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DNA patenting: There’s still hope (maybe)

Written by: Ryan Chiromas
Westerman Hattori Daniels & Adrian, LLP
Posted: June 14, 2013 @ 12:52 pm

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The Supreme Court unanimously ruled yesterday that isolated DNA is not patent eligible under 35 U.S.C. §101. See  Association of Molecular Pathology v. Myriad Genetics. Or, put more precisely, the Court ruled that Myriad’s isolated DNA claims as written are not patent eligible.  The Court further ruled that similar cDNA claims are for the most part patent eligible, seemingly because the information underlying the claimed molecule omits some content of the information which underlies the full gene.

Spoiler alert: If you are the type of person who enjoys reading about convoluted analogies to baseball bats, plucked leaves, mined gold and surgically removed livers, you are out of luck.  Mercifully, and quite amazingly, the Court managed to avoid that morass.

A pivotal point is the question of whether Myriad was claiming information or a chemical compound.  Of course, the unique thing about DNA is that it is both (i) a chemical compound comprised of carbon, oxygen, nitrogen, phosphorus and hydrogen, and can be bound to cellular proteins, and (ii) an informational blueprint for proteins which form the building blocks of every living thing.

So, which was Myriad claiming?  Let’s take a look at the representative claims (from the ‘282 patent):

  1. An isolated DNA coding for a BRCA1 polypeptide, said polypeptide having the amino acid sequence set forth in SEQ ID NO:2.
  2. The isolated DNA of claim 1, wherein said DNA has the nucleotide sequence set forth in SEQ ID NO: 1.
  3. An isolated DNA having at least 15 nucleotides of the DNA of claim 1.

Unfortunately, no Markman hearing was ever done, and thus there was no claim construction at any the three previous proceedings (similar to what occurred in CLS Bank and Mayo).  The claims are all quite brief, and their only real non-informational substance is wholly derived from the phrase “isolated DNA.”   But what does “isolated” mean?  If we look to the patents themselves, the specifications state that:

An “isolated” or “substantially pure” nucleic acid (e.g., an RNA, DNA or a mixed polymer) is one which is substantially separated from other cellular components which naturally accompany a native human sequence or protein, e.g., ribosomes, polymerases, many other human genome sequences and proteins. The term embraces a nucleic acid sequence or protein which has been removed from its naturally occurring environment, and includes recombinant or cloned DNA isolates and chemically synthesized analogs or analogs biologically synthesized by heterologous systems.

Although the claims would seem to recite a chemical structure specifically excluding structure found alongside the genomic DNA, the Court concluded that claim 1 of the ‘282 patent (an isolated DNA claim) “asserts a patent claim on the DNA code that tells a cell to produce the string of BRCA1 amino acids listed in SEQ ID NO: 2”.   Page 5 (emphasis added).  The Court further states that claim 5 (which recites a 15 nucleotide DNA) “claims a subset of the data in claim 1”.  Page 6 (emphasis added).  As to claim 2 of the ‘282 patent (a cDNA claim), the Court uses less strong language, but concludes that this claim “asserts a patent on the cDNA nucleotide sequence listed in SEQ ID NO: 1, which codes for the typical BRCA 1 gene.”  Page 5.

The baffling aspect of the opinion is that the Court seems to agree that both the DNA of claim 1 and the DNA of claim 2 are man-made and do not occur in nature.   Of claim 1, the Court states that “isolating DNA from the human genome severs chemical bonds and thereby creates a nonnaturally occurring molecule”.  Page 14 (emphasis added).  Of claim 2, the Court states that “the lab technician unquestionably creates something new when cDNA is made.”  Page 17 (emphasis added).  According to the way many patent attorneys (and Judge Rader) think, that should be sufficient to comply with §101.  But the Court does not see things this way.

So there we have it:  two molecules each having a structure which never before existed on the planet Earth prior to Myriad’s work, but one of them is not patent eligible under §101.  However, for the Court, the structural argument does not appear to carry any weight, since the claims seem to be interpreted as lacking any significant structure.  Rather, they say “Myriad’s claims are simply not expressed in terms of chemical composition, nor do they rely in any way on the chemical changes that result from the isolation of a particular section of DNA.”  Justice Thomas states that Myriads claims are “concerned primarily with the information contained in the genetic sequence, not with the specific chemical composition of a particular molecule.” (italics in original, underlining added).  Page 15.   In other words, all of the claims are essentially interpreted as claiming only “code” or “data”.

And it is that “code” or “data” that appears to determine why one of the claims fails and one does not.   As to the isolated DNA claims, the Court states that the claims “understandably focus on the genetic information encoded in BRCA1 and BRCA2 genes.”   Pages 14-15 (emphasis added).  In other words, the isolated DNA claims primarily recite information that existed in nature.

On the other hand, as to the cDNA claims, where introns are removed, the underlying information “is distinct from the DNA from which it was derived”.  Page 17.  But, the Court notes that isolated cDNA might be indistinguishable from natural DNA where it is too short of a sequence to have introns removed from it.  In that case, the lab-made short cDNA molecule would be interpreted in the same manner as isolated DNA, it appears.

So where do we stand now?  Patent owners and applicants can rest assured that any claims directed to cDNA are safe and can be written in the traditional way, at least where the cDNA represents a sequence where an intron was removed.  Also, recombinant DNA claims are most likely also safe, since the Court refrains from considering the patentability of “DNA in which the order of the natural occurring nucleotides has been altered.”   For similar reasons, a recombinant vector including naturally occurring DNA, as well as DNA having a radioactive tag or the like should also be safe.

But, perhaps there is still hope for isolated DNA claims, if they are written in a manner which more explicitly recites the chemical structure, and in particular recites structural features which distinguish over the genomic DNA.   In its conclusion, the Court states that “we merely hold that genes and the information they encode” are not patent eligible.  As noted above, the Court appears to interpret the claims such that the structural/chemical recitations in Myriad’s claims as written are trivial and can be ignored.

So, perhaps an isolated DNA claim could be written as follows:

An isolated and purified polymer consisting essentially of:

a plurality of guanine (G), adenine (A), thymine (T) and cytosine (C) molecules arranged in a chain having a sugar-phosphate backbone, the guanine (G), adenine (A), thymine (T) and cytosine (C) molecules being arranged in the order of SEQ ID NO: 1,

wherein said polymer is substantially separated from cellular proteins, and wherein said polymer is not bound by covalent bonds to another polymer.

Would this work?  It is impossible to say until we can see how the USPTO would react, and furthermore how a court would interpret such claims.  But, this would perhaps address the Court’s view that the claims “are simply not expressed in terms of chemical composition”.  If rewriting the claims in this manner would be sufficient to save these claims, or at least give them a fighting chance, patent owners may consider filing a reissue in order to attempt to resurrect the type of claim which the Court has killed today.

About the Author

Ryan B. Chiromas is a Partner in the Biotechnology group at Westerman Hattori Daniels & Adrian, LLP. Any questions or comments may be directed to him at: rchirnomas (at) whda.com. This article is for informational purposes only. The comments herein are the views of the author only and do not necessarily represent the views of Westerman Hattori Daniels & Adrian, LLP or its clients.

11 comments
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  1. Would this work?

    No. You will recieve a severe slap down for playing semantic games with the Court – they already despise the Art of the Scriviner, er, um, I mean patent attorney.

  2. Interesting article, Ryan.

    I think you’re absolutely mistaken if you believe that you can “draft around” the limitation on eligibility of DNA sequences that the Court set forth here. The PTO’s guidelines certainly do not suggest the existence of what could only be characterized as a gaping loophole. I assume, also, that you are not banking on the language “consisting essentially of” to get you through the gate (fyi, nine out of ten Examiners in 1600 will insist that you take the “essentially” language out of the claim and in many cases they would be helping your client by doing so). Lastly, given the Court’s (dubious) repetition of language regarding “encoded information”, I’d bet that you can’t get an eligible claim even if you additionally disclaimed the nucleotide modifications that are inevitably present in most naturally occuring eukaryotic genomes.

    I also have a comment regarding this passage:

    “Of claim 1, the Court states that “isolating DNA from the human genome severs chemical bonds and thereby creates a nonnaturally occurring molecule”. Page 14 (emphasis added). Of claim 2, the Court states that “the lab technician unquestionably creates something new when cDNA is made.” Page 17 (emphasis added). According to the way many patent attorneys (and Judge Rader) think, that should be sufficient to comply with §101.”

    As we now know, a claim to a new polynucleotide which lacks the introns appearing in the corresponding natural sequence >will< comply with 101, so Rader and (most of) the rest of us were on the right track there. While the Court states that a piece of DNA isolated from a longer genome is "non-natural", the Court believes (and I won't defend their reasoning, because it doesn't make sense to me) that, at least in the context of DNA claims, limiting one's claim to a shorter version of a sequence that occurs naturally in the context of a longer sequence is simply not enough to satisfy 101. Such a claim is still "too close" to the identical sequence found in the "natural" longer sequence, according to the Court, and there is no suggestion that reciting a shorter or more specifically described DNA sequence will avoid that result. In fact, the discussion about the possibile ineligibility of short cDNA sequences indicates that the opposite is true.

  3. Ryan,

    What I worry about is not whether patent practitioners will find a way around Myriad in most biotech cases. They will.

    What I worry about is that America is sinking into the morass of being a 3rd world Idiocracy.

    We have judges, even “Supreme” judges, who do not understand the science and yet rule themselves fit for making decisions about things they know not of.

    Take the DNA double helix for example.

    If one side is called the ‘non-complementary’ DNA segment, doesn’t the other strand of the double helix automatically (inherently) have the cDNA segment?

    And yet the “Supremes” (no reverence intended) rule that cDNA is eligible while (non-c)DNA is not?

    It makes no sense.

    We live in an Idiocracy (Google it for movie with same name).
    Also Google the painting “The Scream” for the emotion that goes with this sentiment.

    http://i2.cdn.turner.com/cnn/dam/assets/120223013917-edvard-munch-the-scream-sotheby-s-horizontal-gallery.jpg

  4. @step back

    While I commiserate with your feelings regarding liberal arts majors arguing and deciding scientific merits, your statement:
    “If one side is called the ‘non-complementary’ DNA segment, doesn’t the other strand of the double helix automatically (inherently) have the cDNA segment?”
    is incorrect. The other strand also codes for introns and therefore is not a cDNA segment (as defined by the Justices).

  5. Ryan:

    I appreciate your post.

    You state “Patent owners and applicants can rest assured that any claims directed to cDNA are safe and can be written in the traditional way, at least where the cDNA represents a sequence where an intron was removed.” However, as Gene pointed out in his post from June 13 post, “there are real and very significant limitations on patent eligibility relating to cDNA.” In addition to the exception to patentable subject matter you noted – where the cDNA “naturally” has no introns – the Court said in note 9, “We express no opinion whether cDNA satisfies the other statutory requirements of patentability.” Since cDNA is really a reflection of the genetic code – a law of nature – it is likely that the cDNA at issue in Myriad Genetics – if the issue had been pursued – would be held to be unpatentable under §103, similar to the application of a law of nature without any innovative concept rejected by the Supreme Court in Mayo v. Prometheus, 132 S.Ct. 1289 (2012). See, e.g., “After Prometheus, Are Human Genes Patentable Subject Matter?”, 11 Duke L. & Tech. Rev. 434.

    Also, you seem to imply that anytime some thing is not found in nature, it must be patentable subject matter under 101. However, in Chakrabarty, the Court made clear that simply because human hands were involved, the product did not necessarily become patentable subject matter. In order to be considered a human invention, the Court held the “the patentee has produced a new bacterium with markedly different characteristics from any found in nature and one having the potential for significant utility. His discovery is not nature’s handiwork, but his own; accordingly it is patentable subject matter under §101.” 447 U.S. at 310 (Emphasis added). The Court in Chakrabarty earlier explained, “This human-made, genetically engineered bacterium is capable of breaking down multiple components of crude oil. Because of this property, which is possessed by no naturally occurring bacteria, Chakrabarty’s invention is believed to have significant value for the treatment of oil spills.” 447 U.S. at 304 (Emphasis added). Myriad Genetics is consistent, with Chakrabarty. See, e.g., “After Prometheus, Are Human Genes Patentable Subject Matter?”, 11 Duke L. & Tech. Rev. 434. Since the isolated DNA in claim 1 did not have markedly different characteristics or significantly different utility than the native DNA, claim 1 did not constitute patentable subject matter.

    Thanks.

    Doug Rogers

  6. Thank you for the post, because it helps sharpen our thinking.

    I don’t think your proposed solution will work, because the reason the Supreme Court made its decision is pretty clear. It’s not that the claim was unclear about claiming a chemical. It *was* clear about that. Your solution would claim the same molecules in wordier and more convoluted language. And you’ve now moved the “changes” that Myriad argued were sufficient to make the molecules patent-eligible into your “wherein” clause. But the Court explicitly noted that covalent bonds were broken and the DNA was removed from other cellular components. And the Court explicitly rejected those as sufficient to confer patent-eligibility, so the claim would confront the same problem.

    It would be patent-eligible if you made clear there was an alteration that affected the sequence. One clearly permissible alteration is removal of introns. We don’t know how *much* alteration is needed, but we know that extraction and breaking covalent bonds (a la Lourie logic) is not enough–or whatever else “isolated” means. But claiming the same molecule in the language of chemistry would not solve the problem.

    Used to be folks assumed that saying “isolated” was enough, now we know it isn’t. Judge Bryson was clear in saying if the molecule were tagged (e.g., a probe) it would be patent-eligible. cDNA is clearly eligible because S Ct said it is (along with Bryson and Solicitor General). A vector or recombinant molecule is clearly eligible. The exact boundary is not clear, but my take: using chemistry words instead of biology words and “wherein” clauses won’t do the trick unless the wherein conditions clearly address the problem of pre-emption. You have to change the molecule if you want to claim it, and clearly specify that change.

    Would “wherein the molecule is used to detect changes and make a prognosis or diagnosis” fly? Dunno. But it would free research, which seems to be the reason there was so much concern for pre-emption, and the only tool left in the shed was 101 patentable subject matter.

    But please note, that language applied to claims 1 and 2 would not cover diagnostics, since no one makes a full-length gene for Dx. The individual DNA fragments actually assembled into a sequence (or hybridized) by Myriad and everyone else do *not* encode the protein; the fragments isolated and sequenced are individually too short to encode the protein. So claims 1 and 2 could not effectively protect diagnostics/prognostics. For such shorter fragments, they would have to resort to claim 5, the oligomer claim. Yet that claim is invalid because of prior art (the problem being that 15-bp sequences exist all over the genome unless you specify only those that are truly unique to BRCA1/2, and that’s a lot of work). As written that claim is invalid, even if claim 1 were valid. Rewriting it by adding “wherein it is used to make a diagnosis” solves the pre-emption problem but now confronts the problem of metastatic sequences throughout the genome. They’d have to do the searches and specify the novel molecules, or perhaps “Sequences comprising 15-bp from claim 1… wherein … used… diagnosis or prognosis” maybe.

  7. I agree fully with Roger Cook-Deegan’s first three paragraphs in his 2:29 comment.

    But I strongly disagree with the proposition in the last couple paragraphs that adding a limitation regarding a field of use to an otherwise ineligible composition is going to get you a patent, or even get you to first base. It’s a non-starter, as far as I’m concerned, for the same reason it’s a non-starter when claiming a plainly anticipated composition. I would never advise a client down that path unless they wanted to waste a lot of money obtaining an unenforceable patent. I apologize if I’m missing some nuance in the description of that strategy that might change my views.

    I also disagree with Doug’s statement at 10:40:

    “Since cDNA is really a reflection of the genetic code – a law of nature – it is likely that the cDNA at issue in Myriad Genetics – if the issue had been pursued – would be held to be unpatentable under §103, similar to the application of a law of nature without any innovative concept rejected by the Supreme Court in Mayo v. Prometheus

    Unless I’m mistaken about the facts here, both the structure of the BRCA1 and BRCA2 genes and the structure of the cDNA sequences were unknown as of Myriad’s application date. Assuming those facts, there was nothing “obvious” about those structures and I don’t see how it’s possible to get a 103 rejection without contradicting what the Supreme Court said in Prometheus: “§102 and 103 say nothing about treating laws of nature as if they were part of the prior art when applying those sections”. If anything, based on Prometheus, one might have expected the Court in Myriad to find cDNA sequences to be ineligible under 101, for more or less the same reasons that the “natural genes” were found to be ineligible. But that didn’t happen.

    Now, if the natural gene sequences are in the prior art, then it’s a completely different story. I can assure you that the USPTO already knows how to apply 103 to reject claims to polynucleotides which do nothing more than remove obvious introns (sometimes they are obvious) from the publically available gene sequence. Nothing about the Myriad decision or Prometheus changes that.

  8. Doug: Your point is well taken that any claim complying with §101 must then go through the ringer of §103. As to your second point, your position seems to be similar to that of Judge Newman in the CAFC decisions. She focused on utility, and thought that at least small fragments of isolated DNA should be patent eligible due to their utility as primers and probes.

    Robert: I think this proposed solution is a long-shot too, but I think it is food for thought. In view of the Court’s recognizing that the isolation “technically creates a new molecule” by breaking covalent bonds, but then complaining that the claims are “simply not expressed in terms of chemical composition”, it seems to me that there might be some room for creative drafting by reciting it as a polymer “consisting essentially of” the DNA bases and not bound to another polymer. In other words, I’m not sure that the Court explicitly said the structural changes are insufficient for patent eligibility. I read the decision as saying that the claims did not sufficiently recite the structural changes. See the paragraph beginning at the bottom of page 14 of the decision, which is just about the only time the claims are actually addressed head-on. On the other hand, that would appear to conflict with the pretty clear statement that separating the gene “from its surrounding genetic material is not an act of invention” found earlier in the opinion.

    On a related point, the isolated DNA is free from associations with cellular proteins such as polymerases, ribosomes and histones, which further distinguishes from genomic DNA. This point seemed to have been ignored entirely by the court (despite the definition in the specification), since the focus throughout this litigation was on the so-called “snipping” of the ends of the molecule. So my hypothetical explicitly addresses this feature.

    I also disagree with the point that adding a limitation regarding the intended use of molecule would have any effect. On the preemption issue, I believe that the best solution is for isolated DNA such as this to be patent eligible but in order to address the perceived problem of limiting research, the law should be amended to include a limitation on damages to research and nonprofits, similar to the limitation on damages for medical procedures in §287(c).

  9. Gene:

    I agree with your statement that “If anything, based on Prometheus, one might have expected the Court in Myriad Genetics to find cDNA sequences to be ineligible under 101, for more or less the same reasons that the “natural genes” were found to be ineligible.” In the article I wrote that I cited in my response to Ryan, that is what I argued the Court should hold, but I am not sure that argument was made to the Supreme Court. However, I also agree with you “that didn’t happen.”

    Yet in its short paragraph on cDNA, the Court left many issues unaddressed and therefore open. As Gene Quinn said in his earlier post on the decision (I am not suggesting that Gene agrees with this post), “It is not correct to take from this decision any belief that cDNA is patent eligible. When you unpack the decision and apply it to the claims directly, which the Supreme Court did not do directly, it becomes clear that there are real and very significant limitations on patent eligibility relating to cDNA.”

    In Prometheus the Court said, “the cases have endorsed a bright-line prohibition against patenting laws of nature, mathematical formulas and the like, which serves as a somewhat more easily administered proxy for the underlying ‘building-block’ concern.” 132 S.Ct. at 1303. In other words, laws of nature by themselves cannot be patented.

    The Court in Prometheus also made the statement you quoted that “§102 and 103 say nothing about treating laws of nature as if they were part of the prior art when applying those sections,” but the Court also seemed to reject “studiously ignoring all laws of nature when evaluating a patent application under §§102 and 103.’” 132 S.Ct. at 1304. The Court in Prometheus simply did not address how to consider laws of nature under the obviousness requirement of §103, since §101 was the only issue.

    In Myriad Genetics, the Court seemed to concede that the genetic code reflected in claim 2 of cDNA was an unpatentable law of nature when it said it “may be so” that the “nucleotide sequence of cDNA is dictated by nature, not by the lab technician.” 2013 WL 2631062, *10 (I personally think the genetic code was dictated by God, but in any case humans did not invent the genetic code). However, the Court added that since the lab technician created something markedly different than the naturally occurring DNA, it was “patent eligible under §101, except insofar as very short series of DNA may have no intervening introns to remove when creating cDNA. In that situation, a short strand of cDNA may be indistinguishable from natural DNA.9” Id. Footnote 9 added, however, “We express no opinion whether cDNA satisfies the other statutory requirements of patentability. See, e.g., 35 U.S.C. §§ 102, 103, and 112.” Id. The Court also said, “this case does not involve patents on new applications of knowledge about the BRCA1 and BRCA2 genes.” Id.

    Although presumably we are all still digesting the full meaning of Myriad Genetics, it seems to me that the reference to “new applications of knowledge” is a reference to the statement in Prometheus, citing Benson, that “to transform an unpatentable law of nature into a patent-eligible application of such a law, one must do more than simply state the law of nature while adding the words ‘apply it.’” 132 S.Ct. at 1294. Of course, Prometheus involved a method claim, and the cDNA claims in Myriad Genetics were composition claims, but as Judge Moore said in Myriad Genetics, “the Prometheus discussion of laws of nature (process claims) clearly ought to apply equally to manifestations of nature (composition claims). Myriad’s argument that Prometheus is constrained to methods is an untenable position.” 698 F.3d at 1340.

    The specification in Myriad Genetics revealed only commonly understood methods to transform the unpatentable genetic code in claim 2 into cDNA. As a result, I think an argument will be in some ensuing litigation that cDNA claims such as claim 2 should still fail under the obviousness requirement, because there is no “inventive concept” in the claimed application of the genetic code. 132 S.Ct. at 1299. If any application of a law of nature suffices to bring about a patent, then it would have been meaningless for the Supreme Court to state in Prometheus that “to transform an unpatentable law of nature into a patent-eligible application of such a law, one must do more than simply state the law of nature while adding the words ‘apply it.’” 132 S.Ct. at 1294.

    I recognize you disagree with my above initial thoughts, and you may be right, or there may be a third position that turns out to be correct. I do not think anyone can predict with certainty the outcome in the courts of these incredibly complex issues. In any case I assume there will be additional litigation on the point of the patentability, or not, of applications of new discoveries of laws of nature, which the Supreme Court agreed was not at issue in its recent decision in Myriad Genetics. The outcome of such litigation should be interesting.

    Thanks for your comment.

    Doug Rogers

  10. I appreciate the discussion, Doug. I’m not trying to get a last word in, but I will comment on this as it is the essence of our disagreement:

    “The Court in Prometheus also made the statement you quoted that “§102 and 103 say nothing about treating laws of nature as if they were part of the prior art when applying those sections,” but the Court also seemed to reject “studiously ignoring all laws of nature when evaluating a patent application under §§102 and 103.’” 132 S.Ct. at 1304.”

    Right, and the Court was absolutely correct to reject “studiously ignoring all laws of nature” during a 102 or 103 analysis. Why? Because otherwise we’d have no inherent anticipation and Examiners would not be able to make an argument along the lines of “the laws of physics are well-known to one skilled in the art, therefore it would be obvious to …” This is just the Supreme Court telling us that they aren’t changing how one conducts an obviousness analysis. They used the term “all laws of nature” and not “all products of nature, known or unknown” for a good reason, I believe.

    I wish you luck with the strategy you describe, should any of your clients want or need to spend money on such a defense. But I don’t think you’ll get very far with it. I think it’s worse than a Hail Mary. And if you succeed with it, then we can forget about a patenting not just new cDNAs derived from eukaryotes but a lot of other recombinant biomolecules derived through the engineering of previously undescribed “products of nature.

  11. Ryan,

    I agree with the others that simply changing the description of Myriad’s isolated DNA sequence to the claim structure you proposed doesn’t grapple adequately with the key point n Thomas’ opinion addressing that issue. It’s more than simply claiming the isolated DNA sequence as a chemical molecule. As page 14 of the slip opinion says, Myriad’s claims do not “rely in any way on the chemical changes that result from the isolation of a particular section of DNA.” In other words, how Myriad’s “isolated” DNA sequence was different in terms of utility, chemical properties, etc., from simply the snipped segment from the native DNA nowhere appears in that claim. In particular, the “functionality” of that isolated DNA sequence was no different from that isolated sequence being part of the native DNA. We may not like that thinking or result, but we in the patent world can live with and deal with it.