Personalized Medicine After the ACLU "Gene Patenting" Decision

20 August 2012 Personalized Medicine Bulletin Blog

The biotechnology industry, including those investing in personalized medicine, have been waiting for the Federal Circuit’s decision that answers the questions whether isolated DNA and use of the isolated material are patent-eligible under 35 U.S.C. § 101. As reported in our August 16th post, the same three judges (Lourie, Bryson and Moore) that isolated DNA and cells transformed are patent-eligible. Claims that broadly claim detecting alterations in a gene, in this case the BRCA1 gene, were held to be patent-ineligible. The Ass’n for Molecular Pathology et al. v. USPTO, et al., No. 2010-1406 (Fed. Cir. 2012). In addition, the court determined that the plaintiffs had standing to maintain the action. This decision validates that the tools (DNA and isolated naturally occurring materials) underlying personalized medicine are still patent-eligible. Moreover, the court’s evaluation of the claimed methods are informative to those seeking to patent medical diagnostic tests because the court compared and contrasted a patent-ineligible claimed method to a patent eligible one.

Up and Down the Courts

This is the second time the parties have appeared before the Federal Circuit on the issues. The appeal was returned to the court after the U.S. Supreme Court granted plaintiffs’ petition for certiorari, vacated the Federal Circuit’s prior decision and remanded the case to the Federal Circuit for further consideration in light of its decision in Mayo Collaborative Services v. Prometheus, Inc., 566 U.S. __, 132 S.Ct. 1289 (2012)(“Mayo”). Ass’n for Molecular Pathology v. Myriad Genetics, Inc., 132 S.Ct. 1794 (2012).

The Claims at Issue

The challenged composition claims cover two “isolated” human genes, BRCA1 and BRCA2 (collectively “BRCA1/2” or “BRCA”) and certain alterations or mutations in these genes associated with a predisposition to breast and ovarian cancer. Claims 1, 2 and 5 of challenged U.S. Patent No. 5,747,282 (the ‘282 Patent) are representative compositions claims. Claims 1, 2 and 5 are directed to isolated DNA coding for BRCA1 polypeptides, an isolated cDNA fragment and an isolated DNA probe, respectively. 

Representative challenged method claims cover “analyzing” or “comparing” a patient’s BRCA sequence with the normal or wild-type sequence to identify the presence of cancer-predisposing mutations. Claim 1 of U.S. Patent Nos. 5,709,999 (the ‘999 Patent) and 5,710,001 (the ‘001 Patent) are representative method claims.

The final challenged claim is directed to a method for screening potential cancer therapeutics using a transformed eukaryotic host cell containing an altered BRCA1 gene causing cancer. Claim 20 of U.S. Patent No. 5,747,282 (the ‘282 Patent) is a representative method claim of this type.

Isolated DNA Is Different

Judge Lourie wrote the opinion for the majority. He began his opinion by acknowledging and answering the question  — how would the Federal Circuit apply the Supreme Court’s Mayo decision and analysis to the challenged claims? Judge Lourie answered:

Mayo does not control the question of patent-eligibility of such claims. They are claims to compositions of matter, expressly authorized as suitable patent-eligible subject matter in § 101. As to those claims, the issue of patent-eligibility remains, as it was on the first appeal to this court, whether they claim patent-ineligible products of nature. We hold that they do not. The isolated DNA molecules before us are not found in nature. They are obtained in the laboratory and man-made, the product of human ingenuity. While they are prepared from products of nature, so is every other composition of matter. All new chemical or biological molecules, whether made by synthesis or decompositions, are made from natural materials.”

Slip op. at 38-39.

As to the plaintiff’s and the U.S. Government’s (that do not include the USPTO’s views) assertions that isolated DNA molecules fail to satisfy § 101 because the claims cover naturally occurring phenomena and products of nature, Judge Lourie (as in his prior decision) relied on the Supreme Court’s decisions in Chakrabarty and Funk Brothers and the qualities of the isolated products as compared to the qualities of the products in nature. Isolated DNA, he explained, is not just purified DNA. Although isolated DNA is removed from its native cellular and chromosomal environment, it also has been manipulated chemically so as to produce a molecule that is markedly different from that found in the human body. The claimed isolated DNA molecules are distinct from their natural existence as portions of larger entities, and their informational content (similar to DNA found in the body) is irrelevant to that fact. Judge Lourie recognized that biologists might think of molecules in terms of their uses genes are in fact chemical in nature and as such, best described in patents by their structures rather than their functions. “In fact,” he stated, “many different materials may have the same function (e.g., aspirin, ibuprofen, and naproxen).” Slip op. at 49.

Judge Lourie also cautioned that Congress, not the courts have the appropriate mandate to categorically exclude subject matter such as isolated genes from patenting. Congress, he noted, was aware of the controversial issue when it recently enacted the comprehensive patent reform act, and it is ultimately for Congress to act if it wishes to overturn case law and the long practice of the USPTO to determine that isolated DNA must be treated differently from other compositions of matter.

The judge also took to task the Government’s “magic microscope” test opining that it fails to understand the difference between science and invention and fails to take into account the existence of molecules as separate chemical entities. He explained that the ability to visualize a DNA molecule through a microscope, or by any other means is “worlds apart” from possessing an isolated DNA molecule that is usable. The Government’s microscope could focus in on any portion of any complex molecule making it patent-ineligible, even though that portion never exists in the body or elsewhere in nature, and may have an entirely different utility.

On the issue of preemption (vigorously argued by the plaintiffs, the Government and many amici), Judge Lourie acknowledged that a limited preemption is inherent in every patent. When the patent expires, the public is entitled to practice the invention of the patent. All challenged patents in this dispute expire by December 1, 2015.

Finally, Judge Lourie respected the long-standing practice of the USPTO and the courts in granting patents on this technology. He stated that the Supreme Court has repeatedly stated that changes to longstanding practices should come from Congress, not the courts, citing J.E.M. Ag. Supply, Inc v. Pioneer Hi-Bred International, Inc., 534 U.S. 124, 144 – 45 (2001). Removal of the long-standing practice and expectation regarding gene patenting would adversely effect innovation. Patents, he explained, encourage innovation and even encourage inventing around patented technology.

Diagnostic Method Claims Fall (Again)

Judge Lourie, writing for the panel, again held that the claims directed to comparing and analyzing gene sequences are not patent-eligible because they only claim abstract mental processes.  He noted that limiting the comparison to just the BRCA genes or particular alterations would not rescue the claim because, in applying Mayo, the Supreme Court held that the prohibition against patenting abstract ideas cannot be circumvented by attempting to limit the use of the formula to a particular technological environment. This is in contrast to the application of a formula or abstract idea in a process that may be patent-eligible. The challenged claims, the judge noted, do not apply the step of comparing two nucleotide sequences in a process. Rather, he stated, the step of comparing two DNA sequences is the entire process that is claimed.

Method for Screening Potential Cancer Therapeutics

Claims directed to a method for screening potential cancer therapeutics by changes in cell growth rates of transformed cells were held to be patent-eligible because, as the parties agreed, the transformed cells arose from human effort. The cells, like the cells in Chakrabarty, are not naturally occurring and therefore the claims that use them are more than the abstract mental step of looking at two numbers and comparing two host cells’ growth rates. This claim was also held to meet the patent-eligibility standard set forth in Mayo because it does more than simply apply a law of nature. The claim was noted to apply certain steps to transformed cells that, as pointed out above, are a product of man not nature. In addition, the claim is tied to a specific host cell transformed with a specific gene and grown in the presence or absence of a specific type of therapeutic.

Judge Moore’s Concurrence in Part

Similar to last year’s opinion, Judge Moore joined with Judge Lourie with respect to the patentability of the method claims and isolated cDNA as well as the standing issue (discussed below). However, she wrote separately to explain her reasoning.

She agreed with Judge Lourie as to the controlling nature of Chakrabarty and Funk Brothers to the analysis of the issue. However, she disagreed with Judge Lourie as to the effect of the Supreme Court’s Mayo decision. She stated that as an initial matter, the Mayo decision clearly ought to apply equally to manifestations of nature (compositions) as laws of nature (process claims). In her opinion, the appropriate principles to be applied are: (1) laws of nature/manifestations of nature are not patentable; and (2) a composition of matter with “markedly different characteristics” from that found in nature with the potential for significant utility is directed to patentable subject matter.

Using this framework for analysis, she stated that the claims to cDNA molecules are clearly patentable because the claimed cDNA sequences do not exist in nature. Claims to short DNA sequences that can be used as probes or primers are also patent-eligible because these uses are markedly different from the role of that DNA as it exists in nature. With respect to isolated DNA claims that also encompass full length genes, she stated that the claims are patent-eligible not because the utility of the claimed DNA are markedly different from DNA as it exists in nature, but because of the long history of patenting isolated DNA. She noted that the USPTO began granting patents on isolated human DNA as far back as the 1980s and these patents have been litigated in the courts. Similar to Judge Lourie, she cited the Supreme Court’s warning that courts should not adopt changes that disrupt the settled expectations of the inventing community.

Judge Bryson’s Concurrence and Dissent

Judge Bryson concurred in part and dissented in part. He concurred with respect to standing (discussed below) and the patentability of the cDNA claims and the patentability of the method claims. He dissented with respect to the patentability of the isolated DNA claims that are not limited to cDNA.

He stated that claims to isolated BRCA genes are unpatentable under the application of the principles of Chakrabarty because the genes are not materially different from when they are in the human body. He noted that the primary coding sequence of the gene is the same as it was in the body and reads on the sequences as they appear on chromosomes 13 and 17. He also reiterated several analogies that support his view that the claimed subject matter is not patent-eligible. Isolating a gene in his opinion, while difficult, is similar to plucking a leaf from a tree or carving a baseball bat from an ash tree.

He also disagreed with Judges Lourie as to the effect of Mayo.  He stated that a patent involving a product of nature should have an inventive concept that involves more than merely incidental changes to the naturally occurring product. In a composition of matter that is nearly identical to a product of nature, it is appropriate to ask whether the applicant has done enough to distinguish his alleged invention from the similar product of nature.

He also argued that claims to short DNA fragments should not be patent-eligible because small sequences of DNA are repeated through the human genome, the claims cover portions of DNA of more than 4 % of human genes, and are therefore too broad. Such genes, he opined, could impede innovation in genetic medicine  such as multiplex tests and whole-genome sequencing.

He also dismissed Judge Lourie’s and Moore’s deference to the USPTO’s long-standing history of gene patenting and court’s limitations on crafting new law. Rather, he opined that the court’s role is to interpret the laws of Congress, which in the current situation, would mandate invalidating the contested claims.

The One Issue of Agreement – Plaintiffs’ Standing

The plaintiff’s ability to maintain this action was also before the court. Several of our prior posts address the issue (Sept. 17th, 2011 and May 31st 2012 posts). Judges Lourie, Moore and Bryson all agreed that plaintiffs have alleged a controversy of sufficient immediacy and reality to warrant the issuance of declaratory judgment. The court determined that only Dr. Ostrer had established standing to maintain the declaratory judgment suit even though he was no longer performing the tests using the claimed subject matter. The court noted that the district court, however, failed to limit its jurisdictional holding to affirmative acts by the patentee directed at plaintiffs. Simply disagreeing with the existence of a patent on isolated DNA sequences or even suffering an attenuated, non-proximate, effect from the existence of a patent does not meet the Supreme Court’s requirement for an adverse legal controversy of sufficient immediacy and reality to warrant the issuance of a declaratory judgment.

Myriad and Personalized Medicine

This decision is definitely good news for the biotechnology community, at least in the short term. The patent-eligibility of isolated, naturally occurring materials remains, until further challenged at the Federal Circuit (by an en banc ruling), by appeal to the Supreme Court or by Congressional action. The court also provided further guidance on what “more” is needed to transform a patent-ineligible method to one meeting the requirement of 35 U.S.C. § 101. It appears that any claim that can be performed by mere inspection alone (as by comparing the results of a lab test to a noted control) will not satisfy 35 U.S.C.§ 101. However, if the process is tied to a particular technology, thereby limiting the claim’s scope, then the claim more likely satisfies the statute. This reasoning and application of Mayo also is consistent with the USPTO’s recent guidance on evaluating claims for patent-eligibility. Thus, it is unlikely that the USPTO will further revise the draft guidance on the issue.


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