Illumina, Inc. v. Ariosa Diagnostics, Inc. (Fed. Cir. 2020)

McDonnell Boehnen Hulbert & Berghoff LLP

McDonnell Boehnen Hulbert & Berghoff LLP

Federal Circuit Hands Down Modified Opinion in Illumina, Inc. v. Ariosa Diagnostics, Inc.

Earlier this year, the Federal Circuit (somewhat surprisingly) found claims of two Sequenom patents directed to methods for detecting fetal DNA in maternal blood to satisfy the subject matter eligibility requirements of Section 101 (see "Illumina, Inc. v. Ariosa Diagnostics, Inc. (Fed. Cir. 2020)").  The surprise arose in part due to the Federal Circuit's track record of finding all diagnostic method claims to be ineligible as being directed to a natural law without "something more" to overcome the patentability preclusion created by the Supreme Court in Mayo Collaborative Services v. Prometheus Laboratories, Inc. (see, e.g., Judge Moore's dissent in Athena Diagnostics, Inc. v. Mayo Collaborative Servs., LLC, 927 F.3d 1333, 1352 (Fed. Cir. 2019) ( "Since Mayo, we have held every single diagnostic claim in every case before us ineligible.").  Another reason, of course, is that the Federal Circuit affirmed a finding of patent ineligibility in Ariosa Diagnostics, Inc. v. Sequenom, Inc.  Nevertheless, a divided panel found a patent eligibility-creating distinction in the claims asserted in this most recent case (over a dissent by the author of the Ariosa v. Sequenom decision, Judge Reyna) and today the Court issued a revised opinion in the face of Ariosa's petition for rehearing.

To recap, the case arose over U.S. Patent No. 9,580,751 (the '751 patent) and U.S. Patent No. 9,738,931 (the '931 patent), directed to the solution of an unexpected difficulty in detecting cell-free fetal DNA (cffDNA):

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

The inventors found that cffDNA was significantly smaller (300-500 bp) than the "interfering" maternal DNA, and thus using admittedly conventional techniques of size separation the cffDNA could be isolated and rendered detectable.

Illumina and Sequenom asserted claims 1, 2, 4, 5, 9, and 10 of the '751 patent and claims 1, 2, and 10–14 the '931 patent against Ariosa and Roche Diagnostics; the Court considered claim 1 from each patent to be representative:

'751 patent:

  1. A method for preparing a deoxyribonucleic acid (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 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
            (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).

'931 patent:

  1. A method, comprising:
    (a) extracting DNA comprising maternal and fetal DNA fragments from a substantially cell-free sample of blood plasma or blood serum of a pregnant human female;
        (b) producing a fraction of the DNA extracted in (a) by:
            (i) size discrimination of extracellular circulatory fetal and maternal DNA fragments, and
            (ii) selectively removing the DNA fragments greater than approximately 300 base pairs,
        wherein the DNA fraction after (b) comprises extracellular circulatory fetal and maternal DNA fragments of approximately 300 base pairs and less and a plurality of genetic loci of the extracellular circulatory fetal and maternal DNA fragments; and
        (c) analyzing DNA fragments in the fraction of DNA produced in (b).

The District Court on summary judgment held these claims and all asserted claims to be ineligible under 35 U.S.C. § 101 and the Supreme Court's Alice/Mayo test (see "Illumina, Inc. v. Ariosa Diagnostics, Inc. (N.D. Cal. 2018)"), and Illumina appealed.

In the original opinion, the Federal Circuit reversed, in an opinion by Judge Lourie joined by Judge Moore; Judge Reyna dissenting (as he does in this revised opinion).  Judge Lourie justified the different outcome here by stating "[t]his is not a diagnostic case.  And it is not a method of treatment case.  It is a method of preparation case."  But the majority based its decision on this distinction:  "[h]ere, it is undisputed that the inventors of the '751 and '931 patents discovered a natural phenomenon.  But at step one of the Alice/Mayo test, 'it is not enough to merely identify a patent-ineligible concept underlying the claim; we must determine whether that patent-ineligible concept is what the claim is 'directed to," citing Rapid Litig. Mgmt. Ltd. v. CellzDirect, Inc.  It is undisputed that cell-free fetal DNA (cffDNA) exists in maternal blood and its presence is a natural phenomenon, and moreover that the size differentials and distributions that form the predicate basis for the claims at issue here are also naturally occurring.  But the panel majority held that the claims were not merely "directed to" that natural phenomenon, but rather were directed to a method that exploits the natural phenomenon that renders the claims patent-eligible.  Sounding a theme he first enunciated in Vanda Pharmaceuticals Inc. v. West-Ward Pharmaceuticals, Judge Lourie recognizes the distinction that the claims at issue recited "specific process steps—size discriminating and selectively removing DNA fragments that are above a specified size threshold" that increased the relative amount of cffDNA in the processed sample compared to maternal DNA and thus "change[d] the composition of the mixture" and produced a DNA-containing fraction that was different from what naturally occurs in maternal blood.

Judge Lourie's latest opinion reiterates most of these themes.  The basis of the decision remains that "this is not a diagnostic case.  And it is not a method of treatment case.  It is a method of preparation case."  As in the original opinion, the panel majority are somewhat critical of appellants' inability (in the majority's view) to "clearly identify the natural phenomenon that forms the basis of its challenge" but finds that the parties' differences on this point to be relatively meaningless distinctions and adopts Illumina's definition that the natural phenomenon underlying the claimed invention is that "cell-free fetal DNA tends to be shorter than cell-free maternal DNA in a mother's bloodstream."  But the majority arrives at the same conclusion as before:  although the claims are based on this natural phenomenon they "are not directed to that natural phenomenon but rather to a patent-eligible method that utilizes it" (emphasis in opinion).

And the basis of this conclusion relies at least in part on the specific method steps recited by the claims, which might constitute the ineluctable "something more" mandated by the Supreme Court's jurisprudence that looks enough like novelty to disturb any patent practitioner (or more likely scholar) concerned with doctrinal consistency.  But this insistence also cabins the scope of the claims to the specifically recited steps, which goes a long way towards avoiding the overbroad scope that seems to have been at least part of the Supreme Court's concern regarding preemption motivating the Court's attempts to restrict patent eligibility of certain types of claims.  Also important for the panel majority is that the choice of the size distinctions recited in the claims are not themselves natural phenomenon but are "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."  And the result of the claimed methods are a mixture of DNA fragments having a change in their composition, being enriched in fetal-derived DNA fragments shorter than 500 (the '751 patent) or 300 (the '931 patent) basepairs.

The opinion, like its earlier version, distinguishes the claims at issue here with the claims in Supreme Court and Federal Circuit precedent found to be patent-ineligible, most notably that these claims are not directed to isolated DNA itself (Association for Molecular Pathology v. Myriad Genetics, Inc., 569 U.S. 576 (2013)), or merely detecting its presence in maternal blood (Ariosa), or even determining "whether a cell-free DNA fragment in a previously-prepared sample is fetal or maternal based on the natural size distribution of cell-free DNA fragments" but rather methods for preparing a mixture enriched in cffDNA based on "conventional separation technologies can be used in unconventional ways," specifically the claimed thresholds of 500 bp and 300 bp for separating fetal from material DNA ("Roche[] has presented no evidence that thresholds of 500 base pairs and 300 base pairs were conventional for separating different types of cell-free DNA fragments.").

An admittedly cursory comparison between the majority opinion issued in March and the one issued today finds precious little difference in the reasoning advanced by the Court.  In contrast, Judge Reyna's dissent appears to refine some of the Judge's arguments but at bottom reiterates his opinion that these claims are directed to a patent-ineligible natural phenomenon.

The Court is properly not transparent regarding the internal discussions and arguments asserted by those Judges who share the majority's views and those who share Judge Reyna's views.  But in light of the great similarities of these opinions it seems apparent that the Court was most comfortable not deciding to hear the case as a result of the revisions occasioned in the opinion handed down today.  Whether there are additional motivations (including putting the panel's disparate views in better condition for Supreme Court review) may become apparent if the Court deigns to revisit what it has wrought in the years since deciding the proper metes and bounds of Section 101 became a priority for the Court.

Illumina, Inc. v. Ariosa Diagnostics, Inc. (Fed. Cir. 2020)
Panel: Circuit Judges Lourie, Moore, and Reyna
Opinion by Circuit Judge Lourie; dissenting opinion by Circuit Judge Reyna

DISCLAIMER: Because of the generality of this update, the information provided herein may not be applicable in all situations and should not be acted upon without specific legal advice based on particular situations.

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