On Friday, June 12, 2015, the Federal Circuit 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, and the Federal Circuit’s rigid interpretation of the Mayo framework for determining patent eligibility of diagnostic methods. While the Federal Circuit acknowledged the real-world contribution of the Sequenom methods, it cited the Supreme Court’s decision in Myriad for the proposition that “[groundbreaking], innovative, or even brilliant discovery does not by itself satisfy the § 101 inquiry.” Ariosa, slip op. at 16.

The Claims at Issue

The Sequenom patent at issue was U.S. Patent 6,258,540. The claimed technology relates to diagnostic methods for determining certain fetal characteristics such as gender and genetic defects, based on paternally inherited cell-free fetal DNA (cffDNA) found in maternal plasma and serum.

The independent claims at issue in this appeal recite:

1. 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.

24. A method for detecting a paternally inherited nucleic acid on a maternal blood sample, which method comprises: removing all or substantially all nucleated and anucleated cell populations from the blood sample, amplifying a paternally inherited nucleic acid from the remaining fluid and subjecting the amplified nucleic acid to a test for the paternally [sic] inherited fetal nucleic acid.

25. A method for performing a prenatal diagnosis on a maternal blood sample, which method comprises obtaining a non-cellular fraction of the blood sample amplifying a paternally inherited nucleic acid from the non-cellular fraction and performing nucleic acid analysis on the amplified nucleic acid to detect paternally inherited fetal nucleic acid.

Ariosa, slip op. at 4-5.

The Procedural History

This case dates back to 2011, when 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 applied Mayo’s two-step framework for determining patent eligibility, considering first whether the claims are directed to a patent-ineligible concept, and, if they are, determining whether the additional claim elements “transform the nature of the claim” into a patent-eligible application of the natural phenomenon. Ariosa, slip op. at 8. With regard to the first step, the Federal Circuit noted that the claims recite “a multistep method that starts with cffDNA taken from a sample of maternal plasma or serum . . . [and] ends with paternally inherited cffDNA, which is also a natural phenomenon.” Ariosa, slip op. at 8-9. Having found that “[t]he method begins and ends with a natural phenomenon,” Ariosa, slip op. at 9, the Federal Circuit moved on to the second step of the Mayo framework.

For the second step, the Federal Circuit explained that “for process claims that encompass natural phenomenon, the process steps are the additional features that must be new and useful.” The court followed a methodical approach, studying the individual active steps within the body of the claims, and determining that each were “well-understood, conventional and routine.” Ariosa, slip op. at 11. Instead of focusing on the undisputed novelty of amplifying and detecting a paternally inherited nucleic acid in a serum sample from a pregnant female, the court’s analysis centered on the laboratory techniques used to perform those steps. For example, the court noted that the specification taught that the preparation, amplification and detection “of DNA sequences in a plasma or serum sample were well-understood, routine, conventional activities,” Ariosa, slip op. at 11, even though the specific type of DNA recited in the claims had not been amplified or detected in the specific type of sample recited in the claims. The court also considered several dependent claims, but found none to add anything “inventive” to the claimed methods. Ariosa, slip op. at 12. The court’s conclusion indicates how it may analyze other diagnostic method claims for patent eligibility:

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.

Ariosa, slip op at 13.

Responding to Sequenom's other arguments, the Federal Circuit indicated that the preemption aspect of the subject matter eligibility analysis was more useful as a sword than a shield, noting that “[w]hile preemption may signal patent ineligible subject matter, the absence of preemption does not result in a determination of patent eligibility.” Ariosa, slip op. at 14.

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. 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. Judge Linn urges the Supreme Court to reconsider the Mayo framework, and at least permit the consideration of “post-solution activity” when that activity is novel.

What’s Next for Diagnostic Medicine Patents?

This decision is going to have a ripple effect across the diagnostic and personalized medicine industry. While the contours of this decision have yet to be determined, it at least appears to leave room for patent eligibility where method claims recite novel laboratory techniques or reagents. However, it may make it more difficult to obtain patents related to diagnostic methods, personalized medicine, and other method claims that involve a “natural phenomenon.”

Judge Linn’s concurrence offers one possible solution to this problem, but if the Supreme Court grants certiorari, it will be another year before we could have a different decision. Various groups are working on possible legislative solutions to the patent eligibility problem, but 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.