In Patent Eligibility It's the Claim That Is the Name of the Game*

December 18, 2023

Recently Judge Connolly, Chief Judge of the District Court of Delaware had an opportunity of deciding three motions for summary judgment filed by CareDX in its litigation with Natera, Natera, Inc. v. CareDX, Inc, Dist. DE, CA 20-38, that one patent was invalid as being directed to patent ineligible subject matter. The patents are U.S. Patent Nos. 10,597,724 (‘724), 10,655,180 (‘180), and 11,111,544 (‘544). The ‘724 and ‘180 patents are directed to methods of observing DNA in samples taken from patients. The ‘544 patent is directed to a method of “preparing a preparation of amplified DNA” from the sample of an individual to observe the DNA of a second individual in the sample. The Court found that one claim in each patent was representative of all claims in the respective patent. These representative claims are:

‘724 claim 1

A method for determining genetic data for DNA from a first individual in a biological sample of a second individual, the method comprising:

(a) amplifying a plurality of polymorphic loci on cell-free DNA extracted from the biological sample to generate amplified products;

(b) measuring an amount of the amplified products by sequencing-by-synthesis to obtain genetic data at the plurality of polymorphic loci;

(c) determining the most likely genetic data for DNA from the first individual based on allele frequencies in the genetic data at the plurality of polymorphic loci.

 ‘180 claim 14

A method for measuring an amount of DNA in a biological sample, the method comprising:

(a) performing a targeted PCR amplification for more than 100 SNP loci on one or more chromosomes expected to be disomic in a single reaction mixture using more than 100 PCR primer pairs, wherein the reaction mixture comprises cell- free DNA extracted from a biological sample of a subject comprising DNA of mixed origin, wherein the DNA of mixed origin comprises DNA from the subject and DNA from a genetically distinct individual, wherein neither the subject nor the genetically distinct individual is a fetus, wherein the DNA of mixed origin comprises DNA from a transplant, and wherein the amplified SNP loci comprise SNP loci on at least chromosome 1, 2, or 3;

(b) measuring a quantity of each allele at a plurality of amplified SNP loci that comprise an allele present in the genetically distinct individual but not the subject, wherein the quantity of each allele at a plurality of amplified SNP loci are measured by high-throughput sequencing;

(c) measuring an amount of the DNA from the genetically distinct individual in the biological sample using the quantity of each allele at the SNP loci and an expected quantity of each allele at the SNP loci for different DNA fractions, wherein the method is performed without prior knowledge of genotypes of the genetically distinct individual.  

‘544 claim 21

A method for preparing a preparation of amplified DNA derived from a biological sample of a second individual useful for determining genetic data for DNA from a first individual in the biological sample, the method comprising:

(a) extracting cell-free DNA from the biological sample;

(b) preparing a preparation of amplified DNA by amplifying a plurality of target loci on the cell-free DNA extracted from the biological sample to generate amplified DNA;

(c) analyzing the preparation of amplified DNA by sequencing the amplified DNA using sequencing-by-synthesis to obtain genetic data of the plurality of target loci, and determining the most likely genetic data f or DNA from the first individual based on allele frequencies in the genetic data at the plurality of target loci.

‘724 representative patent claim ineligible

Judge Connolly held the claims of the ‘724 patent to be patent ineligible because DNA-PCR amplification and sequencing by synthesis “were conventional well before the claimed November 26, 2005 priority date” of the patent. Natera does not dispute that these techniques are the only techniques recited in the claim; nor does it dispute that both techniques were conventional as of the patent's priority date. Instead Natera argued ‘724 teaches “specific combinations” of target amplification and analysis amplification but Natera did not cite where these combinations appear in the claim. The §101 “inquiry must focus on the language” of the asserted claims. Synopsys, Inc. v. Mentor Graphics Corp., 839 F.3d 1138, 1149 (Fed. Cir. 2016). Natera’s failure to be able to identify where the specification combinations were recited in the claims was fatal to the argument. In effect, the claim was claiming all combinations including the admittedly conventional ones.

Accordingly, the Court granted CareDX summary judgment that ‘724 were patent ineligible.

‘180 patent – Material fact in dispute

Summary judgment was denied because Natera challenged the CareDX with evidence that the amplifying more than 100 targets simultaneously in a single mixture was unconventional at the time of the priority document. Since this was a fact dispute needing resolution, summary judgment was denied.

‘544 representative claim patent eligible

The ‘544 claims recited “a method for preparing a preparation … .”  CareDX argued that other than the preamble, there was material difference between the ‘544 claims and those of ‘724. The ‘544 claims were infringed only if one prepared the composition using the elements of the claim, quite different from the analysis technique of ‘724. The Court found the claims to be patent eligible relying on Illumina, Inc. v. Ariosa Diagnostics, Inc., 967 F.3d 1319, 1326 (Fed. Cir. 2020), rejecting the CareDX argument, characterizing the claims as detections claims.

The Court’s reliance on claim language is instructive since many of the commentators have criticized prior decisions by considering the invention rather than what is claimed. Sequenom was heavily criticized because the Federal Circuit had found the representative claim 1 to be unpatentable. The commentators ignored the Federal Circuit’s observation that claims 21 and 24, which recited where the CFFDNA was found in the blood serum, were not separately argued but rose or fell with claim 1. See Ariosa Diagnostics, Inc. v. Sequenom, Inc., 788 F.3d 1371, 1374 (Fed. Cir. 2015).

The key lesson from Natera (and Sequenom) is that the claims determine patent eligibility and not the invention, which may or may not be reflected in the claims.