Sequenom is the exclusive licensee of US patent 6,258,540, which Sequenom licensed from Isis
Innovation Limited. The patent relates to prenatal detection methods performed on a maternal serum or plasma sample from a pregnant female, which methods comprise detecting the presence of a paternally inherited nucleic acid of fetal origin in the sample, and is based on the discovery that cell-free fetal DNA (sometimes referred to as “cffDNA”) is detectable in maternal serum or plasma samples. The “invention enables non-invasive prenatal diagnosis, including for example sex determination, blood typing and other genotyping, and detection of pre-eclampsia in the mother.”
Ariosa, formerly known as Aria Diagnostics, sued Sequonom in the Northern District of California seeking a declaratory judgment that it does not infringe the ‘540 patent. On October 30, the court granted summary judgment in favor of Arioso, declaring a number of claims of the ‘540 patent invalid for being directed towards patent ineligible subject matter under 35 USC 101. The decision is available here.
Claim 1 is representative of the invalidated claims. It recites:
1. A method for detecting a paternally inherited nucleic acid of fetal origin performed on a maternal serum or plasma sample from a pregnant female, which method comprises:
amplifying a paternally inherited nucleic acid from the serum or plasma sample and
detecting the presence of a paternally inherited nucleic acid of fetal origin in the sample.
Recent Supreme Court decisions addressing patent eligibility, particularly Mayo v. Prometheus, have emphasized two criteria for assessing patent eligibility of method claims directed towards a practical application of the discovery of a “natural phenomenon.” First, does the claimed method add something to the natural phenomenon beyond what is already “well-understood, routine, or conventional.” Second, does the claimed method “preempt” the natural phenomenon.
With regard to the first criterion, the District Court interpreted the requirement of something more than well understood, routine and conventional activity as imposing a requirement that the claimed method must constitute an “inventive” application of the natural phenomenon. The court held that “use of a newly discovered natural phenomenon  will not render a claim patentable if the use of that natural phenomenon,  is the only innovation contained in the patent.” The court found that the only inventive aspect of the method was the discovery of the presence of cffDNA in maternal plasma, and that the detection of cffDNA using conventional techniques for DNA detection was not sufficiently inventive to render the claim patent eligible.
One way of looking at it is that the court essentially conducted a nonobviousness analysis, usually the province of Section 103, under the guise of Section 101 patent eligibility, treating the newly discovered natural phenomenon which formed the basis for the claim method as something akin to prior art, and concluding that it was not inventive (i.e., it was obvious) to combine the natural phenomenon with prior art methods for DNA detection. It will be interesting to see how the Federal Circuit responds to this interpretation of the “well understood, routine and conventional” language the Supreme Court used in Mayo. Unfortunately, it seems to comport with a literal reading of Mayo. However, in the Federal Circuit’s recent fractured en banc decision in CLS Bank Int’l v. Alice Chief Judge Rader authored an opinion explicitly stating that, in his view, the Supreme Court’s use of the language “well-understood, routine and conventional” does not inject a requirement of inventiveness into the section 101 patent eligibility analysis. Other Federal Circuit judges offered different interpretations, and there appear to be some that are much more receptive to that the Supreme Court has injected an “inventiveness” criterion in the test for patent eligibility.
Regarding the second criterion, the District Court found that the claim would cover all “commercially viable” means of testing for paternal cffDNA and thus preempted use of the natural phenomenon. Sequenom presented evidence that there are alternate methods available for detecting cffDNA that are not covered by the claim, but the court characterized these methods as not “commercially viable,” and hence not relevant to its preemption analysis, which focused on the practical impact of the patent claims. The decision suggests that a method claim such as this is patent ineligible unless, “at the time of the invention or at the time of issuance of the patent,” there are available commercially viable alternatives for applying the claimed natural phenomenon.
If the approach used by this court is upheld by the Federal Circuit and applied generally to diagnostic claims, it would seem to severely limit the availability of patent protection for diagnostics. One well-known patent that immediately comes to mind is Genetic Technology Ltd’s so-called “junk DNA” diagnostic patent, US Patent No. 5,612,179, which involves diagnostic analysis of non-coding DNA and has been asserted against numerous alleged infringers. But even if this approach is adopted, there remains some reason to be optimistic with respect to personalized medicine claims, particularly if the claim includes a step actually applying diagnostic information, for example by administering a drug to a patient. I think the Federal Circuit’s recent decision in Classen Immunotherapies, Inc. v. Biogen IDEC would support that position.