A distinction without a difference?

Updated: Jul 27

Federal Circuit holds claims directed to a process used in a diagnostic test (but not directed to the test itself) to be patent-eligible.

Illumina, Inc., Sequenom, Inc.,

Plaintiffs-Appellants v. Ariosa Diagnostics, Inc., Roche Sequencing Solutions, Inc.,

Roche Molecular Systems, Inc.,



March 17, 2020

Case Summary

Ever since the Supreme Court’s Alice and Mayo decisions, the Federal Circuit has consistently held claims covering medical diagnostic techniques to be directed to natural phenomena and therefore ineligible for patent protection. One such decision (from 2015) is Ariosa v. Sequenom. The patent at issue in that case (6,258,540) was based on a discovery that cell-free fetal DNA (cff-DNA) existed in maternal blood; if extracted and amplified, this DNA could be used to test for genetic abnormalities. Before this discovery, these types of genetic tests required amniocentesis, a much more expensive and risky procedure.

Extracting cff-DNA from a maternal blood sample is not trivial, because these samples also include a large amount of cell-free DNA from the mother. The ‘540 patent solved this problem by recognizing that fetal DNA includes nucleic acid sequences inherited from the father; and by detecting and amplifying paternally-inherited nucleic acids present in a blood sample (using known DNA manipulation techniques), it would be possible to distinguish cff-DNA from maternal DNA.

In its 2015 decision, the Federal Circuit found that claims of that patent fail step one of the Alice/Mayo patent eligibility test because the method they recite “begins and ends with a natural phenomenon"—that cff-DNA exists in maternal blood. And under step two of the Alice/Mayo test, the claimed method (which simply recites conventional DNA detection and amplification techniques) did not transform the natural phenomenon into a patent-eligible application of that phenomenon.

Like the patent discussed in the 2015 Ariosa decision, the patents at issue in this case (9,580,751 and 9,738,931) relate to cff-DNA present in maternal blood; but instead of being directed to a diagnostic test, these claims are directed to methods for removing cell-free maternal DNA from a blood sample, leaving behind a sample with a larger percentage of cff-DNA.

The patents explain that the claimed methods became possible when the inventors discovered that “extracellular fetal DNA has a relatively small size of approximately 500 base pairs or less, whereas the majority of circulatory extracellular maternal DNA in maternal plasma has a size greater than approximately 500 base pairs.” The inventors also realized that they could use existing DNA separation techniques to remove the relatively larger maternal DNA from a sample, leaving behind a sample with a greater percentage of fetal DNA.

After patent owner Illumina filed suit for alleged infringement of these patents, defendant Roche moved for summary judgment that the asserted claims are directed to ineligible subject matter. Following the reasoning in the Federal Circuit’s 2015 Ariosa decision, the District Court granted the motion, finding the claims to be directed to the natural phenomenon that in a maternal blood sample, cff-DNA is smaller in size than cell-free maternal DNA. The District Court also said that the conventional DNA manipulation steps recited in the claims failed to transform them into a patent-eligible application of that natural phenomenon.

Over a dissent by Judge Reyna, the Federal Circuit reversed. The Majority acknowledged that under Mayo, the Federal Circuit had consistently held medical diagnostic claims to be patent-ineligible as directed to natural phenomena. These two judges also agreed that the inventors of the two patents had discovered a natural phenomenon: That in maternal blood, cff-DNA is typically smaller (has fewer base pairs) than cell-free maternal DNA.

But the Majority found that the patent claims are not “directed to” that phenomenon; rather, they are directed to patent-eligible methods that use the natural phenomenon—specifically to methods for preparing a fraction of cell-free DNA that is enriched in fetal DNA.

Because the process steps change the composition of the mixture (resulting in a DNA fraction that is different from the naturally-occurring fraction in the mother's blood), the process achieves more than simply observing that fetal DNA is shorter than maternal DNA, and more than simply detecting the presence of that phenomenon. The claims are therefore not “directed to” this natural phenomenon, they pass Alice/Mayo step one, and are patent-eligible.

In his dissent, Judge Reyna noted that the panel was bound by the 2015 Ariosa decision, and by other later-issued Federal Circuit decisions; these decisions require courts, when evaluating process claims for patent eligibility, to ask whether the “claimed advance” of the patent over the prior art “improves upon a technological process or [is] merely an ineligible concept.” According to Judge Reyna, the claims at issue here must be directed to a natural phenomenon (that cff-DNA in maternal blood is smaller than cell-free maternal DNA) because the specification’s claimed advance over the prior art is the discovery of that phenomenon.

Indeed, the patent specification states that the problem—separating cff-DNA from maternal DNA—was overcome when the inventors made the “surprising” discovery that in maternal blood, fetal DNA is shorter than maternal DNA, and “[t]his surprising finding forms the basis of the present invention.” Therefore, if the specification highlights the discovery of a natural phenomenon as the only “surprising” or “unexpected” aspect of the invention (which the specifications do here), the discovery of this natural phenomenon must constitute the claimed advance over the prior art.

In response to the Majority's assertion that the claims are directed to “a patent-eligible method that utilizes [the natural phenomenon]”—specifically, improvements in “size discriminat[ion]” and “selective[] remov[al]” techniques—Judge Reyna said that since because techniques were well known, they could not (under the Federal Circuit’s earlier Ariosa and Athena decisions), legally constitute a claimed advance over the prior art.

Having determined that the asserted claims are directed to a natural phenomenon and fail to meet Alice/Mayo step one, Judge Reyna then asked whether, under step two of that test, there are additional features of the claim that transform it “into a patent-eligible application” of the natural phenomenon. Because these claims simply adapt commercially available DNA separation techniques to the natural phenomenon (that cff-DNA is smaller than maternal DNA), he concluded that they do not.

202003 Case summary of Illumina v Arios


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