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June 13, 2013 11:51 AM   Subscribe

"We hold that a naturally occurring DNA segment is a product of nature and not patent eligible merely because it has been isolated," Justice Clarence Thomas writes in the court's decision following a unanimous ruling in the case of Association for Molecular Pathology et al. v. Myriad Genetics, Inc., et al.. "Myriad did not create or alter either the genetic information encoded in the BCRA1 and BCRA2 genes or the genetic structure of the DNA. It found an important and useful gene, but groundbreaking, innovative, or even brilliant discovery does not by itself satisfy the §101 inquiry."

Gene patenting began with US patent 4,363,877 in 1982 when the University of California file a patent for the cDNA encoding human growth hormone. The total number of existing gene patents is estimated to be about 30,000 according to the AMA.
posted by Hairy Lobster (100 comments total) 37 users marked this as a favorite

 
Thanks for this glimmer of sanity.
posted by hat_eater at 11:52 AM on June 13, 2013 [28 favorites]


This is great, great news!
posted by medusa at 11:54 AM on June 13, 2013


A *unanimous* Supreme Court decision? They still make those?
posted by FatherDagon at 11:55 AM on June 13, 2013 [22 favorites]


Fuck yeah, science! Fuck yeah, SCOTUS!
posted by filthy light thief at 11:55 AM on June 13, 2013 [10 favorites]


This is a step in the right direction. Sensible healthcare costs include preventative medicine. The absurd cost of the BCRA1 and BCRA2 tests has been an indictment and a blight on us. Although this ruling has far reaching implications, the immediate implication is making a genetic test in reach for many many Americans. I am so relieved and overjoyed by this ruling.
posted by stoneweaver at 11:55 AM on June 13, 2013 [6 favorites]


YESSSSSSSSSSS!!!! *Punches the air*
posted by windykites at 11:57 AM on June 13, 2013 [2 favorites]


I feel like the entire opinion should have just been "Duh." horizontally centered on the page. That leaves the rest of the page free for, you know, whatever. Scalia's unicorn drawings or something.
posted by selfnoise at 11:57 AM on June 13, 2013 [48 favorites]


We got one!
posted by shakespeherian at 11:57 AM on June 13, 2013 [3 favorites]


stoneweaver: " the immediate implication is making a genetic test in reach for many many Americans."

This may or may not be the case. At least Myriad claims that their method is still protected:

"We believe the court appropriately upheld our claims on cDNA and underscored the patent eligibility of our method claims, ensuring strong intellectual property protection for our BRACAnalysis test moving forward," said Peter D. Meldrum, Myriad's president and CEO. "More than 250,000 patients rely upon our BRACAnalysis test annually, and we remain focused on saving and improving peoples' lives and lowering overall healthcare costs."

posted by Hairy Lobster at 11:58 AM on June 13, 2013 [1 favorite]




Yeah, guys. This decision is not at all clear to me. Patents on cDNA (which the court called "composite" rather than "complementary" DNA for some reason) remain valid.
posted by mr_roboto at 12:02 PM on June 13, 2013 [1 favorite]


From SCOTUSblog: Gene patent decision: In Plain English.

"The exclusion of natural substances from eligibility for patents was the theory on which the Court relied Thursday in its unanimous ruling that a company cannot get a patent monopoly on the use and study of human genes that it isolates in the bloodstream, and them takes them out — without changing their natural character — for research."
posted by MonkeyToes at 12:02 PM on June 13, 2013 [2 favorites]


Hairy Lobster: This may or may not be the case. At least Myriad claims that their method is still protected

Won't help them much. I don't know about the specifics of the gene here, but assuming it's a relatively straightforward gene variation with published sequences, a competent molecular biologist could whip up a new analysis within a day.
posted by Mitrovarr at 12:02 PM on June 13, 2013 [2 favorites]


Hold on; they used "composite" in the syllabus and "complementary" elsewhere. Sloppy as hell.
posted by mr_roboto at 12:03 PM on June 13, 2013


Excellent news, thank you.

I posted about lawsuits against Myriad, and their attempt to patent breast cancer genes BRCA1 and BRCA2 back in 2009 and 2010.
posted by zarq at 12:03 PM on June 13, 2013 [2 favorites]


I agree with Justice Thomas?!!??!? UNPOSSIBLE!
posted by Mister_A at 12:05 PM on June 13, 2013 [4 favorites]


The Court held that isolated DNA is not patentable but cDNA is (generally) patentable.

It is also notable that the Court's decision flagrantly ignores the plain language of the Patent Act. "[Myriad] found an important and useful gene, but groundbreaking, innovative, or even brilliant discovery does not by itself satisfy the §101 inquiry."

Section 101: "Whoever invents or discovers any new and useful ... composition of matter ... may obtain a patent therefor ...". (emphasis added).

The Court admits Myriad discovered the claimed DNA molecule (i.e. the gene was a new discovery, as required by § 101). The Court admits the claimed DNA molecule is useful. The Court admits the claimed DNA molecule is a composition of matter. Thus all of the requirements of § 101 are, in fact, met.

What the Court actually did was impose a judicially-created exception to § 101 that has no basis in the Patent Act whatsoever. This is a victory for a Court inventing the law according to its own subjective policy considerations and doing so while making it abundantly clear that it doesn't actually understand the underlying science very well at all.

Hold on; they used "composite" in the syllabus and "complementary" elsewhere. Sloppy as hell.

Only one of many examples of the Court's ignorance on display in this opinion, yet it felt free to build new law on such a shoddy foundation.
posted by jedicus at 12:06 PM on June 13, 2013 [13 favorites]


And I have yet to see any analysis of this decision that either understands the science or addresses the cDNA issue from a legal perspective. ScotusBlog writes: "The Court, however, said that the company might be eligible to get a patent when it created a synthetic form of those genes — in other words, a laboratory imitation of them. Such imitations, according to the ruling, do not exist in nature, and so do not run counter to the rule against patenting nature." This is a rather shallow understanding of cDNA.

To me, it seems that the court has said you cannot patent a gene unless you first identify the exons and introns. Once you identify the exons and introns, you can patent the gene.

This is despite the fact that RNA splicing is a natural process, mRNA is a natural product, and cDNA generation is essentially a rote procedure.
posted by mr_roboto at 12:07 PM on June 13, 2013 [2 favorites]


The fact that we're celebrating a single rational (and some of us likely feel, obvious) decision in a sea of insanity... unsettling at best.
posted by dbiedny at 12:13 PM on June 13, 2013 [6 favorites]


"Whoever invents or discovers any new and useful ... composition of matter ... may obtain a patent therefor ...".

The Court admits Myriad discovered the claimed DNA molecule (i.e. the gene was a new discovery, as required by § 101). The Court admits the claimed DNA molecule is useful. The Court admits the claimed DNA molecule is a composition of matter. Thus all of the requirements of § 101 are, in fact, met.


Except for the NEW requirement.
posted by Kirth Gerson at 12:13 PM on June 13, 2013 [9 favorites]


So it's a judicial decision based on an incorrect understanding of physical law and how that law might apply to patentability?

Okay, I'm not surprised any longer. The dice just happened to come up for us this time.
posted by seanmpuckett at 12:14 PM on June 13, 2013 [4 favorites]


Except for the NEW requirement.

It has long been recognized that the novelty requirement of § 101 adds nothing more than the novelty requirement of § 102 (i.e. that the invention not exist in the prior art, and nature is not prior art).
posted by jedicus at 12:15 PM on June 13, 2013


Suck it, Dr. Leekie!

- Cosima
posted by Rock Steady at 12:15 PM on June 13, 2013 [8 favorites]


Great news. And a unanimous decision? Wow.
posted by homunculus at 12:16 PM on June 13, 2013


I assure you all, despite the generality of any patents or vagueness of any court rulings, natural forces will continue to ensure that we may use our genetic information in the creation of derivative works.
posted by melatonic at 12:19 PM on June 13, 2013 [10 favorites]


Except for the NEW requirement.

Traditionally, natural products have been patentable. If I discover some molecule that some plant produces and find that it acts as a drug, I can patent that molecule. I don't have a good enough legal understanding to describe why the court found this case to be different, but I think it has to do with the fact that the DNA sequence is a piece of information equivalent to a law of nature. So we're thinking not of the DNA molecule as a natural product, but the DNA sequence as a natural phenomenon or law of nature.

If this is in fact the argument, then it seems like the arrangement of introns and exons is similarly a natural phenomenon. Which makes this decision more-or-less nonsense.
posted by mr_roboto at 12:21 PM on June 13, 2013


The Court admits Myriad discovered the claimed DNA molecule (i.e. the gene was a new discovery, as required by § 101). The Court admits the claimed DNA molecule is useful. The Court admits the claimed DNA molecule is a composition of matter. Thus all of the requirements of § 101 are, in fact, met.

Why can't the same logic be applied to discovering a new plant in the Amazon, and owning a patent on the plant itself? Or maybe it can, crazy!
posted by smackfu at 12:22 PM on June 13, 2013 [1 favorite]


I agree with Justice Thomas?!!??!? UNPOSSIBLE!

That's nothing.
posted by Sys Rq at 12:22 PM on June 13, 2013 [1 favorite]


A lot of the Court's recent patent decisions have been unanimous. KSR v. Teleflex, Bowman v. Monsanto, Quanta v. LG (also by Thomas), Global-Tech Appliances v. SEB, Microsoft v. i4i (unanimous plus brief concurrences from Breyer, Scalia, and Alito and Thomas), eBay v. Mercexchange (also unanimous with brief concurrences). Dissenting opinions have been unusual in Supreme Court patent cases in the past decade.
posted by jedicus at 12:24 PM on June 13, 2013


I think that the court might be arguing that the DNA molecule was an "observation," rather than a "discovery" or invention. Myriad did not discover the molecule. They merely discovered what it did.

The DNA pairs were always there, lots of people have long known what they were, but nobody knew what they did.
posted by schmod at 12:24 PM on June 13, 2013 [1 favorite]


It is also notable that the Court's decision flagrantly ignores the plain language of the Patent Act. "[Myriad] found an important and useful gene, but groundbreaking, innovative, or even brilliant discovery does not by itself satisfy the §101 inquiry."

Section 101: "Whoever invents or discovers any new and useful ... composition of matter ... may obtain a patent therefor ...". (emphasis added).

The Court admits Myriad discovered the claimed DNA molecule (i.e. the gene was a new discovery, as required by § 101). The Court admits the claimed DNA molecule is useful. The Court admits the claimed DNA molecule is a composition of matter. Thus all of the requirements of § 101 are, in fact, met.


(emphasis mine)
posted by Sys Rq at 12:25 PM on June 13, 2013 [2 favorites]


(the discovery may be new, but the composition of matter certainly isn't)
posted by Sys Rq at 12:27 PM on June 13, 2013


Yeah, the SCOTUS actually released four unanimous decisions today. Most of them don't get press.
posted by smackfu at 12:29 PM on June 13, 2013 [1 favorite]


the discovery may be new, but the composition of matter certainly isn't

Why does the act contain the word "discovers" then? It is the very nature of the act of discovery that something must exist before one can discover it. By your logic, nothing discovered can ever be new, so the act seems to contain an inherent contradiction.
posted by mr_roboto at 12:29 PM on June 13, 2013 [3 favorites]


Hairy Lobster: "This may or may not be the case. At least Myriad claims that their method is still protected: "

I have a few friends who work in this industry, and they have all been preparing for (and expecting) this verdict.

There's more than one way to skin a cat, and there's a lot of money to be had by the company who can bring a cheap BCRA1/BCRA2 test to market. IIRC, Myriad's patented methods were considered to be slow and expensive, which is one of the reasons why people were arguing so passionately for SCOTUS to rule against Myriad's gene patents in this specific case.

It's only a matter of time before we have a Github for genes.
posted by schmod at 12:32 PM on June 13, 2013 [1 favorite]


Didn't Diamond v Chakrabarty delineate some limits on how "discovery" is interpreted?

“This is not to suggest that § 101 has no limits or that it embraces every discovery. The laws of nature, physical phenomena, and abstract ideas have been held not patentable.”

“Thus, a new mineral discovered in the earth or a new plant found in the wild is not patentable subject matter. Likewise, Einstein could not patent his celebrated law that E=mc2; nor could Newton have patented the law of gravity.”

posted by Kabanos at 12:32 PM on June 13, 2013 [10 favorites]


Laws with inherent contradictions in them? Why, that's impossible. Lawmakers would get a design-time error in their IDE at the drafting stage...
posted by saulgoodman at 12:33 PM on June 13, 2013 [5 favorites]


It is the very nature of the act of discovery that something must exist before one can discover it. By your logic, nothing discovered can ever be new, so the act seems to contain an inherent contradiction.

On can "discover" a new method of doing something (for example, chaining carbon atoms or whatever) that results in a new composition, which can presumably then be patented. This ain't that.

The "new" in the language of the act applies to the words after it, not those before.
posted by Sys Rq at 12:34 PM on June 13, 2013 [2 favorites]


So SCOTUS has effectively invalidated 30,000 patents today? Excellent!
posted by jeffburdges at 12:35 PM on June 13, 2013 [5 favorites]


(emphasis mine)

See above for why this is not the killer counter-argument you may think it to be. Anyway, "discovery" inherently implies novelty. Nobody is arguing that Myriad (or rather the named inventors) wasn't the first to discover these genes. Or at least nobody is arguing that right now, in this immediate case.

(the discovery may be new, but the composition of matter certainly isn't)

The test for novelty is defined by § 102 (for this case you'll want to use the "Original (before AIA)" version, as that's the applicable law). Tell me under which subsection a composition of matter that exists in the universe but has not yet been identified by a human falls (hint: there isn't one).
posted by jedicus at 12:36 PM on June 13, 2013


The more this fucks Myriad, the wider my smile grows. With twenty-two minutes left in the trading day, their stock is down almost 7.5 percent. HAH!

Edit: with twenty minutes left, it's in free-fall. Now off ten percent.
posted by Purposeful Grimace at 12:36 PM on June 13, 2013 [1 favorite]


In The Pipeline
posted by lalochezia at 12:38 PM on June 13, 2013 [1 favorite]


Didn't Diamond v Chakrabarty delineate some limits on how "discovery" is interpreted?

That quote from Chakrabarty was referring to the three main judicially-created exceptions to § 101, exceptions which were created by earlier cases. But they were still entirely made up by judges and are nowhere to be found in the Patent Act.

If DNA molecules should not be patentable, then let Congress pass an amendment to § 101 saying "...except DNA molecules." Or let Congress pass an amendment codifying the judicially-created exceptions. But the Court's patentable subject matter cases have become an unmanageable, unaccountable mess of subjective policy considerations that threaten the underpinnings of some of the country's largest and most internationally competitive industries (biotech, software, and finance).
posted by jedicus at 12:41 PM on June 13, 2013


The discussion in my previous post on this subject is heated but very informative. I recommend it for people interested in more background about the biology.

Some of us do this for a living, so from a non-profit perspective I personally find this ruling heartening for the future of genomics research and the benefits it can deliver to humanity, even if the court's understanding of terminology seems less than clear.
posted by Blazecock Pileon at 12:41 PM on June 13, 2013


That stock trajectory is confusing as hell.

Stock price
earlier today
- Why is Myriad's stock booming after Supreme Court decision?
- Myriad Genetics shares soar on Court decision

Anyone got a good explanation of what happened? Everyone thought it looked good and then realised there was a gotcha, or what?
posted by jacalata at 12:41 PM on June 13, 2013


And Myriad got greedy with cancer patients and people at risk, so it is nice to hear that their investors are going to take a hit today, even if their capital losses will be somewhat subsidized by all of us who are taxpayers.
posted by Blazecock Pileon at 12:43 PM on June 13, 2013 [2 favorites]


the future of genomics research

How many genomics researchers (researchers, not clinicians) had Myriad sued or threatened to sue? How many genomics researchers did Myriad employ, either directly or indirectly by commercializing research done elsewhere (e.g. at the University of Utah, where the BRCA research was originally done)?

How again does this decision help the future of genomics research, when patents on DNA weren't hindering it and companies founded on such patents were helping to drive more research?
posted by jedicus at 12:45 PM on June 13, 2013


Everyone thought it looked good and then realised there was a gotcha, or what?

My best analysis, and IAMNAB, is that MYGN has been having a thirty day downturn over fears of this decision, so when the decision was announced and the management said it wasn't going to affect their patent, buyers went hot. But as the day has worn on, the thirty day and older holders have decided that this might be the best time to get any gain and/or reduce any loss and have sold. As well as negative news coming out that management might be a little too optimistic that this decision won't affect them. YMMV.
posted by Purposeful Grimace at 12:49 PM on June 13, 2013


Anyone got a good explanation of what happened?

A lot of the headline reporting ("Supreme Court rules human genes are unpatentable") has been inaccurate. Also, the BRCA test is not Myriad's only product, and the others may not be as reliant on patents that have just been invalidated.
posted by jedicus at 12:49 PM on June 13, 2013


saulgoodman: Lawmakers would get a design-time error in their IDE at the drafting stage...

With Microsoft Visual Law dot Net, you don't get the error until the contradiction gets JIT compiled by the dot Net Framework. After you download the correct version of the dot Net Framework into your courtroom, of course.
posted by localroger at 12:52 PM on June 13, 2013 [2 favorites]


This ruling reminds me of Sony v. Universal, which pretty much ignored the black-letter law to make home video legal.
posted by whuppy at 12:55 PM on June 13, 2013


But the Court's patentable subject matter cases have become an unmanageable, unaccountable mess of subjective policy considerations that threaten the underpinnings of some of the country's largest and most internationally competitive industries (biotech, software, and finance).

This is me losing sleep worrying about the profit margins of biotech, software, and finance companies.

(researchers, not clinicians)

Because of course these are entirely disjoint and easily distinguishable groups.
posted by kmz at 12:56 PM on June 13, 2013


I choked on a piece of ice when I read the FPP - Clarence Thomas WROTE that? It's opposite day.
posted by PuppyCat at 12:59 PM on June 13, 2013


It's all about wealth creation vs. rent-seeking. This ruling is in the spirit of making patent laws encourage, rather than discourage innovation.
posted by Mental Wimp at 12:59 PM on June 13, 2013


I was pretty delighted to see the decision that natural genomic DNA is not patentable, and that it was unanimous. It's really too bad the Court swallowed the cDNA argument whole though. The information in naturally occurring mRNAs is indistinguishable from their cDNA copies. They are wrong that the natural production of cDNAs by viruses or their incorporation into the cell is rare. At least this leaves the door open to strike down a cDNA patent based on the demonstration that the cDNA does exist in nature, which won't be hard to find in many cases.

I was pretty disappointed by the proud ignorance of Scalia's concurrence:
I join the judgment of the Court, and all of its opinion except Part I–A and some portions of the rest of the opinion going into fine details of molecular biology. I am unable to affirm those details on my own knowledge or even my own belief.
Stay classy, Scalia.

This is me losing sleep worrying about the profit margins of biotech, software, and finance companies.

In aggregate, biotech, software, and finance firms are probably even in favor of the Supreme Court rulings that have limited what is patentable. It's the biotech, software, and finance patent lawyers that deserve your sympathy. Less patentable subject matter means less work for them.
posted by grouse at 1:07 PM on June 13, 2013 [5 favorites]


A lot of the headline reporting ("Supreme Court rules human genes are unpatentable") has been inaccurate. Also, the BRCA test is not Myriad's only product, and the others may not be as reliant on patents that have just been invalidated.

That would explain a drop then jump, but what actually seems to have happened is a giant spike followed by a decline so it's now below the starting point.
posted by jacalata at 1:07 PM on June 13, 2013


Full text of Scalia's concurrence:
JUSTICE SCALIA, concurring in part and concurring in the judgment.

I join the judgment of the Court, and all of its opinion except Part I–A and some portions of the rest of the opinion going into fine details of molecular biology. I am unable to affirm those details on my own knowledge or even my own belief. It suffices for me to affirm, having studied the opinions below and the expert briefs presented here, that the portion of DNA isolated from its natural state sought to be patented is identical to that portion of the DNA in its natural state; and that complementary DNA (cDNA) is a synthetic creation not normally present in nature.
I'm honestly not sure what the deal is with that. If the "belief" line wasn't there it's basically just him saying "I am totally lost with this genetics stuff but I trust the expert testimony," but that one line sticks out.
posted by jason_steakums at 1:10 PM on June 13, 2013 [2 favorites]


How many genomics researchers (researchers, not clinicians) had Myriad sued or threatened to sue?

I appreciate that Myriad only went to far to monetize the IP it was granted, but the relevance or importance of a law is often larger than the apparent lack of belligerence by any one party at any one point in time.

We have laws so that everyone plays by the same set of rules, not just for Myriad today, but also for some GenomiPharmaCo that may more forcefully exploit a patent over its twenty-year lifespan, somewhere down the road.

How again does this decision help the future of genomics research, when patents on DNA weren't hindering it and companies founded on such patents were helping to drive more research?

I am an informed layperson and not a lawyer, and therefore not competent to discuss the legal issues beyond more than what I absorb from lawyers who speak on this issue.

However, as I mentioned in the previous thread, genomic patents technically block off chunks of the human genome as "black boxes" that researchers cannot explore without leaving themselves open to liability.

Further, with how messy genomics is (one can validate the simple combinatorics by scanning a publicly-available publication of a reference human genome for Myriad's patented n-mers, and seeing where those sit outside the BRCA1 and BRCA2 loci) those "black boxes" can be so broadly defined that liability could theoretically be a problem even for researchers not focused on a particular target "owned" by a drug company.

In an increasingly liability-averse society, the outcome for basic life sciences research seems predictable. And most of the genomics-derived pharmacological products are invariably ground in basic research monetized by private research. Patents do hurt private research, even if they appear on the surface to drive it.

One should note that laws can have chilling effects even without a standing history of associated lawsuits. And this is not just genomics, either. For example, those who use compression tools may be interested in learning about arithmetic coding, a generally more efficient compression approach than BW or Huffman encoding, and why bzip2 is historically called bzip2 and not just bzip.
posted by Blazecock Pileon at 1:15 PM on June 13, 2013 [1 favorite]


It has long been recognized that the novelty requirement of § 101 adds nothing more than the novelty requirement of § 102 (i.e. that the invention not exist in the prior art, and nature is not prior art).

Doesn't the quoted bit from Thomas' write-up of the court's decision in the OP directly contradict this view, whether it's long been recognized or not? I mean, the emphasized language here specifically:

"We hold that a naturally occurring DNA segment is a product of nature and not patent eligible merely because it has been isolated..."

By my read, "isolated" = "discovered." So does this decision set a really major new precedent in patent law or what? It seems like it does. (And there goes my million-dollar plans for a start-up based on patenting interesting cloud formations and charging the sky licensing fees...)
posted by saulgoodman at 1:15 PM on June 13, 2013


It has always been my opinion that overturning these patents would have absolutely no effect on Myriad's business. The value is not in the patent, the value is in their database about what each variant in the BRCA1/2 genes means. This will not change that. It will allow others to build their own database of BRCA1 and BRCA2 variants and their clinical implications, but that is a long and slow process, and requires access to lots and lots of samples from people with cancer, and right now it's pretty tough for commercial companies to get access to that.

This is fantastic news for the profits of biotechs, pharmas, and pretty much everyone in the industry.

It's bad news for some patent lawyers. So there's that.

I still don't know what the cDNA thing means; the SCOTUSblog seems just flat out wrong in their interpretation. Reading Justice Thomas's footnotes is extremely worrying, because it seems that he thinks that making cDNA is enough of a transformative procedure to be patentable. However, really the only thing that should be patentable are specific processes of creating cDNA, there's invention there. Otherwise, it's a standard molecular biology technique, achievable through many different means, commercially available in many different kits, that one can learn in a few hours, which would seem that it is trivial to those who are "skilled in the art" of molecular biology. Creating cDNA is fundamentally different from the process of synthesizing a general molecule that was discovered in nature; copying a sequence of nucleic acids is trivial, synthesizing that chiral molecule with three rings from some Amazonian root is something that can consume a team of dozens of PhD-level chemists for a decade or more.
Section 101: "Whoever invents or discovers any new and useful ... composition of matter ... may obtain a patent therefor ...". (emphasis added).

The Court admits Myriad discovered the claimed DNA molecule (i.e. the gene was a new discovery, as required by § 101). The Court admits the claimed DNA molecule is useful. The Court admits the claimed DNA molecule is a composition of matter. Thus all of the requirements of § 101 are, in fact, met.
There's a lot of elision in the Section 101 quote, but I don't see how genomic DNA would be patentable under this, as "composition" seems vague and up to the courts to define specifically. I don't see any need to change the laws.

Also, does anybody know the story of how Myriad was even able to get these patents? I always thought that Marie Claire-King discovered the BRCA genes, and their significance.
posted by Llama-Lime at 1:18 PM on June 13, 2013 [2 favorites]


From Slashdot user Samantha Wright on the cDNA exception:
Let me make an extended computer metaphor to explain this properly.

The human genome is comprised of many different types of information, which we can liken to pieces of text in different languages. Consider a case where we have a long document written in Russian that discusses source code for a program that was heavily commented—but in Greek. (For those of you following along in the lab, Russian is the untranscribed DNA, Greek is transcribed but noncoding, and the ASCII program itself is the coding sequence.) All of this is in UTF-32.

When the cell functions normally, it uses the program's source as a build script: it copies the code out of the document into CP-1253 (the Windows Greek code page), and then cuts out any remaining "??????" left by the transcription, as well as all of the Greek comments in the middle of the code. There are some comments at the start of the code and at the end, but most of the copy is the code itself.

In the Myriad case, they've found a program that works the other way, called reverse transcriptase. It turns the 8-bit Greek/ASCII mixture back into UTF-32, but the Russian and the intragenic comments are still gone, leaving us with a usable sequence that we can do a bitwise search comparison with. This is very convenient to do because there's already a complete set of such sequences available. These are called cDNA libraries, and we rely on them everyday to tell us where the Greek comments are.

What researchers will be forced to [do] instead is to cut the sequences out by hand directly from the wide Unicode source, using a lab technique called PCR splicing. The stupid thing is that there's no chemical difference between the two—it would be impossible to prove one way or the other where the diagnostic sequence came from, unless you knew the sequence's history. It just means that researchers now have to fumble around with splicing a bit more.
posted by alms at 1:22 PM on June 13, 2013 [2 favorites]


Also, does anybody know the story of how Myriad was even able to get these patents? I always thought that Marie Claire-King discovered the BRCA genes, and their significance.

King discovered the existence of the BRCA1 genes and its general location (a small portion of chromosome 17) but it was people at University of Utah and Myriad who patented the sequence of the single gene.
posted by grouse at 1:27 PM on June 13, 2013 [1 favorite]


Washington Post, "Court ruling against gene patents may open BRCA breast cancer tests to more women, experts say":
Hours after the ruling, one company — DNATraits, part of Houston-based Gene By Gene, Ltd. — said it would offer BRCA gene testing in the United States for $995 — less than a third of the current price.
Additionally, Ambry Genetics has just announced that they will immediately add BRCA1 and BRCA2 to their breast cancer sequencing panel starting today at no additional cost:
Please note, all samples received starting June 13, 2013 for BreastNext, CancerNext and OvaNext will automatically include BRCA1/2 gene sequencing and deletion/duplication analyses at no additional cost. Additionally, Ambry will contact clinicians to discuss any clinically-significant BRCA1/2 incidental findings on all in-house samples.
Good for patients, bad for rent-seekers.
posted by grouse at 1:42 PM on June 13, 2013 [13 favorites]


From Slashdot user Samantha Wright on the cDNA exception:

This comment makes very little sense. There seems to be a fundamental misunderstanding that the metaphor to software only bungles further.

In the Myriad case, they've found a program that works the other way, called reverse transcriptase.

Reverse transcriptase was discovered in 1970 and won the Nobel Prize for Baltimore and Temin in 1975. If Myriad had discovered reverse transcriptase or invented the process of in vitro reverse transcription, I can see why they'd have some claim on resulting intellectual property. But it's a standard technique.

This is very convenient to do because there's already a complete set of such sequences available. These are called cDNA libraries, and we rely on them everyday to tell us where the Greek comments are.

Right, and the cDNA libraries were created by reverse transcription. Which is a standard molecular biology technique.

What researchers will be forced to [do] instead is to cut the sequences out by hand directly from the wide Unicode source, using a lab technique called PCR splicing. The stupid thing is that there's no chemical difference between the two—it would be impossible to prove one way or the other where the diagnostic sequence came from, unless you knew the sequence's history. It just means that researchers now have to fumble around with splicing a bit more.

I have no idea what this even means. If you want to generate an actual molecule of the cDNA, you just synthesize it. We have a sequence. It's 29 cents per base pair from GenScript....

But no one really cares about making the molecule of DNA. What's important at this point is knowing the sequence so that you can detect and catalog mutations.
posted by mr_roboto at 1:45 PM on June 13, 2013 [3 favorites]


It's only a matter of time before we have a Github for genes.

Yeah, we have that already. Here's the BRCA1 entry.
posted by mr_roboto at 1:46 PM on June 13, 2013 [2 favorites]


One more comment for now: Splice variants of BRCA1 are known to be oncogenic. If Myriad does have a patent on the cDNA, can they control testing for splice variants?
posted by mr_roboto at 1:49 PM on June 13, 2013


Holy moly, only three digits on that URL?
posted by maryr at 1:50 PM on June 13, 2013


If Myriad does have a patent on the cDNA, can they control testing for splice variants?

You can test for splice variants without making a cDNA. They don't have a patent on the mRNA, which is inarguably a product of nature.
posted by grouse at 2:00 PM on June 13, 2013


And you can test for sequence without making a gene, but when Myriad held a patent on the gene, they prevented other people from making tests with it. It's honestly not clear to me what this ruling means with regard to what exactly Myriad now controls.

If it only restricts people from synthesizing cDNA, then the patent is largely worthless. But gene patents traditionally have controlled the use of sequence information. Is there a reason to think that cDNA patents would behave differently?
posted by mr_roboto at 2:03 PM on June 13, 2013


So is there no value in the transcribed gene that can only be exploited using the cDNA?
posted by nicwolff at 2:05 PM on June 13, 2013


Creating cDNA is the first step for nearly any analysis of RNA, because RNA is very fragile on its own, and DNA is stable.

IMHO, there are going to be as many useful tests that derive from RNA as there are from DNA. RNA tells you the current state of the cell, DNA merely tells you what it's capable of. Both are important.
posted by Llama-Lime at 2:05 PM on June 13, 2013 [1 favorite]


How can Myriad's database of gene variants and clinical implications be private data? Surely to demonstrate the clinical value of the test, they would have to have published studies about variants and likelihood of breast cancer. What doctor would order a $3000 test and just blindly share the result with their patient without open information about which gene variants are clinically relevant?? Just take Myriad's word?
posted by R343L at 2:12 PM on June 13, 2013


Let me make an extended computer metaphor to explain this properly.
Holy shit. That person managed to come up with a metaphor that's probably 20 times more difficult to understand then what's actually happening. I had to read it two or three times to understand what the hell she was even saying in terms of what was actually supposed to be happening to the text she was talking about. In fact, I think she is seriously confused about how character encoding even works, because she says everything is in UTF-32 but also talks about 8-bit ASCII and CP-1253 and whatever.

It would be far simpler just to explain what is actually happening at a molecular level then this nonsense.
posted by delmoi at 2:15 PM on June 13, 2013 [7 favorites]


OK, here's my attempt at a preschool-toy based metaphor:

Imagine you have a toy caterpillar. I'm picturing something a bit like this. It's rainbow colored and the peices are ROYGBIV. Now, the Red piece is clearly a head (it has antenna) and the Violet piece is the butt (only one place to connect over segments) but the other 5 pieces are just segments (legs, connections on either side). Let's make a rule that says you have to keep the pieces in ROYGBIV order. The caterpillar needs at least 4 pieces.

Now, how many different caterpillars can you make from that? Well, you always have to use the head, you always have to use the butt, but your center could be OY, OG, OB, OI, OYG, OYB, OYI, YG, YB, YGBI... But everyone knows that a correctly assembled caterpillar will be ROYGV. Obviously. (Turns out that ROGBIV is an early larval stage though.)

All those ROYGBIV pieces are the chromosomal DNA. The ROYGV product is a spliced mRNA form that you would recover as cDNA. Orginially, Myriad had all the pieces in one nice patent. They could test for any caterpillar you made. But if they're working from a single cDNA piece they can only test for a specific splicing variant. Now, if you already know the splicing variant that causes cancer (oooh, that nasty ROYBV!) and you've isolated it, you can still market your test. However, if you're interested in everything but the correct form (ROYBV and ROYIV and ROYV and ROBV and RYGV and and and...) you're in trouble now.

How does that sound?
posted by maryr at 2:24 PM on June 13, 2013 [1 favorite]


Perhaps someone who knows more about genetics and genetic testing can enlighten me ... how is the BRCA1/BRCA2 test in question different from the very inexpensive "shotgun" DNA microarray tests like those used by 23andMe?

I got a 23andMe profile for $100 and it purports (although with a bunch of disclaimers, naturally) to tell me whether I carry the BRCA 1 and 2 mutations, among many other things.

Is there a significant difference in accuracy between their test and Myriad's? It seems like if you are looking for a well-known mutation, that the microarray tests would be pretty effective. They don't provide whole-genome sequencing or anything, but that's not what most diagnostic tests for specific conditions do or require anyway.
posted by Kadin2048 at 2:28 PM on June 13, 2013


For an extreme real world example of how many gene products a single gene can make, turn to the fly.

That gene contains 4 domains where there are variations available in what to express as a protein. In one, you express one of 12 choices. In the next, 1 of 48 choices. Third, 1 of 33 and finally 1 of 2. That means from a single piece of chromosomal DNA you can (theoretically) express 12*48*33*2 or 38,016 different products. It's a beautiful way to compress information storage, really.

Patenting the chromosomal DNA would cover all 38,016 variants. A cDNA product would only represent one of those. Now, if it's the one variant that causes cancer, it's still a valuable product.

There, that's nearly the same example but without colors and caterpillars.
posted by maryr at 2:36 PM on June 13, 2013 [3 favorites]


Thank you for all the science lessons! One of the best parts of MeFi is learning new things.
posted by stoneweaver at 2:38 PM on June 13, 2013 [1 favorite]


In aggregate, biotech, software, and finance firms are probably even in favor of the Supreme Court rulings that have limited what is patentable. It's the biotech, software, and finance patent lawyers that deserve your sympathy.

Who do you think hires those lawyers? Behind every patent lawyer is one or more (usually a lot more) clients. And look at the amicus briefs. Both PhRMA [pdf] and BIO [pdf] filed briefs in support of Myriad. So "in aggregate" biotech firms support broad patentability.
posted by jedicus at 2:47 PM on June 13, 2013


There's a lot of elision in the Section 101 quote, but I don't see how genomic DNA would be patentable under this, as "composition" seems vague and up to the courts to define specifically. I don't see any need to change the laws.

I elided parts that were entirely irrelevant to the discussion at hand. I linked to the full version so that everyone could see I was not playing games with ellipses.

Composition of matter has already been defined by the courts:
"composition of matter" has been construed consistent with its common usage to include "all compositions of two or more substances and . . . all composite articles, whether they be the results of chemical union, or of mechanical mixture, or whether they be gases, fluids, powders or solids." In choosing such expansive terms as "manufacture" and "composition of matter," modified by the comprehensive "any," Congress plainly contemplated that the patent laws would be given wide scope.

The relevant legislative history also supports a broad construction. The Patent Act of 1793, authored by Thomas Jefferson, defined statutory subject matter as "any new and useful art, machine, manufacture, or composition of matter, or any new or useful improvement [thereof]." The Act embodied Jefferson's philosophy that "ingenuity should receive a liberal encouragement." Subsequent patent statutes in 1836, 1870 and 1874 employed this same broad language. In 1952, when the patent laws were recodified, Congress replaced the word "art" with "process," but otherwise left Jefferson's language intact. The Committee Reports accompanying the 1952 Act inform us that Congress intended statutory subject matter to "include anything under the sun that is made by man."
Diamond v. Chakrabarty, 447 U.S. 303, 308-09 (1980) (citations omitted). The "substances" in "two or more substances" refers to chemical elements; thus isolated, purified DNA is a composition of matter.

Furthermore, isolated, purified DNA molecules are "made by man." Even though the original gene was found in nature, the isolated, purified DNA molecules are produced through various laboratory processes. It is no less a man-made product than cDNA molecules.

The Court worked out the policy result it wanted and invented new law in order to reach that conclusion. That's fine if the Court is working in a common law area, but there is a clear statutory scheme here.
posted by jedicus at 3:01 PM on June 13, 2013


Doesn't the quoted bit from Thomas' write-up of the court's decision in the OP directly contradict this view, whether it's long been recognized or not? I mean, the emphasized language here specifically:

"We hold that a naturally occurring DNA segment is a product of nature and not patent eligible merely because it has been isolated..."


No, it doesn't contradict the view that the novelty requirement of § 101 is the same as the novelty requirement of § 102 and that nature is not prior art. What it does is say that products of nature are not patent eligible at all, regardless of their novelty, and that a DNA molecule that is the same as a DNA molecule that occurs in nature is a product of nature and thus unpatentable.

In other words, it cuts off the analysis before one even considers whether the DNA molecule is novel, useful, nonobvious, etc.

Nature isn't acting as prior art here, though. For example, suppose there was a naturally occurring DNA molecule X. This decision makes molecule X unpatentable. Now suppose a scientist discovers that if you modify molecule X in a certain way you get molecule Y that is new, useful, and nonobvious (sort of like making cDNA). Molecule Y is patentable. Molecule X is not prior art against molecule Y (unless somebody had published an article about it or something). This opinion does not change that.

It's kind of a fine distinction.
posted by jedicus at 3:13 PM on June 13, 2013


Throughout the whole gene patenting issue, I still haven't shaken how really odd it is to me that this is debated in terms of patent law in the first place - I get why it is, because we use the legal tools we have, but it's still weird that the biological makeup of humans was ever even on the table as a patentable thing. It's just.. always been there, in human bodies, for the whole existence of the species. Most of us owned a copy before it was ever discovered. It's an integral part of your body, the only possession you own so fully you can't ever disown it in your lifetime. How do you even start talking commercial ownership of DNA sequences? SO WEIRD.
posted by jason_steakums at 4:23 PM on June 13, 2013 [3 favorites]


Furthermore, isolated, purified DNA molecules are "made by man." Even though the original gene was found in nature, the isolated, purified DNA molecules are produced through various laboratory processes. It is no less a man-made product than cDNA molecules.

The Court worked out the policy result it wanted and invented new law in order to reach that conclusion. That's fine if the Court is working in a common law area, but there is a clear statutory scheme here.
Yeah, and when they overturned segregation that wasn't a change in "policy"? There is nothing wrong with the supreme court considering the wider social and ethical implications of it's decisions.

The fact that patent law had been twisted to produce a result that most people found morally abhorrent doesn't mean it shouldn't be over turned because it makes life more difficult for patent lawyers.

You happen to disagree pretty much everyone who isn't a stockholder in that company or a patent lawyer. And your side lost in a unanimous supreme court ruling, so by definition, you were wrong on the law

Get over it.
In other words, it cuts off the analysis before one even considers whether the DNA molecule is novel, useful, nonobvious, etc.
Aww, so sad. Less money for patent lawyers.
posted by delmoi at 4:36 PM on June 13, 2013 [2 favorites]


But the Court's patentable subject matter cases ... threaten the underpinnings of some of the country's largest and most internationally competitive industries (biotech, software, and finance).

Good riddance. The government has no compelling reason to create and enforce the existance of monopolies. It is a destructive, distortionary tax on consumers and inhibits innovation.
posted by JackFlash at 4:47 PM on June 13, 2013


Yeah, and when they overturned segregation that wasn't a change in "policy"? There is nothing wrong with the supreme court considering the wider social and ethical implications of it's decisions.

That's fair when the Court is considering a matter of constitutional law or common law, areas where it has considerable leeway to interpret or craft the law on its own. But in this case there was a straightforward statutory scheme put in place by Congress. The Court overstepped its bounds.

The government has no compelling reason to create and enforce the existance of monopolies. It is a destructive, distortionary tax on consumers and inhibits innovation.

It's funny how absolutely confident people can be in an economic school of thought when it supports their political views.
posted by jedicus at 5:17 PM on June 13, 2013 [1 favorite]


How do you even start talking commercial ownership of DNA sequences?

You start with the technicality of adapting something from nature into a form that is not found in nature, due to a one base-makeup difference between cDNA and RNA. It's a technicality on the level of arguing a lawsuit over where a comma is placed in a contract, but one that lawyers can bill millions to argue over.
posted by Blazecock Pileon at 5:18 PM on June 13, 2013


Aww, so sad. Less money for patent lawyers.

As I've said on MeFi before (and to you, specifically), I don't give a good god damn about "money for patent lawyers." In an ideal world, the patent system would have zero application costs, zero search costs, zero litigation costs, and zero transaction costs. Everybody would instantly know if their invention was patentable, patents could be instantly and freely registered, everybody would be instantly aware of the patent, everybody would instantly know if a patent was valid and infringed, and negotiating an optimal license would be instantaneous and free. I support a property rights-based system that comes as close to that ideal as possible. In the process, yes, it would actually reduce or eliminate "money for patent lawyers."

It's also worth pointing out that, although I am a lawyer and registered to practice before the USPTO, the vast majority of my income does not come from representing clients. I am primarily an academic. I get paid to do research, write papers, edit books, that kind of thing. If you want to call me a shill or impugn my motives, take it to MeTa.
posted by jedicus at 5:22 PM on June 13, 2013


How do you even start talking commercial ownership of DNA sequences?

First, it's not "commercial ownership of DNA sequences." It's the right to exclude others from making, using, selling, offering to sell, or importing the claimed invention. There is no possessory right or ownership of the DNA sequence as such.

Second, the same way a pharma company can patent a drug molecule or a chemical company can patent a fuel additive molecule or a fabrication company can patent a metal alloy or an agricultural company can patent an insecticide molecule. They discover or invent the substance, patent it, then exclude others from making, using, selling, etc it for a limited time.

In this case, Myriad (or scientists whose work was ultimately assigned to Myriad) discovered a DNA molecule with certain useful properties. It patented the molecule in isolated, purified form. It excluded others from making, using, selling, etc that molecule in isolated, purified form. The Supreme Court ruled that Myriad's kind of molecule, unlike all other kinds of molecule, are not patentable because reasons.
posted by jedicus at 5:28 PM on June 13, 2013


I quote from my comment on another thread:
In the case of BRCA1/2, it is absurd that Myriad would be awarded a patent. The serious intellectual spade work was done by Mary-Claire King in identifying the gene. The sequencing, as I understand it, was mechanical and just a matter of time and resources. It was a race between Myriad and several other groups, including Dr. King. The group with the best resources won, but that should hardly entitle them to patent the gene Dr. King discovered.
posted by Mental Wimp at 5:39 PM on June 13, 2013 [4 favorites]


The Supreme Court ruled that Myriad's kind of molecule, unlike all other kinds of molecule, are not patentable because reasons.

To be fair, one of those reasons is that the molecule in question is an intrinsic part of the cells of every human, and this variant of that molecule strongly predicts whether that human will develop terminal cancer or not. You might not be able to argue that distinction in the dry legal language of the patent code, but it does distinguish that molecule from a fuel additive or a metal alloy.

You may be correct, this is a matter for Congress rather than the Court. However, patent law is pretty screwed up these days, and would probably require a broad overhaul of the entire code to fix this issue. Unsurprisingly, this way is faster.
posted by Existential Dread at 5:40 PM on June 13, 2013


That's fair when the Court is considering a matter of constitutional law or common law, areas where it has considerable leeway to interpret or craft the law on its own. But in this case there was a straightforward statutory scheme put in place by Congress. The Court overstepped its bounds.
The court can do whatever it wants. If Congress feels the law is being misinterpreted they can rewrite it to be more clear.
posted by delmoi at 5:47 PM on June 13, 2013


In this case, Myriad (or scientists whose work was ultimately assigned to Myriad) discovered a DNA molecule with certain useful properties. It patented the molecule in isolated, purified form. It excluded others from making, using, selling, etc that molecule in isolated, purified form. The Supreme Court ruled that Myriad's kind of molecule, unlike all other kinds of molecule, are not patentable because reasons.
"reasons" most people intuitively grok. It's repugnant to allow a company to patent genes in the human body. DNA can be thought of mainly as an information encoding system, it's chemical properties don't really change much when it's sequence changes, so it doesn't make any more sense to patent a sequence then it does to patent a specific stream of magnetic domains on a floppy disk. The actual chemical properties don't emerge until the protein is created and folded.

Anyway you can whine all you want about how this somehow makes patent law "impure," or something, but why would anyone care?
posted by delmoi at 5:57 PM on June 13, 2013


jedicus wrote: The Supreme Court ruled that Myriad's kind of molecule, unlike all other kinds of molecule, are not patentable because reasons.

I'm sympathetic to your view from a legal perspective (IANAL): I think the existing situation was bad, but it was up to Congress and other legislatures to fix it. None the less, I distinguish this case from "all other kinds of molecule" because Myriad's business wasn't "making, using, selling, etc that molecule in isolated, purified form": it was sitting on top of potential tests to identify the presence of that molecule. It's the difference between patenting a newly-recognised form of superphosphate for use in fertiliser, for instance, and claiming to patent any test that would allow miners to detect the presence of that mineral so that they could decide whether to mine it.
posted by Joe in Australia at 6:03 PM on June 13, 2013


It's repugnant to allow a company to patent genes in the human body.

Good thing none of the claims covered genes as they exist in the human body, then, since the human body does not contain isolated, purified copies of the DNA molecules that correspond to the BRCA1 or BRCA2 genes.
posted by jedicus at 8:01 PM on June 13, 2013


Totally honest question here, jedicus, and something I really don't understand. The primary manner in which Myriad has wielded its patent has been to exclude competitors from offering tests for BRCA1 and BRCA2 mutations. To perform such a test, however, it is not necessary to synthesize or even utilize in any way the DNA molecules themselves. You merely need to know the sequences of the molecules, and compare them to the sequence of the DNA in an individual. This seems in substance very different from, for instance, a drug, which must be manufactured and sold as a material in order to be utilized.

I guess what I'm trying to ask is: what's with that?
posted by mr_roboto at 8:45 PM on June 13, 2013 [1 favorite]


Ok, SCOTUS, now take this and apply it to Monsanto, so they can't drive all those small farmers out of business because some butterfly or bee cross pollinated your genetically modified shit to a field down the road.
posted by Kokopuff at 8:28 AM on June 14, 2013 [1 favorite]


Llama-Lime is spot on. The Myriad database is perhaps their most valuable asset. They've tracked a large number of alleles and variant over time and are in the best position to evaluate risk based on a person's BRCA1/2 genes.
posted by Mister_A at 9:37 AM on June 14, 2013 [1 favorite]


Good thing none of the claims covered genes as they exist in the human body, then, since the human body does not contain isolated, purified copies of the DNA molecules that correspond to the BRCA1 or BRCA2 genes.
Genes are genes. There's no reason to distinguish between various "forms", the information is the same.
posted by delmoi at 7:23 PM on June 14, 2013


As much fun as it is to see the assholes who run Myriad's business end get their comeuppance, and it is fun, this Court decision will likely have a drastic effect on the already fragile nascent western phage therapy industry. You already can't patent phages as a living thing, and now you can't patent phages as an undead genome.

As a research community, to get the trials that we need to demonstrate safety and efficacy in a Western context we need hard cash, to get that cash we need to have some plausibly profit generating thing we can show to investors when they ask how they'll get their money back, and in the absence of phage patents all we have left is a trivially duplicatable business model that requires a lot of front end investment by the first player.
posted by Blasdelb at 2:52 AM on June 17, 2013


I'd imagine folks like the CRNS and Gates Foundation recognize plausible advantages in patents not applying. Also, phage therapy can go horrendously wrong, so (a) even copyrights on documentation goes a very long way, and (b) consumers and clinics might not rush to generics.
posted by jeffburdges at 3:55 AM on June 17, 2013


Also, this is where basic research funded by the NIH and DARPA comes in — having ready alternatives to current antibiotics is well within the scope of public health and defense funding. If it is a pressing national security need, one could imagine there would be motivation by government to get things in motion, well beyond existing public funding or private-public collaborations. Being unable to patent genomes wouldn't stop the ability to monetize genome-based therapies, whose IP lies well beyond the simple bases in a sequence, all the way to drug targeting and safety.
posted by Blazecock Pileon at 11:34 PM on June 18, 2013


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