Federal Circuit Holds Sequenom Diagnostic Method Patent Invalid Under 101

15 June 2015 PharmaPatents Blog
Authors: Courtenay C. Brinckerhoff

The Federal Circuit has issued its decision in Ariosa Diagnostics, Inc. v. Sequenom, Inc., affirming the district court’s finding that Sequenom’s claims are invalid under 35 USC § 101. The court’s decision shows the sweeping impact of the Supreme Court’s decision in Mayo v. Prometheus on the patent eligibility of diagnostic methods, and could have a ripple effect across the diagnostic and personalized medicine industry.

The Claims At Issue

The Sequenom patent at issue was U.S. Patent 6,258,540. Claim 1 recites:

A method for detecting a paternally inherited nucleic acid of fetal origin performed on a maternal serum or plasma sample from a pregnant female, which method comprises amplifying a paternally inherited nucleic acid from the serum or plasma sample and detecting the presence of a paternally inherited nucleic acid of fetal origin in the sample.

When the case previously was before the Federal Circuit, the court described the invention as follows:

The ’540 patent discloses methods to identify fetal genetic defects by analyzing … maternal plasma or serum. The ’540 patent discloses that non-nucleated free floating fetal DNA (the cffDNA) exists in maternal blood. … The specification explains that not only does analysis of cffDNA permit more efficient determination of genetic defects (for example, trisomy of chromosome 21) but that a pregnant woman carrying a fetus with certain genetic defects will have more cffDNA in her blood than do women with normal fetuses. … In other words, the ’540 patent claims methods to detect fetal genetic characteristics by analyzing cffDNA obtained from a maternal blood sample. These new tests presented fewer risks and a more dependable rate of abnormality detection.

The Procedural History

This case dates back to 2011, when Aria (now Ariosa) brought a declaratory judgment action seeking a declaration that its “Harmony” test did not infringe the ‘540 patent. Sequenom brought an infringement counterclaim and sought a preliminary injunction. The district court construed the claims, found a substantial question of non-infringement, considered the other factors pertinent to a preliminary injunction inquiry, and denied the preliminary injunction. Sequenom appealed to the Federal Circuit, which vacated and remanded based on a different claim construction. In that decision, the Federal Circuit also directed the district court to consider the patent eligibility issues in view of the Supreme Court’s Myriad decision. (Read more about the first Federal Circuit decision here.) On remand, the district court granted summary judgment of invalidity under 35 USC § 101. It is Sequenom’s appeal of that decision that the Federal Circuit has now decided.

The Patent Eligibility Problem

The Federal Circuit decision was authored by Judge Reyna and joined by Judges Linn and Wallach. Judge Linn also filed a concurring opinion.

The court reviewed the claims and noted that they start and end with naturally occurring material (albeit an amplified material at the end). Thus, the court found them to be caught by the first part of the two-step Mayo framework, and require analysis under the second part, which the court characterized as follows:

In the second step, we examine the elements of the claim to determine whether the claim contains an inventive concept sufficient to “transform” the claimed naturally occurring phenomenon into a patenteligible application. …. [F]or process claims that encompass natural phenomenon, the process steps are the additional features that must be new and useful.

However, instead of considering the process steps as a whole, and recognizing that amplifying a paternally inherited nucleic acid from a serum sample from a pregnant female was new, and that detecting the presence of a paternally inherited nucleic acid of fetal origin in the sample was new and useful, the court found that the method steps did not support patentability because they used conventional amplification and detection techniques.

The court concluded:

The method at issue here amounts to a general instruction to doctors to apply routine, conventional techniques when seeking to detect cffDNA. Because the method steps were well-understood, conventional and routine, the method of detecting paternally inherited cffDNA is not new and useful. The only subject matter new and useful as of the date of the application was the discovery of the presence of cffDNA in maternal plasma or serum.

The court also seemed to pronounce this new “rule”:

Where claims of a method patent are directed to an application that starts and ends with a naturally occurring phenomenon, the patent fails to disclose patent eligible subject matter if the methods themselves are conventional, routine and well understood applications in the art.

Responding to Sequenom’s other arguments, the Federal Circuit indicated that the preemption aspect of the subject matter eligibility analysis was not very persuasive:

While preemption may signal patent ineligible subject matter, the absence of complete preemption does not demonstrate patent eligibility.

The court even acknowledged the real world contribution of the Sequenom methods, but decided that could not carry the day under § 101.

Sequenom also notes that “the method reflects a significant human contribution … that revolutionized prenatal care.” … We agree but note that the Supreme Court instructs that “[g]roundbreaking, innovative, or even brilliant discovery does not by itself satisfy the § 101 inquiry.”

Thus, the Federal Circuit affirmed the district court’s grant of summary judgment of invalidity.

Judge Linn’s Concurrence

Judge Linn’s concurring opinion places blame for the result here squarely on the shoulders of the Supreme Court and its decision in Mayo. Judge Linn urges the Court to reconsider the Mayo framework, and at least permit the consideration of “post-solution activity” when that activity is novel.

Although Judge Linn finds that Sequenom’s claims are distinguished from the claims at issue in Mayo, he feels bound by the language of Mayo to hold the Sequenom claims ineligible:

In short, Sequenom’s invention is nothing like the invention at issue in Mayo. Sequenom “effectuate[d] a practical result and benefit not previously attained,” so its patent would traditionally have been valid. …. But for the sweeping language in the Supreme Court’s Mayo opinion, I see no reason, in policy or statute, why this breakthrough invention should be deemed patent ineligible.

Available For All Or Available For None?

This decision is going to have a ripple effect across the diagnostic and personalize medicine industry. Even if the Supreme Court grants certiorari, it will be another year before we could have a different decision. While various groups are working on possible legislative solutions to the patent eligibility problem, it will take time to negotiate statutory language that is agreeable to all stakeholders, and even longer for any proposed legislation to make is way through Congress.

Although the Supreme Court justifies the judicial exception that bars patenting of products of nature and natural phenomenon on the basis that “manifestations of laws of nature” should be “free to all men and reserved exclusively to none,” new diagnostic methods may be available to none  if a lack of patent protection discourages investment in these important technologies.

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