Illumina has now filed its brief in opposition, completing the certiorari petitions/responses for all parties in the concurrent American Axle and Ariosa patent eligibility cases. True to form, neither of the filings in American Axle referenced Ariosa, and neither of the filings in Ariosa referenced American Axle. Whereas the petition in American Axle was brought by the patent holder, in Ariosa the patent holder was the respondent (Illumina). The respondent and accused infringer Neapco in the American Axle cased filed an opposition running about 40 pages. Illumina’s just-filed opposition is only 25 pages long. In short, Illumina urges that its claims are for processes expressly within the scope of Section 101 and therefore are eligible under either part of the Alice test.

In an almost outline-style form, Illumina begins by explaining what its patents claim: “a new and useful process for enriching the amount of fetal DNA in a maternal blood sample.” Illumina elaborates starting with the basics, i.e., that “a pregnant woman’s plasma contains fragments of both her own DNA and small amounts of DNA from the fetus.” This allows non-invasive fetal genetic testing, but there’s what Illumina characterizes as “a signal-to-noise” problem in that there’s much more maternal DNA than fetal DNA. To address this issue, Illumina looked at the fetal and maternal fragments and found a difference in the size of those fragments—“it was more common for fetal DNA fragments to be smaller.” Based on this observation, Illumina came up with the claimed method, namely: (a) extracting DNA from maternal plasma; (b) producing a fraction of the DNA by size discrimination of the fragments and “selectively removing the DNA fragments greater than approximately 500 base pairs;” and (c) analyzing a genetic locus in that fraction. It is the quoted language in this claim that Illumina focuses on.

How We Got Here

Before arguing why it believes the Federal Circuit was correct in reversing the district court’s determination that the claims are not patent eligible, Illumina provides a quick summary of what the Federal Circuit did: it determined that the claims are not “directed to” a natural phenomenon. The Federal Circuit explained that the natural phenomenon is “that cell-free fetal DNA tends to be shorter than cell-free maternal DNA in a mother’s bloodstream.” What the claims are directed to, according to the Federal Circuit, is a patent-eligible method that uses this phenomenon, i.e., a “method[] for preparing a fraction of the cell-free DNA that is enriched in fetal DNA.” The Federal Circuit determined the claimed size thresholds (e.g., 500 base pairs in the claim recited above) to be “human-engineered parameters that optimize the amount of maternal DNA that is removed from the mixture and the amount of fetal DNA that remains in the mixture in order to create an improved end product that is more useful for genetic testing than the original natural extracted blood sample.” Illumina provides only brief mention to Judge Reyna’s dissent asserting that the only claimed advance was the finding that the fetal DNA fragments tend to be shorter than the maternal fragments.

The Federal Circuit Got It Right

Moving from this background, Illumina quickly explains why it believes the Federal Circuit correctly distinguished Myriad, urged by petitioners (collectively, “Ariosa”) as controlling. For instance, “In Myriad, this Court emphasized that there were ‘no method claims before th[e] Court.’” Illumina then proceeds to walk through the Alice test. Other than sprinkling in adverbs such as “plainly” and “clearly,” this portion of Illumina’s brief is likewise succinct. For context, Illumina begins by arguing that the claims at issue are “for a series of steps definitely conducing to an end: they are for a new, specific method for enriching a blood fraction.” Citing earlier Supreme Court decisions, Illumina states, “Just like a process for enriching ore, refining oil, or purifying water, that process for enriching a blood sample is a ‘process.’” Illumina then moves to the specifics of the two-part test:

To determine whether a patent is “directed to” a natural phenomenon, one must first identify the phenomenon itself. The Federal Circuit correctly identified it as the fact “that cell-free fetal DNA tends to be shorter than cell-free maternal DNA in a mother’s bloodstream.” [Citing to the record, including Judge Reyna’s dissent].

As the Federal Circuit determined, the claims are not “directed to” that tendency, “but rather to a patent-eligible method that utilizes it,” namely a “method[] for preparing a fraction of cell-free DNA that is enriched in fetal DNA.”

Illumina urges that there is no natural law that dictates fetal DNA is always shorter than maternal DNA, or one that “much less dictates a uniform cutoff at approximately 500 (or 300) base pairs.” On the contrary, Illumina points out that the relative size varies greatly from woman to woman.“ For example, in a sample from one pregnant woman, 22% of the fragments shorter than 300 base pairs were determined to be fetal; from another woman, the figure was 87%.” Illumina takes issue with Ariosa’s characterization of the Federal Circuit “as holding ‘that the mere separation of smaller human DNA fragments from larger ones is sufficient to survive a Section 101 challenge, without regard to the inventiveness of techniques used to achieve that separation.’”

Illumina next moves on to step two of the Alice test, saying that its claims would be independently patent-eligible there because those specified thresholds of 500 or 300 base pairs transform the nature of the claim into a patent-eligible application, rather than preempting any natural phenomenon.

No Conflict with Other Case Law

Illumina returns to the theme previewed earlier that the Federal Circuit correctly distinguished both Supreme Court and Federal Circuit case law urged by Ariosa. Instead, the Federal Circuit held the current case to be analogous to CellzDirect, involving use of multiple freeze-thaw cycles to increase a proportion of viable liver cells in a sample. Illumina likewise distinguishes the Funk Brothers case as involving a “discovery of the fact that certain strains of … bacteria can be mixed.” In that case, Illumina observes, “the Court noted that it was not ‘presented the question whether the methods of selecting and testing the non-inhibitive strains are patentable.’”

Observations on Side Effects

Illumina makes two brief parting arguments. The first argument disputes the ripple effects that Ariosa urges, saying, for example, that nothing in this case makes more likely the “risk of patenting DNA itself” or of dismissing with cases by merely labeling them as being in one category or another. Indeed, Illumina argues, “the Federal Court [sic, Circuit] made clear that the Alice test remains the lodestar.” Illumina asserts that it is Ariosa’s arguments that, if adopted, “would cast a cloud of uncertainty over a vast array of important patents on processes like purifying water, cleaning air, enriching gas, refining oil, filtering noise, and ‘thousands of others that recite processes to achieve a desired outcome.’” (quoting CellzDirect)

The second argument is similar to that made by Neapco in the American Axle case: that the current case would be, as Illumina puts it, “a poor vehicle for review.” Not only did Ariosa arise from an interlocutory posture that itself under “ordinary practice” provides sufficient ground for denial, but Illumina adds that the question presented (Alice step one) may not be dispositive since it could still prevail under Alice step two. And finally, Illumina argues, Ariosa’s arguments do not even address all of the claims, some of which involve, for example, the use of microarrays, which have not been previously used with cell-free DNA.

So now, petitions and oppositions are complete for both the Ariosa and American Axle cases. Those interested in a deeper dive can explore the dozen or so amicus briefs filed in American Axle (none in Ariosa). Stay tuned here for further developments.


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