Nantomics, LLC

Patent Trials and Appeals Board

May 26, 2021

2020005510 (P.T.A.B. May. 26, 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.
14/846,290 09/04/2015 John Zachary Sanborn 102402.0006US 1376
149345 7590 05/26/2021
Umberg Zipser, LLP
1920 Main Street, Suite 750
Irvine, CA 92614
EXAMINER
WOITACH, JOSEPH T
ART UNIT PAPER NUMBER
1631
NOTIFICATION DATE DELIVERY MODE
05/26/2021 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):
ipsupport@umbergzipser.com
patents@umbergzipser.com
rdean@umbergzipser.com
PTOL-90A (Rev. 04/07)
UNITED STATES PATENT AND TRADEMARK OFFICE
____________

BEFORE THE PATENT TRIAL AND APPEAL BOARD
____________

Ex parte JOHN ZACHARY SANBORN, CHARLES JOSEPH VASKE,
STEPHEN CHARLES BENZ, SHAHROOZ RABIZADEH
and PATRICK SOON-SHIONG
____________

Appeal 2020-005510
Application 14/846,290
Technology Center 1600
____________

Before ERIC B. GRIMES, JOHN G. NEW, and
MICHAEL A. VALEK, Administrative Patent Judges.

VALEK, Administrative Patent Judge.

DECISION ON APPEAL
Appellant1 submits this appeal under 35 U.S.C. § 134(a) involving
claims to a computer implemented method of analyzing a genomic sequence
of a target tissue of a mammal, which have been rejected as directed to
patent-ineligible subject matter. We have jurisdiction under
35 U.S.C. § 6(b).

1 We use the word “Appellant” to refer to “applicant” as defined in
37 C.F.R. § 1.42(a). Appellant identifies Nantomics, LLC as the real party
in interest. Appeal Br. 2. Herein, we refer to the Final Office Action mailed
July 29, 2019 (“Final Act.”); Appellant’s Appeal Brief filed December 26,
2019 (“Appeal Br.”); and Examiner’s Answer mailed April 20, 2020
(“Ans.”).
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We AFFIRM.
STATEMENT OF THE CASE
Appellant’s Specification describes “methods for genomic analysis in
which idiosyncratic markers or marker constellations are employed to verify
or rule out congruence and/or determine provenance of a biological sample
relative to other genetic samples.” Spec. ¶ 7. These idiosyncratic markers
are preferably single nucleotide polymorphisms (SNPs)2 that may be
“predetermined on the basis of their known position within the genomic
sequence, and/or may be randomly selected.” Id. ¶¶ 7, 11.
According to the Specification, a plurality of such markers are
analyzed in a genomic sequence to build an “idiosyncratic marker profile”
that can be used to compare two sequences:
Most typically, the first idiosyncratic marker profile is based on
characteristics for a plurality of predetermined idiosyncratic
markers in the first genomic sequence of the individual. In
another step, the analysis engine then selects a second genomic
sequence that has an associated second idiosyncratic marker
profile (e.g., from a second individual, retrieved from the same
or other sequence data base), wherein the step of selecting uses
the first and second idiosyncratic marker profiles and a desired
match score between the first idiosyncratic marker profile and
the second idiosyncratic marker profile.
Spec. ¶ 14.
Claims 1–17 are on appeal, and can be found in the Claims Appendix
of the Appeal Brief. Claim 1 is the only independent claim and is

2 “Single nucleotide polymorphism refers to the occurrence of a variant or
change at a single DNA base pair position among genomes of different
individuals.” Spec. ¶ 4.
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reproduced below with numbering added to identify the claimed steps:
1. A computer implemented method of analyzing a genomic
sequence of a target tissue of a mammal, comprising:
[1] coupling a computing device to a sequence database
that stores a genomic sequence for the target tissue of the
mammal;
[2] characterizing, by the computing device, a plurality of
predetermined idiosyncratic markers in the genomic sequence
of the target tissue, and generating an idiosyncratic marker
profile using the characterized idiosyncratic markers;
[3] generating or updating, by the computing device, a
first sample record for the target tissue using the idiosyncratic
marker profile;
[4] comparing, by the computing device, the
idiosyncratic marker profile in the first sample record with a
second idiosyncratic marker profile in a second sample record
to thereby generate a match score; and
[5] identifying the first sample record as belonging to the
same mammal as the second sample record using the match
score.
Appeal Br. 11.
Appellant seeks review of Examiner’s rejection of claims 1–17 under
35 U.S.C. § 101 as directed to patent-ineligible subject matter. Appeal Br. 2.
Claims 2–17 are not argued separately from claim 1. We select claim 1 as
representative for our analysis of Appellant’s arguments regarding these
claims. See 37 C.F.R. § 41.37(c)(1)(iv).
ANALYSIS
I. Subject Matter Eligibility
An invention is patent-eligible if it claims a “new and useful process,
machine, manufacture, or composition of matter.” 35 U.S.C. § 101.
However, the Supreme Court has long interpreted 35 U.S.C. § 101 to include
implicit judicial exceptions: “[l]aws of nature, natural phenomena, and
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abstract ideas” are not patentable. E.g., Alice Corp. Pty. Ltd. v. CLS Bank
Int’l, 573 U.S. 208, 216 (2014).
In determining whether a claim falls within an excluded category, we
are guided by the Supreme Court’s two-step framework, described in Alice.
Id. at 217–18 (citing Mayo Collaborative Servs. v. Prometheus Labs., Inc.,
566 U.S. 66, 75–77 (2012)). In Alice step one, we ask whether the claims
are directed to an exception to patent eligibility, such as an abstract idea or
law of nature. Alice, 573 U.S. at 218. In Alice step two, we examine the
elements of the claims to determine whether they contain an inventive
concept sufficient to transform the claimed judicial exception into a patent-
eligible application. Mayo, 566 U.S. at 71–72 (quoting Alice, 573 U.S. at
217–18).
The Office has published guidance on the application of the Supreme
Court’s Alice analysis. USPTO’s January 7, 2019 Memorandum, 2019
Revised Patent Subject Matter Eligibility Guidance, 84 Fed. Reg. 50
(“Guidance”); see also USPTO’s October 17, 2019 Memorandum, October
2019 Update: Subject Matter Eligibility, available at https://www.uspto.gov/
sites/default/ files/documents/peg_oct _2019 _update.pdf (“Guidance
Update”). According to the Guidance, we look to whether the claim recites:
(1) a judicial exception, including certain groupings of abstract ideas such as
mathematical concepts and mental processes (Guidance Step 2A, prong 1);
and (2) additional elements that integrate the judicial exception into a
practical application (Guidance Step 2A, prong 2). Only if the claim recites
a judicial exception and does not integrate that exception into a practical
application, do we then examine whether the claim adds a specific limitation
beyond the judicial exception that is not “well-understood, routine,
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conventional” in the field (Guidance Step 2B). See Guidance, 84 Fed. Reg.
54–56. Both the Guidance and Guidance Update have been incorporated
into the MPEP.
Examiner’s Findings and Conclusions
Regarding Alice step one, Examiner finds that claim 1 recites an
abstract idea in the form of a mental process, i.e., “a set of instructions for
analysis of sequence data, in this case comparing ‘idiosyncratic markers’
from two sets of data, and if they match based on the ‘match score’
concluding that the sample ‘belongs to the same mammal as the second
sample.’” Ans. 5–6.
Examiner further determines that this judicial exception is not
integrated into a practical application. See Ans. 6–7. According to
Examiner, “the claims have only analysis steps and do not have an additional
element.” Id. at 6. Moreover, the steps are “recited at [a] high level of
generality for the analysis of sequence data (‘characterizing’, ‘comparing’,
‘identifying’ markers in a data set), and [are] not found to be a practical
application of the judicial exception as broadly set forth.” Id. at 7.
Regarding Alice step two, Examiner finds that the “claims do not
recite or require any details on [the] implementation” and encompass the use
of “known types of idiosyncratic markers,” i.e., SNPs, to compare “data . . .
in silico” sequences using “established file formats” on a general purpose
computer. See Ans. 7–9. Examiner also cites evidence demonstrating that
“Appellants are not the first to note that SNPs can be used to compare
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sequences present in genomic data.” Id. at 10 (citing Ghodke3 and Ellonen4)
Accordingly, Examiner determines “there does not appear to [be] any
improvement nor technical problem addressed” and taken “as a whole,
claims 1–17 do not recite something significantly different than a judicial
exception.” Id. at 8–9.
Appellant’s Contentions
Appellant challenges Examiner’s rejection in three respects. First,
Appellant contends that claim 1 is patent eligible because it recites a
practical application, wherein “idiosyncratic markers or marker
constellations are employed to verify or rule out congruence and/or
determine provenance of a genomic sample relative to other genomic
samples.” Appeal Br. 6–7. Second, Appellant argues that claim 1 provides
“an improvement to the computer and genomic analysis technology” by
“using idiosyncratic markers, such as SNPs” to provide “a faster and more
cost-effective technique of comparing two genomic sequences.” Id. at 8.
Third, Appellant urges that Examiner erred in determining that claim 1
recites a mental process because the claimed method “require[s] the use of a
computing device” and “cannot be practically and accurately done in the
mind of a human.” Id. at 9–10.

3 Ghodke et al., Profiling Single Nucleotide Polymorphisms (SNPs) Across
Intracellular Folate Metabolic Pathway in Healthy Indians, Indian J. Med.
Res., Vol. 133, 275–79 (2011) (“Ghodke”).
4 Ellonen et al., Development of SNP Mircroarray for Supplemental
Paternity Testing, Int’l Congress Series, Vol. 1261, 12–14 (2004)
(“Ellonen”).
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Our Review
Applying the Supreme Court’s Alice framework as explained in the
Office’s Guidance, we agree with Examiner that claim 1 is directed to
patent-ineligible subject matter. As explained below, Appellant’s arguments
to the contrary are unpersuasive.
Guidance Step 2A, Prong 1
The Guidance instructs us first to determine whether any judicial
exception to patent eligibility is recited in the claim.5 Claim 1 in steps 2–5
recites the following limitations:
[2] characterizing, by the computing device, a plurality of
predetermined idiosyncratic markers in the genomic sequence
of the target tissue, and generating an idiosyncratic marker
profile using the characterized idiosyncratic markers; [3]
generating or updating, by the computing device, a first sample
record for the target tissue using the idiosyncratic marker
profile; [4] comparing, by the computing device, the
idiosyncratic marker profile in the first sample record with a
second idiosyncratic marker profile in a second sample record
to thereby generate a match score; and [5] identifying the first
sample record as belonging to the same mammal as the second
sample record using the match score.
These limitations, under their broadest reasonable interpretation, recite the
abstract idea of comparing two nucleotide sequences based on the presence
or absence of markers (e.g., SNPs) by looking at portions of the sequence to
determine if the markers are present and generating a profile indicating such
(steps 2 and 3), comparing that profile to the profile for the comparison

5 It is undisputed that Appellants’ claims are directed to one of the statutory
classes of patentable subject matter, i.e., a method or “process,” recited in 35
U.S.C. § 101. Thus, we begin our analysis at Step 2A, prong 1 of the
Guidance.
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sequence (step 4), and based on the extent to which the profiles match (i.e.,
their “match score”) determining provenance (step 5). This abstract idea is a
mental process similar to the judicial exceptions observed in other cases
involving analysis of genomic data. See, e.g., In re BRAC1 & BRAC2-Based
Heredity Cancer Test Patent Litig., 774 F.3d 755, 763 (Fed. Cir. 2014)
(concluding that the concept of “comparing [certain genetic] sequences and
determining the existence of alterations” is an “abstract mental process”).
The fact that claim 1 recites a “computer implemented method”
performed by a “computing device” does not avoid a finding that claim 1
recites an abstract mental process. As the Guidance explains, “[i]f 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 process category unless the claim cannot practically be performed in
the mind.” Guidance at 52 n. 14 (citing cases); see also Versata Dev. Grp. 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.”). Here, the broadest reasonable interpretation of claim 1
encompasses the characterization of two or more (i.e., a “plurality”) SNPs in
a sequence that may comprise only a portion of the genome to generate a
profile for the comparison and identification steps. Absent the recitation of
generic computer elements (i.e., a “computing device” connected to a
“database” storing the requisite data) in claim 1, there is no reason such
steps could not be practically performed in a person’s mind.6 For these

6 This is also true for claim 3, which further limits the plurality of markers in
claim 1 to “between 100 and 10,000” markers. Appeal Br. 11. While it may
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reasons, we agree with Examiner that claim 1 recites a patent-ineligible
mental process.
Guidance Step 2A, Prong 2
Having determined that claim 1 recites a judicial exception, we next
consider whether there are additional elements that integrate the judicial
exception into a practical application (Guidance Step 2A, prong 2).
“Integration into a practical application” requires that the claim recite an
additional element or a combination of elements, that when considered
individually or in combination, “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.” MPEP 2106.04(d).
We begin by observing that claim 1 broadly recites the steps for
performing the mental process in steps 2–5. According to claim 1, any
plurality of markers are characterized to generate a profile that is recorded
and compared to another profile to determine the extent to which they match
(i.e., their match score). None of these steps impose any meaningful limit on
how these activities are performed, nor does claim 1 recite any meaningful
limitation on how the identification of provenance is made based on the
match score.
The only limitation that is not part of the claimed judicial exception is
step 1, which recites coupling the computing device to a database that serves

be faster or more efficient to use a computer when generating a profile for
larger sets of markers, the underlying process of determining whether a
particular SNP appears at a particular location in a sequence is the same
whether performed on a computer, using a pen and paper, or in a person’s
mind.
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as the source of the data analyzed in the subsequent steps. In this regard,
step 1 is merely a data gathering step; it does not integrate the recited
judicial exception into a practical application. See, e.g., Mayo, 566 U.S. at
79 (holding that additional element of measuring metabolites of a drug
administered to a patient was insignificant extra-solution activity); In re
Grams, 888 F.2d 835, 840 (Fed. Cir. 1989) (explaining that a step requiring
“performing clinical tests on individuals to obtain data” to be used in recited
judicial exception does “not render the claim statutory”); see also Guidance,
55, n.31 (describing “data gathering such as a step of obtaining information
about credit card transactions” as an example of “insignificant extra-solution
activity”).
Appellant’s argument that claim 1 recites a practical application, i.e.,
employing markers “to verify or rule out congruence and/or determine
provenance of a genomic sample relative to other genomic samples,” is
unpersuasive. See Appeal Br. 6–7. As explained above, the recited
limitations, considered both individually and as a whole, merely recite a
mental process of comparing two sequences based on the presence or
absence of markers to identify provenance of one sequence to the other.
There is no meaningful limit placed on how that determination is made such
that the claim, as a whole, could be said to be a practical application of the
recited mental process. That claim 1 requires the determination of
provenance as opposed to some other determination (e.g., diagnosis of a
disease associated with particular SNPs) merely limits the recited judicial
exception to a particular technological environment and does not in and of
itself confer patent eligibility. See Mayo, 566 U.S. at 78 (“[T]he prohibition
against patenting abstract ideas cannot be circumvented by attempting to
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limit the use of the formula to a particular technological environment.”)
(internal quotations omitted). For these reasons, we determine that the
judicial exception in claim 1 is not integrated into a practical application and
therefore that claim 1 is directed to the judicial exception itself.
Guidance Step 2B
Proceeding to Alice step 2 (i.e., Step 2B as provided in the Guidance),
we agree with Examiner’s findings that the elements of Appellant’s claims,
considered both individually and in combination, do not provide an
inventive concept beyond the judicial exception itself. See Ans. 7–11. We
incorporate those findings herein and additionally address Appellant’s
arguments below.
Appellant argues that:
The inventors improved the technology of genomic
analysis by developing a faster and more cost-effective
technique of comparing two genomic sequences and
determining whether they are from the same individual. This is
done by using idiosyncratic markers, such as SNPs. Thus, a
subset of SNPs in a genomic sequence is selected for use as
statistical beacons throughout the entire genome in a number
that can be suited to a desired statistical power… Ideally, the
selected SNPs are distributed throughout the entire genome but
only represent a small fraction of the entire genome.
Appeal Br. 8. According to Appellant, “[s]uch a method is an improvement
to both the computer technology as well as genomic analysis technology
because until now, comparing two genomic sequences to see if they are from
the same mammal consumed much more time and money.” Id.
We disagree. Examiner cites evidence, to which Appellant does not
respond, demonstrating that the comparison of a subset of SNPs in genomic
sequences to determine lineage was known and conventional in the art. See
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Ans. 10 (citing Ghodke and Ellonen). Ellonen, for example, was published
ten years before the priority date of Appellant’s application and describes “a
SNP microarray for paternity testing, which contains 10 SNPs and in
addition X and Y chromosome-specific markers.” Ellonen, Abstr. Ellonen
explains that these 10 “SNPs were scattered in the genome” and when used
as markers to compare test samples for paternity “the average exclusion
power of these markers is 86.5%.” Id. at 14. Ellonen further explains that
the specificity of this analysis “can be increased by selecting more SNP loci
[i.e., additional markers] for the array.” Id. Accordingly, Ellonen evidences
that comparing nucleotide sequences based on a subset of SNP markers, as
opposed to the entire genome, to identify provenance was already known in
the art.7
Claim 1 does not recite any particular improvement to the technology
for carrying out such a comparison. As noted by Examiner, claim 1 “does
not provide for any new means or format to compare sequences.” See Ans.
11. Rather, claim 1 generically recites a “computing device” for performing
the steps, which the Specification explains should be broadly interpreted to
“include any suitable combination of computing devices, including servers,
interfaces, systems, databases, agents, peers, engines, controllers, or other
types of computing devices operating individually or collectively.” Spec. ¶

7 Ghodke describes “a study to determine the allelic frequencies” of a subset
of 12 SNPs associated with the folate biosynthetic pathway “in an Indian
ethnic population.” Ghodke, Abstr. Ghodke observes that the frequencies
of these SNPs amongst the Indian participants in its study “were different
from published study data of European and African populations.” Id.
Accordingly, Ghodke also supports Examiner’s finding that the use of a
subset of SNPs to compare genomic sequences was routine and conventional
in the art. See Ans. 10–11 (citing Ghodke).
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40. So too, the Specification indicates that the “characterized idiosyncratic
markers” may be stored or processed in “various digital formats” and that
“[t]he exact format of idiosyncratic marker profile is not limiting to the
inventive subject matter” and includes simply listing those predetermined
markers present in a sample “in bit string form.” Id. ¶¶ 11, 15. As such, this
is not a case where the claim recites a specific improvement to the
underlying computer technology.
“[I]t is not enough” for patent eligibility “to merely improve a
fundamental practice or abstract process by invoking a computer merely as a
tool.” Customedia Techs., LLC v. Dish Network Corp., 951 F.3d 1359, 1364
(Fed. Cir. 2020). But that is all that claim 1 does here. We do not see, nor
does Appellant identify, anything in claim 1 that would enable the recited
computing device “to operate more quickly or efficiently” in performing the
recited judicial exception, nor does claim 1 “solve any technical problem.”
See Id. at 1365. At most, the use of a computer may improve the speed and
efficiency of the process, but such generalized use of a computer as a tool
does not constitute an inventive concept. Id.; see also Intellectual Ventures I
LLC v. Capital One Bank (USA), 792 F.3d 1363, 1369–70 (Fed. Cir. 2015)
(explaining that “claiming the improved speed or efficiency inherent with
applying the abstract idea on a computer” does not constitute an
improvement to computer functionality that might render a claim patent
eligible).
For these reasons, we agree with Examiner that claim 1 does not recite
an inventive concept sufficient to transform the claim into patent eligible
subject matter and, therefore, affirm the rejection of that claim. We affirm
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the rejection of claims 2–17, which are not argued separately, for the same
reasons we affirm the rejection of representative claim 1.
DECISION SUMMARY
In summary:

Claims
Rejected
35 U.S.C. § Reference(s)/Basis Affirmed Reversed
1–17 101 Eligibility 1–17

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). 37 C.F.R.
§ 1.136(a)(1)(iv).

AFFIRMED