Disaster survivors, and even people who just hear about a disaster, are often first overwhelmed by it; they can only rationally process its significance after some time.  During that time they overcome the initial visceral reaction and contemplate the effects the disaster will have on the future (and sometimes, develop remedies to avoid similar disasters in future).  Such is a reasonable reaction to the Federal Circuit's decision on June 12th in the Ariosa v. Sequenom case.

To recap, the technology at issue is non-invasive prenatal diagnosis of sex determination, blood typing, other genetic disorders (including Downs Syndrome) and detection of pre-eclampsia, using a simple blood test that reduces or eliminates the need for amniocentesis and chorionic villus sampling (which incur risks to both mother and child).  Sequenom Inc. is the exclusive licensee of U.S. Patent No. 6,258,540 originally obtained by Isis Inc.; three independent claims were attacked by Ariosa in a declaratory judgment action and asserted by Sequenom in its patent infringement counterclaims:

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 (and co-declaratory judgment plaintiffs Natera Inc. and Diagnostic Center, Inc.) filed a declaratory judgment action against Sequenom on these claims, and the District Court denied Sequenom's motion for preliminary injunction (in July 2012), based on a substantial question of invalidity under Section 101 (this was before the Supreme Court's Myriad decision, and under prevailing Federal Circuit law where both genomic and cDNA was patent eligible).  The Federal Circuit then vacated the District Court's denial of Sequenom's preliminary injunction motion for reconsideration under the Myriad decision.

On remand, the District Court granted Ariosa's summary judgment motion for invalidity on the grounds that the claims were patent ineligible (and denied Sequenom's cross-motion for summary judgment of infringement).  Ariosa's argument was simple:  the claims at issue did not "add enough" to a natural phenomenon (the existence of paternally derived cell-free fetal DNA in maternal blood) to render the claims patent eligible.  Because the additional limitations "either apply well-understood, routine, and conventional activity to the natural phenomenon or limit the natural phenomenon to specific types of the natural phenomenon, which are also unpatentable" the claims do not recited patent eligible subject matter according to Ariosa.

The District Court agreed, providing as its analysis that cffDNA was a natural product that was itself patent ineligible, and that amplifying and detecting DNA from plasma or serum was well known at the time the invention was made, based on "evidence" in the specification.  (This interpretation seems to be a misreading of the specification, which states that amplification was achieved using standard techniques, not that amplifying DNA from plasma or serum was itself a standard technique.)  The prosecution history was cited for the same point with regard to methods for detecting cffDNA, and Sequenom's expert "acknowledged that others before the inventors had amplified and detected nucleic acid in plasma or serum."  The District Court based its decision on a combination of the AMP v. Myriad and Parker v. Flook decisions, concluding that to be patent eligible, Sequenom needed to invent novel ways of detecting cffDNA ("[s]imilarly, had the inventors of the '540 patent created an innovative method of performing DNA detection while searching for paternally inherited cffDNA, such as a new method of amplification or fractionation, those claims would be patentable"), based on dicta from the Myriad case.

Taking its turn, the Federal Circuit first provided its understanding of the proceedings below, in an opinion by Judge Reyna joined by Judge Wallach with Judge Linn concurring.  According to the opinion, the Court appreciated that the inventors had found cell-free fetal DNA (cffDNA) in maternal plasma or serum "that other researchers had previously discarded as medical waste" (emphasis added).  Foreshadowing their reasoning, the panel then state that "[a]pplying a combination of known laboratory techniques to their discovery, Drs. Lo and Wainscoat implemented a method for detecting the small fraction of paternally inherited cffDNA in maternal plasma or serum to determine fetal characteristics, such as gender" (by which the opinion avoids the more significant uses such as detecting Downs syndrome and other fetal genetic defects).  And more foreshadowing occurs when they characterize the development of this test as being a "discovery."

The opinion then acknowledges through the parties that the claims are not directed to cffDNA per se or paternally inherited species thereof.  In language that parallels Justice Thomas's language in Section III of his Myriad opinion, the opinion states that the '540 patent claims methods of using cffDNA and then sets forth the panel's understanding of the technical basis for the claimed methods and the procedural particulars of the case below.

The panel's analysis is best understood using the Court's own language, to better appreciate the basis for this decision:

In Mayo Collaborative Services v. Prometheus Laboratories, Inc., 566 U.S. ___, 132 S. Ct. 1289 (2012), the Supreme Court set forth a framework for distinguishing patents that claim laws of nature, natural phenomena, and abstract ideas from those that claim patent-eligible applications of those concepts.  First, we determine whether the claims at issue are directed to a patent-ineligible concept.  Id. at 1297.  If the answer is yes, then we next consider the elements of each claim both individually and "as an ordered combination" to determine whether additional elements "transform the nature of the claim" into a patent-eligible application.  Id. at 1298.  The Supreme Court has described the second step of this analysis as a search for an "inventive concept" -- i.e., an element or combination of elements that is "sufficient to ensure that the patent in practice amounts to significantly more than a patent upon the [ineligible concept] itself."  Id. at 1294; see also Digitech Image Techs., LLC v. Elecs. For Imaging, Inc., 758 F.3d 1344, 1351 (Fed. Cir. 2014) ("Without additional limitations, a process that employs mathematical algorithms to manipulate existing information to generate additional information is not patent eligible.").

Applying this understanding of the Supreme Court's teachings regarding diagnostic claims, the opinion states:

It is undisputed that the existence of cffDNA in maternal blood is a natural phenomenon.  Sequenom does not contend that Drs. Lo and Wainscoat created or altered any of the genetic information encoded in the cffDNA, and it is undisputed that the location of the nucleic acids existed in nature before Drs. Lo and Wainscoat found them.  The method ends with paternally inherited cffDNA, which is also a natural phenomenon.  The method therefore begins and ends with a natural phenomenon.  Thus, the claims are directed to matter that is naturally occurring.

Of course, what the claimed methods end with are amplified cffDNA and the diagnostic information that is discerned (but not claimed) using the method.

The opinion then takes isolated statements from the specification to support this conclusion (again, stating that cffDNA was "routinely" discarded) and that the inventors surprisingly found that detecting cffDNA could be used to render clinical diagnoses of fetal abnormalities non-invasively.

Of course, it is but a short analytical leap to find that the detection methods were simply "routine, conventional and well-understood" because the panel does not consider the claim as a whole but has broken its analysis into pieces (contrary to Supreme Court's Diamond v. Diehr decision).  Accordingly, the panel determines that there is no "inventive concept" in the claims (bizarrely, relying as did the District Court on Parker v. Flook).  (The applicability of that decision on life science inventions should have been firmly put to bed in Judge Rich's In re Bergy decision.)  The next portion of the opinion nicely sets out the logical and legal flaws in the panel's decision:

Like the patentee in Mayo, Sequenom contends that the claimed methods are patent eligible applications of a natural phenomenon, specifically a method for detecting paternally inherited cffDNA.  Using methods like PCR to amplify and detect cffDNA was well-understood, routine, and conventional activity in 1997.  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.

Unlike the patentee in Mayo, the inventors of the claimed invention here did something not done before their invention (detecting cffDNA in maternal blood).  In contrast, every step in the methods claimed in Mayo had been performed in the prior art; the only inventive aspect in those claims was the therapeutic ratio, which the Court found to be a "natural law."  Accordingly, the Mayo claims did nothing more than recite the natural law.  That is not the case here.  Tragically, the remainder of this portion of the opinion recites the tedious evidence from the specification regarding known amplification and detection methods while ignoring that these methods had never been used to detect cffDNA in maternal blood.

The opinion then visits preemption (sadly, the Circuit Court responsible for interpreting patent law does not correctly state the standard, i.e., undue preemption; after all, all claims are preemptive in nature).  Fortunately, the panel does not follow the District Court through the looking glass of requiring for patent eligibility that every newly claimed method to recite not only a new method but that there be commercially viable, non-infringing alternatives available at the time an application is filed.  Instead, the Court considers the preemption question moot once claims have been determined to be patent ineligible.

Finally, the Court insulates itself from the negative consequences its decision has on innovation by citing language (dicta) in Myriad that "[g]roundbreaking, innovative, or even brilliant discovery does not by itself satisfy the § 101 inquiry," illustrated by the interpretation that "[t]he discovery of the BRCA1 and BRCA2 genes was a significant contribution to the medical field, but it was not patentable" (ignoring the fact acknowledged twelve pages prior in the opinion that the inventors were not claiming cffDNA).

Judge Linn's concurring opinion (which in a rational world would be a dissent) joins "only because [he is] bound by the sweeping language of the test set out in Mayo Collaborative Services v. Prometheus Laboratories, Inc.  And he recognizes the consequences:  "[t]his 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."  His soi-disant concurrence then sets out four ways to distinguish the case at bar from Mayo (although he does not avail himself of any of these grounds as a basis to dissent).  He states:

The Supreme Court's blanket dismissal of conventional post-solution steps leaves no room to distinguish Mayo from this case, even though here no one was amplifying and detecting paternally-inherited cffDNA using the plasma or serum of pregnant mothers.  Indeed, the maternal plasma used to be "routinely discarded," '540 patent col.1 ll.50–53, because, as Dr. Evans testified, "nobody thought that fetal cell-free DNA would be present."

(Perhaps one basis for courts' seeming difficulty in applying Diehr properly is reliance on phrases like "conventional post-solution activity" from Flook; while this may make sense in claims to an alarm limit it is difficult to see how the methods steps recited in Sequenom's claims are properly characterized as such.  Cf, In re Bergy).  He then recites a list of what can only be considered to be secondary considerations (taking the Supreme Court's lead, incorporating concepts of obviousness into the patent-eligibility analysis) to establish how "groundbreaking" the claimed methods were.  And he states:

Unlike in Mayo, the '540 patent claims a new method that should be patent eligible.  While the instructions in the claims at issue in Mayo had been widely used by doctors -- they had been measuring metabolites and recalculating dosages based on toxicity/inefficacy limits for years -- here, the amplification and detection of cffDNA had never before been done.  The new use of the previously discarded maternal plasma to achieve such an advantageous result is deserving of patent protection.

Ironically, he relies upon Rebecca S. Eisenberg, Prometheus Rebound: Diagnostics, Nature, and Mathematical Algorithms, 122 Yale L.J. Online 341, 343–44 (2013) in support of these statements.

Judge Linn hoists the panel's decision on the petard of superior Supreme Court precedent:

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.  Le Roy v. Tatham, 63 U.S. 132, 135–36 (1859) (quoting Househill Coal & Iron Co. v. Neilson, Webster's Patent Case 673, 683 (House of Lords 1843)); Le Roy v. Tatham, 55 U.S. 156, 175 (1852) (same); see generally Jeffrey A. Lefstin, Inventive Application: a History, 67 Fla. L. Rev. (forthcoming 2015), available at http://ssrn.com/abstract=2398696 (last visited June 10, 2015) (analyzing traditional notions of patent eligibility of newly discovered laws of nature).

But while he says he sees no reason "in policy or statute" why these claims are not patent eligible, he believes he is bound by "the sweeping language in the Supreme Court's Mayo opinion" to concur.

It is clear that the Federal Circuit (or at least the members of this panel) believe that they are operating under a mandate from the Supreme Court regarding patent eligibility.  On the contrary, the Court itself has on many occasions made it clear that they view their role (in patent law and otherwise) as setting forth the broad contours of the law that they expect the inferior courts to use to develop the law properly.  In view of the lack of clarity in the Mayo opinion, a third year law student could distinguish this case from that one in arriving at the correct conclusion of patent eligibility.  Nothing more than Supreme Court precedent itself (specifically, the Diamond v. Diehr decision which the Court did not overturn in Mayo) is needed for the task.  The issue is not a lack of analytical and doctrinal tools but the will to employ them, which these members of the Federal Circuit do not seem to have had in rendering this decision.  But shielding the Court from the consequences of their bad decisions does them a disservice.  If the Court intended to exclude from patent eligibility all genetic (nay all types of) diagnostic methods, the Federal Circuit owes it to the Court to give them the opportunity to say so clearly and reap the political consequences.

Sequenom must now contemplate whether to seek en banc review (which is unlikely given the current composition of the Court, and equally fraught with risk for that same reason) or to petition for certiorari.  It is likely that the only way the Court will recognize the significance of this decision will be if that petition is widely and broadly supported by amici from industry, academia and the public through those patient groups who understand that failing to patent such tests today will lead inexorably to a future where all testing is proprietary and testing costs never decrease.  This is surely not what the Court had in mind when deciding Mayo; they deserve the opportunity to clarify the boundaries of patent eligibility with more care.

Ariosa Diagnostics, Inc. v. Sequenom, Inc. (Fed. Cir. 2015)
Panel: Circuit Judges Reyna, Linn, and Wallach
Opinion by Circuit Judge Reyna; concurring opinion by Circuit Judge Linn