Sequencing-by-synthesis: Illumina defeats Columbia’s patents

Columbia University v. Illumina, Inc. (Fed. Cir. 2021) (nonprecedential opinion)

In this IPR decision, the PTAB cancelled claims from five patents owned by Columbia — finding them obvious. US Patent Nos. 9,718,852 (clm 1); 9,719,139 (clm 1); 9,708,358 (clm 1); 9,725,480 (clm 1); and 9,868,985 (clms 1-2).   The patents are all related to methods of sequencing DNA using “sequencing-by-synthesis.”  Illumina believes that it owns the process. Columbia felt otherwise and sued Illumina for patent infringement in D.Del. That lawsuit has been stayed since July 2018 as the court awaits these IPR decisions. On appeal, the Federal Circuit has affirmed.

Here is a fairly easy to understand video about  how this work:

The likelihood of winning an appeal certainly depends upon the merits of your case.  The second most important factor is the level of deference afforded to the lower-tribunal.   The Federal Circuit gives deference to any factual findings made by the PTAB in its IPR decisions.  In particular, a PTAB finding of fact will be affirmed if it is based upon “substantial evidence.”  The words “substantial evidence” might sound like a lot of evidence, it is actually a quite easy threshold.  A decision is based upon “substantial evidence” if it is supported by “more than an iota” of evidence or if “a reasonable mind might accept the evidence to support the finding.”  On the other hand, questions of law are reviewed without deference — de novo.

Obviousness is a question of law reviewed de novo.  However, the ultimate conclusion of obviousness is always based upon a large number of factual findings, “including the scope and content of the prior art, differences between the prior art and the claims at issue, the level of ordinary skill, and relevant evidence of secondary considerations.”   See my simple tip-of-the-mountain drawing below.

Here, the patentee challenged three factual findings by the Board, and the Federal Circuit found that each finding was supported by enough evidence to pass muster.  The three topics: motivation-to-combine; and two reasonable-expectation-of-success arguments.

The patentee argued someone skilled in the art would not have been motivated to combine an allyl capping group into a sequencing-by-synthesis approach.  Their particular argument, was that a prior art reference indicated some problems with use of the capping group and thus discouraged its use.  As supporting evidence, Columbia pointed to the fact that other researchers ceased related experiments after the reference was published.  On appeal, however, the Federal Circuit noted that this “teaching away” argument requires “clear discouragement” which was not proven. Although the reference did not show the experiment to be a smashing success, it also was not a failure.  Thus, while researchers might have considered better alternatives based upon the reference, it did not actually teach-away.

While it may be true that … scientists ultimately chose to research alternative capping groups, “just because better alternatives exist in the prior art” does not mean that an inferior alternative “is inapt for obviousness purposes.” Quoting In re Mouttet (Fed. Cir. 2012).

Thus, the PTAB’s finding of motivation to combine was supported by substantial evidence.

Obviousness affirmed.

31 thoughts on “Sequencing-by-synthesis: Illumina defeats Columbia’s patents

  1. 9

    This is a bunch of nonsense. Obviousness in U.S. patent law is a question of speculation, period. Not law, not facts.

    We need to find a new paradigm. Patent law is totally broken. It hardly ever provides exclusivity for true inventors. It usually rewards corporations and lawyers for their gamesmanship.

    1. 9.1

      The 103 statutory framework – the question of obviousness – is ‘obvious to a person of ordinary skill in the art’ – IMHO is the same legal fiction as the ‘reasonable man’ (person) standard of common law torts. In other words, a jury issue under the 7th – not a de novo legal issue for an appellate court. A lot of water over the dam at this point.

      1. 9.1.3

        I agree with you about the strong analogy between the “skilled artisan” of patent law and the “reasonable man” of common-law torts. I am not sure, however, that this analogy actually leads where you are suggesting that it should go. In the common law of torts, “[g]enerally, the issues of the standard of care and the existence of a duty are legal questions; whereas, the breach of a duty and causation are factual issues.” Lewis v. B & R Corp., 56 S.W.3d 432, 438 (Ky. App. 2001).

        In other words, both common-law torts and patent-law obviousness involve an ultimate conclusion of law that rests on a host of subsidiary fact-findings. That is why—as a mixed question of law and fact—the question of both negligence and obviousness is usually given to the jury, but nevertheless both are typically reviewed de novo on appeal.

        In other words, the law on this point is at is precisely because of—not despite—the analogy between the “reasonable man” and the “skilled artisan.” Even if you back-washed that water under the bridge, there is no reason to suppose that it ought to flow a different way when the forward flow were restored.

  2. 8

    OT but the latest mandamus order from the Fed. Cir. to the new patent suit Valhalla’s judge on venue transfers:
    “..the Federal Circuit (CAFC) ruled on February 1 that Western District of Texas Judge Alan Albright’s handling of a motion to transfer by SK hynix “amounted to egregious delay and blatant disregard for precedent” and ordered the district court to stay all proceedings until it has issued a ruling on the transfer motion “capable of providing meaningful appellate review of the reasons for its decision.”

  3. 7

    The below-linked blog post should really be posted on the comments for Prof. Kumar’s guest essay. If I posted it there, however, no one would see it by now. Everyone should see this blog post, so I am sticking it in this comment thread. Do check it out.

    Derek Lowe, “Myths of Vaccine Manufacturing”
    link to

    1. 7.1


      I keep on coming back to the view that Big Pharma’s development process sure could use some innovation…

  4. 6

    “The motivation we most value . . . is our motivation to invalidate patents. And with all the 101 – 102 – 103 – 112 tricks in our bag, doing so is a virtual piece of cake.”

    “And boy, oh boy, do we love our cake!”

    — CAFC

  5. 5

    For what it’s worth: I wrote a law review article last year opining that motivation-to-combine should be deemed a restatement of the ultimate obviousness inquiry (a question of law), *not* an underlying question of fact. See “Re-Thinking the ‘Motivation to Combine’ in Patent Law,” 48 AIPLA Q.J. 1 (2020). The mountain diagram that Professor Crouch wrote into this blog post is apt: as I argued, treating motivation-to-combine as a question of fact leaves little if anything for a court to resolve as a matter of law, thus eviscerating the rule that obviousness itself is a question of law.

    link to

    1. 5.1

      Great topic Joshua. I have thought about this issue a few times in the past, but thank you for actually doing the work and writing the article. I’ll try to read it this week.

    2. 5.2

      Have not read your article, but query “treating motivation-to-combine as a question of fact leaves little if anything for a court to resolve as a matter of law” in view of the cases reversed on appeal or remanded by the Fed. Cir. for absence of ANY evidence or fact finding on that issue, or for improper such findings, such as the recent reversal for an improper “teaching away” test? Also, is not a major reason those District Courts allowing general jury verdicts that fail to separate fact question decisions from a bare “invalidity not proven” verdict?

      1. 5.2.1

        I haven’t read it either (and can’t as I’m not a member of AIPLA) but it seems to me that it wouldn’t have much of an impact at the initial determination. Even if “reason to combine” were to be a question of law it would still have to be based on facts. The determination would still have to rely on evidence sufficient to support the conclusion. On appeal though that question would get de novo review, not substantial evidence or clear error. That’s a pretty big change. Then again, I can’t really see it impacting that many appellate decisions. It would just allow judges to be a little less unabashed when reversing decisions they don’t like.

    3. 5.3

      I think the question of law is whether a pattern of facts is sufficiently similar to a pattern of facts in another case. Nowadays, the patterns of facts and their articulations in rationales seem to always look like a previous case, and there is little need to be creative on that front. But in theory, a patent challenger could take the risk to use a pattern of facts and an underlying rationale that have never be used in the US. For example, you could try to use the pattern of facts and the rational of the problem-solution approach used at the EPO. I suspect this rationale would be a case of first impression in the US. Now, I am not convinced it is worth taking the risk.

    4. 5.5

      Didn’t KSR overturn the objective evidence standard – you know something in the record, like evidence, in favor of the Breyer “common sense” subjective standard? Do you address that?

  6. 4

    Here a private university can and did lose its patent in an IPR while a state university maintains a claim of sovereign immunity against having its patent(s) challenged in an IPR (per pending petition for rehearing at Fed Cir).

    1. 4.1

      Isn’t it still open to argue that when an IPR is filed by a defendant in defense of a patent lawsuit filed against that defendant by the state university that the state limited-waived its immunity by that suit?

      1. 4.1.1

        Is filing an IPR actually considered a defense in a patent lawsuit (affirmative or otherwise)…?

        Not sure as well that asserting a right would mean waiver of rights — creating such Catch-22’s seems a bit Hellerian in an already Orwellian world.

    1. 3.1

      I am not convinced that the switch from the pre-Zurko clear error standard of review to the post-Zurko APA substantial evidence standard of review was that impactful. What percentage of cases would turn out differently if the standard was clear error (less deferential) instead of substantial evidence (more deferential)?


          I miss that poster who used to whine incessantly about “the illegal Zurko IV panel decision.”


            The en banc Fed. Cir. determined that Zurko was, at last, a case where standard of review mattered and would result in a different outcome so they teed it up for the Supremes. The Supremes clarified (i.e., changed) the standard of review and remanded to the Fed. Cir. The en banc Fed. Cir. remanded the case to the panel. The panel got the same result as before. How do you characterize that sequence of events?

  7. 1

    Note that the test of a PTAB fact finding on appeal as based upon “substantial evidence” (or not) is statutory, from the APA, and was enforced on the Fed. Cir. by a Sup. Ct. decision.

    1. 1.1

      Specifically, as noted earlier on this blog, APA Section 706(E) and the Sup. Ct. in Dickinson v. Zurko (1999).

    2. 1.2

      Being here as a matter of post grant review in which the stick from the bundle of property rights (existence and level of presumption of validity) had been taken at the institution decision point (and not as a function of any adjudged validity), are we ALL still going to pretend that this is somehow OK with that (also) statutory dictate and WHY that presence and level is earned at the point of grant and is [pun intended] part and parcel of the satisfying of the Quid Pro Quo to turn the innovator’s inchoate right into a full legal property right?

      1. 1.2.1

        Because Oil States overturned the reasoning of the Land Grant Patent cases. And ironically, the Land Grant Patent case drew from prior IP patent cases, in that under the US system of government – you can never have the situation of one Commissioner granting a property right, an election, and the new Commissioner (here the pantina of the PTAB) reviewing that grant under guise of ‘mistake’ or other such mumbo jumbo – because the heart of the issue is the injection of the political divisions into the guarantee of an independent judiciary above the political fray. Structural or ordered liberty. Dennis you still teach that?

Comments are closed.