PTAB Finds Method Involving "Growing, Selecting, and Crossing" Sufficient for Integrating Genome Estimation Data Set Into Practical Application

September 17, 2024

f. selecting breeding individuals based on the genomic estimated breeding values; and

g. crossing said selected breeding individuals to create an improved population of breeding individuals.

The Examiner rejected Claims 1, 3-8, and 15 under 35 U.S.C. § 101 as not amounting to significantly more than the abstract idea of “selecting individuals in a breeding program.” The Examiner noted that the claims included several mathematical equations and characterized the phenotyping and genotyping steps as insignificant extra-solution activity[2]. The Examiner ultimately concluded that the “claims do not describe any specific practical steps by which the crossing is performed, nor do they provide any details any specific apparatuses used to perform the cross. This claim element amounts to nothing more than an instruction to apply the abstract idea in an unspecified manner, which does not integrate the abstract idea into the practical application.”

Relying on the 2019 Revised Guidance, the PTAB conducted a full Alice/Mayo Analysis. At Step 1, the PTAB had no problem classifying Claim 1 as a “method” and therefore falling into the eligible “process” category. At Step 2A, Prong 1, the PTAB quickly reasoned that the claim recited the judicial exception of a mathematical concept. At Step 2A, Prong 2, the PTAB tackled the major issue of whether the claim as a whole integrates the recited judicial exception into a practical application of the exception.

The Applicants argued step b of Claim 1 integrates the alleged judicial exception into a practical application, stating “[s]tep b applies the exception in that one or more training candidates from the optimized estimation data set constructed in step a are grown so that the created tangible population has increased GEBV accuracy for future selection candidates.” The Applicants also argued that the claims represented an improvement on conventional breeding processes by creating “an improved population of breeding individuals (see step g) by selecting breeding individuals based on their GEBV, which has increased accuracy due to the constructed optimized estimation data set of step a, and crossing the selected breeding individuals to create a tangible improved population of breeding individuals.” Critically, the Applicants were able to point to the original specification to support this line of reasoning. The specification stated that “[g]enomic prediction greatly facilitates breeding programs, as simulations and empirical studies have shown its advantages over marker-assisted selection and traditional phenotypic selection” and described conventional methods as being disadvantageous for requiring an extra step of “deciding which of the genotyped inbreds are declared either selection candidates or candidates for training.” In contrast, the method of this application improved on the process because “[u]sing linkage disequilibrium means that the future selection candidates coming from populations in the prediction target do not need to be genotyped for this optimization approach.”

The PTAB noted this case was “very close” on “whether growing, selecting, and crossing . . . integrate the optimized estimation data set judicial exception recited in step a into practical application.” Its analysis distinguished In re Bd. of Trs. of Leland Stanford Junior Univ., 989 F.3d 1367, 1370 (Fed. Cir. 2021) (“Stanford”) and Athena Diagnostics, Inc. v. Mayo Collaborative  Servs., LLC, 915 F.3d 743 (Fed. Cir. 2019) (“Athena”) from the classic of § 101 practical application integration: Diamond v. Diehr, 450 U.S. 175 (1981) (“Diehr”).

The claims in Stanford were drawn to “a mathematical method of resolving haplotypes using linkage disequilibrium data, after which the information was stored in a database for display.” The PTAB reasoned, quoting from Stanford, that “[s]imply storing information and providing it upon request does not alone transform the abstract idea into patent eligible subject matter” Stanford, 989 F.3d at 1374. Similarly, the claims in Athena “disclosed identifying disorders related to a particular type of autoantibody by measuring the presence of the autoantibody” and the PTAB reasoned that “[c]laiming a natural cause of an ailment and well-known means of observing it is not eligible for patent because such a claim in effect only encompasses the natural law itself.” Athena, 915 F.3d at 752–753. The PTAB referred to these as “information type claims” with no practical application integration.

In contrast, Diehr was directed to “an improved process for molding rubber articles by solving a practical problem which had risen in the molding of rubber products.” Diehr, 450 U.S. at 180. In Diehr, the claims recited a mathematical equation but were held to be using the mathematical equation in a practical application. Similarly, the claims in the Application included a mathematical equation, but that equation was found to be sufficiently integrated into a method of breeding that included “a step b of growing individuals”, subjecting the individuals to “phenotyping and genotyping steps to use in the mathematical formula to allow selection of particular individuals for further breeding” and finally “a step g to actually breed those individuals to create an improved population.”

Ultimately, the PTAB agreed that the claims were directed to a practical application that “improves a plant or animal population by selecting optimal individuals for breeding the desired phenotypic traits.” The PTAB also noted that “claim 1 does not preclude breeding and crossing generally, but applies a specific approach that was not shown to be anticipated or obvious over the prior art.”

This case represents two pieces of practical advice for practitioners.

First, it is critical to recite sufficiently detailed action steps in the method that can serve as a basis for integrating an abstract idea into a practical application. Some applicants, particularly with applications originating in other jurisdictions, may be wary of including such steps in method claims. Under U.S. practice, however, a step as seemingly expected as “actually breeding the individuals” can be the make-or-break for a rejection under § 101. While it may not be necessary to include them in the claims in all jurisdictions, these steps should always be included in the specification to provide support for U.S. prosecution. Applicants should also be assured that such claims are unlikely to open the door for additional rejections under §§ 102 and 103 and provide robust protection against a broad range of possibly infringing activity. Because the claims are very likely ineligible without such practical application steps, their inclusion does not leave necessarily leave the field to competitors’ applications that may omit such steps.

Second, this case highlights the advantage of a more contemporary approach to drafting that describes how the subject matter of the application contributes to the field as a whole. Telling the “story” of the invention, such as the specific issues in the current art, differences from conventional approaches, and the distinct advantages the present application covers, can give Examiners, the PTAB, and courts critical context that tips the scales in favor of finding an integration into a practical application. The outcome in this “very close” case seems to be linked with the specification providing an explanation of the issues with the field as well as the benefits of the genomic prediction solution offered by the application. While some practitioners are hesitant to characterize the state of the art at the time of the application, including certain details in the specification can provide very convincing support for arguments against both subject matter ineligibility and obviousness.