In an appeal from a final rejection of a pending application, the US Court of Appeals for the Federal Circuit held that claims directed to methods for determining “haplotype phase” were correctly rejected under 35 USC § 101 as subject matter ineligible. In Re Board of Trustees of The Leland Stanford Junior University, Case No. 20-1012 (Fed. Cir. Mar. 11, 2021) (Reyna, J.)

Haplotype phase is a scientific way of describing the methodology of determining from which parent a particular allele (or gene) is inherited. The representative claim involved (i) receiving allele data, (ii) receiving pedigree data, (iii) determining an inheritance state based on the allele data, (iv) receiving transition probability data; (v) receiving linkage disequilibrium data and then- determining a haplotype phase based on the pedigree data, the inheritance state for the information described in the allele data, the transition probability data and the population linkage disequilibrium data; and storing the haplotype phase in a computer system and providing the stored haplotype phase in response to a request.

Steps (i) through (iii) were known in the art for determining haplotype phase. The crux of the improved process depended on steps (iv) and (v). The additional data provided as “linkage disequilibrium data” and “transition probability data” allegedly enable haplotype phase to be inferred in regions of the gene where “inheritance state” may be uninformative. The additional data in the claimed method resulted in an increase in the number of haplotype phase predictions made.

The examiner, and then the Patent Trial & Appeal Board, found that the claimed process was directed toward patent eligible subject matter—a mathematical algorithm. Stanford appealed.

Applying the two-step framework established by the 2014 Supreme Court decision in Alice Corp. v. CLS Bank, the Federal Circuit first determined that the claims were directed to an abstract mathematical calculation under Alice step one.

Under step two of the Alice inquiry, the Federal Circuit found that the claims did not include additional limitations that, taken as a whole, provide an inventive concept that transforms the abstract idea into patent eligible subject matter. The Court reasoned that the representative claim “recites no steps that practically apply the claimed mathematical algorithm; instead [the claim] ends at storing the haplotype phase and ‘providing’ it ‘in response to a request.'” These steps alone were not enough to transform the abstract idea into patent eligible subject matter.

Stanford argued that the claimed process was directed to patent eligible subject matter and represented an improvement on a technological process—namely, an improvement in the number of haplotype phase predictions that this mathematical algorithm could yield. The Federal Circuit was unpersuaded that the pending claims did anything other than “merely enhance[] an ineligible concept.”

The Federal Circuit concluded that the claims only recited the conventional haplotype phase algorithm and then instruct: “apply it,” similar to the claimed subject matter prohibited by the Supreme Court in Alice. Accordingly, the Court affirmed the Board’s decision.