Sunil Kumar et al.

Patent Trials and Appeals Board

May 6, 2021

2020002806 (P.T.A.B. May. 6, 2021)

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.
14/124,261 12/06/2013 Sunil Kumar 2011P00518WOUS 5645
24737 7590 05/06/2021
PHILIPS INTELLECTUAL PROPERTY & STANDARDS
465 Columbus Avenue
Suite 340
Valhalla, NY 10595
EXAMINER
WHALEY, PABLO S
ART UNIT PAPER NUMBER
3619
NOTIFICATION DATE DELIVERY MODE
05/06/2021 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 SUNIL KUMAR, RANDEEP SINGH,
and NEVENKA DIMITROVA
____________________

Appeal 2020-002806
Application 14/124,2611
Technology Center 3600
____________________

Before DEBORAH KATZ, JON M. JURGOVAN, and
JOHN E. SCHNEIDER, Administrative Patent Judges.

JURGOVAN, Administrative Patent Judge.

DECISION ON APPEAL

Appellant seeks review under 35 U.S.C. § 134(a) from a Final
Rejection of claims 1–4 and 7–15, constituting all of the claims pending in
the application.2 We have jurisdiction under 35 U.S.C. § 6(b).
We AFFIRM.3

1 We use the word “Appellant” to refer to “applicant” as defined in
37 C.F.R. § 1.42. According to Appellant, the real party in interest is
Koninklijke Philips N.V. Appeal Br. 3.
2 Claims 5 and 6 were canceled and thus are not on appeal before us.
3 Our Decision refers to the Specification (“Spec.”) filed December 6, 2013;
the Final Office Action (“Final Act.”) mailed April 10, 2019; the Response
after Final Action (“Resp. after Final Act.”) filed June 10, 2019; the
Advisory Action (“Advisory Act.”) mailed July 5, 2019; the Appeal Brief
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CLAIMED INVENTION
The claims recite a method for assembly of nucleic acid sequence
data, which comprises nucleic acid fragment reads, into contiguous
nucleotide sequence segment(s) of a genome sequence. Spec. Abstract. The
method aligns fragment reads to a reference sequence to detect gaps within
the aligned sequence, and performs de novo sequence assembly for the gaps.
Id. The method combines the aligned and de novo assembled fragments to
obtain the contiguous nucleotide sequence segment(s) which is recorded in a
machine-readable storage device. Id.
Claim 1 is independent. The remaining claims depend from claim 1.
Claim 1, reproduced below, is representative of the claimed subject matter.
1. A method for assembly of nucleic acid sequence data
comprising nucleic acid fragment reads into a contiguous
nucleotide sequence segment(s) of a genome sequence,
comprising:
accessing a file comprising one or more digital files
comprising pluralities of nucleic acid sequence data from
pluralities of nucleic acid fragment reads;
selecting, by a computer system, a digital file comprising
a plurality of nucleic acid sequence data from a plurality of
nucleic acid fragment reads corresponding to the genome
sequence, wherein said nucleic acid fragment reads are obtained
from a sequencing device;
selecting, by the computer system, a second digital file
comprising a nucleic acid reference sequence, wherein said
nucleic acid reference sequence is obtained from a nucleic acid
sequence reference source;
performing, by the computer system, a set of alignments
of said nucleic acid sequence data to said nucleic acid reference

(“Appeal Br.”) filed September 3, 2019; the Examiner’s Answer (“Ans.”)
mailed December 30, 2019; and the Reply Brief (“Reply Br.”) filed February
27, 2020.
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sequence by comparing said nucleic acid fragment reads with
genomic or sub-genomic reference sequences within said nucleic
acid reference sequence, to generate a nucleic acid sequence
alignment;
identifying, by the computer system, one or more gaps
within said nucleic acid sequence alignment by comparing said
nucleic acid sequence data with said nucleic acid reference
sequence to which said nucleic acid sequence data has been
aligned, wherein each of the identified one or more gaps
comprises a region within the nucleic acid sequence alignment
which does not align with said nucleic acid reference sequence;
applying, by computer system, a de novo contig sequence
assembly technique to said identified one or more gaps using
nucleic acid sequence data mapping to said identified one or
more gaps, wherein said de novo contig assembly technique
utilizes: (i) a first nucleic acid fragment read, selected from the
plurality of nucleic acid sequence data, which partially overlaps
with both a portion of the gap and a region of the nucleic acid
sequence alignment directly abutting a first side of the gap; and
(ii) a plurality of nucleic acid fragment reads in addition to the
first nucleic acid fragment read, each of the plurality of nucleic
acid fragment reads aligning with a portion of the growing de
novo contig assembly;
determining, by the computer system, a contiguous
nucleotide sequence segment by combining the generated
nucleic acid sequence alignment with the results of said de novo
contig sequence assembly; and
recording said contiguous nucleotide sequence segment in
a rapidly retrievable form on a machine-readable storage device
configured to receive nucleic acid sequence data.

Appeal Br. 25–26 (Claims App.).

REJECTION
Claims 1–4 and 7–15 stand rejected under 35 U.S.C. § 101 as directed
to a judicial exception to patent eligibility without significantly more.
Final Act. 2–10.
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ANALYSIS
Standard of Review
We undertake a limited de novo review of the appealed rejection for
error based upon the issues identified by Appellant, and in light of the
arguments and evidence produced thereon. Ex parte Frye, 94 USPQ2d
1072, 1075 (BPAI 2010) (precedential).
Legal Principles of Patent Eligibility
Patentable subject matter is defined by 35 U.S.C. § 101, as follows:
[w]hoever invents or discovers any new and useful process,
machine, manufacture, or composition of matter, or any new and
useful improvement thereof, may obtain a patent therefor, subject
to the conditions and requirements of this title.
In interpreting this statute, the Supreme Court emphasizes that patent
protection should not preempt “the basic tools of scientific and technological
work.” Gottschalk v. Benson, 409 U.S. 63, 67 (1972) (“Benson”); Mayo
Collaborative Servs. v. Prometheus Labs., Inc., 566 U.S. 66, 71 (2012)
(“Mayo”); Alice Corp. v. CLS Bank Int’l, 573 U.S. 208, 217–18 (2014)
(“Alice”). The rationale is that patents directed to basic building blocks of
technology would not “promote the progress of science and the useful arts”
under the U.S. Constitution, Article I, Section 8, Clause 8, but instead would
impede it. Accordingly, laws of nature, natural phenomena, and abstract
ideas, are not patent-eligible subject matter. Thales Visionix Inc. v. U.S., 850
F.3d 1343, 1346 (Fed. Cir. 2017) (citing Alice, 573 U.S. at 216–17).
The Supreme Court set forth a two-part test for subject matter
eligibility in Alice (573 U.S. at 217–19). The first step is to determine
whether the claim is directed to a patent-ineligible concept. Id. (citing
Mayo, 566 U.S. at 76–77). If so, then the eligibility analysis proceeds to the
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second step of the Alice/Mayo test in which we “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 (quoting Mayo, 566 U.S. at 72, 79). There is no need
to proceed to the second step, however, if the first step of the Alice/Mayo
test yields a determination that the claim is directed to patent eligible subject
matter.
The Patent Office has revised its guidance for how to apply the
Alice/Mayo test in the 2019 Revised Patent Subject Matter Eligibility
Guidance, 84 Fed. Reg. 50–57 (January 7, 2019) (“the Revised Guidance”).
Under the Revised Guidance, the first step of Alice/Mayo is addressed in two
prongs in which we determine whether the claim recites:
(1) any judicial exceptions, including certain groupings of
abstract ideas (i.e., mathematical concepts, mental processes, or
certain methods of organizing human activity such as a
fundamental economic practice or managing personal behavior
or relationships or interactions between people); and
(2) additional elements that integrate the judicial exception into
a practical application (see Manual of Patent Examining
Procedure (“MPEP”) § 2106.05(a)–(c), (e)–(h) (9th Ed., Rev.
10.2019, June 2020)). 84 Fed. Reg. at 51–52, 55.
A claim that integrates a judicial exception into a practical application
applies, relies on, or uses the judicial exception in a manner that imposes a
meaningful limit on the judicial exception, such that the claim is more than a
drafting effort designed to monopolize the judicial exception. 84 Fed. Reg.
at 54. When the judicial exception is so integrated, then the claim is not
directed to a judicial exception and is patent-eligible under § 101. 84 Fed.
Reg. at 54. Only if a claim (1) recites a judicial exception and (2) does not
integrate that exception into a practical application, do we then evaluate
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whether the claim provides an inventive concept in step two of Alice/Mayo.
84 Fed. Reg. at 56; Alice, 573 U.S. at 217–19, 221. Evaluation of the
inventive concept involves consideration of whether an additional element or
combination of elements (1) adds a specific limitation or combination of
limitations that are not well-understood, routine, conventional activity in the
field, which is indicative that an inventive concept may be present; or
(2) simply appends well-understood, routine, conventional activities
previously known to the industry, specified at a high level of generality, to
the judicial exception, which is indicative that an inventive concept may not
be present.
The Examiner’s rejection follows the flowchart shown in MPEP
§ 2106.
Claim 1
USPTO Step 1 – Does the claim recite a statutory category of invention?
The Examiner finds the method for assembly of nucleic acid sequence
data, as recited in claim 1, falls within one of the four statutory categories of
invention. Final Act. 3. The method qualifies as a “process” under
35 U.S.C. § 101, so we agree with the Examiner that Step 1 of the patent
eligibility analysis is satisfied. Final Act. 3. We proceed in our analysis to
USPTO Step 2A, which is the first step of Alice/Mayo.
USPTO Step 2A, Prong 1 – Does the claim recite a judicial exception to
patentability?
The Examiner finds that the “performing,” “identifying,” “applying,”
and “determining” steps of claim 1 recite abstract ideas. Final Act. 3.
Specifically, the Examiner finds that these steps are “mental processes
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because they can be reasonably performed by the human mind and include
evaluation.” Id. at 4. The Examiner finds that “other than reciting these
steps are performed on a computer system, nothing in the claim element
precludes the step from practically being performed in the mind.” Id.
Appellant argues that the claim is not focused on an abstract idea, but
on an improvement. Appeal Br. 14–16; Reply Br. 3. However, USPTO
Step 2A, Prong 1 focuses on whether the claim recites a judicial exception—
improvements are addressed later in Step 2A, Prong 2. See Revised
Guidance, 84 Fed. Reg. at 55. Accordingly, we do not address Appellant’s
argument here, but subsequently under Step 2A, Prong 2.
Appellant contends “[n]ext-generation sequencing (NGS) involving
millions of reads and billions of base pairs is no longer performed using pen
and paper or [in] one’s mind.” Appeal Br. 18; Reply Br. 2. As the
Examiner notes, this argument assumes limitations which are not present in
the claims. Ans. 9–10. Specifically, the claim does not recite “next
generation sequencing.” Appellant appears to be arguing for patentability
based on a limitation reciting a “next generation sequencing (NGS) device”
in an Amendment after Final Office Action filed June 10, 2019. The
Examiner refused entry of this amendment as requiring further search. See
Advisory Act. 3. Accordingly, the amended claims are not considered in
this appeal.
Further, the claims do not recite sequencing involving millions of
reads and billions of base pairs, so Appellant’s argument is not supported by
corresponding language in the claim. Under broadest reasonable
interpretation of the claim, there is no limit on how small the contiguous
nucleotide sequence segment could be, including segment lengths that could
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be determined in one’s mind. See In re Am. Acad. of Sci. Tech Ctr., 367
F.3d 1359, 1369 (Fed. Cir. 2004) (“[T]he PTO is obligated to give claims
their broadest reasonable interpretation during examination.”). As the
claims do not recite the limitations that Appellant argues, we find
Appellant’s argument unpersuasive. In re Self, 671 F.2d 1344, 1348 (CCPA
1982) (stating that limitations not appearing in the claims cannot be relied
upon for patentability).
To the extent Appellant argues that the Examiner has “deconstructed
[the claim] . . . to such a high level of abstraction that it ensures patent
ineligibility” (Appeal Br. 17), we disagree. The Examiner’s finding is that
“with the exception of using a computer system, there is nothing in the
claims themselves that foreclose these steps from being performed by a
human, mentally or with pen and paper.” Ans. 5 (emphasis added); see also
Final Act. 4. The “performing,” “identifying,” “applying,” and
“determining” steps of claim 1 lack specifics that would confine their
performance only to a computer system. In other words, even though the
claim recites performance with a computer system, the recited actions could
be carried out in the human mind or with pen and paper. These steps are
thus properly classified under the “mental processes” category of abstract
ideas constituting judicial exceptions to patent eligibility. See CyberSource
Corp. v. Retail Decisions, Inc., 654 F.3d 1366, 1375 (Fed. Cir. 2011) (“That
purely mental processes can be unpatentable, even when performed by a
computer, was precisely the holding of the Supreme Court in Gottschalk v.
Benson”).
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USPTO Step 2A, Prong 2 – Is the claim directed to a judicial exception?
The Examiner finds that additional elements of claim 1 (other than the
ones reciting judicial exceptions) are the “computer system” and the
“storage device”4 and the steps of “accessing,” “selecting . . . a digital file,”
“selecting . . . a second digital file,” and “recording.” Ans. 6; see also
Final Act. 4–5. The Examiner finds “that the additionally recited elements
do not apply, rely on, or use the judicial exception in a manner that imposes
a meaningful limit on the judicial exception and, as such, does not integrate
the abstract idea into a practical application.” Final Act. 4 (citing MPEP
§ 2106.05(a)–(h)).
We agree with the Examiner. The claim merely recites that the steps
are carried out by a “computer system” and “storage device.” As such, the
claim amounts to nothing more than an instruction to apply the abstract ideas
using a generic computer system and storage device, and this does not render
abstract ideas patent-eligible. See Alice, 573 U.S. at 223; MPEP
§ 2106.05(f). In other words, the claim at issue here merely invokes the
“computer system” and “storage device” as tools to carry out the recited
abstract ideas recited in the claim. See Affinity Labs of Tex., LLC v.
DirectTV, LLC, 838 F.3d 1253, 1262 (Fed. Cir. 2016); TLI Commc’ns LLC
v. AV Auto, LLC, 823 F.3d 607, 613 (Fed. Cir. 2016).
The Examiner further finds the additional elements “amount to
insignificant extra-solution activity and are not indicative of integration into

4 The Examiner does not mention the “sequencer device” here, but does
address it later under the USPTO Step 2B analysis. We view this as
harmless error, however, because the claim does not recite use of the
“sequencer device” in the performance of a step, but merely describes it as
the device from which the nucleic acid fragment reads are obtained.
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a practical application, i.e. no amount of insignificant extra-solution activity
can render the claims statutory.” Ans. 6; see also Final Act. 4–5. We agree
with the Examiner. The “accessing” and the two “selecting” steps amount to
data gathering and do not integrate the steps reciting judicial exceptions into
a practical application. See CyberSource, 654 F.3d at 1375; MPEP
§ 2106.05(g). The “recording” step merely stores the result of the abstract
mental processes, i.e., the contiguous nucleotide sequence segment, on a
machine-readable storage medium capable of storing it. Such storing of data
has been found insufficient to integrate a judicial exception into a practical
application. See, e.g., Content Extraction & Transmission LLC v. Wells
Fargo Bank, Nat’l Ass’n, 776 F.3d 1343, 1348 (Fed. Cir. 2014).
The Examiner further finds that “[t]he claim essentially results in
determining and storing a contiguous nucleic acid sequence inside of a
computer by combining comparative and de novo assembly strategies, i.e.
the claim as a whole generally links the use of the judicial exception to a
particular technological environment (namely a computer system).” Final
Act. 4. We agree. The claim provides little detail of how the computer
system carries out the recited steps. As such, the claim generally links the
use of the judicial exception to a computer system, which is insufficient to
constitute a practical application.
Appellant argues that “the claims are directed to a specific
improvement in the functionality of the computerized NGS system, namely
an improved ability to more quickly and accurately generate a contiguous
nucleotide sequence segment.” Appeal Br. 20. As already noted, the
Examiner did not allow entry of the amendment reciting the computerized
NGS system, so Appellant improperly argues a limitation that is not present
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in the claim as presented on appeal. See Self, supra. For the same reason,
the cases that Appellant cites are inapposite to the facts of this case.
Likewise, Appellant argues that the claim “recites a specific structure
(the visual report comprising the generated and stored contiguous nucleotide
sequence segment, which is more accurate than prior art sequences).”
Appeal Br. 21. No such feature is recited in the claim.
Appellant further argues “[t]here are many practical applications with
direct benefits listed in the application.” Appeal Br. 20 (citing Spec. ¶¶ 4–5,
54–55). Though these practical applications may be set forth in the
Specification, none are recited in the claims, and it is improper to import
limitations from the Specification into the claims. Phillips v. AWH Corp.,
415 F.3d 1303, 1323 (Fed. Cir. 2005) (en banc).
Appellant further contends “the claim as a whole integrates the
alleged abstract idea into a practical application, with regard to the storage
and display of the generated and stored contiguous nucleotide sequence
segment, for review and/or use with other applications.” Appeal Br. 21;
Reply Br. 3–4. As a whole, the claim recites steps that can be classified as
either mental processes or extra-solution activity, and, contrary to
Appellant’s assertions, the claim does not recite any display or use of the
stored sequence segment with other applications. Ans. 4–7; see also Final
Act. 4–5. We agree with the Examiner that the claims, considered as a
whole, do not recite anything that amounts to a practical application.
Step 2B – Does the claim recite an inventive concept sufficient to
transform the judicial exception into patent-eligible subject matter?
The Examiner finds that “[t]he claims do not recite any steps/elements
appended to the judicial exception that amount to ‘significantly more’ than
the judicial exception.” Final Act. 5. The Examiner takes official notice
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that the steps of “accessing” and “selecting” files are well-understood,
routine, and conventional in the art and amount to nothing more than
insignificant extra-solution activity, i.e., routine data collection. Id.
The Examiner also lists numerous cases in which laboratory
techniques in the life science arts were held to be well-understood, routine,
and conventional when claimed in a generic manner or as insignificant extra-
solution activity. Final Act. 5–6 (citing MPEP § 2016.05(d)). These cases
include using polymerase chain reaction to amplify and detect DNA, Genetic
Techs. v. Merial LLC, 818 F.3d 1369, 1376 (Fed. Cir. 2016); Ariosa
Diagnostics, Inc. v. Sequenom, Inc., 788 F.3d 1371, 1377 (Fed. Cir. 2015);
detecting DNA or enzymes in a sample, Ariosa, 788 F.3d at 1377–78;
Cleveland Clinic Foundation v. True Health Diagnostics, LLC, 859 F.3d
1352, 1362 (Fed. Cir. 2017); analyzing DNA to provide sequence
information or detect allelic variants, Genetic Techs., 818 F.3d at 1377;
amplifying and sequencing nucleic acid sequences, and hybridizing a gene
probe, University of Utah Research Foundation v. Ambry Genetics, 774 F.3d
755, 764 (Fed. Cir. 2014). See also In re Board of Trustees of Leland
Stanford Junior Univ., 991 F.3d 1245, 1252 (Fed. Cir. 2021) (receiving and
storing data in a computer memory and extracting a predicted haplotype are
well-understood, routine and conventional). The subject matter of these
cases bears similarity to the present one and lends support to the Examiner’s
finding that the recited steps of claim 1 were well-understood, routine, and
conventional.
The Examiner finds the “recording” step “amounts to nothing more
than mere instructions to implement an abstract idea or a computer as well as
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insignificant extra-solution activity, i.e., data output. Final Act. 6 (citing
MPEP § 2016.05(d)). We agree with the Examiner’s assessment.
The Examiner takes official notice that the claimed “computer
system,” “storage device,” and “sequencer device” are well-understood,
routine, and conventional in the art. Final Act. 6 (citing DDR Holdings, LLC
v. Hotels.com, L.P., 773 F.3d 1245 (Fed. Cir. 2014); Ultramercial, Inc. v.
Hulu, LLC, 772 F.3d 709, 716–717 (Fed. Cir. 2014)); see also Alice, 573
U.S. at 225. We agree with the Examiner’s finding at least as to the
“computer system” and “storage device.” The Specification describes the
“sequencer device” as one of a few different commercial models or “any
other suitable sequencer device.” Spec. 28. As generically described in the
Specification, it is not apparent how the “sequencer device” would constitute
or contribute to an “inventive concept.” Furthermore, as the claim is recited,
the “sequencer device” is merely a device from which nucleic acid fragment
reads are obtained, and it is not used to perform any of the recited steps.
The Examiner further finds that “determining and storing a contiguous
nucleic acid sequence inside of a computer by combining comparative and
de novo assembly strategies” is well known to one of ordinary skill in the
art.” Final Act. 6. For this proposition, the Examiner cites Pop et al.,
BRIEFINGS IN BIOINFORMATICS, 2009, vol. 10, no. 4, pp. 354–366 (“Pop”).
Id.
Appellant argues “the claimed method comprises a complex series of
components and processes that results in a nonconventional method and
system,” and lists several claim features. Appeal Br. 22–23; see also Reply
Br. 4–5. These features include the claimed files comprising nucleic acid
sequence data and reference data; nucleic acid sequence alignment; gaps
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found by comparing nucleic acid sequence data with a reference; de novo
sequence assembly; a contiguous nucleotide sequence segment from the
aligned sequence and de novo sequence assembly; and a machine-readable
storage device to receive and store the nucleic acid sequence data in a
rapidly retrievable form. Appellant does not address, however, the
Examiner’s finding that combining comparative and de novo assembly
strategies was well known, as evidenced by Pop.
Appellant further argues the claimed computerized NGS system is
both novel and non-obvious, and so is not a generic system that would
preempt the field. Appeal Br. 23; Reply Br. 4–5. The claim does not recite
a computerized NGS system, and Appellant’s mere assertion, without
evidence, that the claim is novel and non-obvious is insufficient, particularly
when the Examiner cites Pop as evidence it is not. We further note that “the
absence of complete preemption does not demonstrate patent eligibility.”
Ariosa, 788 F.3d at 1379.
Appellant contends the Examiner “incorrectly imports a new
requirement for Step 2B of the Alice Analysis, that an applicant provide
‘objective evidence of an improvement to the technology.’” Reply Br. 5
(citing Ans. 10). We do not agree that the Examiner imported such a
requirement. The Examiner cited Pop for the proposition that combining
comparative and de novo strategies was known in the art. Appellant
presented no argument or evidence to counter the Examiner’s evidence.
Conclusion for claim 1
In conclusion, Appellant shows in USPTO Step 1 of the patent
eligibility analysis that claim 1 is a statutory process. The Examiner,
however, shows in USPTO Step 2A, Prong 1 that the claim recites judicial
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exceptions, namely, mental processes that are abstract ideas. The Examiner
also shows in USPTO Step 2A, Prong 2 that the claim does not recite
additional elements that integrate those judicial exceptions into a practical
application. The Examiner further demonstrates in USPTO Step 2B that the
additional elements do not set forth an inventive concept. Accordingly, we
sustain the Examiner’s § 101 rejection.
A. Remaining Claims
No arguments were presented for the remaining dependent claims.
See generally, Appeal Br. and Reply Br. Accordingly, we sustain the
Examiner’s § 101 rejection of these dependent claims for the same reasons
stated for claim 1.
CONCLUSION
The Examiner’s rejection of claims 1–4 and 7–15 under 35 U.S.C.
§ 101 is affirmed.
In summary:
Claim(s)
Rejected
35 U.S.C. § Reference(s)/Basis Affirmed Reversed

1–4, 7–15

101

Eligibility

1–4, 7–15

No time period for taking any subsequent action in connection with
this appeal may be extended under 37 C.F.R. § 1.136(a)(1)(iv). See 37
C.F.R. § 41.50(f) (2019).

AFFIRMED