Ex Parte Nelson et al

Patent Trial and Appeal Board

May 3, 2017

13729566 (P.T.A.B. May. 3, 2017)

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.
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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.
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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).
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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
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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
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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).
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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
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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 ’
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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.
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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
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