In re Bd. of Trs. of the Leland Stanford Junior Univ.

In re Bd. of Trs. of the Leland Stanford Junior Univ.

Opinion

 [*1246]  Reyna, Circuit Judge.

The Board of Trustees of the Leland Stanford Junior University appeals the final rejection of patent claims in its patent application. The patent examiner reviewing the application rejected the claims on the grounds that they involve patent ineligible subject matter. On review, the Patent Trial and Appeal Board affirmed the examiner's final rejection of the claims. As discussed below, the rejected claims are drawn to abstract mathematical calculations and statistical modeling, and similar subject matter that is not patent eligible. Accordingly, we affirm the decision of the Patent Trial and Appeal Board.

Background

The Board of Trustees of the Leland Stanford Junior [**2]  University ("Stanford") filed its Application No. 13/486,982 ("'982 application") on June 1, 2012. J.A. 39.¹  [*1247]  The '982 application is directed to computerized statistical methods for determining haplotype phase. A haplotype phase acts as an indication of the parent from whom a gene has been inherited. Haplotype phasing is a process for determining the parent from whom alleles—i.e., versions of a gene—are inherited.

The written description of the '982 application explains that accurately estimating haplotype phase based on genotype data obtained through sequencing an individual's genome "plays pivotal roles in population and medical genetic studies." J.A. 85. The '982 application is directed to methods for inferring haplotype phase in a collection of unrelated individuals. J.A. 65-69. According to the written description, although high-throughput DNA sequencing methods provide genotype data for individuals, those methods do not provide haplotype information. J.A. 65-66. Though difficult, it is possible to infer haplotype phase, even without information about relatives, using statistics-based algorithms. J.A. 66. Prior [**3]  art methods for performing this analysis include PHASE, fastPHASE, and Beagle. J.A. 67-68, 81-82. These methods involve using, among other things, a hidden Markov model ("HMM"), which is a statistical tool used in various applications to make probabilistic determinations of latent variables. See, e.g., J.A. 73, 82.

The written description of the '982 application discloses an embodiment in which a statistical model called PHASEEM is used to predict haplotype phase. PHASE-EM is allegedly a modified version of the preexisting PHASE model and operates more efficiently and accurately than the PHASE model. J.A. 68. Like prior art statistical models, including the fastPHASE model, PHASE-EM uses "a parameterization [expectation maximization] algorithm" in predicting haplotype phase. J.A. 68-69. PHASE-EM "perform[s] optimization on haplotypes rather than MCMC [Markov chain Monte Carlo] sampling," which is used in PHASE. J.A. 68-69. According to the written description, the computational intensiveness of MCMC sampling makes it difficult to use PHASE to analyze large datasets like those generated in genome-wide association studies. J.A. 68.

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