminus enabling the cleaved DNA to function as
an IP in a GMA. For example, a double stranded DNA may be
denatured by heat. Alternately, it may be treated with the T7 gene
6 exonuclease which hydrolyses duplex DNA in a stepwise non-
processive reaction from the 5' termini. The enzyme is not active
on single stranded DNA and thus stops when duplex regions are
no longer present.
McCarthy 1 124, 128. In these passages, McCarty discloses the preparation
of an initiating primer (“IP”) corresponding to Appellants’ inosine-
containing “exonuclease-resistant, inosine-containing primer.” Specifically,
McCarthy discloses that the primer may be constructed by using an
exonuclease to remove the excess double-stranded nucleic acid leaving the
modified primer.
Appellants’ Specification does not explicitly provide a definition of
the claim term “decontaminate.” However, the Specification does provide
examples of what is meant by that term. Paragraph [0007] of the
Specification, for instance, discloses: “Before generating the DNA
amplification mixture, the primer solution, which may further include other
nucleic acid amplification reagents (e.g., dNTPs, buffers, accessory proteins)
may be decontaminated by treating with at least one exonuclease to remove
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Application 13/965,696
any contaminating nucleic acid.” The Specification further discloses that
“The DNA amplification assays described herein further employ an
exonuclease-resistant primer that comprises at least one inosine residue.
The exonuclease-resistant primer solution may be decontaminated prior to
the DNA amplification reaction by treating it with an appropriate
exonuclease.” Spec. 128. Other disclosures of the Specification are, in this
respect, similar. See, e.g., Spec. H 31, 39, 43.
In the absence of an express definition of the claim term, we adopt the
broadest reasonable definition of the term consistent with Appellants’
Specification. See In re Am. Acad. ofSci. Tech Ctr., 367 F.3d 1359, 1364
(Fed. Cir. 2004). McCarthy discloses that, in the preparation of an IP, and
prior to mixing the primer with the target DNA, an IP may be constructed by
using an exonuclease to remove the unwanted double-stranded nucleic acid.
McCarthy 1 124, 128. Employing the broadest reasonable interpretation of
the term “decontaminate,” we find that McCarthy thus discloses removing,
i.e., decontaminating, the unwanted nucleic acid prior to annealing it to the
target DNA. We consequently find that McCarthy discloses the disputed
limitations of claims 1 and 15.
Issue 2
Appellants argue that the Examiner erred in finding that McCarthy
discloses “treating” a primer solution “consisting essentially of an
exonuclease-resistant inosine-containing primer,” as recited in claim 15.
Analysis
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Application 13/965,696
Appellants contend that McCarthy does not disclose any treatment of
a primer solution with any exonucleases. App. Br. 8. According to
Appellants, McCarthy discloses that the exonuclease is contacted with a
double-stranded nucleic acid, indicating that the primer is bound to the target
and, therefore, because the target is present in the reaction, the primer
solution cannot consist essentially of the recited primer. Id.
We are not persuaded. As we have explained, supra, McCarthy
discloses that an IP may be constructed by treating double-stranded DNA
with an exonuclease to remove the unwanted double-stranded nucleic acid.
McCarthy H 24, 28. The primer is thus synthesized prior to mixing it with,
inter alia, the target DNA to make the functioning amplicon, contrary to
Appellants’ arguments.
Issue 3
Appellants argue that the Examiner erred in interpreting claim 15’s
use of the transitional phrase “consisting essentially of “an exonuclease-
resistant inosine-containing primer as being open-ended. App. Br. 8.
Analysis
Appellants argue that the transitional phrase “consisting essentially
of” limits the scope of a claim to the specified materials or steps “and those
that do not materially affect the basic and novel characteristic(s)” of the
claimed invention. App. Br. 8 (quoting In re Herz, 537 F.2d 549, 551-52
(C.C.P.A. 1976) (emphasis in original)).
According to Appellants, the Examiner has failed to provide any
analysis of whether the additional components in the cited reference (i.e.,
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Application 13/965,696
McCarthy’s target and displaced DNA), would materially affect the basic
and novel characteristics of “an exonuclease-resistant, inosine-containing
primer.” App. Br. 8—9. Appellants argue further that their Specification
discloses repeatedly that decontamination of the primer solution (i.e., to
degrade or remove other components) occurs “[bjefore generating the DNA
amplification mixture, the primer solution, may be decontaminated by
treating the primer solution with an appropriate exonuclease to remove any
contaminating nucleic acid.” Id. at 9 (quoting Spec. 131). Appellants
analogize the claimed primer solution to a decontaminated primer solution,
i.e., a primer solution that does not include contaminating nucleic acid.
Therefore, Appellants argue, the presence of McCarthy’s elements would
materially affect the novel characteristics of the claimed primer by
permitting contaminating DNA to be introduced into the amplification. Id.
We disagree. As we have explained, McCarthy discloses the use of an
exonuclease to remove unwanted double-strand nucleic acid in the
construction of the IP prior to combination with the target DNA. See
McCarthy 128. We therefore do not accept Appellants’ interpretation that
McCarthy teaches use of an exonuclease to remove unwanted DNA only
after combination of the primer with the target DNA. We consequently
affirm the Examiner’s rejection of the claims.
Issue 4
Appellants also argue dependent claims 7—9 separately. App. Br. 9.
Claim 7 is exemplary and recites: “The method of claim 1, wherein the
inosine residue of the nuclease-resistant, inosine-containing primer is located
at least 4 nucleotides downstream of the 5' terminal nucleotide.” Id. at 13.
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Appellants argue that the Examiner erred because McCarthy fails to disclose
this limitation. Id. at 9.
Analysis
Appellants note that the Examiner relies upon paragraph [0167] of
McCarthy as disclosing this measure. App. Br. 9. According to Appellants,
the Examiner has pointed to the cleavage and extension of the abasic distal
end as being analogous to the recited inosine location. Id. (citing Advisory
Act. 2, September 24, 2015).
Appellants contend that the recited primer of claim 7 is
decontaminated and then placed on the target DNA. App. Br. 10.
Therefore, Appellants argue, the Examiner cannot rely on strand
displacement and primer extension as disclosing the recited primer but,
rather, must point out where McCarthy discloses a primer that includes an
inosine “located at least 4 nucleotides downstream of the 5' terminal
nucleotide” can be found. Id.
The Examiner responds that claim 7 requires an inosine residue
located at least 4 nucleotides downstream of the 5' terminal nucleotide,
which indicates that the inosine is located anywhere downstream towards 3'
end of the primer, since the claim does not specify the upper limit of the
position. Ans. 5-6. The Examiner finds McCarthy’s primer comprises an
inosine incorporated at or around 3' end. Id. (citing McCarthy 1123). The
Examiner points to paragraph [0167] of McCarthy, which indicates that the
primer in Figure 1, in which the incorporated modified precursor is
recognized by a cleavage enzyme that specifically cleaves phosphodiester
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Application 13/965,696
bond 5' of the abasic site, or distal to phosphate moiety, and generates
upstream fragments having a 3' terminus with a free 3'OH group that can be
extendable by a DNA polymerase. Id. The Examiner finds this disclosure
indicates that the primer comprises a modified precursor that is located at or
near the 3 '-end. Id.
We are not persuaded by Appellants’ arguments. Paragraph [0167] of
McCarthy discloses that:
The method according to the invention was used to cyclically
extend a 25-mer oligonucleotide (Initiating Primer-IP), which
was complementary to a region of an 80-mer oligonucleotide
(Template nucleic acid) which served as the template for the
polymerisation reaction. The complementary region extended
from 10 bases from the 3' end of the 80-mer to 35 bases from the
3' end of the 80-mer.
McCarthy thus discloses a 25-mer (i.e., 25 base) primer with the with the
substituted inosine residue located at the 3' end. See also McCarthy Fig. 1,6
As such, the inosine residue disclosed by McCarthy is necessarily “at least 4
nucleotides downstream of the 5' terminal nucleotide,” as recited in claim 7.
We consequently affirm the Examiner’s rejection.
DECISION
The Examiner’s rejection of claims claims 1—3, 5—9, and 12—16 as
unpatentable under 35 U.S.C. § 102(b) over McCarthy is affirmed.
6 See fii.5
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No time period for taking any subsequent action in connection with
this appeal may be extended under 37 C.F.R. § 1.136(a)(1). See 37 C.F.R.
§ 1.136(a)(l)(iv).
AFFIRMED
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