Last week, Dennis Crouch highlighted recent decisions from the Patent Office Board of Appeals and Interferences that evaluated the patent-eligibility of claims under 35 USC § 101. One case with relevance to biotech and pharmaceutical applicants upheld the § 101 rejection of IBM claims directed to methods for clustering genes having potential functional similarity by comparing gene expression profiles based on both the time and intensity of gene expression. In that case, In re Kelkar, the Board found that the claims failed the “machine or transformation test” (MOT) and were directed to an abstract idea, despite language that invoked the use of a computer.

The Claims At Issue

The Board chose claim 1 as being representative of the claims on appeal:

1. A method for determining similarity between portions of gene expression profiles in a computer comprising the steps of:
processing a number of gene expression profiles with a similar sequences algorithm that is a time and intensity invariant correlation function to obtain a data set of gene expression profile pairs and a match fraction for each gene expression profile pair;
listing gene expression profile pairs in clusters by their match fractions;
removing a first gene expression profile from a cluster when another cluster has another gene expression profile with a higher match fraction with the first gene expression profile, unless the another gene expression profile requires a larger number of subsequences to achieve similarity with the first gene expression profile;
repeating the removing step until all gene expression profiles are listed in only one cluster;
providing output of the listing of clusters of gene expression profiles.

According to the specification, the invention is useful “for discovering functional similarity between portions of gene expression profiles, to cluster all similar genes without a linear search of the genome, thereby characterizing similarity between genes in one or more phases of a cell cycle.”

The § 101 Rejection

The Examiner applied the following tests to assess patent-eligibility under § 101:

  1. Did the invention “transform” an article or physical object to a different state or thing?
    The Examiner found that it did not.
  2. Did the invention otherwise produce “a useful, concrete, and tangible result”?
    The Examiner found that it did not because, for example, it did not include any “output to a user . . . that results in a tangible result.”

The Examiner emphasized that the claimed invention does not “provide for the practical application of results in a concrete, tangible, and useful form, as in a means for output to a user.”

The Appellant’s Arguments

The Appellant argued that the Examiner had incorrectly applied the “useful, concrete, and tangible result” language of the Examination Guidelines in effect at the time by treating it as a three-pronged test that required satisfaction of each prong in order to avoid a § 101 rejection. The Appellant argued that the phrase was intended to screen out inventions that were abstract ideas, laws of nature and natural phenomenon.

The claimed invention passed that test, the Appellant argued because:

Applicants’ process does not convert or process just any data but is limited to useful concrete and non-abstract gene expression profiles in a data base of such profiles. Applicants’ process is but one application of many possible applications of the mathematical steps involved in obtaining the useful result.

The Board Decision

The Board first applied the MOT and found that

  • The claimed invention does not satisfy the “machine” prong because it is “not limited to a particular machine” but “[a]t best” includes a “field-of-use limitation that is insufficient to render the otherwise ineligible process of claim 1 patent-eligible.”
  • The claimed invention does not satisfy the “transformation” prong because it merely “compares a number of gene expression profiles, lists gene expression profiles in clusters, and provides an output of the listing.” Thus, the claimed method “does not transform a particular article into a different state or thing.”

The Board then considered whether the invention was patent-ineligible under § 101 as being directed to an abstract idea. The Board characterized the claimed method as one that “applies the mathematical manipulation of data to determine the similarity between portions of gene expression profiles.” The Board determined that, like the invention at issue in the 1978 Supreme Court Parker v. Flook case, the invention here “is directed to an abstract idea—the mathematical algorithm—as applied to a defined type of data.” The Board cited Flook for the proposition that “attempting to limit the use of [a] formula to a particular technological environment” does not avoid the prohibition against patenting abstract ideas.

Parker v. Flook

As characterized by the Supreme Court, the invention at issue in Parker v. Flook “describes a method of updating alarm limits” in the context of “any process variable involved in a process comprising the catalytic chemical conversion of hydrocarbons.” As summarized in the decision, claim 1 recited:

A method for updating the value of at least one alarm limit on at least one process variable involved in a process comprising the catalytic chemical conversion of hydrocarbons wherein said alarm limit has a current value of Bo + K, wherein Bo is the current alarm base and K is a predetermined alarm offset which comprises:
(1) determining the present value of said process variable, said present value being defined as PVL;
(2) determining a new alarm base B1, using the following equation:
B1 = Bo(1.0-F) + PVL(F)
where F is a predetermined number greater than zero and less than 1.0;
(3) determining an updated alarm limit which is defined as B1 + K; and thereafter
(4) adjusting said alarm limit to said updated alarm limit value.

According to the Court, “The only difference between the conventional methods of changing alarm limits and that described in respondent’s application rests in the second step-the mathematical algorithm or formula.”

The Court recognized that the claims would not “‘wholly preempt the mathematical formula,’ since there are uses of [the] formula outside the petrochemical and oil-refining industries that remain in the public domain,” but still found that the claims were not patent-eligible because the invention was, at its core, directed to an algorithm. The Court rejected the Applicant’s argument that the “‘post-solution’ activity—the adjustment of the alarm limit to the figure computed according to the formula. . . makes his process patentable.”

The Court stated:

The notion that post-solution activity, no matter how conventional or obvious in itself, can transform an unpatentable principle into a patentable process exalts form over substance. A competent draftsman could attach some form of post-solution activity to almost any mathematical formula; the Pythagorean theorem would not have been patentable, or partially patentable, because a patent application contained a final step indicating that the formula, when solved, could be usefully applied to existing surveying techniques.

The Future for Data Mining Patents?

IBM cited two granted patents in support of its position that its “data mining” claims should be patent-eligible under under § 101. The Board dismissed this line of argumentation, stating that “[e]ach case must be decided on its own merits.” Moreover, the cited patents can be distinguished on other grounds.

U.S. Patent 6,406,853 is directed to “[a] method of identifying an intervention that mimics the effects of caloric restriction in cells” and includes a step of “exposing [a] biological sample to an intervention.”  This may constitute a “transformation” that would satisfy the MOT test.

On its face, the claims of U.S. Patent 6,436,642 appear to be more similar to the IBM claims:

1. A method of categorizing a thyroid carcinoma in a subject, the method comprising:
a) providing a test cell population from said subject, wherein at least one cell in said test cell population expresses the nucleic acid sequence MTC: 33;
b) measuring the expression of MTC:33 in said test cell population;
c) comparing the expression of MTC:33 to the expression of MTC:33 in a reference cell population comprising at least one cell whose thyroid carcinoma stage is known; and
d) identifying a difference in expression levels of MTC33, if present, in the test cell population and reference cell population, thereby categorizing said thyroid carcinoma in said subject

But, the “measuring” step involves a physical transformation of the test cell sample. Thus, these claims could pass muster under § 101 following an analysis similar to that applied by the Federal Circuit in Prometheus v. Mayo, which is on remand in the wake of Bilksi.

Both of these patents illustrate the potential value of drafting claims that satisfy the MOT test, even if the Supreme Court rejected the MOT test as a bright-line rule for applying § 101. Such an approach also is consistent with the USPTO’s “Interim Guidance for Determining Subject Matter Eligibility for Process Claims in View of Bilski v. Kappos,” which I previously discussed in the context of Prometheus.

Because the IBM decision is a Board decision that has not been reviewed—let alone affirmed—by the Federal Circuit, and because this area of U.S. patent law is evolving so quickly. I am hesitant to draw “lessons” from the outcome.  Still, it provides useful insight into how the USPTO is evaluating claims for compliance with § 101 until the Federal Circuit provides us all with more guidance.