Tuesday, October 26, 2010

The ACLU Gene Patent Challenge: Analysis of Myriad's Brief

Yesterday I posted a link to the brief filed last Friday by Myriad Genetics with the Federal Circuit in the case of AMP v. PTO (ACLU and Public Patent Foundation challenge to gene patents). In their brief, Myriad argues that (1) the district court should have dismissed the case for lack of jurisdiction, because there was no evidence of any real or immediate dispute between Myriad in any plaintiff; (2) composition of matter claims directed towards isolated DNA molecules are patent eligible, in part because they have "markedly different characteristics" than their naturally occurring counterparts; and (3) method of diagnosis claims are patent eligible, in part because they all require physical transformation of a DNA sample (i.e., isolation, processing and analysis) that satisfies the Bilski machine-or-transformation test.

Lack of Jurisdiction

Myriad argues that the 20 plaintiffs were all recruited by the ACLU and Public Patent Foundation (referred to herein collectively as ACLU) in order to further those group’s agenda of abolishing gene patents, and that there is no evidence of any current dispute between Myriad and any of the plaintiffs. According to Myriad, only three of the plaintiffs have ever been contacted by Myriad, and those three were contacted more than a decade before the filing of the complaint. Myriad argues that none of the plaintiffs has a controversy "of sufficient immediacy and reality to warrant the issuance of a declaratory judgment" under the MedImmune standard.

Composition of Matter Claims

Myriad begins by arguing that the district court was incorrect in its conclusion that "products of nature" are patent ineligible, pointing out that such a "sweeping exception" would bar the patenting of important inventions like pharmaceuticals derived from natural sources (e.g., Taxol), and would be inconsistent with cases finding isolated natural products patentable that date back nearly 100 years.

Myriad goes on to argue that even if the district court is correct, and isolated products of nature are only patent eligible if they display "markedly different characteristics" compared to the product as exists in nature, Myriad's isolated BRCA gene sequences clearly satisfy the test. Myriad points out that it is inconsistent for plaintiffs to argue on the one hand that the claimed isolated BRCA molecules are necessary for performing BRCA diagnostic testing, while at the same time arguing that the claimed isolated molecules have no "markedly different characteristics" from their naturally occurring counterparts. They note that native DNA is useless for the diagnostic and detection applications for which the isolated molecules must be utilized.

Myriad addresses the much discussed dissent by Judge Dyk in his separate opinion in Intervet, which many have interpreted as signaling his skepticism with respect to the patent eligibility of isolated gene sequences. In his opinion, Judge Dyk suggested that it "would be difficult to argue, for instance, that one could patent a leave of a plant merely because the leaves do not occur in nature in an isolated form." Myriad points out that not only would Judge Dyk’s hypothetical leave likely fail under sections 102 and 103 for lack of novelty and obviousness, it would fail the "markedly different characteristics" test "because the plucked leaf would have exactly the same properties as the unplucked leaf-unlike here, where isolated DNA molecules possess significantly different structural and functional characteristics from native DNA."

Method Claims

Critics of Myriad's gene patents have complained that the claims are much too broad, claiming the information content of the BRCA genes, and totally precluding doctors and patients from looking at or discussing the presence of genetic variations in the BRCA genes. For example, some of the challenged method claims could be interpreted broadly to cover comparing a patient's BRCA sequence with wild-type BRCA in order to identify genetic variations (which could be clinically significant).
However, in their brief Myriad argues for a narrower interpretation, under which all the method claims could only be infringed by a party that isolates and analyzes DNA molecules (as opposed to genetic sequence information). This could be a significant limitation that avoids some of the fears that have been raised with respect to the inability to design around these patent claims. For example, I am reading a book called The $1000 Genome, by Kevin Davies, which describes new technology that is rapidly coming online which will enable people to inexpensively determine the sequence of their entire genome. Salzberg and Pertea recently published an article in Genome Biology called "Do-It-Yourself Genetic Testing,” (described recently on the Patent Docs blog), which purports to allow a person who knows her BRCA sequences to analyze for variations predictive of cancer. It seems to me that in the not-too-distant future method claims such as Myriad’s could be readily circumvented by having one's whole genome sequenced (without asking the sequencer to analyze for BRCA mutations), and then using a computational screen such as the one provided by Salzberg and Pertea to analyze for clinically relevant variations.

Myriad argues that because its method claims all require isolation and processing of DNA molecules, they satisfy the transformation prong of Bilski's machine or transformation test. They correctly note that the Federal Circuit's Prometheus decision explicitly held that diagnostic methods that involve processing a biological sample "necessarily involve a transformation,” and thus pass the machine or transformation test. The Supreme Court in Bilski v. Kappos clarified that the machine or transformation test is not the exclusive test for patent eligibility, but acknowledged that in most instances the existence of a machine or transformation is highly relevant to the question of patent eligibility. The Supreme Court vacated the Federal Circuit's original Prometheus decision, and remanded for the Federal Circuit to reconsider in light of Bilski v. Kappos. I predict that when the Federal Circuit issues a new decision in Prometheus, it will maintain the holding that diagnostic methods involving physical manipulation of biological samples are transformative and generally patent eligible.

Myriad goes on to point out that Bilski v. Kappos "remove any suggestion that the rigid 'machine-or-transformation' test provides the exclusive test for patent eligibility, particularly as applied to "Information Age" technologies like the advanced diagnostic techniques claimed injury and patents." In contrast with the method of hedging claims found to be unpatentable abstract ideas in Bilski, Myriad argues that its methods represent "very real ways of diagnosing and treating cancers."
Interestingly, Myriad does not address the question of whether its method claims impermissibly encompass a natural phenomenon. Supreme Court precedent makes clear that natural phenomena are patent ineligible, and prior to the Federal Circuit's In re Bilski decision most patent eligibility challenges to biological method claims (particularly diagnostic claims) focused on arguments that the method claim preempted the practical use of a natural phenomenon. I have discussed this often on this blog, particularly with respect to the Prometheus and Classen cases, and Justice Breyer's often cited dissent from LabCorp.


I don't have a good sense as to how the Federal Circuit will decide the issue of jurisdiction, it seems to me that the threat of being sued for patent infringement was nonexistent for many of the plaintiffs, and highly speculative for others.

However, I do think that if the Federal Circuit finds jurisdiction it will uphold the validity of isolated polynucleotide claims and methods of diagnosis claims, so long as those method claims require the performance of physically transformative processes (isolation, processing and analysis of molecules).

On the other hand, a broad method claim that could be infringed by the mere analysis of genetic information, without requiring any physically transformative step, would I think face a significant threat of invalidation for patent eligibility under Bilski. I suspect this is why Myriad is arguing for a narrower interpretation.


patent litigation said...

Myriad's standing issue seems like a Hail Mary. It doesn't strike me as a terribly strong argument, in the context of the issues at play in this patent litigation. Moreover, what with the DOJ having just decided that isolated genes are unpatentable, Myriad's chances of success on the merits of its case seem increasingly remote. I hope this issue still goes up to the SCOTUS and the Court grants cert, because I'm looking forward to reading that opinion.

Anonymous said...

That was very informative and well written. Mentioned below is an article on gene patent debate:
"The amicus brief submitted by the Department of Justice (DOJ) in the Breast Cancer Gene patent appeal before the Federal Circuit has drawn great attention during the last week. A US District Court had earlier rejected isolated gene sequence claims in Myriad's patent stating that they do not satisfy the patentable subject matter requirement because they are products of nature. Aggrieved by the decision of the District Court, Myriad appealed to the Federal Circuit. The Department of Justice has filed an amicus brief before the Federal Circuit stating that the District Court's opinion was right with respect to genomic DNA sequences. As the DOJ's opinion is very persuasive, it has once again brought the gene patent debate to life."......read more at http://www.patentpill.com/2010/11/gene-patent-debate-is-alive-again.html

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