Patent Baristas

In a 2-1 decision, the Federal Circuit upheld that companies can patent genes but decided that they cannot patent methods to compare the gene sequences.

The Federal Circuit handed down a decision on the Myriad Genetics appeal from the decision of the US District Court holding that a gaggle of medical organizations, researchers, genetic counselors, and patients have standing to challenge Myriad’s patents. See:  Assoc. for Molecular Pathology v. U.S. Patent & Trademark Office, 669 F. Supp. 2d 365 (S.D.N.Y. 2009). Myriad also appealed the district court’s decision granting summary judgment that all of the challenged claims are drawn to non-patentable subject matter under 35 U.S.C. § 101.

1. On the issue of jurisdiction, the Federal Circuit concluded that at least one plaintiff, Dr. Harry Ostrer, has standing to challenge the validity of Myriad’s patents.
2. On the merits, the Federal Circuit reversed the district court’s decision that Myriad’s composition claims to “isolated” DNA molecules cover patent-ineligible products of nature under § 101 since the molecules as claimed do not exist in nature.
3. The Federal Circuit also reversed the district court’s decision that Myriad’s method claim to screening potential cancer therapeutics via changes in cell growth rates is directed to a patent-ineligible scientific principle.
4. The Federal Circuit did, however, affirm the court’s decision that Myriad’s method claims directed to “comparing” or “analyzing” DNA sequences are patent ineligible; such claims include no transformative steps and cover only patent-ineligible abstract, mental steps.

Association For Molecular Pathology v. US Patent And Trademark Office and Myriad Genetics

This whole brouhaha has to do with U.S. Patent Nos. 5,747,282; 5,837,492; 5,693,473; 5,709,999; 5,710,001; 5,753,441; 6,033,857.

The composition claims cover two “isolated” human genes, BRCA1 and BRCA2 and certain mutations in these genes associated with a predisposition to breast and ovarian cancers. Representative composition claims include claims 1, 2, and 5 of the ’282 patent:

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

2.  The isolated DNA of claim 1, wherein said DNA has the nucleotide sequence set forth in SEQ ID NO:1.

5.  An isolated DNA having at least 15 nucleotides of the DNA of claim 1.

SEQ ID NO:2 depicts the amino acid sequence of the BRCA1 protein, and SEQ ID NO: 1 depicts the nucleotide sequence of the BRCA1 DNA coding region.

All but one of the challenged method claims cover methods of “analyzing” or “comparing” a patient’s BRCA sequence with the normal, or wild-type, sequence to identify the presence of cancer-predisposing mutations. Representative method claims include claim 1 of the ’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.

The final method claim challenged by Plaintiffs is directed to a method of screening potential cancer therapeutics. Specifically, claim 20 of the ’282 patent reads as follows:

20. A method for screening potential cancer therapeutics which comprises: growing a transformed eukaryotic host cell containing an altered BRCA1 gene causing cancer in the presence of a compound suspected of being a cancer therapeutic, growing said transformed eukaryotic host cell in the absence of said compound, determining the rate of growth of said host cell in the presence of said compound and the rate of growth of said host cell in the absence of said compound and comparing the growth rate of said host cells, wherein a slower rate of growth of said host cell in the presence of said compound is indicative of a cancer therapeutic.

The challenged claims relate to isolated gene sequences and diagnostic methods of identifying mutations in these sequences.

Declaratory Judgment Jurisdiction

The first question addressed was whether the district court correctly exercised declaratory judgment jurisdiction over this suit:

Although no bright-line rule exists for determining whether a declaratory judgment action satisfies Article III’s case-or-controversy requirement, the Supreme Court has held that the dispute must be “definite and concrete, touching the legal relations of parties having adverse legal interests,” “real and substantial,” and “admi[t] of specific relief through a decree of a conclusive character, as distinguished from an opinion advising what the law would be upon a hypothetical state of facts.” MedImmune, 549 U.S. at 127 (quoting Aetna Life, 300 U.S. at 240-41). “Basically, the question in each case is whether the facts alleged, under all the circumstances, show that there is a substantial controversy, between parties having adverse legal interests, of sufficient immediacy and reality to warrant the issuance of a declaratory judgment.”

Myriad challenged jurisdiction on the grounds that Myriad and the Plaintiffs do not have adverse legal interests and that Plaintiffs failed to allege a controversy of sufficient immediacy and reality to warrant the issuance of a declaratory judgment.

The Plaintiffs responded that they have standing because, not only are they undisputedly prepared to immediately undertake potentially infringing activities, but also Myriad took sufficient affirmative acts with respect to the patents in suit. Regarding the latter, the Plaintiffs cried that Myriad sued, threatened to sue, or demanded license agreements from every known institution offering BRCA clinical testing, including university labs directed by plaintiffs Kazazian, Ganguly, and Ostrer.

Under the facts alleged in this case, we conclude that one Plaintiff, Dr. Ostrer, has established standing to maintain this declaratory judgment suit. All Plaintiffs claim standing under the Declaratory Judgment Act based on the same alleged injury: that they cannot undertake the BRCA-related activities that they desire because of Myriad’s enforcement of its patent rights covering BRCA1/2.³ Only three plaintiffs, however, allege an injury traceable to Myriad; only Drs. Kazazian, Ganguly, and Ostrer allege affirmative patent enforcement actions directed at them by Myriad. Of these three, Dr. Ostrer clearly alleges a sufficiently real and imminent injury because he alleges an intention to actually and immediately engage in allegedly infringing BRCA-related activities.

The court said that Dr. Ostrer could have proceeded with his BRCA-related clinical activities without taking a license from Myriad because he thinks that the patents are invalid since  genes are patent ineligible products of nature. This put Myriad and Dr. Ostrer in adverse legal positions regarding whether or not Ostrer can engage in BRCA genetic testing without infringing any valid claim to “isolated” BRCA DNAs or methods of “analyzing” or “comparing” BRCA sequences, as recited in Myriad’s patents.

 The Supreme Court has required only that it is “likely,” rather than “merely ‘speculative,’” that the alleged injury will be “redressed by a favorable decision.” Lujan, 504 U.S. at 561. The Court has not required certainty.

Patentable Subject Matter

Under the Patent Act, “Whoever invents or discovers any new and useful process, machine, manufacture, or composition of matter, or any new and useful improvement thereof, may obtain a patent therefor, subject to the conditions and requirements of this title.” 35 U.S.C. § 101.

The Supreme Court has consistently construed § 101 broadly, explaining that “[i]n choosing such expansive terms . . . modified by the comprehensive ‘any,’ Congress plainly contemplated that the patent laws would be given wide scope.” Bilski v. Kappos, 130 S. Ct. 3218, 3225 (2010) (quoting Chakrabarty, 447 U.S. at 308).

Supreme Court  precedents provide three judicially created exceptions to § 101’s broad patent-eligibility principles: “laws of nature, physical phenomena, and abstract ideas.”

Here, the Plaintiffs challenge Myriad’s composition claims directed to “isolated” DNA molecules and method claims directed to “analyzing” or “comparing” DNA sequences under § 101.

Composition Claims: Isolated DNA Molecules

Myriad argued that the district court found the claims unpatentable by (1) misreading Supreme Court precedent as excluding from patent eligibility all “products of nature” unless “markedly different” from naturally occurring ones; and (2) incorrectly focusing not on the differences between isolated and native DNAs, but on one similarity: their informational content.

Myriad argued that an isolated DNA molecule is patent eligible because it is, as claimed, “a nonnaturally occurring composition of matter” with “a distinctive name, character, and use.”

The Plaintiffs argued that claims to isolated DNA molecules fail to satisfy § 101 because such claims cover natural phenomena and products of nature. The Plaintiffs assert that to be patent eligible a composition of matter must also have a distinctive name, character, and use, making it “markedly different” from the natural product.

In sum, although the parties and the government appear to agree that isolated DNAs are compositions of matter, they disagree on whether and to what degree such molecules fall within the exception for products of nature. As set forth below, we conclude that the challenged claims to isolated DNAs, whether limited to cDNAs or not, are directed to patent-eligible subject matter under § 101.

Because isolated DNAs, not just cDNAs, have a markedly different chemical structure compared to native DNAs, we reject the government’s proposed “magic microscope” test, as it misunderstands the difference between science and invention and fails to take into account the existence of molecules as separate chemical entities.

Method Claims

The district court’s decision predated the Supreme Court’s decision in Bilski, which rejected this court’s machine-or-transformation test as the exclusive test for determining whether an invention is a patent-eligible process under§ 101, although the test remains “a useful and important clue.”

Methods of “Comparing” or “Analyzing” Sequences

Myriad argued that its claims to methods of “comparing” or “analyzing” BRCA sequences satisfy the machine-or-transformation test as applied in Prometheus because each requires a transformation–extracting and sequencing DNA molecules from a human sample–before the sequences can be compared or analyzed.

The Plaintiffs argued that these method claims are drawn to the abstract idea of comparing one sequence to a reference sequence and preempt a phenomenon of nature–the correlation of genetic mutations with a predisposition to cancer.

We conclude that Myriad’s claims to “comparing” or “analyzing” two gene sequences fall outside the scope of § 101 because they claim only abstract mental processes. The claims recite, for example, a “method for screening a tumor sample,” by “comparing” a first BRCA1 sequence from a tumor sample and a second BRCA1 sequence from a non-tumor sample, wherein a difference in sequence indicates an alteration in the tumor sample.

This claim thus recites 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.

Method of Screening Potential Cancer Therapeutics

The Plaintiffs challenged Myriad’s method claim directed to a method for screening potential cancer therapeutics via changes in cell growth rates as directed to the abstract idea of comparing the growth rates of two cell populations and as preempting a basic scientific principle — that a slower growth rate in the presence of a potential therapeutic compound suggests that the compound is a cancer therapeutic.

The Federal Circuit disagreed:

Starting with the machine-or-transformation test, we conclude that the claim includes transformative steps, an “important clue” that it is drawn to a patent-eligible process. Bilski, 130 S. Ct. at 3227. Specifically, the claim recites a method that comprises the steps of (1) “growing” host cells transformed with an altered BRCA1 gene in the presence or absence of a potential cancer therapeutic, (2) “determining” the growth rate of the host cells with or without the potential therapeutic, and (3) “comparing” the growth rate of the host cells. The claim thus includes more than the abstract mental step of looking at two numbers and “comparing” two host cells’ growth rates.