Illumina, Inc. v. Ariosa Diagnostics, Inc.

• Decision Date: 17 March 2020
• Docket Number: 2019-1419
• Citation: 967 F.3d 1319
• Parties: ILLUMINA, INC., Sequenom, Inc., Plaintiffs-Appellants v. ARIOSA DIAGNOSTICS, INC., Roche Sequencing Solutions, Inc., Roche Molecular Systems, Inc., Defendants-Appellees
• Court: U.S. Court of Appeals — Federal Circuit

967 F.3d 1319

ILLUMINA, INC., Sequenom, Inc., Plaintiffs-Appellants

v.ARIOSA DIAGNOSTICS, INC., Roche Sequencing Solutions, Inc., Roche Molecular Systems, Inc., Defendants-Appellees

2019-1419

United States Court of Appeals, Federal Circuit.

Opinion Issued: March 17, 2020

Opinion Modified: August 3, 2020^*

Edward R. Reines, Weil, Gotshal & Manges LLP, Redwood Shores, CA, argued for plaintiffs-appellants. Also represented by Christopher Shawn Lavin, Derek C. Walter ; Zachary Tripp, Washington, DC.

Daralyn Jeannine Durie, Durie Tangri LLP, San Francisco, CA, argued for all defendants-appellees. Defendant-appellee Ariosa Diagnostics, Inc. also represented by David Floyd McGowan, Laura Miller.

Robert J. Gunther, Jr., Wilmer Cutler Pickering Hale and Dorr LLP, New York, NY, for defendants-appellees Roche Sequencing Solutions, Inc., Roche Molecular Systems, Inc. Also represented by Omar Khan, Christopher R. Noyes ; Thomas Saunders, Washington, DC.

Before Lourie, Moore, and Reyna, Circuit Judges.

Dissenting opinion filed by Circuit Judge REYNA.

Lourie, Circuit Judge.

Illumina, Inc. and Sequenom, Inc. (collectively, "Illumina") appeal from a decision of the United States District Court for the Northern District of California that claims 1–2, 4–5, and 9–10 of U.S. Patent 9,580,751 (the " ’751 patent") and claims 1–2 and 10–14 of U.S. Patent 9,738,931 (the " ’931 patent") are invalid under 35 U.S.C. § 101 as directed to an ineligible natural phenomenon. Illumina, Inc. v. Ariosa Diagnostics, Inc. , 356 F. Supp. 3d 925 (N.D. Cal. 2018) (" Decision "). Because we conclude that the claims are directed to patent-eligible subject matter, we reverse.

BACKGROUND

"In 1996, Drs. Dennis Lo and James Wainscoat discovered cell-free fetal DNA in maternal plasma and serum, the portion of maternal blood samples that other researchers had previously discarded as medical waste." Ariosa Diagnostics, Inc. v. Sequenom, Inc. , 788 F.3d 1371, 1373 (Fed. Cir. 2015). They applied for a patent, and, in 2001, they obtained U.S. Patent 6,258,540, which claimed a method for detecting the small fraction of paternally inherited cell-free fetal DNA in the plasma and serum of a pregnant woman. Id. In 2015, we held that the claims of that patent were invalid under 35 U.S.C. § 101 because they were directed to "matter that is naturally occurring"—i.e. , the natural phenomenon that cell-free fetal DNA exists in maternal blood. Id. at 1376.

The present case involves two patents that are unrelated to the patent held invalid in Ariosa , but rather claim priority from a European patent application filed in 2003. The ’751 and ’931 patents at issue in this case, which are related to each other and have largely identical specifications, begin by acknowledging the natural phenomenon that was at issue in Ariosa : "[I]t has been shown that in the case of a pregnant woman extracellular fetal DNA is present in the maternal circulation and can be detected in maternal plasma ...." ’751 patent col. 1 ll. 23–25. The patents then identify a problem that was the subject of further research on cell-free fetal DNA in maternal blood:

[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.

Id. col. 1 ll. 42–50. In simple terms, the problem that the inventors encountered was that, although it was known that cell-free fetal DNA existed in the mother's bloodstream, there was no known way to distinguish and separate the tiny amount of fetal DNA from the vast amount of maternal DNA.

The inventors of the ’751 and ’931 patents attempted to find a solution to that problem. First, they made a discovery:

An examination of circulatory extracellular fetal DNA and circulatory extracellular maternal DNA in maternal plasma has now shown that, surprisingly, the majority of the circulatory 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.

Id. col. 1 ll. 54–61. To arrive at that discovery, the inventors examined five pregnancies and found that cell-free fetal DNA fragments "were almost completely of sizes smaller than 500 base pairs." ’751 patent col. 4 ll. 50–53. Moreover, the inventors found that 70% of all DNA fragments smaller than 300 base pairs were fetal. Id.

Having made that discovery regarding the relative size distributions of cell-free fetal and maternal DNA fragments in a pregnant mother's bloodstream, the inventors used their discovery to develop a solution to the identified problem of distinguishing the fetal DNA from the maternal DNA:

This surprising finding forms the basis of the present invention according to which separation of circulatory extracellular DNA fragments which are smaller than approximately 500 base pairs provides a possibility to enrich for fetal DNA sequences from the vast bulk of circulatory extracellular maternal DNA.

Id. col. 2 ll. 1–6.

The claims of the ’751 and ’931 patents are directed to that solution. Specifically, they claim methods of preparing a fraction of cell-free DNA that is enriched in fetal DNA. The methods of preparation include size discrimination of the DNA based on size parameters that the inventors selected to balance the need to remove enough longer maternal DNA fragments to enrich the sample but also leave behind enough shorter fetal DNA fragments to allow for testing. As explained in the patent, "depending on the downstream application" of the enriched mixture, the size parameter is not fixed at either 500 or 300 base pairs but can be even smaller. See ’751 patent col. 4 ll. 57–59.

Claim 1 of the ’751 patent, the only independent claim, includes an inventor-chosen size parameter of 500 base pairs to allow for selective removal of longer DNA fragments from the mixture:

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 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 produced in (b).

’751 patent col. 7 l. 54–col. 8 l. 57. In contrast, claim 1 of the ’931 patent imposes a different size parameter, namely, 300 base pairs:

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).

’931 patent col. 7 l. 58–col. 8 l. 63.

Dependent claims in each patent place further limitations on the size discrimination and selective removal processes recited in step (b) of the method claims. For example, dependent claim 7 of the ’751 patent recites that "the size discrimination in (b) comprises centrifugation," and claim 8 further limits it to "density gradient centrifugation." ’751 patent col. 9 ll. 1–4. Likewise, dependent claims 4–10 of the ’931 patent recite that step (b) can comprise "chromatography," "electrophoresis," "centrifugation," and/or "nanotechnological means." ’931 patent col. 9 ll. 1–14.

Illumina filed suit against Ariosa Diagnostics, Inc., Roche Sequencing Solutions, Inc., and Roche Molecular Systems, Inc. (collectively, "Roche") alleging infringement of the ’751 and ’931 patents. Roche moved for summary judgment that the asserted claims are invalid under 35 U.S.C. § 101. The district court granted Roche's motion for summary judgment, holding that the claims of the ’751 and ’931 patents are directed to ineligible subject matter. Decision , 356 F. Supp. 3d at 935. The court entered judgment in favor of Roche, and Illumina appealed. We have jurisdiction under 28 U.S.C. § 1295(a)(1).

DISCUSSION

We review a grant of summary judgment according to the law of the regional circuit. Kaneka Corp. v. Xiamen Kingdomway Grp. Co. , 790 F.3d 1298, 1303 (Fed. Cir. 2015) (citing Halo Elecs., Inc. v. Pulse Elecs., Inc. , 769 F.3d 1371, 1377 (Fed. Cir. 2014) ). In the Ninth Circuit, a grant of summary judgment is reviewed de novo . Leever v. Carson City , 360 F.3d 1014, 1017 (9th Cir. 2004) (citing Hargis v. Foster , 312 F.3d 404, 409 (9th Cir. 2002) ). Summary judgment is appropriate when "there is no genuine dispute as to any material fact and the movant is entitled to judgment as a matter of law." Fed. R. Civ. P. 56.

I

Section 101 provides that "Whoever invents or discovers any new and useful process, machine, manufacture, or composition of matter, or any new and useful improvement thereof, may obtain a patent therefor ...." 35 U.S.C. § 101. Given the expansive terms of § 101, "Congress plainly contemplated that the patent laws would be given wide scope"; the legislative history likewise indicated that "Congress...