Can Any DNA Claims Still Be Patented?

21 January 2015 PharmaPatents Blog

In a decision issued December 17, 2014, in In Re BRCA1- And BRCA2-Based Hereditary Cancer Test Patent Litigation (Myriad II), the Federal Circuit invalidated Myriad’s primer claims and detection method claims under 35 USC § 101. I first reported the decision here, and now revisit that decision and the Supreme Court decision in Association for Molecular Pathology v. Myriad Genetics, Inc. (Myriad I), to consider the patent eligibility of DNA claims, and identify the types of DNA claims that may survive the Myriad decisions. I’ll be presenting some of these views at the USPTO Eligibility Forum later today. 

The Primer Claims At Issue In Myriad I and Myriad II

When considering the impact of the Myriad decisions, it is important to keep in mind the claims that were at issue. Indeed, the primer claims invalidated by the Supreme Court in Myriad I and the Federal Circuit in Myriad II were very broad.

While not limited to primers, several claims invalidated in Myriad I encompassed primers. For example, claim 5 of U.S. Patent 5,747,282 recited “[a]n isolated DNA having at least 15 nucleotides of the DNA of claim 1,” where the DNA of claim 1 was defined as “[a]n isolated DNA coding for a BRCA1 polypeptide.” In Myriad II, the Federal Circuit identified claim 16 of U.S. Patent 5,747,282 as representative of the primer claims:

A pair of single-stranded DNA primers for determination of a nucleotide sequence of a BRCA1 gene by a polymerase chain reaction, the sequence of said primers being derived from human chromosome 17q, wherein the use of said primers in a polymerase chain reaction results in the synthesis of DNA having all or part of the sequence of the BRCA1 gene.

The breadth of these claims may leave room to distinguish more specific claims and defend their patent eligibility.

1. Primer Claims Reciting Specific Sequences

As noted above, the primer claims at issue in Myriad I and Myriad II did not recite specific DNA sequences and were not limited to primers of any specific length. Could claims defining primers by these characteristics satisfy § 101?

While such claims would face the Supreme Court’s pronouncement in Myriad I that “separating [a] gene from its surrounding genetic material is not an act of invention,” a patent holder defending such claims could point to the distinction the Court drew between the open-ended claims at issue, and claims drawn to a specific molecule:

If the patents depended upon the creation of a unique molecule, then a would-be infringer could arguably avoid at least Myriad’s patent claims on entire genes … by isolat¬ing a DNA sequence that included both the BRCA1 or BRCA2 gene and one additional nucleotide pair. Such a molecule would not be chemically identical to the molecule “invented” by Myriad.

While this passage does not expressly discuss patent eligibility, it indicates that the preemption concerns that underlie the Court’s patent eligibility jurisprudence would not be as significant for claims reciting a specific molecule, e.g., primers of limited length having a specific DNA sequence.

2. DNA (or RNA) Constructs With A Different Function Or Utility

In Myriad I, the Supreme Court found that the significance of the Myriad claims was tied to the “genetic information” of the naturally occurring gene, and in Myriad II, the Federal Circuit found that the claimed primers served the same function as naturally occurring DNA. Could DNA (or RNA) constructs that have a fundamentally different function or utility, such as claims directed to binding site decoy constructs or RNAi constructs, satisfy § 101?

Patent holders defending such claims might have to distinguish the Federal Circuit’s analysis in Myriad II, but aspects of that analysis are fundamentally flawed. Myriad argued that the primer sequences “have a fundamentally different function than when they are part of the DNA strand,” e.g., “as a starting material for a DNA polymerization process.” The court rejected that argument, stating:

In fact, the naturally occurring genetic sequences at issue here do not perform a significantly new function. Rather, the naturally occurring material is used to form the first step in a chain reaction—a function that is performed because the primer maintains the exact same nucleotide sequence as the relevant portion of the naturally occurring sequence. One of the primary functions of DNA’s structure in nature is that complementary nucleotide sequences bind to each other. It is this same function that is exploited here—the primer binds to its complementary nucleotide sequence. Thus, just as in nature, primers utilize the innate ability of DNA to bind to itself.

As I read this paragraph, I find that the Federal Circuit has confused the properties of DNA with the different functions (“applications”) to which DNA can be put. The fact that “complementary nucleotide sequences bind to each other” is a property of DNA, but that property can be exploited for different purposes, many of which are not observed in nature. For example, DNA constructs useful as binding site decoys or RNAi constructs perform significantly different functions than the corresponding gene, and are useful in methods that interfere with—rather than duplicate–naturally-occurring processes. While these constructs may exploit the same properties of the naturally-occurring sequence, their different utility certainly represents a new “application” of the naturally-occurring sequences that should qualify as an “invention” under § 101.

3. Labeled DNA Probes

The recited utility for the primer claims at issue in Myriad II related to the synthesis of longer DNA sequences by polymerase chain reaction, but many patents claim short DNA constructs that are useful in detection methods. For such inventions, could claims reciting DNA probes labeled with a detectable label satisfy § 101?

I believe that claims directed to labeled probes should easily satisfy § 101, such as by analogy to the cDNA claims upheld by the Supreme Court in Myriad I. Like cDNA, labeled probes are not naturally occurring, and are “unquestionably … something new” created by a lab technician.

4. DNA Constructs With Sequence Mutations

Another type of DNA claim that should satisfy § 101 is claims reciting constructs having a mutation as compared to the naturally-occurring sequence. As with labeled probe claims, mutated sequence claims should be upheld under an analysis similar to the Supreme Court’s analysis of the cDNA claims in Myriad I. Nevertheless, a patent holder defending such claims may have to reckon with the confusion and contradictory dicta at the end of the Myriad I decision:

 Nor do we consider the patentability of DNA in which the order of the naturally occurring nucleotides has been altered. Scientific alteration of the genetic code presents a different inquiry, and we express no opinion about the application of §101 to such endeavors.

The USPTO’s Interim Guidance On Patent Eligibility

The USPTO issued Interim Guidance on patent eligibility on December 15, 2014, two days before the Federal Circuit issued its decision in Myriad II. As illustrated in the “Natural Products” examples on the USPTO website, claims directed to labeled DNA probes or DNA constructs with sequence mutations should be found to satisfy § 101 under the Interim Guidance. Although the examples do not illustrate any isolated products whose eligibility is based on only functional differences, the Interim Guidance itself provides that “markedly different characteristics” sufficient to satisfy § 101 can be found in a product’s “structure, function, and/or other properties.” Thus, the USPTO might agree with my arguments for the eligibility of DNA constructs having a different function or utility than the naturally-occurring sequence.

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