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ACLU, PUBPAT Seek to Challenge Patentability of Isolated Genes Before Supreme Court


By Turna Ray

The American Civil Liberties Union and the Public Patent Foundation have decided to ask the Supreme Court to take up their case challenging Myriad Genetics' patents on the BRCA 1 and BRCA 2 genes.

Even since American Molecular Pathology et al. v. US Patent and Trademark Office et al. first came before a New York federal district court in late 2009, legal experts have predicted that the case, which could have a broad impact on the patentability of genes, would eventually go the Supreme Court.

This week, ACLU and PUBPAT proved those predictions right by announcing that they will petition the high court following the Federal Circuit Court of Appeals' decision not to rehear the case. The Supreme Court may decide to hear the case, or it may instruct the Court of Appeals to reconsider its decision, which it issued in August.

Myriad spokesperson Rebecca Chambers told PGx Reporter that the company is still considering its options in terms of next steps. "We have not made a public statement regarding our intent to petition the Supreme Court," Chambers said. "We are actively assessing the situation and have until Dec. 15 to decide." She declined to provide any further comment.

The Court of Appeals in August ruled that isolated gene sequences claimed in patents held by the University of Utah and licensed to Myriad are not products of nature and are therefore patentable — a decision that overturned an earlier ruling by the federal district court. The appeals court determined, however, that several of Myriad's method claims that describe "comparing" and "analyzing" gene sequences were invalid (PGx Reporter 8/3/2011).

The appeals court also considered Myriad's allegation that the plaintiffs lacked standing to bring the lawsuit, ultimately deciding that only one researcher, Harry Ostrer, had standing.

In response, Myriad filed a petition with the Federal Circuit, asking the court to reconsider whether Ostrer had standing, since he moved to a new institution that does not have a dispute with Myriad over the BRCA patents. The ACLU and PUBPAT also filed a rehearing petition on behalf of the plaintiffs, claiming that the court "erred" in determining that Myriad's claimed patents on gene fragments are markedly different from those that exist in nature. Additionally, they asserted that the American College of Medical Genetics and Ellen Matloff, a genetic counselor at Yale Cancer Center, also had standing (PGx Reporter 9/7/2011).

However, last month, the federal appeals court shot down both Myriad's and ACLU/PUBPAT's petitions. Subsequently, some legal experts opined that short of going to the Supreme Court, the parties may request the federal appeals court to rehear the case en banc — meaning that the full court would hear the case rather than the three judges who issued their ruling in August.

Although Myriad is still deciding whether to take its case to the Supreme Court, the company has determined that it "cannot ask the Federal Court to hear the case en banc due to procedural rules of the court," Chambers said.

On the other hand, it seems the plaintiffs always had their eye on the Supreme Court. "Whether we went en banc or not, the case was eventually going to be at the Supreme Court, so why wait to get there?" Daniel Ravicher, executive director of PUBPAT said.

Focus on the Molecules

According to Robert Cook-Deegan, director of Duke University's Center for Genome Ethics, Law & Policy, whatever court hears the case next, the defense and plaintiffs are unlikely to focus too heavily on questions of standing and will probably stick strictly to whether DNA molecules corresponding to those occurring in nature can be patented.

Cook-Deegan noted that all the judges that have heard the case so far — in the federal district court as well as the appeals court — have spent "a lot of time and attention, devoting many pages to the question of patentability of DNA molecules that could be found in nature."

As a result, "I would think that will be the focus of any appeal from ACLU," Cook-Deegan said. This issue "is by far the largest and most significant point of uncertainty remaining."

Certainly, there is room for debate on this issue, since the Federal Circuit's three-judge panel, comprising Alan Lourie, Kimberly Moore, and William Bryson, issued a two-to-one decision in AMP v. USPTO upholding Myriad's composition claims on isolated DNA molecules as patent eligible "since the molecules as claimed do not exist in nature."

Lourie wrote the majority opinion for the court, Moore wrote a concurring statement, and Bryson wrote an opinion that agreed with the other two judges about the patentability of cDNA and method claims, but disagreed that isolated gene sequences were patentable. Although Lourie and Moore agreed that isolated gene sequences were patentable, they gave different reasons for their decision.

The conditions under which DNA molecules can and cannot be patented were also the focus of an amicus brief that the Department of Justice filed with the appeals court. In the brief, the DoJ held that the New York Southern District Court wrongly invalidated Myriad Genetics' composition claims "directed solely to cDNAs." However, the government agreed with the lower court that genes as they occur in the body are not products of human invention worthy of a patent (PGx Reporter 11/3/2010).

The fact that the DoJ has weighed in on this question is "significant" if the case is heard by the Supreme Court, Cook-Deegan said.

"The Supreme Court is less patent-oriented than [the Court of Appeals for the Federal Circuit], and has several times and in several ways reined in [the lower court's] pro-patent jurisprudence in recent years (on obviousness, on automatic injunctions, on assessing damages)," Cook-Deegan noted via e-mail. The "DOJ has a good track record defending its positions at the Supreme Court, so I would think their position on not supporting patentability of naturally occurring sequences would get a serious hearing and might be persuasive to the Supreme Court in a way that would not be as true at [the Federal Circuit]."

While Myriad hasn't decided whether to petition the Supreme Court, one reason it might would be to try to get back the five method claims that the federal appeals court invalidated. Myriad has said that its business will be minimally impacted without those patents, some of which are slated to expire in 2014, and has highlighted the fact that it still has more than 200 method patents covering its BRACAnalysis test and a proprietary database of gene-disease associations that can draw on to improve the test.

However, the company may have an uphill climb in trying to reverse the lower court's decision on its method claims, according to Cook-Deegan, since the three circuit judges appeared to generally agree about the patent ineligibility of those claims.

Without the invalidated claims and the "very suspect" claims the company has on short DNA molecules, "Myriad has a much weaker monopoly," Cook-Deegan said. "That is, they would wind up with some claims on fairly narrow methods like PCR and very specific mutations they had discovered and patented, but not the full-length BRCA genes. That would really significantly narrow their claim to royalties (or rights on) full-genome analysis or multi-allele testing."

Impact of Other Cases

Additionally, the Federal Circuit Court of Appeal's recent decision in Classen v. Biogen Idec, as well as the Supreme Court's decision to hear Prometheus v. Mayo, may have an impact on the outcome of AMP v. USPTO.

In Classen v. Biogen Idec, a district court had previously invalidated three patents held by Classen Immunotherapeutics covering the company's discovery that vaccines administered at an early age can lower the risk of chronic immune-mediated side effects. Two of the patents at issue — '139 and '739 — describe methods through which immunization schedules and occurrence of chronic disease are "screened" and "compared," a lower risk of chronic immune-mediated disorders is "identified," and a vaccine is "administered." A third patent — '283 — describes methods of determining the occurrence of immune-mediated disorders by comparing the effects of immunization schedules on rates of disease in treated and control groups.

The district court invalidated all three patents, reasoning that determining the relationship between immunizing infants for infectious diseases and later occurrence of immune-mediated disorders is an "abstract idea" and therefore not patentable.

When this case reached the federal appeals court, circuit judges initially agreed with the district court's findings. However, after the Supreme Court asked the federal appeals court to review its decision in light of more recent legal decisions, the Federal Circuit in August reversed its previous decision for patents '139 and '739, affirming their eligibility, and maintained that patent '283 was patent ineligible.

The impact of this decision is hard to gauge, since there was sharp dissension among circuit judges in Classen v. Biogen Idec. However, the majority opinion appears to hold that it isn't enough to just meet patent-eligibility under 35 USC Section 101 of the patent law, but the claimed invention must also pass muster under the limits of patentability.

In her decision, Judge Pauline Newman wrote that Section 101 — which states that a new and useful process, machine, manufacture, or composition of matter can be patented — is broad and provides only a "coarse eligibility filter." In Newman's view, the patentability conditions outlined in other sections of the law — namely those in section 102 stating that subject matter must be "novel;" section 103 requiring that inventions be "non-obvious;" and section 112 describing the need for a specific and exact description of the invention — are more meaningful when discerning patent eligibility.

According to the majority opinion, Classen's '283 was not patent eligible since "methods that simply collect and compare data, without applying the data in a step of the overall method, may fail to traverse the Section 101 filter." According to some legal experts who have closely followed Classen v. Biogen Idec in order to gauge the case's potential impact on the Myriad case, the patentability of methods comparing isolated gene molecules and naturally occurring DNA sequences — which in AMP v. USPTO district court Judge Sweet deemed invalid as abstract mental processes — may be challenged by similar reasoning.

Separately, the US Supreme Court has decided to hear Prometheus v Mayo, another case that could potentially impact Myriad's method claims should the company seek to challenge the federal appeals court's decision (PGx Reporter 6/22/2011).

Last year, the federal appeals court upheld its earlier decision that Prometheus' contested patents, which cover methods for determining the optimal dosage of drugs to treat stomach disease, were patent eligible under the law. Mayo is challenging that decision before the Supreme Court, asserting that Prometheus' patents claim a natural phenomenon.

Depending on how the Supreme Court rules on the patentability of Prometheus' claims, it could set a precedent for the patentability of other methods based on biological discoveries, such as genetic testing methods. This in turn could affect the advancement of personalized medicine products that rely on the help of a diagnostic to identify patients that have certain gene mutations and would therefore respond to a drug.

If the Supreme Court reverses the appeals court's decision with regard to Prometheus' method claims, deeming them invalid, "then more method claims relevant to diagnostics could be invalid," Cook-Deegan said, adding that "of course, the Supreme Court could also affirm" Prometheus' patents.

Have topics you'd like to see covered in Pharmacogenomics Reporter? Contact the editor at tray [at] genomeweb [.] com.

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