Federal Circuit: Sequenom’s Fetal DNA Claims Are Patent Eligible
April 3 2020
An unborn baby’s DNA (“fetal DNA”) can be used to determine the sex of the baby as well as to test for conditions such as Down’s syndrome. In the past, procedures to get samples of fetal DNA for testing involved sticking a large needle through the abdominal wall and into the uterus of the mother to obtain amniotic fluid, but such procedures are invasive and can be life threatening in some cases. Sequenom Inc. devised and patented less invasive options and licensed them to Illumina, Inc. Ariosa Diagnostics, Inc. and others, however, challenged the patent eligibility of those options when accused of patent infringement.
Specifically, the various lawsuits have repeatedly brought into question whether the patent claims for these new prenatal tests and related methods are patent eligible under 35 U.S.C. §101 or if they are merely directed to ineligible natural phenomena. In fact, in 2015, the Federal Circuit found Sequenom and Illumina’s patents (the “Original Patents”) were invalid as unpatentable because they were directed to a natural phenomenon. This ruling raised many concerns in the industry as to which, if any, inventions of this type could be protected.The Original Patents covered an extremely useful medical test for pregnant mothers and their unborn babies. Researchers determined that several types of DNA are floating around in the plasma of a pregnant mother. While more than 90% of the DNA is the mother’s DNA (“maternal DNA”), other DNA such as bacterial DNA, and most importantly here, fetal DNA is also present in the mother’s plasma. The fetal DNA is identifiable based on the fact that it contains DNA from both the mother and the father (“paternal DNA”). Therefore, using a sample of paternal DNA, the researchers were able to locate fetal DNA in a mother’s plasma by looking for segments of DNA that match the paternal DNA. By using fetal DNA from the mother’s plasma, the researchers determined they could eliminate the need for more invasive, and in some cases life threatening, test procedures. However, in 2015 the Federal Circuit determined the Original Patents covering this new testing approach were patent ineligible because the claimed subject matter was directed to a natural phenomenon.
The issue has arisen again as to two additional patents (the “New Patents”) involving fetal DNA in found in a mother’s plasma and using it to solve the same type of problem—fast, noninvasive testing of the fetal DNA. It turns out that fetal DNA makes up only a small fraction of the DNA present in the plasma and is difficult to distinguish and separate from the maternal DNA. The New Patents, however, take into account that the inventors also learned the fetal DNA fragments in the plasma tend to be shorter than the maternal DNA fragments in the plasma. These New Patents make use of this additional information in claiming methods for preparing the fetal DNA for testing.
As with the Original Patents, the district court found the New Patents ineligible for patent protection. This time, however, in a split decision the Federal Circuit reversed the district court and found these claims “are directed to patent-eligible subject matter.” Illumina, Inc. and Sequenom, Inc. v. Ariosa Diagnostics, Inc. (Fed. Cir. 2020).
Judge Lourie, writing for the majority, noted that while laws of nature and natural phenomena are not patentable, the application of them may be patentable. An otherwise patentable invention does not become ineligible just because it makes use of a natural phenomenon. To distinguish claims that make use of a natural phenomenon from claims that impermissibly attempt to tie up such a natural phenomenon, courts must apply the two-step test set forth in Alice and Mayo. Applying step one, the court determines whether the claims are “directed to a law of nature or natural phenomenon.” If, and only if, they are, then the court proceeds with step two to determine whether the claim limitations “transform the nature of the claim into a patent-eligible application.”
Judge Lourie also noted that “diagnostic” cases have consistently been held ineligible, but method of treatment cases have been held patent-eligible. Here, while the claimed method in the New Patents can be used in conjunction with a diagnostic method, the Federal Circuit stated “This is not a diagnostic case. And it is not a method of treatment case. It is a method of preparation case.”
The Court recognized that the New Patents involve a natural phenomenon, i.e., “that  fetal DNA tends to be shorter than  maternal DNA in a mother’s bloodstream.” But that doesn’t answer the critical question in the first step of the Alice/Mayo test: Are “the claims ‘directed to’ that natural phenomenon”? Applying the first step of the Alice/Mayo test, the Federal Circuit concluded “the claims are not directed to that natural phenomenon but rather to a patent-eligible method that utilizes it.” Instead, “[t]he claims in this case are directed to methods for preparing a fraction of  DNA that is enriched in fetal DNA.” The claimed process steps “change the composition of the mixture,” and thus “achieve more than simply observing that fetal DNA is shorter than maternal DNA or detecting the presence of that phenomenon.” In finding the claims were not directed to a natural phenomenon, the court did not need to proceed to step two of the Alice/Mayo test.
Notably, the Federal Circuit distinguished the claims in the New Patents from those in the Original Patents. The claims in the Original Patents were directed to a method “for detecting a paternally inherited nucleic acid” or a method “for performing a prenatal diagnosis.” Those claims were found ineligible for patent protection, as was the case for invalid diagnostic claims in Mayo, because “they were directed to detecting a natural phenomenon.” (emphasis added).
In dissent, Judge Reyna argued that “[t]he patents’ only claimed advance is the discovery of that natural phenomenon.” “Nothing else in the specification or the record before us indicates there was anything new or useful about the invention.” While the majority agreed that the inventors could not patent a method directed to the natural phenomenon, they concluded the claimed method “utilize[s] the natural phenomenon … by employing physical process steps to selectively remove larger fragments of  DNA and thus enrich a mixture in  fetal DNA.”
In summary, the Court found a way to find the New Patents eligible for patent protection while distinguishing this case from the prior Ariosa decisions. The Federal Circuit, however, may deem this case appropriate for rehearing en banc or the Supreme Court may decide to hear it despite declining to take up the 2015 case. But if this ruling stands, it may provide a path for patent protection for a larger number of inventions of this nature.