On December 2, 2015, an almost unanimous Federal Circuit decision was issued denying the en banc rehearing of Ariosa v. Sequenom, a case having significant consequences for diagnostic patents and Section 101 case law in general. The concurrences and dissent in the Ariosa case offer insight into how the various judges perceive the existing Section 101 case law and attempt to offer applicants guidance in obtaining patent-eligible claims in the diagnostic arena.
The patent at issue
Sequenom is the exclusive licensee of U.S. Patent No. 6,258,540 (the ’540 patent), which claims a “method of detecting paternally inherited nucleic acid of fetal origin performed on the maternal serum or plasma sample from a pregnant female.” ’540 patent at 23:61-63. According to the ’540 patent, the invention enables noninvasive prenatal diagnosis (id. at Abstract) and differs from previous noninvasive tests that detected fetal cells in a mother’s bloodstream. Id. 1:18-36. The independent claims of the ’540 patent recite:
- 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.
- A method of performing a prenatal diagnosis, which method comprises the steps of:
(i) providing a maternal blood sample;
(ii) separating the sample into a cellular and a non-cellular fraction;
(iii) detecting the presence of a nucleic acid of foetal origin in the non-cellular fraction according to the method of claim 1;
(iv) providing a diagnosis based on the presence and/or quantity and/or sequence of the foetal nucleic acid.
- 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 inherited fetal nucleic acid.
- 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.
The district court action
On December 19, 2011, Ariosa filed suit against Sequenom, seeking a declaration that Ariosa’s noninvasive prenatal test did not infringe the ’540 patent. Sequenom counterclaimed, alleging infringement of the ’540 patent. Both parties filed motions for summary judgment regarding invalidity under Section 101. The district court concluded that the only inventive part of the ’540 patent is the application of well-understood, routine, and conventional steps of fractionation, amplification, and detection to a natural phenomenon, i.e., cffDNA. Ariosa Diagnostic, Inc. v. Sequenom, Inc., 19 F.Supp.3d 938 at 953 (N.D. Cal. 2013). Because fractionation, amplification, and detection techniques were previously engaged in by those in the field, albeit on DNA, and because cffDNA is itself not patentable, the district court ruled that the claims of the ’540 patent are directed to patent-ineligible subject matter. Id. at 952-953.
The Federal Circuit affirms the lack of patent-eligible subject matter
The initial Federal Circuit panel (Judge Reyna joined by Judge Linn) applied the two-part test set forth in Mayo and affirmed the district court’s ruling. Ariosa Diagnostic, Inc. v. Sequenom, Inc., 788 F.3d 1371 (Fed. Cir. 2015). Under the first part of the test (whether the claims are directed to a patent-ineligible concept), the court concluded that the claims “begin and end with a natural phenomenon” and are thus “directed to matter that is naturally occurring.” Id. at 1376. Under the second part of the test (whether the claim elements individually and as a whole contain an inventive concept to transform the claim into patent-eligible subject matter), the court concluded that “the practice of the method claims does not result in an inventive concept that transforms the natural phenomenon of cffDNA into a patentable invention.” Id. at 1376. In reaching its decision, the court analyzed the evidence of record, including the specification, expert testimony, and arguments raised by the applicant during prosecution, which, according to the court, established that the process steps did not contain additional features that are new and useful. Id. at 1377. The court held that “[w]here 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.” Id. at 1378.
Judge Linn concurred, but only because he was “bound by the sweeping language of the test set out in Mayo.” Id. at 1380. Judge Linn’s concern for the overly broad test set forth in Mayo is clear from his following statement:
[T]he breadth of the second part of the test was unnecessary to the decision reached in Mayo. This case represents the consequence – perhaps unintended – of that broad language in excluding a meritorious invention from the patent protection it deserves and should have been entitled to retain.
Ariosa, 788 F.3d at 1380.
En banc review denied
In an almost unanimous decision (11-1), the active judges of the Federal Circuit denied the petition for rehearing en banc. Ariosa Diagnostic, Inc. v. Sequenom, Inc., 788 F.3d 1371 (Fed. Cir. 2015), reh’g denied, Nos. 2014-1139, 2014-1144 at 4-5 (Fed. Cir., Dec. 2, 2015). Three opinions were filed with the denial: concurring opinions by Judge Lourie (joined by Judge Moore) and Judge Dyk and a dissent by Judge Newman. Both Judge Lourie and Judge Dyk concurred because they were bound by Supreme Court precedent. According to Judge Lourie, “neither of the traditional preclusions of laws of nature or of abstract ideas ought to prohibit patenting of the subject matter of this case” (Lourie, J., concurring in denial of rehearing en banc at pp. 2-3), but “[a]pplying Mayo, we are unfortunately obliged to divorce the additional steps from the asserted natural phenomenon to arrive at a conclusion that they add nothing innovative to the process.” Id. at p. 6. Similarly, Judge Dyk noted that the court is bound to follow the Mayo decision, and that the court “cannot confine Mayo to its facts or otherwise cabin a clear statement from the Supreme Court.” Dyk, J., concurring in denial of rehearing en banc at p. 1. Judge Newman, on the other hand, dissented, arguing that this case “diverge[s] significantly” from Mayo. Newman, J., dissenting in denial of rehearing en banc at pp. 1-2. According to Judge Newman, whereas the Mayo claims recited a previously known medicinal product and its metabolites, the Sequenom claims recite a “new diagnostic method [that] is novel and unforeseen.” Id. at p. 3.
Guidance offered by the Federal Circuit?
As the diagnostic and life science communities eagerly wait to see whether or not Ariosa will petition the Supreme Court to review this case, the Federal Circuit may have begun to offer applicants guidance on pursuing patentable claims in the diagnostic arena. For example, the original panel decision states that “[f]or process claims that encompass natural phenomenon, the process steps are the additional features that must be new and useful.” Ariosa, 788 F.3d at 1377. Therefore, when the claims include a law of nature, the focus of the claims should be on the process steps, with the inclusion of some new process limitation, as opposed to simply reciting amplifying or sequencing. Furthermore, the Federal Circuit and the district court both focused on the specification and arguments raised by the applicants during prosecution, which established that the method steps can be formed using conventional, well-known techniques. Thus, applicants are advised, depending on the facts of the case, to avoid including broad language regarding well-known or common techniques in the specification.
Judge Lourie suggests drafting the claims as Jepsen claims, i.e., reciting what is in the prior art and the improvement over the prior art. Judge Lourie offers the following example:
In a method of performing a prenatal diagnosis using techniques of fractionation and amplification, the improvement consisting of using the non-cellular fraction of a maternal blood sample.
Lourie, J., concurring in denial of rehearing en banc at pp. 2-3. It is unclear whether this uncommonly used claim strategy will overcome the issues facing diagnostic claims.
Judge Dyk suggests that claims might be patentable if the claims are “both narrow in scope and actually reduced to practice” (Dyk, J., concurring in denial of rehearing en banc at p. 9), such that the claim is “narrowly tailored to the particular application of the law [of nature] that has been developed.” Id. at p. 10. Both Judge Lourie and Judge Dyk offer concerns about the broad scope of the claims in the ’540 patent. Judge Lourie states that “[t]he claims in this case perhaps should be in jeopardy, not because they recite natural laws or abstract ideas, but because they may be indefinite or too broad.” Lourie, J., concurring in denial of rehearing en banc at p. 4. Similarly, Judge Dyk states that “the major defect is not that the claims lack inventive concept but rather that they are overbroad.” Dyk, J., concurring in denial of rehearing en banc at p. 13.
Although there is still a chance that Ariosa will petition the Supreme Court to review the case, the Ariosa decisions continue to narrow the scope of what constitutes patentable subject matter in the diagnostic area. Time will tell whether or not the guidance offered by the Federal Circuit will assist applicants in drafting claims that withstand Section 101 scrutiny going forward.
 Ariosa Diagnostic, Inc. v. Sequenom, Inc., 788 F.3d 1371 (Fed. Cir. 2015), reh’g denied, Nos. 2014-1139, 2014-1144 at 4-5 (Fed. Cir., Dec. 2, 2015).
 The evidence before the court established that fractionation, amplification, and detection techniques, including fractionating, amplifying, and detecting DNA from plasma and serum, were well understood, routine, and conventional. Id. at 949-950. Sequenom acknowledged that the claims of the ’540 patent are directed to applying these “conventional techniques” to the newly discovered cffDNA. Id. at 950.
 Mayo Collaborative Services v. Prometheus Laboratories, Inc., 132 S.Ct. 1289 (2012).