Ex Parte Pont-Kingdon et al

Patent Trial and Appeal Board

Nov 28, 2012

11268433 (P.T.A.B. Nov. 28, 2012)

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.
11/268,433 11/07/2005 Genevieve Pont-Kingdon 50407-5 1912
28441 7590 11/29/2012
BRINKS HOFER GILSON & LIONE/UTAH
UTAH OFFICE
222 South Main Street
Suite 1930
SALT LAKE CITY, UT 84101
EXAMINER
SALMON, KATHERINE D
ART UNIT PAPER NUMBER
1634
MAIL DATE DELIVERY MODE
11/29/2012 PAPER
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.
PTOL-90A (Rev. 04/07)
UNITED STATES PATENT AND TRADEMARK OFFICE
__________

BEFORE THE PATENT TRIAL AND APPEAL BOARD
__________

Ex parte GENEVIEVE PONT-KINGDON, ELAINE LYON,
and JOHN G. WARD
__________

Appeal 2011-013029
Application 11/268,433
Technology Center 1600
__________

Before MELANIE L. McCOLLUM, FRANCISCO C. PRATS, and
STEPHEN WALSH, Administrative Patent Judges.

WALSH, Administrative Patent Judge.

DECISION ON APPEAL
This is an appeal under 35 U.S.C. § 134(a) from the rejection of
claims directed to a chimeric nucleic acid probe and a nucleic acid complex.
The Patent Examiner rejected the claims for obviousness. We have
jurisdiction under 35 U.S.C. § 6(b). We affirm.
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STATEMENT OF THE CASE
“[T]he invention relates to hybridization probes and methods of using
such probes to determine haplotypes and genotypes.” (Spec. 2, [0002].)
The Specification explains that “[t]he genetic sequence at a particular
genetic locus is referred to as the ‘genotype,’ while the particular
combination of genetic sequences or polymorphisms at multiple loci is
referred to as the ‘haplotype.’” (Id., [0003].) According to the
Specification, “[i]dentification and characterization of genotypes and
haplotypes has become a primary focus of genetic research.” (Id.)
Claims 1-16, 28, and 31-35 are on appeal. Appellants state that the
claims stand or fall together. (App. Br. 17.) We select claim 1 as
representative, and claims 2-16, 28, and 31-35 will stand or fall with claim 1.
37 C.F.R. § 41.37(c)(1)(vii).
Claim 1 reads:
1. A chimeric nucleic acid probe comprising:
a first binding region substantially complementary to a first
polymorphic site of a polynucleotide template, and
a second binding region substantially complementary to a second
polymorphic site of a polynucleotide template,
wherein the first polymorphic site and the second polymorphic site are
noncontiguous and wherein the first polymorphic site and the second
polymorphic site of the polynucleotide template are separated by a region of
polynucleotides not complementary to nucleotides in the nucleic acid probe.

The Examiner rejected all the claims under 35 U.S.C. § 103(a) as
unpatentable over Neri1 and Guo.2

1 Bruce Neri et al., US 6,194,149 B1, issued Feb. 27, 2001.
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OBVIOUSNESS
The Issues
The Examiner’s position is that Neri taught (i) a chimeric bridging
probe having binding regions complementary to two or more non-contiguous
sites of a target template (Ans. 6); (ii) a target template having
polymorphisms in a second template region (id., citing Neri at col. 13, ll. 10-
20); and (iii) the first and second sites on Neri’s target template were
separated by at least five nucleotides not complementary to the probe (id.).
The Examiner found the difference between Neri’s probe and Appellants’
probe is that Neri described only one of the sites on the target template as
polymorphic. (Id.)
The Examiner found, however, that “it is well known in the art that
probes can be designed to detect multiple polymorphic sites,” and cited Guo
as teaching probes complementary to multiple polymorphic sites on a
template of interest. (Id. at 10, citing Guo’s Table 1.) The Examiner further
found that Guo (i) taught two or more alleles are needed to define particular
phenotypes, such as HLA, and (ii) motivated the ordinary artisan to design
probes and probe/template complexes to detect multiple polymorphic sites
on a template in order to determine if the sample has a particular phenotype.
(Id. at 11.) The Examiner concluded it would have been “obvious to the
ordinary artisan to modify the probes and complex of Neri et al. to detect
any number of polymorphic sites on templates including a first polymorphic

2 Zhen Guo et al., Oligonucleotide Arrays for High-Throughput SNPs
Detection in the MHC Class I Genes: HLA-8 as a Model System, 12
GENOME RES. 447-457 (2002).
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and second polymorphic site on a polynucleotide temple which is separated
by a noncontiguous region with the reasonable expectation of designing a
probe which detects multiple polymorphic sites associated with a particular
phenotype.” (Id.)
Appellants contend the Examiner erred “because the combination of
Neri and Guo is improper,” and “[o]ne would not be inclined to modify the
probe disclosed by Neri to be complementary to a second polymorphic site
separated from a first polymorphic site by a region of polynucleotides not
complementary to nucleotides in the nucleic acid probe.” (App. Br. 18.)
More specifically, Appellants contend:
(1) “[n]either Neri nor Guo teach or suggest using probes for
haplotyping over distances that would require a loop-out region in a template
with a second polymorphic site;”
(2) “neither reference provid[ed] a reason for the asserted
combination;”
(3) “neither reference provid[ed] a reasonable expectation that the
combination would lead to successful haplotyping.” (Id. at 18-19.)
Findings of Fact
1. We adopt the Examiner’s findings concerning the scope and content
of the prior art.
2. Regarding claim 1’s “template . . . region of polynucleotides not
complementary to nucleotides in the nucleic acid probe,” the Specification
provides:
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The first and second regions of the template are not contiguous, and
are either separated by a region of polynucleotides with respect to
which there are no complementary nucleotides in the nucleic acid
probe, or . . . . The hybridization probe (with its adjacent first and
second regions in close proximity) binds to the first and second
regions of the template, which are brought together in close proximity
to form a probe/template complex, thereby forcing the region of the
template with respect to which there are no complementary
nucleotides in the nucleic acid probe to “loopout”. The single
hybridization probe is used to determine the identity and phase of the
two alleles present on the template, using melting curve analysis of
the hybridization probe.

(Spec. 18, [0064].)
3. The Specification further provides:
The DNA region of interest, and the DNA template
corresponding to the DNA region, which encompass more than one
multi-allelic loci, also includes a region of polynucleotides that
separate the loci. The region of polynucleotides separating the first
and second locus may be a length of nucleotide sequence comprising
one or more nucleotides of any length. The number of nucleotides
separating the first and second locus may be 1, 2, 3, 4, 5, 6, 7, 8, 9, 10,
11, 12, 13, 14 or greater. In particular embodiments, the number of
nucleotides separating the first and second locus may be greater than
15 nucleotides, greater than 20 nucleotides, greater than 25
nucleotides, greater than 50 nucleotides, greater than 100 nucleotides,
or greater than 200 nucleotides.

(Id. at 27, [0091].)

Principles of Law
“During patent examination the pending claims must be interpreted as
broadly as their terms reasonably allow,” and limitations are not to be read
into the claims from the Specification. In re Zletz, 893 F.2d 319, 321 (Fed.
Cir. 1989) (citations omitted).
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“A reference may be read for all that it teaches, including uses beyond
its primary purpose.” In re Mouttet, 686 F.3d 1322, 1331 (Fed. Cir. 2012).
In determining whether the subject matter of a patent claim is obvious,
neither the particular motivation nor the avowed purpose of the
patentee controls. What matters is the objective reach of the claim. If
the claim extends to what is obvious, it is invalid under § 103. One of
the ways in which a patent's subject matter can be proved obvious is
by noting that there existed at the time of invention a known problem
for which there was an obvious solution encompassed by the patent's
claims.

KSR Int’l Co. v. Teleflex Inc., 550 U.S. 398, 419-20 (2007); In re Beattie,
974 F.2d 1309, 1312 (Fed. Cir. 1992) (“the law does not require that the
references be combined for the reasons contemplated by the inventor”).
“A reference is reasonably pertinent if, even though it may be in a
different field from that of the inventor’s endeavor, it is one which,
because of the matter with which it deals, logically would have
commended itself to an inventor’s attention in considering his
problem.” In re Clay, 966 F.2d 656, 659 (Fed. Cir. 1992). In other
words, “familiar items may have obvious uses beyond their primary
purposes.” KSR Int’l Co. v. Teleflex, Inc., 550 U.S. 398, [402], 127
S.Ct. 1727, 1742 (2007).

In re Icon Health and Fitness, Inc., 496 F.3d 1374, 1379-80 (Fed. Cir.
2007).
“Obviousness does not require absolute predictability of success. . . .
[A]ll that is required is a reasonable expectation of success.” In re
O'Farrell, 853 F.2d 894, 903-04 (Fed. Cir. 1988). The presence of a
reasonable expectation of success is measured from the perspective of a
person of ordinary skill in the art at the time the invention was made. Life
Techs., Inc. v. Clontech Labs., Inc., 224 F.3d 1320, 1326 (Fed. Cir. 2000).
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Discussion
After considering the evidence and the arguments, we conclude the
evidence favors the Examiner’s conclusion of obviousness. Accordingly, we
adopt the Examiner’s reasoning (see Grounds of Rejection, Ans. 5-11), and
agree that the Examiner properly found Appellants’ arguments unpersuasive
(see Response to Argument, Ans. 12-24). We provide the following points
for emphasis.
Issue (1)
The Examiner properly found Appellants’ “loopout” argument
unpersuasive because the claims do not contain a loopout limitation. (Ans.
14.) The Specification describes templates that would loopout on
hybridization with the claimed probe. (FF 2.) The Specification also
describes templates that contain only one nucleotide separating the
polymorphic sites. (FF 3.) The Examiner rebuts Appellants’ loopout
contention by pointing to the Specification’s disclosure that as few as one
nucleotide could be the separation in the template (Ans. 14, citing Spec. 27,
[0091].) According to the Examiner, one nucleotide is not enough to form a
loop, and we find the Examiner’s technical reasoning persuasive.
Appellants have not established that the appealed claims must be interpreted
as requiring a loopout region in the template. See Zletz, 893 F.2d at 321.
Issue (2)
Appellants contend that “Neri and Guo relate to different problems
than the claimed invention.” (App. Br. 19.) Even if Appellants’
characterizations are accepted as correct, that alone does not establish a
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reason to disregard other reasons for obviousness. See KSR, 550 U.S. 419-
20. Both Neri and Guo taught probes for analyzing nucleic acids. Neri
explained that its probes permitted the detection and/or identification of
genetic polymorphisms. (Neri, Abstract.) Guo explained that its probes
permitted identifying SNPs in polymorphic targets. (Guo, Abstract.)
According to the Examiner, Guo identified haplotyping as a problem that
could be addressed by using probes complementary to multiple polymorphic
regions on a template. The Examiner explained that changing Neri’s probe
to include regions complementary to two polymorphic regions, as in Guo,
rather than only one, would have provided another way to address Guo’s
haplotyping. Appellants have not produced evidence that the Examiner was
wrong in so reasoning. Any need or problem known in the field may
provide a reason for combining elements in the manner claimed. KSR,
550 U.S. at 420.
Appellants have also argued that a person of ordinary skill in the art
would not have combined the Neri and Guo teachings, as Neri’s purpose was
to assay formation of a secondary structure, and its probes were not designed
for genotyping or haplotyping. (App. Br. 20.) This argument is
unpersuasive because, as the Examiner found, Neri’s disclosure concerned
probes for the detection and identification of polymorphisms (Ans. 6), and
Guo’s disclosure concerned probes for detecting multiple polymorphic sites
(id. at 10). The two references were therefore reasonably pertinent to each
other. See Icon Health, 496 F.3d at 1379-80.
Appellants argue that because the methods Neri and Guo taught were
different, modifying Neri’s probe would change principle of operation of
Neri. This argument is unpersuasive because Neri’s probes operated by
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hybridization, the same mechanism by which Guo’s probes operated. The
two may have extracted different information from their data, but the
principle of operation, hybridization, was not different. If Neri’s probe
having non-contiguous binding sites were modified from being
complementary to one polymorphic site and one non-polymorphic site to
being complemetary to two polymorphic sites, the modified probe would
still operate by hybridization to non-contiguous sites. See Mouttet, 686 F.3d
at 1332 (arguments about changing operational principles inapplicable
where the modified apparatus will operate “on the same principles as
before”). Claim 1 defines a probe, not a method. We agree with the
Examiner that because the claims on appeal define probes, the probes may
have been obvious even if not used to obtain the information Appellants
wish to collect.
Issue (3)
Appellants contend there would have been no “reasonable expectation
that modifying the probe and complex of Neri would result in the successful
identification of a haplotype or genotype of a template which has at least one
genetic locus characterized by multiple alleles.” (App. Br. 25.) The
Examiner responds that Neri allowed mismatches and Guo taught detecting
multiple mismatches, and both references taught extensive template
variations. (Ans. 21-24.) We find the Examiner’s thorough fact-based
analysis persuasive that, from the perspective of a person of ordinary skill in
the art, Neri’s probes, if modified as the rejection proposed, would
reasonably have been expected to identify multiple polymorphic sites on a
template. See Life Techs., 224 F.3d at 1326.
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CONCLUSIONS
The claims do not require template loopout. Neri and Guo were
reasonably pertinent to each other, and properly combined. Guo would have
motivated the ordinary artisan to design probes and probe/template
complexes to detect multiple polymorphic sites on a template in order to
determine if a sample had a particular phenotype. Modifying Neri’s probes
to detect multiple polymorphic sites on a template would have been obvious
in view of Guo’s suggestion. The record evidence supports concluding that
there would have been a reasonable expectation that Neri’s probes, if
modified as the rejection proposed, would detect multiple polymorphic sites.

SUMMARY
We affirm the rejection of claims 1-16, 28, and 31-35 under 35 U.S.C.
§ 103(a) as unpatentable over Neri and Guo.
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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