Nicholas Johnson et al.

Patent Trials and Appeals Board

Oct 16, 2019

13486982 - (D) (P.T.A.B. Oct. 16, 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.
13/486,982 06/01/2012 Nicholas Johnson S31-03828 (S11-077A) 2966
71897 7590 10/16/2019
KPPB LLP
2190 S. Towne Centre Place
Suite 300
Anaheim, CA 92806
EXAMINER
WOITACH, JOSEPH T
ART UNIT PAPER NUMBER
1631
NOTIFICATION DATE DELIVERY MODE
10/16/2019 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):
PAIR@KPPB.COM
PTOL-90A (Rev. 04/07)
UNITED STATES PATENT AND TRADEMARK OFFICE
__________

BEFORE THE PATENT TRIAL AND APPEAL BOARD
__________

Ex parte NICHOLAS JOHNSON, WING H. WONG,
and HUA TANG
__________

Appeal 2018-008016
Application 13/486,982
Technology Center 1600
__________

Before FRANCISCO C. PRATS, TAWEN CHANG, and DAVID COTTA,
Administrative Patent Judges.

PRATS, Administrative Patent Judge.

DECISION ON APPEAL

Pursuant to 35 U.S.C. § 134(a), Appellant1 appeals from the
Examiner’s decision to reject claims 1 and 22–43. We have jurisdiction
under 35 U.S.C. § 6(b).
We AFFIRM.

1 We use the word “Appellant” to refer to “applicant” as defined in
37 C.F.R. § 1.42. Appellant identifies the real party in interest as The Board
of Trustees of the Leland Stanford Junior University (“Stanford”). Appeal
Br. 3 (entered July 10, 2017). An oral hearing was held on September 12,
2019.
Appeal 2018-008016
Application 13/486,982

2

STATEMENT OF THE CASE
Appellant’s invention is directed to methods of inferring (i.e.,
predicting) individuals’ haplotypes, using genotype data obtained by
sequencing the individuals’ genomes. See Spec. ¶¶ 4–10. The Specification
explains that the “term haplotype refers to the combination of alleles at
multiple loci along a chromosome,” i.e., the specific set of genes on a single
particular chromosome inherited from one parent of an individual. Id. ¶ 4.
Haplotype information is useful in population and medical genetics
studies. See id. (“In population genetics studies of evolutionary histories,
haplotype data have been used to detect recombination hotspots as well as
regions that have undergone recent positive selection.”) (citation omitted);
see also id. ¶ 61 (“The ability to accurately construct haplotypes from
unphased genotype data plays pivotal roles in population and medical
genetics studies.”).
The Specification explains that, although high-throughput DNA
sequencing methods provide genotype data for individuals, such methods do
not directly provide haplotype information. See id. ¶ 4 (“[H]igh-throughput
genomic or sequencing technologies . . . generate genotype data-unordered
pairs of alleles.”).
The Specification explains that, “[w]hile reconstructing haplotype
from genotypes is straightforward in some special settings (e.g. in the
presence of relatives, in sperm, or for X chromosomes in males), statistical
inference of haplotype from autosomal genotype data with no known
relatives is challenging.” Id.
Nonetheless, “[n]umerous methods have been developed to infer
haplotypes.” Id. ¶ 6. One known method “begins by identifying a pool of
Appeal 2018-008016
Application 13/486,982

3

unambiguous (homozygous) individuals, and phases the remaining
individuals based on a parsimony heuristic that seeks to minimize the total
number of distinct haplotypes in the sample.” Id.
The Specification focuses on a particular known method of inferring
individuals’ haplotypes, the PHASE program. See id. ¶¶ 7–8; see also id.
¶ 53 (describing “FastPHASE” as a “software package[] used to analyze
large-scale high-density SNP [single nucleotide polymorphism] data”).
Appellant’s invention, in one embodiment, is “a modified version of
the PHASE model . . . that is substantially more accurate than the
FastPHASE model.” Id. ¶ 9. The Specification refers to Appellant’s
inventive and more accurate haplotype modeling method as “PHASE-EM.”
Id. ¶ 8.
The Specification explains that, in one embodiment, Appellant’s
invention uses “a parameterization EM [Expectation-Maximization]
algorithm similar to that of the FastPHASE model . . . to perform
optimization on haplotypes rather than MCMC [Markov Chain Monte Carlo]
sampling.” Id.
More particularly, in one embodiment, “the imputed haplotypes
themselves are used as hidden states in the HMM [Hidden Markov Model]
because this is believed to be important for the PHASE model’s accuracy.
This increase in accuracy becomes more pronounced with increasing sample
size.” Id.
The Specification describes the calculations used in the Hidden
Markov Model as follows:
A Hidden Markov Model (HMM) is developed having a hidden
state sequence H, an emitted sequence B, and jump variables J.
The emitted sequence Bk is produced by taking the element of
Appeal 2018-008016
Application 13/486,982

4

the current imputation AHk,k and changing its value with a small
probability θ. The conditional probabilities of the HMM (for
the jth individual’s haplotypes) are

Id. ¶ 34.
Claim 1 is representative of the subject matter on appeal and reads as
follows:
1. A computerized method for inferring haplotype phase in a
collection of unrelated individuals, comprising:
receiving genotype data describing human genotypes for
a plurality of individuals and storing the genotype data on a
memory of a computer system;
imputing an initial haplotype phase for each individual in
the plurality of individuals based on a statistical model and
storing the initial haplotype phase for each individual in the
plurality of individuals on a computer system comprising a
processor a[nd] memory;
building a data structure describing a Hidden Markov
Model, where the data structure contains:
a set of imputed haplotype phases comprising the
imputed initial haplotype phases for each individual in the
plurality of individuals;
a set of parameters comprising local recombination
rates and mutation rates;
wherein any change to the set of imputed
haplotype phases contained within the data structure
automatically results in re-computation of the set of parameters
comprising local recombination rates and mutation rates
contained within the data structure;
Appeal 2018-008016
Application 13/486,982

5

repeatedly randomly modifying at least one of the
imputed initial haplotype phases in the set of imputed haplotype
phases to automatically re-compute a new set of parameters
comprising local recombination rates and mutation rates that are
stored within the data structure;
automatically replacing an imputed haplotype phase for
an individual with a randomly modified haplotype phase within
the data structure, when the new set of parameters indicate that
the randomly modified haplotype phase is more likely than an
existing imputed haplotype phase;
extracting at least one final predicted haplotype phase
from the data structure as a phased haplotype for an individual;
and
storing the at least one final predicted haplotype phase
for the individual on a memory of a computer system.
Appeal Br. 19 (Supplemental Appeal Brief entered March 2, 2018, in
response to Notice of Defective Brief).
The only rejection before us for review is the Examiner’s rejection of
claims 1 and 22–43 under 35 U.S.C. § 101 as being directed to subject
matter ineligible for patenting. See Final Act. 2–5 (entered February 8,
2017); Ans. 3–11.
DISCUSSION
The Examiner’s Rejection
The Examiner determined that, as process claims, Appellant’s claims
fall within one of the statutory categories of invention. See Final Act. 3.
The Examiner determined, however, that “[f]or the claimed method,
the judicial exception is the abstract idea and mathematical manipulation of
the genetic data of the step of phasing using [the Hidden Markov Model].”
Id. at 4. The Examiner reasoned that, “[a]s such, the instant claims are
drawn only to an abstract process that only manipulates data and, therefore,
Appeal 2018-008016
Application 13/486,982

6

are not directed to statutory subject matter” but instead “are directed towards
a judicial exception, i.e. an abstract idea.” Id.
The Examiner reasoned that, as to Appellant’s claims “being directed
to a process implemented on a computer system or embedded on a computer
readable medium comprising instructions for carrying out the method, it is
the underlying invention that is analyzed to determine subject matter
eligibility, not just the use of a computer system or computer program
product.” Id.
The Examiner, having determined that Appellant’s claims are directed
to a judicial exception, then turned to ascertain “whether any element or
combination of elements, in the claim is sufficient to ensure that the claim as
a whole amounts to significantly more than the judicial exception.” Id. at 5.
In that regard, the Examiner found that “[n]o additional steps are
recited in the instantly claimed invention that would amount to significantly
more than the judicial exception. Without additional limitations, a process
that employs mathematical algorithms to manipulate existing information to
generate additional information is not patent eligible.” Id.
In particular, the Examiner reasoned, 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 non-statutory. In
other words, patenting abstract ideas cannot be circumvented by attempting
to limit the use [the idea] to a particular technological environment.” Id.
(brackets in original).
Moreover, the Examiner reasoned, in Appellant’s claims “the
computer and/or program/product amount to mere instruction to implement
an abstract idea. The hardware recited by the system claims do not offer a
Appeal 2018-008016
Application 13/486,982

7

meaningful limitation beyond generally linking the use of the method to a
particular technological environment, that is, implementation via
computers.” Id. (internal quotations omitted; citing Alice Corp. v. CLS Bank
Int’l, 573 U.S. 208, 216 (2014)).
Based on the above analysis, the Examiner concluded that Appellant’s
claims do not “recite something significantly different than a judicial
exception and thereby are not directed to patent eligible subject matter.” Id.
Principles of Law
An invention is patent-eligible if it claims a “new and useful process,
machine, manufacture, or composition of matter.” 35 U.S.C. § 101. The
Supreme Court has long interpreted 35 U.S.C. § 101 to include implicit
exceptions, however: “[l]aws of nature, natural phenomena, and abstract
ideas” are not patentable. Alice, 573 U.S. at 216.
In determining whether a claim falls within an excluded category, we
are guided by the Supreme Court’s two-step framework, described in Mayo
Collaborative Services v. Prometheus Laboratories., Inc., 566 U.S. 66
(2012) and Alice, 573 U.S. at 217–18 (citing Mayo, 566 U.S. at 75–77). In
accordance with that framework, we first determine what concept the claim
is “directed to.” See Alice, 573 U.S. at 219 (“On their face, the claims
before us are drawn to the concept of intermediated settlement, i.e., the use
of a third party to mitigate settlement risk.”).
Concepts determined to be abstract ideas, and thus patent ineligible,
include certain methods of organizing human activity, such as fundamental
economic practices (Alice, 573 U.S. at 219–20; Bilski v. Kappos, 561 U.S.
593, 611 (2010)); mathematical formulas (Parker v. Flook, 437 U.S. 584,
Appeal 2018-008016
Application 13/486,982

8

594–95 (1978)); and mental processes (Gottschalk v. Benson, 409 U.S. 63,
69 (1972)).
If the claim is “directed to” an abstract idea, we turn to the second
step of the Alice and Mayo framework, where “we must examine the
elements of the claim to determine whether it contains an ‘inventive
concept’ sufficient to ‘transform’ the claimed abstract idea into a patent-
eligible application.” Alice, 573 U.S. at 221 (quotation marks omitted).
Early in 2019, the PTO published revised guidance on the application
of § 101. USPTO, 2019 Revised Patent Subject Matter Eligibility Guidance,
84 Fed. Reg. 50 (January 7, 2019) (“Memorandum” or “2019 Office
Guidance” or “Office Guidance”).2 Following the Office 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
Office 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

2 Available at https://www.govinfo.gov/content/pkg/FR-2019-01-
07/pdf/2018-28282.pdf.
Appeal 2018-008016
Application 13/486,982

9

(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 Memorandum.
Analysis
Office Guidance—Revised Step 2A, Prong 1
We select Appellant’s claim 1 as representative of the claims subject
to this rejection. Applying Revised Step 2A, Prong 1, of the 2019 Office
Guidance, we agree with the Examiner that Appellant’s claim 1 recites
abstract ideas in a number of instances.
Representative claim 1 recites a computerized method for inferring
haplotype phase in a collection of unrelated individuals. Appeal Br. 19.
After an initial step of receiving genotype data from a plurality of
individuals, claim 1 recites the step of imputing an initial haplotype phase
for each individual in the plurality of individuals “based on a statistical
model.” Id. Claim 1 then recites “building a data structure describing a
Hidden Markov Model,” the data structure including the statistically
imputed haplotype phases of the individuals in the target population. Id.
Claim 1 then recites a step of repeatedly randomly modifying at least
one imputed initial haplotype phase “to automatically re-compute a new set
of parameters comprising local recombination rates and mutation rates
stored within the [Hidden Markov Model] data structure.” Id.
As discussed above, a Hidden Markov Model is a mathematical model
that includes a series of calculations. See Spec. ¶ 34. Accordingly, claim 1
expressly recites two mathematical models in its process, the Hidden
Markov Model as well as the statistical model used in the imputing step. In
addition, Claim 1’s “re-comput[ing]” step involves a mathematical
Appeal 2018-008016
Application 13/486,982

10

calculation to determine a new set of parameters comprising local
recombination rates and mutation rates stored within the data structure.
Appeal Br. 19. Claim 1, therefore, recites several mathematical concepts.
Accordingly, we agree with the Examiner that claim 1 recites abstract ideas.
See Office Guidance (84 Fed. Reg. at 52 (abstract ideas include “(a)
Mathematical concepts—mathematical relationships, mathematical formulas
or equations, mathematical calculations”)).
Claim 1 also recites at least two steps that can be performed solely in
the mind. Specifically, the step of “imputing an initial haplotype phase for
each individual in the plurality of individuals based on a statistical model”
(Appeal Br. 19) neither recites nor implies any type of computer
implementation. Because the “imputing” step may therefore be performed
entirely in the human mind, that step is also an abstract idea. See Office
Guidance (84 Fed. Reg. at 52 (abstract ideas include “(c) Mental
processes—concepts performed in the human mind (including an
observation, evaluation, judgment, opinion”) (citations omitted); see also id.
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.”) (Citing Intellectual Ventures I
LLC v. Symantec Corp., 838 F.3d 1307, 1318 (Fed. Cir. 2016)).
Claim 1’s step of automatically replacing an imputed haplotype phase
for an individual with a randomly modified haplotype phase within the data
structure is performed only “when the new set of parameters indicate that the
randomly modified haplotype phase is more likely than an existing imputed
haplotype phase.” Appeal Br. 19. Because claim 1’s automatic replacement
Appeal 2018-008016
Application 13/486,982

11

step is based on an evaluation of likelihood that may be performed entirely
in the mind, the automatic placement step is also an abstract idea, in the
form of a mental process.
Office Guidance—Revised Step 2A, Prong 2
Having determined that Appellant’s representative claim 1 recites
abstract ideas under Revised Step 2A, Prong 1, of the 2019 Office Guidance,
we turn to Revised Step 2A, Prong 2, of the Office Guidance to determine
whether claim 1 recites additional elements that integrate the judicial
exceptions into a practical application. See Office Guidance (84 Fed. Reg. at
54–55). We agree with the Examiner that Appellant’s claim 1 does not
recite additional elements that integrate the judicial exceptions into a
practical application.
Viewed as a whole, claim 1 is directed to a process of using abstract
computational methods to obtain a specific type of information—an inferred
(mathematically predicted) haplotype of an individual. Claim 1, however,
does not recite any step that integrates those abstract computational methods,
or the predicted haplotype information obtained therefrom, into a practical
application.
Specifically, beside the abstract computational steps discussed above,
claim 1 recites the steps of receiving and storing the individuals’ genotype
data in a computer memory, storing the individuals’ imputed haplotype
phases in a computer memory, extracting a predicted haplotype, and storing
a predicted haplotype in a computer memory. See Appeal Br. 19.
Thus, rather than integrating the abstract ideas into a practical
application, the non-abstract steps recited in Appellant’s claim 1 merely
provide a generically-recited computer-implemented methodology by which
Appeal 2018-008016
Application 13/486,982

12

the abstract computational methods are used to arrive at the claimed
haplotype information. We, therefore, agree with the Examiner that
Appellant’s claim 1 does not recite additional elements that integrate the
judicial exceptions into a practical application.
Appellant’s arguments do not persuade us to the contrary. Appellant
contends that, similar to Enfish, LLC v. Microsoft Corp., 822 F.3d 1327
(Fed. Cir. 2016), the claims under rejection “reflect a specific
implementation of a solution not only in the software arts, but in the field of
bioinformatics, and improve the functionality of a computer by enabling it to
yield improved haplotype phasing results.” Appeal Br. 7.
In Enfish, however, the specification of the patents at issue expressly
explained how the claimed data storage and retrieval system improved
computer function. See Enfish, 822 F.3d at 1333 (explaining that the patents
at issue “teach that multiple benefits flow from this design” including “faster
searching,” “more effective storage of data,” and “more flexibility in
configuring the database”). In the present case, in contrast, Appellant does
not identify any specific disclosures in the Specification asserting that
improved computer function results from performing the computations
recited in representative claim 1, nor does Appellant identify persuasive
evidence suggesting an improvement in computer function.
We acknowledge the Specification’s assertion of improved
computational accuracy of haplotype phase using the Hidden Markov
Model. See Appeal Br. 14 (citing Spec. ¶ 9); Reply Br. 6 (citing Spec. ¶¶ 56,
61). However, the fact that Appellant’s abstract computational methods
might be better than other abstract computational methods does not
demonstrate that the claimed steps are integrated into a practical application.
Appeal 2018-008016
Application 13/486,982

13

See Parker v. Flook, 437 at 594–95 (holding alarm limit calculation
ineligible for patenting despite acknowledgment that claimed computational
method “provides a new and presumably better method for calculating alarm
limit values”).
Appellant argues:
[T]he field of haplotype phasing (i.e. identifying groups
of genes on chromosomes inherited together from a single
parent in the absence of knowledge of the parent’s genetic
sequence) is a computer implemented field, and . . . under
McRO[, Inc. v. Bandai Namco Games Am. Inc., 837 F.3d 1229
(Fed. Cir. 2016)], improvements to computer implemented
fields are considered technological improvements. Appellant’s
claims in fact represent an improvement to the computer
implemented field of haplotype phasing by reciting a set of
rules which, when implemented, yield improved haplotype
phasing results previously unobtainable in the field.
Appeal Br. 8; see also Reply Br. 2–5 (arguing that, as in McRO, the claimed
process provides improvement to computer-implemented fields of haplotype
phasing and bioinformatics).
We find the present case distinguishable from McRO. As the court
explained in McRO, “[t]he claimed process uses a combined order of
specific rules that renders information into a specific format that is then
used and applied to create desired results: a sequence of synchronized,
animated characters.” McRO, 837 F.3d at 1315 (emphasis added). In
contrast, in the present case, representative claim 1 merely recites a series of
abstract computational steps to produce mathematically predicted haplotype
information, but does not include any steps that apply that information in a
practical way. See Appeal Br. 19. And, as discussed above, the non-abstract
steps in claim 1 involve generic computer-related steps for performing the
Appeal 2018-008016
Application 13/486,982

14

abstract computational steps (receiving and storing genotype data in a
computer memory, storing imputed haplotype phases in a computer memory,
extracting a predicted haplotype, and storing a predicted haplotype in a
computer memory). See id.
We acknowledge, as noted above, that the inferred haplotype
information computed by the process of claim 1 may be useful in medical or
population genetics studies. See Spec. ¶¶ 4, 61. Nonetheless, given the
absence in representative claim 1 of any specific step that applies that
information in a useful way, such as a therapeutic medical treatment based
on the predicted haplotype, we are not persuaded that claim 1 integrates the
abstract ideas into a practical application. See Office Guidance (84 Fed.
Reg. at 55) (example of additional element that integrates a judicial
exception into a practical application includes “an additional element that
applies or uses a judicial exception to effect a particular treatment or
prophylaxis for a disease or medical condition”) (citing Classen
Immunotherapies, Inc. v. Biogen IDEC, 659 F.3d 1057, 1066–68 (Fed. Cir.
2011); Vanda Pharm. Inc. v. West-Ward Pharm. Int’l Ltd., 887 F.3d 1117,
1135 (Fed. Cir. 2018).
We are not persuaded, moreover, that the process recited in
representative claim 1 is rendered patent-eligible by the claimed generic
computer-related steps used in performing the recited abstract computations.
See Office Guidance (84 Fed. Reg. at 55) (example of a situation in which a
judicial exception has not been integrated into a practical is where claim
“merely uses a computer as a tool to perform an abstract idea”) (citing Alice,
573 U.S. at 222–26; Gottschalk v. Benson, 409 U.S. 63 (1972); Credit
Acceptance Corp. v. Westlake Services, 859 F.3d 1044 (Fed. Cir. 2017)).
Appeal 2018-008016
Application 13/486,982

15

We acknowledge Appellant’s contentions that inferring haplotype
phase can only be performed practically using a computer. See Appeal Br. 9
(“[T]he currently pending claims . . . are not directed to an abstract idea, but
rather to a concrete improvement in the computer-related field of
biotechnology by reciting with particularity processes enabling the
extraction of improved long range haplotype phases.”); Reply Br. 5
(“Looking to only one of the subsets of data discussed in the specification–
13,976 SNPs were analyzed from only the parents in the trios-a single
person would require 4.5 months to analyze this small subset of data. (See
specification, ¶¶ [0047] & [0055].”).)
Representative claim 1, however, only requires performing the
claimed abstract computation using “genotype data describing human
genotypes for a plurality of individuals.” Appeal Br. 19. Claim 1, therefore,
does not require any particular amount or content of genotype data to be
analyzed, and encompasses much smaller data sets than the 13,976 SNPs
described in ¶ 47 of the Specification. See In re Trans Texas Holdings
Corp., 498 F.3d 1290, 1299 (Fed. Cir. 2007) (“[W]hile ‘the specification
[should be used] to interpret the meaning of a claim,’ courts must not
‘import[ ] limitations from the specification into the claim.’ . . . [I]t is
improper to ‘confin[e] the claims to th[e] embodiments’ found in the
specification . . . .”) (Quoting Phillips v. AWH Corp., 415 F.3d 1303, 1323
(Fed. Cir. 2005) (citations omitted, bracketed text in internal quotes in
original). Moreover, the fact that non-computer methods might take a single
individual several months does not persuade us that performing
computations encompassed by claim 1 cannot practically be performed
solely in the human mind.
Appeal 2018-008016
Application 13/486,982

16

In sum, for the reasons discussed, under Revised Step 2A, Prong 2, of
the 2019 Office Guidance we agree with the Examiner that Appellant’s
claim 1 does not recite additional elements that integrate the judicial
exceptions into a practical application.
Office Guidance—Step 2B
For the reasons discussed above, we are persuaded that Appellant’s
representative claim 1 recites judicial exceptions (abstract ideas in the form
of mathematical concepts and mental processes) under Revised Step 2A,
Prong 1, of the 2019 Office Guidance, and does not integrate those judicial
exceptions into a practical application under Revised Step 2A, Prong 2.
Accordingly, we turn to Step 2B of the Office Guidance to determine
whether (a) claim 1 recites specific limitations beyond the judicial
exceptions that are not well-understood, routine, or conventional in the field,
or (b) whether claim 1 simply appends well-understood, routine,
conventional activities previously known to the industry, specified at a high
level of generality, to the judicial exception. See Office Guidance (84 Fed.
Reg. at 56).
As discussed above, the non-abstract steps in claim 1 involve generic
computer-related steps for performing the abstract computation (receiving
and storing genotype data in a computer memory, storing imputed haplotype
phases in a computer memory, extracting a predicted haplotype, and storing
a predicted haplotype in a computer memory). See Appeal Br. 19. The
Examiner finds that these are “necessary and conventional steps in computer
use, and more specifically in genetic analysis of obtaining starting data and
providing/storing the data analysis results, in this case when using a
computer for the HMM modelling.” Ans. 5–6.
Appeal 2018-008016
Application 13/486,982

17

Appellant contends that it is the abstract computational steps that
provide the inventive concept to claim 1:
With respect to the claims at issue, it is the clauses that the
Office action fails to consider including (but not limited to) the
processes of “building a data structure” containing “a set of
imputed haplotype phases” and “repeatedly randomly
modifying[]. . . of the imputed initial haplotype phases[]. . .”
and, “automatically replacing an imputed haplotype phase of an
individual with a randomly modified haplotype phase ... when
... the randomly modified haplotype phase is more likely than
an existing imputed haplotype phase” in order to obtain the
“final predicted haplotype phase from the data structure” as
recited in claim 1 that constitute something more.
Appeal Br. 13.
As explained in the 2019 Office Guidance, however, it is the
“additional elements recited in the claims” beyond the judicial exceptions in
the claim that must provide significantly more than the recited judicial
exception. See Office Guidance (84 Fed. Reg. at 56) (emphasis added).
Thus, the fact that the abstract computational steps recited in Appellant’s
claim 1 might be a highly significant discovery in the field of haplotype
prediction is insufficient to establish eligibility for patenting. See In re
BRCA1- and BRCA2-Based Hereditary Cancer Test Patent Litigation, 774
F.3d 755, 759 (Fed. Cir. 2014) (Even if Appellants “made a
‘[g]roundbreaking, innovative, or even brilliant discovery,’ . . . that is not
enough” to establish patent eligibility.) (Citing Association for Molecular
Pathology v. Myriad, 133 S. Ct. 2107, 2117 (2013)).
Appellant contends that no evidence supports the Examiner’s
determination that the non-abstract computer-related steps recited in claim 1
(receiving and storing genotype and haplotype data, extracting a predicted
Appeal 2018-008016
Application 13/486,982

18

haplotype phase) are well-understood, routine, conventional activities
previously known in the field of haplotype prediction. Reply Br. 13–15.
As noted above, however, Appellant repeatedly contends that
haplotype prediction is a computer-implemented field. See Appeal Br. 8–9;
Reply Br. 3–5. Consistent with the Examiner’s determination, therefore (see
Ans. 5–6), the claimed steps of receiving and storing genotype and
haplotype data in computer memory, and extracting a predicted haplotype
phase therefrom, would not only be necessary in that computer-implemented
field, but would also necessarily be routine and conventional in haplotype
prediction.
Indeed, in describing the state of the art, Appellant’s Specification
cites two known software packages as a basis for comparison to the
inventive method of representative claim 1. See Spec. ¶ 53 (“Two software
packages are used to analyze large-scale high-density SNP data: FastPHASE
. . . and Beagle . . . .”) (citations omitted). On the current record, these
undisputedly art-recognized software packages would appear to necessarily
involve the steps of receiving and storing genotype and haplotype data in
computer memory, and extracting a predicted haplotype phase therefrom.
Appellant does not persuade us, therefore, that the preponderance of the
evidence fails to support a finding that the claimed steps of receiving and
storing genotype and haplotype data in computer memory, and extracting a
predicted haplotype phase therefrom, are well-understood, routine,
conventional activities previously known in the field of haplotype
prediction.
In sum, for the reasons discussed, we agree with the Examiner that, in
reciting the non-abstract steps of receiving and storing genotype and
Appeal 2018-008016
Application 13/486,982

19

haplotype data in computer memory, and extracting a predicted haplotype
phase therefrom, representative claim 1 simply appends well-understood,
routine, conventional activities previously known to the industry, specified
at a high level of generality, to the judicial exceptions recited in the claim.
Eligibility for Patenting—Conclusion
As discussed above, we are persuaded that Appellant’s representative
claim 1 recites judicial exceptions (abstract ideas in the form of
mathematical concepts and mental processes) under Revised Step 2A, Prong
1, of the 2019 Office Guidance, and does not integrate those judicial
exceptions into a practical application under Revised Step 2A, Prong 2. As
also discussed above, we are persuaded that, as to the additional elements
beyond the judicial exceptions recited in the claim, claim 1 simply appends
well-understood, routine, conventional activities previously known to the
industry, specified at a high level of generality, to the judicial exceptions.
Accordingly, applying the principles set forth in the 2019 Office Guidance,
we find that the preponderance of the evidence supports the Examiner’s
determination that Appellant’s claim 1 is directed to subject matter that is
ineligible for patenting.
We acknowledge, but are unpersuaded by, Appellant’s contention that
the process recited in claim 1 does not preempt any and all uses of the
Hidden Markov Model recited in the claims. See Appeal Br. 10–11; Reply
Br. 10–11. Our reviewing court has explained that, “[w]hile preemption
may signal patent ineligible subject matter, the absence of complete
preemption does not demonstrate patent eligibility. . . . Where a patent’s
claims are deemed only to disclose patent ineligible subject matter under the
Mayo framework . . . preemption concerns are fully addressed and made
Appeal 2018-008016
Application 13/486,982

20

moot.” Ariosa Diagnostics, Inc. v. Sequenom, Inc., 788 F.3d 1371, 1379
(Fed. Cir. 2015).
In the present case, as discussed above, under the Mayo framework as
implemented by the 2019 Office Guidance, we are persuaded that the
preponderance of the evidence supports the Examiner’s determination that
Appellant’s claim 1 is directed to subject matter that is ineligible for
patenting. Accordingly, the fact that Appellant’s claim 1 might not preempt
any and all uses of the Hidden Markov Model does not demonstrate patent
eligibility. See Ariosa, 788 F.3d at 1379.
In sum, for the reasons discussed, Appellant does not persuade us
that the Examiner erred in determining that Appellant’s claim 1 is directed to
subject matter that is ineligible for patenting. We, therefore, affirm the
Examiner’s rejection of claim 1 as being ineligible for patenting. Claims
22–43 fall with claim 1. See 37 C.F.R. § 41.37(c)(1)(iv).

CONCLUSION
In summary:
Claims
Rejected
Basis  Affirmed Reversed
1, 22– 43 § 101, ineligibility
for patenting

1, 22– 43
Overall Outcome

1, 22– 43

Appeal 2018-008016
Application 13/486,982

21

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

AFFIRMED