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DBL%20Hendrix%20small.png College chemistry, 1983

Derek Lowe The 2002 Model

Dbl%20new%20portrait%20B%26W.png After 10 years of blogging. . .

Derek Lowe, an Arkansan by birth, got his BA from Hendrix College and his PhD in organic chemistry from Duke before spending time in Germany on a Humboldt Fellowship on his post-doc. He's worked for several major pharmaceutical companies since 1989 on drug discovery projects against schizophrenia, Alzheimer's, diabetes, osteoporosis and other diseases. To contact Derek email him directly: derekb.lowe@gmail.com Twitter: Dereklowe

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August 17, 2012

The Myriad Gene Patent Case: Trickier Than You Might Think

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Posted by Derek

All right, there's been another ruling in the Myriad gene patent case, involving genetic testing for the BRCA mutations in breast cancer. There's been a lot of coverage of this, but not all of it gets the details right. And there are a lot of details, so here goes. First off, here is the latest court opinion (PDF), courtesy of the ACLU, which was a party in this case. (That alone should tell you how involved this has become over the years). Allow me to summarize:

Myriad, and others, began offering genetic testing for these mutations in the mid-1990s. The company obtained several patents directed to the gene sequences and methods of assaying them, and informed other players in this field that they were in violation of Myriad intellectual property, specifically the University of Pennsylvania's Genetic Diagnostic Laboratory. Their cease-and-desist letters did not apply to research uses, only to commercial testing for which money was charged. By 1999, the GDL had stopped testing, and Myriad was now the only company in the US carrying out this diagnostic assay.

The plaintiffs in this case are a wide range of people, ranging from the Penn lab and others who wanted to offer BRCA testing, through people who claimed that they had been denied the opportunity to have such a test done through Myriad's exercise of its patents. The lawsuit went through a challenge in district court about whether the plaintiffs had standing to bring suit in the first place, which is an issue that came up again in this appeal, but I'm going to skip over that. It's certainly of potential interest to attorneys in the field, but doesn't get at the scientific and technical end of the case.

To that, then. the district court decision went against Myriad:

The district court held for Plaintiffs, concluding that the fifteen challenged claims were drawn to non-patentable subject matter and thus invalid under § 101. SJ Op., 702 F. Supp. 2d at 220-37. Regarding the composition claims, the court held that isolated DNA molecules fall within the judicially created “products of nature” exception to § 101 because such isolated DNAs are not “markedly different” from native DNAs. Id. at 222, 232 (quoting Diamond v. Chakrabarty, 447 U.S. 303 (1980)). The court relied on the fact that, unlike other biological molecules, DNAs are the “physical embodiment of information,” and that this information is not only preserved in the claimed isolated DNA molecules, but also essential to their utility as molecular tools.

Turning to the method claims, the court held them patent ineligible under this court’s then-definitive machine-or-transformation test. . .The court held that the claims covered “analyzing” or “comparing” DNA sequences by any method, and thus covered mental processes independent of any physical transformations. Id. at 233-35. In so holding, the court distinguished Myriad’s claims from those at issue in Mayo based on the “determining” step in the latter being construed to include the extraction and measurement of metabolite levels from a patient sample. SJ Op., 702 F. Supp. 2d at 234-35 (citing Prometheus Labs., Inc. v. Mayo Collaborative Servs., 628 F.3d 1347, 1350 (Fed. Cir. 2010), rev’d, 132 S. Ct. 1289 (2012)). Alternatively, the court continued, even if the claims could be read to include the transformations associated with isolating and sequencing human DNA, these transformations would constitute no more than preparatory data-gathering steps. Id. at 236 (citing In re Grams, 888 F.2d 835, 840 (Fed. Cir. 1989)). Finally, the court held that the one method claim to “comparing” the growth rate of cells claimed a basic scientific principle and that the transformative steps amounted to only preparatory data gathering.

I didn't even bother going into detail on this decision at the time, because I expected it to be appealed immediately, and so it was. As you'll see from the comments to that post, though, opinions varied widely about the chances for a reversal, but my informal reading was that the more someone knew about patent law, the more they expected the appeals court to reverse.

And that's just what has happened. The problem is, this isn't as wide-ranging a decision as some people (and some headlines) seem to think it is. I'll quote from the latest opinion again:

. . .it is important to state what this appeal is not about. It is not about whether individuals suspected of having an in- creased risk of developing breast cancer are entitled to a second opinion. Nor is it about whether the University of Utah, the owner of the instant patents, or Myriad, the exclusive licensee, has acted improperly in its licensing or enforcement policies with respect to the patents. The question is also not whether is it desirable for one company to hold a patent or license covering a test that may save people’s lives, or for other companies to be excluded from the market encompassed by such a patent—that is the basic right provided by a patent, i.e., to exclude others from practicing the patented subject matter. It is also not whether the claims at issue are novel or nonobvious or too broad. Those questions are not before us. It is solely whether the claims to isolated BRCA DNA, to methods for comparing DNA sequences, and to a process for screening potential cancer therapeutics meet the threshold test for patent-eligible subject matter under 35 U.S.C. § 101 in light of various Supreme Court holdings, particularly including Mayo. The issue is patent eligibility, not patentability.

In other words, this decision is not designed to address the big issues that so many people think that it has. The court goes on to say, as courts at this level often do, that if someone wants to do something about all these things, then the procedure for remedy is clear:

We would further note, in the context of discussing what this case is not about, that patents on life-saving material and processes, involving large amounts of risky investment, would seem to be precisely the types of subject matter that should be subject to the incentives of exclusive rights. But disapproving of patents on medical methods and novel biological molecules are policy questions best left to Congress, and other general questions relating to patentability and use of patents are issues not before us. . .

Still, even if we're talking about patent eligibility and not patentability per se, we still have a tough question here. Myriad says that the isolated DNA molecules that their patent is directed towards are not found in nature as such, that they have to be manipulated and isolated through human ingenuity, and that they (as opposed to native DNA) can be used in their diagnostic applications. They claim that the district court erred in focusing on the informational content of the molecules, and not the actual composition of matter itself. The plaintiffs argue that the isolated DNA molecules have to have a "distinctive name, character, and use", as the law reads, and that they are not "markedly different" enough from the natural substance, especially since (as they hold) the entire point of them is the informational sequence they represent.

The appeals court comes down in favor of Myriad here. A key part of their argument rests on the decision in the Chakrabarty case involving the patenting of genetically engineered bacteria, so if you didn't like that one, you're not going to like this. The court finds that isolated DNA molecules - unwound from their histones, cleaved at both ends, truncated - are "marked different" enough to be eligible for patents:

. . .Accordingly, BRCA1 and BRCA2 in their isolated states are different molecules from DNA that exists in the body; isolated DNA results from human intervention to cleave or synthesize a discrete portion of a native chromosomal DNA, imparting on that isolated DNA a distinctive chemical identity as compared to native DNA.

As the above description indicates, isolated DNA is not just purified DNA. Purification makes pure what was the same material, but was combined, or contaminated, with other materials. Although isolated DNA is removed from its native cellular and chromosomal environment, it has also been manipulated chemically so as to produce a molecule that is markedly different from that which exists in the body. . .

They go on to say that "an isolated DNA molecule is not a purified form of a natural material, but a distinct chemical entity that is obtained by human intervention". As you might imagine, cDNAs are found under this reasoning to be especially far from nature, and these are already held to be patentable. As to the "informational content" argument that carried the day in the lower court, the appeals court has this to say:

. . .We disagree, as it is the distinctive nature of DNA molecules as isolated compositions of matter that determines their patent eligibility rather than their physiological use or benefit. Uses of chemical substances may be relevant to the nonobviousness of these substances or to method claims embodying those uses, but the patent eligibility of an isolated DNA is not negated because it has similar informational properties to a different, more complex natural material. The claimed isolated DNA molecules are distinct from their natural existence as portions of larger entities, and their informational content is irrelevant to that fact. We recognize that biologists may think of molecules in terms of their uses, but genes are in fact materials having a chemical nature and, as such, are best described in patents by their structures rather than by their functions. . .

In other words, this ruling affirms that molecular biology is, in fact, chemistry, if you want to look at it that way. The court goes on to say that if we as a society want to put DNA in a separate category for terms of patent law (because of its unique informational content, etc.), then Congress should get to work on revising the US Code. It's not a matter for the courts to write that in by themselves. The opinion also rejects arguments (made in the dissenting opinion) that make analogies to snipped a leaf off a tree or removing an organ from a human body. These, they say, are not specific, defined substances, but an isolated DNA molecule most certainly is.

There, that's the first part of the opinion. There's another section as to the methods of use, but I think this is enough legal matter for one day around here. And there's plenty of arguing room staked out already!

Comments (16) + TrackBacks (0) | Category: Patents and IP


COMMENTS

1. Hap on August 17, 2012 10:38 AM writes...

Isn't the informational content of the DNA precisely what's being patented? There isn't a way of comparing two sequences without having purified standards of one, so claiming that the purified sequence (whose reason to exist is the information) is functionally equivalent to claiming the information.

In this case, the purification step seems more akin to patenting the determination of the motion of a blue rubber ball by eliding everything but the mass of the ball, its coefficient of restitution, and the height and speed with which it was dropped - in both cases, what seems to me to be patented is the particular information needed to determine the outcome of interest, and not the method for doing so.

I assume that I am wrong. Why?

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2. daveh on August 17, 2012 10:49 AM writes...

As isolation of DNA fragments is known to those skilled in the art,I would find it hard to believe that the lack of novelty has no bearing on the validity of these claims. It appears that this discovery is just routine experimentation targeting a different sequence. (Others skilled in this area may know better...)

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3. PtX on August 17, 2012 11:44 AM writes...

But if you disregard that it's information that matters and treat this isolated DNA as patentable chemical molecules, then a test which doesn't isolate those specific DNA molecules at any step by for example sequencing mRNA or using some sort of restiction analysis should be in the clear.

Also if it's cleaving that matters and makes DNA different from natural product then the same original DNA cleaved in different places should constitute different chemical matter and not be covered by original patent.

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4. Will on August 17, 2012 12:11 PM writes...

@2 - you are conflating novelty with obviousness. I don't think novelty was ever in play, as the DNA fragments had presumably never existed isolated from other cellular components prior to the inventors getting their hands on it.

Obviousness with any chemical/biotechnologicla invention can be very difficult to prove, and courts have steadily applied a very high standard of proof for obviousness to pharmaceutical/biotechnology patents. It would certainly not be a slam dunk case. The fact that the plaintiffs only went after 101 patent eligibiliy and not an obviousness attack may indicate where they thought there best chances were

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5. Hibob on August 17, 2012 12:54 PM writes...

Won't this all be irrelevant shortly? Sequencing methods that don't rely on chemically modified templates or isolated BRCA genes avoid the composition claims entirely. More importantly, pretty soon it will be cheaper to just have your entire genome sequenced than it will be to have a single genetic test ($2500 for BRCA) performed. At that point no one will be paying for genetic testing ever again, they'll just pay for genetic counseling.

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6. RKN on August 17, 2012 1:30 PM writes...

@Hap,

My take was that it's not the information content that makes it eligible for patent, but rather the fact that BRCA1 (or 2) is a *piece* of a naturally occurring polymer (DNA), and when isolated and chemically modified becomes (is transformed into) something that is unnatural (novel).

Pretty slippery reasoning if you ask me. But as Hibob points out, the implications of the decision may soon become clinically irrelevant.

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7. Carl Lumma on August 17, 2012 2:55 PM writes...

This blows my mind. If I understand correctly, the court held that any DNA segment having the properties claimed are patented 'machines', like any vacuum cleaner having a patented feature would be a patented machine. In other words, forget the method, and think about the DNA segments themselves.

But the test being sold *is* a method -- the DNA isn't being sold. It would be like suing a cleaning company for patent infringement, if they produced vacuum cleaners only for their own use. Is that possible?

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8. David Young, MD on August 17, 2012 8:22 PM writes...

I think that such a ruling as the patent on the BRCA test should have to stand up to the general population. Get 100 ordinary people and ask them if this patent makes sense. I would estimate that 99 out of 100 would say no. If I am correct, then the courts should think twice about how they ruled in this case. As for myself, I think that ruling that Myriad has a patent because of certain strand of DNA is novel and unique does not cut it. That strand of DNA is from a person, it is not something made in a laboratory... it belongs to the patient (individual), not to a company. It should not be patentable. Perhaps certain methods of testing for it may be patentable, perhaps not. I would think that 99 our of 100 people would agree with me.

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9. Arne on August 18, 2012 9:23 AM writes...

(sequence of native DNA or RNA) So I am not an expert in patent law but have been following the Myriad case. If some one could answer this isolated vs purified question. We are currently developing a method that allows us to determine the sequence of native DNA or RNA. No amplification or labeling is required. We start the read at a point that we are interested in using differences in electrical conductivity between the different nucleotides as they pass through a nanopore. So my question is if the argument of patent-ability revolves around isolated DNA what exactly constitutes isolated and does sequencing purified native DNA create an alternative method that is not patent-able.

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10. Will on August 18, 2012 10:21 AM writes...

@8 - the problem with reasoning like that is that line of thinking would also lead to natural products not being patentable. For instance, the compound taxol is produced by a tree. Thus, the compound itself cannot be patented. However, it is possible to patent isolated/purified taxol, or taxol in formulation for treating a person. That patent protections makes it worthwhile for people to go looking for useful drugs in nature in the first place.

The district court recognized this problem, and tried to get around it by elevating DNA as special by virtue of their "chemical information" property, and thus not 101 eligible. This was a clever effort, but the Fed. Cir. shut it down. I doubt the SC will take this case up, but we will see.

If you are correct and 99/100 people don't believe an isolated sequence should be patentable, it will be an easy matter to amend the current law to specifically exclude them, even given the dysfunctional nature of our democracy.

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11. Arne on August 18, 2012 10:59 AM writes...

Certainly we all know that the majority of representatives in Washington unfortunately do not represent the will of the people but rather their financial supporters who would be out in full force if congress looked at this with any kind of specificity. I would hope that if the American people were better informed they would put more pressure on congress to act.

This may be a basic question but what exactly is patented. Is it the information obtained from the isolated DNA or the isolated DNA itself?

I believe amplification of a specific area of DNA by PCR is the same as taking a book and copying a page out of the book. The process of making a copy is quite complicated but the page and its content that are still considered part of the book no matter how many times you copy it. That page would still fall under copyright law because the page although isolated from the book is just a copy of a tiny portion of the book.

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12. Anonymous on August 20, 2012 1:49 PM writes...

The claims being challenged were of three types - 1) composition of matter claims which covered a few very specific molecules. These molecules consist of chains of nucleic acids bound in specific sequences.
2) method claims which consisted of comparing a specific gene in a tumor sample to the same gene in a non-tumor sample.
3) method claims which consisted of growing transformed cell lines containing specific gene sequences in the presence or absence of potential anti-tumour compounds and comparing their rate of growth under the two conditions.

The claims were evaluated in this decision under a single criterion, whether or not the claims contained patent-eligible material against a very narrow judicially-created exclusion that included ONLY natural principles or laws, strictly mental processes, or natural phenomena. The court took great pains to point out that they were NOT deciding whether this material was patentable, whether it was novel or non-obvious, whether there were any infringement or licensing issues, or anything at all with respect to the desirability of patenting these compounds.

The only truly difficult decision in here appears to be the claim to a molecule consisting of a specific sequence of DNA. Note - the inventors are not claiming the sequence of DNA, they are not claiming any of the information contained in the sequence, they are claiming only a set of specific molecules. And these are specific molecules which do not, in fact, exist in nature. In nature, each end of the sequence is always bound to something else. The court made a distinction between compounds that must be separated from a mixture to be purified (which may and may not be patent-eligible) and compounds which "can be imagined to be made" by cleaving chemical bonds which would bind the compound to a far larger molecule. I say "can be imagined to be made" because this is not, in fact, how the isolated DNA sequences are produced. They are instead synthesized from complementary sequences, and are thus even further separated from natural products. The court characterized the compositions of matter as pure compounds which did not exist in nature in their isolated forms, and therefore not being patent-ineligible under the natural phenomena exception.

The method claims which only claimed comparing a sequence from a non-tumor source to a sequence from a tumor source were all held to be patent-ineligible under the mental process exception. Although Myriad argued that there was a lot of prep work and transformation required to get to the point where you could compare the two sequences, the court noted that these steps were not included in the method claim, and that the comparison of the two sequences was a mental process. Consequently, all of the claims of that type were declared patent-ineligible.

The last method claim considered, however, involved transforming cells with the tumour gene and testing it against potential inhibitors. This was no longer a mental process, and the transformed cells were not cells that appeared in nature and hence not natural phenomena, so this method claim also was not declared patent ineligible.

It is important to note that just because a particular invention is not barred from patentability by one very low threshold set up in the patent code does not mean that it could or should be patented. The much higher barriers of novelty and non-obviousness must still be overcome before a patent can be issued, and Congress has the power to decide what should be patented, for how long, and under what conditions, under Article I section 8, the mandate "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." If Congress does not feel that a limited time, exclusive right to a compound consisting of a specific gene sequence promotes the progress of Science, they can always amend the patent law to make them patent-ineligible.

However, consider what the alternative to a patent covering this technology might be. I don't mean that all research would immediately stop - that's a doomsday scenario and doesn't take account of the individual desire to know and to make a profit off of their knowledge. No, the alternative to patenting an invention and profiting off of it for a few years while making the entire invention public domain is to simply keep the invention secret. "You want to know if you might be susceptible to breast cancer? Send us a biopsy and $29.95 and we'll tell you by return mail!" Under these conditions, they would never have to reveal the nature of their screen to anybody, and could profit by it for as long as they could keep it secret.

And the time is very short - these patents expire in 2015, so only three more years before the entire test and all of the claimed material becomes public domain.

Permalink to Comment

13. Arne on August 20, 2012 7:11 PM writes...

Here is the latest patent on genetic test for PRCD-PRA. How are any of these claims novel and non-obviousness? Over the past 10 years they have 3 patents on the same prcd-PRA test.

Patent# 8,206,911

The invention claimed is:

1. A method for identifying a dog as genetically normal, as a carrier of, or as affected with or predisposed to progressive rod cone degeneration comprising: a) providing a biological sample obtained from the dog, said biological sample comprising nucleic acids; and b) detecting in the biological sample whether or not there is a change from G to A at position 1298 in SEQ ID NO:1, identifying the dog to be a carrier of progressive rod cone degeneration, affected with or predisposed to progressive rod cone degeneration, or normal, wherein the G to A change in one allele is indicative of a carrier of progressive rod-cone degeneration, the G to A change in both alleles is indicative of a dog affected with or predisposed to progressive rod-cone degeneration, and the absence of the G to A change is indicative of a genetically normal dog.

2. The method of claim 1, wherein the nucleic acid is DNA.

3. The method of claim 1, wherein the nucleic acid is mRNA.

4. The method of claim 1, wherein the biological sample is any tissue containing genomic DNA or mRNA.

5. The method of claim 1, wherein the biological sample is selected from the group consisting of blood, hair, mucosal scrapings, semen, tissue biopsy and saliva.

6. The method of claim 1, wherein the biological sample is saliva.

7. A method for identifying a dog as genetically normal, as a carrier of, or as affected with or predisposed to progressive rod cone degeneration comprising: a) providing a biological sample obtained from the dog, said biological sample comprising nucleic acids; b) detecting in the biological sample whether or not there is a change from G to A at position 1298 in SEQ ID NO:1; c) based on the detecting in b), identifying the dog to be a carrier of progressive rod cone degeneration, affected with or predisposed to progressive rod cone degeneration, or normal, wherein the G to A change in one allele is indicative of a carrier of progressive rod-cone degeneration, the G to A change in both alleles is indicative of a dog affected with or predisposed to progressive rod-cone degeneration, and the absence of the G to A change is indicative of a genetically normal dog.

8. The method of claim 7, wherein the nucleic acid is DNA.

9. The method of claim 7, wherein the nucleic acid is mRNA.

10. The method of claim 7, wherein the biological sample is any tissue containing genomic DNA or mRNA.

11. The method of claim 10, wherein the biological sample is selected from the group consisting of blood, hair, mucosal scrapings, semen, tissue biopsy and saliva.

12. The method of claim 11, wherein the biological sample is saliva.

Permalink to Comment

14. cliffintokyo on August 21, 2012 3:47 AM writes...

It is definitely worthwhile to mull over this issue some more.

"...it is the distinctive nature of DNA molecules as isolated compositions of matter that determines their patent eligibility rather than their physiological use or benefit."

Using this argument as a basis, I should expect to be able to patent a natural product, that I have isolated from *a leaf* snipped off a plant, and have shown by accepted methods to be a distinct composition of matter, but of course not expect to be able to patent the leaf or the plant.

I would normally expect to also have to show some evidence of a use to justify applying for a patent.

More insight, anyone?

Permalink to Comment

15. Anonymous on August 21, 2012 7:49 AM writes...

@cliffintokyo - exactly so. The phrase "have shown by accepted methods to be a distinct composition of matter" is key here. The CAFC decision notes that "In this case, the claimed isolated DNA molecules do not exist in nature within a physical mixture to be purified. They have to be chemically cleaved from their native chemical combination with other genetic materials. In other words, in nature, the claimed isolated DNAs are covalently bonded to such other materials. Thus, when cleaved, an isolated DNA molecule is not a purified form of a natural material, but a distinct chemical entity that is obtained by human intervention." So one "accepted" method of showing that your molecule is a distinct composition of matter, per this decision, would be to show that the natural product is a larger molecule with additional groups covalently bonded to the structure of your claimed invention.

And yes, this is the barest threshold to eligibility to get a patent, merely showing that the field of invention is such that a patent would even be available to the type of invention. You still have to demonstrate all of the other necessary conditions of usefulness, novelty, non-obviousness, and so forth. All the court decided was that these types of compounds were not "natural phenomena" in the sense of judicially created exceptions to patent-eligible material. It did not consider any other criterion of patent validity.

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16. Anonymous on September 1, 2012 2:26 PM writes...

I think the Supreme Court is going to backhand the CAFC hard, and I can't fucking wait.

If they want to patent a method for reading the data out of DNA (isolating it, cleaving it, etc), then go ahead. But they can't, they didn't invent that.

The real meat of the patent is "detecting in the biological sample whether or not there is a change from G to A at position 1298 in SEQ ID NO."

You can't patent that. This is Metabolite vs Labcorp meets Gottschalk vs Benson.

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