Until I read that another commentator wrote that the split panel decision in Illumina v. Ariosa Diagnostics, Appeal No. 2019-1419 (Fed. Cir., March 17, 2020) struck a hopeful note in the patent eligibility wars, I confess that I had missed this decision altogether. I can only blame this on the general chaos that the pandemic has brought to all of our affairs.

But this decision is entitled to some analysis, a fact that becomes abundantly clear when you read it with a copy of Ariosa Diagnostics v. Sequenom, Appeal no. 2014-1139, 2014-1141 (Fed. Cir., June 12, 2015) at hand. Here is claim 1 of the Ariosa decision:

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 [cff DNA] from the serum or plasma sample and

detecting the presence of a paternally inherited nucleic acid of fetal origin in the  sample.

The unanimous panel of Judges Reyna, Linn and Wallach held that this was a patent-ineligible attempt to claim a natural phenomenon: “Thus the claims at issue…are generally directed to detecting the presence of a naturally occurring thing or a natural phenomenon, cffDNA, in maternal plasma or serum. …[T]he claimed invention begins and ends with a naturally occurring phenomenon”. That is the end of the Mayo/Alice step 2A – in the MPEP – analysis, and the panel jumped right into the Sep B analysis, and we know h0w that turned out.

Judge Linn concurred but his opinion sounded more like a dissent: “In short, Sequenom’s invention is nothing like the invention at issue in Mayo. Sequenom ‘effectuated a practical result and benefit not  previously attained.’” He seemed to be arguing for  an “improvement standard” that would be a part of the s. 2A analysis of whether or not a claim is “directed to” a natural phenomenon.

Now let’s jump about 20 years into the future of s. 101 jurisprudence and see how Illumina’s claims fared:

Claim 1 [of U.S. Pat. No. 9,580,751]. A method for preparing a [DNA]  fraction from  a pregnant human female

Useful for analyzing a genetic locus involed in a fetal chromosomal aberration, comprising:

a. extracting DNA from a substantially 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 of DNA produced in (b).

After the usual discussion of the Alive/Mayo test, the Judges Lourie and Moore –both technically versed—get down to their brass tacks analysis, beginning: “This a not a diagnostic case. And it is not a method of treatment case, it is a method of preparation case.” The Judges note that, while method of medical treatments are patent eligible and diagnostic methods are not, “The claims of this case do not fall into either bucket, and we consider the claims under the Alice/Mayo test.”

The Judges begin with the undeniable fact that the inventors in this case discovered a natural phenomenon, but that alone dose not resolve the step 2A analysis of whether a patent-ineligible phenomenon is what the claims are “’directed to’” [citing the CellzDirect decision], i.e. “whether they claim the discovered natural phenomenon itself vs. eligible subject matter that exploits the discovery of the natural phenomenon [that cell-free fetal DNA tends to be shorter than cell-free maternal DNA in a mother’s bloodstream]…We conclude that the claims are not directed to that natural phenomenon but rather to a patent eligible method that utilizes it.”

The Judges’ rationale is that the specific process steps recited in the claims change the change the composition of the “mixture”—the sample of cell-free plasma or serum—to yield a DNA fraction that is different from the naturally-occurring fraction in the mother’s blood. So, in the Judge’s eyes, the DNA fraction that is the end-product of step (b) of the claim is not a natural product, but is a product of the hand of man—a fraction of cell-free DNA  “that is enriched in fetal DNA.”

Distinguishing Ariosa is a task the Judges face head-on:

“In essence, the inventors in Ariosa 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. Here in contrast, the claims are directed to more than just the correlation between a DNA fragment’s size and its tendency to be either fetal or maternal.  And the claims do not merely cover a method for detecting whether a cell-free DNA fragment is fetal or maternal based on its size. Rather the claimed method removes some maternal DNA for the mother’s blood to prepare a fraction of cell-free DNA that is enriched in fetal DNA…These methods are ‘directed to’ more than merely the natural phenomenon that the inventors discovered. Accordingly, we conclude at step one (PTO 2A) of the Mayo/Alice test that the claims are not directed to a patent-ineligible concept and we need not reach step 2 [PTO step 2B] of the test.”

And so, unlike Ariosa, the claimed method does not begin and end with the natural phenomenon.  But does the Judges’ rationale hold legal water? Would the Fed. Cir. decide Ariosa differently if it was argued post-Illumina? What if the Ariosa claims had been worded slightly differently so, that instead of beginning “a method for detection” or “a method for performing a prenatal diagnosis”, they had begun more like the process claims in Illumina, e.g., “a method for preparing paternally inherited nucleic acid of fetal origin” and ended with an “isolating” step. As in the Illumina claims, the process steps per se were well-known. However, now the Ariosa claims are using PCR to prepare and isolate a product that does not exist in nature – or at least is markedly different from its natural counterpart—amplified paternally inherited DNA extracted from the jungle of nature – a sample of maternal serum or plasma.

This post is already too long, so I will not comment on Judge Reyna’s dissent, except to note that he references the language of Ariosa—he was on that panel—that the invention begins and ends with a “naturally occurring substance”. But so does Cellzdirect’s process, and I don’t think that that “rule”—if it even is a rule—resolves the “directed to” inquiry.

I plan to do a further post on Judge Reyna’s dissent. Any “pre-comments” are welcomed. Stay safe!