By Kevin E. Noonan —

The Federal Circuit affirmed a decision by the U.S. Patent and Trademark Office Patent Trial and Appeal Board (PTAB) rejecting claims for failure to satisfy the subject matter eligibility standard under 35 U.S.C. § 101, in ex parte examination of claims to methods and related computing systems for genetic haplotyping in In re Board of Trustees of the Leland Stanford Junior University.

The claimed method is recited in representative claim 1:

1.  A method for resolving haplotype phase, comprising:
    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 system comprising a processor and a memory;
    determining an inheritance state for the allele information described in the allele data based on identity between single nucleotide variants contained in the genotypes for the family using a Hidden Markov Model having hidden states implemented on a computer system comprising a processor and a memory,
        wherein the hidden states comprise inheritance states, a compression fixed error state, and a[ Mendelian inheritance error]- rich fixed error state,
        wherein the inheritance states are maternal identical, paternal identical, identical, and non-identical;
    receiving transition probability data describing transition probabilities for inheritance states and storing the transition probability data on a computer 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 information described in the allele data, the transition probability data, and the population linkage disequilibrium data using a computer system comprising a processor and a memory;
    storing the haplotype phase for at least one member of the family using a computer system comprising 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.

As explained in the opinion, the claimed method involves determining haplotype phase, i.e., "a process for determining the parent from whom alleles—i.e., versions of a gene—are inherited."  The specification describes using genotype data and pedigree data and applying a known prior art method as disclosed in Roach et al., Analysis of Genetic Inheritance in a Family Quartet by Whole Genome Sequencing, 328 SCIENCE 636 (2010).  This method uses a statistical tool termed a hidden Markov model for these predictions.  The specification discloses that prior art methods were inadequate and that the disclosed methods cure such shortcomings, increasing the number of possible prediction to 97.9% by "factoring additional data into the analysis."  These additional data include linkage disequilibrium data (a measure of reduction of expected crossing over frequency events during meiosis produced, inter alia, by marker genes being adjacent to one another on a chromosome) obtained from an art-available database of single nucleotide polymorphisms, as well as "transition probability date," wherein "transition probabilities are set depending on 'the expected number of state transitions and the total number of allele assortments in the pedigree.'"

The Examiner, affirmed by the PTAB, rejected the claims based on their being directed to "abstract mathematical algorithms and mental processes."  According to the Federal Circuit's opinion, the Examiner and the Board applied the two-step test set forth by the Supreme Court in Alice Corp. Pty. Ltd. v. CLS Bank Int'l, 573 U.S. 208 (2014), in making this determination.  With regard to step 1 of the test, the Examiner and Board determined that all steps recited in claim 1 were "directed to" either "mental steps of receiving, storing, or providing information[ or ]mathematical concepts"; the rationale is that the steps recited receiving or analyzing information, "which humans could process in their minds," or mathematical algorithms.  (It would be doctrinally beneficial for both the USPTO and the Federal Circuit to abandon the charade that the types of processes recited in claims related to computer implementation could be performed in the human mind; surely there must be a better rationale for the question-begging conclusion than this!)  Further, the Board also held that these mathematical algorithms, steps, and processes were not "integrated into a practical application" (which might be a surprise to patentees and patients who benefit from the application of the claimed methods).  The distinction drawn by the Board was that the method does not improve computer technology, citing Enfish, LLC v. Microsoft Corp., 822 F.3d 1327 (Fed. Cir. 2016), but rather provides an improved mathematical analysis (which results in a seemingly unappreciated practical application in genetic analysis).

Completing its Alice analysis, the Board concluded that the claims did not satisfy the requirements of step 2 either, insofar as they did not "include additional limitations that, when taken individually or as a whole, provide an inventive concept that transforms the abstract idea into patent eligible subject matter" (an analysis that illustrates one again the wisdom Congress demonstrated generations ago in substituting obviousness for "inventive concept").  The recited steps "did not go beyond the well-known, routine, and conventional" according to the Board.  And in the philosophical coup de grace stemming from dicta in Justice Thomas's opinion in AMP v Myriad Genetics, the Board stated that the claimed invention was patent-ineligible "although the claims may provide a valuable contribution to science."

Certain other claims, which recited as an affirmative step "providing the drug for treatment" did not transform the genetic analysis claims to patent-eligible ones for failing to satisfy the "five specificities" recited by Judge Lourie in Vanda Pharmaceuticals Inc. v. West-Ward Pharmaceuticals International Ltd., 887 F.3d 1117 (Fed. Cir. 2018), because "they are not directed to a specific method of treatment, do not identify specific patients, do not recite a specific compound, do not prescribe particular doses, and do not identify the resulting outcome."

The Federal Circuit affirmed (not surprisingly, under the circumstances) in an opinion by Judge Reyna joined by Chief Judge Prost and Judge Lourie.  The opinion recited the Court's familiar litany of purported obeisance to the Supreme Court's subject matter eligibility jurisprudence, down to Gottschalk v. Benson, 409 U.S. 63 (1972), and Parker v. Flook, 437 U.S. 584 (1978), with regard to claims relying on mathematical algorithms.  After parsing claim 1 according to the context of its analytical steps, the Federal Circuit held that the Board was correct in finding this claim patent-ineligible because "Claim 1 recites no concrete application for the haplotype phase beyond storing it and providing it upon request."  The Court's response to Stanford's argument that "the specific application of the steps is novel and enables scientists to ascertain more haplotype information than was previously possible" was that "we are not persuaded" even if they were to accept Stanford's argument, nor was this panel convinced even if the invention provides the claimed advance in genetic analysis that the process is "an improved technological process" (which raises the question of the wisdom of denying patent eligibility to an invention that provides an improvement in genetic analysis that does not require a concommittant improvement in the technological process).

Having found no legal (not logical) fault in the Board's determinations regarding step 1 of the Alice test, the Court turned to step 2, finding no error in the Board's determination regarding this step, because "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.'"  This rhetorical formulation evokes Justice Breyer's objection to the claims Mayo Collaborative Services v. Prometheus Laboratories, Inc. (2012), which curiously was not cited in the opinion.  This is perhaps because the clear distinction with the case before the Court is that everything except the correlation recited in the Mayo case was known in the prior art.  And the failure to recite "a specialized computer or a computer with a specialized memory or processor" in claim 1 here was enough to confirm patent ineligibility, analogous to the use of known detection methods that the Court used to sustain invalidation of claims directed to detecting cell-free fetal DNA in maternal blood in Ariosa v. Sequenom.  The opinion states:

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.  . . .  Thus, taken individually, the limitations of claim 1 fail to transform the claims into a patent eligible application [emphasis added].

Illustrating that a willingness to apply Alice seems to include a similar willingness to ignore Diamond v. Diehr (1981).  To Stanford's argument that the claim recites an ordered combination of elements, it is enough for this panel to conclude that because "[t]he alleged innovation accomplished in claim 1 is in the mathematical analysis itself, namely, in the receipt of data, executing mathematical calculations, and storing the resulting data, [t]he alleged innovation therefore subsists in 'the basic tools of scientific and technological work.'"

And none of the limitations recited in any of the dependent claims in the application, including those directed towards drug treatment, rise (in this panel's view) above the characterization of the claims "do[ing] nothing more than recite the haplotype phase algorithm and instruct, 'apply it,' as the Supreme Court has prohibited," citing Alice instead of Mayo.

Nothing about this decision is surprising; fortunately it is also non-precedential.  But that very fact should be enough to illustrate the importance of the Supreme Court granting certiorari in American Axle & Mfg. v. Neapco Holdings to perhaps straighten out the illogical morass that is subject matter eligibility at the Federal Circuit.

In re Board of Trustees of the Leland Stanford Junior University (Fed. Cir. 2021)
Panel: Chief Judge Prost and Circuit Judges Lourie and Reyna
Opinion by Circuit Judge Reyna