DOJ, Patent Holder Briefs Debate Patentability of Isolated DNA

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The U.S. Department of Justice filed an unsolicited amicus curiae brief Oct. 29 in the highly controversial Myriad case and asked the U.S. Court of Appeals for the Federal Circuit to affirm a lower court judgment that patent claims on isolated gene sequences--“without material change to its naturally occurring chemical structure and function”--are not patentable subject matter (Association for Molecular Pathology v. U.S. Patent and Trademark Office, Fed. Cir., No. 2010-1406, briefing 10/29/10).

Isolated DNA molecules represented only a subset of the claims at issue in the case, the DOJ noted. It faulted the district court for not distinguishing claims drawn to patent-eligible “man-made compositions,” representative of claims in other patents directed to vaccines and genetically modified crops.

However, an Oct. 22 brief filed by the appellant patent owners noted that the Patent and Trademark Office has issued about 2,645 patents with claims to “isolated DNA,” and over 50,000 patents containing at least one claim directed to a nucleic acid sequence in humans, other animals, plants, or bacteria.

The DOJ's position--challenging patents issued by the PTO--essentially puts the two Obama administration agencies at odds with one another. It is unclear which among the 50,000 issued DNA patents mentioned by the appellant could be struck down as ineligible for patenting if the Federal Circuit follows the DOJ's advice. However, Peter Pappas, the PTO's chief communications officer, told BNA that his agency “will maintain the status quo as regards examination practice while the issue is pending before the Circuit Court of Appeals.”

The Complaint in the Case.

A May 2009 declaratory judgment complaint against the PTO and patent owners alleged that patents on two human genes associated with hereditary breast and ovarian cancer monopolistically stifle research that could lead to cures, limit women's options regarding their medical care, and are unconstitutional (78 PTCJ 64, 5/15/09).

The lawsuit was filed by the American Civil Liberties Union and the Public Patent Foundation at Benjamin N. Cardozo School of Law on behalf of the Association of Molecular Pathology and other medical associations, eight individuals involved in medical research, two breast cancer counselors, and six women diagnosed with or seeking diagnosis for cancer.

The complaint challenged the patent eligibility of 15 claims of patents (5,747,282; 5,837,492; 5,693,473; 5,709,999; 5,170,001, 5,753,441; and 6,033,857) on the BRCA1 and BRCA2 genes, owned or part-owned by the University of Utah Research Foundation, under Section 101 of the Patent Act, 35 U.S.C. §101. Myriad Genetics Inc. is the exclusive licensee of the patents and the sole clinical provider of full sequencing of the BRCA1/2 genes in the United States.

The complaint against the PTO was that the agency's policy that allows naturally-recurring genes to be patented if they are “isolated from their natural state and purified” is unconstitutional. The plaintiffs charged that the claims “constitute patents on thought, knowledge, and ideas in violation of the First Amendment,” and that the claims also violate the intellectual property clause of the Constitution--Art. 1, Sec. 8, Cl. 8--because they “impede rather than advance science.”

In August 2009, the plaintiffs moved for summary judgment, alleging that the claims at issue--including composition of matter claims drawn to the gene sequences and method claims on testing methods--fall within one of the three judicially-recognized exceptions to patentability--natural phenomena, laws of nature, and abstract ideas (78 PTCJ 561, 9/4/09).

The District Court on Isolated DNA.

On Nov. 1, 2009, Judge Robert W. Sweet of the U.S. District Court for the Southern District of New York denied Myriad's motions to dismiss for lack of subject matter and personal jurisdiction and for failure to state a claim (79 PTCJ 4, 11/6/09). The judge found that the court had subject matter and personal jurisdiction over all the defendants; that the plaintiffs had standing against all the named defendants, including the PTO; and that the claims were adequately pled.

Both sides then filed new motions for summary judgment (79 PTCJ 246, 1/8/10). Several amicus briefs were filed, and, in a proceeding more reminiscent of appellate advocacy, oral arguments were heard Feb. 2 (79 PTCJ 395, 2/5/10).

On March 29, Sweet ruled in favor of the plaintiffs on the merits on both the composition of matter and method claims at issue. No. 09 Civ. 4515, 94 USPQ2d 1683 (S.D.N.Y. March 29, 2010) (79 PTCJ 661, 4/2/10).

“DNA, and in particular the ordering of its nucleotides,” he said, “serves as the physical embodiment of laws of nature--those that define the construction of the human body.”

“[P]urification of a product of nature, without more, cannot transform it into patentable subject matter,” Sweet said. Isolated and purified DNA lacking “markedly different characteristics” from native DNA is not a patentable composition under Section 101 of the Patent Act, according to the judge.

The court repeatedly used the term “product of nature” to identify the isolated DNA, and subsequently considered, in footnote 40, whether it would be a fourth judicial exception to patentability or whether a product of nature is equivalent to one or more of the well known three exceptions:  

Myriad distinguishes between “laws of nature,” “natural phenomena,” and “abstract ideas,” which it concedes are not patentable, and “products of nature,” for which it appears to argue no prohibition to patentability exists. Although the distinction between these two categories is unclear, it is well established that “products of nature” are not patentable. See, e.g., Chakrabarty, 447 U.S. at 13 (stating that relevant distinction for §101 patentability is “between products of nature, whether living or not, and human-made inventions”). 




The District Court on Diagnostic Methods.

Sweet further cited the Federal Circuit's Bilski opinion as controlling law as to Section 101 patentability of the method claims at issue. In re Bilski, 545 F.3d 943, 88 USPQ2d 1385 (Fed. Cir. 2008) (en banc) (77 PTCJ 4, 11/7/08). But his analysis was driven more by a comparison to the Federal Circuit's follow-on decision that diagnostic method tests were patent eligible in their transformative effects, in Prometheus Laboratories Inc. v. Mayo Collaborative Services, 581 F.3d 1336, 92 USPQ2d 1075 (Fed. Cir. 2009) (78 PTCJ 635, 9/25/09).

However, Sweet distinguished the claims in the instant case from the claims at issue in Prometheus. A representative claim from Prometheus showed a “transformation of the human body as well as the chemical and physical changes of the drug's metabolites,” he said. That claim included a transformation in the determining step, he noted, but that step was “central to the claimed methods.” In contrast, the particular method claims challenged by the ACLU in the instant case, he said, “are directed only to the abstract mental processes of 'comparing' or 'analyzing' gene sequences.”

The Supreme Court has since ruled that the Bilski “machine or transformation” test is not the exclusive test for process claim patent eligibility. Bilski v. Kappos, 129 S.Ct. 2735, 95 USPQ2d 1001 (2010) (80 PTCJ 285, 7/2/10). The high court further vacated and remanded Prometheus in light of Bilski (80 PTCJ 288, 7/2/10), though most analysts expect the appellate court to reach the same conclusion (80 PTCJ 726, 10/1/10).

Sweet concluded by dismissing the plaintiffs' constitutional claims against the PTO. Given the judgments of unpatentability, he said, “The doctrine of constitutional avoidance, which states that courts should not reach unnecessary constitutional questions, thereby becomes applicable.”

Myriad appealed June 16. The plaintiffs did not cross appeal, so the PTO's role in the case as a party is likely ended.

Myriad Appeals Jurisdiction.

The Oct. 22 brief for the appellant, patent holder Myriad, which is represented by Gregory A. Castanias of Jones Day, Washington, D.C., contested both the jurisdiction and merits decisions.

On the jurisdiction judgment, Myriad distinguished two categories of plaintiffs in the case. “The first consists of organizations and individuals that share these attributes: (1) there is no allegation or evidence that any of these plaintiffs ever communicated with Myriad, or that Myriad communicated with them, regarding the patents-in-suit, let alone the specific disputed claims selected for challenge; and (2) there is no allegation or evidence that Myriad ever evaluated any conduct of any of these plaintiffs for purposes of determining infringement,” the company said.

“The plaintiffs in the second category,” Myriad continued, are three research physicians who “share a common attribute in that the complaint alleges, or the court found, that they had communications with Myriad more than a decade ago concerning certain of the patents-in-suit.”

Citing MedImmune Inc. v. Genentech Inc., 549 U.S. 118, 81 USPQ2d 1225 (2007) (73 PTCJ 242, 1/12/07, Myriad argued that the plaintiffs were required to show “a substantial controversy, between parties having adverse legal interests, of sufficient immediacy and reality.”

Therefore, the company said, “Under the proper standard, there is no adversity here--just a complaint manufactured to serve the ends of two public-advocacy groups. This is precisely the type of 'abstract' dispute that the constitutional case-or-controversy requirement excludes from federal jurisdiction.”

Myriad's Attack on Patentability Judgments.

As to patent eligibility issues, Myriad first attacked the lower court's conclusions that isolated DNA is no more than the physical embodiment of genetic information, that the “markedly different characteristics” is the basis for a Section 101 test, and that there is a judicial exception to patent eligibility for “products of nature.”

To support its argument that isolated DNA molecules are compositions of matter and thus patent-eligible under Section 101, Myriad cited support from the PTO's 2001 Utility Examination Guidelines (61 PTCJ 262, 1/12/01) and the text of Section 103(b) on obviousness. Section 103(b) references “a biotechnological process using or resulting in a composition of matter,” and Section 103(b)(3) defines a biotechnological process as “a process of genetically altering or otherwise inducing a single- or multi-celled organism to … (i) express an exogenous nucleotide sequence.”

The brief then looked at Supreme Court precedents to argue that isolated DNA molecules do not fall within the judicially created exceptions to patent eligibility. Noting the one-time-only reference to “markedly different characteristics” in Diamond v. Chakrabarty, 447 U.S. 303, 206 USPQ 193 (1980)(484 PTCJ A-1, 6/19/80), Myriad contended that the high court did not mean to create a new test for patent eligibility in the phrase. “ 'Markedly different' is a fine term for judges to use when describing the particular facts of a particular case, as in Chakrabarty, but it surely was not meant as a legal standard to govern all future cases decided under the statute,” the appellants argued.

The brief further addressed a Federal Circuit judge's apparent predisposition toward patent ineligibility of nucleotide sequences in a dissenting opinion in Intervet Inc. v. Merial Ltd., No. 2009-1568, 95 USPQ2d 1956 (Fed. Cir. Aug. 4, 2010) (80 PTCJ 502, 8/13/10).

“It is far from clear that an 'isolated' DNA sequence is qualitatively different from the product occurring in nature such that it would pass the test laid out in Funk Brothers and Chakrabarty,” Judge Timothy B. Dyk said in Intervet, referring to Funk Brothers Seed Co. v. Kalo Inoculant Co., 333 U.S. 127, 76 USPQ 280 (1948). “The mere fact that such a DNA molecule does not occur in isolated form in nature does not, by itself, answer the question. It would be difficult to argue, for instance, that one could patent the leaves of a plant merely because the leaves do not occur in nature in their isolated form.”

But, Myriad argued, that analogy--and the court's opinion in Funk Brothers--is directed to obviousness analysis under Section 103, and not patent eligibility under Section 101. And, for the second time in the brief, the appellant reminded the court that the plaintiffs did not challenge Myriad's patent claims for invalidity by reason of anticipation or obviousness.

Finally, Myriad criticized the lower court for distinguishing its diagnostic method claims from those that the Federal Circuit deemed patent eligible in Prometheus. The district court found no transformative process in Myriad's claims due to, the brief stated, “an erroneous claim construction--it construed the term 'sequence' in the method claims as mere information (i.e., letters from the alphabet), rather than as a physical molecule.”

“Under a proper claim construction, the claims require the transformation of a human sample, and the transformation of the specific BRCA molecules in that sample,” Myriad said, and the claims are thus patent-eligible.

DOJ Makes Distinction in Claims.

The stance taken by the DOJ in its brief was not unexpected, as the rumor had spread during the prior week's annual meeting of the American Intellectual Property Law Association that the PTO's voice was being drowned out by the interests of other government “components” (80 PTCJ 848, 10/29/10). In the introduction to the brief, the DOJ mentioned “the Patent and Trademark Office (PTO), the National Institutes of Health (NIH), the Antitrust Division of the Department of Justice, the Centers for Disease Control and Prevention, the Office of Science and Technology Policy, and the National Economic Council, among others,” as government agencies implicated by the appeal in this case.

The brief addressed only the questions on patent eligibility of DNA and ignored the jurisdictional and method claim issues.

The DOJ identified a difference between post-Chakrabarty grants of patents on “man-made complementary DNA molecules (cDNA) in combination with vectors” and “eventually,” the PTO's decision to grant patents on “isolated but otherwise unaltered genomic DNA itself … without material change to its naturally occurring chemical structure and function.”

The district court erred, the DOJ brief said, in not distinguishing, for example, the naturally occurring BRCA1 protein in Claim 1 of the '282 patent and the claims limited to cDNAs that encode the BRCA1 protein, such as Claim 2 of that patent.

The DOJ summarized its position as follows:  

The scope of Section 101 is purposefully wide and its threshold is not difficult to cross. See Bilski, 130 S.Ct. at 3225. New and useful methods of identifying, isolating, extracting, or using genes and genetic information may be patented (subject to the prohibition against patenting abstract ideas), as may nearly any man-made transformation or manipulation of the raw materials of the genome, such as cDNAs. Thus, the patent laws embrace gene replacement therapies, engineered biologic drugs, methods of modifying the properties of plants or generating biofuels, and similar advanced applications of biotechnology. Crossing the threshold of section 101, however, requires something more than identifying and isolating what has always existed in nature, no matter how difficult or useful that discovery may be. 




The DOJ brief further distinguished patent eligible methods of identifying, isolating, and using DNA molecules from genomic DNA itself. In so doing, the agency labeled the latter as a product of nature, and said, “'the relevant distinction' for purposes of section 101 is not 'between living and inanimate things, but between products of nature … and human-made inventions,” per J.E.M. Ag Supply Inc. v. Pioneer Hi-Bred International Inc., 534 U.S. 124, 130, 60 USPQ2d 1865 (2001) (63 PTCJ 132, 12/14/01).

“We acknowledge that this conclusion is contrary to the longstanding practice of the Patent and Trademark Office, as well as the practice of the National Institutes of Health and other government agencies that have in the past sought and obtained patents for isolated genomic DNA,” according to the government's brief. “The district court's judgment in this case, however, prompted the United States to reevaluate the relationship between such patents and the settled principle under Supreme Court precedent that the patent laws do not extend to products of nature.”

Other Briefs Generally Support Reversal.

The case is widely predicted to reach the en banc Federal Circuit at least, if not the Supreme Court. Nonetheless, even though a three-member panel of the appellate court has yet to be named, at least 14 other briefs were filed by friends of the court on or before Oct. 29:

• Alnylam Pharmaceuticals Inc., filed by Mary M. Calkins of Foley & Lardner, Washington, D.C.;

• the American Intellectual Property Law Association, by Barbara R. Rudolph of Finnegan, Henderson, Farabow, Garrett & Dunner, Washington, D.C.;

• the Animal Health Institute, by Kent D. McClure of the Washington, D.C., organization;

• the Biotechnology Industry Organization and the Association of University Technology Managers, by former solicitor general Seth P. Waxman of Wilmer Cutler Pickering Hale and Dorr, Washington, D.C.;

• the Boston Patent Law Association, by Lee Carl Bromberg of McCarter & English, Boston;

• the Genetic Alliance, by Douglas S. Forman of Finnegan, Henderson, Farabow, Garrett & Dunner, Washington, D.C.;

• Genomic Health Inc., Celera Corp., XDx Inc., Target Discovery Inc., the Coalition for 21st Century Medicine, and Burrill & Co., by William G. Gaede of McDermott Will & Emery, Menlo Park, Calif.;

• Christopher M. Holman, professor at the University of Missouri-Kansas City School of Law, and Robert Cook-Deegan, of the Duke Institute for Genome Sciences & Policy, Durham, N.C.;

•  The Intellectual Property Owners Association, signed by Executive Director Herbert C. Wamsley, with Paul H. Berghoff of McDonnell Boehnen Hulbert & Berghoff, Chicago, listed as counsel of record;

• Kane Biotech, by Brian R. Dorn of Merchant & Gould, Minneapolis;

• Merial Ltd., by Judy Jarecki-Black of the Duluth, Ga., firm;

• Novartis Corp., but Aaron Stiefel of Kaye Scholer, New York;

• Rosetta Genomics Ltd. and George Mason University, by Jacqueline D. Wright Bonilla of Foley & Lardner, Washington, D.C.; and

• the University of New Hampshire School of Law in Concord, N.H., by professor Ann M. McCrackin.


The IPO brief cited different statistics than Myriad for the number of patents at risk: “almost a thousand U.S. patents that claim isolated plant DNA, almost 25,000 U.S. patents on isolated animal DNA, almost 3,000 U.S. patents on isolated bacterial DNA, over 3,000 U.S. patents on isolated viral DNA, and 50 U.S. patents claiming vaccines based on isolated DNA, primarily DNA encoding antigens from viral and other pathogens.”

Another Controversy in the Case.

Myriad's concern about Dyk's apparent predisposition in the case reflects half of another controversy in the case. The ACLU and PUBPAT challenged Chief Judge Randall R. Rader to recuse himself from the case (80 PTCJ 371, 7/23/10), for comments Rader was reported to have made as a panelist at the Biotech Industry Organization's BIO 2010 conference May 4 in Chicago (80 PTCJ 47, 5/14/10), and at an April Fordham University School of Law conference.

The appellees' motion stated that Rader “expressed his views on the correctness of the district court's decision in this case” at the BIO conference, and that “he insinuated disagreement with Plaintiffs/Appellees' view of the law” when the case was discussed at the Fordham conference.

The Federal Circuit Bar Association already submitted an amicus brief Aug. 3 on that issue alone (80 PTCJ 499, 8/13/10). But the court, in a July 29 letter to the ACLU co-counsel Christopher A. Hansen, wrote that “the panel in this case has not yet been chosen. In the event that Judge Rader is assigned, the motion will be transmitted to him.”

The plaintiff-appellees' brief is due Dec. 6.

By Tony Dutra