Gene Patent in Cancer Test Upheld by Appeals Panel(nytimes.com)
nytimes.com
Gene Patent in Cancer Test Upheld by Appeals Panel
http://www.nytimes.com/2011/07/30/business/gene-patent-in-cancer-test-upheld-by-appeals-panel.html
5 comments
Were all the claims upheld? The article's penultimate paragraph suggests that some fell short.
Nope. At least one claim was rejected.
* The appeals court ruled against Myriad in another part of the case, however. The court said that Myriad’s patent claims on the process of analyzing whether a patient’s genes had mutations that raised the risk of cancer was not patentable because it involved only “patent-ineligible abstract mental steps.” *
The result that the gene is patentable but that the test is not patentable is intriguing.
From the standpoint of genetic research, I may not care whether I have the gene itself, but I do care whether I can test for the gene and its mutations. For example, if my methodology needs to isolate the gene in order to test for it (e.g. exome sequencing), then the "isolation patent" prevents me from using this methodology but allows me to find another methodology that does not require isolation (e.g. whole-genome sequencing).
Daniel MacArthur will probably have a compelling blog post shortly: http://www.wired.com/wiredscience/geneticfuture/
* The appeals court ruled against Myriad in another part of the case, however. The court said that Myriad’s patent claims on the process of analyzing whether a patient’s genes had mutations that raised the risk of cancer was not patentable because it involved only “patent-ineligible abstract mental steps.” *
The result that the gene is patentable but that the test is not patentable is intriguing.
From the standpoint of genetic research, I may not care whether I have the gene itself, but I do care whether I can test for the gene and its mutations. For example, if my methodology needs to isolate the gene in order to test for it (e.g. exome sequencing), then the "isolation patent" prevents me from using this methodology but allows me to find another methodology that does not require isolation (e.g. whole-genome sequencing).
Daniel MacArthur will probably have a compelling blog post shortly: http://www.wired.com/wiredscience/geneticfuture/
This kind of gene patent is not relevant for drug companies who are trying to make therapeutic proteins.
1. if the whole concept of a "gene patent" (as described in this article) were shut down then drug companies will still be fine, since DNA is not the drug, the protein is the drug.
2. On the other hand, if all 25k human genes were patented by many different parties as diagnostic markers (as described in this article), then it wouldn't hurt drug companies either, since that's not where the money really is. And if something turned out to be important for a drug treatment, then at least there is a patent which can be purchased.
3. Actually, if all human genes (and their proteins) were patented to prevent any use by any other parties, then that would be a good thing, because if it turns out that one of them is really useful to treat a disease, then a drug company would be more likely to pursue that as a drug candidate because they could license the patent and protect themselves from generics for a few years to pay off all the R&D costs.
4. if there is a protein or chemical of some sort which is already in the public domain for your intended use and can't be patented - then there is no way to protect your huge investment. This is the worst case scenario for drug companies. Or, if suddenly there was no way to get a patent for a drug based on a naturally occurring chemical of human protein, then that would be bad for business, too.
Also, this whole gene patent thing becomes a little absurd since it now costs only $4000 to sequence the entire human genome. According to this article, Myriad is charging $3000 to sequence 2 different genes (or maybe just to check for a couple common SNPs in those genes?). So, the problem is, what happens when you get your whole genome sequenced? Does the company who does the sequencing need to withhold the BRCA1 and BRCA2 genes from their product that they return to you? What about all the other "thousands" of gene patents? Maybe when you get your genome sequenced then the company which does it just can't interpret the patented parts of the genome? Well, from this article it look like the interpretation of the gene sequence is unpatentable since it is an "abstract mental step." So, maybe everything is fine and all these patents can exist and we can go ahead and get our genomes sequenced without any fear of getting sued by a Myriad of companies.
1. if the whole concept of a "gene patent" (as described in this article) were shut down then drug companies will still be fine, since DNA is not the drug, the protein is the drug.
2. On the other hand, if all 25k human genes were patented by many different parties as diagnostic markers (as described in this article), then it wouldn't hurt drug companies either, since that's not where the money really is. And if something turned out to be important for a drug treatment, then at least there is a patent which can be purchased.
3. Actually, if all human genes (and their proteins) were patented to prevent any use by any other parties, then that would be a good thing, because if it turns out that one of them is really useful to treat a disease, then a drug company would be more likely to pursue that as a drug candidate because they could license the patent and protect themselves from generics for a few years to pay off all the R&D costs.
4. if there is a protein or chemical of some sort which is already in the public domain for your intended use and can't be patented - then there is no way to protect your huge investment. This is the worst case scenario for drug companies. Or, if suddenly there was no way to get a patent for a drug based on a naturally occurring chemical of human protein, then that would be bad for business, too.
Also, this whole gene patent thing becomes a little absurd since it now costs only $4000 to sequence the entire human genome. According to this article, Myriad is charging $3000 to sequence 2 different genes (or maybe just to check for a couple common SNPs in those genes?). So, the problem is, what happens when you get your whole genome sequenced? Does the company who does the sequencing need to withhold the BRCA1 and BRCA2 genes from their product that they return to you? What about all the other "thousands" of gene patents? Maybe when you get your genome sequenced then the company which does it just can't interpret the patented parts of the genome? Well, from this article it look like the interpretation of the gene sequence is unpatentable since it is an "abstract mental step." So, maybe everything is fine and all these patents can exist and we can go ahead and get our genomes sequenced without any fear of getting sued by a Myriad of companies.
> 3. Actually, if all human genes (and their proteins) were patented to prevent any use by any other parties, then that would be a good thing, because if it turns out that one of them is really useful to treat a disease, then a drug company would be more likely to pursue that as a drug candidate because they could license the patent and protect themselves from generics for a few years to pay off all the R&D costs.
Your hypothesis has been tested and empirically shown to be false. Genes that have ever been patented have had less subsequent innovation than genes that have never been patented: http://papers.nber.org/papers/w16213
The reason that this lawsuit is being brought at all is that your interpretation in your final paragraph differs from Myriad's interpretation, so I would not say that everything is 'fine' from either party's perspective.
Your hypothesis has been tested and empirically shown to be false. Genes that have ever been patented have had less subsequent innovation than genes that have never been patented: http://papers.nber.org/papers/w16213
The reason that this lawsuit is being brought at all is that your interpretation in your final paragraph differs from Myriad's interpretation, so I would not say that everything is 'fine' from either party's perspective.
My understanding is that its not the gene that is patented, but the processes surrounding the isolation of it, or the actual isolated product.
There would be no patent infringement if you sequence an entire genome (including BRCA1 and BRCA2), as you are not dealing with the actual chemical processes or products covered by the patent.
They have a monopoly on their specific test, as it uses the chemical products covered by their patents (although the test aspect of the patent appears to have been thrown out).
Creating a different test based around, say Illumina or SOLiD sequencing is not going to infringe on this patent.
There would be no patent infringement if you sequence an entire genome (including BRCA1 and BRCA2), as you are not dealing with the actual chemical processes or products covered by the patent.
They have a monopoly on their specific test, as it uses the chemical products covered by their patents (although the test aspect of the patent appears to have been thrown out).
Creating a different test based around, say Illumina or SOLiD sequencing is not going to infringe on this patent.
[citation needed]
Both Illumina and SOLiD are methods of sequencing by synthesis. Depending on how broadly you interpret the patent, both would potentially cause you to infringe.
Both Illumina and SOLiD are methods of sequencing by synthesis. Depending on how broadly you interpret the patent, both would potentially cause you to infringe.
>DNA is not the drug, the protein is the drug.
The most accurate comparison is source code to binary. DNA is the source code; it gets compiled to protein. It's really hard to say that one is patentable and the other isn't.
The most accurate comparison is source code to binary. DNA is the source code; it gets compiled to protein. It's really hard to say that one is patentable and the other isn't.
Could someone with more expert knowledge explain how the isolated DNA is different from DNA already in cells in the body, in terms of chemical structure and information (ACGT) content?
I'd be surprised if the appellate court could give you a set of criteria for what exactly makes "a distinctive chemical identity and nature".
Inside the body, your DNA is packed up into chromatin by wrapping around other proteins called histones, and then coiling those thicker strands around itself a few more times. One could make the argument that it's shape is different from isolated DNA, which doesn't have the histones, and is going to be much closer to a short string. However, trying to make the claim that this is a chemically distinct molecule is dubious at best, since the chemical structure and identity of the DNA molecule is unchanged.
There are, however, chemical modifications to the DNA itself that that may not get preserved in the extraction technique (but that really depends on your technique), and almost certainly won't be preserved if you need to amplify your sample to sequence it. The most common way is to put a methyl group (CH3) onto a particular part of the DNA molecule. Single-molecule sequencing techniques exist (but aren't comparably cheap to Illumina or SOLID sequencing yet) that would preserve this chemical structure.
Finally, Illumina sequencing (and probably SOLID too, though I'm not sure) involves adding on extra sequences at the end of your DNA fragments, which allow the sequencer to start it's work. I'd doubt if the patent covers this approach, so doing high-throughput genome sequencing like this ought to be fine, based on their "markedly different structure" standard, but who knows what the court would actually say.
But the appellate decision Friday rejected Judge Sweet’s reasoning, saying that since DNA is a chemical, the chemical structure is what matters and that “informational content is irrelevant to that fact.”
This paragraph is the most troubling to me. In the most obvious definition of the terms, the informational content and the chemical structure of DNA are two different ways of saying the same thing. It would be like saying, "the shape of the splotches of ink on this paper are what's being patented, and the informational content is irrelevant"
Inside the body, your DNA is packed up into chromatin by wrapping around other proteins called histones, and then coiling those thicker strands around itself a few more times. One could make the argument that it's shape is different from isolated DNA, which doesn't have the histones, and is going to be much closer to a short string. However, trying to make the claim that this is a chemically distinct molecule is dubious at best, since the chemical structure and identity of the DNA molecule is unchanged.
There are, however, chemical modifications to the DNA itself that that may not get preserved in the extraction technique (but that really depends on your technique), and almost certainly won't be preserved if you need to amplify your sample to sequence it. The most common way is to put a methyl group (CH3) onto a particular part of the DNA molecule. Single-molecule sequencing techniques exist (but aren't comparably cheap to Illumina or SOLID sequencing yet) that would preserve this chemical structure.
Finally, Illumina sequencing (and probably SOLID too, though I'm not sure) involves adding on extra sequences at the end of your DNA fragments, which allow the sequencer to start it's work. I'd doubt if the patent covers this approach, so doing high-throughput genome sequencing like this ought to be fine, based on their "markedly different structure" standard, but who knows what the court would actually say.
But the appellate decision Friday rejected Judge Sweet’s reasoning, saying that since DNA is a chemical, the chemical structure is what matters and that “informational content is irrelevant to that fact.”
This paragraph is the most troubling to me. In the most obvious definition of the terms, the informational content and the chemical structure of DNA are two different ways of saying the same thing. It would be like saying, "the shape of the splotches of ink on this paper are what's being patented, and the informational content is irrelevant"
Isolated DNA is artificially synthesized DNA derived from a biologically produced mRNA transcript.
If you pretend the mRNA is object code, DNA is source code, and isolated DNA is reverse-engineered object code, you have a pretty solid metaphor. Oh, and comments = introns.
If you pretend the mRNA is object code, DNA is source code, and isolated DNA is reverse-engineered object code, you have a pretty solid metaphor. Oh, and comments = introns.
You're using "Isolated DNA" to mean cDNA (a point that I think needs clarifying; you can isolate DNA from cells through other methods). Your metaphor doesn't seem particularly solid to me; it would be more accurate to say that DNA is source code, proteins (and hence enzymes) are object code, and mRNA is code that has been pulled out from disk (the genome), had its comments (introns, as you point out) removed, but is not yet compiled. The computing metaphor obviously breaks down; the best way to characterize cDNA I can think of is as code that's been intercepted on its way to the compiler and placed back into storage - for it to be reverse-engineered object code, it would need to be derived from proteins, which it is not.
We could always call the proteins the binaries, that is to say the output of the linker!
Either way, I was just trying to phrase it in terms familiar to programmers. No metaphor is perfect.
Either way, I was just trying to phrase it in terms familiar to programmers. No metaphor is perfect.
That metaphor really only holds up if your "compiler" does nothing but remove comments (and introduce errors at a low rate).
Obviously DNA is low level. This means it must be assembler- and assembly often is as simple as removing comments and translating "written" code into "machine" code.
Yes, if your "compiler" translates "assembly with comments" to "assembly without comments," then your metaphor is apt.
Update: After reconsidering, I take it back. Introns are important, especially intron boundaries. So, my new assertion: so long as your "compiler" translates "assembly with comments" into "assembly with the same comments intact," then I agree that your metaphor is apt.
Update: After reconsidering, I take it back. Introns are important, especially intron boundaries. So, my new assertion: so long as your "compiler" translates "assembly with comments" into "assembly with the same comments intact," then I agree that your metaphor is apt.
So... compiler directives? ;)
"patent-ineligible abstract mental steps"
This the phrase we need in order to kick the nuts off of software patent trolls!
This the phrase we need in order to kick the nuts off of software patent trolls!
I'm looking forward to this going to SCOTUS...