Ex Parte PETER

Patent Trial and Appeal Board

May 24, 2018

13777842 (P.T.A.B. May. 24, 2018)

UNITED STA TES p A TENT AND TRADEMARK OFFICE
APPLICATION NO. FILING DATE
13/777,842 02/26/2013
22878 7590
Agilent Technologies, Inc.
Global IP Operations
5301 Stevens Creek Blvd
Santa Clara, CA 95051
05/29/2018
FIRST NAMED INVENTOR
BRIAN JON PETER
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.
20100165-01 2560
EXAMINER
SISSON, BRADLEY L
ART UNIT PAPER NUMBER
1634
NOTIFICATION DATE DELIVERY MODE
05/29/2018 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):
IPOPS.LEGAL@agilent.com
Agilentdocketing@cpaglobal.com
PTOL-90A (Rev. 04/07)
UNITED STATES PATENT AND TRADEMARK OFFICE
BEFORE THE PATENT TRIAL AND APPEAL BOARD
Ex parte BRIAN JON PETER
Appeal2017-008386 1
Application 13/777 ,842 2
Technology Center 1600
Before TONI R. SCHEINER, ULRIKE W. JENKS, and
JAMES A. WORTH, Administrative Patent Judges.
WORTH, Administrative Patent Judge.
DECISION ON APPEAL
Appellant appeals under 35 U.S.C. § 134(a) from the Examiner's
Final Rejection of claims 1-20, which are all pending claims. We have
jurisdiction under 35 U.S.C. §§ 134 and 6(b).
We reverse.
1 Our Decision refers to Appellant's Appeal Brief ("Appeal Br.," filed June
9, 2016) and Reply Brief ("Reply Br.," filed May 15, 2017), and the
Examiner's Final Office Action ("Final Act.," mailed Feb. 1, 2016) and
Answer ("Ans.," mailed Mar. 16, 2017).
2 According to Appellant, the real party in interest is Agilent Technologies,
Inc. Appeal Br. 3.
Appeal2017-008386
Application 13/777,842
Statement of the Case
Background
Appellant's application "relates, in part, to a method for genome
partitioning." Spec. 1:7. "Methods for genome partitioning, i.e., separating
selected regions of a genome from other regions, find use in a variety of
genomic analysis applications, including, but not limited to SNP analysis,
sequencing, mutation detection and the detection of chromosomal
rearrangements." Id. at 1:4--7.
A C-probe is an oligonucleotide, consisting of RNA, DNA, or a
combination of RNA and DNA, and is called a "C-probe" because it forms a
"C" shape when it hybridizes to a target nucleic acid. See Spec. 14:13-19.
In one embodiment, C-probe 2 contains oligonucleotide sequence 18 ( a
sequence of defined length), first region 10' and second region 12', where
the first region 10' hybridizes to a first genomic sequence 10 and the second
region 12' hybridizes to a second genomic sequence 12. Id. at 14:6-9, Fig.
1. According to the disclosure, exonuclease T may be used to trim the 3'
end of the target nucleic acid. Id. at 16: 17. After the 3' end of the target
nucleic acid has been trimmed, the 3' end of the first sequence is extended
using the C-probe as a template. Id. at 16:24--25. The target sequence may
be further processed, e.g., by removing the 5' end of the target sequence and
ligating the resulting ends of the DNA containing the target sequence, i.e.,
intoacovalentlyclosedcircularDNAmolecule. Id. at 17:6-7, 19:11-15.
The C-probe may be used in this manner to capture the target sequence. See
id. at 20:6-7, Figs. 2A, 2B. In one further embodiment, the methylation
status of the target sequence can be compared from different samples. Id. at
21:1-2.
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Application 13/777,842
The Claims
Claims 1 and 20 are the independent claims on appeal. Claim 1,
reproduced below, is illustrative of the subject matter on appeal:
1. A method of processing a nucleic acid, comprising:
(a) hybridizing a C-probe to a strand of a target nucleic
acid to produce a complex, wherein:
(i) said strand comprises a target sequence that is
flanked by a first sequence and a second sequence,
and
(ii) said C-probe comprises a first region that
hybridizes to said first sequence, a second region
that hybridizes to said second sequence, and an
oligonucleotide sequence between said first and
second regions,
(b) enzymatically removing any 3' overhang from the
target nucleic acid of said complex to produce a 3' hydroxyl
group at the 3' end of said first sequence;
( c) extending the 3' end of said first sequence using the
oligonucleotide sequence of said C-probe as a template,
wherein said extending results in a 3' hydroxyl group that is
adjacent to the 5' end of said second sequence;
( d) enzymatically removing any 5' overhanging from the
target nucleic acid, either before or after said extending of step
( c ), to produce a 5' phosphate group at the end of said second
sequence; and
( e) ligating the 5' phosphate group at the end of the
second sequence to the 3' hydroxyl group that is adjacent to the
5' end of said second sequence to produce a circular DNA
molecule that contains said target sequence and the complement
of said oligonucleotide sequence.
Appeal Br., Claims App.
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Application 13/777,842
The Issues
A. The Examiner rejected claim 20 under 35 U.S.C. § 101 as being
directed to patent ineligible subject matter.
B. The Examiner rejected claims 1-20 under pre-AIA 35 U.S.C.
§ 112, first paragraph, as failing to comply with the enablement requirement.
C. The Examiner rejected claims 1-20 under pre-AIA 35 U.S.C.
§ 112, first paragraph, as failing to comply with the written description
requirement. 3
A. 35 U.S.C. § 1 OJ
The Examiner determines that claim 20 is directed to a kit that
comprises a C-probe as well as a "one or more enzymes that remove 5' and
3' single stranded overhangs; and a DNA ligase." Final Act. 2. The
Examiner determines that "one or more enzymes that remove 5' and 3'
single stranded overhangs" as well as DNA polymerase and DNA ligase, are
all recognized as being products of nature without significantly more, and
therefore fall under the laws of nature or natural phenomena exceptions. See
id. at 2-3. The Examiner determines that no evidence has been presented
showing that the presence of the probe will result in markedly different
characteristics to either the "one or more enzymes" or to the "DNA ligase."
Id. at 3.
Appellant argues, inter alia, that "[t]he inclusion in the kit of
additional components, even components derived from a natural source, in
no way negates that clearly statutory C-probe component of the kit (which
3 Certain other rejections, i.e., under 35 U.S.C. §§ 102 and 103, have been
withdrawn. Ans. 18-19.
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Application 13/777,842
the Examiner has acknowledged does not occur in nature)." Appeal Br. 4.
Appellant also contends that the Examiner has failed to comply with the
recently published guidelines entitled "Subject Matter Eligibility Examples:
Life Sciences" (May 2016). Id. at 5.
The statutory provision at issue, 35 U.S.C. § 101, states that
"[ w ]hoever invents or discovers any new and useful process, machine,
manufacture, or composition of matter, or any new and useful improvement
thereof, may obtain a patent therefor, subject to the conditions and
requirements of this title."
"Laws of nature, natural phenomena, and abstract ideas are not
patentable." Mayo Collaborative Services v. Prometheus Labs., Inc., 132 S.
Ct. 1289, 1293 (2012) (citation omitted). The Supreme Court articulated a
two-step test for patent eligibility under § 101 that "distinguish[ es] patents
that claim laws of nature, natural phenomena, and abstract ideas from those
that claim patent-eligible applications of those concepts." Alice Corp. Pty.
Ltd. v. CLS Bank Int'!, 134 S. Ct. 2347, 2355 (2014) (citing Mayo, 132 S. Ct.
at 1296-97). "First," Alice instructs a court to "determine whether the
claims at issue are directed to one of those patent-ineligible concepts." Id.
( citation and quotations omitted). If the claims are directed to a patent
ineligible concept then the court must proceed to the second step of the
test-the "search for an inventive concept-i.e., an element or combination
of elements that is sufficient to ensure that the patent in practice amounts to
significantly more than a patent upon the ineligible concept itself." Id.
( quotations and alterations omitted).
Turning to the first step of the Alice test, although certain of the
individual elements of claim 20 are naturally occurring, we are persuaded by
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Appellant's contention that the C-probe and the combination of elements, as
recited in the kit of claim 20, are not naturally occurring. In particular, we
agree with Appellant that the recited C-probe has not been shown to be a
product of nature. Independent claim 20 recites that "the 3' end of said C-
probe is blocked to prevent the addition of nucleotides by a polymerase or a
ligase." Appeal Br. 19, Claim App. As defined in the Specification,
[t]he term "blocked", in the context of an oligonucleotide that is
blocked at its 3' end when it is annealed to a target nucleic acid,
refers to an oligonucleotide that cannot be extended by a
template-dependent polymerase, either because the 3' end of the
oligonucleotide has a non-natural nucleotide at the 3' end (e.g.,
by a dideoxy nucleotide or any of a multitude of nucleotides that
are not substrates for the polymerase) or because the 3' end of
the oligonucleotide is mis-matched with the target, i.e., because
one or more nucleotides at the 3' end of the oligonucleotide are
not complementary to correspondingly positioned nucleotides in
the target sequence). In certain cases, blocked oligonucleotides
cannot be digested by a 3' to 5' exonuclease, e.g., because one
or more phosphodiester linkages has been altered to become, for
example, a phosphothioate linkage.
Spec. 13:23-14:2. Accordingly, the C-probe either contains a non-natural
nucleotide or contains one or more non-complementary nucleotides at the 3'
end such that the 3' end is functionally blocked. The Examiner has not
shown such a C-probe to be naturally occurring, neither alone nor with the
correspondingly-recited enzymes, i.e., as in the kit of independent claim 20.
Accordingly, we reverse the Examiner's rejection based on that
ground.
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B. 35 U.S. C. § 112 (Enablement)
The Examiner determines, inter alia, that:
[ t ]he nucleotide sequence for the genome of any given species of
bacteria is highly unpredictable .
. . . In order to practice the full scope of the invention, one would
have to first determine the nucleotide sequence for each and
every organism, much less any gene of interest, in order to
identify the correct nucleotide sequences for all probes and/or
primers essential to the claimed invention. Such information is
neither provided by the disclosure nor the art of record.
Final Act. 10-11. Thus, as we understand it, the Examiner's rejection is
based on the fact that the claims encompass, prospectively, the detection of
any and all target nucleic acids, in any and all types of organisms, for which
the nucleotide sequences, as well as the sequences of suitable probes, have
not yet been determined. Therefore, the Examiner reasons, practicing the
full scope of the claimed method requires sequencing any and all organisms,
which would take a significant amount of time and effort. See id. at 11 ("In
order to determine the appropriate primers for the tens of millions of bacteria
that are not known yet encompassed by the claimed method, one would need
to determine the nucleotide sequence of the various target sequences.").
Appellant asserts that "the specification provides a detailed
description of how the method can be implemented and that several 7 6
million individual sequences from over 260,000 named organisms (including
the entire human and mouse genomes) were publicly available from NCBI' s
Genbank database at the time of filing (see, e.g., Nucl. Acids Res. 2008 36:
D25-D30)." Appeal Br. 7.
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The issue with respect to this rejection is: Does a preponderance of
the evidence of record support the Examiner's conclusion that there is a lack
of enablement for claims 1-20?
We are persuaded by Appellant that a preponderance of the evidence
of record does not support the Examiner's conclusion of non-enablement.
As our reviewing court has explained, the Examiner "bears an initial
burden of setting forth a reasonable explanation as to why it believes that the
scope of protection provided by that claim is not adequately enabled by the
description of the invention provided in the specification of the application."
In re Wright, 999 F.2d 1557, 1561-62 (Fed. Cir. 1993).
"The scope of enablement ... is that which is disclosed in the
specification plus the scope of what would be known to one of ordinary skill
in the art without undue experimentation." National Recovery Technols.,
Inc. v. Magnetic Separation Sys., Inc., 166 F.3d 1190, 1196 (Fed. Cir. 1999).
While the Specification must enable the skilled artisan to practice the
full scope of the claimed subject matter, " [ i ]t is well settled that patent
applicants are not required to disclose every species encompassed by their
claims, even in an unpredictable art." In re Vaeck, 947 F.2d 488, 496 (Fed.
Cir. 1991 ). Moreover, a claim does not lack enablement merely because it
encompasses inoperative embodiments. Atlas Powder Co. v. E.I. du Pont
De Nemours & Co., 750 F.2d 1569, 1576 (Fed. Cir. 1984).
Rather, as the Federal Circuit has explained:
[T]here must be sufficient disclosure, either through
illustrative examples or terminology, to teach those of ordinary
skill [in the art] how to make and how to use the invention as
broadly as it is claimed. This means that the disclosure must
adequately guide the art worker to determine, without undue
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experimentation, which species among all those encompassed by
the claimed genus possess the disclosed utility.
Vaeck, 947 F.2d at 496 (footnote omitted).
In the present case, Appellant's claims are directed to a method and a
kit for capturing a target sequence of DNA by hybridizing a C-probe to a
target nucleic acid and extending the target sequence using the C-probe as a
template. See Spec. 16:8-10, 16:24--25, 20:5-7, Figs. 1, 2A, 2B.
We agree with the Examiner that, given its broadest reasonable
interpretation consistent with the Specification, Appellant's claim 1
encompasses detecting numerous target nucleic acids in addition to those
exemplified in the Specification. The Examiner does not, however, advance
specific persuasive evidence demonstrating sufficiently that an ordinary
artisan (see Appeal Br. 7 (discussing knowledge in art); Ans. 25), would
have needed to experiment unduly to determine suitable probe and target
sequences for practicing the claimed invention.
We do not agree, with the Examiner's implication (see Final Act. 11)
that Appellant must draft its claims in a manner that excludes application of
the claimed process to such as yet undiscovered target sequences. See In re
Anderson, 471 F.2d 1237, 1242 (CCPA 1973) ("It is always possible to put
something into a combination to render it inoperative. It is not the function
of the claims to exclude all such matters but to point out what the
combination is."). In the present case, the claims are not directed to methods
of sequencing every known organism. Rather, the claims are directed to a
method and kit for capturing a target sequence using a C-probe and DNA
processing enzymes. As noted above, Appellant's Specification describes
how to perform the claimed process.
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Accordingly, for the reasons discussed, we agree with Appellant that a
preponderance of the evidence does not support the Examiner's prima facie
case of lack of enablement. We, therefore, reverse the Examiner's rejection
on that ground.
C. 35 U.S. C. § 112 (Written Description)
The Examiner determines, inter alia, that "[f]or purposes of
examination, the claimed method ( claims 1-19) as well as the claimed kit
( claim 20), which is to comprise the C-probe, have been construed as
encompassing probes that will hybridize to any conceivable target." Final
Act. 23. The Examiner further states: "[i]n addition to no teaching of any
actual and useful nucleic acid probes sequences (35 USC 101; specific,
substantial, and credible utility), the disclosure has not been found to teach
those nucleotide sequences that are useful in the bacteria, plants, viruses,
etc., that are fairly encompassed by the claims yet not known to the public."
Id. at 25.
Appellant argues that "the written description requirement does not
require a specific description of every species encompassed by a claim."
Appeal Br. 9. Appellant further asserts that the written description
requirement is satisfied because "the specification provides a detailed
description of how the method can be implemented and that several 7 6
million individual sequences from over 260,000 named organisms (including
the entire human and mouse genomes) were publicly available from NCBI's
Genbank database (see, e.g., Nucl. Acids Res. 2008 36: D25-D30)." Id. at
10.
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The issue with respect to this rejection is: Does a preponderance of
the evidence of record support the Examiner's conclusion that the
Specification fails to provide descriptive support for the claims?
The Federal Circuit has explained:
[T]he determination of what is needed to support generic
claims to biological subject matter depends on a variety of
factors, such as the existing knowledge in the particular field, the
extent and content of the prior art, the maturity of the science or
technology, the predictability of the aspect at issue, and other
considerations appropriate to the subject matter.
Capon v. Eshhar, 418 F.3d 1349, 1359 (Fed. Cir. 2005).
We find Appellant has the better position. The instant invention is not
in the target sequences themselves, but rather the method of capturing target
sequences using a C-probe and DNA processing enzymes.
The Specification refers to the deposit of sequences at NCBI' s
Genbank database for reference genomic regions. Spec. 8: 13-30, 10:28-30.
The instant facts are therefore also similar to those in F alko-Gunter,
which teaches that "where, as in this case, accessible literature sources
clearly provided, as of the relevant date, genes and their nucleotide
sequences (here 'essential genes'), satisfaction of the written description
requirement does not require either the recitation or incorporation by
reference ( where permitted) of such genes and sequences." F alko-Gunter
Falkner v. Inglis, 448 F.3d 1357, 1368 (Fed. Cir. 2006) (footnote omitted).
We recognize, but find unpersuasive, the Examiner's finding that the
Specification does not teach probe sequences. Final Act. 25. The
Specification discloses the use of substantially complementary sequences
and optionally, particular mismatches, e.g., G-A mismatches. E.g., Spec.,
5:24---6:20, 9:28-10:2, 18:9-17. We, therefore, conclude that the evidence of
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record does not support the Examiner's conclusion that the Specification
fails to provide descriptive support for the claims. Accordingly, we reverse
the Examiner's rejection on that ground.
DECISION
The Examiner's decision to reject claims 1-20 is reversed.
REVERSED
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