Last month, in Illumina, Inc. v. Natera, Inc., District Judge Susan Illston of the U.S. District Court for the Northern District of California denied a motion to dismiss filed by Defendant Natera, Inc., to dismiss a complaint filed by Plaintiff Illumina, Inc. against Natera.  Illumina initiated the dispute between the parties by filing a patent infringement action against Natera, asserting that Natera's sale of its Panorama™ Prenatal Screen, a non-invasive prenatal test for Down syndrome, infringed U.S. Patent No. 9,493,831.  In response to Illumina's complaint, Natera filed a motion to dismiss under Federal Rule of Civil Procedure 12(b)(6), arguing that the claims of the '831 patent are invalid under 35 U.S.C. § 101 as being directed to patent-ineligible subject matter and for being void of any inventive concept.

The '831 patent, which is entitled "Methods for Fetal Abnormality Detection," is directed to methods for "selectively enriching non-random polynucleotide sequences," "generating libraries of sequences," and "detect[ing] fetal aneuploidy."  Representative claim 1 recites:

1.  A method for preparing a sequencing library from a maternal blood sample, the method comprising:
    a.  obtaining a maternal blood sample comprising fetal and maternal cell-free DNA;
    b.  selectively enriching a plurality of non-random polynucleotide sequences of genomic DNA from said fetal and maternal cell-free DNA to generate a library of enriched non-random polynucleotide sequences, wherein said plurality of non-random polynucleotide sequences comprises at least 100 different nonrandom polynucleotide sequences selected from a chromosome tested for being aneuploid, said enriching comprising:
        (i)  a first amplification step to generate a plurality of first reaction products, said amplification comprising at least 100 first primers configured to amplify at least 100 different non-random polynucleotide sequences;
        (ii)  a second amplification step to generate a second reaction product, said amplification comprising a second set of primers comprising sequences contained in the first reaction products; and
        (iii)  a third amplification step to generate a third reaction product comprising said library of enriched non-random polynucleotide sequences, said amplification comprising a third set of primers comprising sequences contained in the second reaction products;
        wherein at least one primer of at least one of the second and third sets of primers includes a sequence configured to be added to the different non-random polynucleotide sequences to permit the enriched non-random polynucleotide sequences of the library to anneal to a same sequencing primer for the enriched non-random polynucleotide sequences of the library.

In considering Natera's motion to dismiss, the District Court began by noting that the Supreme Court set forth a two-step analytic framework for distinguishing patents that claim laws of nature, natural phenomena, and abstract ideas from those that claim patent-eligible applications of those concepts.  The District Court then cited to the Federal Circuit's decision in Ariosa Diagnostics, Inc. v. Sequenom, Inc. for an articulation of this two-step analysis:

The first step looks to determine whether claims are directed to a patent-ineligible concept.  If they are, the second step is to consider whether the additional elements recited in the claim transform the nature of the claim into a patent-eligible application by reciting an inventive concept that is sufficient to ensure that the patent in practice amounts to significantly more than a patent upon the [ineligible concept] itself.

88 F.3d 1371, 1380 (Fed. Cir. 2015) (internal quotations and citations omitted).

With respect to the first step of the patent eligibility analysis, Natera argued that the '831 patent is directed to a patent-ineligible concept because it is concerned primarily with obtaining a library that contains non-altered DNA sequences that are naturally occurring, and further, that the addition of sequence tags or indexing sequences does not confer patent eligibility because they do not otherwise alter the naturally occurring genetic information contained in the DNA sequences of interest.  Illumina countered that the '831 patent is directed to a method of preparing a synthetic nucleic acid library comprised of non-naturally occurring nucleic acid molecules, wherein the resulting nucleic acid molecules include the same sequencing primer (claim 1) and/or an index sequence (claims 2, 3, and 14).

Looking to the Federal Circuit's decision in Ariosa Diagnostics, Inc. v. Sequenom, Inc., the District Court concluded that:

The claims of the '831 patent similarly use cffDNA, beginning with samples of naturally occurring "fetal and maternal cell-free DNA."  '831 Patent col. 63 l. 41-42.  The '831 patent is also directed towards amplifying specific sequences of the cell-free DNA and detecting fetal aneuploidies.  See '831 Patent at [57].  Like the claims in Ariosa that were directed to the detection of naturally occurring cffDNA, the claims of the '831 patent only enable aneuploidy detection if the non-random sequences retain their natural arrangement.  Consequently, the method claims of the '831 patent also "end[] with a natural phenomenon."  See Ariosa, 788 F.3d at 1376.

The District Court therefore determined that the '831 patent is directed to patent-ineligible subject matter.

With respect to the second step of the patent eligibility analysis, Natera argued that the '831 patent does not contain an inventive concept because the selective enrichment of DNA in the patent involves well-known, routine, and conventional amplification techniques.  Illumina responded by arguing that the '831 patent improves upon prior art techniques by addressing a need for selective enrichment of DNA sequencing for aneuploidy analysis to avoid producing non-target amplification products.

In denying Natera's motion, however, Judge Illston determined that "at this stage in litigation the factual record is not sufficient for the Court to conclude whether there is an inventive concept."  In particular, the District Court noted that it "cannot determine whether the amplification of 'at least 100 different non-random polynucleotide sequences' and the performance of 'successive rounds of amplification using primers that are directed to sequences within the products of prior amplification reactions' are routine or conventional" (emphasis in order).  In addition, the District Court noted that it "cannot determine whether the claimed selective enrichment leads to a technological improvement."

Illumina, Inc. v. Natera, Inc. (N.D. Cal. 2018)
Order Denying Motion to Dismiss by District Judge Illston