Important Development in Patent Subject Matter Eligibility for Diagnostic Method Claims: Federal Circuit Denies Sequenom Petition for Rehearing En Banc

December 4, 2015

On December 2, 2015, the U.S. Court of Appeals for the Federal Circuit issued an order denying a petition for rehearing en banc in the closely watched Sequenom case.1 Earlier this year, on appeal from the U.S. District Court for the Northern District of California, a three-judge Federal Circuit tribunal ruled that the asserted claims in U.S. Patent No. 6,258,540 (the '540 patent) were invalid for not being directed to patent-eligible subject matter.

The inventors on the '540 patent discovered that cell-free fetal DNA (cffDNA), which circulates in maternal blood plasma and serum, could be used to determine fetal characteristics (e.g., gender). Previously, diagnostics were inaccurate or invasive, risky, and expensive. The cffDNA diagnostic, commercialized by Sequenom as the MaterniT21 test, created a prenatal diagnostic alternative using maternal blood or plasma, which provided accuracy but avoided the invasive risks of earlier diagnostics. The inventors patented their test in the '540 patent.2

Patent Subject Matter Eligibility

One requirement to obtain a patent is that Section 101 of the Patent Statute be satisfied, i.e., that each patent claim be drawn to patent-eligible subject matter. The plain language of the patent subject matter eligibility statute is broad3 and has historically presented a low bar to patentability—until recently. Interpretations of recent U.S. Supreme Court cases by the United States Patent and Trademark Office (USPTO) and the lower federal courts, however, have made patent subject matter eligibility a significant hurdle to: 1) patenting diagnostic method claims; and 2) defending diagnostic method patent claims from challenge. The current state of patent subject matter eligibility could hinder the ability of diagnostic test developers from attracting investment; and therefore, result in a reduction of new diagnostic tests on the market. This, in turn, has significant ramifications for patients, physicians, and the practice of medicine.4 For these reasons, Sequenom—a case about the patent subject matter eligibility of diagnostic method claims—has been closely watched.

Patent Subject Matter Eligibility Analysis (The Mayo Test)

Sequenom presents a representative example of the current state of patent subject matter analysis in the U.S. federal courts and the USPTO. The present high bar to diagnostic method claim patent subject matter eligibility is a significant deviation from the historical norm. In Sequenom, the Federal Circuit interpreted and employed the two-part patent subject matter eligibility test from Mayo Collaborative Services v. Prometheus Laboratories, Inc. (i.e., the Mayo test):

    First, we determine whether the claims at issue are directed to a patent-ineligible matter. If the answer is yes, then we next consider the elements of each claim both individually and "as an ordered combination" to determination whether additional elements "transform the nature of the claim" into a patent-eligible application.5

In applying the Mayo test, the Federal Circuit first determined if the '540 patent's at-issue claims contained a judicial exception (e.g., if the claims contained an abstract idea, natural phenomenon, or law of nature), thereby satisfying the first Mayo test prong. The Federal Circuit maintained that the claims started and ended with natural phenomena—cffDNA and paternal cffDNA respectively—and so contained a natural phenomenon.6, 7 Next, the Federal Circuit looked at whether the remaining claim elements amounted to something more than merely conventional steps (e.g., amplification of the cffDNA by polymerase chain reaction or PCR, detecting (sequencing) the amplified cffDNA, and in some cases using the resulting sequence data for diagnostic purposes). The Federal Circuit held that using "methods like PCR to amplify and detect cffDNA was well-understood, routine, and conventional activity …"8 Thus, as it interpreted and applied the Mayo test, the Federal Circuit held that the as-issue claims of the '540 patent were not drawn to patent eligible subject matter.9

The Time Is Ripe for Supreme Court Clarification of the Mayo Test

For multiple reasons, the time is right for the U.S. Supreme Court to clarify how its test for patent subject matter eligibility should be applied to diagnostic method claims.

First, as Judge Linn noted, and as currently applied, the Mayo test excludes meritorious inventions such as Sequenom's diagnostic test from being patent subject matter eligible. "I concur … only because I am bound by the sweeping language of the test set out in Mayo …" because it "is hard to deny that Sequenom's invention is truly meritorious."10 "[P]rior to the '540 patent, prenatal diagnoses required invasive methods, which 'presented a degree of risk to the mother and the pregnancy …'" and the "Royal Society lauded [Sequenom's test] as 'a paradigm shift in non-invasive prenatal diagnosis.'"11

Second, as raised by Judge Dyk, the Mayo test as applied discourages the development of diagnostics increasingly critical to providing good medical care. "I too share the concerns … that a too restrictive test … (reflected in some of the language in Mayo) may discourage development of new diagnostic and therapeutic methods in the life sciences, which are often driven by discovery of new natural laws and phenomena."12 "This leads me to think that some further illumination as to the scope of Mayo would be beneficial … and any further guidance must come from the Supreme Court …"13

Third, the current application of the Mayo test by the federal courts and the USPTO is, in some cases, arguably yielding incorrect results. In her dissent, Judge Newman stated her opinion that this "subject matter is not ineligible under Section 101, but warrants standard legal analysis for compliance with the requirements of patentability …"14

Will Sequenom Seek Certiorari?

At this point, Sequenom has about 90 days to file a certiorari petition with the U.S. Supreme Court. If Sequenom files a certiorari petition, and if the petition is accepted, the Supreme Court will have the opportunity to provide further guidance on interpreting and applying its test for patent subject matter eligibility.

Recommendations for Companies Developing Diagnostic Methods

In light of the continuing changes in patent subject matter eligibility law, below are several current recommended practices when drafting patent applications with claims drawn to diagnostic methods. The list is not exhaustive. If you have questions, please contact your WSGR patent professional.

    1) Draft the application with an explanation of the problem found in the art and how the invention overcomes the problem in a way that is not routine or conventional.

    2) Draft claims of broad, intermediate, and narrow scope. Even if the broader claims are found patent subject matter ineligible, the intermediate and narrow scope claims may surmount the Section 101 bar.

    3) When possible, draft claims that map to representative allowable claims in the USPTO Section 101 guidance. Showing parallels between model patent subject matter eligible claims and your claims can be a strong argument for traversing the Section 101 bar.

    4) If novel detection reagents can be employed in the diagnostic method (e.g., novel primers, novel antibody-dye conjugates), include claims employing these. The use of novel reagents in a claim can help show that the claim steps were not known and routine.

    5) Interview each diagnostic method claim case at the USPTO. Interviews provide the opportunity to educate the examiner on the merits of your case, and to pressure test different claim amendments and arguments to see if one or more is likely to advance prosecution.

    6) Draft claims to companion diagnostics if applicable.


U.S. patent subject matter eligibility law is in flux. Developers of diagnostic tests should continue to seek patent protection, draft patent applications and claims to maximize the chances of surmounting the patent subject matter eligibility bar, and keep abreast of continuing developments in the law. For questions regarding any of these topics, please contact Maya Skubatch, Richard Torczon, or any member of the patent and innovation strategies practice at Wilson Sonsini Goodrich & Rosati.

Charles Andres contributed to the preparation of this WSGR Alert.

1 Order denying petition for rehearing en banc, 2014-1139, -1114 (Fed. Cir. Dec. 2, 2015).
2 Ariosa Diagnostics, Inc. v. Sequenom, Inc., 2014-1139, -1144 (Fed. Cir. June 12, 2015).
3 35 U.S.C. § 101 recites: 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.
4 As an example of the increasingly important role diagnostics play in medicine, a subset of diagnostics are companion diagnostics. The U.S. Food and Drug Administration or FDA defines a companion diagnostic as providing "information that is essential for the safe and effective use of a corresponding therapeutic product." Emphasis added. "Guidance for Industry and Food and Drug Administration Staff — In Vitro Companion Diagnostic Devices", FDA, (2014), at 7.
5 Slip op. at 8.
6 Id. at 8-9.
7 The at-issue claims of the '540 patent fell roughly into two types: 1) 'detecting' claims and 2) 'diagnosing' claims. For an example, claim 25 of the '540 patent, a diagnosing claim, recites: "A method of 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 faction and performing nucleic acid analysis on the amplified nucleic acid to detect paternally inherited fetal nucleic acid."
8 Slip op. at 11.
9 The authors of this WSGR alert co-authored an amicus brief to the Federal Circuit in support of the petition for rehearing. In the brief, we reasoned that the USPTO and the lower federal courts were not correctly applying the U.S. Supreme Court's test for patent subject matter eligibility. Specifically, we argued that the Mayo test's first prong requires that: i) each claim be construed (considered) as a whole ii) in light of the specification iii) from the perspective of the skilled artisan iv) as well as the problem being solved by, and the v) state of the art at the time of, the claimed invention. The alternative, simply looking for the presence of a judicial exception, de-contextualizes the claim and makes meeting both the first and second test prongs, in most cases, a foregone conclusion. See Brief of Amici Curiae Amarantus Bioscience Holdings, Inc., Personalis, Inc., and Population Diagnostics, Inc. in Support of Appellants' Petition for Rehearing En Banc, Ariosa Diagnostics, Inc. v. Sequenom, Inc., On Writ of Certiorari to the United States Court of Appeals for the Federal Circuit, No. 2014-1139, -1144.
10 Linn Concurrence to Slip Op. at 1, 3.
11 Id. at 3-4.
12 Dyk Concurrence to Order at 2.
13 Id.
14 Newman dissent to Order at 3. Emphasis added.