On June 27, 2016, the Supreme Court of the United States (“SCOTUS”) denied Sequenom’s petition for a writ of certiorari, leaving in place the decision of the Federal Circuit to invalidate Sequenom’s patent in Ariosa Diagnostics, Inc v Sequenom, Inc. (“Sequenom”).  Sequenom is noteworthy because many of the Federal Circuit judges found the invention to be highly meritorious, and that invalidating the patent would impede innovation, but nonetheless concurred with invalidating the patent because they considered themselves bound by the test SCOTUS prescribed in Mayo.  Sequenom’s patented invention enabled fetal DNA to be determined from a maternal blood sample “by identifying genetic fragments containing paternally inherited sequences the mother did not share”.  This permitted fetal genetic conditions to be diagnosed without resorting to invasive techniques like amniocentesis, which carry a risk of miscarriage. 
The denial of Sequenom’s petition makes it clear that SCOTUS accepts, at least for the time being, that patents for highly meritorious inventions may be invalidated as judicial exceptions to patent protection under 35 USC § 101 even when doing so may impede innovation. Beyond its dire significance to life science patents, this result is important to patent subject matter eligibility generally, especially in the computer-implemented arts.
Sequenom filed a petition for a writ of certiorari (more details available here). In their petition, they asked SCOTUS “whether a novel method is patent-eligible where: (1) a researcher is the first to discover a natural phenomenon; (2) that unique knowledge motivates him to apply a new combination of known techniques to that discovery; and (3) he thereby achieves a previously impossible result without preempting other users of the discovery.”  The petition argues that this pre-emption analysis should be central to a Section 101 analysis and that courts should not frustrate the legislative purpose of patent law to promote innovation by invalidating patents for covering judicial exceptions even when these patents do not pre-empt all uses of the judicial exception. The failure of both of these arguments suggests that analogous arguments for the patentability of computer-implemented inventions are likely to fail.
Sequenom quoted from Alice to describe the purpose of pre-emption analysis: “the very reason we distinguish patents that claim the building blocks of human ingenuity from those that integrate the building blocks into something more, is that the latter pose no comparable risk of pre-emption.”  The particular natural phenomenon at issue, that fetal DNA carries paternal contribution, was combined with known techniques to define the claimed invention. Thus, the patent did not pre-empt other users from using this natural phenomenon for other purposes. The Federal Circuit appears to have accepted that the patent did not pre-empt all uses of the natural phenomenon, but also determined that while “preemption may signal patent ineligible subject matter, the absence of complete preemption does not demonstrate patent eligibility.” 
Sequenom also argued that the purpose of patent law is to promote innovation, and that by invalidating their patent, the Court would reduce the predictability and certainty of the patent system and thereby deter innovation. The Federal Circuit agreed with this argument but invalidated the patent nonetheless.  That is, the Federal Circuit appeared to accept that the Sequenom patent does not pre-empt other uses of the natural phenomenon, and that invalidating the patent is likely to impede innovation in the medical diagnosis space. Nonetheless, they invalidated the patent as they considered themselves bound by SCOTUS precedent to do so.
Implications for Computer-Implemented Technologies
Whatever else judicial exception cases are about, they need not be about interpreting patent legislation so as to promote innovation, nor are they primarily concerned with pre-emption of the judicial exceptions. Clearly, patent practitioners in the computer arts should not exclusively rely on such arguments. Beyond this general observation, Sequenom can also help shape claim drafting approaches, as well as arguments regarding the eligibility of computer-implemented inventions based on other decisions, such as Alice.
In invalidating the patent at issue in Alice, Judge Thomas pointed out that the innovation claimed did not improve the operation of a computer or another area of technology.  This has sometimes been taken to mean that innovations that improve the operation of the computer or another area of technology are eligible for patent protection. Sequenom makes it clear that this is not necessarily the case. The innovation at issue in Sequenom was a profound breakthrough, allowing a dangerous and intrusive procedure, amniocentesis, to be replaced with a simple blood sample – undoubtedly a procedure that improved its area of technology. To distance arguments based on Judge Thomas’ decision in Alice from Sequenom, it may be helpful to argue that the particular computer-implemented invention claimed improves the operation of some kind of system or machine, such as a computer system, or a rubber mold.  Further, in drafting patent claims, it may be advisable to define the invention in terms of the improved operation of such system or machine.
Sequenom also reinforces the current position of the USPTO and its guidelines on subject matter eligibility.  In drafting these guidelines, the USPTO was handicapped by the failure of the courts to provide a justification for the judicial exceptions that consistently explains when patent claims define ineligible abstract ideas. Lacking such explanations or the authority to craft its own explanation, the USPTO has instead instructed examiners to reject claims as abstract ideas if and only if the claims cover subject matter that is similar to what the courts have determined to be abstract ideas. Sequenom provides a very clear example of why this approach is required, exemplifying the futility of principles when it comes to questions of subject matter eligibility.
Patents and patent applications are creatures of statute. In general, courts are obliged to interpret legislation to accomplish legislative objectives. In the case of the Patent Act, this legislative objective is to promote innovation.  Clearly, however, this legislative objective is of little assistance in identifying ineligible abstract ideas. Further, claims can define ineligible abstract ideas without pre-empting all applications of these abstract ideas. At present, no principles exist for accurately predicting patent eligibility. Given this absence of general principles, it is best to focus on specifics. For example, when drafting claims, it is best to draft patent claims with arguments in mind as to why the subject matter covered by the claims is materially different from subject matter determined to be ineligible in the case law.