Detecting Natural Phenomena Using Conventional Techniques Found “Directed to” Natural Phenomena at Alice/Mayo Step One
| September 16, 2022
CAREDX, INC. v. NATERA, INC.
Lourie, Bryson, and Hughes. Opinion by Lourie.
Summary
The CAFC held that genetic diagnostic method claims are ineligible for patent, finding that the claims reciting conventional laboratory techniques to perform diagnosis using a naturally occurring correlation are directed to natural phenomena under Alice/Mayo step one, and also lack additional elements to constitute enough inventive concept under Alice/Mayo step two.
Details
CareDx sued Natera and Eurofins in the U.S. District Court for the District of Delaware, asserting that their products infringed one or more patents licensed to CareDx. The district court awarded summary judgment for the defendants, holding that the patents are ineligible for patent under 35 U.S.C. §101. CareDx appealed the district court’s grant of the summary judgment motions of ineligibility.
The patents at issue, U.S. Patents 8,703,652, 9,845,497, and 10,329,607, relate to diagnosis of organ transplant status by detecting a donor’s cell-free DNA (“cfDNA”) circulating in a recipient’s body. The specification, common to all three patents, depicts prior findings that the existence of cfDNA in blood is mostly attributed to dead cells, and had been used for various diagnostic purposes, such as cancer diagnostics and prenatal testing. The specification notes that the cfDNA-based diagnostic scheme is applicable to organ transplant situations, where the recipient’s immune system kills incompatible donor’s cells which in turn release their nucleic acids into the recipient’s stream, such that an increased level of the donor-derived cfDNA may allow for detection of the transplant rejection.
Claim 1 of ‘652 patent recites:
1. A method for detecting transplant rejection, graft dysfunction, or organ failure, the method comprising:
(a) providing a sample comprising cell-free nucleic acids from a subject who has received a transplant from a donor;
(b) obtaining a genotype of donor-specific polymorphisms or a genotype of subject-specific polymorphisms, or obtaining both a genotype of donor-specific polymorphisms and subject-specific polymorphisms, to establish a polymorphism profile for detecting donor cell-free nucleic acids, wherein at least one single nucleotide polymorphism (SNP) is homozygous for the subject if the genotype comprises subject-specific polymorphisms comprising SNPs;
(c) multiplex sequencing of the cell-free nucleic acids in the sample followed by analysis of the sequencing results using the polymorphism profile to detect donor cell-free nucleic acids and subject cell-free nucleic acids; and
(d) diagnosing, predicting, or monitoring a transplant status or outcome of the subject who has received the transplant by determining a quantity of the donor cell-free nucleic acids based on the detection of the donor cell-free nucleic acids and subject cell-free nucleic acids by the multiplexed sequencing, wherein an increase in the quantity of the donor cell-free nucleic acids over time is indicative of transplant rejection, graft dysfunction or organ failure, and wherein sensitivity of the method is greater than 56% compared to sensitivity of current surveillance methods for cardiac allograft vasculopathy (CAV).
The representative claims of the three patents recite somewhat similar procedures, which may be summarized as:
- collecting a bodily sample from the recipient,
- “genotyping” or identifying genetic features that allow for distinction between the donor and recipient,
- “sequencing” or determining the makeup of cfDNA included in the sample, and
- determining, using the genetic features, the amount of cfDNA originating from the donor in the sample.
The specification depicts that the methods are performed using specific techniques that are “standard,” “well-established” and/or reported in prior patents and scientific articles, including sophisticated polymerase chain reaction (“PCR”), such as digital PCR and selective amplification, and next-generation sequencing (“NGS”), all of which are advanced, but already known, techniques in the field.
The district court held that that the asserted claims were patent ineligible as they were “directed to the detection of natural phenomena, specifically, the presence of donor cfDNA in a transplant recipient and the correlation between donor cfDNA and transplant rejection” and also, “recited only conventional techniques.”
On appeal, the CAFC performed the two-step Alice/Mayo analysis to determine patent-eligibility.
- Are the claims “directed to” laws of nature or natural phenomena? – Yes.
CareDx sought to characterize the claimed invention as directed to “improved measurement methods,” in particular, patent-eligible “use of digital PCR, NGS, and selective amplification” allowing for improved accuracy in cfDNA measurement, as opposed to “discovery of a natural correlation between organ rejection and the donor’s cfDNA levels in the recipient’s blood.” CareDx also asserted that the district court improperly considered conventionality of the claimed techniques at step one, essentially merging the two steps into a single-step analysis centered on conventionality.
The CAFC found that the claims satisfy the step one. Two contrasting precedents are notable: Illumina, Inc. v. Ariosa Diagnostics, Inc., 952 F.3d 1367, opinion modified by 967 F.3d 1319, 1327 (Fed. Cir. 2020), and Ariosa Diagnostics, Inc. v. Sequenom, Inc., 788 F.3d 1371 (Fed. Cir. 2015). The CAFC noted that this case is different from Illumina, where the claimed improvement was a patent-eligible “method for preparing” a cfDNA fraction that would not occur naturally without manipulation of a starting sample; rather, the asserted claims are akin to those in Ariosa, wherein the claimed diagnostic methods, including the steps of “amplifying” (i.e., making many copies of) a cfDNA sample using PCR and “detecting” a certain type of cfDNA, so as to perform diagnosis using a natural correlation between certain conditions and the level of cfDNA, were found to be “directed to a natural phenomenon.”
The CAFC noted that the conventionally considerations are not limited to step two, and precedents have routinely performed overlapping conventionality inquiry at both stages of Alice/Mayo. The CAFC found that the use of specific laboratory techniques relied on by CareDx only amounts to “conventional use of existing techniques to detect naturally occurring cfDNA.” The CAFC added that the conventionality is supported by the specification’s numerous remarks characterizing the claimed techniques as “any suitable method known in the art” and similar boilerplate language.
- Do the claims recite additional elements, aside from the natural phenomena, which transform the nature of the claim’ into a patent-eligible application? – No.
CareDx’s main argument at step two was that the inventive concept resides in the use of the specific advanced techniques to identify and measure donor-derived cfDNA.
The CAFC disagreed, concluding that the claimed methods lack requisite inventive concept. In reaching the conclusion, the CAFC again pointed to the specification’s admissions of the conventionality of the individual techniques recited in the claims. The CAFC went on to state that “[t]he specification confirms that the claimed combination of steps … was a straightforward, logical, and conventional method for detecting cfDNA previously used in other contexts,” which adds nothing inventive to the detection of natural phenomena.
Takeaway
This case provides a reminder that conventionality of claimed elements may affect both steps of Alice/Mayo test. At step one, the effort to characterize the claim as being “directed to” a patent-eligible subject matter can be thwarted where the claimed elements are undisputedly conventional, in the absence of an unconventional element that is not a judicial exception to eligibility. And at step two, the conventionality of the individual elements and their combination prohibits finding of inventive concept.
For Biotech, “Method of Preparation” Claims May Survive §101
| April 15, 2020
Illumina, Inc. v. Ariosa Diagnostics, Inc.
March 17, 2020
Lourie, Moore, and Reyna (Opinion by Lourie; Dissent by Reyna)
Summary
In a patent infringement litigation between the same parties that were involved in the earlier case, Ariosa Diagnostics, Inc. v. Sequenom, Inc., 788 F.3d 1371 (Fed. Cir. 2015) (diagnostic patent deemed patent ineligible under 35 U.S.C. §101), the United States Court of Appeals for the Federal Circuit (“Federal Circuit”) found the claimed “method of preparation” of a fraction of cell-free fetal DNA (“cff-DNA”) enriched in fetal DNA to be patent eligible, reversing the district court’s grant of summary judgment of patent ineligibility. A dissent by J. Reyna (author of the earlier Ariosa decision) asserts that there is nothing new and useful in the claims, other than the discovery that cff-DNA tends to be shorter than cell-free maternal DNA, and that use of known laboratory techniques and commercially available testing kits to isolate the naturally occurring shorter cff-DNA does not make the claims patent eligible.
Details
Illumina and Sequenom (collectively, “Illumina”) appealed a
summary judgment ruling of patent ineligibility by the United States District
Court for the Northern District of California.
The two patents at issue, USP 9,580,751 (the ‘751 patent) and USP
9,738,931 (the ‘931 patent), are unrelated to the diagnostic patent held
ineligible in the 2015 Ariosa decision. While the earlier litigated patent claimed a
method for detecting the small fraction of cff-DNA in the plasma and serum of a
pregnant woman that were previously discarded as medical waste, the present
‘751 and ‘931 patents claim methods for preparing a fraction of cff-DNA that is
enriched in fetal DNA. A problem with
maternal plasma is that it was difficult, if not impossible, to determine fetal
genetic markers (e.g., for certain diseases) because the proportion of circulatory
extracellular fetal DNA in maternal plasma was tiny as compared to the majority
of it (>90%) being circulatory extracellular maternal DNA. The inventor’s
“surprising” discovery was that the majority of circulatory extracellular fetal
DNA has a relatively small size of approximately 500 base pairs or less, as
compared to the larger circulatory extracellular maternal DNA. With this discovery, they developed the
following claimed methods for preparing a DNA fraction that separated fetal DNA
from maternal DNA from the maternal plasma and serum, to create a DNA fraction
enriched with fetal DNA.
‘931 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 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:
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 Federal Circuit had consistently found diagnostic claims patent ineligible (as directed to natural phenomenon) (Athena Diagnostics, Inc. v. Mayo Collaborative Servs., LLC, 927 F.3d 1333 (Fed. Cir. 2019); Athena Diagnostics, Inc. v. Mayo Collaborative Servs., LLC, 915 F.3d 743 (Fed. Cir. 2019); Cleveland Clinic Found. v. True Health Diagnostics LLC, 859 F.3d 1352 (Fed. Cir. 2017)). In contrast, the Federal Circuit had also held that method of treatment claims are patent eligible (Endo Pharm. Inc. v. Teva Pharm. USA, Inc., 919 F.3d 1347 (Fed. Cir. 2019); Natural Alternative Int’l, Inc. v. Creative Compounds, LLC, 918 F.3d 1338 (Fed. Cir. 2019); and Vanda Pharm. Inc. v. West-Ward Pharm. Int’l Ltd., 887 F.3d 1117 (Fed. Cir. 2018)). However, this is not a diagnostic case, nor a method of treatment case. This is a method of preparation case – which the Federal Circuit found to be patent eligible.
The natural phenomenon at issue is that cell-free fetal DNA tends to be shorter than cell-free maternal DNA in the mother’s bloodstream. However, under the Alice/Mayo Step 1, the Federal Circuit held that these claims are not directed to a natural phenomenon. Instead, the claims are directed to a method that utilizes that phenomenon. The claimed method recites specific process steps – size discrimination and selective removal of DNA fragments above a specified size threshold. These process steps change the composition of the normal maternal plasma or serum, creating a fetal DNA enriched mixture having a higher percentage of cff-DNA fraction different from the naturally occurring fraction in the normal mother’s blood. “Thus, the process achieves more than simply observing that fetal DNA is shorter than maternal DNA or detecting the presence of that phenomenon.”
In distinguishing the earlier Ariosa case, the Federal Circuit stated, “the claims do not merely cover a method for detecting whether a cell-free DNA fragment is fetal or maternal based on its size.”
In distinguishing the Supreme Court decision in Association for Molecular Pathology v. Myriad Genetics, Inc., 569 U.S. 576 (2013), the Federal Circuit noted that the “Supreme Court in Myriad expressly declined to extend its holding to method claims reciting a process used to isolate DNA” and that “in Myriad, the claims were ineligible because they covered a gene rather than a process for isolating it.” Here, the method “claims do not cover cell-free fetal DNA itself but rather a process for selective removal of non-fetal DNA to enrich a mixture in fetal DNA.” This is the opposite of Myriad.
As for whether the techniques for size discrimination and selective removal of DNA fragments were well-known and conventional, those considerations are relevant to the Alice/Mayo Step 2 analysis, or to 102/103 issues – not for Alice/Mayo Step 1. The majority concluded patent eligibility under Step 1 and did not proceed to Step 2.
J. Reyna’s dissent focused on the claims being directed to a natural phenomenon because the “only claimed advance is the discovery of that natural phenomenon.” In particular, referring to a “string of cases reciting process claims” since 2016, the “directed to” inquiry under Alice/Mayo Step 1 asks “whether the ‘claimed advance’ of the patent ‘improves upon a technological process or is merely an ineligible concept.’” citing Athena, 915 F.3d at 750 and Genetic Techs., 818 F.3d at 1375. “Here, the claimed advance is merely the inventors’ ‘surprising[]’ discovery of a natural phenomenon – that cff-DNA tends to be shorter than cell-free maternal DNA in a mother’s bloodstream.” J. Reyna criticizes the majority for ignoring the “claimed advance” inquiry altogether.
Under the claimed advance inquiry, one looks to the written description. Here, the written description identifies the use of well-known and commercially available tools/kits to perform the claimed method. Checking for 300 and 500 base pairs using commercially available DNA size markers and kits does not constitute any “advance.” There is no improvement in the underlying DNA processing technology, but for checking the natural phenomenon of sizes indicative of cff-DNA.
J. Reyna also criticized the majority’s “change in the composition of the mixture” justification. “A process that merely changes the composition of a sample of naturally occurring substances, without altering the naturally occurring substances themselves, is not patent eligible.” Here, one begins and ends with the same naturally occurring substances – cell-free fetal DNA and cell free maternal DNA. There is no creation or alteration of any genetic information encoded in the cff-DNA. Therefore, the claims are directed to a natural phenomenon under Alice/Mayo Step 1.
J. Reyna also found no inventive concept under Alice/Mayo Step 2.
Take Away
- Until there is an en banc rehearing or a Supreme Court review of this case, this case is an example of a patent eligible method of preparation claim.
- For defendants, the “claimed advance” inquiry could help sink a claimed method under Alice/Mayo Step 1.
Tags: 101 > biotech > diagnostics > eligibility > Mayo/Alice Test > preparation > treatment
