Federal Circuit disposition — 20-1012

United States Court of Appeals
for the Federal Circuit
______________________
IN RE: BOARD OF TRUSTEES OF THE LELAND
STANFORD JUNIOR UNIVERSITY,
Appellant
______________________
2020-1012
______________________
Appeal from the United States Patent and Trademark
Office, Patent Trial and Appeal Board in No. 13/445,925.
______________________
Decided: March 11, 2021
______________________
JOEL K AUTH , KPPB LLP, Anaheim, CA, argued for ap-
pellant. Also represented by D AVID B AILEY, CHRISTIAN
H ANS , M ARK Y EH .
M AUREEN D ONOVAN Q UELER, Office of the Solicitor,
United States Patent and Trademark Office, Alexandria,
VA, argued for appellee Andrew Hirshfeld. Also repre-
sented by THOMAS W. K RAUSE , AMY J. N ELSON .
______________________
Before PROST, Chief Judge, LOURIE and REYNA, Circuit
Judges.
REYNA, Circuit Judge.
The Board of Trustees of the Leland Stanford Junior
University appeals the final rejection of patent claims con-
tained in its patent application. The patent examiner
Case: 20-1012 Document: 38 Page: 1 Filed: 03/11/2021

-- 1 of 13 --

IN RE: THE BOARD OF TRUSTEES 2
reviewing the application rejected the claims on grounds
that they involve patent ineligible subject matter. On re-
view, the Patent Trial and Appeal Board affirmed the ex-
aminer’s final rejection of the claims. As discussed below,
we hold that the rejected claims are drawn to abstract
mathematical calculations and statistical modeling, and
similar subject matter that is not patent eligible. Accord-
ingly, we affirm the decision of the Patent Trial and Appeal
Board.
BACKGROUND
The Board of Trustees of the Leland Stanford Junior
University (“Stanford”) filed its Application No. 13/445,925
(“’925 application”) on April 13, 2012. The ’925 application
is directed to methods and computing systems for deter-
mining haplotype phase. J.A. 270, 906–07. Haplotype
phasing is a process for determining the parent from whom
alleles—i.e., versions of a gene—are inherited. A haplotype
phase acts as an indication of the parent from whom a gene
has been inherited.
According to the written description of the ’925 appli-
cation, improved haplotype phasing techniques “promise[]
to revolutionize personalized health care by tailoring risk
modification, medications, and health surveillance to pa-
tients’ individual genetic backgrounds.” J.A. 269–70.
Achieving the understanding necessary to accomplish
those goals has long challenged scientists because it re-
quires “interpretation of massive amounts of genetic data
produced with each genome sequence.” J.A. 270, 296. The
’925 application purports to meet that challenge via a
method for receiving certain types of genetic data and pro-
cessing the data by performing mathematical calculations
and statistical modeling to arrive at a haplotype phase de-
termination.
The claimed methods first involve using two types of
information, namely genotype data and pedigree data, to
determine alleles’ inheritance state using a method
Case: 20-1012 Document: 38 Page: 2 Filed: 03/11/2021

-- 2 of 13 --

IN RE: THE BOARD OF TRUSTEES 3
published in the prior art, namely Roach et al., Analysis of
Genetic Inheritance in a Family Quartet by Whole Genome
Sequencing, 328 SCIENCE 636 (2010). The Roach reference
teaches the use of a hidden Markov model (“HMM”)—a sta-
tistical tool used in various applications to make probabil-
istic determinations of latent variables—to predict
inheritance state. See J.A. 272–73, 282, 294–95, 319–20.
The written description also explains that, in the prior
art, methods of determining haplotype phase based on in-
heritance state yielded an incomplete number of the alleles’
haplotypes. See, e.g., J.A. 297 (discussing the “trio” method
that predicted haplotype phases for approximately 80 per-
cent of heterozygous positions); see also J.A. 909; Appel-
lant’s Br. 7 (explaining that “the inheritance state
information produced by the HMM is uninformative in
some regions of the allele data”). The claimed methods al-
legedly increase the number of possible haplotype phase
predictions. See, e.g., J.A. 298–99 (explaining that the
claimed methods result in “phase resolution of 97.9% of
heterozygous positions”); see also Appellant’s Br. 5 (con-
trasting the inventions from the “‘trio’” method”).
The increase in haplotype phase predictions is made
possible by factoring additional data into the analysis. See
J.A. 296–99; see also Appellant’s Br. 7. The first type of
additional data, known as “linkage disequilibrium data,”
could at the time be obtained from the “SNP Annotation
and Proxy Search” or “SNAP” database, which launched in
approximately 2008. See J.A. 283. The second type of ad-
ditional data is referred to as “transition probability data.”
According to the written description, transition probabili-
ties are set depending on “the expected number of state
transitions and the total number of allele assortments in
the pedigree.” J.A. 273, 295. These two types of additional
data allegedly enable haplotype phase to be inferred in re-
gions where inheritance state is uninformative. See
J.A. 273, 298–99; see also Appellant’s Br. 3.
Case: 20-1012 Document: 38 Page: 3 Filed: 03/11/2021

-- 3 of 13 --

IN RE: THE BOARD OF TRUSTEES 4
Stanford appeals the Patent Trial and Appeal Board’s
(“Board”) affirmance of the examiner’s rejection of claims
1, 4–11, 14–25, and 27–30 as covering patent ineligible ab-
stract mathematical algorithms and mental processes. See
J.A. 871–72, 1101–10. Independent claim 1 is representa-
tive and recites:
1. A method for resolving haplotype phase, com-
prising:
receiving allele data describing allele information
regarding genotypes for a family comprising at
least a mother, a father, and at least two children
of the mother and the father, where the genotypes
for the family contain single nucleotide variants
and storing the allele data on a computer system
comprising a processor and a memory;
receiving pedigree data for the family describing
information regarding a pedigree for the family
and storing the pedigree data on a computer sys-
tem comprising a processor and a memory;
determining an inheritance state for the allele in-
formation described in the allele data based on
identity between single nucleotide variants con-
tained in the genotypes for the family using a Hid-
den Markov Model having hidden states
implemented on a computer system comprising a
processor and a memory,
wherein the hidden states comprise inher-
itance states, a compression fixed error
state, and a[ Mendelian inheritance error]-
rich fixed error state,
wherein the inheritance states are mater-
nal identical, paternal identical, identical,
and non-identical;
Case: 20-1012 Document: 38 Page: 4 Filed: 03/11/2021

-- 4 of 13 --

IN RE: THE BOARD OF TRUSTEES 5
receiving transition probability data describing
transition probabilities for inheritance states and
storing the transition probability data on a com-
puter system comprising a processor and a
memory;
receiving population linkage disequilibrium data
and storing the population disequilibrium data on
a computer system comprising a processor and a
memory;
determining a haplotype phase for at least one
member of the family based on the pedigree data
for the family, the inheritance state for the infor-
mation described in the allele data, the transition
probability data, and the population linkage dise-
quilibrium data using a computer system compris-
ing a processor and a memory;
storing the haplotype phase for at least one mem-
ber of the family using a computer system compris-
ing a processor and a memory; and
providing the stored haplotype phase for at least
one member of the family in response to a request
using a computer system comprising a processor
and a memory.
J.A. 1101–02.1
1 Claims 11 and 21, the two other independent
claims in the ’925 application, both recite computer hard-
ware for carrying out the steps of claim 1. See J.A. 1101–
10. The claims depending from claim 1 (claims 4–10 and
22–25) recite the same substantive limitations as the cor-
responding claims that depend from claim 11 (claims 14–
20 and 27–30). J.A. 1101–10. No claims depend from claim
21.
Case: 20-1012 Document: 38 Page: 5 Filed: 03/11/2021

-- 5 of 13 --

IN RE: THE BOARD OF TRUSTEES 6
In its analysis of the examiner’s rejections, the Board
applied the two-step framework established by the Su-
preme Court for determining patent eligibility. See Alice
Corp. Pty. Ltd. v. CLS Bank Int’l, 573 U.S. 208 (2014);
J.A. 5–18. Addressing step one of the Alice inquiry, the
Board determined that the eight steps in claim 1 are di-
rected to either the “mental steps of receiving, storing, or
providing information” or “mathematical concepts.” See
J.A. 7–9. The Board reasoned that the claim recites steps
for receiving and analyzing information, which humans
could process in their minds, or by mathematical algo-
rithms, which are mental processes within the abstract-
idea category. J.A. 10. The Board concluded that the
mathematical process recited in the claims is not inte-
grated into a practical application. The Board specifically
found that the claims, unlike those in Enfish, LLC v. Mi-
crosoft Corp., 822 F.3d 1327 (Fed. Cir. 2016), do not im-
prove computer technology but rather use off-the-shelf
computing equipment to perform an improved mathemati-
cal analysis. See J.A. 12–13. The Board explained that the
claims are also unlike those covering animation of 3-D
characters in McRO, Inc. v. Bandai Namco Games America
Inc., 837 F.3d 1299, 1315 (Fed. Cir. 2016), which improve
“the computer animation process itself.” J.A. 13–15. The
Board concluded that claim 1 is directed to patent ineligible
subject matter under § 101. J.A. 11, 15; 35 U.S.C. § 101.
Turning to step two of the Alice inquiry, the Board con-
cluded that the claims did not include additional limita-
tions that, when taken individually or as a whole, provide
an inventive concept that transforms the abstract idea into
patent eligible subject matter. The Board found that the
steps of receiving data, performing calculations using that
data, storing the results, and providing the results upon
request using a computer did not go beyond the well-
known, routine, and conventional. See J.A. 16–17 (“We
find that Appellants’ claims do not require anything other
than the use of conventional and well-understood
Case: 20-1012 Document: 38 Page: 6 Filed: 03/11/2021

-- 6 of 13 --

IN RE: THE BOARD OF TRUSTEES 7
techniques and equipment to gather and process data ac-
cording to the recited judicial exception.”). The Board ex-
plained that, although the claims may provide a valuable
contribution to science, that contribution does not go be-
yond patent ineligible mental processes and mathematical
operations. See J.A. 16.
The Board addressed the remaining claims and con-
cluded that the analysis applied to claim 1 also applied to
claims 7, 8, 10, 11, 17, 18, 20, and 21. J.A. 17. It separately
addressed claims 9 and 19, which recite certain steps cul-
minating in a final step of “providing the drug for treat-
ment.” The steps recited in claim 9 appear as follows and
are the same as those in claim 19 in all respects material
to this appeal:
determining whether at least one genetic variant
associated with disease is within the stored haplo-
type phase by utilizing the haplotype phase to
query a disease associated-single nucleotide poly-
morphism database using a computer system com-
prising a processor and a memory;
determining a drug for treatment of at least one
member of the family based on information regard-
ing drug-variant-phenotype associations from a
pharmacogenomics database and the determina-
tion whether the at least one genetic variant asso-
ciated with disease is within the stored haplotype
phase using a computer system comprising a pro-
cessor and a memory;
storing the determined drug using a computer sys-
tem comprising a processor and a memory; and
providing the determined drug in response to a re-
quest using a computer system comprising a pro-
cessor and a memory.
J.A. 1103–04, 1106–07. The Board determined that claims
9 and 19 are drawn to patent ineligible subject matter
Case: 20-1012 Document: 38 Page: 7 Filed: 03/11/2021

-- 7 of 13 --

IN RE: THE BOARD OF TRUSTEES 8
because they “are not directed to a specific method of treat-
ment, do not identify specific patients, do not recite a spe-
cific compound, do not prescribe particular doses, and do
not identify the resulting outcome.” J.A. 18. The Board
distinguished claims 9 and 19 from the patent eligible
claims discussed in Vanda Pharmaceuticals Inc. v. West-
Ward Pharmaceuticals International Ltd., 887 F.3d 1117
(Fed. Cir. 2018), because the claims in Vanda were directed
to a “specific method of treatment for specific patients us-
ing a specific compound at specific doses to achieve a spe-
cific outcome.” J.A. 17–18. For these reasons, the Board
affirmed the examiner’s rejection of claims 1, 4–11, 14–25,
and 27–30 under § 101. Stanford appeals. We have juris-
diction pursuant to 35 U.S.C. § 141(a) and 28 U.S.C.
§ 1295(a)(4)(A).
STANDARD OF R EVIEW
We review Board decisions in accordance with the Ad-
ministrative Procedure Act (“APA”), 5 U.S.C. § 706(2).
Dickinson v. Zurko, 527 U.S. 150, 152 (1999). Under the
APA, we review the Board’s legal conclusions de novo and
its factual findings for substantial evidence. ACCO Brands
Corp. v. Fellowes, Inc., 813 F.3d 1361, 1365 (Fed. Cir.
2016). Substantial evidence is “such relevant evidence as
a reasonable mind might accept as adequate to support a
conclusion.” In re Gartside, 203 F.3d 1305, 1312 (Fed. Cir.
2000) (quoting Consol. Edison Co. v. NLRB, 305 U.S. 197,
229 (1938)).
D ISCUSSION
The Supreme Court has articulated a two-step analysis
to determine patent eligibility under 35 U.S.C. § 101. Al-
ice, 573 U.S. at 217–18. In the first step, we examine
whether a claim is directed to patent ineligible subject mat-
ter, such as an abstract idea. Id. If so, we turn to the sec-
ond step and examine whether the claims contain an
inventive concept sufficient to transform the abstract idea
into patent eligible subject matter. Id. at 221. In this
Case: 20-1012 Document: 38 Page: 8 Filed: 03/11/2021

-- 8 of 13 --

IN RE: THE BOARD OF TRUSTEES 9
second step we consider the claim elements individually
and as an ordered combination to determine whether any
additional limitations amount to significantly more than
the ineligible concept. Id. at 217–18, 221. A patent eligible
claim must do more than simply recite the abstract idea
“while adding the words ‘apply it.’” Id. at 221.
We conclude that all the reviewed claims of the ’925
application are directed to patent ineligible abstract ideas.
Courts have long held that mathematical algorithms for
performing calculations, without more, are patent ineligi-
ble under § 101. See, e.g., Parker v. Flook, 437 U.S. 584,
595 (1978) (“[I]f a claim is directed essentially to a method
of calculating, using a mathematical formula, even if the
solution is for a specific purpose, the claimed method is
nonstatutory.” (internal citation and quotation marks
omitted)); Gottschalk v. Benson, 409 U.S. 63, 72 (1972)
(finding claims patent ineligible because they “would
wholly pre-empt the mathematical formula and in practical
effect would be a patent on the algorithm itself”); SAP Am.,
Inc. v. InvestPic, LLC, 898 F.3d 1161, 1167 (Fed. Cir. 2018)
(explaining that the focus of the claims, namely selecting
certain information, analyzing it using mathematical tech-
niques, and reporting or displaying the results of the anal-
ysis, “is all abstract”); Digitech Image Techs., LLC v. Elecs.
for Imaging, Inc., 758 F.3d 1344, 1351 (Fed. Cir. 2014)
(“Without additional limitations, a process that employs
mathematical algorithms to manipulate existing infor-
mation to generate additional information is not patent el-
igible.”); In re Schrader, 22 F.3d 290, 294 (Fed. Cir. 1994)
(holding that a data gathering step of entering bids was
“insufficient to impart patentability to a claim involving
the solving of a mathematical algorithm”).
On its face, representative claim 1 is drawn to a
“method for resolving haplotype phase.” J.A. 1101. The
method first involves “receiving” allele data and pedigree
data and “determining an inheritance state” based on the
received data “using [an HMM].” Id. The method then
Case: 20-1012 Document: 38 Page: 9 Filed: 03/11/2021

-- 9 of 13 --

IN RE: THE BOARD OF TRUSTEES 10
involves “receiving” transition probability data and popu-
lation linkage disequilibrium data and “determining a hap-
lotype phase” based on that received data as well as the
earlier-calculated inheritance state “using a computer sys-
tem comprising a processor and a memory.” Id. Lastly, the
method involves “storing the haplotype phase” and “provid-
ing” it “in response to a request using a computer system
comprising a processor and a memory.” Id. at 1101–02.
Claim 1 recites no concrete application for the haplotype
phase beyond storing it and providing it upon request.
Stanford argues that claim 1 is not directed to an ab-
stract idea because the specific application of the steps is
novel and enables scientists to ascertain more haplotype
information than was previously possible. See, e.g., Appel-
lant’s Br. 5 (“While the ‘trio’ method may be able to provide
long-range haplotype phasing for approximately 80% of
heterozygous positions, the method of the present inven-
tion provides accurate, long-range phasing at 97.9% of all
heterozygous positions.” (citing the ’925 application at
¶¶ 91–92)). Even accepting the argument that the claimed
process results in improved data, we are not persuaded
that claim 1 is not directed to an abstract mathematical
calculation. Synopsys, Inc. v. Mentor Graphics Corp.,
839 F.3d 1138, 1151 (Fed. Cir. 2016) (“[A] claim for a new
abstract idea is still an abstract idea.”); SAP, 898 F.3d at
1170 (“[P]atent law does not protect such claims, without
more, no matter how groundbreaking the advance.”).
We have also examined, consistent with our precedent,
whether the claimed advance demonstrates an improve-
ment on a technological process or merely enhances an in-
eligible concept. See, e.g., Athena Diagnostics, Inc. v. Mayo
Collaborative Servs., LLC, 915 F.3d 743, 750 (Fed. Cir.
2019). The claimed advance proffered by Stanford, that the
process yields a greater number of haplotype phase predic-
tions, may constitute a new or different use of a mathemat-
ical process, but we are not persuaded that the process is
an improved technological process. We therefore conclude
Case: 20-1012 Document: 38 Page: 10 Filed: 03/11/2021

-- 10 of 13 --

IN RE: THE BOARD OF TRUSTEES 11
that claim 1 is directed to the abstract idea of mathemati-
cally calculating alleles’ haplotype phase.
Because claim 1 is directed to a patent ineligible math-
ematical algorithm, we turn next to Alice step two. We con-
clude that claim 1 is not transformed at step two into
patent eligible subject matter. Claim 1 recites no steps
that practically apply the claimed mathematical algorithm;
instead, claim 1 ends at storing the haplotype phase and
“providing” it “in response to a request.” Simply storing
information and providing it upon request does not alone
transform the abstract idea into patent eligible subject
matter. See, e.g., In re Greenstein, 774 F. App’x 661, 664
(Fed. Cir. 2019) (explaining that the claims at issue only
invoked a computer as a generic tool to store information
and record transactions).
Notably, claim 1 neither requires, nor results in, a spe-
cialized computer or a computer with a specialized memory
or processor. Indeed, it is hard to imagine a patent claim
that recites hardware limitations in more generic terms
than the terms employed by claim 1. See J.A. 1101–02 (re-
citing method steps carried out by a “computer” with a “pro-
cessor” and a “memory”); see also Alice, 573 U.S. at 226
(explaining that the hardware-related terms “data pro-
cessing system,” “communications controller,” and “data
storage unit” are “purely functional and generic”); In re TLI
Commc’ns LLC Pat. Litig., 823 F.3d 607, 614 (Fed. Cir.
2016) (holding generic computer components insufficient to
add an inventive concept to an otherwise abstract idea).
The written description makes clear that the mathematical
steps performed, and the types of data received, as claimed,
are conventional and well understood in the prior art. See,
e.g., J.A. 272–73, 282–83, 294–99, 319–20. Thus, taken in-
dividually, the limitations of claim 1 fail to transform the
claims into a patent eligible application.
Although Stanford faults the Board for failing to assess
the elements of claim 1 as an ordered combination,
Case: 20-1012 Document: 38 Page: 11 Filed: 03/11/2021

-- 11 of 13 --

IN RE: THE BOARD OF TRUSTEES 12
Stanford fails to explain how that combination of elements
moves the claimed subject matter beyond the abstract and
into the practical. See Appellant’s Br. 41–43; see also Af-
finity Labs of Tex., LLC v. DIRECTV, LLC, 838 F.3d 1253,
1263 (Fed. Cir. 2016) (explaining that novelty does not nec-
essarily avoid abstractness). That a specific or different
combination of mathematical steps yields a greater num-
ber of haplotype predictions than previously achievable un-
der the prior art is not enough to transform claim 1 into a
patent eligible application. See SAP, 898 F.3d at 1170
(holding an advance in financial mathematical techniques
does not constitute an inventive concept). The alleged in-
novation accomplished in claim 1 is in the mathematical
analysis itself, namely, in the receipt of data, executing
mathematical calculations, and storing the resulting data.
The alleged innovation therefore subsists in “the basic tools
of scientific and technological work.” See Alice, 573 U.S. at
216.
The remaining claims contain no limitations that,
when considered individually or as an ordered combina-
tion, transform them into patent eligible applications. In-
dependent claims 11 and 21 recite generic computer
hardware for performing the calculations covered in claim
1. Such hardware by itself is insufficient to provide an in-
ventive concept. See, e.g., Alice, 573 U.S. at 222–24; SAP,
898 F.3d at 1168–70. Dependent claims 4–7, 14–17, 22–25,
and 27–30 recite additional calculation steps and specify
certain aspects of the haplotype phase algorithm covered
by claim 1. But none of these additional steps move the
claims beyond patent ineligible abstract mathematical al-
gorithms. See SAP, 898 F.3d at 1169 (holding dependent
claims patent ineligible where they add features that
“simply provide further narrowing of what are still mathe-
matical operations”)).
Dependent claims 8–10 and 18–20 contain limitations
drawn to making non-specific determinations of a “diagno-
sis,” “drug treatment,” and “prognosis” based on the
Case: 20-1012 Document: 38 Page: 12 Filed: 03/11/2021

-- 12 of 13 --

IN RE: THE BOARD OF TRUSTEES 13
haplotype phase calculation. Without further limitations,
these claims do nothing more than recite the haplotype
phase algorithm and instruct, “apply it,” as the Supreme
Court has prohibited. See Alice, 573 U.S. at 221. These
claims are devoid of an inventive concept that transforms
the claims into a patent eligible application.
CONCLUSION
We have considered Stanford’s remaining arguments
and find them unpersuasive. For the above reasons, the
Board’s conclusion that claims 1, 4–11, 14–25, and 27–30
are drawn to patent ineligible subject matter under § 101
is affirmed.
AFFIRMED
Case: 20-1012 Document: 38 Page: 13 Filed: 03/11/2021

-- 13 of 13 --