International Business Machines Corporation

Patent Trials and Appeals Board

Sep 1, 2020

14511702 - (D) (P.T.A.B. Sep. 1, 2020)

UNITED STATES PATENT AND TRADEMARK OFFICE
UNITED STATES DEPARTMENT OF COMMERCE
United States Patent and Trademark Office
Address: COMMISSIONER FOR PATENTS
P.O. Box 1450
Alexandria, Virginia 22313-1450
www.uspto.gov
APPLICATION NO. FILING DATE FIRST NAMED INVENTOR ATTORNEY DOCKET NO. CONFIRMATION NO.
14/511,702 10/10/2014 Thomas C. Conway YOR920140444US1 3604
48063 7590 09/01/2020
RYAN, MASON & LEWIS, LLP
48 South Service Road
Suite 100
Melville, NY 11747
EXAMINER
WOITACH, JOSEPH T
ART UNIT PAPER NUMBER
1631
NOTIFICATION DATE DELIVERY MODE
09/01/2020 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):
nyoffice@rml-law.com
wel@rml-law.com
PTOL-90A (Rev. 04/07)
UNITED STATES PATENT AND TRADEMARK OFFICE
________________
BEFORE THE PATENT TRIAL AND APPEAL BOARD
________________

Ex parte THOMAS C. CONWAY and KELLY L. WYRES1
________________

Appeal 2020-001476
Application 14/511,702
Technology Center 1600
________________

Before JEFFREY N. FREDMAN, ULRIKE W. JENKS, and
JOHN G. NEW, Administrative Patent Judges.

NEW, Administrative Patent Judge.

DECISION ON APPEAL

1 We use the term “Appellant” to refer to the “applicant” as defined in
37 C.F.R. § 1.142. Appellant identifies International Business
Machines Corporation as the real party-in-interest. App. Br. 1.
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SUMMARY
Appellant files this appeal under 35 U.S.C. § 134(a) from the
Examiner’s Final Rejection of claims 21–38 as unpatentable under 35 U.S.C.
§ 101 as being directed to nonstatutory subject matter.
We have jurisdiction under 35 U.S.C. § 6(b).
We AFFIRM.

NATURE OF THE CLAIMED INVENTION
Appellant’s claimed invention is directed to a method of extracting
short fixed-length source sub-sequences from a collection of source
sequences derived from a sample for which a biological signature is to be
determined. Abstr.
REPRESENTATIVE CLAIM
Claim 21 is representative of the claims on appeal and recites:
21. An article of manufacture comprising a computer readable
storage medium for storing computer readable program code and
data for identifying a biological signature of a sample which,
when executed, causes a computer node to perform the steps of:
extracting short fixed length source sub-sequences from a
collection of source biological sequence data obtained from a
biological sequence data source operatively coupled to a
processor device of the computer node via a communications
network, wherein the collection of source biological sequence
data is derived from a sample for which a biological signature is
to be identified, wherein the collection of source biological
sequence data and the extracted short fixed length source sub-
sequences are stored in the storage medium;
compiling the extracted short fixed length source sub-
sequences to determine the frequency of each within the
collection, wherein the respective frequencies of the extracted
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short fixed length source sub-sequences are stored in the storage
medium;
using overlaps between the short fixed length source sub-
sequences to find a chain of overlaps from one or more first sub-
sequences to one or more second sub-sequences, wherein each of
the one or more first sub-sequences is equivalent to a pre-
flanking reference marker sequence, wherein each of the one or
more second sub-sequences is equivalent to a post-flanking
reference marker sequence, and wherein each of the reference
marker sequences flank a region containing a repetitive sequence
region, wherein the references marker sequences are obtained
from a reference database operatively coupled to the processor
device via the communications network, and wherein the chain
of overlaps from the one or more first sub-sequences to the one
or more second sub-sequences is stored in the storage medium;
in response to determining that the chain comprises a cycle
containing multiple instances of the one or more short fixed
length source sub-sequences, analyzing the source biological
sequence data to find one or more sequences that span the cycle,
and at least one of: (i) using the lengths of the spanning
sequences to determine the length of the cycle and (ii) counting
the number of repeat motif copies within each spanning
sequence, wherein the results of the analysis are stored in the
storage medium;
identifying the biological signature for the sample based
on the analysis and the at least one of the length of the cycle and
the number of repeat motif copies within each spanning
sequence, wherein the identified biological signature is stored in
the storage medium; and
presenting the identified biological signature to at least
one of a system or a user device for use in one or more of
determining a genetic relatedness of subjects and observing an
epidemiological trend, wherein the system and the user device
are operatively coupled to the processor device via the
communications network.
App. Br. 18–19.
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ISSUES AND ANALYSES
We adopt the Examiner’s findings, reasoning, and conclusion that the
claims on appeal are directed to non-statutory subject matter. We address
the arguments raised by Appellant below.

Issue
Appellant argues that the Examiner erred in concluding that the claims
recite no more than “the analysis and calculation of overlapping sequences
to obtain a number representing the copy number of a repeat motif in a
sequence data” and are therefore directed to a judicial exception to 35 U.S.C.
§ 101. App. Br. 8 (quoting Final Act. 3).

Analysis
The Examiner finds that independent claim 21 recites identifying a
number of repeats based on the number of compiled sequences in a given
span, and includes that results of analysis steps are “stored in the storage
medium” and the additional step of “presenting the identified biological
signature to at least one of a system or a user device.” Final Act. 3.
The Examiner finds that the claims are directed to the statutory
category of a product, i.e., a readable storage medium. Final Act. 3. The
Examiner next finds that the recited steps for the analysis and calculation of
overlapping sequences to obtain a number representing the copy number of a
repeat motif in a sequence data is an abstract idea and, consequently, a
judicial exception to Section 101. Id. Furthermore, the Examiner finds that
the claims recite no additional steps or elements which have to be performed
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and which would produce a physical nucleic acid molecule based on the
assessment of the sequence data provided in the recited steps. Id. at 3–4.
The Examiner additionally finds that the claims are directed to
nonstatutory subject matter because they recite only “a computer readable
medium” and the claims, as recited, read on carrier waves, which are
transitory propagating signals and therefore are not proper patentable subject
matter. Final Act. 4 (citing In re Nuijten, 500 F.3d 1346, 1353–4 (Fed. Cir.
2006)).
Appellant argues that the Examiner erred in failing to consider claim
21 as a whole. App. Br. 8. Appellant argues that the Examiner’s
characterization of the claim limitations are mere paraphrased fragments of
various features of independent claim 21. Id.
Specifically, Appellant argues that claim 21 is directed to an article of
manufacture comprising a computer readable storage medium for storing
computer readable program code and data for identifying a biological
signature of a sample. App. Br. 8. According to Appellant, the computer
program code, when executed, causes a computer node to perform various
steps, including “extracting short fixed length source sub-sequences from a
collection of source biological sequence data,” “compiling the extracted
short fixed length source sub-sequences to determine the frequency of each
within the collection,” “using overlaps between the short fixed length source
sub-sequences to find a chain of overlaps from one or more first
subsequences to one or more second sub-sequences,” and “in response to
determining that the chain comprises a cycle containing multiple instances
of the one or more short fixed length source subsequences, analyzing the
source biological sequence data to find one or more sequences that span the
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cycle.” Id. Appellant contends that, in allegedly ignoring these limitations
of the claims, the Examiner has failed to consider independent claim 21 as a
whole, because, when evaluating the scope of a claim, every limitation of the
claim must be considered. Id. (citing Diamond v. Diehr, 450 U.S. 175, 188–
89 (1981)).
Appellant argues further that, even if one were to assume, arguendo,
that claim 21 is directed to a judicial exception as the Examiner concludes,
the claim is integrated into a practical application of the alleged judicial
exception that imposes meaningful limits on the alleged judicial exception.
App. Br. 9. Appellant asserts that claim 21 is directed to the practical
application of identifying a biological signature for a sample. Id. Appellant
argues that this goes well beyond the alleged abstract idea or judicial
exception of “an abstract process that only manipulates data.” Id. (citing
Final Act. 7). According to Appellant, elements in a claim that reflect “an
improvement in the functioning of a computer, or an improvement to other
technology or technical field” is evidence of integration into a practical
application. Id. (quoting United States Patent and Trademark Office’s 2019
Revised Patent Subject Matter Eligibility Guidance, 84(4) Fed. Reg. 50, 53
(January 7, 2019) (the “2019 Guidance”)).
Specifically, Appellant argues that genotypic characterization or
genotyping “is an important method for the identification of organisms and
the determination of relationships between them, often using DNA sequence
data.” App. Br. 9 (quoting Spec. 2). Appellant points to the Specification as
disclosing illustrative embodiments of the independent claim 21 that provide
improvements in genotyping, including in Multiple Locus Variable number
tandem repeat Analysis (“MLVA”). Id. at 9–10 (citing Spec. 5). Appellant
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asserts that next-generation sequencing (“NGS”) technologies, as disclosed
in the Specification, generate large numbers (e.g., millions) of short,
overlapping sequence reads, in which each base of a true sequence is
sampled or sequenced multiple times, the extent of which is referred to as
“coverage depth” where the true coverage depth varies across the sample
sequence. Id. (citing Spec. 5–6). Appellant particularly points to the
Specification’s disclosure that:
In silico derivation of existing assays from NGS data is an
important area of research and development, and is essential to
enable compatibility between data sources. For MLVA in
particular, no NGS based method exists to reliably derive the
typing information (repeat motif numbers/amplicon lengths at
each locus of interest).

Id. (quoting Spec. 6). Appellant asserts that illustrative embodiments of the
claimed arrangements meet the need for reliably deriving typing
information, such as the number of repeat motif numbers and amplicon
lengths at each locus of interest, for MLVA analysis, and that, prior to the
invention of the Appellant’s claimed technique, there was no reliable method
for doing so. Id. Appellant argues that the lack of any prior art rejection by
the Examiner against any of the claims of the present application sustains
this contention. Id.
Summarizing, Appellant argues that claim 21 recites features
including identifying a biological signature for a sample based on at least
one of: (1) a length of a cycle containing multiple instance of one or more
short fixed length source sub-sequences; and (2) a number of repeat motif
copies within each spanning sequence. Appellant asserts that such features
solve a technological problem in genotyping, particularly in MLVA analysis.
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Final Act. 10. As such, Appellant argues claim 21 integrates the alleged
judicial exception of “manipulating data” into a practical application that
provides improvements to the technological field of MLVA analysis and
genotyping. Id. at 9–10.
Appellant next points to the Examiner’s finding that “while the
instructions of the judicial exception recite to obtain or store data, there are
no additional steps or elements of the claims which actually have to be
performed and would be considered producing a physical nucleic acid
molecule based on the assessment of the sequence data.” App. Br. 11
(quoting Final Act. 3–4). Appellant responds that there is no requirement
that in genotyping or MLVA, that a “physical nucleic acid molecule” is
produced. Id. Appellant contends that that is not the “goal” or end result of
genotyping or MLVA; rather, biological sequence data is derived from a
sample for which a biological signature is to be identified, as recited in claim
21. Id.
Appellant argues further that the Examiner's analysis does not address
whether independent claim 21 recites “significantly more” than the alleged
judicial exception. App. Br. 11. Appellant points to the Examiner’s
conclusion that “[n]o additional steps are recited in the instantly claimed
invention that would amount to significantly more than the [alleged] judicial
exception,” without any reference to or discussion of the actual features
recited in independent claim 21. Id. (alterations in original).
Appellant asserts that the Supreme Court has identified various
examples of limitations that qualify as “significantly more” when recited in a
claim with an abstract idea including: (1) improvements to another
technology or technical field; improvements to the function of the computer
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itself; (2) applying the judicial exception with, or by use of, a particular
machine; (3) effecting a transformation or reduction of a particular article to
a different state or thing; (4) adding a specific limitation other than what is
well-understood, routine and conventional in the field; or (5) adding
unconventional steps that confine the claim to a particular useful application;
and other meaningful limitations beyond generally linking the use of a
judicial exception to a particular technological environment. App. Br. 12
(citing United States Patent and Trademark Office, 2014 Interim Guidance
on Patent Subject Matter Eligibility, 79(241) Fed. Reg. 74618, 74624 (2014)
(the “Interim Guidance”)).
Appellant contends MLVA and genotyping, as recited in claim 21,
provide improvements to technology or the technical field. App. Br. 12.
Appellant contends that embodiments of claim 21 disclosed in Appellant’s
Specification overcome particular problems arising in the technological field
of genotyping. Id. (citing, e.g., Spec. 5–6). Appellant asserts that the
features recited by claim 21 provide solutions to overcome disadvantages
associated with conventional biological sequence data processing
techniques, such as in processing large numbers (e.g., millions) of short,
overlapping sequences. Id. Appellant argues that a person of ordinary skill
in the art would have appreciated the benefits and advantages provided by
illustrative embodiments of independent claim 21 will increase as the
number of sequences to be analyzed increases. Id.
Appellant also contends that claim 21 recites features other than what
is well understood, routine and conventional in the field and/or adds
unconventional steps that confine independent claim 21 to particular useful
applications. App. Br. 13. Appellant contends that the Final Office Action
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is devoid of any analysis of the features of claim 21 with regards to their
being “well-understood, routine and conventional” as required by the
Federal Circuit in Berkheimer v. HP Inc., 881 F.3d 1360, 1368 (Fed. Cir.
2018). Id.
Appellant also points out that, in the present appeal, there are no prior
art rejections of claim 21. App. Br. 14. According to Appellant, the
Examiner’s implicit acknowledgment that a set of specific claim limitations
are not anticipated, taught, or even suggested by a field of available art,
while simultaneously alleging that the same specific claim limitations are
somehow “well-understood, routine and conventional in the field” is
counterintuitive and contrary to the clear standard put forth by the Supreme
Court and the guidance detailed by the Federal Circuit. App. Br. 15 (citing,
e.g., Ultramercial, LLC v Hulu, LLC, 772 F.3d 709 (Fed. Cir. 2014).
Finally, Appellant disputes the Examiner’s characterization that claim
21 recites only a computer readable medium and therefore reads on
transitory carrier waves. App. Br. 15. Appellant contends that claim 21
rather recites a computer readable storage medium, and that Appellant’s
Specification discloses that a computer readable storage medium is not to be
construed as being transitory signals. Id. (citing Spec. 18).
As an initial matter, we agree with Appellant’s argument that the
claim 21’s recitations of “a computer readable storage medium” is not
directed to non-statutory subject matter because it fails to expressly exclude
non-transitory signals. In Nuijten, upon which the Examiner relies, our
reviewing court held that “physical but transitory forms of signal
transmission such as radio broadcasts, electrical signals through a wire, and
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light pulses through a fiber-optic cable, …. are not directed to statutory
subject matter.” Nuijten, 500 F.3d at 1353 (emphasis added).
Appellant’s Specification expressly discloses that:
A computer readable storage medium, as used herein, is not to be
construed as being transitory signals per se, such as radio waves
or other freely propagating electromagnetic waves,
electromagnetic waves propagating through a waveguide or
other transmission media (e.g., light pulses passing through a
fiber-optic cable), or electrical signals transmitted through a
wire.
Spec. 18. The claims on appeal are thus directed to a storage medium, and
not to a transitory signal, as in Nuijten2, and we are consequently not
persuaded by the Examiner’s analysis in this respect.
In performing an analysis of patentability under 35 U.S.C. § 101, we
follow the framework set forth by the Supreme Court in Mayo Collaborative
Services v. Prometheus Laboratories, Inc., 566 U.S. 66 (2012). We are also
mindful of, and guided by, the 2019 Guidance.
Appellant’s independent claim 21 recites: “An article of manufacture
comprising a computer readable storage medium….” Independent claim 30
recites: “A non-transitory processor readable storage medium configured to
store….” Following the first step of the Mayo analysis, we find that the

2 Nuitjen’s Claim 14, the sole independent claim, recited:
A signal with embedded supplemental data, the signal being
encoded in accordance with a given encoding process and
selected samples of the signal representing the supplemental
data, and at least one of the samples preceding the selected
samples is different from the sample corresponding to the given
encoding process.
Nuitjen, 500 F.3d at 1351.
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claims are directed to a manufacture or composition of matter, and therefore
fall into one of the broad statutory categories of patent-eligible subject
matter under 35 U.S.C. § 101.
In the next step of the Mayo analysis, we determine whether the claim
at issue is directed to a nonstatutory, patent-ineligible concept, i.e., a law of
nature, a phenomenon of nature, or an abstract idea. Mayo, 566 U.S. at 70–
71. If the claim is so directed, we next consider the elements of the claim
both individually and “as an ordered combination” to determine whether
additional elements “transform the nature of the claim” into a patent-eligible
application. Id. at 78–79; see also Ariosa Diagnostics, Inc. v. Sequenom,
Inc., 788 F.3d 1371, 1375 (Fed. Cir. 2015). Specifically, the Supreme Court
considered this second step as determining whether the claim recites 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.” Mayo, 566 U.S. at 72–73.
More specifically, in this second step of the Mayo analysis, we look to
whether the claim recites one of the judicially-created exceptions to 35
U.S.C. § 101, i.e., an abstract idea, a law of nature, or a natural phenomenon.
See 2019 Guidance 54 (Step 2A, Prong 1). If we determine that the claim
recites a judicial exception, we then determine whether the limitations of the
claim reciting the judicial exception are integrated into a practical
application. Id. (Step 2A, Prong 2).
Finally, if we determine that the claim is directed to a judicially-
created exception to Section 101, we evaluate the claim under the next step
of the Mayo analysis, considering the elements of each claim both
individually and “as an ordered combination” to determine whether
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additional elements “transform the nature of the claim” into a patent-eligible
application. Mayo, 566 U.S. at 78–79; see also 2019 Guidance 56 (Step
2B).
Claim 21 recites a computer readable storage medium for
storing readable program code and data, and performing, at a computer
node, the following steps: (1) extracting short fixed-length source sub-
sequences from a collection of source biological sequence data derived from
a sample; (2) compiling the extracted short fixed-length source sub-
sequences to determine their frequency; (3) using overlaps between the short
fixed-length source sub-sequences to find a chain of overlaps from one or
more first sub-sequences to one or more second sub-sequences; (4)
analyzing the source biological sequence data to find one or more sequences
that span the cycle, and (a) using the lengths of the spanning sequences to
determine the length of the cycle and/or (b) counting the number of repeat
motif copies within each spanning sequence; (5) identifying the biological
signature for the sample based on the analysis; and (6) presenting the
identified biological signature to at least one of a system or a user device.
All of these steps may be performed on a generic computer processor. See
Spec. 20 (“These computer readable program instructions may be provided
to a processor of a general purpose computer, special purpose computer, or
other programmable data processing apparatus”).
Independent claims 21 and 30 are so-called “Beauregard claims,” i.e.,
claims reciting a computer readable medium (e.g., a disk, hard drive, or
other data storage device) containing program instructions for a computer to
perform a particular process. See In re Beauregard, 53 F.3d 1583 (Fed. Cir.
1995). Consequently, the claims on appeal recite nothing more than a
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computer readable medium containing program instructions for executing
the method recited in the limitations of the claims. See CyberSource Corp.
v. Retail Decisions, Inc., 654 F.3d 1366, 1374 (Fed. Cir. 2011).
We find that each of the recited steps of the method of claims 21 and
30, i.e., (1) extracting short fixed-length source sub-sequences stored in the
storage medium; (2) compiling the sequences; (3) using overlaps between
the sub-sequences to find a chain of overlaps; (4) analyzing the biological
sequence data to find one or more sequences that span the cycle; (5) using
the analysis to identifying the biological signature of the sample; and (6)
presenting the results to a user, represent steps or processes that an
individual could perform either mentally or with a pencil and paper. See
Cybersource, 654 F.3d at 1373.
What is essentially happening in these steps is that fixed-length base
sequences are retrieved from memory and compiled, overlaps between the
sequences are compared to construct a chain of overlaps spanning the cycle,
and the analysis is used to identify the biological signature of the sample.
Each of these steps involves either the retrieval and compiling of
information or comparing the retrieved information to identify a pattern. All
of these tasks are capable of being performed by a person without the use of
a computer. Granted, such a task would be laborious and time consuming,
but the essential question is whether a person, either mentally or with paper
and pencil, could perform the steps recited in the claim. See Cybersource,
654 F.3d at 1372–73. Appellant has made no argument, or adduced any
evidence, that the steps recited in the claims are beyond the mental
capacities of an individual, or that they require a specialized computer or
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device. We therefore conclude that claim 21 recites a judicial exception to
35 U.S.C. § 101, viz., an abstract idea.
Turning to the next step of our analysis (Step 2A, Prong 2) we inquire
as to whether the abstract idea recited in the claims is integrated into a
practical application. 2019 Guidance 54 (step 2A, prong 2). The Guidance
provides additional context for this analysis, stating that: “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.” Id. at 53.
In the present case, we find that the claims recite no additional steps
other than the abstract idea recite in steps (1)–(6), as implemented on a
general-purpose computer, that would constitute integration into a practical
application. As such, we find that the claims do not impose meaningful
limits upon the abstract idea recited in the claims.
For the same reason, we find that, considering the elements of each
claim both individually and “as an ordered combination” the claims recite no
additional elements or steps that would suffice to “transform the nature of
the claim” into a patent-eligible application. Mayo, 566 U.S. at 78–79; 2019
Guidance at 56 (Step 2B).
We are not persuaded by Appellant’s argument that the claims
constitute “an improvement in the functioning of a computer, or an
improvement to other technology or technical field” as evidence that the
claims are integrated into a practical application. See App. Br. 12. In this
analysis, we inquire whether the claims are directed to a specific
improvement in the capabilities of computing devices, or, instead, to “a
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process that qualifies as an ‘abstract idea’ for which computers are invoked
merely as a tool.” Enfish, LLC v. Microsoft Corp., 822 F.3d 1327, 1336
(Fed. Cir. 2016). In this instance, Appellant adduces no evidence that the
claimed invention improves the capability of the computer employed in
performing the calculations. On the contrary, Appellant’s Specification
discloses that the recited steps can be performed upon a generic computer.
See Spec. 18.
Nor are we persuaded of the relevancy of Appellant’s argument with
respect to Berkheimer’s requirement of an evidence-supported finding of
fact that any additional steps are “conventional, routine and well
understood,” for the simple reason that the claims do not recite any
additional steps beyond those reciting the abstract idea itself. See
Berkheimer, 881 F.3d at 1370. That the abstract idea is embedded in code
stored on a computer readable medium that allows communication of the
results of the method to a person is evidence that the claim elements, other
than the abstract idea, are conventional. Appellant does not assert that the
computer readable medium, generic processors, or communications
networks are anything other than conventional, routine, and well-understood
technologies.
In summary, we conclude that (1) independent claims 21 and 30 recite
an abstract idea, which is a judicial exception to Section 101 (Step 2A,
Prong 1); (2) that the abstract idea is not integrated into a practical
application (Step 2A, Prong 2); and (3) that there are no additional elements
of the claims that transform the nature of the claim into a patent-eligible
application. (Step 2B). We consequently affirm the Examiner’s rejection of
independent claims 21 and 30 upon this ground.
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Furthermore, Appellant relies upon essentially the same arguments
with respect to the patentability of dependent claims 22–29 and 31–38. For
the reasons we have explained, we similarly affirm the Examiner’s rejection
of these claims.

CONCLUSION
The Examiner’s rejection of claims 21–38 under 35 U.S.C. § 101 is
affirmed.
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

Claims
Rejected
35 U.S.C.
§
Reference(s)/Basis Affirmed Reversed
21–38 101 Nonstatutory
subject matter

21–38