Ex Parte WHITMAN et al

Patent Trials and Appeals Board

May 30, 2019

14270785 - (D) (P.T.A.B. May. 30, 2019)

UNITED STA TES p A TENT AND TRADEMARK OFFICE
APPLICATION NO. FILING DATE FIRST NAMED INVENTOR
14/270,785 05/06/2014 Douglas F. WHITMAN
108120 7590 06/03/2019
Parker Highlander PLLC
1120 S. Capital of Texas Hwy
Bldg 1, Suite 200
Austin, TX 78746
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
ATTORNEY DOCKET NO. CONFIRMATION NO.
LUMN.P0036US.D1 2525
EXAMINER
CHUNDURU, SURYAPRABHA
ART UNIT PAPER NUMBER
1637
NOTIFICATION DATE DELIVERY MODE
06/03/2019 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):
docket@phiplaw.com
PTOL-90A (Rev. 04/07)
UNITED STATES PATENT AND TRADEMARK OFFICE
BEFORE THE PATENT TRIAL AND APPEAL BOARD
Ex parte DOUGLAS F. WHITMAN and HONGWEI ZHANG 1
Appeal2018-003489
Application 14/270, 785
Technology Center 1600
Before DEBORAH KATZ, ULRIKE W. JENKS, and
JOHN G. NEW, Administrative Patent Judges.
Opinion for the Board filed by Administrative Patent Judge NEW.
Opinion Concurring filed by Administrative Patent Judge KATZ.
NEW, Administrative Patent Judge.
DECISION ON APPEAL
1 Appellants identify the real party-in-interest as Luminex Corp. App. Br. 3.
Appeal2018-003489
Application 14/270, 785
SUMMARY
Appellants file this Appeal under 35 U.S.C. § I34(a) from the
Examiner's Final Rejection of claims 56-61 and 67-78. Specifically, claims
74, 76, and 77 stand rejected as unpatentable under 35 U.S.C. § I02(b) as
being anticipated by Mast et al. (US 2004/0203035 Al, October 14, 2004)
("Mast").
Claims 55---61 and 67-78 as unpatentable under 35 U.S.C. § I03(a) as
being obvious over the combination of Mast and Collier et al. (WO
2006/071770 A2, July 6, 2006) ("Collier"). 2
We have jurisdiction under 35 U.S.C. § 6(b).
We REVERSE.
NATURE OF THE CLAIMED INVENTION
Appellants' invention is directed to a method for detecting a target
nucleic acid using a probe that includes a target-specific primer sequence, an
anti-tag sequence, a tag sequence, and a blocker between the anti-tag
sequence and tag sequence. Spec. Abstr.
REPRESENTATIVE CLAIM
Claim 74 is representative of the claims on appeal and recites:
74. A method for detecting a target nucleic acid comprising:
(a) hybridizing a first oligonucleotide probe to a target nucleic
acid, the first oligonucleotide probe comprising a hybridizing
region that is complementary to at least a portion of the target
2 Claims 1-54 and 62-66 are cancelled. App. Br. 3.
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Application 14/270, 785
nucleic acid and a non-hybridizing region that 1s not
complementary to the target nucleic acid;
(b) cleaving the non-hybridizing region from the first
oligonucleotide probe to form a cleavage product;
( c) hybridizing the cleavage product to a second oligonucleotide
probe, the second oligonucleotide probe comprising, in a 3' to
5' direction, a hybridizing region that is complementary to the
cleavage product and a non-hybridizing region that is not
complementary to the cleavage product;
( d) extending the cleavage product along the second
oligonucleotide probe to form an amplicon; and
( e) detecting the target nucleic acid by detecting the amplicon.
App. Br. 11.
ISSUES AND ANALYSIS
We decline to adopt the Examiner's findings, reasoning, and
conclusion that the claims are primafacie anticipated and/or obvious over
the cited prior art. We address below the arguments raised by Appellants.
A. Rejection of claims 74, 76, and 77 under 35 U.S.C. § 102(b)
Issue
Appellants argue that the Examiner erred in concluding Mast
discloses Appellants' method for detecting a target nucleic acid. See App.
Br. 6.
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Application 14/270, 785
Analysis
The Examiner finds Mast discloses a method of:
(a) hybridizing a first oligonucleotide probe comprising a non-
complementary flap region (WT probe) and a target
complementary region;
(b) cleaving the non-hybridizing region with a nuclease;
( c) hybridizing a second oligonucleotide probe (FRET cassette) with
the cleavage product; and
( d) detecting the cleavage product.
Ans. 6-7 (citing Mast ,r,r 110-111, Fig. 1). The Examiner finds that Mast
teaches "extending the cleavage product by polymerase chain reaction or
rolling circle amplification (isothermal amplification) and detecting the
amplicon." Id. at 7 (citing Mast ,r,r 16, 110). The Examiner finds "[t]he
broad[] scope of 'extending' as presented in the claims read[s] on [the]
detection step comprising polymerase chain reaction, rolling circle
amplification (isothermal amplification), cycling probe assays, ARMS
assays, [and] sequencing." Id. (citing Mast ,r 16). The Examiner further
finds that Mast teaches: "the cleavage agent is a 5' nuclease that comprises a
polymerase and the detection step includes polymerase chain reaction." Id.
( citing Mast 20, claims 14--23, 29). Therefore, the Examiner concludes,
"claim 7 4 as presented requires extending the cleavage product and
detecting the cleavage product amplicon" as taught by Mast. Id.
Appellants argue that Mast does not disclose a method that comprises
"extending the cleavage product along the second oligonucleotide probe to
form an amplicon." App. Br. 6. With respect to paragraphs [0110]-[0111]
and Figure 1, upon which the Examiner relies, Appellants argue that Mast
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Appeal2018-003489
Application 14/270, 785
discusses the INV ADER assay, which includes "a two-part reaction, in
which the reaction in both parts is mediated by a cleavase enzyme cleaving
an overlapping oligonucleotide structure." Id.; see also Reply Br. 6-7.
Figure 1 of Mast is reproduced below:
A.
FIG. 1 shows a schematic diagram of INVADER
oligonucleotides, probe oligonucleotides, and FRET cassettes
for detecting a two different alleles (e.g., differing by a single
nucleotide) in a single reaction. Mast. ,r 81
Appellants argue that neither part of the reaction includes extending
the cleavage product along a second nucleotide. See Reply Br. 7-8. With
respect to Mast's listing of various polymerases, Appellants argue that: "all
of the polymerases contemplated are known to have flap endonuclease
activity, and ... does not teach extension of any polynucleotide using the
polymerase, only use of the endonuclease activity to cleave an invasive
cleavage structure." Id. at 6. Furthermore, Appellants argue that nothing in
Mast paragraph 16 connects primer extension, rolling circle amplification,
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Application 14/270, 785
and polymerase chain reaction with extension of a cleavage product along a
second nucleotide. Id.
We agree with Appellants that Mast does not disclose the step of
"extending the cleavage product along the second oligonucleotide probe to
form an amplicon." For example, the two-part process described in
paragraphs [0110]-[0111], and depicted in Figure 1 of Mast does not
disclose extending the cleavage product. See Mast ,r,r 110-111. Rather, as
argued by Appellants, Mast discloses amplifying the number of cleavage
products (5'-flaps) and FRET cassettes by cycling on the target DNA. Id.
Although Mast generally discloses numerous detection assays, many of
which may extend primers or other oligonucleotides to form amplicons, the
reference does not disclose all of the limitations of claim 7 4 arranged or
combined in the same way as recited in the claim. See Net MoneyIN, Inc. v.
VeriSign, Inc., 545 F.3d 1359, 1371 (Fed. Cir. 2008). We therefore find the
Examiner erred in concluding Mast anticipates claims 74, 76, and 77.
B. Rejection of claims 55-61 and 67-78 under 35 U.S.C. § 103(a)
Issue
Appellants argue there would have been no reason for a person of
ordinary skill in the art to combine Mast and Collier. See App. Br. 7.
Analysis
As discussed above, the Examiner finds Mast teaches a method for
detecting a nucleic acid using a hybridizing probe that generates a cleavage
product that is bound to a second probe. Ans. 6-7. The Examiner
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Application 14/270, 785
acknowledges Mast "did not specifically teach a blocking moiety between a
tag region and anti-tag region of the probe." Id. at 5.
The Examiner finds Collier teaches "a method for detecting a target
nucleic acid using oligonucleotides in a PCR assay wherein clam-like
oligonucleotides comprise a blocker moiety between tag sequence and anti-
tag sequence to prevent the polymerase from extending into the tag sequence
region." Ans. 5 (citing Collier 30-31, 11. 1-14; 46-47, 11. 10-47, 1. 29). The
Examiner finds Collier teaches using the Invader assay with the probes. Id.
(citing Collier 39, 11. 18-25, 41--42, 11. 29-5). The Examiner finds the
person of ordinary skill in the art would have combined the Collier with
Mast, "because ... use of the blocking moiety between tag and anti-tag or
first and second sequences would prevent polymerase to extend and reduces
... non-specific amplification." Id. at 5---6.
Appellants argue that "Mast's 'amplification' method ... involves
neither the amplification of nucleic acids nor a polymerase (i.e., Mast
teaches neither PCR nor primer extension). As such, there is no motivation
to combine the blocking moiety of Collier with the method of Mast." App.
Br. 7. With respect to claims 55---61 and 67-73, Appellants argue Collier
only uses blocking moieties to block polymerase extension in order to
maintain a single-stranded overhand on the end of the extended, double-
stranded molecule. Reply Br. 8-9. Appellants argue that Mast does not
extend a hybridized oligonucleotide or cleavage product and, therefore, there
is no reason to incorporate a nucleic acid having a blocking moiety for
preventing polymerase extension activity. Id. at 9.
We are persuaded by Appellants' arguments. As discussed above, we
do not agree with the Examiner that Mast teaches the step of "extending the
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Application 14/270, 785
cleavage product along the second oligonucleotide probe to form an
amplicon." Because the Examiner expressly relies upon Mast as disclosing
this step, we do not sustain the obviousness rejection of claim 7 4 and its
dependent claims ( claims 7 5-7 8).
With respect to claims 55---61 and 67-73, we agree with Appellants
that because Mast does not teach extending a hybridized oligonucleotide or
cleavage product, there would be no reason to modify Mast with the
blocking moiety of Collier. In the absence of a reason to prevent
polymerase extension, we do not agree with the Examiner's finding that the
"combination would result in an efficient and sensitive method for target
nucleic acid detection." See Ans. 5. "We must still be careful not to allow
hindsight reconstruction of references to reach the claimed invention without
any explanation as to how or why the references would be combined to
produce the claimed invention." Innogenetics, NV. v. Abbott Labs., 512
F.3d 1363, 1374 n.3 (Fed. Cir. 2008). We therefore do not sustain the
rejection of claims 55---61 and 67-78 as obvious over the prior art.
DECISION
The Examiner's rejection of claims 74, 76, and 77 under 35 U.S.C.
§ 102 (b) is reversed.
The Examiner's rejection of claims 56-61 and 67-78 under 35 U.S.C.
§ 103(a) is reversed.
REVERSED
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UNITED STATES PATENT AND TRADEMARK OFFICE
BEFORE THE PATENT TRIAL AND APPEAL BOARD
Ex parte DOUGLAS F. WHITMAN and HONGWEI ZHANG3
Appeal2018-003489
Application 14/270, 785
Technology Center 1600
Before DEBORAH KATZ, ULRIKE W. JENKS, and
JOHN G. NEW, Administrative Patent Judges.
KATZ, Administrative Patent Judge, concurring.
I write separately because, while I concur with my colleagues that
Mast does not anticipate claim 74, I believe that Mast renders it obvious for
reasons that differ from the Examiner's reasoning. Mast teaches the
INVADER assay, wherein the 5'-end of the "Primary Probe" includes a 5'-
flap that does not hybridize to the target DNA, and an enzyme recognizes
this structure and cleaves off the unpaired 5'-flap of the "Primary Probe."
See Mast ,r [0110] and Figure 1. Thus, Mast teaches steps (a) and (b) of
Appellants' claim 74.
3 Appellants identify the real party-in-interest as Luminex Corp. App. Br. 3.
Appeal2018-003489
Application 14/270, 785
Mast also teaches that oligonucleotides, such as the cleavage product
produced by steps (a) and (b) of claim 7 4, can be detected by a number of
methods known at the time. Specifically, in paragraph 16, Mast teaches
oligonucleotide detection assays including polymerase chain reaction,
primer extension, and rolling circle replication assays. See Mast ,r 16.
These techniques would include hybridizing the cleavage product to a
second oligonucleotide, as recited in step ( c) of claim 74, extending the
cleavage product along the second oligonucleotide probe to form an
amplicon, and detecting the target nucleic acid by detection the amplicon, as
recited in steps (d), and (e) of claim 74. Although Mast does not teach
extending the cleavage product along the FRET Cassette of the INVADER
assay (see Mast ,r 111 ), and thus does not anticipate claim 7 4, one of
ordinary skill in the art would have understood that FRET Cassette could be
used as a template for the oligonucleotide detection assays taught by Mast in
paragraph 16. Thus, given the teachings of the INV ADER Assay in
paragraphs 110 and 111 of Mast, one of ordinary skill in the art would have
understood steps ( d) and ( e) to have been an obvious variation of detecting
the target nucleic acid, in light of the teachings of the oligonucleotide
detection assays in paragraph 16 of Mast. The Examiner fails to articulate
this reasoning in the rejection of claim 74 under 35 U.S.C. § 103(a). See
Ans. 5. Therefore, I concur with the majority in reversing the Examiner's
rejection of claim 74.
2