Introduction

The Federal Circuit, in Illumina, Inc., v. Ariosia, reversed the summary judgment decision of a lower trial court and upheld—as patent subject matter eligible—claims in two patents (U.S. 9,580,751; U.S. 9,738,931). The patented claims, the patentee asserted, address a problem with trying to diagnose fetal abnormalities using fetal cell-free DNA. This is a noteworthy case for diagnostic test manufacturers. We summarize the case below, and then provide our thoughts.

The Problem

The court, quoting from one of the patents, noted that:

The major proportion (generally >90%) of the extracellular DNA in material circulation is derived from the mother. This vast bulk of maternal circulatory extracellular DNA renders it difficult, if not impossible, to determine fetal genetic [alterations] . . . from the small amount of circulatory extracellular [fetal] DNA.

Hence, the patentee asserted they identified a problem for diagnosing fetal abnormalities using fetal cell-free DNA circulating in a mother's blood: that there is a small amount of fetal cell-free DNA relative to the much larger amount of maternal cell-free DNA; and this makes diagnoses based on the small amount of fetal cell-free DNA difficult.

Solving the Problem

To address this problem, the inventors noticed that the majority of circulating fetal cell-free DNA was small-in-size—500 base pairs or less; and contrastingly, the majority of circulating maternal cell-free DNA larger in size—greater than 500 base pairs. The solution, the patentee asserted, enriching the amount of fetal-cell free DNA in a sample—arose from this observation.

The claims of the two patents are directed to methods directed toward this solution to the problem, for which the claim recited below is representative:

A method for preparing a DNA fraction from a pregnant human female useful for analyzing a genetic locus involved in a fetal chromosomal aberration, comprising

(a) extracting DNA from a cell-free sample of blood plasma or blood serum of a pregnant human female to obtain extracellular circulatory fetal and maternal DNA fragments;

(b) producing a fraction of the DNA extracted in (a) by:

(i) size discrimination of extracellular circulatory DNA fragments, and

(ii) selectively removing the DNA fragments greater than approximately 500 base pairs,

wherein the DNA fraction after (b) comprises a plurality of genetic loci of the extracellular circulatory fetal and maternal DNA; and

(c) analyzing a genetic locus in the fraction of DNA produced in (b).

Thus, the patentees: i) asserted they solved the problem, which they identified, by enriching the amount of fetal cell-free DNA in the maternal blood sample; and ii) claimed their solution to the problem.

The Court's Analysis

The court began its analysis by noting that this was not a diagnostic case, not a method of treatment case, but rather a preparation case (e.g., preparation of a sample for diagnostic testing). Having made that distinction, the court proceeded to determine if the claims were patent eligible.

Briefly, courts determine if method claims are patent subject matter eligible by employing the Supreme Court's Alice/Mayo test. If the method claim contains or relies upon a judicial exception that, by itself, would not be patent eligible, courts apply the two-step Alice/Mayo test to determine patent subject matter eligibility.

Step one of the test can be stated: Is a method claim, which contains a patent ineligible exception, drawn to more than the patent ineligible exception. Critically, the court determined that the claims "are not directed to [ a patent ineligible exception] (i.e., a natural phenomenon) but rather to a patent-eligible method that utilizes it." (Emphasis in original.) The court found this dispositive in determining the claims were patent subject matter eligible, without needing to proceed to the second step of the Alice/Mayo test.

The court noted that the process steps in the claim "change the composition of the mixture, resulting in a DNA fraction that is different from the naturally-occurring fraction in the mother's blood"; and that the process "achieves more than simply observing that fetal DNA is shorter than maternal DNA or detecting the presence of that phenomenon."

The court then distinguished the contested claims from an earlier case where claims were found patent ineligible because they "were directed to detecting a natural phenomenon." In essence, the inventors [in the earlier case] "discovered that cell-free fetal DNA exists, and then obtained patent claims that covered only the knowledge that [cell-free DNA] exists and a method to see that it exists."

In contrast, the court found that the currently contested claims "are directed to more than just the correlation between a DNA fragment's size and its tendency to be either fetal or maternal." […] "The claimed method removes some maternal DNA from the mother's blood to prepare a fraction of cell-free DNA that is enriched in fetal DNA. Thus, the claims in this case are different from the claims that we held invalid [in the earlier case]."

Further, the court noted that the claims "do not cover cell-free DNA itself (which the court hints would likely be patent ineligible) but rather a process for selective removal of non-fetal DNA to enrich a mixture in fetal DNA."

In summary, the court held:

Rather … than focusing on what the inventors … did not invent, we focus our Alice/Mayo step one analysis on what the inventors did purport to invent and what they claimed in their patents: methods for preparing a fraction of cell-free DNA by the physical process of size discriminating and selectively removing DNA fragments longer than a specified threshold. Those methods are "directed to" more than merely the natural phenomenon that the inventors discovered. Accordingly, we conclude at step one of the Alice/Mayo test that the claims are not directed to a patent-ineligible concept, and we need not reach step two of the test.

Our Thoughts

At the very beginning of the case, the court laid a foundation for distinguishing this case from earlier cases by placing the claims at issue in a separate category from earlier cases where the claims from those earlier cases were found patent ineligible (diagnostic cases), and earlier cases where claims were found patent subject matter eligible (method of treatment cases). Thus, the court was setting the stage to determine that the claims in this case—drawn to preparation of a sample for diagnostic testing—could set a precedent for being a type of claim that could pass the patent subject matter eligibility test in a diagnostic context.

Also, in the current case, the patent applications presented claims in a problem-solution approach framework, which the judges found helpful. We note, that although not universally applicable, presenting claims in a problem solution approach can also be valuable when prosecuting claims in some international jurisdictions (e.g., Europe).

Further, the court determined that the claims were drawn to patent eligible subject matter based solely on the first prong of the Alice/Mayo test, without needing to resort to the test's second prong. This is important, because failure to determine that a claim is patent subject matter eligible based solely on the test's first prong can lead to a claim being at risk of found patent ineligible at the second test prong either during prosecution or subsequent challenge—because many methods arguably use conventional and routine procedures. Drafting applications to frame inventions in ways that can help courts, and patent examiners, to determine patent eligibility based on the first Mayo/Alice test prong is not only a prerequisite for eligibility, but can eliminate the need for further proofs.

Also, if a patentee drafts claims along the lines presented here, and the claims are found to be patent eligible (and patentable), this opens up interesting possibilities for dependent, diagnostic method claims. Diagnostic claim steps can be appended as dependent claims—and found patentable based on the patent eligibility of the separation process—even if the diagnostic steps, on their own, might not be patent subject matter eligible. Moreover, if taking this approach, split-infringement considerations should be taken into account and minimized.

Finally, we note that one judge dissented and would have instead held that the claimed invention merely applied a natural phenomenon.

Charles Andres and Prashant Girinath contributed to the preparation of this Wilson Sonsini alert.