Mishra, Bhubaneswar et al.

Patent Trials and Appeals Board

Jun 9, 2020

2019004726 (P.T.A.B. Jun. 9, 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.
13/139,809 10/26/2011 Bhubaneswar Mishra 190904WOUS01-32882-214274 4078
120944 7590 06/09/2020
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
06/09/2020 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):
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 NARZISI

Appeal 2019-0047261
Application 13/139,809
Technology Center 1600
____________

Before ULRIKE W. JENKS, RACHEL H. TOWNSEND, and
CYNTHIA M. HARDMAN, Administrative Patent Judges.

JENKS, Administrative Patent Judge.

DECISION ON APPEAL
Pursuant to 35 U.S.C. § 134(a), Appellant2 appeals from the
Examiner’s decision to reject claims as directed to patent ineligible subject
matter. We have jurisdiction under 35 U.S.C. § 6(b).
We REVERSE.

1 A telephonic hearing was held on April 9, 2020. See Transcript 1.
2 Appellant identifies New York University of New York, New York as the
real party in interest. Appeal Br. 2. We use the word “Appellant” to refer to
“applicant” as defined in 37 C.F.R. § 1.42(a).
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STATEMENT OF THE CASE
According to the Specification, advances in genomic sciences have
now made it possible to “generate a massive amount of short reads covering
a whole genome many times.” Spec. ¶ 9. These “massively large number of
such non-contextual short-reads can only lend themselves to biological
interpretations and biomedical applications when they can be assembled into
contiguous overlapping sequences encompassing the information contained
in each haplotype chromosome.” Id. ¶ 15. It is the combination of optical
mapping procedures, that use long-range information in the form of single
molecule based ordered restriction maps, in conjunction with non-contextual
short sequence reads, that allows for the assembly of “a genome wide
personalized haplotype sequence.” Id. ¶ 69.
Claims 74–136 are on appeal, and can be found in the Claims
Appendix of the Appeal Brief. Claim 95 below is representative of the
claims on appeal, and reads as follows:
95. A method for assembling at least one part of at least one
of at least one haplotype sequence or at least one genotype
sequence of at least one genome, comprising:
(a) obtaining (i) a plurality of randomly located short
sequence reads, and (ii) overlap information about overlaps
between the randomly located short sequence reads;
(b) obtaining long range information for the randomly
located short sequence reads, wherein the long range
information includes optical map data and mate-pair data;
(c) automatically randomly selecting a first read from the
randomly located short sequence reads;
(d) automatically identifying one or more overlapping
second reads of the randomly located short sequence reads that
overlap with the first read;
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(e) automatically generating one or more scores
regarding the one or more overlapping second reads using the
overlap information and the long range information;
(f) selecting a particular read of the one or more second
overlapping reads based on the one or more scores;
(g) automatically generating a path through the plurality
of randomly located short sequence reads by repeating
procedures (e) and (f); and
(h) using a computer hardware arrangement,
automatically assembling the at least one part of the at least one
of the at least one haplotype sequence or the at least one
genotype sequence of the genome based on the path.
Appeal Br., Claims Appendix A6–A7.
Appellant requests review of Examiner’s rejection of claims 74–136
under 35 U.S.C. § 101, as being directed to patent ineligible subject matter.
ANALYSIS
Examiner finds that the claims are directed to nothing more than an
abstract idea, and that the claim as a whole, considering all the claim
elements both individually and in combination, do not amount to
significantly more than the abstract idea. Ans. 3. Examiner identifies steps
(e) and (g) of the independent claims, claims 74, 95, and 116, as reciting a
mathematical concept or algorithm. Ans. 3. Examiner finds that the
additional steps in the claims are directed to analyzing and organizing
information. Ans. 3–4. Examiner finds that “[t]he claims do not describe any
specific computational steps by which the computer performs or carries out
the abstract idea, nor do they provide any details of how specific structures
of the computer are used to implement these functions.” Ans. 4.
When the claims are considered as a whole, they do not
integrate the abstract idea into a practical application; they do
not confine the use of the abstract idea to a particular
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technology; they do not solve a problem rooted in or arising
from the use of a particular technology; they do not improve a
technology by allowing the technology to perform a function
that it previously was not capable of performing; and they do
not provide any limitations beyond generally linking the use of
the abstract idea to a broad technological environment (i.e.
computerized analysis of nucleic acid sequence data).

Ans. 6–7. Examiner finds that “[t]he step of ‘generating one or more scores
for the one or more reads using the overlap information and the long-rang[e]
information’ is a mathematical operation.” Ans. 8.
Appellant contends that the claims are not directed to an abstract idea
because “none of the claims recite, much less are directed to, a mathematical
operation. Indeed, there is no mathematical operation recited in any of the
claims of the present application.” Appeal Br. 22. Appellant contends “the
claimed solution of the present application is rooted in computer technology
by solving the problem of genetic sequencing.” Id. at 23. Appellant contends
that the “sheer complexity of generating a haplotype or genotype sequence
(e.g., based on overlapping sequence reads, scoring reads, and generating a
path through the reads), []would make it impossible to be performed
mentally by human.” Id. at 24–25 (emphasis omitted). Appellant contends
that the claims present an improvement “over the art due to the decreased
computational space and time that result from the use of the claimed subject
matter.” Id. at 23 (citing Spec. ¶ 75).
The Supreme Court has established a two-step framework for
“distinguishing patents that claim laws of nature, natural phenomena, and
abstract ideas from those that claim patent-eligible applications of those
concepts.” Alice Corp. Pty. Ltd. v. CLS Bank Int’l, 573 U.S. 208, 217 (2014).
The United States Patent and Trademark Office (PTO) issued the 2019
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Revised Patent Subject Matter Eligibility Guidance (“Guidance”), indicating
how the PTO can analyze patent eligibility under the Supreme Court’s two-
step framework, and the October 2019 Update to the Revised 2019 Guidance
(“Update,” or “2019 Update Guidance, 84 Fed. Reg.”), which provides
further details regarding how the PTO is to analyze patent-eligibility
questions under 35 U.S.C. § 101. See 84 Fed. Reg. 50−57; see also 2019
Update Guidance, 84 Fed. Reg. 55,942. Following the Guidance, under
Revised Step 2A, we first look to whether the claim recites the following:
(1) any judicial exceptions, including certain groupings of
abstract ideas (i.e., mathematical concepts, certain methods of
organizing human activity such as a fundamental economic practice,
or mental processes); and
(2) additional elements that integrate the judicial exception into
a practical application (see MPEP § 2106.05(a)-(c), (e)-(h)).
Only if a claim (1) recites a judicial exception and (2) does not
integrate that exception into a practical application, do we then look,
under Step 2B of the Guidance, to whether the claim:
(3) adds specific limitations beyond the judicial exception that
are not “well-understood, routine, conventional” in the field (see
MPEP § 2106.05(d)); or
(4) simply appends well-understood, routine, conventional
activities previously known to the industry, specified at a high level of
generality, to the judicial exception.
See Guidance, 84 Fed. Reg.
Appellant does not argue the claims separately. We select claim 95 as
representative.
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STEP 1:
We first find that claim 95 is directed to “[a] method for assembling at
least one part of at least one of at least one haplotype sequence or at least
one genotype sequence of at least one genome.” We therefore conclude that
the claim is directed to a “process” for carrying out a sequence assembly and
thus falls into one of the broad categories of patentable subject matter under
section 101. See 35 U.S.C. § 100 (In “(b) [t]he term ‘process’ means
process, art, or method, and includes a new use of a known process,
machine, manufacture, composition of matter, or material.”).
STEP 2A, Prong One:
Under the Guidance, in determining what concept a claim is “directed
to” in step one of the Supreme Court’s two-step framework, we first look to
whether the claim recites any judicial exceptions to section 101, such as an
abstract idea, a law of nature, or a natural phenomenon. See Guidance, 84
Fed. Reg. 52, 54 (Step 2A, Prong One).
In Mayo, the Supreme Court found “mental processes and abstract
intellectual concepts are not patentable, as they are the basic tools of
scientific and technological work.” Mayo Collaborative Servs. v.
Prometheus Labs., Inc., 566 U.S. 66, 71 (2012) (quoting Gottschalk v.
Benson, 409 U.S. 63, 67 (1972)).
Claim 95 is directed to a method of assembling a gene sequence from
a collection of obtained short sequence reads. See Appeal Br., Claims App.
A6–A7 (Claim 95 contains step “(a) obtaining (i) a plurality of randomly
located short sequence reads, and (ii) overlap information about overlaps
between the randomly located short sequence reads.”). Claim 95 contains
additional steps (b)–(h) beyond (a) obtaining the short read sequence
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collection, with the end result of these steps producing a long sequence read
based on the collection of short sequence comparisons. The creation of the
long sequence read in claim 95 is accomplished by stitching together
numerous short sequences based on their overlapping nucleotide sequence
information, which just involves a comparison between two nucleic acid
sequences to assess the overlap and therefore represents an abstract idea.
Comparison between two gene sequences represents a mental process, i.e.,
an abstract idea. See In re BRCA1- and BRCA2-Based Hereditary Cancer
Test Patent Litigation, 774 F.3d 755, 762 (2014). We discern no distinction
between comparing full-length gene sequences made up of a string of
nucleic acids or short nucleic acid segments also made up of a string of
nucleic acids.
We are not persuaded by Appellant’s contention that that the sheer
complexity of generating a sequence based on the numerous short sequence
reads needed to create a long sequence is so complex that it would make it
impossible to be performed mentally by a human. Appeal Br. 24–25; see
also Reply Br. 10; and Transcript 17:11–20. The claims embrace assembling
a gene sequence of any size, including small viral genomes, which could
contain a small number (e.g., 100–200) of short sequence reads. Transcript
21:2–7. Moreover, just because the number of short sequences could involve
a large number of short sequence reads does not mean that given enough
time one of ordinary skill in the art would not be able to generate the
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sequence using pencil and paper.3 Accordingly, we are not persuaded by
Appellant’s contention that the claim is not drawn to an abstract idea.
We are also not persuaded by Appellant’s contention that the claims
do not include a mathematical formula and thereby do not embrace an
abstract idea. See Appeal Br. 22 (“[T]here is no mathematical operation
recited in any of the claims of the present application.”). Just because the
claim does not contain a mathematical formula in the form of equations does
not mean that an algorithm is not required to achieve the step of creating a
score, i.e. creating more data. We look to the Specification to determine
what is encompassed by “generating one or more scores regarding the one or
more overlapping second reads.” We understand this step to be what is
described in the Specification as the score function. See, e.g., Spec. ¶¶ 16,
72, 73,102–112. The Specification provides an exemplary score function as
follows:
If (Overlap(A,B) && Overlap(B,C)) {Score(A, B, C)
=[Score(A,B) + Score(B,C)]+ [Overlap(A,C)? Score(A,C): O]}
Spec. ¶ 103.
A score-function according to the Specification “can be used to guide the
manner in which the short-sequence reads are arranged and further
combined into haplotype sequence information (either in its entirety or in
parts in terms of contigs).” Id. ¶ 79. Based on these disclosures in the
Specification, we agree with Examiner that “[t]he step of ‘generating one or
more scores for the one or more reads using the overlap information and the

3 See CyberSource Corp. v. Retail Decisions, Inc., 654 F.3d 1366, 1372–73
(Fed. Cir. 2011) (Holding that a claim whose “steps can be performed in the
human mind, or by a human using a pen and paper” is directed to an
“unpatentable mental process[].”).
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long-range information’ is a mathematical operation.” Ans. 8; see also
Transcript 23:3–21.
We, therefore, agree with Examiner that the claim recites an abstract
idea because in addition to the underlying algorithm needed to create scores
that are used for the assembly of the gene sequence, the assembly of a gene
sequence (the final step of the process) itself is a process that can be
achieved in the human mind with the help of pencil and paper, but for the
recitation of “using a computer hardware arrangement.” Versata Dev. Grp.,
Inc. v. SAP Am., Inc., 793 F.3d 1306, 1335 (Fed. Cir. 2015) (“Courts have
examined claims that required the use of a computer and still found that the
underlying, patent-ineligible invention could be performed via pen and paper
or in a person's mind.”); see also Guidance 84 Fed. Reg. at 52 n.14 (“If a
claim, under its broadest reasonable interpretation, covers performance in
the mind but for the recitation of generic computer components, then it is
still in the mental processes category unless the claim cannot practically be
performed in the mind.”). Accordingly, we determine that the claim recites
an abstract idea.
STEP 2A, Prong Two:
Having made the determination that claim 95 recites an abstract idea,
under the Guidance, we next examine whether there are additional elements
beyond the abstract idea that integrate the judicial exception into a practical
application. Under the Guidance, this is referred to as the “Prong Two”
inquiry under “Step 2A.” Guidance, 84 Fed. Reg. 54–55. Under the Prong
Two analysis, we look to whether the claim as a whole “appl[ies], rel[ies]
on, or use[s] the judicial exception in a manner that imposes a meaningful
limit on the judicial exception.” Id.
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Appellant contends that “the claimed solution of the present
application is rooted in computer technology by solving the problem of
genetic sequencing.” Appeal Br. 23 (citing Spec. ¶¶ 4–31). We are not
persuaded because claim 95 uses a computer only for its most basic
functions to perform repetitive calculations to form alignments in order to
implement the abstract idea of determining scores in order to string together
multiple short sequences to arrive at a full-length gene sequence. We agree
with Examiner that, contrary to Appellant’s assertion, the problem is not
rooted in computer technology but instead is rooted in the problem of
meaningfully organizing collected information in genetic sequencing. See
Ans. 10.
Appellant contends that the claim integrates the judicial exception into
a practical application. See Appeal Br. 25–26. We are not persuaded.
In making a determination under Step 2A, Prong Two we look to see
if the claims recite additional elements such as improvements to computer
functioning or another technological field, applying the judicial exception by
use of particular machine, transformational reduction of a particular article
to different state or thing, or using the judicial exception in some other
meaningful way beyond generally linking the use of the judicial exception to
a particular technological environment. See MPEP 2106.05 (9th ed., rev.
08.2017 (Jan. 2018)); Guidance, 84 Fed. Reg. 54–55.
Examiner finds that “[t]here is no practical element [integration] in
either the assembly or the sequence.” Ans. 12. We agree with Examiner that
the judicial exceptions are not linked to the process of obtaining the short
sequence reads. See Spec. ¶ 9; see also Ans. 6 (citing multiple references),
id. at 14. The judicial exceptions are also not integrated into the data
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gathering of the optical map data or mate-pair data as these function the
same way regardless of the additional algorithm. See Transcript 27:6–8 (“the
fact that you performed these additional specific algorithm steps doesn’t
affect the way that the optical map is obtained in the first place.”), 25:24–
26:4; see Ans. 13 (“computerizing a sequence assembly algorithm as
claimed was a practice that was well-understood, routine and conventional in
the art prior to the time of invention.”); see also Spec. ¶¶ 9, 23. We also
agree with Examiner that the claim does not integrate the judicial exception
into a particular computer or processing system. See Ans. 13 (“[T]he
Specification expressly states that the invention was implemented using a
‘typical personal computer[,]’ which indicates that computerizing a sequence
assembly algorithm as claimed was a practice that was well-understood,
routine and conventional in the art prior to the time of invention.”); see also
Spec. ¶ 126.
Furthermore, the steps of obtaining (a and b), selecting (c), and
identifying (d) are data gathering steps that themselves do not apply the
abstract score function step, and while the selection step (f) is based on
applying the score function, neither that step nor the generating step (g)
applies the abstract assembling step, they are simply more data gathering for
the abstract idea that is the assembly of the sequence step based on the
collected and organized data. See e.g., MPEP § 2106.05(g); see also
CyberSource, 654 F.3d at 1370 (“We have held that mere ‘[data-gathering]
step[s] cannot make an otherwise nonstatutory claim statutory.”’ (alterations
in original)). Thus, even if one abstract idea can be considered to be
integrated because it is applied in further steps to create the assembled
sequence, the assembling step is not integrated into a practical application.
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Because the judicial exception is not integrated into a practical
application, we conclude that claim 95 is directed to an abstract idea.
STEP 2B:
Step 2B requires that we look to whether the claim “adds a specific
limitation beyond the judicial exception that [is] not ‘well-understood,
routine, conventional’ in the field.” See MPEP § 2106.05(d).
Appellant contends that “the improvement in the claims of the present
application is system/method/computer-accessible medium that can quickly
and accurately assemble a haplotype or genotype sequence, and reduces time
and complexity as compared to previous systems.” Appeal. Br. 28 (citing
Thales Visionix, Inc. v. US, 850 F. 3d 1343 (Fed. Cir. 2017)).
Here, the claimed method takes in two streams of information, the
overlap information from step (a) and the optical map data and mate-pair
data from step (b), and based on these two input streams the claim then
determines a score in step (e), based on this score the method prunes the
overlap reads in step (f), and by using the combination of the score and
pruned overlap reads the method generates a path in step (g) from which to
ultimately assemble the gene sequence in step (h). See generally
Specification; see also Transcript 24:9–13, 27:25–28:3. Thus, the claimed
process incorporates the algorithms to generate scores that improve the
accuracy of assembling short nucleic acids sequences into a long contiguous
string of nucleic acids. See Spec. ¶¶ 75, 115, 123 (Scoring-and-Unfolding
Trimmed Tree Assembler (SUTTA) “outperforms the assemblies from both
TIGR and Arachne in terms of, e.g., assembly quality.”), 125 and Figs.
3−11; see also Transcript 19:19–20:2.
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As the Guidance indicates, unconventional data gathering in
combination with a specifically recited application can render a claim patent
eligible under section 101 despite the fact that the judicial exception is not
considered to be integrated into a practical application. Id. at 56 and n.39
(citing Exergen Corp. v. Kaz USA, Inc., 725 F. App’x 959, 966 (Fed. Cir.
2018).). Here, claim 95 recites the collection of data in the form of short
sequence reads, created using standard protocols, as well as gathering more
data in the form of optical map data and mate-pair data, both of which are
also known protocols, and applying mathematical equations in order to
combine these two data streams to arrive at a full-length gene sequence. See
Spec. ¶¶ 9, 10. Although each data gathering steps is conventional, what is
unconventional is using both data streams at the same time to feed into the
scoring step (e) and pruning step (f) in order to achieve higher accuracy in
the long continuous sequence. When the process steps of the claim are
considered as an ordered combination, we find that the scoring step adds an
inventive concept and thus amounts to significantly more than the judicial
exception.
Thus, we reverse the Examiner’s rejection of claims 74–136 under
35 U.S.C. § 101 as being directed to non-statutory subject matter.

DECISION SUMMARY
In summary:
Claims
Rejected
35 U.S.C.
§
Reference(s)/Basis Affirmed Reversed
74–136 101 Eligibility 74–136

REVERSED