Stanford’s Abstract Idea: A Method for Resolving Haplotype Phase

In re Stanford University (Fed. Cir. 2021).

This case appears to potential be a good test case on patent eligibility for the U.S. Supreme Court. The Federal Circuit here held that Stanford’s bioinformatics innovation – “a method for resolving haplotype phase” – lacks eligibility under Section 101 because it is directed to an abstract idea under Alice Corp.

Gene inheritance is a super interesting biologic process.  Each person inherits a set of chromosomes from each parent.  At times, it is helpful to understand which genes came from which parent — especially if tracing disease patterns or researching various diseases.  The problem though is that the chromosomes are not labelled “dad” & “mom” (except potentially the sex linked one).

The general purpose of the invention is to provide a better method for figuring out which genes are associated with which parent.  The approach is to first obtain allele data from the subject as well as three other family members (two parents and a sibling).  The claims then use a statistical inference process (Hidden Markov Model) to identify the likely inheritance state.  The claims define key parameters of the model (the hidden states). In addition to HMM, the claims also require a series of error-reduction techniques that use population data as well as consideration of sequencing errors. The prior art includes other methods of resolving haplotype phase, and other would-be non-infringing methods have also been developed since then. [Read Claim 1].  Apparently, the prior-art method had ~80% accuracy while the invention here boosts accuracy to ~98% (for heterozygous positions).

Prosecution History: Stanford researchers filed a couple of provisional applications back in 2011 followed in 2012 by the non-provisional application at issue here (App. No. 13/445,925).  After two rejections, an RCE, and several claim amendments, the examiner eventually issued a notice of allowance in 2016. Stanford paid the issue fee and the patent issued on September 13, 2016.  The next day (on September 14, 2016), the USPTO withdrew the patent from issue on order of the Tech Center 1600 director, and the subsequently issued a new rejection focusing on patent eligibility.  That rejection was affirmed by the PTAB and how has been affirmed by the Federal Circuit.

Patenting Math: On appeal, the Federal Circuit found the claims directed to an abstract mathematical calculation. In its analysis, the court broke-down the claim into a three step process:

  1. Receive data
  2. Process data
  3. Store or output data.

This is an information processing claim, but it does not “DO” anything with the information. The court explains “claim 1 recites no concrete application for the haplotype phase beyond storing it and providing it upon request.”  Now, some data processing approaches have been patentable, but those have focused on improving computer functionality itself.  The distinguishing point here is that Stanford’s innovation simply provides a better data output.

With Alice Step 2, the court found no inventive concept beyond the abstract idea.  Rather, all of the innovative features were basically combining various mathematical algorithms to do a better job of processing data — but we already said that is an abstract idea.

That a specific or different combination of mathematical steps yields a greater number of haplotype predictions than previously achievable under the prior art is not enough to transform claim 1 into a patent eligible application.

Slip Op.

Some of the dependent claims include a “diagnosis” or providing a “drug treatment.” However, the court found that the generalized element was equivalent to saying “apply it.”  In other words, a specific application is required before a mathematical algorithm such as this will be deemed patent eligible.

48 thoughts on “Stanford’s Abstract Idea: A Method for Resolving Haplotype Phase

  1. 9

    “After two rejections, an RCE, and several claim amendments, the examiner eventually issued a notice of allowance in 2016. Stanford paid the issue fee and the patent issued on September 13, 2016. The next day (on September 14, 2016), the USPTO withdrew the patent from issue on order of the Tech Center 1600 director…”


    The PTO does not have statutory authority to withdraw from issue AFTER a patent has issued. How did Stanford not contest the “withdrawal” from issue?

  2. 8

    One could add the steps of 1) obtaining a biological sample from the subject and at least the biological mother, father, and a sibling and 2) determining allele data for each biological sample. These steps are not just performed mentally. But, then, the specter of divided infringement arises.

    Let’s also ponder that the TC Director of Group 1600 withdrew the patent from issue.

    1. 8.1

      I do believe that it is already recognized that it was the TC Director that invoked the action.

      I think that the larger point here is under what LEGAL authority did the TC Director invoke that action – and perhaps critically, WHEN was the OFFICIAL date of the action taken.

      Reflections of purported action in an Image File Wrapper do not count as actions ‘to be taken in writing.’

      1. 8.1.1

        Exactly. When was the official action taken. The Transaction History says the withdrawal was the day before issue, but the IFW shows the withdrawal has a date the day after issue, both handwritten on the document, and the mail date. The written record should be clear.

        Applicants who petition to withdraw must have the decision on the petition levied before the date of issuance.


          I am not sure that we are on the same page (although we may be) – the written record is NOT the IFW.

          It is the Official Mail Date. As far as I can tell, that Official Date is actually in conflict with the IFW (and the position of the TC Director).

          From what I have been able to gather (and granted, this is stemming mostly from conversation of my colleagues), the TC Director’s actions have no support in law.

  3. 7

    More grist (gist!) for my mill:

    Is it a method? Yes. Is the result of performing the method only an item of information? Yes. Does the utility of the information arise from human consumption of the meaning of the information? Yes. Ineligible for patenting.

    If this method were instead a series of steps in another claimset, where the information was consumed by a non-human actor toward some purpose, the steps would be eligible in my mind- such as a new drug claim. The result of a new drug is a chemical change- not just an item of information.

    Policy wise, these claims are essentially scientific facts, and we ought not to patent scientific facts, even new and useful ones.

    1. 7.1

      How are ‘a series of steps’ being ‘essentially scientific facts?’

      facts are not steps, let alone a series of them

      Your “policy wise…essentially” is nonsense.

      Your “ought” that then flows from your nonsense is – likewise – nonsense.

      You would be FAR better off not chasing your (wind) mill.

      1. 7.1.1


        Just bizarre isn’t it anon. The ignorance is just stunning.

        The sad thing is that things keep getting worse and worse. I fully expect the witch of San Jose State to put out strong trade mark bill that will cut patents down another 50%.

        People are skating on mighty thin ice right now.


          The true display of ignorance is failure to recognize the unworkable and unconstitutional overreach of “everything under the sun” and the patent acts sheer incoherence in dealing with items of information as both subject matter and claim elements.

          What has occurred is no accident, and no conspiracy. It’s the inevitable result of manifest injustice. Failure to recognize the prime cause means further failure to either not recognize potential solutions or suffer further consequences of the original problem.


            The Ends do not justify the Means — and certainly the “Ends” of your feelings are even further removed.


              You keep saying that, as if it’s some kind of unimpeachable truth.

              But sometimes the Ends do Justify the Means.

              The sad fact is that they do here. The ends could be reached by better means, but you would rather just wave away the problem requiring the suboptimal means.


                It is an impeachable truth not because I say it.

                I say it because it IS an impeachable truth.

                You might not recognize the terrain, but the impeachable truth also goes by the nomenclature of Rule of Law.

                Also, see Sir Thomas More.

                1. The so called Rule of Law has all kinds of exceptions for when reality bites, including the continued existence of equity & sovereign immunity.

                  also see, plain common sense. Sometimes the ends do justify the means, and even toddlers know it.

                2. Sorry but no – the Ends NEVER justifies the Means.

                  Especially in the legal terrain.

                  (Your desired path is the epitome of Tyranny – the very opposite of Rule of Law).

                  But keep on showing that you just don’t understand this terrain…

  4. 6

    If what is claimed is “a statistical inference process (Hidden Markov Model) to identify the likely inheritance state .. [with] defined key parameters of the model (the hidden states) [and] .. a series of error-reduction techniques that use population data as well as consideration of sequencing errors.” then should not the first two questions be if all of these techniques are previously known and being used here unmodified, and even if so is their use for this purpose, or in this combination, 103 unobvious to a POSITA?

    1. 6.1

      No. The issue is that the Pharaoh did something similar to this back in the first dynasty in that they had math and understood that things could relate to one another.

      1. 6.1.1

        Well, to be ‘fair,’ Night Writer, Paul’s question may be taken as a criticism of the court for conflating the different sections of law.

        And is that not something that both you and I have postulated for the better part of a decade?

        He may be late to the party, but should we not at least welcome him?


          Thanks for reading. What I said seems particularly relevant in this case, because this is was an appeal of a pending application. A pending application can far more easily and vastly less expensively have such a proper 103 analysis before [and likely avoiding] relying on 101 judicial exceptions. The expressed desire of the Sup. Ct. for “unpatentable subject matter” to be a “preliminary issue” in patent litigation makes far less sense for applications, and can even conceal inadequate prior art searches and treatment.


            I am going to have to say no and reject that reasoning, Paul.

            Compact prosecution (at the extreme minimum), and the plain fact that an applicant pays for a full and complete examination under the law, dictates that there is NO such “shortcut” or preference of one section of law as opposed to any other section of law.


            Actually Paul when the claim is properly read it is quite narrow and specific and a bit shocking that it would be held ineligible under 101.

            I suspect that the reason this was held ineligible is that it comes close to the examiner a DNA molecule and figure out something important about the person.


          anon >>He may be late to the party, but should we not at least welcome him?

          Late to the party? Are you having delusions of grandeur again anon?

    2. 6.2

      Your characterization of this as the “first” question(s) is interesting.

      The frustration that so many express with use of the implicit judicial exception to 101 is that it punts this well-developed question to the side, and instead alleges a lack of an “inventive concept” at step two without any of the developed jurisprudence or judicial safeguards that pertain to the Supreme Court’s Hotchkiss condition for patentable invention codified as 35 USC 103.

      In Flook, the Court explicitly incorporated the Hotchkiss/inventiveness/obviousness inquiry into its evaluation of whether the subject claim involving an ineligble concept contained an “inventive concept in its application.” Parker v. Flook, 437 U.S. 584, 594 (1978). Specifically, the Court considered whether, “once that [ineligible concept] is assumed to be within the prior art, the [claim], considered as a whole, contains no patentable invention.” Flook, 437 U.S. at 594.

      In the face of this, patent claims are frequently concluded to have no inventive concept without ever performing this analysis. Here, the Fed. Cir. “conclude[d] that claim 1 is directed to the abstract idea of mathematically calculating alleles’ haplotype phase.” Slip op. at 10-11. But the Court never evaluates or considers whether the specific claimed method is inventive over this broad idea.

      1. 6.2.1

        *I should change that to: never explicitly considers/discusses. Obviously, it is possible that they considered it and reached their own conclusion, but the lack of explicit analysis is striking.

      2. 6.2.2

        J. Doerre,

        It is this type of near-mindless recitation of Flook that shows your flaws as an attorney.

        While you may correctly point out flaws below in view of Flook, you suffer the mistake of accepting ALL of Flook in an unthinking manner.

        Flook existed in a specific point of time, with specific Justices having different and competing views (pay attention, for example, to Justice Stevens).

        Further, Flook was cabined by Diehr – See Bilski (again, paying attention to which Justices weighed in how).

        You are diligent — but you need to grasp the bigger picture if you are going to turn that diligence into true gold for your clients.


          This made me laugh. Given the expressed views regarding the S. Ct. and Fed. Cir., I guess I am in good company.

          If you’re bored, I would be curious to see an attempt to point out with specific quotation to my post where I “suffer the mistake of accepting ALL of Flook in an unthinking manner”. This is not really possible to do, but if you want to try, knock yourself out! (Incidentially, bonus points to you for the cojones to characterize a quote from a case as “near-mindless recitation of [the case].”)

          My post literally just noted the Court’s analysis in Flook, and then used that as a jumping off point to suggest that it seems troubling when “patent claims are … concluded to have no inventive concept without ever … evaluat[ing] or consider[ing] whether the specific claimed method is inventive over th[e] [alleged abstract] idea.” Still seems troubling to me.



            Did I stutter?

            Yes – you used a quote from the case — in a blind manner as not reflecting or understanding the nature of the case, who was saying what, when, and why — and what happened in subsequent cases.

            Maybe apply that diligence that you have (which IS a good trait) to track down in Bilski the notion of how Diehr cabined Flook.

            Then consider just what that means.

  5. 5


    Before PROST, Chief Judge, LOURIE and REYNA, Circuit

    REYNA, Circuit Judge.

    For someone known to have pushed back against “lazy” CAFC Rule 36 use, one has to wonder why the reticence to posting the panel members.

    It’s not like people have not made note of this lack of information….

  6. 4

    I prefer debating eligibility of contributions in the biotech space than the business methods space. That’s because I’m European and so am concentrated on patents for non-obvious technical solutions to objective technical problems. To me, it is hard to deny the technical character of the problem here, and its solution.

    Then there’s that other European mainstay, that the scope of protection granted by the patent should be “commensurate” with the magnitude of the contribution to the art. In other words, when an inventor provides an enabling disclosure to the technical solution to a technical problem, and the scope of the claim in suit accurately corresponds to that solution, well then you need a pretty convincing reason to say there is no eligibility.

    Instead of which, we have here a lazy dismissal: Nothing more than data processing. Go away.

    Patents for pure business methods are a very different kettle of fish. It’s patents on human behaviour I find problematic.

    1. 4.1

      You are talking about the junk circuity and Reyna is a junk judge selected by SV and nominated by Obama to burn the patent system down.

    2. 4.2

      To me, it is hard to deny the technical character of the problem here, and its solution.

      your “preferences” aside, even the EPO is more permissive towards patents “directed to” business methods, as long as there is a ‘technical component.”

      The caveats of “as such” and “per se” are open invitations to scriviners.

      It’s more than odd that you do not seem to even recognize this, seeing how much time you spend on US patent law blogs…

      1. 4.2.1

        Yes, anon, you’re right. The EPC excludes methods of doing business from patentability only to the extent that the subject matter claimed amounts to no more than the method “as such”. And yes, the internationally recognised general principle that statutory exceptions are to be construed narrowly is indeed an invitation to scriveners.

        But no amount of scrivening will get you any further forward at the EPO, when the invention you describe in your patent application is (as I wrote above) a “pure” business method.


          You note too Max that the EPO is sadly behind the USA, China, Korea, and Japan in business methods and software.

          So, being proud that you don’t grant patents for a huge area of innovation and then hiding the fact that you are sadly behind the rest of the world.

          Germany does better.


            Night, I don’t follow you, when you state that Germany does it better than the EPO. Can you expand on that, perhaps.


          Can you define “pure” business method?

          Can you ALSO recognize – and respect – that different Sovereigns have set forth different choices as to what their patent systems cover (completely aside from any international treaties of comity)?

          Do you recognize HERE a point that I have corrected you time and again (and again) over the years?

          Do you recognize how impolite it is to NOT recognize the differences that have been pointed out and explained to you (whether or not you ‘like’ or ‘prefer’ those differences)?


            Good catch, anon. The EPC excludes from patentability any claim that is directed to a method of doing business, but the exclusion, the statutory exception, is confined to the category “as such”. So when I use the adjective “pure” it is intended to have the same meaning as “as such”.

            In other words, nothing “more” than a method of doing business.


              which circles back to…

              How big of a truck do you have driving through that loop-hole?

              What example of a “pure” business method could not be quickly and easily ‘spun’ so as to have the “as such” NOT apply?

              This is NOT an idle question, as I just had one of my partners remark last week that it is EASIER to obtain patent coverage in the EPO for software and business methods than it is to do so in the US – AND our laws have NO SUCH edicts (written by Congress, mind you) against such — without or without such wiggle words as “as such” and “per se.”

              The ‘wiggle’ has swallowed your rule, while here, a NON-rule has swallowed our broader embrace of Useful Arts.

              THIS should cause every reasonable US patent attorney** consternation.

              ** real patent attorneys – not merely litigation attorneys who happen to do patent litigation cases. Even though those TOO should be offended.


                If you claim a method of doing business comprising…..method steps, you will fall foul of the exception. If you claim that same invention in a claim that recites a computer programmed to perform (same method steps) you have overcome the eligibility hurdle under the EPC because a computer has “technical character”.

                But you don’t get to issue till you have got past the obviousness filter, which shuts out any method which fails inventively to solve a technical problem with technical features recited in the claim.

                OK, it might be “easier” at the EPO to get through to issue than at the USPTO with a wide range of subject matter in the “computer-implemented invention” space. But that does not mean that the EPC exclusions to patentability are toothless.

                If SCOTUS could tell us all what “useful arts” includes and what it does not, progress could be made. The EPO tells us what “technical” means in an evolutionary way, with thousands of decisions over decades of evolving jurisprudence. That’s the civil law way. Ask your partner about the level of confidence, whether any given claim is eligible o not i) in Europe and ii) in the USA.

                Perhaps Night can chime in. He seems to think that the courts in Germany hew to a standard different from that of the established case law of the Boards of Appeal of the EPO. Me, I don’t think so.

                1. This is NOT a conversation about the obviousness filter.

                  Let’s avoid conflation, if you don’t mind.

  7. 3

    No way will this get cert. This is exactly the type of invention that the Scotus has decided privately that is not patentable.

    The court doesn’t really get it either. The invention is look at DNA and figure something important out. Seems like a huge mistake to me to not allow these types of inventions. The rest of the claim is just filler.

    1. 3.1

      The other aspect of this is the Scotus, who are to a person ignorant of science, business, and innovation, deciding what is an invention based on their 19th century iron-age thinking.

      The question should be how it fits into the modern world and not, “do it look like a plough?”

      1. 3.1.1

        … or “can I drop it on my foot” (except if it is a computing device – even if I can drop a computing device on my foot – those are not allowed).

  8. 1

    This is exactly what happens when a court refuses to remove their Alice-colored glasses when deciding a case.

    Stanford’s invention is eligible; including as claimed (and it’s not even close).

    Critically important resultant question for Stanford:

    Time now to join the just cause of returning patent eligibility to all areas of innovation — including for all of your plethora of current — and future — innovations?

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