Skip to main content
Premium Trial:

Request an Annual Quote

USPTO Guidance on Patent Eligibility of Products Derived from Nature Raises Industry Concerns

Premium

NEW YORK (GenomeWeb) – Following the release of the US Patent and Trademark Office's guidelines on how its examiners should interpret the US Supreme Court's decision in Association for Molecular Pathology et al. v. Myriad Genetics, life sciences industry players and legal experts are concerned that the patent office has overreached its authority.

"I think there is consensus that the guidelines went further than the Supreme Court decision [in AMP v. Myriad] required, or perhaps even envisioned," patent law expert Courtenay Brinckerhoff told PGx Reporter. Brinckerhoff is a partner with the law firm Foley & Lardner, where she chairs the IP law and practice division.

In the guidelines issued in March, the USPTO laid out a three-step framework that examiners should follow in determining whether a patent application for a product derived from natural materials is eligible for IP protection.

First, the examiner should determine if the claimed product falls into one of four categories describing patent-eligible subject matter under 35 USC Section 101-- "any new and useful process, machine, manufacture, or composition of matter." If it does, then the examiner must determine if the claim is limited by any of the judicial exceptions to Section 101, that is if the claim describes a law of nature, abstract idea, a natural phenomenon, or a natural product. If it does not, then it is patent eligible. If it does, then the examiner must ask a third question: "Does the claim as a whole recite something significantly different than the judicial exception?"

With regard to this third question, the USPTO guidelines provide the following examples of non-patent-eligible natural products such as "chemicals derived from natural sources (e.g., antibiotics, fats, oils, petroleum derivatives, resins, toxins, etc.); foods (e.g., fruits, grains, meats and vegetables); metals and metallic compounds that exist in nature; minerals; natural materials (e.g., rocks, sands, soils); nucleic acids; organisms (e.g., bacteria, plants and multicellular animals); proteins and peptides; and other substances found in or derived from nature."

Myriad for one doesn't believe the USPTO is interpreting correctly how the Supreme Court's decision against its patent claims should impact the life sciences industry at large."We believe strong patent protection is essential to innovation because it guarantees a period of reward for the significant investment underlying innovation. Patent protection provides the research-based industries with an incentive to invest in research and development," spokesperson Ron Rogers told PGx Reporter. "We have significant concerns over the breadth of what may be ineligible for patenting under the USPTO guidelines."

The latest guidance reflects the USPTO's interpretation of the Supreme Court's decision last year in AMP v. Myriad. In that case, the court held a number of Myriad's claims on isolated BRCA1/2 gene sequences patent ineligible under Section 101, stating that such claims describe naturally occurring products. However, the court decided that Myriad's claims on cDNA were patent eligible when the nucleotide sequences are different than DNA that exists in the body.

"Myriad did not create or alter either the genetic information encoded in the BRCA1 and BRCA2 genes or the genetic structure of the DNA. It found an important and useful gene, but groundbreaking, innovative, or even brilliant discovery does not by itself satisfy the Section 101 inquiry," the court wrote. "Finding the location of the BRCA1 and BRCA2 genes does not render the genes patent eligible 'new . . . composition[s] of matter.'" Overall, the Supreme Court held that a DNA segment is a product of nature and the fact that the segment has been "isolated" does not render it patent eligible.

Robert Cook-Deegan, research professor of genome ethics, law, and policy at Duke University, told PGx Reporter that the life sciences industry is very confused right now about how to read the Supreme Court's ruling in AMP v. Myriad. "No one quite knows what the Supreme Court meant, or how to draw the line," he said in an e-mail.

Immediately following this ruling last year, the USPTO issued a preliminary guidance to its examiners instructing them to reject claims drawn only to naturally occurring nucleic acids regardless of whether the sequences have been isolated or not. However, the USPTO told examiners to uphold claims drawn to cDNA where the sequence of nucleotides is different than those in naturally occurring DNA. The patent office warned that method claims involving naturally occurring nucleic acids would likely need to be examined under existing guidance.

"The patent office could have stopped there," with that first guidance, Brinckerhoff reflected. "I don't think there would have been as much of a surprise or outcry if the patent office also just applied Myriad to single component claims."

LIfe sciences firms are particularly concerned with the USPTO's interpretation of the Supreme Court's ruling because the guidance seems to suggest that even the individual components that comprise a product must be "markedly different" from what exists in nature. "MDx firms are going to be trying to figure this stuff out; I would think most therapeutics will survive," Cook-Deegan said. "But there is potential spillover to things like vaccines, proteins, and other macro-molecues and organisms and parts of organisms that might be 'found in nature,' since the UPSTO seems to be looking for structural differences to denote [what is] 'markedly different.'"

For example, in training materials for examiners, the USPTO uses the example of a patent application for a beverage comprising pomelo juice and a preservative. Pomelo juice exists in nature so it's not patent eligible, but if the preservative is something that also occurs in nature, such as Vitamin E, then the beverage as a whole doesn't meet the patent eligibility test, as the USPTO interprets it.

While, the applicant might argue that the claim is eligible since pomelo juice and vitamin E don't occur in nature together, the USPTO would not find such an argument convincing since the product must be both not naturally occurring and markedly different in structure. And adding a certain amount of vitamin E to pomelo juice doesn't impart a structural change. Meanwhile, if the claim was for "pasteurized pomelo juice," where the juice is heated to a certain temperature resulting in a structural change to the beverage, that would render the claim patent eligible, according to the USPTO.

"Myriad … clarified that not every change to a product will result in a marked difference, and that the mere recitation of particular words (e.g., 'isolated') in the claims does not automatically confer eligibility," the USPTO wrote in its March guidance. "Thus, while the holding in Myriad was limited to nucleic acids, Myriad is a reminder that claims reciting or involving natural products should be examined for a marked difference under Chakrabarty." In 1980, the Supreme Court decided in Diamond v. Chakrabarty that genetically modified bacterium was patent eligible because, unlike naturally occurring bacteria, it could break down crude oil.

Although structural changes are one example of how the USPTO is defining the extent to which a patented product must be "markedly different" from naturally occurring substances, Kevin Marks, general counsel and chief compliance officer for Roche Molecular Diagnostics, still finds the guidelines ambiguous in this regard. "The guidance is intended to 'assist examiners in determining whether a claim reflects a significant difference from what exists in nature and thus is [101] eligible, or whether a claim is effectively drawn to something that is naturally occurring, like the claims found ineligible by the Supreme Court in Myriad.' However, there is little, if any, insight as to what is the 'significantly different' standard," Marks reflected.

"In addition, with respect to natural products, the guidance offers that what is claimed should be 'non-naturally occurring and markedly different in structure from the naturally occurring products,'" he said. "Again, it is unclear as to what constitutes 'markedly different' and to what 'degree.'"

Brinckerhoff further pointed out that the claims at issue in Myriad were just isolated DNA molecules themselves; those claims didn't involve formulations of any kind. After the Supreme Court's ruling, "people were predicting that the patent office would extrapolate that decision to other products that could be isolated from nature, such as proteins, antibodies, and chemicals that can be isolated from a plant." What has been surprising and concerning to industry players, according to Brinckerhoff, is that the USPTO "dug up" the Supreme Court ruling in Funk Brothers Seed Co. v. Kalo Inoculant Co. and put it together with the Supreme Court's ruling in AMP v. Myriad, to interpret how examiners should apply Section 101 to composition of matter claims where multiple components are combined.

In the Funk Brothers case in 1948, the Supreme Court struck down Kalo Inoculant's patent claims on mixing strains of bacteria that scientists found didn't have a mutually inhibitive effect and that could be used together in a mixture to inoculate plants. Unlike in Chakrabarty, the court in this case decided that although the patentee had discovered a phenomenon of nature that certain strains of bacteria had mutually non-inhibiting properties when mixed together, this discovery did not deserve a patent because the individual bacteria strains were found in nature. "The combination of species produces no new bacteria, no change in the six species of bacteria, and no enlargement of the range of their utility," the court wrote.

In its guidance, now, "the patent office [has taken] the position that if all of the components that you're mixing together could be found in a natural source then even that combination is not patent eligible," Brinckerhoff said. "That's where it could reach to pharmaceutical compositions, vaccines, and other products."

Roche's Marks further pointed out that the Supreme Court's ruling that naturally occurring gene sequences are not patent eligible was based on the reasoning that the disease associated information contained in nucleic acids is the same whether DNA is in the body or isolated from the body. "The USPTO guidelines now not only extend the prohibition to any naturally occurring molecule, but also exclude any molecule 'found in or derived from nature,'" he said. "Potentially, not only may it affect compound claim patentability, it may also throw the validity of many compound claims in doubt on the argument that the compound could have been 'derived from nature,'"

In a post about the USPTO guidance in the blog "Patent Docs," IP legal expert Kevin Noonan tried to quell industry fears by reminding that the guidelines are not legally binding and that the limits of Section 101 in light of recent Supreme Court decisions will likely be further defined in the courts.

These "guidelines have no force of law; they are merely administrative tools for how the office will administer the law under its (mis)understanding of the Supreme Court's rubrics," wrote Noonan, a partner with law firm McDonnell Boehnen Hulbert & Berghoff. "While the Federal Circuit has occasionally referenced such guidelines … courts have consistently recognized that they are not bound by the office's understanding of how to apply the law. Thus, bemoaning the loss of thousands of granted patents is at best premature; until this interpretation of subject matter eligibility gets judicial imprimatur these guidelines have no effect on existing patents."

In an effort to gather more input on its guidelines for determining eligibility of claims on laws of nature, natural phenomena, and natural products, the USPTO is hosting a public meeting on May 9 to collect stakeholder input.

"It's the province of the courts to decide what Section 101 means," Brinckerhoff added. "I don't think it's the patent office's place to interpret Section 101 in a more narrow way than the Supreme Court decisions indicates."

The Scan

Purnell Choppin Dies

Purnell Choppin, a virologist who led the Howard Hughes Medical Institute, has died at 91, according to the Washington Post.

Effectiveness May Decline, Data From Israel Suggests

The New York Times reports that new Israeli data suggests a decline in Pfizer-BioNTech SARS-CoV-2 vaccine effectiveness against Delta variant infection, though protection against severe disease remains high.

To See Future Risk

Slate looks into the use of polygenic risk scores in embryo screening.

PLOS Papers on Methicillin-Resistant Staphylococcus, Bone Marrow Smear Sequencing, More

In PLOS this week: genomic analysis of methicillin-resistant Staphylococcus pseudintermedius, archived bone marrow sequencing, and more.