Sequenom Back Again: This time Patent Eligible

by Dennis Crouch

Illumina, Inc. and Sequenom, Inc. v. Ariosa Diagnostics, Inc. (Fed. Cir. 2020)

These parties were before the Court back in 2015 in a case that ended with a big holding that Illumina & Sequenom’s patents were invalid as directed to an unpatentable natural phenomenon.  The discovery here is super interesting — a pregnant mother has the baby’s DNA floating around in her plasma.  Turns out that there is lots of DNA floating around in a human body: mother DNA; baby DNA; bacterial DNA; viruses; mitochondrial; etc.  The researchers here used a smart way to find the baby-DNA in the mess that relies on the fact (i.e., natural phenom) that baby-DNA is part mother and part father.  The researchers got a sample of paternal DNA (from the father) and then looked for DNA in the mother’s plasma that included segments that matched the father’s DNA.  Prior to this breakthrough some parents agonized over whether to collect some baby DNA by sticking a big needle into the amniotic sac.  That approach had the problem of causing death in a small number of cases.   In any event, the 2015 Federal Circuit held the patent claims ineligible and the Supreme Court denied certiorari.

The present case involves two additional patents that use the same natural phenomena to solve the same problems.  An important added element here is that the inventors also found that baby-DNA fragments in the plasma tend to be shorter than the mother-DNA in the plasma.  Both patents here take advantage of this phenomenon to claim methods of preparing DNA for testing. The patent document explains this finding as follows:

[S]urprisingly, 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. . . . This surprising finding forms the basis of the present invention according to 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.

‘751 Specification.

The district court ruled the asserted claims ineligible.  On appeal here, however, the Federal Circuit has reversed — holding that these claims are directed at a technical solution that crosses the threshold into a patent eligible invention.

We conclude that the claims are not directed to that natural phenomenon but rather to a patent-eligible method that utilizes it.

This is a split decision with Judge Lourie explaining why the claims are patent eligible and Judge Reyna dissenting. Judge Moore signed-on with the Louri opinion making the result 2-1.

= = = =

The patents here both relate to preparing sample to be tested. U.S. Patent 9,580,751 claims a method of “preparing a DNA fraction from a pregnant human female.” Claim 1 includes three steps:

(a) extracting DNA from pregnant mother’s blood plasma [this should include both fetal and maternal DNA fragments];

(b) using “size discrimination” to remove DNA fragments greater than ~500 bp; [This results in what the claims call a “fraction of the DNA”.]

(c) analyzing a genetic locus in the fraction of DNA produced in (b). [Although not stated, this analysis could discern whether the DNA is fetal and the presence of genotypic abnormalities.]

U.S. Patent 9,580,751 Claim 1. The ‘931 patent is almost identical — it removes DNA fragments < 300 bp instead of 500 bp.

Note here that prior to the invention researchers already knew how to do all of these steps individually. However, there was no reason to separate-out the <500 bp fragments prior to the discovery of the phenomenon that most of those would be fetal DNA. This is what lead Judge Reyna to reject the claims as ineligible:

The patents’ only claimed advance is the discovery of that natural phenomenon. The claims, the written description, and the legal precedent applicable to this case all support the conclusion that the patents are ineligible. . . .

The inventors discovered a natural phenomenon: that cff-DNA tends to be shorter than cell-free maternal DNA in a mother’s blood. . . . Other than the surprising discovery, nothing else in the specification or the record before us indicates there was anything new or useful about the claimed invention.

Bottom line, researchers discovered that most of the fetal DNA in the plasma is <500 bp and the resulting invention directly applies that and broadly claims fractioning-out DNA from the plasma that is <500 bp.

The majority agreed that “the inventors were not entitled to patent the natural phenomenon that cell-free fetal DNA tends to be shorter than cell-free maternal DNA.”  Here, however, the majority concludes that the claimed method merely takes advantage of that phenomenon “by employing
physical process steps to selectively remove larger fragments of cell-free DNA and thus enrich a mixture in cellfree fetal DNA.”

In prior cases the Federal Circuit has distinguished between unpatentable diagnostic methods and patent eligible methods of treatments. In this case, the court places the inventions at issue in a third category: method of preparation.

This is not a diagnostic case. And it is not a method of treatment case. It is a method of preparation case.

This line allows the court to distinguish the case from the prior Ariosa decisions and find the claims patent eligible.

28 thoughts on “Sequenom Back Again: This time Patent Eligible

  1. 9

    About. @#$%^&*. Time.

    No surprise that Moore got it right, no surprise that Reyna got it wrong. Pleasant surprise that Lourie got it right (he whiffs alot).

  2. 8

    Kudos to the court! Application of a natural phenomenon is not the same as claiming a natural phenomenon on its own.
    For example, we rely upon gravity but we do no claim gravity in the following claim.
    “A method of breaking glass by dropping a hammer on the glass.”
    “Subject matter eligible” for sure, although not “patentable” because of anticipation.

    1. 8.1

      And yet Reyna got it wrong.

      Again.

      Wait for the request for rehearing en banc.

      1. 8.1.1

        Reyna should do us all a favor and resign. He is a disgrace. It is an insult to those of us that spent many years learning science, technology, and patent law that a complete novice was appointed. And he was selected by SV to burn the patent system down.

        Reyna is –flat out–a disgrace.

    2. 8.2

      Worth emphasizing:

      on its own

      By the way, this decision and the prior one are irreconcilable to anyone employing inte11ectual honesty. All we get is another layer of non-statutory mumbo-jumbo (now with ‘method of preparation’).

  3. 7

    “patents that use the same natural phenomena to solve the same problems”

    This case is as good an illustration as any, that, for policy reasons, we should consider restricting patents to those that use unnatural or supernatural phenomena to solve problems.

    1. 7.1

      — as a proxy for the “S” sign…

      Two memes come to mind. For the “unnatural,” the exchange between Anakin Skywalker and Senator Palpatine (there are many that consider the powers of the dark side to be… (dramatic pause) unnatural); and for the supernatural the portion of the Monty Python bit of ‘She’s a Witch’ (she turned me into a newt once (dramatic pause) I got better).

    2. 7.2

      Anon2 that is my first laugh of the day!

  4. 6

    Only a tangent to the topic, but I found the article on quantum computing (it discusses a link to bio chem processing) to be interesting, but ‘off’ in its attempt to ‘set the bar’…:

    link to phys.org

    1. 6.1

      Thanks!

  5. 5

    >>is not preempting all possible fetal diagnostic tests from the maternal blood sample.

    What basis in patent law do people think this comes from? This is a judge made-up rule that is applied at some level of abstraction (of the ladders of abstraction) and is —completely arbitrary.

    At 2.3 Pika included the claim that was invalidated. The claim appears to be inline with what was actually invented.

    1. 5.1

      “preempting all possible X” is just a pretext to invalidate a claim a judge does not like.

      If the claim is not invalid based on enablement and prior art, then the reason above is a pretext to invalidate the claim. What it means is the inventor is claiming the scope of what they invented.

      And again, what is the patent law basis of such a reason to invalidate a claim? It would have to come from a judicial exception and be justified by the text of the Constitution.

      The argument goes like this. That the claim is so broad that it is actually hindering innovation, so therefore the grant of the claim is unconstitutional.

      It is another outrageous piece of the Scotus’s jurisprudence on patent law.

      1. 5.1.1

        Completely agree — and would add the plain fact that ALL claims pre-empt everything within their scope, as that it what claims are intended to do.

        As to the hand-wringing of “blocking,” there is a simple adage that fits: Necessity is the mother of invention. Being blocked is a good thing (for innovation).

  6. 4

    Reyna tells us that the majority has “sidestepped” the binding precedent. As if that’s a bad thing to do. But if the precedent is intellectually indefensible the adroit sidestep around it by the majority is something for which it should attract kudos, not disparagement.

    The 1973 European Patent Convention declares as ineligible not only methods of treatment of the human or animal body by surgery or therapy but also methods of diagnosis. But mindful of the need to confine the exclusion tightly, lest it spread out of control, it also declares the exclusion to be limited to each of these methods AS SUCH. The 40 years of European case law since then have vindicated the statutory wording, and the US cases confirm it.

    Presumably, the courts from now on will be better able to distinguish on the substance (as opposed to the scrivening) in the field of advances in the technical field of diagnosis of disease, which claims are eligible and which are not.

    1. 4.1

      Rule
      Of
      Law

    2. 4.2

      … there are SO many things wrong with your post, MaxDrei, that the Rule of Law utterance is but a start.

      Instead of throwing CRP against the wall, you have presented a wall of CRP.

      1. 4.2.1

        On this one, we agree.

        1. 4.2.1.1

          I would but point out that we agree FAR more than we disagree.

  7. 3

    Who ever invents or DISCOVERS….

    1. 3.1

      any new and useful process, machine, manufacture, or composition of matter…

      A law of nature per se is neither a new process, a new machine, a new manufacture, nor a new composition of matter. At best, there is the question of what Congress intended for a claim to fall under the category of a new process: is it any act or series of acts that is new, or is it less than that? The response of the Supreme Court to this question is clear. Then, if it is less than any act or series of acts that is new, how much less is it? Personally, I find the response of the Supreme Court to that question to be murky, but several contributors to this blog have a response that they find clearer and more practical than the response of the Supreme Court.

      1. 3.1.1

        PiKa,

        It is important to distinguish the point that you present: “A law of nature per se”, as that ‘per se’ is an extremely LOW bar to meet (and one done so by most all scriviners).

        Further, Congress dictated exactly which party has the power to and responsibility for overcoming that low bar: the applicant, and NOT the Court.

        It is the Court that acts ultra vires with its legislating from the Bench and its disdain for what IT sees as a “too easy” ability to obtain a patent (can you say ‘Flash of Genius’…?)

        I would further posit that there is NO such “question of what Congress intended” as you seem to suggest. The words of Congress are indeed clear as to their breadth, and instead it is merely a breadth that the Court does not like. The more important point here is that this is simply something that the Court has no legitimate power over.

        You also mention that the Court’s action has resulted in murkiness. There is a different legal phrase that fits: Void for Vagueness.

    2. 3.2

      I wrote an article going down that path several years ago when the first case on this issue came up. “Discover” is a rather important word, but it isn’t the only place where the Supreme Court has messed up.

      link to law360.com

      1. 3.2.1

        … paywall …

  8. 2

    Unlike the invalid broad claim in Ariosa Diagnostics, Inc. v. Sequenom, Inc., 788 F.3d 1371, 1373 (Fed. Cir. 2015), the relatively narrow claim here is not preempting all possible fetal diagnostic tests from the maternal blood sample.

    1. 2.1

      Uh sure, Paul. If you say so.

    2. 2.2

      Nope. In the 2015 case there were at least 3 noninfringing ways in the record for testing for the same natural phenomenon. Preemption wasn’t the issue then any more than it is in this case.

    3. 2.3

      Paul, in Ariosa, the claim scope was definitely not as broad as preempting all fetal diagnostic tests from maternal blood sample. At worst, claim 1 would have preempted all methods of detecting the presence of a paternally inherited nucleic acid of fetal origin in a serum or plasma sample of the mother.

      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..

  9. 1

    Nope, no problem here with the CAFC acting in an extremely predictable manner…

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