Agilent Technologies, Inc.

Patent Trials and Appeals Board

Oct 27, 2020

14684242 - (D) (P.T.A.B. Oct. 27, 2020)

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.
14/684,242 04/10/2015 Ashutosh 20150050-01 7642
22878 7590 10/27/2020
Agilent Technologies, Inc.
Global IP Operations
5301 Stevens Creek Blvd
Santa Clara, CA 95051
EXAMINER
WISE, OLIVIA M.
ART UNIT PAPER NUMBER
1631
NOTIFICATION DATE DELIVERY MODE
10/27/2020 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,
ARJUN VADAPALLI, and JAYATI GHOSH
____________

Appeal 2019-006566
Application 14/684,242
Technology Center 1600
____________

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

ADAMS, Administrative Patent Judge.

DECISION ON APPEAL
Pursuant to 35 U.S.C. § 134(a), Appellant1 Appeals2 from Examiner’s
decision to reject claims 1–17 (Final Act.3 2). We have jurisdiction under
35 U.S.C. § 6(b).
We AFFIRM.

1 Appellant identifies “Agilent Technologies, Inc.” as the real party in
interest (Appellant’s May 1, 2019 Appeal Brief (Appeal Br.) 2).
2 Appellant acknowledges that this Appeal is related to Appeal 2019–002083
(Application 14/288,299, now abandoned) (Appeal Br. 2). A Decision
affirming the subject matter eligibility rejection in Appeal 2019-002083 was
entered August 2, 2019 (see generally Appellant’s September 3, 2019 Reply
Brief (Reply Br.) 2).
3 Examiner’s December 13, 2018 Final Office Action.
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STATEMENT OF THE CASE
Appellant’s disclosure relates to methods for detecting genomic
alterations, (Spec.4 5). Appellant’s claims 1, 2, 4, 12, and 16 are reproduced
below:
1. A method for detecting genomic alterations, comprising:
enriching a genomic sample for a plurality of genomic
backbone regions and a plurality of genomic mutation regions
of interest in a genomic locus of a subject;
obtaining a plurality of sequence reads from the enriched
genomic sample that includes sequence reads for the plurality
of genomic backbone regions and sequence reads for the
plurality of genomic mutation regions of interest;
obtaining a plurality of sequence reads from
corresponding genomic backbone regions and genomic
mutation regions of at least one reference genomic sample;
assembling, via a processor, an assembly of the plurality
of sequence reads from the enriched genomic sample and the at
least one reference genomic sample; and
determining, via the processor utilizing the assembly,
whether the genomic locus has a copy number variation (CNV)
or a sequence variation, or a CNV and a sequence variation.
(Appeal Br. 29.)
2. The method of claim 1, wherein determining whether the
genomic locus has a sequence variation comprises:
(i) identifying genetic differences in the plurality of
sequence reads of the enriched genomic sample as compared to
the sequence reads from the reference genomic sample; and
(ii) determining which potential variants are true and
which potential variants are artifacts by examining the sequence
reads that make up each of the discrete sequence assemblies.
(Id.)

4 Appellant’s April 10, 2015 Specification.
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4. The method of claim 1, wherein determining whether the
genomic locus comprises a sequence variation further
comprises determining whether the genomic locus has a loss of
heterozygosity (LOH), comprising:
(i) identifying genetic differences in the sequence reads
of the enriched genomic sample as compared to the sequence
reads from the at least one reference genomic sample; and
(ii) comparing the identified genetic differences to known
frequencies of genetic differences in a population to identify a
genomic region in the first genomic locus that has a LOH.
(Id. at 30.)
12. The method of claim 1, wherein the assembling uses graph
theory.
(Id. at 31.)
16. A system for detecting genomic alterations comprising:
a database configured to store reference sequence reads
for one or more reference genomes; and
a genomic sequence computing device configured to:
obtain information from a probe or bait design used for
enrichment of a plurality of genomic backbone regions and a
plurality of genomic mutation regions of interest in a genomic
locus of a subject;
obtain a plurality of sequence reads from the enriched
genomic sample that includes sequence reads for the plurality
of genomic backbone regions and sequence reads for the
plurality of genomic mutation regions of interest in a genomic
locus of a subject;
obtain from the database a plurality of reference
sequence reads from corresponding genomic backbone regions
and genomic mutation regions of at least one reference genome;
assemble an assembly of the plurality of sequence reads
from the enriched genomic sample and the at least one
reference genomic sample; and
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determine, based on the assembly, whether the genomic
locus has a copy number variation (CNV) or a sequence
variation, or a CNV and a sequence variation.
(Id. at 32.)

Grounds of rejection before this Panel for review:5
Claims 1–17 stand rejected under 35 U.S.C. § 112(b).
Claims 1–3 and 6–17 stand rejected under 35 U.S.C. § 102(a)(1) as
anticipated by Ashutosh ’724.6
Claims 1, 6, 7, 10, 11, and 15–17 stand rejected under 35 U.S.C.
§ 103(a) as unpatentable over the combination of Ohgami7 and NCBI.8
Claims 1, 6, 7, 10, 11, and 15–17 stand rejected under 35 U.S.C.
§ 103(a) as unpatentable over the combination of Ohgami, NCBI, and
Ashutosh 2014.9

5 Copending Application 14/288,299 abandoned November October 24,
2019. Therefore, the nonstatutory double patenting rejection over this
copending Application 14/288,299 is moot and will not be discussed further
(see generally Reply Br. 2).
6 Ashutosh et al., US 2015/0073724 A1, published Mar. 12, 2015.
7 Ohgami et al., Next-generation sequencing of acute myeloid leukemia
identifies the significance of TP53, U2AF1, ASXL1, and TET2 mutations, 28
Modern Pathology 706–714 (2015).
8 GRCh37-hg19-Genome-Assembly-NCBI (Feb. 27, 2009), available at
https://www.ncbi.nlm.nih.gov/assembly/GCA_000001405.1, last accessed
June 22, 2018.
9 Ashutosh et al., SNPPET: A Fast and Sensitive Algorithm for Variant
Detection and Confirmation From Targeted Sequencing Data, Poster
presented at American Society of Human Genetics (ASHG) (Oct. 18-22
(2014).
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Claims 1, 2, 4–8, 10, 11, and 15–17 stand rejected under 35 U.S.C.
§ 103(a) as unpatentable over the combination of Koboldt10 and Cancer
Network.11
Claims 12–14 stand rejected under 35 U.S.C. § 103(a) as unpatentable
over the combination of Koboldt, Cancer Network, and Kaptcianos.12
Claims 1–17 stand rejected under 35 U.S.C. § 101.

DEFINITENESS:
ISSUE
Does the preponderance of evidence support Examiner’s conclusion
that the term “genomic backbone regions,” as set forth in Appellant’s claims,
is indefinite?

10 Koboldt et al., VarScan 2: Somatic mutation and copy number alteration
discovery in cancer by exome sequencing, 22 Genome Research 568–576
(2012).
11 The Cancer Genome Atlas Research Network, Integrated gemonic
analyses of ovarian carcinoma, 474 Nature 609–615 (2011).
12 Kaptcianos, A Graph Theoretical Approach to DNA Fragment Assembly, 7
American Journal of Undergraduate Research 1–18 (2008).
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FACTUAL FINDINGS (FF)
FF 1. Appellant’s Figure 3 is reproduced below:

Figure 3 provides a schematic of different genomic regions in a
genomic locus and the baits used to generate an enriched
genomic sample that includes a plurality of genomic backbone
regions (for the “Genomic Backbone”) and a plurality of
genomic mutation regions of interest (for the SNPs, clinical
disease-associated regions, and other targeted exons).
(Spec. ¶ 59; see also id. ¶ 13 (Appellant’s Figure 3 illustrates “[b]ait design
schema used for genomic sequence enrichment showing backbone, SNP,
clinical gene (ClinGen) disease associated region, and targeted exon
regions”).)
FF 2. Appellant discloses:
[E]nriched genomic samples (for both the test/sample and
reference genomes) include a plurality of genomic backbone
regions and a plurality of genomic mutation regions of interest
in a genomic locus of a subject. Genomic backbone regions are
generally used to determine the genome-wide copy number of
the locus of interest whereas genomic mutation regions are

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employed to determine both copy-number and genetic
alterations at the desired regions in the genomic locus.
(Spec. ¶ 59.)
FF 3. Ghosh declares that “[a] person working in the field of sequencing-
based genomic analysis would understand that a ‘genomic background
region’ is a region of the genome that does not include SNPs, clinical
disease-associated regions, and other targeted exons, in comparison to other
regions of the genome which are also being analyzed” (Ghosh Decl.13 ¶ 4;
see also id. ¶ 6 (Ghosh declares that “[a] skilled person would also
understand that at least some sequence reads for the genomic backbone
regions are different than the sequence reads for the genomic mutation
regions”)).
FF 4. Ghosh declares that “[t]he use of the term ‘genomic backbone
regions’ in . . . [Appellant’s Specification] is consistent with the use of that
term in the field” (Ghosh Decl. ¶ 7; see also id. ¶¶ 7–9 (Ghosh provides
evidence to establish that the term “genomic backbone regions” is a
recognized term in this art)).
ANALYSIS
Examiner finds that “[t]he metes and bounds of the term ‘genomic
backbone regions’ is not clearly defined in the instant specification and is
not a well-known term in the art” (Ans.14 15). We are not persuaded.
Appellant’s Specification discloses two different regions of an
enriched genomic sample: (1) genomic backbone regions and (2) genomic
mutation regions of interest (FF 1–2). Appellant’s Specification further

13 Declaration of Jayali Ghosh signed September 26, 2018.
14 Examiner’s July 1, 2019 Answer.
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discloses that genomic mutation regions of interest are those that contain
SNPs, clinical disease-associated regions, and other targeted exons (FF 1;
see also FF 2). Consistent with Appellant’s Specification, Ghosh declares
that those of ordinary skill in this art “would understand that a ‘genomic
background region’ is a region of the genome that does not include SNPs,
clinical disease-associated regions, and other targeted exons” (FF 3; see also
FF 4; see generally Reply Br. 4–7). Thus, those of ordinary skill in this art
would understand that once genomic mutation regions of interest are
identified, those regions that are not genomic mutation regions of interest are
genomic backbone regions, from which, according to Appellant’s claimed
invention, sequence reads may be obtained from a plurality of these genomic
backbone regions.
Therefore, even if, as Examiner asserts, “‘clinical-disease associated
regions’ and ‘other targeted exons’ are subjective and variable terms that can
vary based on the user of the invention as each user may have a different
definition of which exons are targeted or which regions are clinically-disease
associated” (Ans. 16); once those regions and exons are identified a person
of ordinary skill in the art would understand what regions represent genomic
backbone regions (see FF 1–4; see generally Reply Br. 8–9). See also In re
Miller, 441 F.2d 689, 693 (CCPA 1971) (“[B]readth is not to be equated
with indefiniteness.”).
For the foregoing reasons, we are not persuaded by Examiner’s
assertion that because various prior art references make use of different
genomic backbone regions “the term ‘genomic backbone’ is not a well-

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established term of the art” (Ans. 16). In addition, we recognize Examiner’s
reliance on Zepeda-Mendoza.15 Zepeda-Mendoza discloses:
Identical sequences with a minimal length of about 300 base
pairs (bp) have been involved in the generation of various
meiotic/mitotic genomic rearrangements through non-allelic
homologous recombination (NAHR) events. Genomic
disorders and structural variation, together with gene
remodelling processes have been associated with many of these
rearrangements. Based on these observations, we identified and
integrated all the 100% identical repeats of at least 300 bp in the
NCBI version 36.2 human genome reference assembly into
nonoverlapping regions, thus defining the Identical Repeated
Backbone (IRB) of the reference human genome.
(Zepeda-Mendoza 1; see also id. at 9 (Zepeda-Mendoza discloses that
Identical Repeated Backbone (IRB) “need not . . . be identical in different
individuals due to the presence of SNPs, microindels, and structural
variation”)). Examiner failed to establish an evidentiary basis on this record
to support a finding that those of ordinary skill in this art would consider
IRBs to represent genetic backbone regions (see generally Zepeda-Mendoza
2–3 (providing a definition of the term IRB); cf. FF 1–4 (defining the term
genetic backbone regions)). Therefore, we are not persuaded by Examiner’s
reliance on Zepeda-Mendoza to support an assertion that genomic backbone
regions “can include SNPs or structural variations and are therefore not
identical in different individuals” (Ans. 16 (citing Zepeda-Mendoza 9: col. 2,
para. 3); see generally Reply Br. 8).

15 Zepeda-Mendoza et al., Identical repeated backbone of the human
genome, 11 BMC Genomics 60 (2010) (available at
http://www.biomedcentral.com/1471-2164/11/60).
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CONCLUSION
The preponderance of evidence fails to support Examiner’s conclusion
that the term “genomic backbone regions,” as set forth in Appellant’s claims,
is indefinite. The rejection of claims 1–17 under 35 U.S.C. § 112(b) is
reversed.

ANTICIPATION:
ISSUE
Does the preponderance of evidence on this record support
Examiner’s finding that Ashutosh ’724 teaches Appellant’s claimed
invention?
FACTUAL FINDINGS (FF)
FF 5. Ashutosh ’724 discloses:
Provided herein is 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.
(Ashutosh ’724, Abstract; see also id. ¶ 6; Ans. 3–4.)
FF 6. Ashutosh ’724 discloses “a computer system comprising a memory
comprising: a) a database of sequences; and b) an executable program for
performing the present method” and “a computer-readable storage medium
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comprising instructions for performing the present method” (Ashutosh ’724
¶¶ 7–8; see also id. ¶ 73 (Ashutosh ’724 discloses that its “method can be
implemented on a computer”); Ans. 3–4).
FF 7. Ashutosh ’724 defines “[t]he term ‘sequence variant’” as “a nucleic
acid sequence that is different from a reference sequence at at least one
position. Examples of sequence variants include sequences containing SNPs
and somatic mutations” (Ashutosh ’724 ¶ 24).
FF 8. Ashutosh ’724’s
method may be performed on sequence reads that have been
obtained from an sample that has been enriched for a particular
genomic region, i.e., a sample that contains fragments of
genomic DNA that correspond to a particular genomic region,
where the fragments have been enriched from fragmented total
genomic DNA. In some cases, the enriched genomic region
may contain a gene that has a mutation that is associated with
one or more cancers. . . . In particular cases the sample may
contain fragments of genomic DNA that correspond to multiple
different genomic regions . . . that have been enriched, where
each region may correspond 10 to a gene, e.g., an oncogene.
(Ashutosh ’724 ¶ 38; see also id. ¶¶ 39–40 (disclosing sources of enriched
genomic regions); Ans. 3–4.)
FF 9. Ashutosh ’724 discloses that
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. . . . In yet
other embodiments, sequence reads can be assembled by
aligning each read to a reference sequence such as a reference
genome.
(Ashutosh ’724 ¶ 47; see Ans. 4.)
FF 10. Ashutosh ’724 discloses that “graph theory is used to assemble the
reads,” wherein “assembling the sequence reads may comprise making a
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directed graph, such as a de Bruijn graph” or “directed weighted graph,”
wherein “[a] potential sequence is represented in the directed weighted
graph by an Euler path.”
In such cases, a minimum de-Bruin 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).
(Ashutosh ’724 ¶¶ 48–50.)
FF 11. Ashutosh ’724 discloses that its
method may involve enriching for one or more pairs of
genomic regions, where each pair of genomic regions is
composed of a genomic region of interest (e.g., a cancer-
associated gene) and a region that is adjacent to (and, in some
cases, overlapping with) the genomic region of interest. . . . In
some cases, the sequence reads for the adjacent region can be
used to, for example, adjust the results to accommodate any
sampling bias.
(Ashutosh ’724 ¶ 55; see Ans. 3.)
ANALYSIS
Examiner finds that Ashutosh ’724 anticipates Appellant’s claimed
invention (see Ans. 3–7; FF 5–11).
Appellant contends that Ashutosh ’724 “does not disclose the step of
obtaining a plurality of sequence reads from an enriched genomic sample
that includes a plurality of genomic backbone regions and a plurality of
genomic mutation regions of interest” (Appeal Br. 23; see also Reply Br.
16). We are not persuaded. Ashutosh ’724’s method comprises obtaining:
a plurality of sequence reads from a sample that has been enriched for a
genomic region and that its “method may involve enriching for one or more
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pairs of genomic regions, where each pair of genomic regions is composed
of a genomic region of interest (e.g., a cancer-associated gene) and a region
that is adjacent to . . . the genomic region of interest” (FF 5 and 11; see,
generally, Ans. 3 and 31 (Examiner found that a region that is adjacent to a
genomic region of interest is a genomic backbone region). Appellant failed
to establish an evidentiary basis on this record to support a finding that a
region that is adjacent to a genomic region of interest is not a genomic
backbone region (see Appeal Br. 23 (Appellant recognizes that Ashutosh
’724 “teaches that each pair of genomic regions is composed of a genomic
region of interest and a region that is adjacent to the genomic region of
interest, but [contends that] this is not a teaching of the element which is
recited in the claim”); see also Reply Br. 16 (Ashutosh ’724 “does not teach
that genomic backbone regions are enriched, nor any of the other steps
where sequence reads for genomic backbone regions are required”)).
Ashutosh ’724 discloses the use of “a computer system comprising a
memory comprising: a) a database of sequences; and b) an executable
program for performing [its] method,” which comprises, inter alia,
“assembling . . . sequence reads to obtain a plurality of discrete sequence
assemblies that correspond to potential variants” and “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” (FF
5–6). Ashutosh ’724 defines “[t]he term ‘sequence variant’” as “a nucleic
acid sequence that is different from a reference sequence at at least one
position. Examples of sequence variants include sequences containing SNPs
and somatic mutations” (FF 7). Therefore we are not persuaded by
Appellant’s contention that Ashutosh ’724 “does not disclose the step of
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determining, via the processor utilizing the assembly, whether the genomic
locus has . . . a sequence variation” (Appeal Br. 23).
CONCLUSION
The preponderance of evidence on this record supports Examiner’s
finding that Ashutosh ’724 teaches Appellant’s claimed invention. The
rejection of claim 1 under 35 U.S.C. § 102(a)(1) as being anticipated by
Ashutosh ’724 is affirmed. Claims 2, 3, and 6–17 are not separately argued
and fall with claim 1.

OBVIOUSNESS:
ISSUE
Does the preponderance of evidence relied upon by Examiner support
a conclusion of obviousness?
FACTUAL FINDINGS (FF)
FF 12. Ohgami discloses the design of “a panel of genes that are commonly
mutated in myeloid neoplasms and assess[ment] [of] their frequency in a
well-defined cohort of AML patients and the relevance of these gene
mutations in diagnosis and prognosis” (Ohgami 706; see generally Ans. 8).
FF 13. Ohgami discloses the design of “[a] Haloplex . . . target enrichment
panel of 45 selected exons in 19 genes (RUNX1, ASXL1, TET2, CEBPA,
IDH1, IDH2, DNMT3A, FLT2, NPM1, TP53, NRAS, EZH2, CBL, 2AF1,
SF3B1, SRSF2, JAK2, CSF2R, and SETBP1)” (Ohgami 707).
FF 14. Ohgami discloses the identification of “specific frequencies and
patterns of mutations in AML, and novel associations of mutations in the
genes TP53, U2AF1, ASXL1, and TET2 with AML subtype, morphology,
and prognosis” (Ohgami 706–707; see generally Ans. 8).
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FF 15. Examiner finds that Ohgami fails to disclose the assembly of a
“plurality of sequence reads from the at least one reference genomic sample”
and relies on NCBI to disclose the “assembly of reads from PCR and whole
genome sequencing products from human subjects that represent [a]
reference human genome” (Ans. 9 (citing NCBI 1–2)).
FF 16. Examiner finds that the combination of Ohgami and NCBI fails to
suggest
determining which of the potential variants are true and which
are the potential variants are artifacts by examining the
sequence reads that make up each of the discrete sequence
assemblies in claim 2; determining whether the genomic locus
has a sequence variation comprises using a SNPPET algorithm
in claim 3; outputting a report comprising whether the enriched
genomic sample has a sequence variation in claim 8; and
wherein the report indicates whether the enriched genomic
sample contains a mutation and provides publicly available
information about the reference sequence in claim 9
and relies on Ashutosh 2014 to make up for these deficiencies in the
combination of Ohgami and NCBI (Ans. 10).
FF 17. Examiner finds that Koboldt
discloses a software algorithm for detecting somatic mutations
and copy number alterations in exome data from tumor-normal
pairs . . .[,] applying the algorithm to exome sequence data from
151 patients with high-grade serous ovarian adenocarcinoma
obtained from . . . [Cancer Network] for tumor-normal pairs[,
and] . . . utilizing the exome sequence data to perform both
variant detection and copy number alteration
detections . . . [wherein] a computer with a memory system to
store the data operated on the [software algorithm] program and
processor [is used] in order to run the software.
(Ans. 11 (citing Koboldt Abstract, 568, 569, 574, and 575).)

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FF 18. Examiner finds that Koboldt fails to
disclose enriching a genomic sample for a plurality of genomic
backbone regions and a plurality of genomic mutation regions
of interest in a genomic locus of a subject, obtaining a plurality
of sequence reads from the enriched genomic sample that
includes the plurality of genomic backbone regions and the
plurality of genomic mutation regions of interest, obtaining a
plurality of sequence reads from corresponding genomic
backbone regions and genomic mutation regions of at least one
reference genomic sample, and assembling the plurality of
sequence reads from the enriched genomic sample and the at
least one reference genomic sample in claims 1, 16 and 17;
wherein the enriched genomic sample is from a human in claim
11; and wherein the enriched genomic sample is obtained using
baits designed to target locations in the genome based on
known SNP allelic frequency and estimated properties of the
genomic regions of interest in the reference genome in claim 15
and relies on Cancer Network to make up for these deficiencies in Koboldt
(Ans. 13).
FF 19. Examiner finds that the combination of Koboldt and Cancer Network
fails to suggest “assembling us[ing] graph theory in claim 12; wherein the
assembling is done using a minimal de-Bruijn sequence in claim 13; and
wherein the assembling is done using a BEST theorem in claim 14” and
relies on Kaptcianos to make up for these deficiencies in the combination of
Koboldt and Cancer Network (Ans. 14).
ANALYSIS
The rejection over the combination of Ohgami and NCBI:
Based on the combination of Ohgami and NCBI, Examiner concludes
that, at the time Appellant’s invention was made, it would have been prima
facie obvious “to obtain the reads and assemble them in order to obtain the
reference sequence taught by Ohgami . . . that inherently includes the
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corresponding regions in the enriched genomic sample because the reference
sequence is for the entire human genome” (Ans. 9). In this regard, Examiner
reasons that
each region in [Ohgami’s] target enrichment panel includes
both the . . . region encompassing the mutation of interest as
well as regions other than the mutation of interest within the
sequence read as there is no limitation on the size of the regions
necessary nor a requirement that the regions must reside in
different genes or exons.
(Ans. 9.) We are not persuaded.
“Inherency . . . may not be established by probabilities or possibilities.
The mere fact that a certain thing may result from a given set of
circumstances is not sufficient.” In re Robertson, 169 F.3d 743, 745 (Fed.
Cir. 1999) (citations and internal quotation marks omitted). As Appellant
explains, “Ohgami indicates that the target enrichment panel was for
genomic mutation regions of interest” (Appeal Br. 25; see also FF 12–13).
Thus, Appellant contends, although Examiner
asserts that Ohgami discloses obtaining reads for a target
enrichment panel for a plurality of genomic regions in the
patient samples, and that this reads on the broadest reasonable
interpretation of “obtaining a plurality of sequence reads from
an enriched genomic sample that includes a plurality of
genomic backbone regions” . . . there is no basis [in Ohgami]
for assuming that a plurality of genomic regions would include
genome backbone regions.
(Appeal Br. 25; see also Reply Br. 17.) We agree. Examiner failed to
establish an evidentiary basis on this record to support a conclusion that the
combination of Ohgami and NCBI makes obvious a plurality of genomic
regions that includes genome backbone regions. See, In re Kahn, 441 F.3d
977, 988 (Fed. Cir. 2006) (“[R]ejections on obviousness grounds cannot be
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sustained by mere conclusory statements; instead, there must be some
articulated reasoning with some rational underpinning to support the legal
conclusion of obviousness.”).

The rejection over the combination of Ohgami, NCBI, and Ashutosh 2014:
Based on the combination of Ohgami, NCBI, and Ashutosh 2014,
Examiner concludes that, at the time Appellant’s invention was made, it
would have been prima facie obvious
to utilize the SNPPET algorithm taught by Ashutosh [2014] . . .
for sequence variant calling in the method taught by Ohgami . .
. and NCBI, in order to improve sequence variant detection for
low allele fraction variants or in complex genotypes.
Furthermore, one of ordinary skill in the art would predict that
SNPPET algorithm taught by Ashutosh [2014] . . . could be
readily applied to the method taught by Ohgami . . . and NCBI
with a reasonable expectation of success since Ohgami . . .
discloses utilizing . . . software that includes the SNPPET
algorithm.
(Ans. 11.) We are not persuaded.
Examiner failed to establish that Ashutosh 2014 makes up for the
deficiencies in the combination of Ohgami and NCBI discussed above (see
Appeal Br. 25 (Appellant contends that Ashutosh 2014 “does not disclose or
suggest the use of ‘genome backbone regions’. For at least the reasons in
the preceding section, this rejection is improper and should be reversed”);
see also Reply Br. 18).

The rejection over the combination of Koboldt and Cancer Network:
Based on the combination of Koboldt and Cancer Network, Examiner
concludes that, at the time Appellant’s invention was made, it would have
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been prima facie obvious “to perform the steps disclosed by . . . [Cancer
Network] to produce the data utilized in Koboldt . . . [and] to enter the data
into the software taught by Koboldt . . . in order to analyze the [data]” to
determine genomic variations (Ans. 14). According to Examiner, Cancer
Network
discloses that the exome sequence data from the tumor DNA
and normal DNA was prepared by preparing sequencing
libraries for the exomes using an exome kit, and then
sequencing and aligning the reads . . ., which reads on the
broadest reasonable interpretation of “enriching a genomic
sample for a plurality of genomic backbone regions and a
plurality of genomic mutation regions of interest in a genomic
locus of a subject and obtaining a plurality of sequence reads
from an enriched genomic sample that includes a plurality of
genomic backbone regions”. . . . Specifically, each region in
the exome sequence data [disclosed by Cancer Network]
includes both the a region encompassing the mutation of
interest as well as regions other than the mutation of interest
within the sequence read as there is no limitation on the size of
the regions necessary nor a requirement that the regions must
reside in different genes or exons.
(Ans. 33.) We are not persuaded.
As Appellant explains, neither Koboldt nor Cancer Network disclose
“enriching for a plurality of genomic backbone regions” or recognizes “the
use of genomic backbone regions in addition to genomic mutation regions of
interest” (Appeal Br. 26; see also Reply Br. 18 (Appellant contends that “the
‘broadest reasonable interpretation’ does not mean that claim limitations can
be ignored”)). We agree. Examiner failed to establish an evidentiary basis
on this record to support a conclusion that the combination of Koboldt and
Cancer Network makes obvious the enrichment of a genomic sample for a
plurality of genomic backbone regions in addition to a plurality of genomic
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mutation regions of interest and obtaining sequence reads from both sets of
regions (cf. FF 17–19). See, In re Kahn, 441 F.3d at 988 (“[R]ejections on
obviousness grounds cannot be sustained by mere conclusory statements;
instead, there must be some articulated reasoning with some rational
underpinning to support the legal conclusion of obviousness.”).

The rejection over the combination of Koboldt, Cancer Network, and
Kaptcianos:
Based on the combination of Koboldt, Cancer Network, and
Kaptcianos, Examiner concludes that, at the time Appellant’s invention was
made, it would have been prima facie obvious to utilize graph theory and the
BEST theorem, as disclosed by Kaptcianos, to assemble the sequence reads
suggested by the combination of Koboldt and Cancer Network (see Ans. 15).
We are not persuaded.
Examiner failed to establish that Kaptcianos makes up for the
deficiencies in the combination of Koboldt and Cancer Network discussed
above (see generally Appeal Br. 27; Reply Br. 19).
CONCLUSION
The preponderance of evidence relied upon by Examiner fails to
support a conclusion of obviousness. The rejection of claims 1, 6, 7, 10, 11,
and 15–17 under 35 U.S.C. § 103(a) as unpatentable over the combination of
Ohgami and NCBI is reversed.
The rejection of claims 1, 6, 7, 10, 11, and 15–17 under 35 U.S.C.
§ 103(a) as unpatentable over the combination of Ohgami, NCBI, and
Ashutosh 2014 is reversed.
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The rejection of claims 1, 2, 4–8, 10, 11, and 15–17 under 35 U.S.C.
§ 103(a) as unpatentable over the combination of Koboldt and Cancer
Network is reversed.
The rejection of claims 12–14 under 35 U.S.C. § 103(a) as
unpatentable over the combination of Koboldt, Cancer Network, and
Kaptcianos is reversed.

SUBJECT MATTER ELIGIBILITY:
ISSUE
Does the preponderance of evidence of record support Examiner’s
finding that Appellant’s claimed invention is directed to patent ineligible
subject matter?
PRINCIPLES OF LAW
A. Section 101
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 U.S. 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. Pty. Ltd. 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 Court’s two-part 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
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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, 67 (1972)). Concepts
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 (1854))); and manufacturing flour (Benson, 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
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 187; 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 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. (citation omitted)
(citing Benson and Flook); see, e.g., id. at 187 (“It is now commonplace that
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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
ensure ‘that the [claim] is more than a drafting effort designed to
monopolize the [abstract idea].’” Id. (alterations in original) (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.
B. USPTO Section 101 Guidance
In January 2019, the U.S. Patent and Trademark Office (USPTO)
published revised guidance on the application of § 101. 2019 Revised Patent
Subject Matter Eligibility Guidance, 84 Fed. Reg. 50 (Jan. 7, 2019)
(“Guidance”).16 “All USPTO personnel are, as a matter of internal agency
management, expected to follow the guidance.” Id. at 51; see also October
2019 Update at 1.
Under the Guidance and the October 2019 Update, we first look to
whether the claim recites:

16 In response to received public comments, the Office issued further
guidance on October 17, 2019, clarifying the 2019 Revised Guidance.
USPTO, October 2019 Update: Subject Matter Eligibility (the “October
2019 Update”) (available at
https://www.uspto.gov/sites/default/files/documents/peg_oct_2019_update.p
df).
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(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) (“Step 2A, Prong One”); and
(2) additional elements that integrate the judicial exception into
a practical application (see MPEP § 2106.05(a)–(c), (e)–(h) (9th
ed. Rev. 08.2017, Jan. 2018)) (“Step 2A, Prong Two”).17
Guidance, 84 Fed. Reg. at 52–55.
Only if a claim (1) recites a judicial exception and (2) does not
integrate that exception into a practical application, do we then look, under
Step 2B, 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.
Guidance, 84 Fed. Reg. at 52–56.
ANALYSIS
(Step 1)
We first consider whether the claimed subject matter falls within the
four statutory categories set forth in 35 U.S.C. § 101, namely “[p]rocess,
machine, manufacture, or composition of matter.” Guidance, 84 Fed. Reg.
at 53–54; see 35 U.S.C. § 101. Appellant’s independent claims 1, 16, and

17 This evaluation is performed by (a) identifying whether there are any
additional elements recited in the claim beyond the judicial exception, and
(b) evaluating those additional elements individually and in combination to
determine whether the claim as a whole integrates the exception into a
practical application. See Guidance — Section III(A)(2), 84 Fed. Reg. at
54–55.
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17, and their respective dependent claims, are directed to a method
(process), system (apparatus), and a non-transitory computer readable
medium (product), respectively, and are reasonably understood to be
properly directed to one of the four recognized statutory classes of invention
designated by 35 U.S.C. § 101. Therefore, we proceed to the next steps of
the analysis.
(Step 2A, Prong 1)
The method of Appellant’s claim 1 comprises, inter alia,
assembling, via a processor, an assembly of the plurality
of sequence reads from the enriched genomic sample and the at
least one reference genomic sample; and
determining, via the processor utilizing the assembly,
whether the genomic locus has a copy number variation (CNV)
or a sequence variation, or a CNV and a sequence variation.
(Appeal Br. 29.)
Examiner finds that Appellant’s claim 1 “recite[s] limitations for
assembling the plurality of sequence reads from the enriched genomic
sample and the at least one reference sample and determining whether the
genomic locus has a copy number variation, sequence variation, or a CNV
and sequence variation based on analysis of the assembly” that can be
performed by the human mind and, thus, represent mental processes, an
abstract idea under the Guidance (Ans. 17–18; see Guidance, 84 Fed. Reg. at
52 (Abstract ideas include “[m]ental processes––concepts performed in the
human mind (including an observation, evaluation, judgment, opinion)”
(footnotes omitted)).
We find no error in Examiner’s finding that Appellant’s claims recite
a judicial exception (see, e.g., Ans. 3; cf. Appeal Br. 14–17 (Appellant
contends that its claims do not recite an abstract idea)).
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(Step 2A, Prong 2)
Having determined that Appellant’s claims recite a judicial exception,
the Guidance requires an evaluation as to whether the claim as a whole
integrates the recited judicial exception into a practical application of the
exception. See Guidance, 84 Fed. Reg. at 54. The Guidance explains:
[C]ourts have . . . identified examples in which a judicial
exception has not been integrated into a practical application:
 An additional element . . . merely includes
instructions to implement an abstract idea on a computer, or
merely uses a computer as a tool to perform an abstract idea;
[and]
 an additional element adds insignificant extra-solution
activity to the judicial exception
Id. at 55 (footnotes omitted).
The remaining limitations in the method of Appellant’s claim 1 recite:
enriching a genomic sample for a plurality of genomic
backbone regions and a plurality of genomic mutation regions
of interest in a genomic locus of a subject;
obtaining a plurality of sequence reads from the enriched
genomic sample that includes sequence reads for the plurality
of genomic backbone regions and sequence reads for the
plurality of genomic mutation regions of interest; [and]
obtaining a plurality of sequence reads from
corresponding genomic backbone regions and genomic
mutation regions of at least one reference genomic sample;
(Appeal Br. 29; see generally Reply Br. 11.) These additional elements of
Appellant’s claimed invention, when considered both individually and in
combination, relate to data gathering steps (i.e. insignificant extra-solution
activity to the judicial exception). See Manual of Patent Examining
Procedure § 2106.05(g) (“Extra-solution activity includes both pre-solution
and post-solution activity. An example of pre-solution activity is a step of
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gathering data for use in a claimed process”); see also Mayo, 566 U.S. at 79
(Determining the level of a biomarker in blood is a pre-solution activity that
“is normally not sufficient to transform an unpatentable law of nature into a
patent-eligible application of such a law”).
In addition, we agree with Examiner’s finding that although
Appellant’s claimed invention recites the use of a processor “there are no
additional limitations to indicate that anything other than a generic computer
is required” (see Ans. 18). When considered individually and in
combination with the remainder of the claim, we agree with Examiner’s
finding that the processor limitation simply instructs one to implement the
abstract idea on a generic computer, wherein the computer is merely used as
a tool to perform the abstract idea (see Ans. 20; see also Appeal Br. 17
(Appellant recognizes that “[T]he mere recitation of a generic computer
cannot transform a patent-ineligible abstract idea into a patent-eligible
invention.”) (alteration original; internal quotations omitted.)). See
Guidance, 84 Fed. Reg. at 55.
On this record, Appellant’s claimed invention directs a person of
ordinary skill in this art to generate data, i.e., “a plurality of sequence reads”
from the genomic backbone regions and genomic mutation regions of: (a)
an enriched genomic sample and (b) at least one reference gnomic sample,
manipulate this data, and produce additional data, i.e., determining whether a
genomic locus has a copy number variation (CVN) or a sequence variation,
or a CNV and a sequence variation. Appellant’s claimed invention,
however, does not do anything practical with this information. 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
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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 (see generally
Appeal Br. 17–18).
Thus, on this record, we find no error in Examiner’s finding that the
judicial exception recited in Appellant’s claimed invention “is not integrated
into a practical application” (Ans. 18).
(Step 2B)
Having determined that Appellant’s claims: (1) recite a judicial
exception and (2) do not integrate that exception into a practical application,
the Guidance requires that we evaluate whether Appellant’s claims: (a) add
a specific limitation beyond the judicial exception that is not “well-
understood, routine, conventional” in the field or (b) simply appends well-
understood, routine, conventional activities previously known to the
industry, specified at a high level of generality, to the judicial exception.
Guidance, 84 Fed. Reg. at 52–56.
As discussed above, with respect to the anticipation rejection over
Ashutosh ’724, we agree with Examiner’s finding that Appellant’s claimed
invention does “not include additional elements that are sufficient to amount
to significantly more than the judicial exception because the . . . additional
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element[s] . . . equate to well-understood, routine and conventional activities
known in the art at the time of the effective filing date of the invention”
(Ans. 18). For the foregoing reasons, we are not persuaded by Appellant’s
contention that Examiner failed to establish that the additional elements of
Appellant’s claimed invention are not well-understood, routine, conventional
in this field (see Appeal Br. 20–22; Reply Br. 14–15). In addition, as
Examiner explains, Appellant discloses that the enriching and obtaining
steps may be performed with commercially available systems, which further
supports a finding that these additional elements are well-understood,
routine, convention in this field (Ans. 30 (citing Spec. ¶¶ 32, 33, and 67).
Therefore, we are not persuaded by Appellant’s contention that Examiner
“has not established that enriching for genomic backbone regions and
genome mutations regions of interest was a routine or conventional
technique” (Reply Br. 13).
As discussed above, Appellant’s claimed invention directs a person of
ordinary skill in this art to generate data, i.e., “a plurality of sequence reads”
from the genomic backbone regions and genomic mutation regions of: (a)
an enriched genomic sample and (b) at least one reference gnomic sample,
manipulate this data, and produce additional data, i.e., determining whether a
genomic locus has a copy number variation (CVN) or a sequence variation,
or a CNV and a sequence variation. Appellant’s claimed invention,
however, does not do anything practical with this information. When
considered as a whole, Appellant’s claimed invention is not directed to a
practical application, and the additional elements of Appellant’s claimed
invention, when considered individually and in combination, simply append
well-understood, routine, conventional activities previously known to the
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industry, specified at a high level of generality, to the judicial exception.
Therefore, we are not persuaded by Appellant’s contention that their claimed
invention provides an improved technological result over the prior art (see
Appeal Br. 18–20; see also Reply Br. 11–14). 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). For example, the claims do not recite how the assembling
and sequence variations are determined, but rather, in contrast to McRO and
BASCOM, are stated in a result-oriented way. Further, Appellant’s claim
invention does not transform matter; to the contrary, Appellant’s claimed
invention, 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).
To be complete, we are not persuaded by Appellant’s contentions
regarding preemption (see Appeal Br. 16; Reply Br. 13). Although
preemption “might tend to impede innovation more than it would tend to
promote it, ‘thereby thwarting the primary object of the patent laws,”’
(Alice, 573 U.S. at 216 (citing Mayo, 566 U.S. at 70-71)), “the absence of
complete preemption does not demonstrate patent eligibility.” Ariosa
Diagnostics, Inc. v. Sequenom, Inc., 788 F.3d 1371, 1379 (Fed. Cir. 2015).

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Claim 4:
The method of Appellant’s claim 4 depends from and further limits
the step of determining whether the genomic locus comprises a sequence
variation in Appellant’s claim 1 to further comprise
determining whether the genomic locus has a loss of
heterozygosity (LOH),
comprising:
(i) identifying genetic differences in the sequence reads
of the enriched genomic sample as compared to the sequence
reads from the at least one reference genomic sample; and
(ii) comparing the identified genetic differences to known
frequencies of genetic differences in a population to identify a
genomic region in the first genomic locus that has a LOH.
(see Appeal Br. 30.)
Appellant contends that claim 4 is “analogous to the rules or
requirements which are indicated by McRO as conferring patent eligibility”
(Appeal Br. 22; see also Reply Br. 15). We are not persuaded. For the
reasons discussed above, the additional determining steps of Appellant’s
claim 4 simply manipulate data to generate additional data without
identifying the specific implementation on the steps are accomplished,
which is not sufficient to confer eligibility to a patent ineligible claim. 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. McRO,
Inc. v. Bandai Namco Games America Inc., 837 F.3d 1299, 1316 (Fed. Cir.
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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).

Claim 16:
Appellant’s claim 16 requires, inter alia, that information is obtained
“from a probe or bait design used for enrichment of a plurality of genomic
backbone regions and a plurality of genomic mutation regions of interest in a
genomic locus of a subject” (see Appeal Br. 32; see also Reply Br. 16).
Appellant contends that
information from a probe or bait design used for enrichment of
a plurality of genomic backbone regions and a plurality of
genomic mutation regions of interest in a genomic locus of a
subject. As explained above, enrichment of a plurality of
genomic backbone regions and a plurality of genomic mutation
regions of interest in a genomic locus of a subject adds
significantly more to the alleged abstract idea.
(Appeal Br. 22.) We are not persuaded.
Appellant defines “[t]he term ‘obtaining’ . . . [as] any way of coming
into possession of something, including accessing a data file in silico, as
well as receiving a data file from a remote location” (Spec. ¶ 29). As
Examiner explains, receiving or transmitting data over a network is not
sufficient to make an abstract idea patent eligible (Ans. 30). See buySAFE,
Inc. v. Google, Inc., 765 F.3d 1350, 1354–55 (Fed. Cir. 2014) (reciting
generic computer functions of receiving and sending information over a
network was insufficient to make the abstract idea patent eligible).
In addition, Examiner finds that “[e]ven under the interpretation that
obtaining the sequencing reads and design information are physical
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steps, . . . [Appellant’s] [S]pecification . . . indicates that both of these steps
are performed with commercially available systems and thus are
conventional in combination” (Ans. 30 (citing Spec. ¶¶ 32, 33, and 67)). In
this regard, we note that Ashutosh ’724 discloses probe design for
enrichment of a genomic region from a genomic sample (see Ashutosh ’724
¶ 39; see also Ans. 6–7).
Thus, we find the additional elements recited in Appellant’s claim 16,
when considered both individually and in combination, do not integrate the
judicial exception into a practical application or add a specific limitation
beyond the judicial exception that is not “well-understood, routine,
conventional” in the field. Therefore, we are not persuaded by Appellant’s
contention that “the enrichment of a plurality of genomic backbone regions
and a plurality of genomic mutation regions of interest in a genomic locus of
a subject adds significantly more to the alleged abstract idea” (Reply Br. 16).
CONCLUSION
The preponderance of evidence of record fails to support Examiner’s
finding that Appellant’s claimed invention is directed to patent ineligible
subject matter. The rejection of claims 1, 4, and 16 under 35 U.S.C. § 101 is
affirmed. Claims 2, 3, and 7–15 are not separately argued and fall with
claim 1. Claim 5 and 6 are not separately argued and fall with claim 4.
Claim 17 was not separately argued and falls with claim 16.

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DECISION SUMMARY
In summary:
Claims
Rejected
35 U.S.C. § Reference(s)/Basis Affirmed Reversed
1–17 101 Eligibility 1–17
1–17 112(b) Indefiniteness 1–17
1–3, 6–17 102(a)(1) Ashutosh ’724 1–3, 6–17
1, 6, 7, 10,
11, 15–17
103 Ohgami, NCBI 1, 6, 7, 10,
11, 15–17
2, 3, 8, 9 103 Ohbami, NCBI,
Ashutosh 2014
2, 3, 8, 9
1, 2, 4–8, 10,
11, 15–17
103 Koboldt, Cancer
Network
1, 2, 4–8,
10, 11,
15–17
12–14 103 Koboldt, Cancer
Network,
Kaptcianos
12–14
Overall
Outcome
1–17

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