Myriad: The PTO’s Preliminary Guidance

By Jason Rantanen

Within hours of the Court's Association for Molecular Pathology v. Myriad Genetics, Inc. decision yesterday, the USPTO published its preliminary guidance to the Patent Examining Corps relating to nucleic acid-related technology.  From the memorandum:

As of today, naturally occurring nucleic acids are not patent eligible merely because they have been isolated. Examiners should now reject product claims drawn solely to naturally occuning nucleic acids or fragments thereof, whether isolated or not, as being ineligible subject matter under 35 U.S.C. § 101. Claims clearly limited to non-naturally-occurring nucleic acids, such as a cDNA or a nucleic acid in which the order of the naturallyoccuning nucleotides has been altered (e.g., a man-made variant sequence), remain eligible. Other claims, including method claims, that involve naturally occurring nucleic acids may give rise to eligibility issues and should be examined under the existing guidance in MPEP 2106, Patent Subject Matter Eligibility.

Read the entire memorandum (it's short) here: Download Myriad_20130613

56 thoughts on “Myriad: The PTO’s Preliminary Guidance

  1. Different capabilities of PTOs are manufactured for each type of vehicle such as earth mounting, truck mounting cranes and other applications.

  2. Great discussion points from Couretnay. More at her blog page, linked above.

    LOL – yes more and even better ones at

    especailly as she explains exactly what I told Malcolm and that Malcolm still does not have the nuts to admit that I was right and he was wrong.

  3. Courtenay Brinckerhoff shares her analysis of some of Myriad’s remaining claims at her PharmaPatents blog:

    link to pharmapatentsblog.com

    I don’t agree with some of her conclusions, but she makes some very astute observations about claim terms that weren’t addressed by the Court or in the comments here:

    10. An expression system which comprises the isolated DNA of claim 1 or parts thereof operably linked to suitable control sequences.

    Likely not invalid, assuming the expression system necessarily is something “created by man.”

    That may be a big assumption, even if the expression system is “created by man”, given that the broadest reasonable construction of “expresssion system” (apparently defined in the claim itself, in this instance) is a gene with some regulatory sequence in front of it. That would include, of course, the “natural sequence” in the human chromosome.

    16. A pair of single-stranded DNA primers for determination of a nuycleotide [sic] sequence of a BRCA1 gene by a polymerase chin [sic] reaction, the sequence of said primers being derived from human chromosomne sic] 17q, wherein the use of said primers in a polymerase chain reaction results in the synthesis of DNA having all or part of the sequence of the BRCA1 gene.

    ????? Does the “pair” of primers distinguish this claim from claims to a single fragment? Can this claim be distinguished from the Funk Brothers case?

    That’s a really interesting question, given that the “meaning” of Funk Brothers seems to evolve at the whim of the Supreme Court. In this claim we have two primers, each of which would clearly be ineligible if claimed separately. If I had to guess, I would guess that this mixture is ineligible not because of Funk Brothers but because, like any “merely isolated” DNA molecule describing a natural sequence, the mixture of two such molecules claimed in this manner is not “an act of invention”. The analysis might change if the two primers in the mixture were shown to be the “best” of a subset (at least) of tested primers for the recited use. Definitely a bit of a head-scratcher: can one make an eligible composition by combining two ineligible compositions, without changing the chemical structure of either composition?

    18. A kit for detecting mutations in the BRCA1 gene resulting in a susceptibility to breast and ovariann [sic] cancers comprising at least one oligonucleotide prime [sic] specific for a BRCA1 gene mutation and instructions relatiing [sic] to detectiong [sic] mutations in the BRCA1 gene.

    Likely not invalid, at least not for any reasons specific addressed by the Supreme Court.

    I have to disagree here. I would be stunned if the Supreme Court (or even the Federal Circuit) is going to uphold the validity of a claim that recites only an ineligible composition and the likewise ineligible instructions for using it. Or is the argument that paper is per se eligible (I used to think that about man-made chemicals but of course that’s out the window now)? Does it matter what’s on the piece of paper? Why would it have to be “instructions”? It seems that if this strategy works, then you get around the eligibility issue by citing any old eligible subject matter, e.g., a “container” for the ineligible nucleic acid. That would seem like a genuine end-around the holding in Myriad.

    Great discussion points from Couretnay. More at her blog page, linked above.

  4. Further down:
    “Some innovations may be difficult to patent, such as a software development or perhaps a future cure for disease, and companies may thus be forced to rely on trade secret measures to maintain their market position, thereby depriving the world of technological disclosure.”

    So Van Dyke thinks: the FDA would allow secret APIs through the drug approval process, pharmas would forgo composition/method of treatment patents on a natural product in favor of a trade secret, and competitors would be unable to reverse engineer the drug composition.

  5. Is it any wonder you cannot see with you eyes clenched so tightly?

    Or did you not think that the natural sequence which you use as your baseline for the variant sequences NOT make those variant sequences obvious?

    You are aware of the rationale the court was keying on, right?

    LOL, of course you do pumpkin, I told you what it was.

  6. To which I ever so graciously replied to his smarminess with

    anon said in reply to MM…
    I would like you to actually (honestly) address the points onthis board that are made in good faith and for you to stop being a complete @_$$ about pushing your agenda.
    And as I previously told 6, the main thrust of this case will be based on the Product of Nature exception.
    The court fully may venture into a slight dictum on utility – angels do dance on the heads of pins. But clearly, your emphasis, when compared to my emphasis, shows which of us is the master on this topic (hint: it’s not you).
    Do me a favor and find me your quote from the last Myriad post where you finally came full circle and admitted a view that I tried from the onset to impress upon you. That was so yummy!

    Yes, that last comment was after Malcolm franticly danced to the exact thing that I had long told him in a conversation with another PhD. The thing he thought was English as a second language, and the very thing he is trying so very hard to NOT understand now.
    With his final bit of ‘class,’ Malcolm reflects on the fact that he had taken to repeating me with:

      MM said in reply to anon…
      The court fully may venture into a slight dictum on utility
      Right. So STEffUP.

    So graceful, so cool under pressure, so full of CRP.

    Did you miss something? LOL – you shouldn’t have – I held your hand for every step of the way.

    Bow

  7. anon said in reply to MM…
    “And that brings us back to the utility issue.”
    Except it does not, as there is no “utility issue” for the Supreme Court in the Myriad case, as you fully know (or should know).
    That should be a clue as to why no party or jurist has addressed this.
    D’Oh! (said in the best Homer Simpson tones)

    To which Malcolm replied:

      MM said in reply to anon…

      Would you like to bet on that, Hxmpty?

  8. Snapshot of the hypocrite.

    Compare Malcolm’s smarmy “Did I miss something” at 9:24 with his equally smarmy (just out of the other side of his face) exchange with yours truly on

    starting at 1:41 PM, May 1:

  9. I think that the lefties would be far happier to have no diagnostic test at all (for anyone) than to have one that is expensive.

    Pretty sure you’re wrong about that but keep shoveling.

  10. lack of utility = patent ineligible;

    having utility = patent eligible.

    Sure. That’s old news. I don’t see any indication from the decision that the Court found Myriad’s claimed compositions ineligible as lacking utility.

    I think an argument could have made that Myriad’s claims were so broad and covered such an extraordinary number of useless molecules that they could have been deemed ineligible under those grounds. That would have been a welcome decision. I would have applauded that decision (and I wouldn’t have been alone). But that wasn’t in the cards, mainly because the ACLU was looking to fry a much bigger fish.

  11. I think that the lefties would be far happier to have no diagnostic test at all (for anyone) than to have one that is expensive.

  12. Just confused by the reasoning and not sure what the actual holding is.

    LOL. Maybe poor poor Malcolm is ‘just confused because the Supremes have English as a second language.

    Maybe he can ask Francis, or Robert, or Keeping It real to explain this to him. You know, those three words are just so difficult to understand: product of nature.

    LOL

  13. If that turns out that even small oligonucleotides are patent-ineligible, that could have a chilling effect on R&D investment.

    They are certainly ineligible, unless this decision is even more internally contradictory than it appears at first glance. Thomas made it clear when he discusses the ineligibility of short “cDNA” molecules.

    I doubt the chilling effect is significant as it was nearly impossible to obtain a patent on a small oliogonucleotides anyway. That space is “used up.”

    I’m not troubled by that result at all. Just confused by the reasoning and not sure what the actual holding is.

  14. competitors will simply use the natural sequence

    You seem unaware of the fact that the “natural sequences” are often less useful than the variants due to differences in codon usage by different organisms. It’s called “codon optimization.” Look it up. Old, basic stuff.

    In a nutshell, one variant may work poorly in a recombinant organism; another variant may work much better. It’s usually not the “naturally occuring” sequence, however.

  15. It’s too bad that Malcolm was not the first to link to the USPTO guidance, as it would have been a delicious second course to his Prometheus linking.

    Just had a wonderful time going through some of the Patently-O Myriad archives.

    What a hoot.

    These are especially delicious for repeated drubbings of all of the little circle club members:

    link to patentlyo.com

    link to patentlyo.com

    Does anyone know how to hyperlink to explicit and particular blog posts? There are like pages and pages of archived comments to rub Malcolm’s nose in.

  16. Oops – need to update that (vacuous) logic, and now aim not just for any and all medical methods, but for any and all medical manufacture or any and all medical composition of matter…

    /off sarcasm

  17. There are a lot of people who sit around all day looking for something to be outraged about. It’s a sign of a wealthy society where people’s bellies are full. Myriad’s test costs about the same as an MRI scan, and it’s so widely covered by health insurance that the US is now the country with the widest patient access to BRCA testing anywhere in the world. In the universal payor health bureaucracies of Europe – where these patents aren’t enforced – women have to jump more hurdles, wait longer, and have less access to BRCA testing than in the US. So long as there are neither profits nor patents, complainers would apparently be quite happy with such a state of affairs.

  18. Congressional action would be needed to re-write patent law to insert a tie to the amount of profit allowed,…

    to basically destroy the exclusive nature of patents (of course there are other ways than strictly through Congress to make such a constitutional amendment that would be needed for that change),…

    and ‘independent research’ of a sort already is not blocked. Sure, ‘independent research’ which aim is to eviscerate the patent right is blocked, but that circles back to that exclusive nature thing.

    In other words, eliminate the exclusive nature thing, and you would be OK?

    /facepalm

  19. So if the profit margin were smaller, and second opinions were possible, and ‘independent research’ were not blocked, then you would be OK?

  20. And no second opinion should simply be banned.

    Do you realize that you mean to gut patents for the medical field?

    LOL – I sense an impending revival of the ‘all medical methods’ are categorically banned because one medical method was banned logic…

  21. Yes – quite simple, when you think about it (and if you are not trying to kick up a dust storm to hide in).

  22. Another day or two of gloating over Malcolm and enjoying his mad dash to find some spin that he can hide behind, all the while knowing that he knows that I was perfectly right and that he was perfectly wrong in the Myriad case, and then I might bother with the Bosch decision.

    Malcolm, more popcorn please.

  23. Oh noes, big costs!

    LOL – careful thre 6, you are firing on one of the central ‘beliefs’ of patents are only ‘but for’

    Who knows, you might just next post that patents are not only for the genius (or flash of genius).

  24. if you claim all variant nucleotide sequences which encode the identical protein except for the naturally occurring sequence, then you really have no protection at all. competitors will simply use the natural sequence. so…i don’t get the loophole.

  25. 900% profit margin is too high for live saving routine. And no second opinion should simply be banned. (That most probably mean forced licensing of every patent that is used for DIAGNOSING).

    And I’m more inclined for right side of political scene.

    And war was already lost on that patent. Myriad BLOCKED independent research. So go find better example for your “theory” about loosing war. This do not hold water.

  26. I think that there is exact wording in the verdict that support you conclusion.

    Eg. cDNA indistinguishable from DNA is not patent eligible.

    But that make sense.

    If you can find new ore, with profound use cases, you can not patent its chemical structure. If you alter it (improve or degrade), then you can patent your alteration…

  27. Laws of nature have utilities. Plenty of them actually. Even everything we do we base on laws of nature.

    And they are not patent eligable. They are too usefull.
    ;)

    And for MM.

    Why not patent production of such drug? Why patenting piece of information?
    (DNA is information as words that compose book are.. You can’t take few words from book and then patent them. For same reason you can’t patent nature. You DID NOT INVENTED THEM. It was author or it was nature. And in case of author it was most probably derivative work, so you would need to get “whole humanity” into “inventor” field for patent aplication.)

  28. lack of utility = patent ineligible;

    having utility = patent eligible.

    See pages 10-11 of the decision

  29. I haven’t seen a poll; it’s my assessment based on circumstantial evidence. It just seems that almost everyone I’ve observed who is opposed to the granting of gene patents leans left in their political views.

    The left-leaning pundits are particularly distressed about Myriad’s test that costs $3000. I just hope that, with the SCOTUS ruling, they don’t end up “winning the battle but losing the war”

  30. Note that I did not use the phrase “naturally occurring molecule”… I used the phrase “naturally occurring sequence”. Big difference.

    I any case, I am troubled by the decision insofar as short DNA sequences are concerned, particularly for the case where the cDNA is identical to the naturally occurring sequence. If that turns out that even small oligonucleotides are patent-ineligible, that could have a chilling effect on R&D investment.

  31. some people on the political left get all hysterical about someone getting a patent claim to a measly oligonucleotide

    I don’t think it’s a right/left thing. Did you take a poll or are you aware of one?

  32. lack of utility

    I don’t think “lack of utility” was an issue in Myriad, at least not from the Supreme Court’s perspective. Did I miss something?

  33. I think we’ll see claims like that (all variant nucleotide sequences …except for the naturally occurring one).

    Assuming you’re correct, how long do you think they will last before the legal broom comes by to “clean up”?

    Not a loophole, because the naturally occurring sequence would still remain in the public domain.

    Round and round we go. Even Myriad’s “isolated” DNA didn’t cover any “naturally occurring” molecule (according to the Supreme Court, anyway). The naturally occurring molecule “remained in the public domain.” The Court was concerned with something else, or they at least pretended to be. What was all that business about “information”?

    This is where we’re at: a claim to a fantastically useful 100 nucleotide polymer of a defined sequence and length is ineligible for patenting if the identical stretch of nucleotides is buried somewhere in the 3 billion nucleotide chromosome of an extinct flea, but if I make a non-coding change to one nucleotide in that 3 billion nucleotide chromosome, I’m good to go. It’s perfectly eligible. And the reason has something to do with the “public domain”? Huh.

  34. Yes, there are plenty of pharmacologically active tetrapeptides that could be “encoded” by a 12-mer oligonucleotide.

    A 12-mer oligonucleotide should not have to be rejected for lack of utility merely because it happens to coincide with a 12-mer sequence in the human genome.

  35. I agree…. it’s not really a “loophole”

    I think we’ll see claims like that (all variant nucleotide sequences …except for the naturally occurring one).

    Not a loophole, because the naturally occurring sequence would still remain in the public domain.

  36. Why would that be a loophole? Claiming a non-naturally occurring DNA molecule, having a non-naturally occurring sequence that encodes a natural protein – what exactly do you find objectionable about that?

    I don’t find anything objectionable about it. I’m just trying to make sense of what the Court wrote as their holding:

    genes and the information they encode are not patent eligible under §101 simply because they have been isolated from the surrounding genetic material.

    In your view, is the holding of the case simply that a claimed DNA polymer is ineligible ONLY when the recited sequence is identical to a “naturally occurring” sequence of the same length or longer? If so, then what is the point of the phrase “and the information they encode”? What does it add to the meaning of that sentence? If the PTO’s understanding of the holding is correct, then that clause can be deleted without changing the meaning of the case.

    Consider that the Court went way out of its way to let us know that you can patent a “natural” gene “and the information it encodes” but you have to delete all the introns from the gene first. Um … okay, Court, if you say so! But somehow they forgot to mention that an “isolated” 1,000 nucleotide gene with a single conservative nucleotide change relative to the “natural” sequence is also eligible for patenting? Hmmm…

    If the PTO’s intepretation is correct, here’s the weird world the Supreme Court just created: I can make a single conservative (non-coding) change in the genome of an monkey, one base out of a billion, a change that doesn’t change the organism in any other detectable way, and that organism is now eligible for patenting as a non-natural man-made composition. But if I discover a bacterium in the gut of that monkey, discover a way to culture that bacterium, dissolve the membrane of the collected cultured bacterium so I can study its proteins, identify a protein of interest, then chop the chromosomes up into a billion tiny pieces, purify the piece of DNA that encodes my protein of interest to 100% purity, and show that this purified piece of nucleic acid cures cancer when administered to a kid, I’m screwed. I can’t patent my nucleic acid because … “it’s not an invention.” Thus sayeth the Supreme Court. That result just doesn’t make much sense. Mind you, I’m not saying that the DNA fragment should be eligible, necessarily. I’m just saying that if the PTO’s interpretation is correct, then the holding really is purely arbitrary, or worse.

    In a related vein, I wonder whether the holding applies to fragments of synthetic (non-natural) DNA molecules as well as to natural molecules? In other words, consider a synthetic DNA molecule in the public domain, not identical to any “natural molecule”. If I discover that a new, non-obvious sub-fragment of that molecule has a useful function, can I patent the fragment? If not, why not? There’s no “product of nature” issue in this fact pattern so … what’s the answer?

  37. Funny how some people on the political left get all hysterical about someone getting a patent claim to a measly oligonucleotide (that happens to exist in humans), but no one cares about the patenting of peptides and proteins that are produced by polynucleotides.

  38. It’s the dustcloud being kicked up on the ‘information’ front so that Malcolm can hide from the actual beatdown on the product of nature decision.

    He finds it objectionable that I am proven right, he proven wrong and everyone sees his nose is full of his own CRP.

  39. Why would that be a loophole? Claiming a non-naturally occurring DNA molecule, having a non-naturally occurring sequence that encodes a natural protein – what exactly do you find objectionable about that?

  40. I haven’t read the dissent yet. I think it’s actually 7-2 on the first question, and 5-4 on the second.

    Any thoughts on the consequences of this decision?

  41. Night, are you suggesting providing patents to discoverers of new laws of nature is authorized regardless there may be no use for them identified?

  42. Hal Wegner had this out – 5-4 Old Guard/New Guard split with a fiery O’Malley dissing the ‘special status’ of the CAFC…

  43. The Congress shall have power…To promote the progress of science and useful arts, by securing for limited times to authors and inventors the exclusive right to their respective writings and discoveries;

    Could that be what it says, Ned?

  44. he extensive research and development costs expended to discover a genetic correlation — such as in this case, for an insidious cancer — may be enormous, with great cost and great risk.”

    That’s nice. Granting patents on “correlations” is a really silly way of encouraging people to discover those correlations.

    Some people have great difficulty processing the fact that “more patents” is not the answer to every problem that involves money or “risk.” Of course, those same people tend to be the ones that decry the use of their taxes for public education or government funded research. You know: the type of people who think that the money set aside for Social Security would “better used” if it were invested in their friend’s business instead.

  45. USPTO:

    Claims clearly limited to non-naturally-occurring nucleic acids, such as a cDNA or a nucleic acid in which the order of the naturally occuring nucleotides has been altered (e.g., a man-made variant sequence), remain eligible.

    This seems to contradict the (strange) final paragraphs of the Supreme Court’s opinion. Didn’t Thomas say that you couldn’t protect the natural gene “and the encoded information” with an eligible claim?

    This would seem to create a significant loophole (assuming the Court did not intend it for it be created): applicants can identify a natural gene or even a natural protein sequence, and then, relying on the genetic code, claim all variant nucleotide sequences which encode the identical protein except for the naturally occuring sequence. That seems to be what the USPTO is suggesting here.

    Maybe someone should ask the Supreme Court to correct that last paragraph or explain to everyone what the h-ll it means. It’s impossible to be sure from reading it but it seems highly likely that Thomas was trying to say something important and straightforward. He just miserably failed to do so.

  46. This the problem with the current assault on patent rights in general.

    Casualities of common sense are always a risk in a dishonest intellectual war.

  47. We sua sponte took this case en banc to answer two
    questions. First, does 28 U.S.C. § 1292(c)(2) confer jurisdiction on this court to entertain appeals from patent infringement liability determinations when a trial on damages has not yet occurred? Second, does 28 U.S.C. 1292(c)(2) confer jurisdiction on this court to entertain appeals from patent infringement liability determinations when willfulness issues are outstanding and remain undecided?

    We answer both questions in the affirmative

    Seems reasonable. Certainly a favorable decision for defendants.

  48. Patents for “useful” discoveries are authorized by the Const. It is just that laws of nature are not inventions and are not machines, etc.

    Why don’t we consider extending the patent statutes to include discoveries of laws of nature?

  49. Oh noes, big costs! The traditional gifting of downstream techs they invent after being the first to discover the correlation is NO LONGER SUFFICIENT, we must change this immediately!

  50. “A troubling aspect of the Myriad ruling is the Court’s adamant position that all of the efforts of discovery were meaningless. In some areas of technology, the extensive research and development costs expended to discover a genetic correlation — such as in this case, for an insidious cancer — may be enormous, with great cost and great risk.”

    link to technewsworld.com

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