By Kevin E. Noonan —

A little more than one year after the Supreme Court issued its opinion on the patent-eligibility of (business) method claims in Bilski v. Kappos, the Court has granted certiorari in one case (Prometheus Laboratories, Inc.  v. Mayo Collaborative Services) and may consider two others (Classen Immunotherapies, Inc. v. Biogen Idec. and Association for Molecular Pathology v. U.S. Patent and Trademark Office) relating to diagnostic methods.  The Court handed down its decision in Bilski on the last day of the 2010 term (June 28, 2010), and shortly thereafter granted certiorari, vacated the Federal Circuit opinion, and remanded both the Prometheus and Classen cases.  The Federal Circuit decided the Prometheus case on remand on December 17, 2010, and on June 20, 2011, the Court again granted certiorari.  Since the question of patent eligibility is completely dependent on the scope and meaning of properly construed claims (see "Is Claim Construction the Key to Patent-eligibility of Isolated DNA?"), a comparison of the claims in Prometheus, Myriad, and Classen might shed some light on the reasoning used by the Federal Circuit in arriving at the answers to the patent-eligibility question posed in each of these cases.

Perhaps the most clear-cut decision by the Federal Circuit involves the method claims in the patents at issue in the Myriad case.  These claims all require the steps of "analyzing" or "comparing" a mutated BRCA gene sequence with the wildtype, "normal" sequence without any express claim language requiring that either sequence be determined as part of the claim:

U.S. Patent No. 5,709,999:

1.  A method for detecting a germline alteration in a BRCA1 gene, said alteration selected from the group consisting of the alterations set forth in Tables 12A, 14, 18 or 19 in a human which comprises analyzing a sequence of a BRCA1 gene or BRCA1 RNA from a human sample or analyzing a sequence of BRCA1 cDNA made from mRNA from said human sample with the proviso that said germline alteration is not a deletion of 4 nucleotides corresponding to base numbers 4184-4187 of SEQ ID NO:1.

U.S. Patent No. 5,710,001:

1.  A method for screening a tumor sample from a human subject for a somatic alteration in a BRCA1 gene in said tumor which comprises gene comparing a first sequence selected form the group consisting of a BRCA1 gene from said tumor sample, BRCA1 RNA from said tumor sample and BRCA1 cDNA made from mRNA from said tumor sample with a second sequence selected from the group consisting of BRCA1 gene from a nontumor sample of said subject, BRCA1 RNA from said nontumor sample and BRCA1 cDNA made from mRNA from said nontumor sample, wherein a difference in the sequence of the BRCA1 gene, BRCA1 RNA or BRCA1 cDNA from said tumor sample from the sequence of the BRCA1 gene, BRCA1 RNA or BRCA1 cDNA from said nontumor sample indicates a somatic alteration in the BRCA1 gene in said tumor sample.

U.S. Patent No. 5,753,441:

1.  A method for screening germline of a human subject for an alteration of a BRCA1 gene which comprises comparing germline sequence of a BRCA1 gene or BRCA1 RNA from a tissue sample from said subject or a sequence of BRCA1 cDNA made from mRNA from said sample with germline sequences of wild-type BRCA1 gene, wild-type BRCA1 RNA or wild-type BRCA1 cDNA, wherein a difference in the sequence of the BRCA1 gene, BRCA1 RNA or BRCA1 cDNA of the subject from wild-type indicates an alteration in the BRCA1 gene in said subject.

U.S. Patent No. 6,033,857:

1.  A method for identifying a mutant BRCA2 nucleotide sequence in a suspected mutant BRCA2 allele which comprises comparing the nucleotide sequence of the suspected mutant BRCA2 allele with the wild-type BRCA2 nucleotide sequence, wherein a difference between the suspected mutant and the wild-type sequences identifies a mutant BRCA2 nucleotide sequence.

2.  A method for diagnosing a predisposition for breast cancer in a human subject which comprises comparing the germline sequence of the BRCA2 gene or the sequence of its mRNA in a tissue sample from said subject with the germline sequence of the wild-type BRCA2 gene or the sequence of its mRNA, wherein an alteration in the germline sequence of the BRCA2 gene or the sequence of its mRNA of the subject indicates a predisposition to said cancer.

Significantly, other diagnostic method claims, including ones using antibodies to detect altered BRCA proteins, were not recited in the complaint and thus not at issue.  Also not recited in these claims were "additional, transformative steps," including "the steps of (1) extracting DNA from a human sample, and (2) sequencing the BRCA DNA molecule, . . . steps [that] necessarily precede the step of comparing nucleotide sequences."

The Federal Circuit panel unanimously agreed that these claims do not satisfy the "machine or transformation" (MOT) test under Bilski.  These claims "recite[] nothing more than the abstract mental steps necessary to compare two different nucleotide sequences:  look at the first position in a first sequence; determine the nucleotide sequence at that first position; look at the first position in a second sequence; determine the nucleotide sequence at that first position; determine if the nucleotide at the first position in the first sequence and the first position in the second sequence are the same or different, wherein the latter indicates an alternation; and repeat for the next position," according to Judge Lourie's majority opinion.  Also significant for the Court is that the specification required the term "sequence" to refer "more broadly to the linear sequence of nucleotide bases of a DNA molecule" per se.  The panel found that Myriad's method claims can be satisfied (i.e., infringed) by "mere inspection" alone, and thus encompass merely an abstract idea.

In contrast, on remand, the Federal Circuit found the claims in Prometheus to satisfy the MOT test and thus recite patent-eligible subject matter, whether the claim recites an affirmative administration step or not:

U.S. Patent No. 6,355,623:

1.  A method of optimizing therapeutic efficacy for treatment of an immune-mediated gastrointestinal disorder, comprising:
    (a)  administering a drug providing 6-thioguanine to a subject having said immune-mediated gastrointestinal disorder; and

    (b)  determining the level of 6-thioguanine in said subject having said immune-mediated gastrointestinal disorder,

    wherein the level of 6-thioguanine less than about 230 pmol per 8×10⁸ red blood cells indicates a need to increase the amount of said drug subsequently administered to said subject and

    wherein the level of 6-thioguanine greater than about 400 pmol per 8×10⁸ red blood cells indicates a need to decrease the amount of said drug subsequently administered to said subject.

46.  A method of optimizing therapeutic efficacy and reducing toxicity associated with treatment of an immune-mediated gastrointestinal disorder, comprising:
    (a)  determining the level of 6-thioguanine or 6-methylmercaptopurine in a subject administered a drug selected from the group consisting of 6-mercaptopurine, azathiop[u]rine, 6-thioguanine, and 6-methyl-mercaptoriboside, said subject having said immune-mediated gastrointestinal disorder,

    wherein the level of 6-thioguanine less than about 230 pmol per 8×10⁸ red blood cells indicates a need to increase the[] amount of said drug subsequently administered to said subject, and

    wherein the level of 6-thioguanine greater than about 400 pmol per 8×10⁸ red blood cells or a level of 6-methylmercaptopurine greater than about 7000 pmol per 8×10⁸ red blood cells indicates a need to decrease the amount of said drug subsequently administered to said subject.

The distinction between the claims in Myriad and claim 1 of the '623 patent can be appreciated in light of the difference in what is being detected in each claim:  a naturally occurring nucleic acid in the Myriad claims and an administered drug or its metabolite in Prometheus.  Insofar as patent eligibility for method claims must either satisfy the Bilski machine or transformation test or otherwise not be so abstract as to entirely preempt an abstract idea, law of nature, or natural phenomenon, the absence of the drug or its metabolite without administration of the drug would appear to provide the Federal Circuit with its rationale regarding the patent eligibility of claim 1 of the '623 patent.  Claim 46 of the '623 patent does not have an affirmatively recited administration step.  However, the "detecting" step recites that 6-thiopurine or one of its metabolites is performed on "a subject administered [one of the recited] drug[s]," again encompassing only those patients who have been transformed by drug administration.  It would seem that the Court refused to exalt form over substance in making a distinction between claims that recite administration of the drug to a subject and claims that are restricted to detecting a drug or its metabolites only in that subset of subjects to whom the drug has been administered; in either case, the Federal Circuit discerned a transformation.  Neither of these considerations are likely to be before the Supreme Court, however, since defendant's certiorari petition focused on the purported interference with the practice of medicine and the non-inventiveness of the portions of the claim that recited the transformation step.  In this regard it should be remembered that the case that raised this aspect of medical diagnostic method claims, Laboratory Corp. v. Metabolite Labs., Inc. (LabCorp), was like Myriad, directed at detecting a naturally occurring metabolite, homocysteine, and not an administered drug as in the Prometheus claims.

The most surprising Federal Circuit decision relating to diagnostic method claims is the most recent, in the Classen case.  There, a divided panel (Judge Newman joined by Chief Judge Rader, with Judge Moore dissenting) found a distinction between the claims of U.S. Patent No. 5,723,283:

A method of determining whether an immunization schedule affects the incidence or severity of a chronic immune-mediated disorder in a treatment group of mammals, relative to a control group of mammals, which comprises immunizing mammals in the treatment group of mammals with one or more doses of one or more immunogens, according to said immunization schedule, and comparing the incidence, prevalence, frequency or severity of said chronic immune-mediated disorder or the level of a marker of such a disorder, in the treatment group, with that in the control group.

Which the majority found not to be patent-eligible, with the claims of U.S. Patent Nos. 6,420,139 and 6,638,739 (claim 1 of the '739 patent being representative):

1.  A method of immunizing a mammalian subject which comprises:
    (i)  screening a plurality of immunization schedules, by
        (a)  identifying a first group of mammals and at least a second group of mammals, said mammals being of the same species, the first group of mammals having been immunized with one or more doses of one or more infectious disease-causing organism-associated immunogens according to a first screened immunization schedule, and the second group of mammals having been immunized with one or more doses of one or more infectious disease-causing organism-associated immunogens according to a second screened immunization schedule, each group of mammals having been immunized according to a different immunization schedule, and

        (b)  comparing the effectiveness of said first and second screened immunization schedules in protecting against or inducing a chronic immune-mediated disorder in said first and second groups, as a result of which one of said screened immunization schedules may be identified as a lower risk screened immunization schedule and the other of said screened schedules as a higher risk screened immunization schedule with regard to the risk of developing said chronic immune mediated disorder(s),

    (ii)  immunizing said subject according to a subject immunization schedule, according to which at least one of said infectious disease-causing organism-associated immunogens of said lower risk schedule is administered in accordance with said lower risk screened immunization schedule, which administration is associated with a lower risk of development of said chronic immune-mediated disorder(s) than when said immunogen was administered according to said higher risk screened immunization schedule.

Which the panel found were patent-eligible.  Judge Moore, on the other hand, found no difference.  The difference appears to be in whether the determination of an appropriate immunization schedule directs an affirmative (and transformative) step or steps.  In the '283 claim, the majority construed the scope of the claim to encompass mere comparison of the results of immunization schedules that produce a conclusion (i.e., information) without any further steps in the claimed method.  The claims in the '739 patent, in contrast, require that an appropriate immunization schedule be determined, and then that a mammal or mammals be immunized according to that schedule to achieve the beneficial result of immunization with the least "incidence, prevalence, frequency or severity" of deleterious side effects.

Seen in this light, the question can be framed (according to Supreme Court precedent) as whether immunizing according to different immunization schedules in the '283 patent is considered "mere data gathering" activity and could be performed by evaluating previously performed immunizations, and whether the immunization step recited in the '739 patent can be considered to be "insignificant post-solution activity."  It is evident that the first proposition is better supported that the second; as in the Myriad claims, the structure of the '283 patent claim encompasses activity (immunization according to a plurality of immunization schedules) not performed in the practice of the claimed method (as opposed to the comparison, in this view the only active step in the claim).  The immunization step in the '739 patent claim is harder to construe as "insignificant post-solution activity" since the claim is directed towards "a method for immunizing a mammalian subject."

This analysis may seem like an exercise in counting dancing angels on the head of a pin, but it is the path set out by the Supreme Court in Benson v. Gottschalk, Parker v. Flook, Diamond v. Diehr, and Bilski v. Kappos (and for some members of the Court and commentators, LabCorp).  While Judge Moore recites a common-sense conclusion that the scope of the '283 and '739 claims should not logically be different, they must be when considered under the relevant Supreme Court rubrics, which give significance (no matter how undeserved) to these distinctions.  That is not to say that reciting the immunization step should be enough to render the '739 patent claims patent eligible, but like drug administration in Prometheus, immunization is transformative (as Judge Moore recognized by expressly equating immunization with drug administration).

Perhaps another way of performing the analysis is to recognize that another salient difference between the Myriad claims and the '283 claim in Classen on the one hand, and the Prometheus claims and the '739 patent claims in Classen, on the other, is that the former claims involve producing intangible information, while the latter use the information to direct the claim practitioner to perform a tangible, transformative step.  Claims that produce information may not be patent-ineligible per se (see "Patenting Information"); however, as in Bilski (and Benson and Flook) they are more likely to raise patent eligibility concerns.  Indeed these considerations arose in the concurring Justices' opinion in Bilski:

For even when patents encourage innovation and disclosure, "too much patent protection can impede rather than 'promote the Progress of . . . useful Arts.'" Laboratory Corp. of America Holdings v. Metabolite Laboratories, Inc., 548 U. S. 124, 126–127 (2006) (BREYER, J., dissenting from dismissal of certiorari).  . . .  Patents "can discourage research by impeding the free exchange of information," for example, by forcing people to "avoid the use of potentially patented ideas, by leading them to conduct costly and time-consuming searches of existing or pending patents, by requiring complex licensing arrangements, and by raising the costs of using the patented" methods.  Id., at 127.

While the Supreme Court gave the Federal Circuit precious little time or opportunity to flesh out its patent eligibility jurisprudence after the Bilski v. Kappos decision by granting certiorari in Prometheus, the Supreme Court's Bilski decision provided no clear instruction for resolving the different results in the Prometheus and Classen cases.  Thus, its guidance may be necessary (provided that such guidance is more "pellucid" than the Court's opinion in Bilski).

For biotechnology, it remains the case that including active, technology-dependent steps in method claims is prudent, and to draft claims that minimize the likelihood that the invention will be characterized as merely an "abstract idea."