Ashutosh et al.

Patent Trials and Appeals Board

Aug 2, 2019

14288299 - (D) (P.T.A.B. Aug. 2, 2019)

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.
14/288,299 05/27/2014 Ashutosh 20130278-02 2376
22878 7590 08/02/2019
Agilent Technologies, Inc.
Global IP Operations
5301 Stevens Creek Blvd
Santa Clara, CA 95051
EXAMINER
WOITACH, JOSEPH T
ART UNIT PAPER NUMBER
1631
NOTIFICATION DATE DELIVERY MODE
08/02/2019 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):
Agilentdocketing@cpaglobal.com
ipopsadmin@agilent.foundationip.com
PTOL-90A (Rev. 04/07)

UNITED STATES PATENT AND TRADEMARK OFFICE
____________

BEFORE THE PATENT TRIAL AND APPEAL BOARD
____________

Ex parte ASHUTOSH,
DEVENDRA JOSHI, and CHRISTIAN A. LE COCQ
(APPLICANT: AGILENT TECHNOLOGIES, INC.)
____________

Appeal 2019-002083
Application 14/288,2991
Technology Center 1600
____________

Before DONALD E. ADAMS, ERIC B. GRIMES, and
RICHARD M. LEBOVITZ, Administrative Patent Judges.

ADAMS, Administrative Patent Judge.

DECISION ON APPEAL
This Appeal under 35 U.S.C. § 134(a) involves claims 1–19 (Final
Act.2 2). Examiner entered a rejection under 35 U.S.C. § 101. We have
jurisdiction under 35 U.S.C. § 6(b).
We AFFIRM.

1 Appellants identify “Agilent Technologies, Inc.” as the real party in
interest (Appellants’ August 7, 2018 Appeal Brief (App. Br.) 2).
2 Examiner’s January 16, 2018 Final Office Action.
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STATEMENT OF THE CASE
Appellants’ disclosure relates to
a method for identifying a sequence variant in an enriched
sample. In certain embodiments, this method may comprise:
(a) obtaining: (i) a plurality of sequence reads from a sample
that has been enriched for a genomic region and (ii) a reference
sequence for the genomic region; (b) assembling the sequence
reads to obtain a plurality of discrete sequence assemblies that
correspond to potential variants; (c) determining which of the
potential variants are true and which are artifacts by examining
the sequence reads that make up each of the discrete sequence
assemblies; (d) optionally determining whether each of the true
potential variants contains a mutation that is known to be
associated with the reference sequence; and (e) outputting a
report indicating whether the sample comprises a sequence
variant[;] . . . a computer system comprising a memory
comprising: a) a database of sequences; and b) an executable
program for performing the present method[;] . . . a computer-
readable storage medium comprising instructions for
performing the present method[; and] . . . a method of
identifying a variant sequence. In certain embodiments, this
method may comprise: a) inputting sequence information into a
computer system comprising a program comprising instructions
for performing the present method; b) executing the program;
and c) receiving an output from the computer system.
(Spec. 2–3.)
Appellants’ claims 1 and 10–12 are representative and reproduced
below:
1. A method for identifying a sequence variant comprising:
(a) generating a plurality of at least 100 sequence reads
from a sample that has been enriched for a genomic region and
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obtaining a reference sequence for the genomic region, wherein
the sequence reads are generated by:
i. enriching for the genomic region; and
ii. sequencing the enriched genomic region;
(b) assembling the sequence reads to obtain a plurality of
discrete sequence assemblies each of which corresponding to a
potential variant;
(c) examining, using a computer, the sequence reads that
make up each of the discrete sequence assemblies to determine
which of the potential variants are true and which are artifacts;
(d) optionally determining whether each of the true
potential variants contains a mutation that is known to be
associated with the reference sequence; and
(e) identifying a true sequence variant in the sample
based on the determination of which variants are true and which
variants are artifacts.
(App. Br. 11.)
10. The method of claim 1, wherein said assembling uses graph
theory.
(Id. at 12.)
11. The method of claim 10, wherein said assembling is done
using a minimal de-Bruijn sequence.
(Id.)
12. The method of claim 10, wherein said assembling is done
using a BEST theorem.
(Id.)

Ground of rejection before this Panel for review:
Claims 1–19 stand rejected under 35 U.S.C. § 101.
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ISSUE
Does the preponderance of evidence of record support Examiner’s
finding that Appellants’ claimed invention is directed to patent ineligible
subject matter?
PRINCIPLES OF LAW
An invention is patent-eligible if it claims a “new and useful process,
machine, manufacture, or composition of matter.” 35 U.S.C. § 101.
However, the Supreme Court has long interpreted 35 U.S.C. § 101 to include
implicit exceptions: “‘[l]aws of nature, natural phenomena, and abstract
ideas’” are not patentable. E.g., Alice Corp. v. CLS Bank Int’l, 573 U.S.
208, 216 (2014).
In determining whether a claim falls within an excluded category, we
are guided by the Supreme Court’s two-step framework, described in Mayo
and Alice. Id. at 217–18 (citing Mayo Collaborative Servs. v. Prometheus
Labs., Inc., 566 U.S. 66, 75–77 (2012)). In accordance with that framework,
we first determine what concept the claim is “directed to.” See Alice, 573
U.S. at 219 (“On their face, the claims before us are drawn to the concept of
intermediated settlement, i.e., the use of a third party to mitigate settlement
risk.”); see also Bilski v. Kappos, 561 U.S. 593, 611 (2010) (“Claims 1 and 4
in petitioners’ application explain the basic concept of hedging, or protecting
against risk.”).
Concepts determined to be abstract ideas, and thus patent ineligible,
include certain methods of organizing human activity, such as fundamental
economic practices (Alice, 573 U.S. at 219–20; Bilski, 561 U.S. at 611);
mathematical formulas (Parker v. Flook, 437 U.S. 584, 594–95 (1978)); and
mental processes (Gottschalk v. Benson, 409 U.S. 63, 69 (1972)). Concepts
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determined to be patent eligible include physical and chemical processes,
such as “molding rubber products” (Diamond v. Diehr, 450 U.S. 175, 191
(1981)); “tanning, dyeing, making water-proof cloth, vulcanizing India
rubber, smelting ores” (id. at 182 n.7 (quoting Corning v. Burden, 56 U.S.
252, 267–68 (1853))); and manufacturing flour (Gottschalk, 409 U.S. at 69
(citing Cochrane v. Deener, 94 U.S. 780, 785 (1876))).
In Diehr, the claim at issue recited a mathematical formula, but the
Supreme Court held that “[a] claim drawn to subject matter otherwise
statutory does not become nonstatutory simply because it uses a
mathematical formula.” Diehr, 450 U.S. at 176; see also id. at 191 (“We
view respondents’ claims as nothing more than a process for molding rubber
products and not as an attempt to patent a mathematical formula.”). Having
said that, the Supreme Court also indicated that a claim “seeking patent
protection for that formula in the abstract . . . is not accorded the protection
of our patent laws, . . . and this principle cannot be circumvented by
attempting to limit the use of the formula to a particular technological
environment.” Id. (citing Gottschalk and Parker); see, e.g., id. at 187 (“It is
now commonplace that an application of a law of nature or mathematical
formula to a known structure or process may well be deserving of patent
protection.”).
If the claim is “directed to” an abstract idea, we turn to the second
step of the Alice and Mayo framework, where “we must examine the
elements of the claim to determine whether it contains an ‘inventive
concept’ sufficient to ‘transform’ the claimed abstract idea into a patent-
eligible application.” Alice, 573 U.S. at 221 (quotation marks omitted). “A
claim that recites an abstract idea must include ‘additional features’ to
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ensure ‘that the [claim] is more than a drafting effort designed to
monopolize the [abstract idea].’” Id. (quoting Mayo, 566 U.S. at 77).
“[M]erely requir[ing] generic computer implementation[] fail[s] to transform
that abstract idea into a patent-eligible invention.” Id.
The PTO recently published revised guidance on the application of
§ 101. USPTO, 2019 Revised Patent Subject Matter Eligibility Guidance,
84 Fed. Reg. 50 (January 7, 2019) (“Revised Guidance”). Under that
guidance, we first look to whether the claim recites:
(1) any judicial exceptions, including certain groupings of
abstract ideas (i.e., mathematical concepts, certain methods of
organizing human activity such as a fundamental economic
practice, or mental processes); and
(2) additional elements that integrate the judicial exception into
a practical application (see MPEP § 2106.05(a)–(c), (e)–(h)).
See 84 Fed. Reg. 54–55. Only if a claim (1) recites a judicial exception and
(2) does not integrate that exception into a practical application, do we then
look to whether the claim:
(3) adds a specific limitation beyond the judicial exception that
is not “well-understood, routine, conventional” in the field (see
MPEP § 2106.05(d)); or
(4) simply appends well-understood, routine, conventional
activities previously known to the industry, specified at a high
level of generality, to the judicial exception.
See 84 Fed. Reg. 51.
ANALYSIS
The method for identifying a sequence variant, set forth in Appellants’
claim 1 requires, as step (a), the generation of “a plurality of at least 100
sequence reads from a sample that has been enriched for a genomic region and
obtaining a reference sequence for the genomic region” (App. Br. 11).
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Step (a) of Appellants’ claim 1 further requires that “the sequence reads
are generated by: i. enriching for the genomic regions; and ii. sequencing the
enriched genomic region” (id.).
Step (b) of Appellants’ claim 1 requires that “the sequence reads [are
assembled] to obtain a plurality of discrete sequence assemblies each of which
correspond[] to a potential variant” (id.; see Ans. 4 (citing Spec. 5) (Examiner
finds that Appellants’ Specification defines the term “‘assembling’ . . . as
‘aligning sequences that represent fragments of a longer nucleic acid’”)).
Step (c) of Appellants’ claim 1 requires that “the sequence reads that
make up each of the discrete sequence assemblies [are examined, using a
computer,] to determine which of the potential variants are true and which are
artifacts” (id.; see Ans. 4 (Examiner finds that the term “‘examining’ [is] not
specifically defined [in Appellants’ Specification] and . . . [that the term] is
general and broad on how it is to be performed to establish [a] ‘potential’
variant”)).
Step (d) of Appellants’ claim 1 provides an optional requirement,
wherein “each of the true potential variants [are evaluated to determine whether
they] contain[] a mutation that is known to be associated with the reference
sequence” (id.; see Ans. 4–5 (Examiner finds that this optional step is “not
required nor specifically defined, but could be performed by search of [a]
commercial database”)).
Step (e) of Appellants’ claim 1 requires that “a true sequence variant in
the sample [is identified] based on the determination of which variants are true
and which variants are artifacts” (id.; see Ans. 5 (Examiner finds that the
requirement of “‘identifying a true sequence variant in the sample based on the
determination . . .’ [is] not defined and [represents a] broad general self-
referring step that a true or artifact variant is identified”)).
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The Revised Guidance instructs us first to determine whether any
judicial exception to patent eligibility is recited in the claim. The Revised
Guidance identifies three judicially-excepted groupings identified by the courts
as abstract ideas: (1) mathematical concepts, (2) certain methods of organizing
human behavior such as fundamental economic practices, and (3) mental
processes.
Examiner finds that a judicial exception is found in method steps (b)–
(e) of Appellants’ claim 1 (Ans.3 4; see also id. at 7–9). More specifically,
Examiner finds that method steps (b)–(e) represent a mental process under
the Revised Guidance. We agree with the Examiner’s finding because the
steps comprise “examining,” “determining,” and “identifying,” which can be
performed in the mind of the user. See Elec. Power Grp., LLC v. Alstom
S.A., 830 F.3d 1350, 1354 (Fed. Cir. 2016) (“analyzing information by steps
people go through in their minds, or by mathematical algorithms, without
more, [are] essentially mental processes falling within the abstract idea
category”).
Having determined that Appellants’ claim 1 recites a judicial
exception, the Revised Guidance directs us to next consider whether the
claims integrate the judicial exception into a practical application. On this
record, we find tht Appellants’ claim 1 does not integrate the abstract idea,
i.e., the mental process, into a practical application. To the contrary,
Appellants’ claimed method directs a person of ordinary skill in this art to
generate data, i.e., “a plurality of at least 100 sequence reads from a
sample,” manipulate this data, and produce additional data, i.e., the
identification of “a true sequence variant in the sample based on the

3 Examiner’s November 29, 2018 Answer.
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determination of which variants are true and which variants are artifacts”
(see generally App. Br. 11). The claim identifies a “true sequence,” but does
not do anything practical with the sequence, other than observe it. See
Digitech Image Techs., LLC. v. Elecs. For Imaging, Inc., 758 F.3d 1344,
1351 (Fed. Cir. 2014) (“Without additional limitations, a process that
employs mathematical algorithms to manipulate existing information to
generate additional information is not patent eligible”); see also Gottschalk,
409 U.S. at 71–72 (holding that a computer based algorithm that merely
transforms data from one form to another is not patent-eligible); cf. Diehr,
450 U.S. at 179 n.5 (the claims in Diehr recited a method for operating a
rubber-molding press including the step of “opening the press automatically
when a said comparison [of calculated cure time vs. elapsed time] indicates
equivalence.” Thus, the recited mathematical equation in Diehr had the
practical application of automatically operating a press). Therefore, on this
record, we conclude that the ineligible subject matter in Appellants’ claim 1
is not integrated into a practical application.
Having determined that the judicial exception is not integrated into a
practical application, the Revised Guidance requires us to evaluate the
additional elements of Appellants’ claimed invention, individually and in
combination, to determine whether they provide an inventive concept, such
as a specific limitation beyond the judicial exception that is not well-
understood, routine, and conventional in the field, or instead simply appends
well-understood, routine, conventional activities previously known to the
industry, specified at a high level of generality, to the judicial exception.
See 84 Fed. Reg. 51. “Whether something is well-understood, routine, and
conventional to a skilled artisan at the time of the patent, however, is a
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factual determination.” Berkheimer v. HP Inc., 881 F.3d 1360, 1369 (Fed.
Cir. 2018).
On this record, Examiner finds that Van Eijk4 discloses
obtain[ing] enriched forms of DNA from the whole genome and
the sequence information from multiple human biopsy samples
and . . . methodology [to analyze the samples] for specific
cancer associated sequences with a normal . . . reference
sequence and provide a report of sensitivity as well as false
positives/negatives as verification of the variants within a
sample.
(Ans. 6.) In addition, Examiner finds that Dahl5 discloses “a method of
using massive parallel sequencing (MPS) for analysis and discovery of
cancer mutations, more specifically for enriched genomic sequences by
using purified DNA from cell lines and clinical blood samples, and provide
enrichment through PCR for a variety of cancer associated genes” (id. at 5–
6). Examiner further finds that Boisvert6
provides for methods of assembly and analysis of sequence
reads using de Bruijn graphs and the analysis of genomic
sequences. In the comparison of assemblers and sequence data
analysis, Boisvert . . . teaches that different methods and data
for various depths are important in determining sequence
variants and artifacts.
(Id. at 6.)
In addition, Appellants disclose:

4 R. Van Eijk et al., Sensitive and Specific KRAS Somatic Mutation Analysis
on Whole-Genome Amplified DNA from Archival Tissues, 12 JOURNAL OF
MOLECULAR DIAGNOSTICS 27–34 (2010).
5 F. Dahl et al., Multigene amplification and massively parallel sequencing
for cancer mutation discovery, 104 PNAS 9387–9392 (2007).
6 S. Boisvert et al., Ray: Simultaneous Assembly of Reads from a Mix of
High-Throughput Sequencing Technologies, 17 JOURNAL OF
COMPUTATIONAL BIOLOGY 1519–1533 (2010).
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The sequence reads can be assembled to obtain a
plurality of discrete sequence assemblies that each corresponds
to a potential variant using a variety of different methods.
Sequence reads may be assembled using any suitable method,
basic steps of which are described in a variety of publications
such as Myers et al. (Science 200 287: 2196–204), Batzoglou et
al (Genome Research 2002 12: 177–89), Dohm et al (Genome
Research 2007 17 : 1697–706) and Boisvert et al (Journal of
Computational Biology 2010 17: 1519–33), which are al
incorporated by reference for disclosure of those methods.
(Spec. 10: 14–20.) Appellants further disclose that “[t]he use of de-Bruijn
graphs to assemble reads is described in US Pat 8,209,130; U.S. Pub.
2011/0004413, U.S. Pub. 2011/0015863, and U.S. Pub. 2010/0063742” and
a minimum de-Bruin [sic] sequence may be defined by a
spanning subgraph, or tree of the directed weighted graph,
using the BEST (de Bruijn, Ehrenfest, Smith and Tutte)
theorem (which provides a product formula for the number of
Eulerian circuits in directed (oriented) graphs, and relates the
number of Eulerian circuits to the number of rooted spanning
trees at a given vertex). Determining spanning trees of a
directed graph may be achieved by any convenient method (see,
e.g., Tarjan et al. Proc FOCS 1984 12-20).
(Spec. 11: 7–9 and 21–27.)
Based on Examiner’s findings and the evidence cited in Appellants’
Specification, we find that when elements of Appellants’ claimed invention
are evaluated, individually and in combination, they simply append well-
understood, routine, conventional activities previously known to the
industry, specified at a high level of generality, to the judicial exception (see
id. at 7–10; see also Spec. 10: 14–20, 11: 7–9, and 11: 21–27).
For the foregoing reasons, we are not persuaded by Appellants’
contention that step (a) of Appellants’ claimed method “recites more than
just generating or obtaining sequence data,” because step (a) requires that “a
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sample . . . has been enriched for a genomic region” and that “[t]he
sequence reads are generated by: i. enriching for the genomic region; and
ii. sequencing the enriched genomic region” and that Examiner failed to
consider: “the combination of elements in claim 1” or “the claim as a
whole” (App. Br. 4–5; see also Reply Br. 2–4). For the same reasons, we
are not persuaded by Appellants’ contention that “the recitations of claim 1
include the physical step of generating sequencing reads from an enriched
genomic region, specific steps that add meaningful limits, particularly with
regard to the assembly of a plurality of discrete sequence assemblies, each of
which corresponds to a potential variant” (id. at 6; see also id. at 10
(“Appellant[s] submit[] that the Office has failed to show that the additional
elements recited in the dependent claims are well-understood, routine, or
conventional”)).
As discussed above, Appellants’ claimed method directs a person of
ordinary skill in this art to generate data, i.e., “a plurality of at least 100
sequence reads from a sample,” manipulate this data, and produce additional
data, i.e., the identification of “a true sequence variant in the sample based
on the determination of which variants are true and which variants are
artifacts” (see generally App. Br. 11). When considered as a whole,
Appellants’ claimed invention is not directed to a practical application, and
the additional elements of Appellants’ claim, when considered individually
and in combination, simply append well-understood, routine, conventional
activities previously known to the industry, specified at a high level of
generality, to the judicial exception. Therefore, we are not persuaded by
Appellants’ contention that their claimed method provides an improved
technological result over the prior art (see App. Br. 6–8; see also Reply Br.
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4–6). Cf. McRO, Inc. v. Bandai Namco Games America Inc., 837 F.3d 1299,
1316 (Fed. Cir. 2016) (holding that the claim in that case is directed to a
technological improvement over existing 3-D animation techniques and,
therefore, not directed to an abstract idea); BASCOM Global Internet Servs.,
Inc. v. AT&T Mobility LLC, 827 F.3d 1341, 1351 (Fed. Cir. 2016) (holding
that the ‘606 patent is claiming a technology-based solution (not an abstract
idea based solution) to filter content on the Internet that overcomes existing
problems with other Internet filtering systems); see generally Ans. 11–12.
Further, the method of Appellants’ claim 1 does not transform matter; to the
contrary, Appellants’ method, at best, transforms information, i.e., data. See
Gottschalk, 409 U.S. at 71–72 (holding that a computer based algorithm that
merely transforms data from one form to another is not patent-eligible).
We are not persuaded by Appellants’ contention that Dahl fails to
disclose step (b) of Appellants’ claimed invention, which is disclosed by
Boisvert (App. Br. 8; cf. Ans. 6–7; see also Spec. 10: 14–20, 11: 7–9, and
11: 21–27). We are also not persuaded by Appellants’ contention that
Examiner “does not identify anything in Boisvest [sic] . . . to show that
assembling sequence reads from an enriched genomic region was
conventional” (Reply Br. 6). On this record, notwithstanding Appellants’
unsupported assertion to the contrary, the weight of the evidence as cited by
Examiner, and disclosed in Appellants’ Specification, weighs in favor of a
finding that graph theory, a minimal de-Bruijn sequence, or a BEST theorem
were well-understood, routine, conventional activities previously known to
the industry, specified at a high level of generality in Appellants’ claimed
invention (see Ans. 6–7; see also Spec. 10: 14–20, 11: 7–9, and 11: 21–27).
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We are not persuaded by Appellants’ contention that “the combination
of elements must not be well-understood, routine and conventional to a
skilled artisan,” because Appellants’ claimed invention is free of a prior art
rejection (see App. Br. 9). Initially, we note that the additional elements of
Appellants’ claims, such as assembling the sequence reads using processes
such as graph theory and using a computer to examine sequence reads, are
computer based algorithms. “[T]he novelty of the mathematical algorithm is
not a determining factor at all,” but is “treated as though it were a familiar
part of the prior art.” Flook, 437 U.S. at 591–92. Appellants have given us
no reason to depart from this guiding principle. As the Court in Flook
explained, “[v]ery simply, our holding today is that a claim for an improved
method of calculation, even when tied to a specific end use, is unpatentable
subject matter under § 101.” Flook, 437 U.S. at 595 (fn. 18). Thus,
Appellants’ additional elements, even if novel when combined, do not make
the claim eligible for a patent under § 101.
Further, we note that the Supreme Court cautioned that even though
the § 101 patent-eligibility inquiry and prior art inquiries might sometimes
overlap, “to shift the patent-eligibility inquiry entirely to these later sections
risks creating significantly greater legal uncertainty, while assuming that
those sections can do work that they are not equipped to do.” Mayo
Collaborative Servs. v. Prometheus Labs., Inc., 566 U.S. 66, 90 (2012). See
also Diamond v. Diehr, 450 U.S. 175, 188–89 (1981) (“[t]he ‘novelty’ of
any element or steps in a process, or even of the process itself, is of no
relevance in determining whether the subject matter of a claim falls within
the § 101 categories of possibly patentable subject matter.”). Putting this
into practice, the Federal Circuit has held that “a claim for a new abstract
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idea is still an abstract idea. The search for a § 101 inventive concept is thus
distinct from demonstrating § 102 novelty.” Synopsys, Inc. v. Mentor
Graphics Corp., 839 F.3d 1138, 1151 (Fed. Cir. 2016) (holding claims to a
method for converting a hardware-independent user description of a logic
circuit are ineligible because the use of assignment conditions as an
intermediate step in the translation process is an aid to a mental process and
does not change the nature of the claims to being directed to more than an
abstract idea).

Claims 10–12:
Appellants contend that “claims 10 to 12 recite[] various techniques
for assembling the sequence reads, such as using graph theory, a minimal
de-Bruijn sequence, or a BEST theorem. These elements in combination
with the elements recited in claim 1 are not well-understood, routine, or
conventional” (App. Br. 10; see Reply Br. 7). We are not persuaded. For
the reasons set forth above, we find that the weight of the evidence on this
record weighs in favor of a finding that graph theory, a minimal de-Bruijn
sequence, or a BEST theorem were well-understood, routine, conventional
activities previously known to the industry, specified at a high level of
generality in Appellants’ claimed invention (see Ans. 6–7; see also Spec. 10:
14–20, 11: 7–9, and 11: 21–27).
CONCLUSION OF LAW
The preponderance of evidence of record fails to support Examiner’s
finding that Appellants’ claimed invention is directed to patent ineligible
subject matter. The rejection of claims 1 and 10–12 under 35 U.S.C. § 101
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is affirmed. Claims 2–9 and 13–19 are not separately argued and fall with
claim 1.

TIME PERIOD FOR RESPONSE
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