CAFC Holds Sequenom’s Prenatal DNA Patent Claims Eligible Under 101

By Eileen McDermott
March 17, 2020

“This is not a diagnostic case. And it is not a method of treatment case. It is a method of preparation case,” wrote the CAFC. “The claims in this case do not fall into either bucket.” U.S. Court of Appeals for the Federal Circuit (CAFC) has reversed a district court decision finding certain claims of two patents covering prenatal DNA testing patent ineligible. The CAFC held that “the claimed methods utilize the natural phenomenon that the inventors discovered by employing physical process steps” and thus were patent-eligible. The patents at issue in the case acknowledge but are not related to the patented invention held invalid in Ariosa Diagnostics, Inc. v. Sequenom, Inc., 788 F.3d 1371, 1373 (Fed. Cir. 2015). The opinion was authored by Judge Lourie, with Judge Reyna dissenting.

U.S. Patent 9,738,931 (the ’931 patent) and U.S. Patent 9,580,751  (the ’751 patent) are owned by Sequenom and licensed by Illumina. The two companies brought suit against Ariosa Diagnostics, Inc., Roche Sequencing Solutions, Inc., and Roche Molecular Systems, Inc. (Roche) for infringement in the United States District Court for the Northern District of California in 2018, three years after the decision in Ariosa v. Sequenom. The district court found the asserted claims invalid under 35 U.S.C. § 101 as directed to an ineligible natural phenomenon and granted summary judgment to Roche.

According to the Federal Circuit, the inventors in the present case were attempting to solve the following problem: “Although it was known that cell-free fetal DNA existed in the mother’s bloodstream, there was no known way to distinguish and separate the tiny amount of fetal DNA from the vast amount of maternal DNA.”

To find a solution, the inventors first made the discovery that “the majority of the circulatory extracellular fetal DNA has a relatively small size of approximately 500 base pairs or less, whereas the majority of circulatory extracellular maternal DNA in maternal plasma has a size greater than approximately 500 base pairs.”

Next, they developed a solution, articulating an invention in which “separation of circulatory extracellular DNA fragments which are smaller than approximately 500 base pairs provides a possibility to enrich for fetal DNA sequences from the vast bulk of circulatory extracellular maternal DNA.”

The claims of the ’931 and ’751 patents are directed to “methods of preparing a fraction of cell-free DNA that is enriched in fetal DNA.”

“Laws of nature and natural phenomena are not patentable, but applications and uses of such laws and phenomena may be patentable,” explained the CAFC.  Turning to the two-step Alice test, the Court distinguished the case from the many diagnostics cases in which it has held patents in this field ineligible, such as Athena Diagnostics and Cleveland Clinic, as well as from method-of-treatment cases in which it has held patents eligible, such as Endo Pharmaceuticals, Natural Alternatives Int’l, Inc. and Vanda.

“This is not a diagnostic case. And it is not a method of treatment case. It is a method of preparation case,” wrote the Court. “The claims in this case do not fall into either bucket, and we consider the claims under the Alice/Mayo test.”

Ultimately, the CAFC said that the claims at issue were not directed to a natural phenomenon, but “include specific process steps—size discriminating and selectively removing DNA fragments that are above a specified size threshold—to increase the relative amount of fetal DNA as compared to maternal DNA in the sample.”

These steps result in a DNA fraction that is distinct from the naturally occurring fraction in the mother’s blood, said the court. “Thus, the process achieves more than simply observing that fetal DNA is shorter than maternal DNA or detecting the presence of that phenomenon.”

The Court dismissed Roche’s arguments that the claims are no more eligible than the claims at issue in Ariosa:

In essence, the inventors in Ariosa discovered that cell-free fetal DNA exists, and then obtained patent claims that covered only the knowledge that it exists and a method to see that it exists. Here, in contrast, the claims are directed to more than just the correlation between a DNA fragment’s size and its tendency to be either fetal or maternal.

The CAFC likewise dismissed the argument that the claims were invalid under Myriad, which held that “a naturally occurring DNA segment is a  product of nature and not patent eligible merely because it has been isolated.” 569 U.S. 576, 580 (2013). Judge Lourie wrote: “The claims do not cover cell-free fetal DNA itself but rather a process for selective removal of non-fetal DNA to enrich a mixture in fetal DNA.”

The Court added that Rapid Litig. Mgmt. Ltd. v. CellzDirect, Inc. is instructive on this and other points made by the majority. The opinion concluded:

The invention in this case is the product of further research on cell-free fetal DNA. This time, the inventors discovered that, not only does the fetal DNA exist in the bloodstream of a pregnant mother, but it has characteristics that make it distinguishable, and therefore separable, from the maternal DNA.

The district court’s decision was thus reversed and remanded for further proceedings.

Judge Reyna was not moved by the majority’s distinction between this case and the Court’s previous precedent in diagnostics cases. He said in his dissent that “the claims are directed to a natural phenomenon. The patents’ only claimed advance is the discovery of that natural phenomenon.” He continued:

The Majority sidesteps well-established precedent by reasoning that the claims in this case belongin a unique “bucket” reserved for patents that claim “a method of preparation.” By placing this case in that bucket and not in a “diagnostic case” bucket, the Majority summarily dismisses precedent like Athena, Roche Molecular, Cleveland Clinic, Genetic Techs., Ariosa, and others.

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Copyright: almoond 

The Author

Eileen McDermott

Eileen McDermott is the Editor-in-Chief of Eileen is a veteran IP and legal journalist, and no stranger to the intellectual property world, having held editorial and managerial positions at several publications and industry organizations. She has acted as editorial consultant for the International Trademark Association (INTA), chiefly overseeing the editorial process for the Association’s twice-monthly newsletter, the INTA Bulletin. Eileen has also served as a freelance editor for the World Intellectual Property Organization (WIPO); as senior consulting editor for the Intellectual Property Owners Association (IPO) from 2015 to 2017; as Managing Editor and Editor-in-Chief at INTA from 2013 to 2016; and was Americas Editor for Managing Intellectual Property magazine from 2007 to 2013.

Warning & Disclaimer: The pages, articles and comments on do not constitute legal advice, nor do they create any attorney-client relationship. The articles published express the personal opinion and views of the author as of the time of publication and should not be attributed to the author’s employer, clients or the sponsors of Read more.

Discuss this

There are currently 12 Comments comments.

  1. MaxDrei March 18, 2020 4:26 am

    The 1973 EPC denies eligibility to methods of diagnosis, (as well as methods of treatment of the human or animal body by surgery or therapy) but it’s a narrow exclusion, denying patentability ONLY to the method “as such”. EPO case law since then only serves to vindicate that a narrow exclusion is the proper way to handle such advances in medical science.

    Judge Reyna complains that the majority “sidesteps” established precedent. He sees sidestepping as wrong. I don’t. The precedent he relies upon might be binding but if it is intellectually indefensible it deserves to be sidestepped.

  2. Anon March 18, 2020 6:15 am

    The Rule of Law is offended BOTH by sidestepping binding precedent AND by the binding precedent itself.

    The better path is to recognize that the scoreboard is broken; that is, that the binding precedent is ultra vires to what OUR Congress has actually written.

    One path for realization of this concept: the Kavanaugh Scissors, looks unlikely to be deployed as the denial of very by the Supreme Court has, what, bypassed the 50 case mark now?

    The other path, by direct action of Congress (somewhat reminiscent of the Act of 1952), looks doubtful in an age of Citizens United and the unchecked power of the “voice” of the lobbying screams of large established entities.

    Sadly, it must get worse before it gets better. This calls for fortitude and stamina.

  3. EG March 18, 2020 8:06 am

    Hey Gene,

    About time the Federal Circuit reversed course on patent eligibility of what might be arguably be a medical diagnostic method. Also time to tell SCOTUS to either put up or shut up in this area of technology.

  4. Anon March 18, 2020 8:48 am

    Auto correct be dammed…

    denial of very ==> denial of cert

  5. AAA JJ March 18, 2020 9:16 am

    Putting cases, or claims, in a “bucket” rather than applying the facts and the law to them is part of the reason we’re in this mess.

  6. TFCFM March 18, 2020 11:31 am

    The outcome seems right to me. In this case, the patentee claimed an actual process (‘do this, and then this, and then this’), rather than the vague idea of “perform any process that achieves this end,” as in the earlier decision adverse to Sequenom.

  7. Pro Say March 18, 2020 11:56 am

    Dear CAFC: More of these please.

    With SCOTUS covering their eyes, and Congress sitting on their hands, American innovation needs you now like never before.

  8. Anon March 18, 2020 4:20 pm

    I have to laugh at anyone that is attempting to distinguish this case from the prior case.

  9. stepback March 19, 2020 8:56 pm

    AAA JJ @5

    Spot on. All of this is just circular reasoning disguised as judicial prudence. First you chose the result you want. Then you pick the “bucket” that will get you to that pre-picked result. Then you a lay out a story line that involves surprise discovery of the “bucket” and subsequent unraveling of the result that the bucket leads one to.

    All we can say to these circle forming judicial pretenders is, Just one leaf plucking moment there!

  10. B March 24, 2020 8:02 pm

    @ MaxDrei “Judge Reyna complains that the majority “sidesteps” established precedent. He sees sidestepping as wrong. I don’t. The precedent he relies upon might be binding but if it is intellectually indefensible it deserves to be sidestepped.”

    Judge Reyna is as clueless of law as he is of technology.

    That said, one thing Reyna is right about is the majority did sidestep some of the trash the CAFC spewed. However, 101 in the CAFC is nothing more than a panel majority getting to ignore whatever contradictions they desire, and lie about the facts or Rule 36 a case when they have nothing. Judge Giles Rich rewrote the patent law to rid this country of judicial overstepping, and our Art3 courts rewrote the patent law from the bench

  11. Anon March 25, 2020 7:35 am


    But that is the elephant in the room — and one that certain sets of people willfully ignore (as long as their Ends are the ones being arrived at).

    The lessons of history are lost on such.

  12. B March 25, 2020 12:23 pm

    @Anon “The lessons of history are lost on such.”

    And they think they’re smarter than all of us. Justice Stevens was dead set on ignoring the 1952 Patent Act to the point of making absolutely retarded statutory constructions. The courts’ just told themselves “Oh, the 1952 Patent Act did nothing more than confirm our judicial decisions” when the opposite was true. What hubris and dishonesty.