Illumina v. Ariosa Diagnostics: A Closer Look

The Federal Circuit recently found that a method for preparing an extracellular DNA fraction from a pregnant human female and using it for analyzing a genetic locus involved in a fetal chromosomal aberration was not directed to a natural phenomenon, and thus eligible for patenting. Illumina, Inc. v. Ariosa Diagnostics, Inc., No. 2019-1419 (Fed. Cir. March 17, 2020) (“Illumina v. Ariosa”). The decision includes a dissent. Appreciation of the reasoning of both the Majority and the Dissent is essential to understanding the current state of the debate on subject matter eligibility of processes involving natural phenomenon. The all-important question in such cases centers on how to determine whether such an invention is directed to a judicial exception. Stated differently, when does an invention that uses a natural phenomenon turn into a patent-eligible process rather than being directed merely to the natural phenomenon?

The claimed methods at issue are covered by U.S. Patents 9,580,751 and 9,738,931, owned by Illumina. The extracellular DNA fraction prepared by the methods are enriched in the DNA of fetal origin. The natural phenomenon involved is that the extracellular (or cell-free) DNA of fetal origin found in the mother’s bloodstream tends to be shorter than the cell-free DNA of the mother. Generally, over 90% of the extracellular DNA in the maternal circulation is derived from the mother and only a very small fraction from the fetus. As such, determining fetal genetic alternation using the extracellular DNA obtained straight from the maternal circulation is difficult. Illumina v. Ariosa, Majority Opinion at 3. Enriching for extracellular DNA of fetal origin solves this problem.

The Majority

In keeping with the trend started in 2016, the Majority (judges Lourie and Moore) focused on whether at step one of the Alice/Mayo test, the claims of Illumina’s patents were directed to a natural phenomenon or to subject matter that exploited the discovery of the natural phenomenon.

The Majority made two points. First, it reasoned that the claimed methods include process steps that lead to a DNA fraction that is different from the naturally-occurring fraction present in the mother’s blood (due to enrichment of cell-free fetal DNA). Thus, the process achieves more than simply observing that fetal DNA is shorter than maternal DNA or detecting the presence of that phenomenon. Id. at 10. Next, the Majority noted that the dependent claims, which name specific techniques for carrying out the steps of the method, illustrated the concrete nature of the claimed process steps. Id. at 10. These concrete process steps were used, not merely to observe the presence of the phenomenon that fetal DNA is shorter than maternal DNA, but to exploit that discovery in a method for preparation of a mixture enriched in fetal DNA. Id. at 11.

The Majority contrasted this case to Ariosa Diagnostics, Inc. v. Sequenom, Inc., 788 F.3d 1371 (Fed. Cir. 2015) (“Ariosa”), observing that in Ariosa, the inventors had discovered that cell-free fetal DNA exists, and then obtained patent claims that covered only the knowledge that it exists and a method to see that it exists. Illumina v. Ariosa, Majority Opinion at 11.

The Majority referred also to Rapid Litig. Mgmt. Ltd. v. CellzDirect, Inc., 827 F.3d 1042, 1050 (Fed. Cir. 2016) (“CellzDirect”), observing that in CellzDirect, having discovered that some fraction of hepatocytes are capable of surviving multiple freeze-thaw cycles, the inventors patented an improved process of preserving hepatocytes that required freezing hepatocytes, thawing the hepatocytes, removing the non-viable hepatocytes, and refreezing the viable hepatocytes. Illumina v. Ariosa, Majority Opinion at 12-13. The invention was patent eligible because it was not simply an observation or detection of the ability of hepatocytes to survive multiple freeze-thaw cycles; rather, the claims were directed to a new and useful method of preserving hepatocyte cells. Id. Likewise, the Majority observed, the Illumina inventors used their discovery to invent a method of preparing a fraction of DNA that includes physical process steps to selectively remove some maternal DNA in blood to produce a mixture enriched in fetal DNA. Id. at 13.

Therefore, the “methods are “directed to” more than merely the natural phenomenon that the inventors discovered,” the Majority stated. Id. at 14 (emphasis added). Accordingly, at step one of the Alice/Mayo test the claims were found to be not directed to a patent-ineligible concept.

Thus, in order for a method reciting a natural phenomenon to be “directed to more than a natural phenomenon” the method must use the natural phenomenon to achieve something more than simply the observing of the natural phenomenon. How much more needs to be achieved, however, is not clear. Unlike the Majority, the Dissent did not think that much was achieved beyond observing the natural phenomenon.

The Dissent

The Dissent’s (Judge Reyna’s) main point was that the Majority had disregarded “the well-established precedent for conducting the Alice, step one, “directed to” inquiry by failing to consider the patent’s claimed advance.” Since 2016, in a string of cases reciting process claims, the Federal Circuit had begun conducting the “directed to” inquiry by asking whether the “claimed advance” of the patent “improve[d] upon a technological process or [was] merely an ineligible concept based on both written description and the claims” (citing Athena Diagnostics, Inc. v. Mayo Collaborative Servs., LLC, 915 F.3d 743, 750 (Fed. Cir. 20l9).

Judge Reyna observed that if a written description highlighted the discovery of a natural phenomenon, e.g., by describing the natural phenomenon as the only “surprising” or “unexpected” aspect of the invention or that the invention was “based” on the discovery” of a natural law – the natural phenomenon likely constituted the claimed advance. Illumina v. Ariosa Dissenting Opinion at 7. The judge pointed to the specification of the ’751 patent for stating that the surprising finding that “the majority of the circulating extracellular fetal DNA has a relatively small size of approximately 500 base pairs or less…[which] forms the basis of the present invention” concluding therefrom that the claimed advance was a natural phenomenon. In the judge’s view, the claimed methods began and ended with naturally occurring substances and that the method steps did not alter those substances, again showing that the claimed methods were directed to a natural phenomenon. Id. at 8.

Dismissing the importance attached by the Majority to the use of concrete process steps, Judge Reyna noted that whether the steps are concrete is not the appropriate analysis for determining the claimed advance and wrote: “[w]here a written description identifies a technology as well-known or performed using commercially available tools or kits, that technology cannot logically constitute a claimed advance.” Id. at 9. The judge noted that in the instant case, “the claimed advance was “not an improvement in the underlying DNA-processing technology,” (unlike as hinted by the Majority) since the written description identified the claimed method steps as well-known or performed using commercially available tools or kits. Id. at 9 (emphasis added).

Judge Reyna also compared the instant case to CellzDirect, finding, however, that unlike CellzDirect, the claimed method steps here were not new, nor were the claimed techniques used in a new or unconventional way. Id. at 11.

The clear implication of Judge Reyna’s view is that the “directed to” inquiry requires asking whether the method involving the use of a natural phenomenon represents a real improvement over existing methods.

Discussion

This Dissent’s view appears to be more in line with many of the court’s decisions in the area of computer related inventions, where the “directed to” inquiry focuses on whether the invention led to improvements in computer related technologies. For example, in Enfish, LLC, v. Microsoft Corp. No. 2015-1244 (Fed. Cir. May, 2016) (“Enfish”), the Federal Circuit described the first step of the Alice/Mayo test as asking “whether the focus of the claims [was] on the specific asserted improvement in computer capabilities … or, instead, on a process that qualifies as an “abstract idea” for which computers are invoked merely as a tool.” Enfish at 11(emphasis added). On the other hand, in another case, finding claims directed to methods and systems for broadcasting signals to cellular telephones ineligible, the court said, “in this case, the claims are directed not to an improvement in cellular telephones but simply to the use of cellular telephones as tools in the aid of a process focused on an abstract idea.” Affinity Labs of Texas, LLC v. Directv, LLC, Nos. 2015-1845, 2015-1846, 2015-1847, 2015-1848 (Fed. Cir. Sept. 2016) at 15. (“Affinity Labs”) (emphasis added).

 Enfish and Affinity Labs support also the notion of determining what the claimed advance is by looking in part in the specification. For example, in Enfish the court stated, “[T]he “directed to” inquiry applies a stage-one filter to claims, considered in light of the specification, based on whether “their character as a whole is directed to excluded subject matter,” and in Affinity Labs, the court wrote, “[t]he “abstract idea” step of the inquiry calls upon us to look at the “focus of the claimed advance over the prior art” to determine if the claim’s “character as a whole” is directed to excluded subject matter.” Affinity Labs at 6. (emphasis added).

Finally, Judge Reyna’s dissent in Amdocs (Israel) Ltd. V. Openet Telecom, Inc. No. 2015-1180, (Fed. Cir. 2016) (“Amdocs”) is instructive. In this case, the judge noted that “the step one inquiry cannot be settled in the affirmative by the observation of an underlying abstract idea nor in the negative by recitation of just any additional limitations.” Amdocs Dissent at 7-8. Rather, the step one inquiry is a legal analysis that must focus on determining “what type of discovery is sought to be patented.” Id. (citing Parker v. Flook, 437 U.S. 584, 593) (emphasis added).

To summarize, the more a claim is seen to go beyond applying known techniques to the newly discovered natural phenomenon, resulting thereby in a new or improved process, the more likely it is to be found not directed to the natural phenomenon. And, Illumina v. Ariosa notwithstanding, it is quite likely that a court would examine the claim in light of the specification to determine the claimed advance over the prior art in order to decide whether the character of the claim as a whole is directed to ineligible subject matter.

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