Bhubaneswar Mishra et al.

Patent Trials and Appeals Board

Aug 29, 2019

13266662 - (D) (P.T.A.B. Aug. 29, 2019)

UNITED STATES PATENT AND TRADEMARK OFFICE
UNITED STATES DEPARTMENT OF COMMERCE
United States Patent and Trademark Office
Address: COMMISSIONER FOR PATENTS
P.O. Box 1450
Alexandria, Virginia 22313-1450
www.uspto.gov
APPLICATION NO. FILING DATE FIRST NAMED INVENTOR ATTORNEY DOCKET NO. CONFIRMATION NO.
13/266,662 10/27/2011 Bhubaneswar Mishra 191263.US.02-32882-214035 1573
120944 7590 08/29/2019
Hunton Andrews Kurth LLP/HAK NY
Attention: Intellectual Property - Patent Docket
200 Park Avenue
New York, NY 10016
EXAMINER
HARWARD, SOREN T
ART UNIT PAPER NUMBER
1631
NOTIFICATION DATE DELIVERY MODE
08/29/2019 ELECTRONIC
Please find below and/or attached an Office communication concerning this application or proceeding.
The time period for reply, if any, is set in the attached communication.
Notice of the Office communication was sent electronically on above-indicated "Notification Date" to the
following e-mail address(es):
nydocket@andrewskurth.com
ptony@andrewskurth.com
PTOL-90A (Rev. 04/07)
UNITED STATES PATENT AND TRADEMARK OFFICE
____________

BEFORE THE PATENT TRIAL AND APPEAL BOARD
____________

Ex parte BHUBANESWAR MISHRA
and GIUSEPPE NARZISI1
____________

Appeal 2019-001691
Application 13/266,662
Technology Center 1600
____________

Before TONI R. SCHEINER, RICHARD M. LEBOVITZ, and
DEBORAH KATZ, Administrative Patent Judges.

LEBOVITZ, Administrative Patent Judge.

DECISION ON APPEAL
The claims is this appeal are directed to computer executable
instructions, methods, and systems for assembling a genetic sequence. The
Examiner rejected the claims under 35 U.S.C. § 101 as directed to non-
statutory subject matter. Pursuant to 35 U.S.C. § 134, Appellant appeals
the Examiner’s determination that the claims are unpatentable. We have
jurisdiction for the appeal under 35 U.S.C. § 6(b). The Examiner’s decision
is affirmed.

1 The Appeal Brief (“Appeal Br.” entered Sept. 5, 2018) lists New York
University of New York, New York as the Real Party in Interest. Appeal Br.
3.
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STATEMENT OF THE CASE
Claims 42–75 stand rejected by the Examiner under 35 U.S.C. § 101
as directed to non-statutory subject matter ineligible for a patent. Ans. 3.
There are three independent claims, claims 42, 53, and 65. Claim 42 is
directed to a “non-transitory computer-accessible medium having stored
thereon computer executable instructions for assembling at least one genetic
sequence,” claim 53 is to a “method for assembling at least one genetic
sequence,” and claim 65 is to a “system for assembling at least one genetic
sequence.” Appellants did not provide separate arguments for the claims.
Because the claims were not argued separately by Appellants and because
the steps are the same, or substantially similar (Appeal Br. 25), we address
all three independent claims together, as well as the dependent claims. The
claims stand or fall together. 37 C.F.R. § 41.37(c)(1)(iv).
Claim 53, which is representative of the appealed claims, is
reproduced below:
53. A method for assembling at least one genetic
sequence, comprising:
(a) obtaining a series of raw intensity outputs from a
sequencing platform configured to be used for reading a
fragment of at least one genome;
(b) obtaining at least one reference sequence for the at
least one genome, wherein the at least one reference sequence
for the at least one genome is obtained independently from the
series of raw intensity outputs obtained from the sequencing
platform;
(c) automatically generating a search tree comprising a
plurality of nodes, wherein each of the plurality of nodes
corresponds to a particular nucleotide base;
(d) automatically selecting a node of the plurality of
nodes in the search tree;
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(e) automatically expanding the selected node by creating
a plurality of child nodes, each of the child nodes corresponding
to a particular further nucleotide base;
(f) automatically generating a score for one or more of
the child nodes, wherein the score is a function of (i) at least
one raw intensity output from the series of raw intensity
outputs, (ii) the plurality of reference sequences, and (iii) the
nucleotide base to which a particular one of the plurality of
child nodes corresponds;
(g) automatically selecting one or more of the plurality of
child nodes based on the score;
(h) automatically repeating procedures (e)–(g) for the
selected child node;
(i) automatically generating a path through the plurality
of nodes; and
(j) using a computer hardware arrangement,
automatically assembling the at least one genetic sequence
based on the path.

REJECTION UNDER § 101
The Examiner rejected claims 42–75 under 35 U.S.C. § 101 as
directed to a judicial exception to patent eligibility. Ans. 3. The Examiner
found that the claims are directed to an abstract idea which is a judicial
exception to patent eligibility under § 101. Ans. 6.
Under 35 U.S.C. § 101, an invention is patent-eligible if it claims a
“new and useful process, machine, manufacture, or composition of matter.”
However, not every discovery is eligible for patent protection. Diamond v.
Diehr, 450 U.S. 175, 185 (1981). “Excluded from such patent protection are
laws of nature, natural phenomena, and abstract ideas.” Id. The Supreme
Court articulated a two-step analysis to determine whether a claim falls
within an excluded category of invention. Alice Corp. v. CLS Bank Int’l,
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573 U.S. 208, 216 (2014); Mayo Collaborative Servs. v. Prometheus Labs,
Inc., 566 U.S. 66, 75–77 (2012).
In the first step, it is determined “whether the claims at issue are
directed to one of those patent-ineligible concepts.” Alice, 566 U.S. at 217.
If it is determined that the claims are directed to an ineligible concept, then
the second step of the two-part analysis is applied in which it is asked
“‘[w]hat else is there in the claims before us?’” Id. The Court explained
that this step involves
. . . 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.”
Alice, 566 U.S. at 217–18 (citing from Mayo, 566 U.S. at 75–77).
Alice, relying on the analysis in Mayo of a claim directed to a law of
nature, stated that in the second part of the analysis “the elements of each
claim both individually and ‘as an ordered combination’” must be
considered “to determine whether the additional elements ‘transform the
nature of the claim’ into a patent-eligible application. Alice, 566 U.S. at
217.
The PTO recently published revised guidance on the application of
§ 101. USPTO’s January 7, 2019 Memorandum, 2019 Revised Patent
Subject Matter Eligibility Guidance, 84 Fed. Reg. 50, 51–57 (2019) (“2019
Eligibility Guidance”). This guidance provides direction on how to
implement the two-part analysis of Mayo and Alice.
Step 2A, Prong One, of the 2019 Guidelines, looks at the specific
limitations in the claim to determine whether the claim recites a judicial
exception to patent eligibility. In Step 2A, Prong Two, the claims are
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examined to identify whether there are additional elements in the claims that
integrate the exception in a practical application, namely, is there 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 53 (“2. Prong Two”).
If the exception is not integrated into a practical application, then as in
the Mayo/Alice framework, Step 2B of the 2019 Guidelines asks whether
there is an inventive concept to ensure that the patent is significantly more
than a patent on the ineligible concept, itself. In making this determination,
it must be considered whether there are specific limitations or elements
recited in the claim “that are not well-understood, routine, conventional
activity in the field, which is indicative that an inventive concept may be
present” or whether the claim “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.” 84 Fed. Reg. at 56.
With these guiding principles, we proceed to determine whether the
claimed subject matter in this appeal is eligible for patent protection under
35 U.S.C. § 101. As explained in more detail below, we conclude that the
claims are directed to patent-ineligible subject matter.

Step 2A, Prong One
In Step 2A, Prong One, of the 2019 Guidelines, the specific
limitations in the claim are examined to determine whether the claim recites
a judicial exception to patent eligibility, i.e., whether the claim recites an
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abstract idea, law of nature, or natural phenomenon. The Examiner found
that the claim recites an abstract idea.
The 2019 Eligibility Guidance identifies three groupings (a)–(c) as
abstract ideas. 84 Fed. Reg. 52. As explained in more detail below, the
claim recites subject matter which fits into grouping (a), “Mathematical
concepts–mathematical relationships, mathematical formulas or equations,
mathematical calculation.”
Claim 53 is directed to a “method for assembling at least one genetic
sequence.” In broad terms, the method is for identifying nucleotides at
specific positions of a genome fragment by applying mathematical
operations to raw intensity outputs obtained from nucleotide sequencing
technology. The process is also called “base-calling” because the identity of
a nucleotide base at a position in a genome sequence is “called out” by
carrying out the steps of the method. See Spec. ¶ 32. By using the method,
and aligning it with a reference sequence, accurate nucleotide sequence
polymorphisms can be identified. See Spec. ¶ 6.
Step (a) of the claim is directed to “obtaining . . . raw intensity outputs
obtained from the sequencing platform.” The “sequencing platform” is the
nucleotide base sequencing technology used to detect the nucleotides in the
recited “genome fragment.” Spec. ¶ 34. “Raw intensity outputs” represent
the intensity values generated by the nucleotide base sequencing, namely the
signal intensities for each of the A, C, G, and T bases. Spec. ¶ 101. The
example in the Specification is fluorescence light intensity using the
Illumina sequencing technology. Id. The sequence data from step (a) is
obtained from reading the nucleotide base sequence of a fragment of a
genome. The sequence data of claims (b) is from a reference nucleotide
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sequence from the genome. Steps (a) and (b) thus comprise obtaining
nucleotide sequence data.
Steps (c) through (i) each use the term “automatically” to describe a
step in the claim, indicating that the subsequently recited instructions are
computations performed by a computer with no human intervention. The
instructions or steps recited in these steps are mathematical operations
performed on nodes in a search tree, where the nodes represent nucleotides.
As explained in the Appeal Brief and the Specification, the purpose of the
steps is to identify the particular nucleotide, A, T, C, and G, at a specific
location in the genome fragment, i.e., base-calling. Appeal Br. 9–14. The
Specification explains:
Figure 4 shows a diagram of an exemplary tree
that can be generated by an exemplary base-caller
procedure in accordance with certain exemplary
embodiments of the present disclosure. As shown in
Figure 4, an exemplary tree 400 can include root 401
corresponding to cycle 0. The tree 400 can be a
quaternary tree (e.g., branching factor = 4), where, at
each cycle, each node can be expanded by 4,
corresponding to A, T, C, and G, for example.
Spec. ¶ 98.
Step (f) of the claim specifically recites “generating a score for one or
more of the child nodes” where “the score is a function of (i) at least one raw
intensity output from the series of raw intensity outputs, (ii) the plurality of
reference sequences, and (iii) the nucleotide base to which a particular one
of the plurality of child nodes corresponds.” The score, described in the
Specification as a “score function” is derived using mathematical operations:
The exemplary score function (and/or components thereof) can
be built from (e.g., generated, derived from, based upon, etc.)
the logarithm of intensity information from each base-read and
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its variance-based weighting of squared deviations computed
using a distribution of similar positional intensities stored in an
exemplary database.
Spec. ¶ 81. Thus, the Specification defines step (f) as a mathematical
concept and an abstract idea.
The last step (j) of the method comprises “automatically assembling
the at least one genetic sequence based on the path.” (Claims App. A–5).
The Specification does not define “assembling,” but we understand it to
mean producing one genome nucleotide sequence from the “series of raw
intensity outputs” obtained in step (a) of the claim by following the
instructions recited in steps (c)–(i) of the claim. Id.
In sum, the steps performed in claim 53 comprise “Mathematical
concepts” and “mathematical calculations,” falling into grouping (a) of the
three groupings identified as abstract ideas. 84 Fed. Reg. 52. We reach this
conclusion, consistent with the Examiner’s analysis, because steps (c)–(i) of
the claim each involve performing mathematical operations on a node,
where the node is mathematical representation of nucleotide. Spec. ¶¶ 62,
64, 80, 98. For example, as explained in the Specification, the nodes are
repeatedly expanded by branching to form a path that is used to determine
the sequence of the genome fragment. See Spec. ¶ 62, Fig. 4. The
Specification defines these steps mathematically and thus the steps are
abstract ideas. Step (j) of the claim is assembling a nucleotide base sequence
(the “genetic sequence” of the claims) based on the preceding mathematical
operations and thus is a mathematical operation, itself.
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Step 2A, Prong Two
In the second step of the analysis, when the claim is found to recite a
judicial exception, the 2019 Guidelines direct us to “evaluate whether the
claim as a whole integrates the recited judicial exception into a practical
application of the exception.” 84 Fed. Reg. 54 (in section titled “2. Prong
Two”). Thus, because claim 53 is directed to a judicial exception – an
abstract idea – , we proceed to the second step of the analysis. The 2019
Guidelines explains:
A claim that integrates a judicial exception into a
practical application will apply, rely on, or use 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. 54.
In this case, the mathematical operations recited in the claim are for
the purpose of assembling a nucleotide sequence from raw intensity outputs
obtained from a nucleotide sequencing platform. The issue is whether these
mathematical operations to assemble a nucleotide sequence constitute a
practical application.
Appellants argue that the claims are “directed to an improvement of
an existing technology” which they characterize as “assembling genetic
sequences,” because the method “improves the reliability in generating
genome sequences, and improves the reliability of population-wide genomic
studies.” Appeal Br. 28. However, not every improvement to a technology
is patent-eligible.
In Parker v. Flook, 437 U.S. 584, 594–95, claims to updating alarm
limits were found to be ineligible for patent, despite providing “a new and
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presumably better method for calculating alarm limit values.” In Flook, the
claim was directed to a “method for updating the value of at least one alarm
limit on at least one process variable involved in a process comprising the
catalytic chemical conversion of hydrocarbons.” Flook, 437 U.S. at 596–97
(Appendix to Opinion). The steps comprised determining a new alarm base
using a mathematical algorithm, using the alarm base to update an alarm
limit, and then adjusting the alarm limit to the updated value. Id. The Court
found the claim to be unpatentable under Section 101. The Court held that
“[t]he process itself, not merely the mathematical algorithm, must be new
and useful.” Id. at 591.
All the independent claims in this appeal perform mathematical
operations on raw sequencing data (“raw intensity outputs”) to improve the
sequencing technology to assemble a genetic sequence. Appellants argue
that “there is no mathematical operation recited in any of the claims of the
present application” (Appeal Br. 27), but do not explain what the steps
involving generating “a search tree comprising a plurality of nodes” as
recited in step (c), and then selecting nodes (step (d)), expanding nodes (step
(e)), and automatically generating score for nodes (step (f)) are, if not
mathematical operations or concepts.2 Consistent with the finding that the

2 Mathematics is defined as “the science of numbers and their
operations . . . , interrelations, combinations, generalizations, and
abstractions and of space . . . configurations and their structure,
measurement, transformations, and generalizations // Algebra, arithmetic,
calculus, geometry, and trigonometry are branches of mathematics.”
https://www.merriam-webster.com/dictionary/mathematics (last accessed
June 26, 2019). Appellants made the conclusory statement that the search
trees utilized in the claims are not mathematical operations, but did not
provide evidence that one of ordinary skill in the art would not have
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steps constitute mathematical operations, the Specification describes the
processes performed on the nodes in terms of mathematical concepts:
It is possible to perform global optimization (or near
optimization) by searching the hypotheses space potentially
exhaustively (or near exhaustively) utilizing an intelligent
pruning procedure using exemplary branch-and-bound
heuristics. For example, the search tree can be a pruned
quaternary tree (e.g., branching factor = 4), where each node in
position j can be expanded to the j+1) position by augmenting
the path with the base A, T, C, and G, and scoring a new
resulting path for the hypothesis that it could have generated the
data, which, in reality, can be obtained from the sequencing
platform. If the score for a new node is below the desired range,
the node can be pruned. In a more aggressive approach, it can
be possible to utilize an exemplary embodiment using beam-
search heuristics where at any point only a fixed number (e.g., k
= 20} of the best possible hypotheses can be allowed to survive
pruning and be included.
Spec. ¶ 62 (emphasis added).
Generate a QUATERNARY Tree by, e.g., starting with
an unexplored leaf node (labeled by a nucleotide base) with the
best score-value, selecting all four possible nucleotide bases
(e.g., A, T, C, G) to expand the node by making them its
children and computing their scores, and repeating until the tree
cannot be expanded any further.
Spec. ¶ 80 (emphasis added).
As shown in Figure 2, it is possible to start with a null set of
leaves T 203 = 0, and a set of live nodes L 204. The set of live

considered them to embody mathematical concepts which the 2019
Guidelines characterize as abstract ideas. We recognize that the steps are
not simple mathematical calculations as they were in Flook, but rather are
mathematical operations performed on a computer. However, Appellants
have not explained why such operations are not abstract ideas as the
“algorithms” were in Flook.
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nodes L 204 can include nodes queued in a first in, first out
(FIFO) basis, such that L = {(Ro.g(Ro))}.
Spec. ¶ 95.3
Step (a) comprises obtaining the nucleotide information in the form of
“raw intensity outputs.” Step (b) is obtaining a reference sequence. These
steps are not a practical application of the abstract idea recited in the claims,
but rather involve the collection of information that is necessary to perform
the abstract idea.4
The result of steps (c)–(i) is recited in step (j) of claim 53 to be
“automatically assembling the at least one genetic sequence based on the
path.” The assembled “genetic sequence” is therefore the solution when the
steps of the claimed method are accomplished on the “raw intensity
outputs.” The skilled worker is not instructed to do anything with the
assembled genetic sequence that would integrate it into a practical
application.
Indeed, the solution to following the instructions in claim 53 is to
discover the naturally-occurring sequence of the recited “fragment of at least
one genome.” Spec. ¶ 33. The discovery of a natural phenomenon, namely
the sequence of a genome fragment, is not itself patent eligible under Mayo,
566 U.S. at 77–78 (“tell[ing] a doctor about the relevant natural laws” does
not make an otherwise patent-ineligible claim, eligible).

3 The letters T, L, R, and g appear in an italicized font in the Specification,
but are shown as Times New Roman here because the specific font could not
be identified
4 The collection of information in the context of analyzing it and displaying
the result was still found to be an abstract idea in Electric Power Group,
LLC v. Alstom S.A., 830 F.3d 1350, 1354–55 (2016).
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We have not been directed by Appellants to any additional element
in the claims beyond the judicial exception. See 84 Fed. Reg. 55. As
explained in the 2019, the additional element must apply or use “the judicial
exception in some other meaningful way beyond generally linking the use of
the judicial exception to a particular technological environment, such that
the claim as a whole is more than a drafting effort designed to monopolize
the exception.” Id. at 55. In this case, the mathematical operations are
performed on output obtained from a specific environment, namely
nucleotide sequencing, but we have not been directed to an element outside
the mathematical operations applied to the nodes and score function that
involve a practical application or that improve the technology involved in
obtaining the raw intensity outputs.
Independent claims 53, 62, and 65 are limited to an improvement in
the mathematical operations performed on raw intensity outputs from a
sequencing platform. However, “the prohibition against patenting abstract
ideas ‘cannot be circumvented by attempting to limit the use of the formula
to a particular technological environment.’” Bilski v. Kappos, 561 U.S. 593,
610 (2010).
Without additional limitations, a process that employs
mathematical algorithms to manipulate existing information to
generate additional information is not patent eligible. “If a
claim is directed essentially to a method of calculating, using a
mathematical formula, even if the solution is for a specific
purpose, the claimed method is nonstatutory.” Parker v. Flook,
437 U.S. 584, 595, 98 S.Ct. 2522, 57 L.Ed.2d 451 (1978)
(internal quotations omitted).
Digitech Image Technologies LLC v. Electronics for Imaging Inc., 758 F.3d
1344, 1351 (Fed. Cir. 2014).
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Here, while the specific purpose of the claim is to assemble a genetic
sequence, the steps recited in the claim that instruct one of ordinary skill in
the art to make that sequence are simply calculations/instructions that
manipulate the existing raw intensity output to arrive at the mathematical
solution of “at least one genetic sequence based on the path” of the
preceding steps performed on nodes.
Appellants cite to a number of cases from the Federal Circuit Court
of Appeals to support their argument that the rejected claims are patent-
eligible. The core of their argument is that the claims in these cases were
directed to technological improvements, as are the rejected claims in this
appeal. Appellants cite the following cases:
- “directed to an improvement of an existing technology” (“a self-
referential table for a computer database”) (Enfish, LLC v. Microsoft
Corporation, et al., 822 F.3d 1327 (Fed. Cir. 2016)) (Appeal Br. 21);
- “the claims solve a technological problem, improve the performance
of the system itself” (Amdocs (Israel) Ltd. V. Openet Telecom, Inc. 841 F.3d
1288 (Fed. Cir. 2016)) (Appeal Br. 23);
- “the claims in Thales ‘result in a system that reduces errors in an
inertial system that tracks an object on a moving platform.’ . . . the
improvement in Thales is not directed to a computer itself. Rather, the
improvement in the technology in Thales is a system that reduces errors in
inertial tracking systems.” (Thales Visionix, Inc. v. U.S., 850 F.3d 1343 (Fed.
Cir. 2017)) (Appeal Br. 23).
Appellants contend that the claims involved in this appeal are similar
to the claims in these cases because they “are directed to an improvement of
an existing technology (e.g., assembling genetic sequences at least because it
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improves the reliability in generating genome sequences, and improves the
reliability of population-wide genomic studies)” and they are an
improvement “due to the decreased complexity and the high level of
accuracy that result from the use of the claimed subject matter.” Appeal Br.
28. “In particular, similar to [DDR Holdings, LLC v. Hotels.com, L.P. 773
F.3d 1245 (Fed. Cir. 2014)], the claimed solution of the present application
is rooted in computer technology by solving the problem of genetic
sequencing.” Appeal Br. 27. Appellants also argue that the claims do not
preempt other approaches.
These arguments do not persuade us that the Examiner erred in
finding the claims nonstatutory and ineligible for a patent. Appellants
provided evidence in the background section of their application that the
claimed method is an improvement to genetic sequencing technology. The
Examiner did not dispute this assertion. However as explained above, the
improvement is not to the sequencing technology itself (e.g., producing the
raw intensity outputs), but to the mathematical operations and concepts
which improve nucleotide base-calling using the existing sequencing
technology. As discussed in Sap America, Inc. v. Investpic, LLC, 898 F.3d
1161, 1167 (2018):
We have explained that claims focused on “collecting
information, analyzing it, and displaying certain results of the
collection and analysis” are directed to an abstract idea. Electric
Power, 830 F.3d at 1353. “Information as such is an
intangible,” hence abstract, and “collecting information,
including when limited to particular content (which does not
change its character as information), [i]s within the realm of
abstract ideas.” Id. (citing cases). So, too, is “analyzing
information ... by mathematical algorithms, without more.” Id.
at 1354 (citing cases, including Parker v. Flook, 437 U.S. 584,
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98 S.Ct. 2522, 57 L.Ed.2d 451 (1978), and Gottschalk v.
Benson, 409 U.S. 63, 93 S.Ct. 253, 34 L.Ed.2d 273 (1972)).
And “merely presenting the results of abstract processes of
collecting and analyzing information, without more (such as
identifying a particular tool for presentation), is abstract as an
ancillary part of such collection and analysis.” Id. (citing cases).

The bottom line here is that Appellants are asking us to find that
improvements to nucleotide sequencing technology, and specifically to the
mathematical concepts applied in assembling a genetic sequence of a
genome fragment, is patent-eligible subject matter in the same way that
improvements to website visitor retention in DDR, processing network
information in Amdocs, and improving a data storage and retrieval system
for a computer memory in Enfish were patent-eligible. We have not been
directed to a case that holds that mathematical improvements to nucleotide
sequencing technology constitute a practical, patent-eligible, application. As
emphasized above, the improvements pointed out by Appellants, i.e.,
“reliability in generating genome sequences,” “high level of accuracy,”
“accurately assembl[ing] a genetic sequence, and reduc[ing] errors as
compared to previous systems”, etc., (Appeal Br. 28, 32) are all achieved by
the mathematical concepts embodied by the claims (e.g., operations
performed on the nodes representing nucleotides). The steps are performed
on a computer with no improvement to the computer, itself, but instead use
generic computer parts to carry out computer executable instructions (see
preamble of claim 42).
What distinguishes the claims found to be patent eligible in DDR,
Amdocs, Enfish, etc., from the rejected claims in this appeal is that
the improvements in the cited cases were to a technology, and not to a
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mathematical operation, itself. Thus, in DDR, there was an improvement to
internet function, in Amdocs to how network information is handled, and in
Enfish, to computer memory. Here, the claim is not directed to improving
how physical nucleotide sequencing is performed; instead, all the steps of
the claim involve performing mathematical operations on information
obtained from a sequencing platform to make the base-calling more accurate
and reliable by using mathematical operations. Nothing is done with the
resulting assembled sequence except to reveal it.
Because we have determined that the rejected claims are directed to a
judicial exception and not integrated into a practical application, we move to
Step 2B in which the claims are examined to determine if an inventive
concept is provided.
Step 2B
As explained in the 2019 Guidelines, if the exception is not integrated
into a practical application, then Step 2B of the 2109 Guidelines, as in the
Mayo/Alice framework, asks whether there is an inventive concept. To
determine whether an unpatentable law of nature has been transformed “into
a patent-eligible application of such law,” the Court in Mayo held that the
claim as a whole must be examined to determine whether it “also contain[s]
other elements or a combination of elements, sometimes referred to as an
‘inventive concept,’ sufficient to ensure that the patent in practice amounts
to significantly more than a patent upon the natural law itself.” Mayo, 566
U.S. at 72–73. Under this step, we are directed to ask whether an additional
element or combination of elements recited in the claims:
• Adds a specific limitation or combination of
limitations that are not well-understood, routine,
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conventional activity in the field, which is indicative that
an inventive concept may be present; or
• 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.
84 Fed. Reg. 56.
While Appellants recognized that a claim is patent eligible when
additional elements that amount to “significantly more than the abstract
idea” are present in the claims (Appeal Br. 21, 22, 25, 26). Appellants did
not identify an element in the claim that adds “significantly more” to the
judicial exception. The steps of obtaining the series of raw intensity outputs
from a sequencing platform and obtaining at least one reference sequence
were found by the Examiner to be well-understood, routine, conventional
activities previously known to the industry. Ans. 5; 84 Fed. Reg. 56.
Appellants do not purport to have invented sequencing, and prior art
sequencing methods are disclosed in the Specification (e.g., Spec. ¶¶ 8–16).
Thus, the Examiner’s finding is supported by a preponderance of the
evidence.
Summary
For the foregoing reasons, the rejection of claim 53 as ineligible for a
patent under 35 U.S.C. § 101 is affirmed. Claims 42–52 and 54–75 fall with
claim 53.

Appeal 2019-001691
Application 13/266,662

19
TIME PERIOD
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).

AFFIRMED