Gene patent ruled invalid

[dragon]

At least the judge has some common sense.

A federal court has ruled that key patents held by Myriad Genetics, a diagnostics company based in Salt Lake City, UT, on the BRCA 1 and 2 genes are invalid. Specific mutations in these genes are responsible for the majority of hereditary forms of breast and ovarian cancers, and many women with a family history of these cancers undergo screening to help them make medical decisions around preventing the disease.

The suit, brought by the American Civil Liberties Union (ACLU), patients and medical groups, argued that the patents restricted research and patients' access to healthcare. Myriad's critics have long argued that they give the company a monopoly over this type of genetic screening, allowing it to keep prices high--the test costs more than $3000, despite continual decreases in the cost of genomic analysis tools--and preventing women from seeking confirmatory tests from other sources.

According to a statement from the ACLU, "The precedent-setting ruling marks the first time a court has found patents on genes unlawful and calls into question the validity of patents now held on approximately 2000 human genes." That amounts to about 20 percent of human genes, including those associated with Alzheimer's disease, colon cancer, asthma and other illnesses. "Because the ACLU's lawsuit challenges the whole notion of gene patenting, its outcome could have far-reaching effects beyond the patents on the BRCA genes."

Dan Vorhaus at the Genomics Law Report discusses the ruling in more detail:

Judge Sweet's ruling invalidates both Myriad's composition of matter claims (its patents on isolated DNA sequences to all or a portion of the breast cancer genes) and its method claims (those patent claims that relate to analyzing or comparing isolated DNA sequences in order to detect mutations in a patient's BRCA1/2 genes that might cause breast cancer).

The overall tone of the Court's ruling is best captured by this passage (from page 135):

The identification of the BRCA1 and BRCA2 gene sequences is unquestionably a valuable scientific achievement for which Myriad deserves recognition, but that is not the same as concluding that it is something for which they are entitled to a patent.

The ruling follows decades of debate over gene patenting. An article in the New York Times points out that such patents "have been granted for decades; the Supreme Court upheld patents on living organisms in 1980," an argument Myriad made when asking the court to dismiss the case. The company is expected to appeal the decision

Many patent experts were surprised by the court's decision and predict it will have a negative impact on young start-ups in the biotech industry. It's not yet clear how it will affect the market for BRCA screening. "For the moment, however, we do not foresee this decision producing any radical changes in commercial, clinical or other activity surrounding Myriad's BRCA patents, or gene patents more broadly," Vorhaus wrote in his post.

In the broader policy debate surrounding gene and biotechnology patents, however, this decision is the latest, unmistakable shot across the bow of gene patent holders, particularly those such as Myriad Genetics that have developed businesses around patent-protected genetic tests supported by exclusive rights in underlying gene patents.

link

[Simon_Jester]

The problem I see is:

It makes sense for you to be able to patent something that you invented, whether that thing is a modified gene, a new breed of horse you created by selective breeding, or a widget you built in the garage. It might make sense for Myriad to patent its process for testing genes, under that rule.

It does not make sense for you to be able to patent a naturally occuring phenomenon, such as air, sunlight, or the gene that causes breast cancer. Even if you were the first person to discover it, you didn't create it, and you don't own it in any real sense, because it existed before you even thought to look for it. So I definitely agree with the court that it does not make sense for Myriad to be able to patent the BRCA gene, which it did not create... even if it makes sense for Myriad to be able to patent a device for testing the BRCA gene.

[SCRawl]

The problem I see is:

It makes sense for you to be able to patent something that you invented, whether that thing is a modified gene, a new breed of horse you created by selective breeding, or a widget you built in the garage. It might make sense for Myriad to patent its process for testing genes, under that rule.

It does not make sense for you to be able to patent a naturally occuring phenomenon, such as air, sunlight, or the gene that causes breast cancer. Even if you were the first person to discover it, you didn't create it, and you don't own it in any real sense, because it existed before you even thought to look for it. So I definitely agree with the court that it does not make sense for Myriad to be able to patent the BRCA gene, which it did not create... even if it makes sense for Myriad to be able to patent a device for testing the BRCA gene.

You're right: it doesn't make logical sense to be able to patent a (naturally occurring) gene in the same way that someone would patent a device or a process. You can see the reason for allowing it though, right? If you take away the patent protection, then you take away the economic incentive for discovering the genetic tests necessary to exploit that discovery. I agree that there has been gouging going on in these cases, and that that should be either discouraged or (if necessary) regulated. Perhaps a new class of patent-like protections could be extended to these sorts of discoveries, along with the means to control the costs of the tests or treatments.

[Samuel]

Have the government take possession of the patent and pay the company who discovered the gene enough to insure there is an incentive to continue finding genes?

[ArmorPierce]

That would make mores sense but we always are going to be facing people raging against this governmental expenditure.

[Drooling Iguana]

You're right: it doesn't make logical sense to be able to patent a (naturally occurring) gene in the same way that someone would patent a device or a process. You can see the reason for allowing it though, right? If you take away the patent protection, then you take away the economic incentive for discovering the genetic tests necessary to exploit that discovery. I agree that there has been gouging going on in these cases, and that that should be either discouraged or (if necessary) regulated. Perhaps a new class of patent-like protections could be extended to these sorts of discoveries, along with the means to control the costs of the tests or treatments.

Or perhaps we should just stop depending on market forces to handle important medical research.

[Alyrium Denryle]

Have the government take possession of the patent and pay the company who discovered the gene enough to insure there is an incentive to continue finding genes?

Because biologists already do that, the finding of genes. We also do it for a lot less monetary cost to the GDP.

When a biologist finds a gene, annotates it etc, it goes on a massive public database called Genebank, where any scientist anywhere in the world can BLAST a sequence against that gene, search for functions, find exon splicing sites etc.

Patenting genes is frankly, the antithesis of the scientific process, to make knowledge like that, basic knowledge, proprietary. It should ever be allowed under any circumstance.

If you take away the patent protection, then you take away the economic incentive for discovering the genetic tests necessary to exploit that discovery.

No you dont. Because biologists employed at universities do it without those same incentives.

The claim that we should depend on market forces for basic research is patently (pun intended) absurd.

[General Zod]

The problem I see is:

It makes sense for you to be able to patent something that you invented, whether that thing is a modified gene, a new breed of horse you created by selective breeding, or a widget you built in the garage. It might make sense for Myriad to patent its process for testing genes, under that rule.

It does not make sense for you to be able to patent a naturally occuring phenomenon, such as air, sunlight, or the gene that causes breast cancer. Even if you were the first person to discover it, you didn't create it, and you don't own it in any real sense, because it existed before you even thought to look for it. So I definitely agree with the court that it does not make sense for Myriad to be able to patent the BRCA gene, which it did not create... even if it makes sense for Myriad to be able to patent a device for testing the BRCA gene.

Here's a better article. Full thing in the link, but I quoted most of it.

Yesterday, a judge in New York issued a sweeping decision that, if upheld following a seemingly inevitable appeal, may put most gene patents on shaky ground. The ACLU, various researchers, and medical advocacy groups had sued Myriad genetics and the University of Utah, which held patents that covered tests for mutations in the BRCA genes, which predispose their carriers to breast and ovarian cancers (the US Patent and Trademark Office was also sued, for good measure). Just about everyone involved requested summary judgement, and the ruling grants it in favor of the plaintiffs, invalidating Myriad's patents in the process.

Summary judgment requires that there be little dispute over the basic facts of the matter. And, not surprisingly, all of the parties agree on the history of modern genetics, which the decision recites, starting with Mendel and moving through Watson and Crick to the biotechnology era.

The are a number of disputed issues, however, mostly focused on whether gene patents are a public good. The plaintiffs argue that Myriad's patents block the option of second opinions, while Myriad points out that it has licensed the patents to other groups. The two sides disagree about whether gene patents foster research, with Myriad arguing that the lure of profits does, while the plaintiffs suggest that the fear of running afoul of intellectual property ends up intimidating researchers.

To a large extent, however, the judge in this case, Robert Sweet, has indicated that the public good disputes aren't central to the decision, which largely hinges on the facts that aren't disputed. Precedent indicates that laws of nature or natural substances can't be patented, although significant transformations to natural products can lead to a patentable process or product. The USPTO grants patents to isolated DNA based on the conclusion that they are "distinctly different in character" from the DNA that is present in human cells.

The court has chosen to essentially reanalyze the USPTO's decision in that regard, noting that it sees no reason to defer to the organization, given that roughly 40 percent of the patents challenged in court are ruled to be invalid. To do so, it divides Myriad's patents into two features: the patent on the genes themselves, and the analysis process by which an individual's genes are scanned for potential mutations.
DNA as an information carrier

Sweet's analysis of the former focuses heavily on a Supreme Court decision called Funk Brothers, in which the court overturned a patent that was granted to a specific mix of bacterial species that doesn't occur naturally. In contrast, a single species of naturally occurring bacteria that was transformed with a combination of genes that don't occur naturally was ruled patentable, because the addition of foreign DNA was transformative. So, the question becomes one of whether the isolation of the BRCA genes as part of the genetic test involves some sort of transformative process.

It doesn't, according to Sweet, but he uses a very novel bit of reasoning to get there. Chemically, he notes, DNA is rather inert, and the process of testing performed by Myriad doesn't really rely on any chemical properties that are distinct to the BRCA genes. (It does rely on chemical behaviors, like base pairing, as part of procedures like PCR, but those properties are common to all DNA molecules.) Instead, the BRCA patents rely on the second aspect of what the decision terms the "dual nature" of DNA: its role as a carrier of information.

To draw an analogy, the chemical nature of DNA can be thought of as akin to the magnetic nature of the surface of a hard disk. The patent doesn't deal with that aspect; instead, it deals with the information encoded by the DNA/disk.

Sweet considers both biology and the patents themselves to reach this conclusion. For example, there's what's termed a pseudogene copy of one of the BRCA genes, which has inactivating mutations in it, and no longer produces any protein. Nevertheless, chemically, large stretches of the pseudogene are identical to the active form—it's only the complete informational context that distinguishes the two. Myriad's patents also regularly switch among different versions of the genes—the full genomic sequence, the processed RNA transcript, even small fragments of the gene—suggesting, in Sweet's view, that it's the informational context that matters.

From this perspective, it's clear that Myriad doesn't rely on anything that transforms the BRCA genes—it's simply relying on their sequence as generated by evolution. It does isolate the DNA from cells, but that's not transformative, and simply involves "techniques well known to those skilled in the art." So, that aspect of the patents fails the test of precedent as defined in Funk Brothers.
Sequence comparisons and the scientific method

The decision then turns to the other aspect of the patents, the process of comparing the sequences obtained to determine whether they contain mutations that might predispose their carriers to cancer. Myriad claimed that the Prometheus decision applies to its patents; this indicated that a common lab technique for isolating chemicals from blood was sufficiently transformative that the process of analyzing the levels of those chemicals could be patented. Purifying DNA from cells, then, is a similarly transformative step during the process of DNA analysis.

Unfortunately, the patents themselves don't include a description of the process of isolating the DNA for sequencing. As such, obtaining the sequences is a generic data-gathering process, and not central to Myriad's claims. Prometheus doesn't apply as precedent, and the patent is invalid.

Sweet wasn't done with Myriad yet. The patents also covered a process by which BRCA mutations could be engineered into a cell line, and chemicals tested for therapeutic activity. Again, this is a fairly generic lab technique, and the ruling is very dismissive, stating, "this claimed 'process' is, in fact, the scientific method itself."

About the only defendant that comes out well is the USPTO, which was sued on constitutional grounds, under the claim that it stifled free speech by granting a patent that restricted discussions of diagnostic information to licensees of Myriad's patents. Since the patents are invalid, the court could avoid considering constitutional issues, so it did.

[Alyrium Denryle]

It is nice to see a scientifically literate judge.

[SCRawl]

If you take away the patent protection, then you take away the economic incentive for discovering the genetic tests necessary to exploit that discovery.

No you dont. Because biologists employed at universities do it without those same incentives.

The claim that we should depend on market forces for basic research is patently (pun intended) absurd.

I'm not a firm believer in the market -- I only make the argument I do because it's the system we have, not the system I want. But I'm a dirty socialist commie fascist Canucklehead, so my opinion means very little.

The only way to make the system work the way you suggest -- with the current rate of advancement in this field -- would be to nationalize the sciences. In other words, if you want to work in medical research, you have to work for the government, and (presumably) make a government salary, which would be an order of magnitude lower than what these golden geese currently pull down for making these kinds of discoveries. (I don't have the actual figures in front of me, but my impression is that the private sector guys get paid way more than their university and government counterparts.)

(Edited for typo)

[General Zod]

(I don't have the actual figures in front of me, but my impression is that the private sector guys get paid way more than their university and government counterparts.)

(Edited for typo)

That really depends on the field and the sector, as always. Some fields will get paid more in the government sector than private and vice versa, simply because having steady funding is a good thing. Unfortunately I can't quote any specific figures since I'd wind up violating a bunch of NDAs in the process.

[Simon_Jester]

You're right: it doesn't make logical sense to be able to patent a (naturally occurring) gene in the same way that someone would patent a device or a process. You can see the reason for allowing it though, right? If you take away the patent protection, then you take away the economic incentive for discovering the genetic tests necessary to exploit that discovery.

Why not make the testing process patentable, but not the genes themselves?

I mean, the fact that I can't patent the moon doesn't stop me from setting up a lucrative telescope business, because I can patent those.

I agree that there has been gouging going on in these cases, and that that should be either discouraged or (if necessary) regulated. Perhaps a new class of patent-like protections could be extended to these sorts of discoveries, along with the means to control the costs of the tests or treatments.

Fair enough, so long as we don't end up with the absurd outcome of people being able to patent natural phenomena they did not create.

[General Zod]

You're right: it doesn't make logical sense to be able to patent a (naturally occurring) gene in the same way that someone would patent a device or a process. You can see the reason for allowing it though, right? If you take away the patent protection, then you take away the economic incentive for discovering the genetic tests necessary to exploit that discovery.

Why not make the testing process patentable, but not the genes themselves?

I mean, the fact that I can't patent the moon doesn't stop me from setting up a lucrative telescope business, because I can patent those.

I agree that there has been gouging going on in these cases, and that that should be either discouraged or (if necessary) regulated. Perhaps a new class of patent-like protections could be extended to these sorts of discoveries, along with the means to control the costs of the tests or treatments.

Fair enough, so long as we don't end up with the absurd outcome of people being able to patent natural phenomena they did not create.

Did you read the expanded article I posted?

To a large extent, however, the judge in this case, Robert Sweet, has indicated that the public good disputes aren't central to the decision, which largely hinges on the facts that aren't disputed. Precedent indicates that laws of nature or natural substances can't be patented, although significant transformations to natural products can lead to a patentable process or product.

[Simon_Jester]

Why not make the testing process patentable, but not the genes themselves?

I mean, the fact that I can't patent the moon doesn't stop me from setting up a lucrative telescope business, because I can patent those...

Fair enough, so long as we don't end up with the absurd outcome of people being able to patent natural phenomena they did not create.

Did you read the expanded article I posted?

Yes, in point of fact.

I fail to see the inconsistency between: "Precedent indicates that laws of nature or natural substances can't be patented, although significant transformations to natural products can lead to a patentable process or product" and the notion that "people being able to patent natural phenomena they did not create" is an absurd outcome.

That's my entire point: it would be absurd for a mutated version of BRCA that exists in nature to be patentable. As the precedent you cite says, that is not permissible. I agree with the precedent 100%, and agree with the court's decision to follow that precedent when it comes to a patent on the gene.

Patents on naturally occuring genes are absurd and contradict a long standing precedent. What should be patentable is the process by which I can look at someone's DNA and say "Ah-ha! This woman has a mutated version of BRCA!" Whether the testing process can be patented is an entirely different question, or it ought to be.

[Alyrium Denryle]

I mean, the fact that I can't patent the moon doesn't stop me from setting up a lucrative telescope business, because I can patent those.

The problem is, they are patenting a process that is already commonly used for other applications. The process they patented was not actually new, it was a process As Applied To That One Gene.

It is like trying to patent a frog, and also patent the dip-net and flashlight combination used to catch that particular frog, when that combination of dip-net and flashlight is already commonly used to catch all species of pond-breeding frog.

[Admiral Valdemar]

It's not just this one gene though. They were trying to patent EVERY gene humans possess with this one. A patent filed in '98 was examined for the extent of the claims on intellectual property this would have regarding BRCA1. The claim was for a 15 letter sequence of nucleotides that coded for any protein made by BRCA1. Guess what? That coding sequence turns up over 300,000 times on chromosome one, and at least once on every other chromosome.

So, had the US kept up with allowing these patents to carry on, one company could, literally, own the entire human genome and hold back ALL genomic research by simply filing a suit against any company that happened to utilise a horrible common function of biochemical programming. It, for all intents and purposes, is entirely analogous to the joke of Microsoft patenting zero and one, and claiming all computer software infringes on their patent at the machine code level.

[Simon_Jester]

I mean, the fact that I can't patent the moon doesn't stop me from setting up a lucrative telescope business, because I can patent those.

The problem is, they are patenting a process that is already commonly used for other applications. The process they patented was not actually new, it was a process As Applied To That One Gene.

It is like trying to patent a frog, and also patent the dip-net and flashlight combination used to catch that particular frog, when that combination of dip-net and flashlight is already commonly used to catch all species of pond-breeding frog.

Ah. I see.

In that case, they're not selling anything unique or of their own devising, and the only thing they "own" is a naturally occuring phenomenon. They don't have a right to a monopoly in that case, and it's their own damn fault for setting up a business model that relied on their own ability to patent a naturally occuring phenomenon.