Makkapati, Vishnu Vardhan. et al.

Patent Trials and Appeals Board

Sep 24, 2020

13979908 - (D) (P.T.A.B. Sep. 24, 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.
13/979,908 07/16/2013 Vishnu Vardhan Makkapati 2011P00017WOUS 5991
24737 7590 09/24/2020
PHILIPS INTELLECTUAL PROPERTY & STANDARDS
465 Columbus Avenue
Suite 340
Valhalla, NY 10595
EXAMINER
BRUSCA, JOHN S
ART UNIT PAPER NUMBER
1631
NOTIFICATION DATE DELIVERY MODE
09/24/2020 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):
katelyn.mulroy@philips.com
marianne.fox@philips.com
patti.demichele@Philips.com
PTOL-90A (Rev. 04/07)

UNITED STATES PATENT AND TRADEMARK OFFICE
BEFORE THE PATENT TRIAL AND APPEAL BOARD
Ex parte VISHNU VARDHAN MAKKAPATI,
NEVENKA DIMITROVA, RANDEEP SINGH, and SUNIL KUMAR
Appeal 2019-005485
Application 13/979,908
Technology Center 1600
Before DONALD E. ADAMS, FRANCISCO C. PRATS, and
TAWEN CHANG, Administrative Patent Judges.
CHANG, Administrative Patent Judge.
DECISION ON APPEAL
Pursuant to 35 U.S.C. § 134(a), Appellant1 appeals from the
Examiner’s decision to reject claims 1–4, 6, 8, 9, and 11–18. We have
jurisdiction under 35 U.S.C. § 6(b).
We AFFIRM.

1 We use the word “Appellant” to refer to “applicant” as defined in 37
C.F.R. § 1.42. Appellant identifies the real party in interest as Koninklijke
Philips N.V. Appeal Br. 3.
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STATEMENT OF THE CASE
The Specification states that voluminous genomic sequence data
requires “significant amounts of storage capacity” and “high-end
computational devices for its analysis.” Spec. 1:30–32. The Specification
further states that, moreover, “most of the genomic sequence data obtained
during whole genome sequencing runs will rather hamper than improve . . .
diagnostic possibilities” for a professional “who is concerned with a specific
clinical question and would like to have focused information with regard to
identified symptoms or suspected diseases.” Id. 2:4–8.
According to the Specification, therefore, “[t]here is . . . a need for a
method allowing a time and resource preserving handling of a patient’s
genomic data.” Spec. 2:9–10. Further according to the Specification, “[t]he
present invention relates to a method for processing a subject’s genomic data
comprising (a) obtaining a subject’s genomic sequence; (b) reducing the
complexity and/or amount of the genomic sequence information; and (c)
storing the genomic sequence information of step(b) in a rapidly retrievable
form.” Id. at 1:5–8.
CLAIMED SUBJECT MATTER
The claims are directed to a method for processing a subject’s
genomic sequence data. Claim 1 is illustrative:
1. A method for processing a subject’s genomic
sequence data, the method comprising:
obtaining the subject’s genomic sequence data
using a next generation sequencing apparatus, the genomic
sequence data comprising coverage of at least 90% and
including signature data comprising a plurality of genetic or
genomic variations specific to one or more disorders, diseases,
predispositions for a disorder or a disease, or risk factors for
development of a disease or disorder;
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using a processor configured to reduce complexity
included in the subject’s genomic sequence data by: (i) aligning
the subject’s genomic sequence data with a reference sequence
comprising signature data, (ii) detecting the subject’s genomic
sequence data comprising signature data, and (iii) removing,
from the subject’s genomic sequence data, data other than the
signature data to generate reduced complexity genomic
sequence data;
storing the reduced complexity genomic sequence
data in a storage structure comprising annotated database
entries in a differential DNA storage structure format, wherein
the storage structure encodes acquisition time information
associated with the reduced complexity genomic sequence data
and allows for locally unrestrained access to the reduced
complexity genomic data and associated time information and
other medical data; and
providing access to the reduced complexity
genomic data and associated time information and other
medical data in a clinical environment, thereby facilitating
clinical decision-making pertaining to the subject;
wherein the signature data comprises two or more
of a missense mutation, nonsense mutation, single nucleotide
polymorphism (SNP), copy number variation (CNV), splicing
variation, variation of a regulatory sequence, small deletion,
small insertion, small indel, gross deletion, gross insertion,
complex genetic rearrangement, inter chromosomal
rearrangement, intra chromosomal rearrangement, loss of
heterozygosity, and insertion of repeats and deletion of repeats.
Appeal Br. 35 (Claims App.).

REJECTION(S)
A. Claims 1–4, 6, 8, 9, and 11–18 are rejected under 35 U.S.C. § 101 as
being directed to an abstract idea without significantly more. Ans. 3.
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B. Claims 1, 8, 14, and 15 are rejected under pre-AIA 35 U.S.C. § 103(a)
as being unpatentable over Chang,2 Gatawood,3 Sherry,4 Metzker,5
and Kane.6 Final Act. 10–11.
C. Claims 2, 13, and 16–18 are rejected under pre-AIA 35 U.S.C.
§ 103(a) as being unpatentable over Chang, Gatawood, Sherry,
Metzker, Kane, and Greenman.7 Final Act. 14.
D. Claims 3, 4, and 12 are rejected under pre-AIA 35 U.S.C. § 103(a) as
being unpatentable over Chang, Gatawood, Sherry, Metzker, Kane,
and Bollet.8 Final Act. 15.
E. Claim 6 is rejected under pre-AIA 35 U.S.C. § 103(a) as being
unpatentable over Chang, Gatawood, Sherry, Metzker, Kane, and
Langmead.9 Final Act. 16.

2 H. Chang et al., Seq-SNPing: Multiple-Alignment Tool for SNP Discovery,
SNP ID Identification, and RFLP Genotyping, 13 OMICS: J. INTEGRATIVE
BIOLOGY 253 (2009).
3 Gatawood et al., US 2008/0077607 A1, published Mar. 27, 2008.
4 S. T. Sherry et al., dbSNP: the NCBI Database of Genetic Variation, 29
NUCLEIC ACIDS RES. 308 (2001).
5 M. L. Metzker, Sequencing Technologies – the Next Generation, 11
NATURE REVIEWS GENETICS 31 (2010).
6 Kane et al., WO 2009/108802 A2, published Sep. 3, 2009.
7 C. Greenman et al., Pattern of Somatic Mutation in Human Cancer
Genomes, 446 NATURE 153 (2007).
8 M. A. Bollet, High-Resolution Mapping of DNA Breakpoints to Define
True Recurrences Among Ipsilateral Breast Cancers, 100 JNCI 48 (2008).
9 Ben Langmead et al., Ultrafast and Memory-Efficient Alignment of Short
DNA Sequences to the Human Genome, 10 GENOME BIOLOGY R25 (2009)
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F. Claim 9 is rejected under pre-AIA 35 U.S.C. § 103(a) as being
unpatentable over Chang, Gatawood, Sherry, Metzker, Kane, and
Rhodes.10 Final Act. 17.
G. Claim 11 is rejected under pre-AIA 35 U.S.C. § 103(a) as being
unpatentable over Chang, Gatawood, Sherry, Metzker, Kane, and
Hwang.11 Final Act. 17.

OPINION
A. Subject matter eligibility rejection under § 101
1. Issue
The Examiner concludes that “[t]he process of claim 1, but for the
limitation of using a generic computer processor, falls within the mental
processes grouping of abstract ideas.” Ans. 3. The Examiner concludes that
this judicial exception is not integrated into a practical application because
independent claim 1 comprises only the additional elements of “use of a
computer processor, inputting data, storing data, . . . outputting data,” and
“using a next-generation sequencing procedure to produce sequence data.”
Id. at 5–6. The Examiner finds that “[t]he recited computer functions are
functions of a generic computer that do not represent an improvement in the
functioning of a computer or any other practical application of the recited

10 D. R. Rhodes, Oncomine 3.0: Genes, Pathways, and Networks in a
Collection of 18,000 Cancer Gene Expression Profiles, 9 NEOPLASIA 166
(2007).
11 D. G. Hwang & Phil Green, Bayesian Markov Chain Monte Carlo
Sequence Analysis Reveals Varying Neutral Substitution Patterns in
Mammalian Evolution, 101 PNAS 13994 (2004).
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judicial exception,” and “[t]he sequencing steps are data gathering that does
not represent a practical application of the recited judicial exception.” Id.
The Examiner further finds that “[t]he claims do not include
additional elements that are sufficient to amount to significantly more than
the judicial exception,” because the additional elements of claim 1 are
merely “conventional functions and components of a generic computer.”
Ans. 6.
Appellant argues that the claims are not directed to an abstract idea
because they are “directed to a specific improvement in: (1) improved
storage efficiency for a database and (2) retrieval of relevant portions of a
subject’s whole genome sequence, which facilitates clinical decision-making
pertaining to the subject.” Appeal Br. 19. More specifically, Appellant
argues that the claims relates to “storing the [relevant] portions [of a
subject’s whole genome] in a manner that allows for unrestrained access in a
clinical setting.” Id. Appellant argues that “[d]ue to the reduced complexity
of the [stored] genetic data, . . . memory and storage space required for
storing the genetic information can be reduced drastically[,]” and “the
matching/analysis of the data is significantly faster.” Id. at 19, 21–22.
The issue with respect to this rejection is whether a preponderance of
the evidence supports the Examiner’s conclusion that claim 1 recites a
judicial exception to patent eligibility, without significantly more.
2. Analysis
We analyze this case under the framework set forth by the Supreme
Court in Mayo Collaborative Services v. Prometheus Laboratories, Inc., 566
U.S. 66 (2012), and applied by our reviewing court in Ariosa Diagnostics,
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Inc. v. Sequenom, Inc., 788 F.3d 1371 (Fed. Cir. 2015). As the Ariosa court
explained:
In Mayo . . . , the Supreme Court set forth a framework for
distinguishing patents that claim laws of nature, natural
phenomena, and abstract ideas from those that claim
patent-eligible applications of those concepts. First, we
determine whether the claims at issue are directed to a
patent-ineligible concept. . . . If the answer is yes, then we
next consider the elements of each claim both individually
and “as an ordered combination” to determine whether
additional elements “transform the nature of the claim”
into a patent-eligible application. . . . The Supreme Court
has described the second step of this analysis as a 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. at 1375.
Mayo Step One: Whether Claim 1 Is Directed to Abstract Idea
We begin with the first step of the Mayo test, namely whether a claim
is “directed to” a patent-ineligible concept.
On January 7, 2019, the Director of the USPTO issued the “2019
Revised Patent Subject Matter Eligibility Guidance” (“Revised Guidance”),
which provides further details regarding how the Patent Office analyzes
patent-eligibility questions under 35 U.S.C. § 101. Revised Guidance, 84
Fed. Reg. 50–57 (Jan. 7, 2019). Under the Revised Guidance, the first step
of the Mayo test (i.e., Step 2A of the Revised Guidance) is “a two-pronged
inquiry.” Id. at 54. In prong one, we evaluate whether the claim recites a
judicial exception, such as laws of nature, natural phenomena, or abstract
ideas. Id. The Revised Guidance explains that the abstract idea exception
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includes the following groupings of subject matter, when recited as such in a
claim limitation(s) (that is, when recited on their own or per se):
(a) Mathematical concepts—mathematical
relationships, mathematical formulas or equations,
mathematical calculations;
(b) Certain methods of organizing human
activity—fundamental economic principles or practices
(including hedging, insurance, mitigating risk);
commercial or legal interactions (including agreements
in the form of contracts; legal obligations; advertising,
marketing or sales activities or behaviors; business
relations); managing personal behavior or relationships
or interactions between people (including social
activities, teaching, and following rules or instructions);
and
(c) Mental processes—concepts performed in
the human mind (including an observation, evaluation,
judgment, opinion).
Id. at 52 (footnotes omitted). If the claim recites a judicial exception, the
claim is further analyzed under prong two, which requires “evaluat[ion of]
whether the claim recites additional elements that integrate the exception
into a practical application of that exception.”

First Prong of Revised Guidance Step 2A
With respect to the first prong of Step 2A of the Revised Guidance,
we agree with the Examiner that claim 1 recites a patent-ineligible abstract
idea. In particular, claim 1 recites a method of processing a subject’s
genomic data, the method comprising
using a processor configured to reduce complexity
included in the subject’s genomic sequence data by: (i)
aligning the subject’s genomic sequence data with a
reference sequence comprising signature data, (ii)
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detecting the subject’s genomic sequence data
comprising signature data, and (iii) removing, from the
subject’s genomic sequence data, data other than the
signature data to generate reduced complexity genomic
sequence data.
Appeal Br. 35 (Claims App.). Each of steps (i)–(iii) above, however, are
mental processes, i.e., concepts that may be performed in the human mind or
by a human using pen and paper. See Revised Guidance, 84 Fed. Reg. at 52;
see also Cybersource Corp. v. Retail Decisions, Inc., 654 F.3d 1366, 1373
(explaining that “[i]t is clear that unpatentable mental processes are the
subject matter of [the] claim” because “[a]ll of [the] method steps can be
performed in the human mind, or by a human using a pen and paper”). Such
mental processes are not patentable. Mayo, 566 U.S. at 71; see also Genetic
Technologies, Ltd. v. Merial L.L.C., 818 F.3d 1369, 1378 (Fed. Cir. 2016)
(holding that “[t]he term ‘to detect the allele’ (in the sense of examining the
non-coding region to detect an allele in the coding region) is a mental
process step, . . . because it merely sets forth a routine comparison that can
be performed in the human mind”).
Second Prong of Revised Guidance Step 2A
The second prong of Step 2A asks whether the claims as a whole
integrate the judicial exception into a practical application of the exception.
Revised Guidance, 84 Fed. Reg. at 54. We find that claim 1 does not recite
additional elements that integrate the recited abstract idea into a practical
application of the idea.
The elements of claim 1 in addition to mental processes are: (1)
“obtaining the subject’s genomic sequence data using a next generation
sequencing apparatus, the genomic sequence data comprising coverage of at
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least 90% and including signature data . . . ”; (2) a processor; (3) “storing the
reduced complexity genomic sequence data in a storage structure comprising
annotated database entries in a differential DNA storage format, wherein the
storage structure encodes acquisition time information . . . and allows for
locally unrestrained access to . . . data”; and (4) “providing access to the . . .
data in a clinical environment . . . .” Appeal Br. 35 (Claims App.).
The limitations relating to “obtaining the subject’s genomic sequence
data” and “storing the reduced complexity genomic sequence data” in the
recited manner do not integrate the recited abstract mental processes into a
practical application, because they merely “add[] insignificant extra-solution
activity to the judicial exception.” 84 Fed. Reg. at 55. In particular, the
limitations relating to obtaining the subject’s genomic sequence merely
gather data for practicing the abstract mental process. Cybersource, 654
F.3d at 1372 (explaining that, “even if some physical steps are required to
obtain information from the database” regarding credit card transactions for
purposes of fraud detection, “such data-gathering steps cannot alone confer
patentability”); see also Mayo, 566 U.S. at 1297–1298 (holding that
“[p]urely ‘conventional or obvious’ ‘[pre]-solution activity’,” such as a step
of determining the level of a recited metabolite, “is normally not sufficient to
transform an unpatentable law of nature into a patent-eligible application of
such a law) (alteration original).
Likewise, the limitations regarding “storing the reduced complexity
genomic sequence data” are insignificant post-solution activity even if the
claim specifies particular additional information (e.g., acquisition time
information) to be stored. In Electric Power Group, LLC v. Alstom S.A., 830
F.3d 1350 (Fed. Cir. 2016), for instance, the Court held the claims as drafted
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in that case to be patent-ineligible, even though the claim required
displaying information in a particular format, i.e., “‘displaying concurrent
visualization’ of two or more types of information,” possibly in a “time-
synchronized” manner. Id. at 1355.
As to the limitations regarding “providing access to . . . data in a
clinical environment,” we note that they merely “limit[] [the] abstract idea to
one field of use” – i.e., “in a clinical environment” – and thus also do not
serve to integrate the idea into a practical application. Bancorp Servs.,
L.L.C. v. Sun Life Assurance Co. of Canada (U.S.), 687 F.3d 1266, 1275–
1276, 1280 (Fed. Cir. 2012) (citing Bilski for the proposition that “‘limiting
an abstract idea to one field of use or adding token post-solution components
d[oes] not make the concept patentable’” and holding that limiting claims to
“use in the life insurance market” does not render them patent-eligible)
(alteration in original).
Finally, the limitation of “a processor” merely implements on a
computer the abstract mental processes of “aligning . . . sequence data,”
“detecting . . . signature data,” and “removing . . . data other than the
signature data.” As explained in the Revised Guidance, a judicial exception
has not been integrated into a practical application if the additional elements
of the claim “merely include[] instructions to implement an abstract idea on
a computer, or merely uses a computer as a tool to perform an abstract idea.”
Revised Guidance, 84 Fed. Reg. at 55.
Mayo Step Two: Whether Claim 1 Amounts to “Significantly More”
Finally, the Revised Guidance directs us to consider whether claim 1
includes “additional elements . . . [that] provide[] ‘significantly more’ than
the recited judicial exception.” 84 Fed. Reg. at 56. The Revised Guidance
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states that an additional element that “simply appends well-understood,
routine, conventional activities previously known in the industry, specified
at a high level of generality, to the judicial exception, . . . is indicative that
an inventive concept may not be present.” Id.
Here, as discussed, the only elements recited in claim 1, other than the
abstract idea itself, are (1) “obtaining the subject’s genomic sequence data
using a next generation sequencing apparatus, the genomic sequence data
comprising coverage of at least 90% and including signature data . . . ”; (2) a
processor; (3) “storing the reduced complexity genomic sequence data in a
storage structure comprising annotated database entries in a differential
DNA storage format, wherein the storage structure encodes acquisition time
information . . . and allows for locally unrestrained access to . . . data”; and
(4) “providing access to the . . . data in a clinical environment . . . .”
The evidence of record makes clear that all of these additional
elements are well-understood, routine, and conventional. With respect to
limitations regarding obtaining the subject’s genomic sequence data using a
next generation sequencing apparatus, the Specification states that “[t]he
present invention . . . focuses on the implementation of the sequence
information available, prepared, and obtained according to suitable
contemporary sequencing techniques.” Spec. 9:16–18 (emphasis added);
see also Spec. 7:33–8:2 (stating that “[m]ethods for sequence determination
are known to the person skilled in the art” and that “[p]referred are next
generation sequencing methods or high throughput sequencing methods”),
1:23–27 (explaining that “next generation sequencing techniques” has
dramatically reduced the costs and time needed for obtaining sequence
information and that whole genome sequencing is becoming a cost effective
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alternative to existing biochemical and genetic tests and assays”), Final Act.
6 (citing references discussing next generation sequencing, including data
showing “next generation sequencing can routinely achieve coverage of
greater than 90%).
The recitation of a generic “processor” also does not transform the
recited patent-ineligible abstract idea into a patent-eligible invention. Alice,
573 U.S. at 223. In particular, the claim recites that the processor is
configured to “align[] the subject’s genomic sequence data with a reference
sequence comprising signature data,” “detect[] the subject’s genomic
sequence data comprising signature data,” and “remov[e] from the subject’s
genomic sequence data, data other than the signature data.” These steps
require the processor to do no more than perform the generic functions of
comparing data and deleting data. See also Spec. 15:29–31 (stating that
“alignment algorithms as known to the person skilled in the art may be
employed in order to detect differences between the two genomic
sequences), 25:1–3 (stating that “[t]he alignment between the signature
reference sequence and the genome sequence obtained from a subject may
be carried out according to any suitable alignment method or technique”).
The storage structure recited in claim 1 is likewise generic and/or
well-known, routine, and conventional. Although claim 1 recites that the
storage structure comprises “annotated database entries in a differential DNA
storage structure format,” this phrase does not appear to denote any
characteristics that distinguishes the storage structure from a generic
database, other than by the content of the information (e.g., inclusion of
acquisition time information) that is stored. The Specification, for instance,
states that “electronic picture/data archiving and communication system”
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currently on the market, such as Philips’ iSite PACS systems, may be used
as the clinical decision support and storage system of the present invention
and may be “adjusted or modified in order to comply with the requirements
of the methods of the present invention and/or in order to be able to carry out
a computer program or algorithm as described herein, and/or in order to
store genomic sequence information and/or functional genetic information as
defined herein.” Spec. 32:26–33.
As to the limitation regarding “providing access to . . . data in a
clinical environment,” we have noted above that merely limiting a recited
abstract idea to a field of use – i.e., “a clinical environment” – does not
render the abstract idea patent-eligible. Bancorp Servs., 687 F.3d at 1275–
1276, 1280 (Fed. Cir. 2012). In addition, the potential use of genomic data
in a clinical environment is well-known, routine, and conventional. See,
e.g., Gatawood ¶ 5 (“Current social, medical, and scientific thinking
converges on the idea of ‘personalized medicine’, broadly interpreted as
tailoring clinical decision making based on a patient’s genetics.”).
Finally, considered as an ordered combination and in the context of
the claim as a whole, the additional limitations of claim 1 add nothing that is
not already present when the elements are separately considered.
Accordingly, we affirm the Examiner’s rejection of claim 1 as being directed
to an abstract idea without significantly more. Claims 2–4, 6, 8, 9, and 11–
18, which are not separately argued, fall with claim 1.
Appellant’s Arguments
Appellant first contends that “[t]he ‘character as a whole’ of the
claims is not directed to an abstract idea.” Appeal Br. 19; see also id. at 24.
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As an initial matter, Appellant contends that “the Patent Office has not
performed several of the procedural steps required under . . . the 2019
Eligibility Guidance.” Appeal Br. 23. Appellant asserts that, “[f]or
example, the Patent Office appears to assert that several steps equate to
information,” but “‘information’ does not fall within any of the subject
matter groupings of abstract ideas enumerated in the 2019 Eligibility
Guidance.” Id. at 24.
We are not persuaded. The Final Rejection was mailed on December
11, 2018, prior to the issuance of the Revised Guidance. The Examiner
provided the analysis described in the Revised Guidance in the Answer,
including explaining that the claim recites mental processes, which is one of
the subject matter groups of abstract ideas enumerated in the Revised
Guidance. Appellant has not submitted a Reply Brief disputing the
Examiner’s analysis.
Appellant contends that the steps recited in the claims “cannot be
accomplished by the human mind alone,” because
[t]he claimed invention requires alignment of a reference
genome and the genomic sequence data in order to detect
signature data in the genomic sequence data, and then
requires generation of reduced complexity genomic
sequence data by removing certain data from the
genomic sequence data. Comparing millions or billions
of base pairs, and processing the results of that
comparison (including identifying specific signature data
and creating new genomes with that signature data
removed) is more than a human mind could perform in a
lifetime or multiple lifetimes.
Appeal Br. 25.
We are not persuaded. As the Examiner points out, although the
claim requires obtaining a subject’s genomic sequence data comprising
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“coverage of at least 90%,” under the broadest reasonable interpretation the
claim does not limit the size of the subject’s genomic sequence data or the
reference sequence that must be aligned. Ans. 3–4; see also In re BRCA1-
and BRCA2-Based Hereditary Cancer Test Patent Litigation, 774 F.3d 755,
763–764 (holding that merely “comparing BRCA [gene] sequences and
determining the existence of alternations” is a patent-ineligible mental
process).
Appellant next contends that “the claims are directed to a specific
improvement in: (1) improved storage efficiency for a database; and (2)
retrieval of relevant portions of a subject’s whole genome sequence, which
facilitates the clinical decision-making pertaining to the subject.” Appeal
Br. 19. More particularly, Appellant contends that “the claims are directed
to reducing the complexity of genomic sequencing data, and storing that data
in a specialized storage structure and format that enables unrestrained access
to the reduced complexity genomic data and associated time information and
other medical data in a clinical environment to facilitate clinical decision-
making pertaining to the subject.” Id. at 24; see also id. at 25, 26. Appellant
contends that “[t]his processing and specialized storage structure and format
is an important application that provides the value of the claimed method”:
Appellant contends that “the outcome of the method provides clinicians with
actionable information that improves patient treatment and care,” for
example because the data generated by the processing steps “is far more
accessible and is immediately available in a clinical environment to facilitate
clinical decision-making” as compared to previous data. Id. at 24–25, 26.
We are not persuaded. The improvement Appellant refers to is not an
improvement in computer technology or another technical field. Instead, the
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alleged improvement in data storage and retrieval results from the abstract
idea of deleting non-signature data (i.e., “reducing the complexity of
genomic sequencing data”) prior to data storage (e.g., because less data is
being stored), and the association of the remaining reduced complexity data
with additional information such as acquisition time. Even assuming such
an abstract idea constitutes a significant improvement in genomic data
analysis and storage, an abstract idea that is “[g]roundbreaking, innovative,
or even brilliant . . . does not by itself satisfy the § 101 inquiry.” Assoc. for
Molecular Pathology v. Myriad Genetics, Inc., 569 U.S. 576, 591 (2013).
Appellant contends that the claimed invention in fact improves
computer technology, in that “[t]he claimed method . . . recites specific steps
that . . . allow[] a database to store significantly more genetic data for
significantly more people in a manner that enables faster retrieval and
analysis of the genetic data.” Id. at 21–22; see also id. at 24, 25. Appellant
contends that “[t]his result is not something that current computer systems
can accomplish.” Id. at 22; see also id. at 26. Appellant contends that “[a]
computer system implementing the claimed method/system is no longer a
generic computer, it is a modified computer with improved functionality
(both in storage and analytics),” and further argues that “[t]hese
improvements transform the claims into patent-eligible subject matter.” Id.
at 27.
We are not persuaded for reasons already discussed above. Appellant
does not suggest that the claim allows the database to store more data in the
absolute sense – e.g., that the same database would be capable of storing
more bits of data. Rather, Appellant appears to argue that the claimed
method allows a database to store more “relevant” data and retrieve such
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data more rapidly by not storing data deemed to be irrelevant (i.e., data other
than the signature data). Such increased storage and faster retrieval times,
however, does not change how the computer functions; it merely changes
the amount and content of genetic data stored and/or processed for each
subject. Neither do we agree that a computer system implementing the
claimed method/system is thereby transformed into patent-eligible subject
matter. Courts have made clear that “merely claiming a software
implementation of a purely mental process that could otherwise be
performed without the use of a computer” does not render an otherwise
ineligible claim patent eligible. Cybersource, 654 F.3d at 1375.
Citing Enfish, LLC v. Microsoft Corp., 822 F.3d 1327 (Fed. Cir. 2016)
and McRO, Inc. v. Bandai Namco Games Am. Inc., 837 F.3d 1299 (Fed. Cir.
2016), Appellant contends that the fact “the invention comprises a unique
data structure in memory, rather than a physical component, does not negate
the non-abstract nature of the data structure.” Appeal Br. 27; see also id. at
20. Appellant argues that, as in Enfish, the claimed “novel data structure
makes a non-abstract improvement to the computer technology in this
system, by formatting the information into a format and data structure that
enables faster and more efficient storage and retrieval.” Id. at 27–28.
Appellant’s citation to Enfish and McRO are inapposite. The claims at
issue in Enfish are directed to “an innovative logical model for a computer
database.” 822 F.3d at 1330. As the Enfish court explains, “[a] logical
model is a model of data for a computer database explaining how the various
elements of information are related to one another,” and “generally results in
the creation of particular tables of data.” Id. In contrast to the conventional
“relational” databases, where “each entity (i.e., each type of thing) that is
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modeled is provided in a separate table,” the “self-referential” database
recited in the Enfish claims “includes all data entitles in a single table, with
column definitions provided by rows in that same table.” Id. The patent at
issue in Enfish teaches that the “self-referential” databases “allow[] for faster
searing of data than would be possible with the relational model,” “more
effective storage of data other than structured text,” and “more flexibility in
configuring the database.” Id. at 1333.
In other words, “the self-referential table recited in the claims on
appeal is a specific type of data structure designed to improve the way a
computer stores and retrieves data in memory.” Id. at 1339. In contrast, the
claims on appeal do not improve the manner in which a computer stores and
retrieves data in memory; rather, they are directed to determining the content
of the information to be stored in the database.
Similarly, the claims on appeal are not analogous to the claims at
issue in McRO, which “uses a combined order of specific rules that renders
information into a specific format that is then used and applied to create
desired results: a sequence of synchronized, animated characters.” 837 F.3d
at 1315. As the court explained in its decision, and in contrast to the claims
on appeal, the claims do not “simply use a computer as a tool to automate
conventional activity” and also “goes beyond merely ‘organizing [existing]
information into a new form.’” Id. at 1314–1315 (alteration original).
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Appellant also references Thales,12 Visual Memory,13 Finjan,14 and
Core Wireless15 as supporting the proposition that “a claim reciting a
software-related invention focused on improving computer technology is not
directed to an abstract idea.” Appeal Br. 21. These cases are also inapposite
for the reason already discussed, namely that claim 1 is not focused on
improving computer technology and instead uses the computer only to
implement the recited abstract idea.
Finally, with respect to Step 2B of the Alice/Mayo analysis, Appellant
contends that the Examiner fails to show that “the physical data structure
recited in the claims, which stores the reduced complexity genomic sequence
data comprising annotated database entries in a differential DNA storage
structure format, was well-understood, routine, and conventional.” Appeal
Br. 28.
We are not persuaded. Although the claim recites “a differential DNA
storage structure format,” the Specification does not define this term, and
Appellant has not provided a construction for the term or suggested that the
term has a plain and ordinary meaning to a skilled artisan. In addition, there
is no evidence that the term refers to a specific logical model for databases,
as in Enfish; instead, the term at most appears to refer to the content of the
information (e.g., the differences between DNA sequences, acquisition time
information) to be stored. Under the broadest reasonable interpretation of

12 Thales Visionix Inc. v. United States, 850 F.3d 1343 (Fed. Cir. 2017).
13 Visual Memory LLC v. NVIDIA Corp., 867 F.3d 1253 (Fed Cir. 2017).
14 Finjan, Inc. v. Blue Coat Sys., Inc., 879 F.3d 1299 (Fed. Cir. 2018).
15 Core Wireless Licensing S.A.R.L. v. LG Electronics, Inc., 880 F.3d 1356
(Fed. Cir. 2018).
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the claim, therefore, claim 1 requires that the reduced complexity genomic
sequence data be stored as annotated entries in a database that also stores
associated acquisition time information and other medical data. As
discussed above, such a requirement merely calls for a generic computer
component (i.e., a database) performing its conventional function (storing
and associating information). See also Spec. 32:26–33 (stating that the
invention may be implemented in an “electronic picture/data archiving and
communication system” currently on the market).
Accordingly, we affirm the Examiner’s rejection of claim 1 under 35
U.S.C. § 101 as directed to an abstract idea without significantly more.
Claims 2–4, 6, 8, 9, and 11–18, which are not separately argued, fall with
claim 1.
B. Obviousness rejections under § 103(a)
1. Issue
The same issue is dispositive as to all of the obviousness rejections;
we therefore discuss them together.
The Examiner finds that Chang teaches a “computer-mediated process
of comparing a query sequence to a single nucleotide polymorphism (SNP)
database,” which meets a number of the limitations of claim 1. Final Act.
11–12. However, the Examiner finds that Chang does not explicitly show
“sequencing a genome using next-generation sequencing to a coverage of at
least 90%,” a database “compris[ing] a reference sequence with
annotations,” “deletion of a portion of the genomic sequence that is not
related to sequences pertaining to a disease, . . . linking the sequence data to
an individual’s medical data, or storing time information.” Id. at 12.
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Nevertheless, the Examiner finds that the other cited references teach
these limitations. In particular, the Examiner finds Metzker teaches that
“next generation sequencing [technologies] can routinely achieve coverage
of greater than 90%” of genomic sequence data. Final Act. 13.
The Examiner also finds that Sherry describes the dbSNP database
used by Chang and shows that the “SNPs are shown in association studies
showing functional and pharmacogenomics,” that date of submission (i.e.,
time information) is included with the SNP data provided with each
submission to the database, and that “entries in dbSNP are annotated.” Final
Act. 12.
The Examiner further finds that Gatawood teaches the “advantage in
storing compressed DNA sequences to conserve computer storage space and
facilitate transmission and analysis of DNA sequence data,” and also teaches
“delta compression” wherein “only the differences relative to a reference
sequence” is stored. Final Act. 12.
Finally, the Examiner finds that Kane teaches a “database that
combines patient’s electronic health record (EHR) . . . , a patient’s genotypic
record . . . , and a genotype database,” wherein data is obtained and/or stored
regarding “health risks associated with each genotype,” including
associations with oncogenesis and associations between SNPs and adverse
drug reactions. Final Act. 13. The Examiner finds that Kane also teaches a
database including time information (i.e., “the most recent update date for
data relevant to a patient’s genotype”). Id. at 13. The Examiner further
finds that Kane teaches paring down patient genotypic data to SNPs that are
in a database of risk linkages, and eliminating DNA sequences that does not
constitute SNP data. Final Act. 13.
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The Examiner concludes that
[i]t would have been obvious to a person of ordinary skill
in the art at the time the invention was made to modify
the process of Chang . . . by pruning genotype
information because Gatawood . . . shows that retaining
only differences in sequences relative to a reference
sequence allows for reduction in the amount of data
needed to characterize variations in genomic samples. It
would have been further obvious to link data to an
individual’s medical record for clinical use because
Chang . . . and Sherry . . . show that SNPs can be related
to disease[,] and Kane . . . shows pruning of genotype
information to retain SNP data relevant to risk of disease
or adverse drug reactions and . . . that analysis of
individual patients can be performed by including patient
genotype data and patient medical record information. It
would have been further obvious to include acquisition
time information in SNP data because Sherry . . . shows
searching SNP data with limiters on time of submission.
It would have been further obvious to sequence a genome
using next generation sequencing to a coverage of at least
90% because Metzker shows that next generation
sequencing has advantages in low cost and allows for
high coverage of a genome that is greater than 90%.
Final Act. 14.
Appellant contends that the Examiner has not identified a prior art
teaching wherein “a portion of the genomic sequence that is not related to
sequences pertaining to one or more specific disorders, diseases,
predispositions for a disorder or a disease, or risk factors for development of
a disease or disorder is deleted from the obtained genome sequence.”
Appeal Br. 29.
Appellant does not separately argue the claims. We, therefore, focus
our analysis on claim 1 as representative. The issue with respect to these
rejections is whether a preponderance of evidence of record supports the
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Examiner’s conclusion that the cited combination of prior art suggests the
limitation of “removing, from [a] subject’s genomic sequence data, data
other than the signature data to generate reduced complexity genomic
sequence data.”
2. Analysis
Unless otherwise noted, we adopt the Examiner's findings of fact and
reasoning regarding the Examiner’s rejection of claim 1 (Final Act. 10–14;
Ans. 12) and agree that a preponderance of the evidence of record supports
the Examiner’s conclusion that claim 1 is obvious in light of the cited prior
art. We address Appellant's arguments below.
Appellant contends that neither Gatawood nor Kane discloses deleting
“a portion of the genomic sequence that is not related to sequences
pertaining to one or more specific disorders, diseases, predispositions for a
disorder or a disease, or risk factors for development of a disease or disorder
. . . from the obtained genome sequence.” Appeal Br. 29. Thus, the
corresponding claim limitation at issue is “removing, from the subject’s
genomic sequence data, data other than the signature data to generate
reduced complexity genomic sequence data.” Id. at 35 (Claim App.)
In particular, Appellant concedes that “Gatawood . . . discloses delta
compression to store ‘differences relative to a reference sequence.’” Appeal
Br. 25. However, Appellant contends that this differs from the claimed
invention because,
if the claimed invention stored “differences relative to a
reference sequence,” it would include the millions of
bases at which any sequence will differ from a reference
sequence, most of which [will have] no relationship to
any “genetic or genomic variations specific to one or
more disorders, diseases, predispositions for a disorder or
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a disease, or risk factors for development of a disease or
disorder.” Furthermore, storing only “differences relative
to a reference sequence” will necessarily omit the
signature data also found in the reference sequence.
Accordingly, retaining only differences in sequences
relative to a reference sequence is not a suitable method
for reducing complexity, and is not the method utilized
by the present invention.
Id. at 30.
We are not persuaded by Appellant’s argument. The Specification
defines “signature data” as follows:
The term “signature data” as used herein refers to
information on a genetic or genomic variation.
Preferably, such a signature data may be information on a
genetic or genomic variation specific to a disorder,
disease, predisposition for disorders or diseases, risk
factors for the development of diseases etc. Alternatively,
signature data may also comprise data which is not per se
linked to a disease or disorder, but provide information
on a subject’s fitness, robustness, adaptation to specific
conditions, potential of adaptability, history of
modifications, or information necessary for the subject's
or the subject's progeny’s identification, e.g. in criminal
investigations, fingerprinting approaches, paternity tests
etc.
Spec. 20:25–32. Thus, we agree with the Examiner that “differences relative
to a reference sequence” is “signature data” within the broadest
interpretation of that term, and delta compression to store such differences,
which Appellant admits is taught by Gatawood, meets the limitation of
“removing . . . data other than the signature data to generate reduced
complexity genomic sequence data.” Ans. 12.
In this regard, we note that while the claim requires obtaining
signature data comprising genetic or genomic variations specific to diseases,
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disorders, or predispositions or risk factors therefor, the claim recites
removing data other than signature data (i.e., information on a genetic or
genomic variation), not data other than the subset of signature data
consisting of “genetic or genomic variations specific to” diseases, disorders,
or predispositions or risk factors therefor. We further note that while the
Specification states that the step of reducing the complexity of genomic data
is “preferably carried out on all parts of the genomic sequence except for
signature data pertaining to a disease or disorder,” see, e.g., Spec. 3:11–15,
the Federal Circuit has counseled that “the PTO should avoid . . . limit[ing]
broad claim terms solely on the basis of specification passages” and that,
“[a]bsent claim language carrying a narrow meaning, the PTO should only
limit the claim based on the specification or prosecution history when those
sources expressly disclaim the broader definition.” In re Bigio, 381 F.3d
1320, 1325 (Fed. Cir. 2004).
Likewise, we are not persuaded by Appellant’s argument that
Gatawood differs from the claimed invention because Gatawood’s method
would “necessarily omit the signature data also found in the reference
sequence.” Appeal Br. 30. The claim requires storage of “reduced
complexity genomic sequence data,” which is obtained by “removing, from
the subject’s genomic sequence data, data other than the signature data.”
Appeal Br. 35 (Claims App.) (emphasis added). Thus, under the broadest
reasonable interpretation, claim 1 does not require storage of “signature data
also found in the reference sequence.”
Appellant similarly contends that Kane does not suggest the limitation
at issue because
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Kane teaches retention and storage of information about
every SNP that is maintained in a “[SNP] database of risk
linkages” rather than the retention and storage of a
plurality of genetic or genomic variations specific to one
or more disorders, diseases, predispositions for a disorder
or a disease, or risk factors for development of a disease
or disorder. Furthermore, in contrast to Kane, the claimed
method comprises more than just SNP data, and thus a
database comprising only SNPs with some risk linkage
would not enable capture of the claimed signature data.
Appeal Br. 31.
We are not persuaded. As an initial matter and as discussed above,
the claim does not require retention and storage only of signature data
consisting of genetic or genomic variations “specific to one or more
disorders, diseases,” or predispositions or risk factors therefor. Furthermore,
Appellant concedes that Kane teaches retention and storage of information
about SNPs maintained in a SNP database of risk linkages. Kane explains
this database “comprises a collection of established SNP-risk linkages and
detailed information about each risk” that allows determination of “a link
between the genetic information and the adverse drug reaction information
for a single or plurality of patients.” Kane ¶ 13. Appellant does not explain
why SNPs linked to risks of adverse drug reactions would not fall within the
scope of “genetic or genomic variations specific to one or more disorders,
diseases,” or predispositions or risk factors therefor under the broadest
interpretation of the claim.
Finally, we are not persuaded by Appellant’s argument that Kane does
not suggest the claimed method because “the claimed comprises more than
just SNP data, and thus a database comprising only SNPs with some risk
linkage would not enable capture of the claimed signature data.” As
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discussed above, the Specification defines “signature data” as “information
on a genetic or genomic variation.” Spec. 20:25–26 (emphasis added).
Claim 1 recites “removing, from the subject’s genomic sequence data, data
other than the signature data,” and further recites
wherein the signature data comprises two or more of a
missense mutation, nonsense mutation, single nucleotide
polymorphism (SNP), copy number variation (CNV),
splicing variation, variation of a regulatory sequence,
small deletion, small insertion, small indel, gross
deletion, gross insertion, complex genetic rearrangement,
inter chromosomal rearrangement, intra chromosomal
rearrangement, loss of heterozygosity, and insertion of
repeats and deletion of repeats.
Appeal Br. 35 (Claims App.) (emphasis added).
Under the broadest reasonable interpretation, therefore, claim 1 does
not require that all possible signature data (i.e., all possible information on a
genetic or genomic variation) in the subject’s genomic sequence data be
stored. In this case, Kane teaches retention and storage of information about
SNPs maintained in a SNP database of risk linkages and thus teaches or
suggests retaining/storing two or more of SNPs as recited by claim 1.
Accordingly, we affirm the Examiner’s rejection of claim 1 as
obvious over Chang, Gatawood, Sherry, Metzker, and Kane. Claims 8, 14,
and 15, which are not separately argued, fall with claim 1. Appellant does
not make any additional arguments with respect to the rejections of claims 2,
13, and 16–18 as obvious over Chang, Gatawood, Sherry, Metzker, Kane,
and Greenman; claims 3, 4, and 12 as obvious over Chang, Gatawood,
Sherry, Metzker, Kane, and Bollet; claim 6 as obvious over Chang,
Gatawood, Sherry, Metzker, Kane, and Langmead; claim 9 as obvious over
Chang, Gatawood, Sherry, Metzker, Kane, and Rhodes; and claim 11 as
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obvious over Chang, Gatawood, Sherry, Metzker, Kane, and Hwang.
Accordingly, we affirm these rejections based on the same reasoning
discussed above.

CONCLUSION
In summary:
Claims
Rejected
35 U.S.C. § Reference(s)/Basis Affirmed Reversed
1–4, 6, 8, 9,
11–18
101 Eligibility 1–4, 6, 8, 9,
11–18

1, 8, 14, 15 103(a) Chang, Gatawood,
Sherry, Metzker,
Kane
1, 8, 14, 15
2, 13, 16–18 103(a) Chang, Gatawood,
Sherry, Metzker,
Kane, Greenman
2, 13, 16–18
3, 4, 12 103(a) Chang, Gatawood,
Sherry, Metzker,
Kane, Bollet
3, 4, 12
6 103(a) Chang, Gatawood,
Sherry, Metzker,
Kane, Langmead
6
9 103(a) Chang, Gatawood,
Sherry, Metzker,
Kane, Rhodes
9
11 103(a) Chang, Gatawood,
Sherry, Metzker,
Kane, Hwang
11
Overall
Outcome
1–4, 6, 8, 9,
11–18

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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). See 37 C.F.R.
§ 1.136(a)(1)(iv).

AFFIRMED