Subject Matter Eligibility for Medical Diagnostic Claims – a Possible Path Forward?


On March 11, 2021, the Federal Circuit in In re PTAB of the Trustees of Leland Stanford Junior University issued a priority decision confirming a decision by the Patent Trial and Appeal Board (PTAB) denying the investigator’s claims related to the analysis genetic data to maintain heredity to determine heredity. The Federal Circuit found that the disputed claims were in fact directed to unpatented subject matter. This case highlights the difficulties in obtaining medical diagnostic claims, but also highlights that a potential way forward could have been with the disclosure of specific treatment regimens in the specification.

The application in question

Application series No. 13 / 445,925 – the ‘925 application for short – was directed to methods of haplotype phasing. Haplotype phasing is a process of determining which genetic alleles in a patient have been inherited from each parent.

Claim 1 of the ‘925 application reads as follows in the relevant part:

  1. A method for resolving the haplotype phase comprising:

Receiving allele data describing allelic information regarding genotypes for a family … and storing the allele data on a computer system comprising a processor and memory;

Receiving family tree data for the family … and storing the family tree data on a computer system including a processor and memory;

Determining an inheritance state for the allelic information … using a hidden Markov model with hidden states implemented on a computer system comprising a processor and memory;

wherein the hidden states include inheritance states, a compression-proof error state, and a[ Mendelian inheritance error]- Rich Fixed Error State,

where the inheritance says …;

Receiving transition probability data describing transition probabilities for inheritance states and storing the transition probability data on a computer system comprising a processor and memory;

Receiving population link imbalance data and storing the population imbalance data on a computer system including a processor and memory;

Determining a haplotype phase … using a computer system comprising a processor and memory;

Storing the haplotype phase … using a computer system comprising a processor and memory; and

Providing the stored haplotype … using a computer system comprising a processor and a memory.

Evaluation and decision of the PTAB

The ‘925 was rejected by the examiner under 35 USC §101 as being directed to unpatented subject matter. The PTAB used the two-step analysis developed by Alice Corp. Pty. Ltd., V. CLS Bank International, 573 US 208 (2014). In step one of the Alice investigation, the PTAB determined that the steps of representative claim 1 were directed to “mental steps of receiving, storing or providing information” or “mathematical concepts”. The PTAB expressly stated that the claims do not improve computer technology, but use off-the-shelf computer equipment to perform improved mathematical analysis.

In step two of the Alice investigation, the PTAB came to the conclusion that the claims did not constitute an inventive concept that converted the abstract idea into patentable subject matter. While the patent claims can make a valuable contribution to science, the PTAB is of the opinion that this is insufficient to go beyond patent-prohibited mental processes and mathematical operations. Even in claims 9 and 19, in which steps were listed that culminated in a final step of “providing the drug for treatment”, the PTAB stated that the claims “are not directed to a specific treatment method, do not identify certain patients Do not recite a certain compound, do not prescribe specific doses, and do not identify the resulting result. “The PTAB distinguished these claims from the patentable claims in Vanda Pharmaceuticals Inc. against West-Ward Pharmaceuticals International Ltd., 887 F.3d 1117 (Fed. Cir. 2018), which claims a“ specific treatment method for certain patients who use a specific compound in specific doses to get a specific result. “

Evaluation and decision of the Federal Circuit

The Federal Circuit came to the same results as the PTAB by also using the two-step Alice test.

With respect to step one, the ‘925 application disclosed that prior methods “may be able to provide long-range haplotype phasing for approximately 80% of the heterozygous positions, the method of the present invention providing accurate long-range phasing provides positions in 97.9% of all heterozygous positions. “The Federal Circuit stated,” Even if we accept the argument that the claimed process leads to improved data, we are not convinced that Claim 1 is not directed to an abstract mathematical calculation is. “

With respect to step two, the “written description makes it clear that the mathematical steps performed and the types of data received are as claimed to be conventional and well understood in the art.” The Court found that “a specific or other combination of mathematical steps yields a greater number of haplotype predictions than has been possible in the prior art, is not sufficient to convert Claim 1 into a patentable application.” Furthermore, the “alleged innovation achieved in claim 1 resides in the mathematical analysis itself”. The Court concluded that the remaining claims contained limitations on unspecific determinations of a “diagnosis”, a “drug treatment” and a “prognosis” based on the haplotype calculation.


This case suggests that the claims might have been considered patentable subject matter had the independent claims included restrictions on the specific diagnosis, drug treatment, and prognosis based on the data manipulation. The case demonstrates the need to include disclosure of specifics of treatment regimens, including therapeutics and dosages, which are supported by a variety of examples and literature citations describing such regimens.

While subject eligibility remains an area of ​​patent law that is constantly changing, the area may continue to change if the Supreme Court of American Axle & Mfg. Vs Neapco Holdings is considering a case where the Court has granted Certiorari and been asked to reconsider the standard for determining whether a claim is “directed” to an inoperable concept under Step 1 of the Alice Framework.