Illumina v. Ariosa Diagnostics: A Closer Look

“Appreciation of the reasoning of both the Majority and the Dissent in Illumina v. Ariosa is essential to understanding the current state of the debate on subject matter eligibility of processes involving natural phenomenon.” Federal Circuit recently found that a method for preparing an extracellular DNA fraction from a pregnant human female and using it for analyzing a genetic locus involved in a fetal chromosomal aberration was not directed to a natural phenomenon, and thus eligible for patenting. Illumina, Inc. v. Ariosa Diagnostics, Inc., No. 2019-1419 (Fed. Cir. March 17, 2020) (“Illumina v. Ariosa”). The decision includes a dissent. Appreciation of the reasoning of both the Majority and the Dissent is essential to understanding the current state of the debate on subject matter eligibility of processes involving natural phenomenon. The all-important question in such cases centers on how to determine whether such an invention is directed to a judicial exception. Stated differently, when does an invention that uses a natural phenomenon turn into a patent-eligible process rather than being directed merely to the natural phenomenon?

The claimed methods at issue are covered by U.S. Patents 9,580,751 and 9,738,931, owned by Illumina. The extracellular DNA fraction prepared by the methods are enriched in the DNA of fetal origin. The natural phenomenon involved is that the extracellular (or cell-free) DNA of fetal origin found in the mother’s bloodstream tends to be shorter than the cell-free DNA of the mother. Generally, over 90% of the extracellular DNA in the maternal circulation is derived from the mother and only a very small fraction from the fetus. As such, determining fetal genetic alternation using the extracellular DNA obtained straight from the maternal circulation is difficult. Illumina v. Ariosa, Majority Opinion at 3. Enriching for extracellular DNA of fetal origin solves this problem.

The Majority

In keeping with the trend started in 2016, the Majority (judges Lourie and Moore) focused on whether at step one of the Alice/Mayo test, the claims of Illumina’s patents were directed to a natural phenomenon or to subject matter that exploited the discovery of the natural phenomenon.

The Majority made two points. First, it reasoned that the claimed methods include process steps that lead to a DNA fraction that is different from the naturally-occurring fraction present in the mother’s blood (due to enrichment of cell-free fetal DNA). Thus, the process achieves more than simply observing that fetal DNA is shorter than maternal DNA or detecting the presence of that phenomenon. Id. at 10. Next, the Majority noted that the dependent claims, which name specific techniques for carrying out the steps of the method, illustrated the concrete nature of the claimed process steps. Id. at 10. These concrete process steps were used, not merely to observe the presence of the phenomenon that fetal DNA is shorter than maternal DNA, but to exploit that discovery in a method for preparation of a mixture enriched in fetal DNA. Id. at 11.

The Majority contrasted this case to Ariosa Diagnostics, Inc. v. Sequenom, Inc., 788 F.3d 1371 (Fed. Cir. 2015) (“Ariosa”), observing that in Ariosa, the inventors had 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. Illumina v. Ariosa, Majority Opinion at 11.

The Majority referred also to Rapid Litig. Mgmt. Ltd. v. CellzDirect, Inc., 827 F.3d 1042, 1050 (Fed. Cir. 2016) (“CellzDirect”), observing that in CellzDirect, having discovered that some fraction of hepatocytes are capable of surviving multiple freeze-thaw cycles, the inventors patented an improved process of preserving hepatocytes that required freezing hepatocytes, thawing the hepatocytes, removing the non-viable hepatocytes, and refreezing the viable hepatocytes. Illumina v. Ariosa, Majority Opinion at 12-13. The invention was patent eligible because it was not simply an observation or detection of the ability of hepatocytes to survive multiple freeze-thaw cycles; rather, the claims were directed to a new and useful method of preserving hepatocyte cells. Id. Likewise, the Majority observed, the Illumina inventors used their discovery to invent a method of preparing a fraction of DNA that includes physical process steps to selectively remove some maternal DNA in blood to produce a mixture enriched in fetal DNA. Id. at 13.

Therefore, the “methods are “directed to” more than merely the natural phenomenon that the inventors discovered,” the Majority stated. Id. at 14 (emphasis added). Accordingly, at step one of the Alice/Mayo test the claims were found to be not directed to a patent-ineligible concept.

Thus, in order for a method reciting a natural phenomenon to be “directed to more than a natural phenomenon” the method must use the natural phenomenon to achieve something more than simply the observing of the natural phenomenon. How much more needs to be achieved, however, is not clear. Unlike the Majority, the Dissent did not think that much was achieved beyond observing the natural phenomenon.

The Dissent

The Dissent’s (Judge Reyna’s) main point was that the Majority had disregarded “the well-established precedent for conducting the Alice, step one, “directed to” inquiry by failing to consider the patent’s claimed advance.” Since 2016, in a string of cases reciting process claims, the Federal Circuit had begun conducting the “directed to” inquiry by asking whether the “claimed advance” of the patent “improve[d] upon a technological process or [was] merely an ineligible concept based on both written description and the claims” (citing Athena Diagnostics, Inc. v. Mayo Collaborative Servs., LLC, 915 F.3d 743, 750 (Fed. Cir. 20l9).

Judge Reyna observed that if a written description highlighted the discovery of a natural phenomenon, e.g., by describing the natural phenomenon as the only “surprising” or “unexpected” aspect of the invention or that the invention was “based” on the discovery” of a natural law – the natural phenomenon likely constituted the claimed advance. Illumina v. Ariosa Dissenting Opinion at 7. The judge pointed to the specification of the ’751 patent for stating that the surprising finding that “the majority of the circulating extracellular fetal DNA has a relatively small size of approximately 500 base pairs or less…[which] forms the basis of the present invention” concluding therefrom that the claimed advance was a natural phenomenon. In the judge’s view, the claimed methods began and ended with naturally occurring substances and that the method steps did not alter those substances, again showing that the claimed methods were directed to a natural phenomenon. Id. at 8.

Dismissing the importance attached by the Majority to the use of concrete process steps, Judge Reyna noted that whether the steps are concrete is not the appropriate analysis for determining the claimed advance and wrote: “[w]here a written description identifies a technology as well-known or performed using commercially available tools or kits, that technology cannot logically constitute a claimed advance.” Id. at 9. The judge noted that in the instant case, “the claimed advance was “not an improvement in the underlying DNA-processing technology,” (unlike as hinted by the Majority) since the written description identified the claimed method steps as well-known or performed using commercially available tools or kits. Id. at 9 (emphasis added).

Judge Reyna also compared the instant case to CellzDirect, finding, however, that unlike CellzDirect, the claimed method steps here were not new, nor were the claimed techniques used in a new or unconventional way. Id. at 11.

The clear implication of Judge Reyna’s view is that the “directed to” inquiry requires asking whether the method involving the use of a natural phenomenon represents a real improvement over existing methods.


This Dissent’s view appears to be more in line with many of the court’s decisions in the area of computer related inventions, where the “directed to” inquiry focuses on whether the invention led to improvements in computer related technologies. For example, in Enfish, LLC, v. Microsoft Corp. No. 2015-1244 (Fed. Cir. May, 2016) (“Enfish”), the Federal Circuit described the first step of the Alice/Mayo test as asking “whether the focus of the claims [was] on the specific asserted improvement in computer capabilities … or, instead, on a process that qualifies as an “abstract idea” for which computers are invoked merely as a tool.” Enfish at 11(emphasis added). On the other hand, in another case, finding claims directed to methods and systems for broadcasting signals to cellular telephones ineligible, the court said, “in this case, the claims are directed not to an improvement in cellular telephones but simply to the use of cellular telephones as tools in the aid of a process focused on an abstract idea.” Affinity Labs of Texas, LLC v. Directv, LLC, Nos. 2015-1845, 2015-1846, 2015-1847, 2015-1848 (Fed. Cir. Sept. 2016) at 15. (“Affinity Labs”) (emphasis added).

 Enfish and Affinity Labs support also the notion of determining what the claimed advance is by looking in part in the specification. For example, in Enfish the court stated, “[T]he “directed to” inquiry applies a stage-one filter to claims, considered in light of the specification, based on whether “their character as a whole is directed to excluded subject matter,” and in Affinity Labs, the court wrote, “[t]he “abstract idea” step of the inquiry calls upon us to look at the “focus of the claimed advance over the prior art” to determine if the claim’s “character as a whole” is directed to excluded subject matter.” Affinity Labs at 6. (emphasis added).

Finally, Judge Reyna’s dissent in Amdocs (Israel) Ltd. V. Openet Telecom, Inc. No. 2015-1180, (Fed. Cir. 2016) (“Amdocs”) is instructive. In this case, the judge noted that “the step one inquiry cannot be settled in the affirmative by the observation of an underlying abstract idea nor in the negative by recitation of just any additional limitations.” Amdocs Dissent at 7-8. Rather, the step one inquiry is a legal analysis that must focus on determining “what type of discovery is sought to be patented.Id. (citing Parker v. Flook, 437 U.S. 584, 593) (emphasis added).

To summarize, the more a claim is seen to go beyond applying known techniques to the newly discovered natural phenomenon, resulting thereby in a new or improved process, the more likely it is to be found not directed to the natural phenomenon. And, Illumina v. Ariosa notwithstanding, it is quite likely that a court would examine the claim in light of the specification to determine the claimed advance over the prior art in order to decide whether the character of the claim as a whole is directed to ineligible subject matter.

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Author jamesgroup
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Join the Discussion

21 comments so far.

  • [Avatar for Anon]
    May 30, 2020 07:22 am

    Take the biscuit?

    And yet, MaxDrei, you yourself would take the biscuit by failing to grasp the rest of the post.

    Do you really think that Mr. Cole’s “but I am a alien” schtick was a “thinking” position in relation to his choice of attacking one level of the US Sovereign judicial branch but not another (and that one not chosen being the source of a problem)…?

    Your entreaty to someone else while you misplay the facts is thus based in falsity itself.

  • [Avatar for MaxDrei]
    May 30, 2020 04:47 am

    That last really does take the biscuit. Justifying “wild” words in reply to Paul Cole as being necessary to assault “the unthinking”. Mr Quinn, your opportunity now, to explain to us all what you mean by “respectfully”.

  • [Avatar for Anon]
    May 29, 2020 05:11 pm

    Words ought to be a little wild, for they are the assaults of thoughts on the unthinking.

    – John Maynard Keynes

  • [Avatar for Anon]
    May 29, 2020 05:06 pm

    Max Drei and Paul,

    You are free to entertain whatever feelings that you want to entertain.

    But you do NOT get to have your very own set of facts.

    The plain facts are that I hit hard – but I also hit with substance. You may not like that substance, but frankly my dear, I REALLY do not give a damn.

    If in fact, my posts had zero substance, then Paul would NOT be so upset.


    In fact, I have correctly called out his ‘but I am an alien” stance coupled with NO cognitive difference in HIS attacking one level of the US judicial branch while choosing to NOT attack a different level.

    The ONLY aspect for those that may find my posts tiresome is that I am relentless on actual points that should be noted, acknowledged, and addressed. Those that would claim my posts to be so ‘tiresome’ are the same one that suffer NOT engaging on these points, while insisting on peddling a ‘same song and dance’ as if counter points were never presented.

    Do NOT confuse the ‘politeness’ of NOT being challenged with ANY type of meaningful attractiveness for a legal blog.

    If you want a bubble chamber effect for politeness, I suggest that the topic of law is not for you.

  • [Avatar for MaxDrei]
    May 29, 2020 04:15 pm

    Mr Quinn, I have known Professor Paul Cole for several decades, and know of his work with the European and UK Institutes of Patent Attorneys, his editorship and authorship of standard works for the European and UK patent attorney profession, and his several commissioned briefs to the Supreme Court. Even though I post under a pseudonym, you know me and I ask you to reflect thoughtfully on the recommendation advanced by Paul, to ban anon from your comment threads.

    Specifically, I respectfully invite you to consider seriously whether “anon” is consistently and wilfully ignoring your “house rules”, to add to the thread “respectfully”.

    I agree with Paul, that anon’s stream of comments is consistently unprofessional. A lack of professionalism is of course OK if the commenter is not a patent professional, any to your credit you have any number of such commenters. But when anon holds himself out to be a patent professional, with “clients”, and on that basis lectures others with sentences like:

    “As for long hours of study of relevant case law, I guarantee that I have matched and most likely put in more hours of diligent study and critical thinking than you.”

    even while he continues with his offensive texts, it brings disrepute not only on the blog but also on the entire profession.

    anon also enjoys assaulting my postings. It might be thought that this is why I am here seconding Paul. But I am conceited enough to suppose that his assaults on my postings fail to dent my positions and instead make him look ridiculous. So I don’t care.

    Posting anonymously, I don’t need to worry about my own reputation here, nor do I have to worry about that of your blog. All the same, I agree with Paul, that anon’s tiresome postings, far from bringing anything to these blog threads, render them less attractive to readers. And that would be a shame.

  • [Avatar for Anon]
    May 29, 2020 12:54 pm

    Whine whine whine, Paul.

    Maybe do more than merely accuse “sarcasm,” and answer the points that accompany the sarcasm.

    Here’s a hint: if you would actually engage on the points, you would see LESS sarcasm.

    Give it a try.

  • [Avatar for Paul Cole]
    Paul Cole
    May 29, 2020 09:28 am

    @ Anon 2,4,6,8, 10, 12, 14

    Apart from sarcastic comments on the opinions of others, what have you positively contributed or done to entitle you to criticise the comments of others in the way that you do? How many articles have you written and where? How many briefs have you written and how long have you spent on them?

    WHERE ARE your articles? HOW MANY amicus briefs have you written supporting eligibility? What have you done to HELP our profession? How many books have you written or edited?

    Regrettably the useful information content in your comments is ZERO. You have been a waste of space and a waste of time, i.e. a continuum of waste. I hereby undertake that, unless you apologise, I will NEVER take seriously or respond to a comment of yours again. it is my recommendation that you should be banned from this blog for repeated inappropriate and unprofessional comments.

  • [Avatar for Anon]
    May 28, 2020 04:12 pm

    I laugh at your attempted put-down Mr. Cole, the last refuse of a man who will not face the points that I have put to you directly here.

    The “out yourself and use your real name” is a very disingenuous retort, and absolutely misses THIS Sovereign’s long and venerable tradition of pseudonymous and anonymous contributions.

    Nice miss there.

    As to “well, I wrote a real brief and that took time.”

    Great. Did I ever argue differently? This amounts to a rather EMPTY strawman.

    The fact is that you DID choose to write a brief (as well as engage in a forum in which “I use My Real Name” is simply not required) in obvious efforts to influence the law in this Sovereign.

    So much for your “but I am an alien” weak-@$$ excuse.

    As for long hours of study of relevant case law, I guarantee that I have matched and most likely put in more hours of diligent study and critical thinking than you.

    My ammunition of reasoned argument surpasses yours. Perhaps this is why you choose to flail at such a p00r rejoinder at this point of our exchange.

    The war is simply more than you have chosen to politely (daintily?) partake in. You still offer NO cogent reason for the distinction of ‘attack’ between different levels of our judicial system. That you are willing to attack one but not another is not — and cannot be — a function of your “being an alien.”

  • [Avatar for Paul Cole]
    Paul Cole
    May 28, 2020 03:53 pm

    @ Anon

    If this is a war, the only ammunition I have or could possibly have is reasoned argument.

    In addition to my articles and comments, I have fired four amicus briefs at SCOTUS, two on behalf of CIPA, one on behalf of the EPI, and one in person. I have also submitted or lead authored a number of briefs to the Federal Circuit. In case you have never written a brief, it takes some hours of careful work, even after prolonged study of the relevant case law.

    Apart from sarcastic comments on the opinions of others, what have you positively contributed or done to entitle you to criticise the comments of others in the way that you do? How many articles have you written and where? How many briefs have you written and how long have you spent on them? Why, you cannot even stand up and give your own proper name.

  • [Avatar for Anon]
    May 28, 2020 02:49 pm

    Mr. Cole,

    While I certainly enjoy (and myself employ) invoking historical references, your invocation of the Dunkirk evacuation misapprehends the statement in regards to a win of a battle is not winning the war.

    Of course, winning a war will most always entail winning some battles. At the same time, LOSING a war will ALSO most always entail winning some battles.

    There is NO sense of “this step forward” to be a step that will not be surrendered (even in an immediately next decision).

    You miss the point also of the LARGER picture that ALL of these back and forths currently EXIST simultaneously in the Supreme Court unleashed “write the statutory law of 35 USC 101” by an uncontrolled (out of control) Common Law writing style.

    Your small step carries with it NO meaningful consequence, and that you want to focus on that illusionary advance, while seemingly oblivious to the affront on statutory law and the ultra vires run away nature of Common Law casts a long shadow on the perception of your critical thinking.

    As to fair game, as I noted YOU have chosen to engage in advocacy of OUR Sovereign’s laws. It is simply NOT UP TO YOU to decide that ‘tact and politeness are not unreasonable, nor should ANY absence of such BE considered unreasonable.

    That is merely advancing a FALSE sense of civility in a very real war on innovation and the protection of innovation. You are getting in the way of a real fix, and I will not ‘be civil’ to the point that excuses your chosen actions. There remains NO cognitive distinction that YOU have chosen in your willingness to ‘attack’ one level of OUR judicial branch, but to purposefully refrain from ‘attack’ of the much more meaningful branch.

    You are of course (even as an alien) to choose differently. But your choices and this utter silly notion that ‘tact and politeness somehow put critical thinking on the shelf and create a ‘no-critique zone’ for the very entity MOST responsible for the mess is most emphatically rejected.

    This goes well beyond merely not giving a damn (about your feelings).
    This is a war every bit as real as a war with military. The casualties may be different, but the stakes are every bit as high.

  • [Avatar for Paul Cole]
    Paul Cole
    May 28, 2020 11:49 am

    @ Anon

    If you recall Operation Dynamo whose 80th anniversary has been recalled this year over here, you will appreciate that though it did not win the war it was a step in the right direction. Similarly the Illumina decision, though not a total fix of the problem is a small step in a favourable direction.

    As to SCOTUS, tact and politeness are not unreasonable and should not render a commentator “fair game”.

  • [Avatar for Anon]
    May 28, 2020 08:57 am

    As an alien, I feel free to criticise the CAFC, but not the US Supreme Court which I feel would be unhelpful and a step too far.

    I cannot fathom what would drive such a distinction.

    At all.

    Being an alien has nothing at all to do with critical thinking and ‘attacking’ in an even handed and objective manner.

    As such, there is NO “entitlement” to NOT attack at the very source.

    Worse, by not doing so, you guarantee to NOT fix the problem at the source and you will forever be chasing symptoms rather than the cause.

    For all of your good advice (and you have plenty of solid ‘best practices’ type of advice), this reticence of yours is most puzzling.

    It mars [pun intended] your attempts to weigh in – and I fear that for whatever reason you proffer, the effect will be that all of your advice will obtain a taint of suspicion, and lower the gravity of your effects.

    Lastly, while you do offer “I am an alien” as a reason, I will once again point out that US attorneys have an ethical obligation to challenge Supreme Court when the entity a the top of that ‘only one of three’ branches of the government acts beyond its limited authority and treats itself as if it is above the Constitution. You may not have that same ethical responsibility, but it does not mean that your attempts to ‘go light’ are either necessary, nor are they helpful.

    If you are not being helpful, you are being a part of the problem. A problem, as you admit, in a Sovereign not your own, but one in which you do choose to involve yourself with by advocating through avenues such as blog posts and amici briefs.

    You do choose to involve yourself.

    Thus, you make yourself fair game. I reject your sense of “feeling” and your sense of “but that would be unhelpful” and posit that your current course IS unhelpful, and about your feelings (to quote Rhett Butler), “Frankly, my dear, I don’t give a damn.”

  • [Avatar for Paul Cole]
    Paul Cole
    May 28, 2020 04:58 am

    @ Anon

    As you are aware, I am an alien as I used to be reminded every time I visited the US. There were signs directing “aliens” at every airport. Some years ago at a session at the AIPLA annual meeting a member of the audience questioning a speaker discussed at some length the views of a man form Mars. I followed with an opening remark that I would be giving an alien viewpoint, creating slightly unexpected but unforgettable laughter amongst the whole audience.

    As an alien, I feel free to criticise the CAFC, but not the US Supreme Court which I feel would be unhelpful and a step too far. I feel free to and have attempted to analyse SCOTUS decisions and point out their conservative nature and the unfortunate “gold plating” by the Federal Circuit, but that it as far as I feel entitled to go. I am not disputing your position, merely explaining that because of geography I am not able to go as far as you can.

  • [Avatar for Anon]
    May 27, 2020 01:17 pm

    Mr. Cole,

    The main reason of my counter point presented is that a battle does not the war win.

    The fact that this decision IS as it is, and yet, other decisions — entirely contradictory — are what they are, and ALL of this remains in the SAME jurisprudence points to the elephant in the room:

    The scoreboard is broken.

    And I will add one more item that I have not yet seen you fully embrace: the party MOST responsible for breaking that scoreboard is the US Supreme Court itself.

  • [Avatar for Paul Cole]
    Paul Cole
    May 27, 2020 11:39 am

    @ Anon – Exceptions are to items that otherwise are within categories.

    With that I 100% agree with you and sent an e-mail this morning making this very point.

    But these two patents were directed essentially to a diagnostic method but were nevertheless held to be patent-eligible. Consequently the panel majority here made a breach in the categorical exclusion. I accept what you say about “the ongoing MUCK may STILL violate treaty obligations vis a vis TRIPS”, but a frequently applied exclusion is less helpful vis-a-vis TRIPS than a complete exclusion.

    In the life sciences area, repeated Federal Circuit decisions have been deeply grounded in both legal and scientific fact error, the latter errors reminding me of the error of the Inquisition when Galileo was brought before them. Spare me Judge Reyna’s opinion!

  • [Avatar for Anon]
    May 27, 2020 10:33 am

    Mr. Cole,

    It is uncertain what your view is within your post at 5, given that your past writings on “categorical exclusion” have suffered a fundamental misunderstanding of what the word ‘exception’ means.

    Exceptions are to items that otherwise are within categories.

    The fact that this decision differs from the prior decision really is no reason to celebrate.

    If anything, the analysis and juxtaposition of the reasoning ‘from both sides’ and from both decisions reveals that the jurisprudence is an irreconcilable muck of a Gordian Knot.

    For example, take the headings away (majority and dissent) from both cases and one can easily interchange the reasoning, with the controlling result thus shown to be completely arbitrary.

    The additional fact that the ongoing MUCK may STILL violate treaty obligations vis a vis TRIPS does NOT go away with this decision.

  • [Avatar for Paul Cole]
    Paul Cole
    May 27, 2020 02:09 am

    In briefs I have written I have taken note of the categorical exclusion for diagnostic methods identified in the Athena decision and commented that such exclusion is contrary to TRIPS. From this decision it appears that the identification of the categorical exclusion went too far, for which we should be thankful. Hopefully there will neither be an en banc stage nor a successful petition.

  • [Avatar for Anon]
    May 26, 2020 02:48 pm

    Mr. Morgan,

    Every possible use? Every application?Were the claims that you so you indicate method claims?

    If so, then the appropriate rejection would have been under 112.

    Defending the (horrible) 101 jurisprudence is NOT – in any way – a noble thing to do.

  • [Avatar for Paul F. Morgan]
    Paul F. Morgan
    May 26, 2020 12:20 pm

    The claims held not 101-unpatentable by the majority in Illumina, Inc. v. Ariosa Diagnostics, Inc., No. 2019-1419 (Fed. Cir. March 17, 2020) can also be distinguished from the claims held 101 unpatentable on the same subject [of detecting fetal DNA in pregnant women] in Illumina v. Ariosa by claims in the latter being so broad as to encompass or preempt every possible use or application of the discovery of its existence.

  • [Avatar for Anon]
    May 25, 2020 05:21 pm

    I do not find this article compelling in the least.

    A closer look only reveals the strands of the rope that make up the Gordian Knot of current 101 jurisprudence.

    Any sanity said to be found is only an illusion.

  • [Avatar for Kevin E Noonan]
    Kevin E Noonan
    May 25, 2020 04:05 pm

    Judge Reyna was wrong about CellzDirect – the steps in the claim was routine and conventional; what was different is that they did them twice.