District Court Rules That Genes and Genetic Tests Are Not Patentable

30 March 2010 Publication
Author(s): Courtenay C. Brinckerhoff Antoinette F. Konski Stephen B. Maebius

Legal News Alert: Life Sciences

On March 29, 2010, the U.S. District Court for the Southern District of New York issued its decision in Association for Molecular Pathology v. U.S. Patent & Trademark Office, No. 09-Civ-4515. The District Court’s decision on cross-motions for summary judgment invalidated all raised claims in Myriad’s seven patents at issue. If the District Court’s judgment is sustained on appeal, this decision will have a profound effect on the intellectual property assets and strategies used by a wide range of biotechnology and pharmaceutical companies.

In this case, a coalition of plaintiffs, led by the ACLU, sought a precedential court decision that claims in patents assigned to Myriad Genetics are invalid. The plaintiffs include women who cannot afford Myriad’s tests, researchers who want to perform the patented tests in their laboratories, and associations representing professionals who perform and interpret these tests. Plaintiffs advanced two theories in support of its motion. First, plaintiffs argued that the patents are invalid because they claim subject matter that is not patentable under 35 U.S.C. § 101. Second, plaintiffs argued that the Patent & Trademark Office (“PTO”) had exceeded its constitutional authority in granting the patents.

Defendant Myriad is the owner or exclusive licensee of a series of patents claiming isolated genes and methods for testing for the presence of mutations in the BRCA1 and BRCA2 genes. Mutations in these genes are linked to increased likelihood of breast and ovarian cancers. Myriad offers several different tests for the presence of these mutations and has asserted the patents to preclude competitors.

The claims in Myriad's patents can be divided into two categories: (1) claims to compositions of matter consisting of isolated DNA encoding all or part of the BRCA1 or BRCA2 genes (which are associated with breast cancer), and (2) claims to methods of using the isolated genes to detect the mutations in BRCA1 and BRCA2 by analysis of the gene sequences or by comparison of the sequence of the patient’s gene with the sequence of a normally occurring gene. The District Court found that both categories of claims are invalid because they are directed to non-statutory subject matter.

Claims Directed to Isolated Genes
The District Court determined that the claims to the isolated genes are not patentable because the claims encompass products of nature, which are not patentable under 35 U.S.C. § 101. Claim 1 of U.S. Pat. No. 5,747,282 is representative of this category of claims:

An isolated DNA coding for a BRCA1 polypeptide, said polypeptide having the amino acid sequence set forth in SEQ ID NO:2.

In the course of determining that composition of matter claims to isolated DNA are invalid, the District Court had to resolve several questions: (1) Whether the Court could appropriately address the issues presented in the case; (2) How to interpret the statutory language in 35 U.S.C. § 101 that defines patentable subject matter; and (3)  Whether the claims directed to isolated genes fall within this definition of patentable subject matter.

First, the District Court determined that it could decide the issues presented because it should not defer to the PTO’s long-standing interpretation of the patent statute. The PTO has granted many patents with claims directed to isolated DNA sequences. Myriad argued that this demonstrated that the PTO had interpreted the patent statute as encompassing such claims within the category of patentable subject matter, and that the District Court should defer to this interpretation. The District Court rejected these arguments, noting that the Federal Circuit does not defer to the PTO’s legal determinations. Furthermore, the District Court noted that plaintiffs’ argument that these types of claims are not patentable subject matter had not been raised before.

Second, the District Court undertook a lengthy survey of the cases that interpreted 35 U.S.C. § 101. While the Court acknowledged that previous cases had stated that the scope of patentable subject matter is very broad, it noted that several cases had established that a naturally occurring substance was not patentable subject matter. Placing particular reliance on three Supreme Court decisions, American Fruit Growers, Inc. v. Brogdex Co., 283 U.S. 1 (1931); Funk Bros. Seed Co. v. Kalo Inoculant Co., 333 U.S. 127 (1948); and Diamond v. Chakrabarty, 447 U.S. 303 (1980), the District Court held that “the purification of a product of nature, without more, cannot transform it into patentable subject matter. Rather, the purified product must possess ‘markedly different characteristics’ in order to satisfy the requirements of § 101” (emphasis supplied).

Third, the District Court determined that the isolated DNA that was the subject of Myriad’s claims was not “markedly different” from the native DNA. In concluding that the isolated DNA could not meet its test for patentable subject matter, the District Court focused not on the chemical structure or nature of the DNA molecule. Rather, the Court emphasized the role of the DNA as an information carrier, and noted that the native DNA and the claimed isolated DNA convey the same genetic information. “The preservation of this defining characteristic of DNA in its native and isolated forms mandates the conclusion that the challenged composition claims are directed to unpatentable products of nature.”

Claims Directed to Methods for Detection or Use of Mutant Genes
The Court also held five claims directed to methods for using the claimed DNA sequences invalid for failure to define patent-eligible subject matter. Claim 1 of U.S. patent 5,709,999 (“the ’999 patent”) is representative of the group of method claims considered by the Court:

A method for detecting a germline alteration in a BRCA1 gene, said alteration selected from a 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.

Common among the challenged method claims is the step of “comparing” an individual’s BRCA DNA sequence with the known wild-type gene sequences, or alternatively, a step of “analyzing” the two sequences.

The Court began its analysis by noting that “[p]henomena of nature, though just discovered, mental processes, and abstract intellectual concepts are not patentable, as they are the basic tools of scientific and technological work.” Gottschalk v. Benson, 409 U.S. 63, 67 (1972). The Court determined that the method claims are the basic tools of scientific and technological work as they failed the Federal Circuit’s “machine or transformation” test, elucidated in In re Bilski, 545 F.3d 943 (Fed. Cir. 2008), cert. granted, 129 S. Ct. 2735 (2009).

Under the “machine or transformation” test, a process or method is patent eligible if it is tied to a particular machine or apparatus or, alternatively, if it transforms a particular article or thing. Additionally, the use of the machine or apparatus must impose a significant limitation on the claim’s scope and the involvement of the machine or transformation in the claimed process must not merely be insignificant extra-solution activity.

The Court determined that the only meaningful limitations of the claims are the steps of analyzing or comparing the individual’s gene sequences to the wild-type gene sequences. The Court dismissed Myriad’s argument that the claims incorporate a “transformation” step similar to the claims held patent-eligible by the Federal Circuit in Prometheus Laboratories., Inc. v. Mayo Collective Services, 581 F.3d 1336 (Fed. Cir. 2009). In Prometheus, the claims under consideration were directed to methods for calibrating the proper dosage of thiopurine drugs by measuring metabolites in individuals having gastrointestinal disorders. The Federal Circuit determined that these claims are patent-eligible as the methods transformed the individual when a drug is administered to the individual or when it is metabolized by the individual in vivo. The Court also stated that the claimed step of “determining the level of the metabolite” satisfies the “machine or transformation” test because this step necessarily involves a transformation because those levels cannot be determined by mere inspection.

Myriad argued that the “analyzing” and “comparing” steps of its claims should be interpreted to be transformative in accordance with Prometheus, as each requires the isolation and analysis of a biological sample. The Court rejected this argument, strictly construing the claims as being directed only to comparing and analyzing DNA sequences, not DNA molecules, which are abstract mental processes. Moreover, the Court stated that even if the method claims were read to include the transformation associated with isolating and sequencing human DNA, these steps would be no more than “data-gathering steps” that are not “central to the purpose of the claimed process” and so cannot confer patent eligibility under 35 U.S.C. § 101.

The Court concluded that the method claims are closely analogous to those considered by the Federal Circuit in In re Grams, 888 F.2d 835 (Fed. Cir. 1989), where the Court held claims to diagnosing an abnormal condition in an individual to be unpatentable under 35 U.S.C. § 101. The methods claimed in Grams were determined to consist only of two steps: (1) performing clinical laboratory tests on an individual to obtain data for the parameters, and (2) analyzing that data to ascertain the existence and identity of an abnormality.

The Court also held unpatentable claim 20 of U.S. Patent No. 5,747,282, which is directed to a method screening for potential cancer therapeutics by growing transformed eukaryotic host cells containing an altered BRCA1 gene in the presence and absence of a potential cancer therapeutic and comparing the growth rates of the cells. The Court determined that although the claim arguably satisfies the “transformation” element of the Bilski test, the essence of the claim when considered in its entirety is comparing the growth rate of the cells. Thus, the Court reasoned, the “process” is in fact, the scientific method itself.

The PTO’s Constitutional Authority
As noted above, plaintiffs also argued that the PTO had exceeded its constitutional authority by granting the patents in question. Because the District Court invalidated the claims as being directed to non-statutory subject matter under 35 U.S.C. § 101, it declined to reach this question.

It is almost inevitable that Myriad and other defendants will appeal the District Court’s holdings to the Federal Circuit. Furthermore, no matter what the outcome of that appeal, the losing party is likely to seek Supreme Court review. The initial appeal process at the Federal Circuit alone is likely to take an additional 18 months to two years, with even more time potentially needed at the Supreme Court. If the District Court’s holding is ultimately affirmed by either Court, the scope of subject matter that can be patented in the United States will be considerably narrowed, and many existing patents will become vulnerable to challenge.

Many in the biotechnology, diagnostic, and personalized medicine industries may be anxious for a prompt reversal of what they may view as a controversial and damaging decision by the District Court. The District Court's finding that isolated DNA composition claims are unpatentable under 35 U.S.C. § 101 is the first decision of its kind on this issue. Moreover, the District Court's finding that certain diagnostic method claims are unpatentable steps into a hornet’s nest of current controversy that may or may not be addressed by the Supreme Court in Bilski or Prometheus. Because of the complexity of these issues, it may take some time for the Federal Circuit and/or Supreme Court to render their decisions. Until these matters are resolved, the District Court decision may influence pending patent cases or encourage new challenges to gene patents and patented genetic screening methods. It also is interesting to note that all seven patents at issue in this case will expire in 2014 or 2015; thus, it is clear that this case is not really about the Myriad patents in particular, but rather about the patentability of isolated genes and genetic screening methods in general.

Until the case is resolved, companies isolating genes and developing tests for genetic mutations may consider reevaluating their strategies for protecting their intellectual property. For example, when considering options including those running counter to the ideals behind patent law, companies may consider maintaining the sequences and mutations associated with particular diseases as trade secrets, rather than making them available through publication and patenting. On the other hand, international companies and companies that pursue international patent strategies remain likely to continue to patent their discoveries, on the assumption that the Federal Circuit (and Supreme Court) will maintain status quo for the biotechnology industry, and keep U.S. patent law consistent with the patent laws of other developed countries, which also permit the patenting of isolated genes.

Legal News Alert is part of our ongoing commitment to providing up-to-the-minute information about pressing concerns or industry issues affecting our clients and colleagues. If you have any questions about this alert or would like to discuss the topic further, please contact your Foley attorney or the following:

George C. Best
Palo Alto, California

Courtenay C. Brinckerhoff
Washington, D.C.

Jacqueline Wright Bonilla
Washington, D.C.

Antoinette F. Konski
Palo Alto, California
650. 251.1129

Stephen B. Maebius
Washington, D.C.