While Judge found that isolated genes are patentable, he stated that Myriad’s patents covering methods of analyzing those genes aren’t.

In a long awaited decision, it is now clear that isolated genes will remain patentable subject matter. The American Civil Liberties Union (ACLU), the Public Patent Foundation, and others filed a lawsuit in 2009 (Association for Molecular Pathology, et al. v. United States Patent and Trademark Office, et al.) challenging patents on two human genes associated with breast and ovarian cancer.

Today, the Court of Appeals for the Federal Circuit affirmed in part and reversed in part the original decision. There are three key parts to the decision reflecting three claim sets that were reviewed: genes, method of diagnosis, and methods of screening for therapeutics.

The patents at the center of the lawsuit against the U.S. Patent and Trademark Office (USPTO) and owners of the patents on mutations in the BRCA genes, Myriad Genetics and the University of Utah Research Foundation are based on the initial identification of mutations within two genes, called BRCA1 and BRCA2. These two genes appear to be the cause of the majority of cases of hereditary breast and ovarian cancers.

The lawsuit stated that the patents on the two human genes are unconstitutional and invalid because “human genes are products of nature, laws of nature and/or natural phenomena, and abstract ideas or basic human knowledge or thought.”  In that case which was originally decided in the United States District Court for the Southern District of New York, it was held that genes were not patentable subject matter.

In the most recent decision, the Court reversed the district court’s judgment with regard to Myriad’s composition claims to isolated DNAs; affirmed the district court’s judgment with regard to Myriad’s method claims to comparing or analyzing gene sequences; and reversed the district court’s judgment with regard to Myriad’s method claim to screening potential cancer therapeutics via changes in cell growth rates.

The Court stated that genes are “products of nature” and not eligible for patent protection. According to the decision, genes will be considered patentable subject matter based on the Court’s reading of the intent of Congress and under the patent laws in the U.S. Therefore, patents will continue to be granted to applicants who “isolate” nucleic acid sequences from their natural environment, sequence them, and identify functions and uses for those sequences, and existing patents will remain enforceable.

“It is undisputed that Myriad’s claimed isolated DNAs exist in a distinctive chemical form—as distinctive chemical molecules—from DNAs in the human body, i.e., native DNA . Accordingly, BRCA1 and BRCA2 in their isolated state are not the same molecules as DNA as it exists in the body; human intervention in cleaving or synthesizing a portion of a native chromosomal DNA imparts on that isolated DNA a distinctive chemical identity from that possessed by native DNA.”

Further, the Court stated that “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.

“The ability to visualize a DNA molecule through a microscope or by any other means when it is bonded to other genetic material is worlds apart from possessing an isolated DNA molecule that is in hand and usable. It is the difference between knowledge of nature and reducing a portion of nature to concrete form, the latter activity being what the patent laws seek to encourage and protect.”

The Court also noted that “if the law is to be changed, and DNA inventions excluded from the broad scope of § 101 contrary to the settled expectation of the inventing community, the decision must come not from the courts, but from Congress.”

As to the second issue, the Court has ruled that patents covering methods of analyzing or comparing genes (diagnostics), per se, will not be considered patentable. “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. See Benson, 409 U.S. at 67 (“Phenomena of nature, . . . mental processes, and abstract intellectual concepts are not patentable, as they are the basic tools of scientific and technological work.”).”

The Court distinguished the Myriad claims from the recently decided Prometheus case in that “Myriad’s claims, in contrast, do not include the step of “determining” the sequence of BRCA genes by, e.g., isolating the genes from a blood sample and sequencing them, or any other necessarily transformative step.

Rather, the comparison between the two sequences can be accomplished by mere inspection alone. However, a close reading of the decision leads one to surmise that it may be possible to patent such methods by adding steps that include a transformative process (e.g., extracting and isolating the DNA, then sequencing it before doing the comparison). Myriad’s claims do not include this “transformative” language before the “comparing” steps, and the Court concluded that Myriad’s claims were nothing more than observations.

Finally, methods of screening for cancer compounds based on the facts in this case and the claim language are considered patentable because the steps of growing cells containing a BRCA1 or BRCA2 gene and the manipulation of those cells growing in the presence or absence of the proposed cancer therapeutic requires transformation of the cell culture and not just mere observation without intervention.

“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. 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. The claim includes the steps of “growing” transformed cells in the presence or absence of a potential cancer therapeutic, an inherently transformative step involving the manipulation of the cells and their growth medium.”

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