Appeals court concludes that Myriad can patent BRCA genes

By Grant Jacobs 30/07/2011 19


Friday saw the US Court of Appeals for the Federal Circuit (which we’re told by the New York Times told specialises in patent cases) rule that Myriad can patent the isolated BRCA1 and BRCA2 genes, mutations in which are diagnostic for (some) cases of breast and ovarian cancers.

The three judges didn’t rule unanimously, with the ruling based on a majority. Most sources are citing a 2:1 ruling. My reading of it is that all three judges differed in reasoning.

While the ruling has sided with patenting of the genes, the judges ruled against Myriad’s method of diagnosing the patients.

Below I’ve offered a few links for those interested in this decision.

  • New York Times (brief but good; includes brief takes on the Judge’s reasoning)
  • The CAFC ruling (PDF file; this is the actual legal ruling – while long it is for the most part quite readable; I’d encourage reading Judge Bryson’s dissenting views, some of which I have excerpted below.)
  • Genome Web News (or this article; free registration required)
  • ArsTechnica (good discussion and more depth; recommended)

My thoughts? I’m not a lawyer, and this will come down to understanding how their actions sit compared to current law in the USA (something I know nothing about), but colour me surprised. Regardless of the details, I would like to think I’m not a long in thinking that the Judges not putting forward a unified front suggests a need for clarity.

The argument that genes are chemically different through being extracted seems at first blush–to paraphrase Judge Sweet’s earlier remark–’a lawyer’s trick’. It reads to me to be a shifting of the target from sequences (which are information and–surely–what is sought) to ‘chemicals’ (the DNA) in order to try win favour in court.

While this ruling clearly touches on many different aspects in a complex way, let’s look at what Judge Bryson offers in the ruling document where he, to use the language of the ruling document, ’concurs in part and dissents in part’ (see also the New York Times piece and my Footnote):

I concur with the portions of this court’s judgment that are directed to standing, the patentability of the cDNA claims, and the patentability of the method claims. I respectfully dissent, however, from the court’s holding that Myriad’s BRCA gene claims and its claims to gene fragments are patent-eligible. In my view, those claims are not directed to patentable subject matter, and if sustained the court’s decision will likely have broad consequences, such as preempting methods for whole- genome sequencing, even though Myriad’s contribution to the field is not remotely consonant with such effects.

In its simplest form, the question in this case is whether an individual can obtain patent rights to a human gene. From a common-sense point of view, most observers would answer, ’Of course not. Patents are for inventions. A human gene is not an invention.’ The essence of Myriad’s argument in this case is to say that it has not patented a human gene, but something quite different–an isolated human gene, which differs from a native gene because the process of extracting it results in changes in its molecular structure (although not in its genetic code). We are therefore required to decide whether the process of isolating genetic material from a human DNA molecule makes the isolated genetic mate- rial a patentable invention. The court concludes that it does; I conclude that it does not. [Italics as in original.]

Judge Bryson then gives a detailed reasoning for this opinion, citing previous cases. This explanation includes the remark the New York Times cited, here in longer form:

[…] Yet some of Myriad’s challenged composition claims effectively preempt any attempt to sequence the BRCA genes, including whole-genome sequencing. In my view, those claims encompass unpatentable subject matter, and a contrary ruling is likely to have substantial adverse effects on research and treatment in this important field.

and:

In each case, merely isolating the products of nature by extracting them from their natural location and making those alterations attendant to their extraction does not give the extractor the right to patent the products themselves.

Bryson also tackles that the sequences for which patents were sought contain variable regions, a much talked-about point in these patents. (Long story short: these claims are very broad and have impact outside of the BRCA genes.)

Opinions are out everywhere, of course. ‘Rochefort’ in the ArsTechnica comments opined (shown here in full):

Wow, the appeals court got it exactly wrong, IMO. Comparing the sequences from a patient with carcinogenic sequences first discovered by Myriad according to a specific protocol is arguably something that should be patentable. The naturally occurring sequences themselves should not. The court missed a golden opportunity to straighten out some of the worst aspects of current patent law.

You’re welcome to chime in with your own thoughts in the comments.

Footnotes

This article is opinion. I am not a lawyer.

More on Judge Bryon’s dissenting opinion.

I’m struck by Judge Bryson’s words, which I take to be a summary of Myriad’s position, that:

Because the native BRCA genes are chemically bonded to other genes and histone proteins, the majority concludes that cleaving those bonds to isolate the BRCA genes turns the isolated genes into ’different materials.’

My reaction was to think that in removing the histone proteins and other other genes, the gene isolated–what the patent seeks protection for–is left substantially unaltered; it’s a removal of stuff that is not part of the gene, in effect, not a modification of the gene itself. (Small alterations needed for isolation not withstanding.) Reading down, Bryson goes on to write:

[…] In order to isolate the BRCA gene, it is necessary to break chemical bonds that hold the gene in its place in the body, but the genetic coding sequence that is the subject of each of the BRCA gene claims remains the same whether the gene is in the body or isolated. The majority, however, does not agree that the cases are analogous, and indeed appears to have adopted the following rule: Isolated atoms are not patent eligible, but isolated molecules are.

Apart from the arbitrariness of such a rule, if we are to apply the conventional nomenclature of any field to determine whether Myriad’s isolated DNA claims are ’new,’ it would seem to make more sense to look to genetics, which provides the language of the claims, than to chemistry. […]

By ‘the majority’, Bryson is referring to the other judges. (Is it just me, or couldn’t the final sentence of the first paragraph cited is that be read as quite the poke at his colleagues’ reasoning?) There’s much more, but much of it centres on the issue of the material for which patent is sought being the same as in the natural gene. For example Bryson offers:

[…] The use to which the genetic material can be put, i.e., determining its sequence in a clinical setting, is not a new use; it is only a consequence of possession. In order to sequence an isolated gene, each gene must function in the same manner in the laboratory as it does in the human body. Indeed, that identity of function in the isolated gene is the key to its value. […]

I’m curious about the ruling of patenting cDNAs, too. I’d have thought that they were ‘merely’ derived products, but then I’m not a lawyer and true novelty may not be an issue.

I’ve haven’t read the full ruling as yet (and may never find time) – it is very long. Bear this in mind, as my excerpts here are from just one portion of the ruling document.


Other articles on Code for life:

Gene patents, an amicus curiae

Myriad Genetics patent of BRCA (breast cancer) genes denied

Haemophilia – towards a cure using genetic engineering

Fainting kittens – feline myotonia congenita?

I remember because my DNA was methylated


19 Responses to “Appeals court concludes that Myriad can patent BRCA genes”

  • The case is now with the Supreme Court, who are deciding if they should take the case, and also with in an Australian federal court, who are hearing a challenge against Myraid‘s patents there. (I’m short on time to flesh out the details, I’m afraid; better this than nothing, I hope!)

  • Grant,

    I am a retired patent attorney/lawyer. I also have an MSc in chemistry and have been learning about the science and the law on the job for over 44+ years. And if I come across as patronising that is not my intention. I hope this comment adds a bit of background to the discussion.

    To start with, patents are an economic tool intended to encourage investment in innovation through commercialisation of inventions. The theoretical basis for this is discussed in a Treasury paper at the link:

    http://www.treasury.govt.nz/publications/research-policy/tprp/08-05

    “Another characteristic often attributed to knowledge is non-excludability. Non-excludability means that once a good has been created, it is impossible to prevent other people from gaining access to it (or more realistically, is extremely costly to do so).”

    ~ Page 10

    “If knowledge is not perfectly excludable, others can benefit from the knowledge other than the creator. The knowledge “spills over” to others – a positive externality. This outcome is good from a social point of view, because the benefit to society as a whole outweighs the loss of potential economic rents the creator could have made from keeping the knowledge to herself (because knowledge is non-rival). However, the creator’s ex post inability to capture enough of those rents will diminish the incentive to invest in developing knowledge in the first place.”

    ~ Page 12

    Applied to the Myriad Genetics patent tale, the knowledge is what the BRCA DNA sequence codes for. That “knowledge” was discovered by researchers (mostly from the University of Utah. Myriad Genetics is a spinoff company that was established to “capture” the “rents” by commercialising the invention. The patent was the economic device used to do so.

    A great deal of the original New York District Court Decision was devoted to why patients had been denied access to first tests and, sometimes, second opinions. It is apparent that the problem of access was because health insurers and Myriad could not agree on what they insurers would pay. This illustrates the public policy problem that a new health technology creates. How do you incentivise the application of knowledge for the public good while not putting the cost of it beyond the reach of the average citizen?

    Those who advocate the there should be no patents do not offer a commercially viable alternative. The evidence presented by the plaintiffs did not include any testing organisation prepared to carry out testing on a commercial scale. President Obama can testify that introducing a publicly funded health system in the US is not politically possible.

    So my conclusion is that gene patents are the most preferable of a lot of politically unpalatable alternatives.

    Last year the US amended its patent law with its America Invents Act (AIA). One of the compromises made during the passing of the AIA was a section that required the US Patent Office (USPTO) to conduct hearings into whether patent owners of genetic testing patents should be required to allow another entity to conduct a second test. The first day of those hearings is reported at:

    http://www.patentdocs.org/2012/02/uspto-holds-hearing-on-second-opinion-genetic-testing.html

    While some might regard this report as being as one-eyed as the Aussi Channel 9 cricket commentators, it is an informed one-eyed view.

    And today, the same blog reports on new direct to consumer genetic diagnostic tests that could do an end run around gene patents. The link is:

    http://www.patentdocs.org/2012/02/impact-of-advances-in-dna-sequencing-technology-on-genetic-diagnostic-testing.html

    And if you’re still with me, there is an Aussi patent attorney’s blog that discusses the wider aspect of the Australian case currently in progress. That link is:

    http://blog.patentology.com.au/2012/02/as-myriad-gene-trial-starts-are-cancer.html

    And the position in New Zealand?

    The government accepted the 2001 GM Royal Commission’s recommendation that there should be no ban on the patenting of isolated DNA sequences. (Disclosure of interest – I appeared before the Commission and advocated in favour of that recommendation.)

    Curiously, Clause 15 (3) of the Patents Bill (that has been waiting patiently for a 2nd reading since 30 March 2010) prohibits patents for diagnostic methods carried out on humans. I say “curiously” because a method of testing a sample (like saliva) is not excluded, but something like an MRI scan is – because it is carried out on a human.

    If I have piqued your curiosity about government patent policy you might also be interested in my guest post on SticKnz:

    http://sticknz.net/2012/02/16/do-patents-really-have-nothing-to-do-with-innovation/

    Cheers,
    Doug Calhoun
    IP Mentor

  • Grant,

    Having laid out the background and broader issues as I see them in this case I thought it might be helpful to respond to your comments from July:

    “My thoughts? I’m not a lawyer, and this will come down to understanding how their actions sit compared to current law in the USA (something I know nothing about), but colour me surprised. Regardless of the details, I would like to think I’m not alone in thinking that the Judges not putting forward a unified front suggests a need for clarity.”

    “The argument that genes are chemically different through being extracted seems at first blush—to paraphrase Judge Sweet’s earlier remark—“a lawyer’s trick”. It reads to me to be a shifting of the target from sequences (which are information and—surely—what is sought) to ‘chemicals’ (the DNA) in order to try to win favour in court.”

    Patent law tends to operate in a bit of a silo. Its experts are well versed in both law and science/technology. Judge Sweet in the district court was an 87-year-old “senior” (mostly retired but can make appearances when he chooses) judge. By his own admission he had not studied much science beyond high school. The author of the lead appeal judgement, Judge Lourie has a PhD in chemistry. It may seem that they are coming from different planets, but the reality is how they have framed the legal question and then have come to their conclusions.

    Patent law is best understood by thinking in compartments. And when you are in one compartment do not become distracted by any other. Patents are granted after an examination process that is intended to determine if the invention “claimed” is:
    1. patent eligible,
    2. novel,
    3. inventive, and
    4. useful.

    If a claim fails in any one compartment it is invalid and cannot be enforced.

    Working in our compartments:

    – The claims at the end of a patent specification define the invention and are the most critical part. Patents usually contain multiple claims. The shortest are the broadest. The intention of broad claims is to define the invention in as abstract a way as possible while not also capturing anything that has been described before. The claims get progressively narrower until they focus on the embodiment expected to be commercialised. In the Myriad patents there were claims to DNA sequences, cDNA sequences and methods of diagnosing the presence of the BRCA sequences.

    – Whether or not a claimed invention is novel in the US is done by comparing it with what had been published one year before the patent application was filed. The relevant year in this case was 1994 – although the novelty of the claims was not an issue before the court. This needs to be borne in mind when judging the novelty of a claim in 2012 – you have to look at it through a 1994 lens.

    – Determining whether or not an invention is obvious is a step beyond novelty. It is an objective test done on a subjective basis – would the invention have been obvious to a “person skilled in the art” given all that was known to that person a year before the application was filed. Again, obviousness was not an issue before the court here.

    – An invention is considered to be useful if the descriptive part of the patent document describes a use that is “substantial, specific and credible”. That test was introduced so that patents would not be granted for expressed sequence tags that did not have any substantial, specific and credible use other than a vaguely defined future use in finding “useful” sequences.

    – Finally, the issue that was decided in the Myriad case – what is patent eligible? The definition is “any new and useful process, machine, manufacture, or composition of matter”. The diagnostic method claims were considered under the heading “process”; the DNA and cDNA sequence claims under the heading “composition of matter”.

    It’s useful to remember that the courts were working in the last compartment and were meant to ignore each of the other compartments I have identified above. Many of the criticisms I have read cross these boundaries and are irrelevant to what was actually at play.

    Although largely forgotten now, Marshall McLuhan:

    http://en.wikipedia.org/wiki/Marshall_McLuhan

    was famous in his time for the observation, “The medium is the message.” That metaphor is applicable here. The medium is the sequence – the message is what it encodes for. Judges Sweet and Bryson were McLuhan men – Judges Lourie was of the opinion that what is patented is the medium – full stop – and Judge Moore was a bit in between. If the US Supreme Court (SCOTUS is the acronym favoured by US lawyers) agrees to hear the case it will decide who is right.

    When this issue last came before SCOTUS in 1980 the court held that a genetically modified organism (with an appetite for oil spills) was patent eligible. The phrase “anything under the sun made by man” was central to their reasoning. The “made by man” part of that phrase is at the guts of the issue here. That is because the court also mentioned in passing what was on the ineligible side of the line. The key words defining what is on that side of the line are “natural phenomena”. Do DNA sequences fall on the “man made” or on the ‘natural phenomena” side of the line?

    The analogy that the Myriad lawyer used to apply the man made – natural phenomenon test to was a baseball bat. In his view a baseball bat is a tree that has been felled, dried and from which all the bits that are not a baseball bat have been removed. But the molecular structure of the bat is identical to that in the tree. If you frame the question as how did the bat get from being a tree to being a bat then the conclusion is that it is man made. If you frame the question as how much does the molecular structure of the bat resemble the molecular structure of the tree then the answer is that a baseball bat is a natural phenomenon.

    If you take one of the bits of the tree discarded in making the bat, and isolate its DNA sequences that give rise to its usefulness as a baseball bat, are those sequences man made or natural phenomena. As with a baseball bat, it depends on how you frame the question.

    There is a yuck (or moral) factor at play in the Myriad case as well because the DNA sequences were isolated from a human rather than a tree. But morality is not an explicit ground of ineligibility in US patent law. One can speculate that it was an influence behind the interpretations of judges Sweet (district court) and Bryson (dissent appeal court) who chose to frame the question as how much does the molecular structure and biological activity of the claimed sequences resemble the structure and activity of those found in the human body?

    That is my take, for the take of a US attorney and former US Patent Office examiner you might want to read:

    http://www.ipwatchdog.com/2011/09/25/myriad-isolated-dna-claims/id=19397/.

    Some of the comments are enlightening but others are soapboxing opinions without much regard for others.

    Cheers,

    Doug Calhoun
    IP Mentor

  • Doug,

    (As I pointed out earlier) I’m rather busy at this time and aren’t able to put much time to the blog at the moment. I appreciate your very long efforts. As much as I’d like to I haven’t time to “defend” myself, which leaves me a little frustrated.

    In that respect, you might have more luck if you offered your thoughts to readers in general rather than just me. Others: please feel free to offer comment.

    My own concerns are based on science involved and the general area of industry (of gene-based diagnosis). That human genes are involved is not ‘of the essence’.

    (As a afterthought: while this may not help what is a complex issue, it might pay to be careful about considering the DNA molecule and it’s sequence to be conceptually the same thing.)

  • News is that the Supreme Court has thrown out the decision (that isolated DNA [DNA extracted from cells] can be patented) turning the case handing the case back to the Appeal Court for re-hearing.

    More later if/when I’ve time and if I feel so inclined. (Hey, writing articles here is voluntary!)

    This article has a little more (ignore the headline):

    http://news.smh.com.au/breaking-news-world/top-us-court-throws-out-human-gene-patents-20120327-1vv6d.html?skin=text-only

    I’d link to something more substantive, but at the moment the only one (of the few available) I’ve encountered is subscription-only.

  • I have to say, I struggle with the idea that DNA that’s simply been isolated from a cell can be patented. It’s not a novel invention, which would seem to be one of the requirements (as per Doug’s comment above). Now a test using that sequence for some purpose eg identifying the presence of a particular gene: that I can see as a subject for patent.

  • Hi Alison,

    I struggle with the idea that DNA that’s simply been isolated from a cell can be patented.

    That and a bunch of other things. It’s compounded in my eyes that what is relevant for their purposes is not that particular DNA molecule itself, but an interpretation of what biological impact (variants of) the DNA sequence would have in a particular context ; in other contexts the same DNA sequence(s) would have completely different properties. (It’s not the DNA sequence in itself that is relevant to them, but the fact that translated to a protein each variant would have a particular effect on one particular protein – that’s all interpretative stuff, observations derived from properties of the molecules ‘processed’ particular ways in a particular biological setting, not the molecule itself.)

  • The US Supreme Court deals with cases, not in isolation, but in relation to each other. The reason they have referred the Myriad Genetics case back to the CAFC (the specialist Court of Appeal of the Federal Circuit set up in 1982 to bring consistency to patent law interpretation) is because of its decision on 20 March in the case of Mayo v Prometheus.
    I have discussed that case at:

    http://sciblogs.co.nz/stick/2012/03/23/optimising-autoimmune-treatment-patent-invalid-a-%e2%80%98law-of-nature%e2%80%99-is-not-a-law-passed-by-congress/

    That decision has attracted a lot of criticism from patent lawyers, probably because the Supreme Court judges operate in a completely different paradigm from patent attorneys and CAFC judges. To give you an example of what is being said, have a look at:

    http://www.patentdocs.org/2012/03/mayo-collaborative-services-v-prometheus-laboratories-what-the-courts-decision-means.html

    “I have to say, I struggle with the idea that DNA that’s simply been isolated from a cell can be patented. It’s not a novel invention, which would seem to be one of the requirements (as per Doug’s comment above).”

    I think that statement nicely illustrates the gap in understanding of patent law. “Novel” does not mean that a particular DNA sequence does not exist, it means that the sequence and the property that it codes for has not been discovered and that discovery made available to the public (through publication or use). And at the date the original patent application for the BRCA genes was filed in 1994, the sequences and what they code for had not been published. So under patent law the claimed DNA sequences were novel.

    “Now a test using that sequence for some purpose eg identifying the presence of a particular gene: that I can see as a subject for patent.”

    The Mayo V Prometheus case was about a patent for a diagnostic test. But the Supreme Court equated a discovery, that there was a goldilocks range of metabolites from the thiopurine drug being administered, with a “natural law” and then in effect disregarded existing case law and held that a newly discovered “natural law” was not new.

    “That and a bunch of other things. It’s compounded in my eyes that what is relevant for their purposes is not that particular DNA molecule itself, but an interpretation of what biological impact (variants of) the DNA sequence would have in a particular context; in other contexts the same DNA sequence(s) would have completely different properties. (It’s not the DNA sequence in itself that is relevant to them, but the fact that translated to a protein each variant would have a particular effect on one particular protein – that’s all interpretative stuff, observations derived from properties of the molecules ‘processed’ particular ways in a particular biological setting, not the molecule itself.)”

    Patent law has struggled with the concept of whether patents should be granted for new entities, however they are used, or whether patents should be restricted to the particular use or uses initially discovered. For more than a century it has been well established law that “composition of matter” claims (as they are called) may be granted provided the description in the patent specification is of a “specific, substantial and credible” utility. Such patents are infringed by any unauthorised use of the composition of matter that is patented.

    If someone other than the original patent owner discovers that the same DNA sequence has a different property (as described above) then it is possible to get another patent for (say) a diagnostic test based on that newly discovered property. That would create a relationship between the basic and the dependent patent. For the remainder of the life of the basic patent the owner of the dependent patent would need to have a licence to commercialise the dependent invention – but the owner of the basic patent would also need to have a licence to commercialise the dependent invention. And that is where patent management starts – how do the two patent owners best cooperate with each other?

  • Doug,

    Re your first paragraph – thanks but I was aware that it follows the Mayo v Prometheus case: the short blurb I pointed to says the same as does just about everyone reporting on this 😉

    “I think that statement nicely illustrates the gap in understanding of patent law. ”

    (Just a loose thought – try a lighter tone?)

    Take this well, but I have to admit I’m not sure you know the argument that’s being presented for in this patent or not or if you are ‘just’ opposing anything that strikes a patent down as some sort of defence of patents in general.

    Myriad may well have cloned the BRCA1 gene, but that’s not an invention (whatever legal opinion is). They tried to argue that the isolated DNA fragment is novel by it’s extraction. (That’s what your previous baseball bat analogy refers to.)

    Now you refer to the ‘design’ element of novelty. I say design only as it’s a legal nonsense in my eyes to be patenting observations or properties in themselves, no matter how someone wriggles for it – patent a ‘device’ that records the observations/properties, sure, but not the observations or properties themselves.

    Myriad is no doubt trying to (separately) patent a diagnostic method (they’ve other patents, I just haven’t time to check them), but here they’re also trying to patent the DNA molecules/DNA sequences themselves.

    then it is possible to get another patent for (say) a diagnostic test based on that newly discovered property.

    Yes, but somehow you’re walked around the key problem – they’re not patenting ‘just’ “a diagnostic test” (as Alison also referred to), but also trying to protect their diagnostic test via patenting the DNA molecules or DNA sequences in themselves. That is where researcher’s concern are.

    (Note I’m distinguishing DNA [molecule] and DNA sequences – not sure you’ve got my point on that; pretty sure you haven’t as you’re still using them interchangeably to my reading – ? In this context DNA sequences are properties, not a physical thing – as I wrote earlier “It’s not the DNA sequence in itself that is relevant to them, but the fact that translated to a protein each variant would have a particular effect on one particular protein”)

  • I can see that we are never going to agree on what constitutes novelty under patent law – so I won’t waste my breath.

    We do have a different understanding of DNA and DNA sequences. I use the former expression for a continuous strand of DNA and DNA sequences for a shorter strand of DNA – known colloquially as a “gene”. In a patent specification these shorter strands are given the name “SEQ ID No, xxx”.

    In one of the 5 Myriad patents being considered by the CAFC, claim 2 claims an isolated DNA “having the nucleotide sequence set forth in SEQ ID NO:1” The full text of the patent can be downloaded from:

    http://www.google.com/patents?id=lpgnAAAAEBAJ&printsec=frontcover&dq=5,747,282&hl=en

    At the end of the description are found the endless pages of “sequence ID listings”. That is what I mean by a DNA sequence. Probably I should have used the express “nucleotide sequence” to make it clearer.

    And you might be interested in this post by an American academic who gives the Myriad “gene” claims a 50/50 chance of being valid/invalid.

    http://holmansbiotechipblog.blogspot.co.nz/2012/03/supreme-court-sends-myriad-back-to.html

    Cheers!

  • Doug, I’m not sure if it’s disagreement or difficulty getting my head around the concept of patenting DNA that’s been extracted from an individual. The DNA exists, period. The bit that’s been sequenced may or may not be peculiar to the individual from whence it came. So I struggle to see how it can be defined as an ‘invention’. The test using it – yes, sure, I can follow the logic there. But not the simple DNA sequence (which, incidentally, isn’t necessarily the same as a ‘gene'; it is in the case under discussion, is all).

  • I can see that we are never going to agree on what constitutes novelty under patent law – so I won’t waste my breath.

    I wasn’t trying to ‘define’ novelty or oppose your definition – I don’t quite know where this is coming from or what I’m supposed to say in reply! :-)

    “We do have a different understanding of DNA and DNA sequences. I use the former expression for a continuous strand of DNA and DNA sequences for a shorter strand of DNA – known colloquially as a “gene”. In a patent specification these shorter strands are given the name “SEQ ID No, xxx”.

    You’re distinguishing by length, then – ? The point I was raising was the difference between the molecule itself and properties of the molecule – and not in general, but with respect to this particular patent.

    (About distinguishing by length – DNA molecules and DNA sequences can both be very short and very long. Proteins and peptides are distinguished this way but there isn’t really any widely-accepted equivalent for DNA (outside of the very short molecules, oligmers). If you’re referring to a particular functional unit from a chromosome, it’s more usual – in biology anyway – to simply refer to the function unit, e.g. the gene sequence, the coding sequence, promoter, enhancer, first intron, etc.)

    Anyway, getting back to it (don’t over-read my words here, just try get the gist – I’m not trying to be terribly precise).

    First up – there’s a difference here in, say, creating an artificial construct (DNA molecule entirely made in a laboratory for a ‘designed’ purpose) and something that is an observation of what already existed in nature. The former is more clearly ‘created by man’ for want of a better term.

    Secondly, and perhaps a little over-intellectual of me (?!) – it’s not the DNA itself that is of interest to Myriad – it’s the outcome of translation of the coding sequence and the implications of that which are of interest. This might seem nitpicky of me, but to me it clarifies that what they’re dealing with is not a ‘thing’ but an inferred observation (confirmed in studies).

    As a thought experiment, consider the exact same DNA as (part of) a pseudo gene* – it wouldn’t be of any interest to them. Point is it’s not the DNA itself they are interested in, or even the DNA sequence, but how it is ‘interpreted’ inside the cell in it’s normal context as part of that gene.

    I see this patent as trying to find a way to patent that, but that’s an observation not an invention and I can’t see that patents should cover observations in and off themselves. (I’ve a silly sunset analogy that gives my thinking on this, but I’ll stop here!)

    Myriad’s interest is that the DNA in it’s natural setting codes for a particular protein and that particular variants of that coding sequence code for variant proteins that are associated with breast cancer. The DNA sequence is a proxy for the protein, relying on how human coding sequences are translated into proteins by the cell and impact of variants on the protein that would result. But all those things are observations, not inventions.

    Excuse my rambling 😉


    * Some thing that ‘looks like’ a gene, but isn’t used.

  • Alison and Grant,

    Alison recently authored a post asking how do you communicate with someone who has a completely different belief system from the concept you are trying to explain. That is the dilemma I am facing.

    For over a hundred years patents have been granted for “composition of matter” claims. A chemical compound is an example of such a claim. To be eligible for a patent the compound must be new, inventive and have a “use”.

    The history of acetylsalicylic acid:

    http://en.wikipedia.org/wiki/History_of_aspirin

    illustrates the point. It has been known since antiquity that salicylate rich plants such as willow can be used to produce medicines. But Bayer were able to patent aspirin because that particular derivative was new, and its utility (less irritating and therefore acceptable for most patients) was both new and not obvious. That the compound might have been among the salicylates produced naturally was not a bar to its being patented. The compound and its properties had not been published.

    Microorganisms that have been isolated from nature and cultured in an “unnatural” environment are treated as patentable compositions of matter. There is even an international treaty specifying how patented cultures are to be maintained so that anyone who wants to practice the invention after the patent expires may do so. And the TRIPS treaty (that sets minimum patent standards that member countries must meet) states expressly that countries may not exclude patents for microorganisms or microbiological processes.

    It was a logically consistent step that DNA molecules (or however you want to define them) should be patent eligible applying the same eligibility principles. The “useful” eligibility principle was redefined in the US (and this requirement is to become the law in New Zealand) as a result of the rush to the US Patent Office to claim all sorts of DNA sequences including primers whose utility was to identify other DNA molecules of indeterminate usefulness. That is why the requirement is that the utility must be specific, substantial and credible.

    The Myriad “gene patent” claims are for a DNA molecule (the one I gave the reference to) and the molecule’s utility is that it can be used in a diagnostic test for identifying women highly likely to get breast cancer. This was consistent with the interpretation of the law by the US Patent Office since the 1980 US Supreme Court Chakrabarty decision holding that the fact that a microorganism was living did not bar it from being a patentable composition of matter.

    And the approach used by Myriad’s patent attorneys was to claim as many aspects of the invention as possible. Some claims are for the DNA molecules per se, some for the diagnostic tests and some for the test kit. The patent attorney’s role is to identify how the invention is to be put into practice by the patent owner or licensee and then to claim the invention as broadly and in as many ways as possible without capturing was has already been published.

    Patents have played a significant role in the development of the biotechnology industry in the US. And for the last 30 + years the law has been settled. But the relative certainty in the minds of investors in biotech has been undermined by the new uncertainty in what is patentable. For a take on this read:

    http://holmansbiotechipblog.blogspot.co.nz/2010/04/aclu-gene-patent-decision-from.html

    My belief system is based on an understanding of how patent law has evolved over the last 40+ years. I doubt that explaining that will change you belief systems – so I suggest we leave it there. At least until after the next round in the CAFC.

    Cheers

  • Doug,

    Hey, my views aren’t based on or about belief systems! :-) I think you want to replace ‘belief system’ with ‘opinion’ – ? (BTW, do you mean this post of Alison’s?)

    Your clear explanations are useful to readers. (I hope!) I agree with the summary you’ve just offered – it’s been my understanding too. (If you’re intending this a countering or opposing what I’m writing or whatever, I’m not disagreeing with that.)

    You mention that Myriad have claims “for the DNA molecules per se, some for the diagnostic tests and some for the test kit” (as I was already aware). My concern, like others’, is with the first, i.e. “for the DNA molecules per se, […]” as I hope is already clear.

    Clearly opinion is divided on this particular patent – it’s why it’s in the courts in the first place. I have to admit I’m personally a bit disappointed you seem not to want to engage with others’ opinions but it’s your choice, it’s a free world and all.

    Nevertheless a thought – you wrote “Bayer were able to patent aspirin because that particular derivative was new” – by contrast cloning of a gene is usually to make a copy that has, as much as possible, the same properties as the natural gene.

  • Doug, like Grant I think it’s more a case of ‘understandings’ rather than belief systems. The reason Bayer could patent aspirin was that they were using a compound synthesised de novo in the lab. A DNA sequence isolated from an individual is not a de novo invention, but a test based on that molecule is. I suspect our cross-communication is probably due to the fact that you’ve got the patent law background & I’m a biologist :-) ie we are seeing the world differently. That shouldn’t stop us having a robust discussion around those differences, though, as it may help us come to a common understanding.

  • Nice to get some affirmative feedback about my posts and comments. Thank you.

    Aspirin was probably a bad example. (But given the timing of the patent I wonder if Einstein was the examiner when the Swiss equivalent patent application went through.)

    In the early 1980s I was the patent attorney for the Development Finance Corporation, a crown corporation, (they were a client of my firm) who ran the “applied technology programme”. That programme was intended to commercialise inventions may by research funded by the government. Roy Daniel and Hugh Morgan and a couple of their students from the University of Waikato, had collected samples from a hot pool in Rotorua and isolated a thermophilic micro-organism that metabolised both a protease and an asparaginase with industrial utilities. They were granted patents in a number of countries including both New Zealand and the US.

    The Google link to the US patent 4,442,214 for the microorganism is:

    http://www.google.com/patents?id=-y4UAAAAEBAJ&pg=PA8&dq=thermus+aquaticus+t-351&hl=en#v=onepage&q=thermus%20aquaticus%20t-351&f=false

    The Google link to the US patent 4,473,646 for the asparaginase is:

    http://www.google.com/patents?id=63QyAAAAEBAJ&pg=PA4&dq=thermus+aquaticus+t-351&hl=en#v=onepage&q=thermus%20aquaticus%20t-351&f=false

    The Google link to the US patent 4,480,036 for the protease is:

    http://www.google.com/patents?id=CV08AAAAEBAJ&pg=PA10&dq=thermus+aquaticus+t-351&hl=en#v=onepage&q=thermus%20aquaticus%20t-351&f=false

    The microorganism and the two enzymes that were patented were identical to what was found in the hot pool. That is the basis for my statement that pre-existence of something is, of itself, not a bar to novelty. It was a development of the patent law of the 1980s to extend the principle to DNA molecules. That is why 30 years on those of us on the dark side are wondering what the all fuss is about.

    However, as I said yesterday, I think it is time to adjourn the debate at least until the courts in both Australia and the US have spoken again.

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