Court Opinion

ID: 4666753
Source: CourtListenerOpinion
Date Created: 2021-03-11 16:00:58.283361+00
Date Added: 2024-06-11T08:02:51.492026
License: Public Domain

Case: 20-1012    Document: 38     Page: 1    Filed: 03/11/2021

   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 KAUTH, KPPB LLP, Anaheim, CA, argued for ap-
 pellant. Also represented by DAVID BAILEY, CHRISTIAN
 HANS, MARK YEH.

    MAUREEN DONOVAN QUELER, Office of the Solicitor,
 United States Patent and Trademark Office, Alexandria,
 VA, argued for appellee Andrew Hirshfeld. Also repre-
 sented by THOMAS W. KRAUSE, AMY J. NELSON.
                 ______________________

   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
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 2                              IN RE: THE BOARD OF TRUSTEES

 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
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 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.
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     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;
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 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.
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 6                              IN RE: THE BOARD OF TRUSTEES

     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
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 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
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 8                              IN RE: THE BOARD OF TRUSTEES

 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 REVIEW
      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)).
                         DISCUSSION
      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
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 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
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 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
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 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,
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 12                             IN RE: THE BOARD OF TRUSTEES

 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
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 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