On March 11, 2021, the Federal Circuit affirmed the PTAB’s finding that claims directed to a novel mathematical process to generate genetic inheritance data was patent ineligible under 35 U.S.C.S. § 101 and Alice. In In re Bd. of Trs. of the Leland Stanford Junior Univ., 2021 U.S. App. LEXIS 7148, *1 (Fed. Cir. 2021), Prost, Lourie, and Reyna concluded that the claimed method was merely an algorithm and lacked any improvement of a technological process.

On April 13, 2012, The Board of Trustees of the Leland Stanford Junior University (“Stanford”) filed Application No. 13/445,925 directed to computing systems for determining haplotype phase, which is the statistical process for determining the parent from whom alleles of various genes are inherited.¹ The specification explained that haplotype phasing previously involved interpreting “massive amounts of genetic data” and that the claimed method would simplify this process by utilizing mathematical calculations and modeling to make the haplotype phase determination.² It posited that improved techniques for haplotype phasing techniques would improve human health by tailoring a patient’s treatments to their unique genetic background.³

The claimed method utilized both genotype and pedigree data in a previously known statistical tool to determine haplotype phase. Independent claim 1 is representative and recited:

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.⁴

The application’s specification explained how the claimed method improved over prior art methods by utilizing additional data, such as “linkage disequilibrium data” and “transition probability data,” which results in an increased number of possible haplotype phase predictions.⁵

The examiner rejected the claims under 35 U.S.C.S. § 101 as patent ineligible because they were directed to abstract mathematical calculations and statistical modeling.⁶ Stanford appealed the rejection of claims 1, 4-11, 14-25, and 27-30 to the PTAB.⁷

In considering the appeal, the PTAB applied the two-part test set forth in Alice Corp. Pty. Ltd. v. CLS Bank Int’l, 573 U.S. 208, (2014) for determining patent eligibility under §101.⁸ First, it considered whether the claims were directed to a patent-ineligible concept.⁹ Here, the Board concluded that the independent claim “recites steps for receiving and analyzing information, which humans could process in their minds, or by mathematical algorithms, which are mental processes within the abstract-idea category.”¹⁰ The Board noted that all eight steps of independent claim 1 were directed to “mental steps of receiving, storing, or providing information” or “mathematical concepts.”¹¹ Under step two of the Alice inquiry, the Board considered whether the claim’s elements, both individually and as whole, transformed the nature of the claims into patent-eligible subject matter.¹² Here, the Board reasoned that the claims contained no additional limitations that provided an inventive concept that transformed the abstract idea into patent eligible subject matter.¹³ The Board concluded 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.”¹⁴ The Board held that the same analysis it carried out with respect to claim 1 was applicable to claims 7, 8, 10, 11, 17, 18, 20, and 21.¹⁵

The Board addressed claims 9 and 19 separately, as these claims recited additional steps, including the step of providing a subsequent drug for treatment.¹⁶ But the Board found these claims also to be patent ineligible because they were not directed to any specific method of treatment, compounds, or doses, and did not identify a resulting outcome.¹⁷

On appeal, the Federal Circuit considered Standford’s argument that because claim 1 contained novel steps that allowed for more phase predictions than was possible under prior art methods, it could therefore not be directed to an “abstract idea.”¹⁸ The Federal Circuit found that this was immaterial to the § 101 analysis, as new or not, “[c]ourts have long held that mathematical algorithms for performing calculations, without more, are patent ineligible under § 101.”¹⁹ The Federal Circuit then found that there was no transformation into patent eligible subject matter, because claim 1 did not go past “storing the haplotype phase and ‘providing’ it ‘in response to a request’” and “neither requires, nor results in, a specialized computer or a computer with a specialized memory or processor.”²⁰

The Federal Circuit also rejected Stanford’s argument that the Board had erred by failing to consider the steps of claim 1 as a combination, stating that Stanford had failed to explain how the combination of elements would take the claim “beyond the abstract and into the practical.”²¹ The Federal Circuit noted that “[i]ndeed, it is hard to imagine a patent claim that recites hardware limitations in more generic terms than the terms employed by claim 1” and that the alleged “innovation therefore subsists in ‘the basic tools of scientific and technological work.’”²²

The Federal Circuit then found that the other independent claims, which recited generic computer hardware for performing the calculations of claim 1, also did not contain limitations that would transform them into patent eligible claims.²³ The dependent claims at issue also merely instructed that the claimed algorithm be applied, as prohibited under Alice.²⁴