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« Patents and the State of the Union -- A Response | Main | ACI Life Sciences Collaborative Agreements and Acquisitions Conference »

January 30, 2014



I do wish Sequenom well in its effort to convince the Federal Circuit to render order out of this utter chaos that patent-eligibility under 35 USC 101 become. As I've stated before, the primarily responsibility for this mess lies at the foot of Our Judicial Mount Olympus who have so mucked up this area of patent law that no one (including them) knows how to apply this patent-eligibility precedent other than subjectively, irrationally, illogically and with no consistency.

Very nice article I appreciate the thoroughness. I think this is a very tricky arena. I am not an attorney but a scientist. I think '540 is a very weak patent from a methods point of view (and not from a Myriad point of view). First let's examine an empirical argument that, I believe, has not much legal merit but is still a valid argument from a rational scientific viewpoint. This patent is old from the point of view of DNA sequencing technology. If there really was a workable method in the patent based upon PCR (which was already an old technique at the time), how come it took so long for Sequenom and Lo to come up with a method that actually works? Instead they spent a lot of time on another method that fell outside the domain of '540 the so-called PLAC RNA method. This method doesn't work even though Sequenom and Dr. Lo said it did and it led to the fraud that destroyed Sequenom's market capitalization in 2009. If there really was a workable "method" in '540 then a) MathernT21 would have appeared 10 years ago and b) they wouldn't have needed the paternal DNA limitation. If I decide to patent consciousness on a chip, and 15 years later someone actually figures out how to do it can I then claim "Hey, I invented that". Unfortunately, the patent portfolio of the US is littered with patents like this - many of which end up getting enforced anyway.

In my opinion, Ilston's claim construction of the use of the word paternal, was thrown aside erroneously. The reason for the need to use paternal DNA was that, at the time, massively parallel DNA sequencing did not exist. Therefore, there was a real question as to how one would count the excess fetal DNA that would lead to a diagnosis of aneuploidy in the presence of the huge maternal background. This was a vexing scientific question and it is pretty obvious to any scientist with experience in this domaIn (though apparently not to judges) that '540 does not provide a method for how to do this. Therefore, in the original patent examination they were required to use the paternal limitation in claim 1 (and that is a limitation inherited in every subsequent claim in that patent) as that was the only means, at the time, that could readily distinguish between the maternal and fetal DNA. Fast forward a few years and Fan and Quake from Stanford put out a patent in '017 or "Non-invasive Fetal Genetic Screening by Digital Analysis" in which one of the claims is to use massively parallel sequencing to determine aneuploidies. Once one sees this it is now obvious how to go about counting the DNA to anyone skilled in the field. It is also obvious that one doesn't need the paternal limitation (although it is true that by counting both the fetal and maternal DNA that some of the DNA came from the father - DUH). Frankly, from an inventive scientific viewpoint the only real novelty in '540 is the idea of using cell free fetal DNA in maternal plasma. A great idea to be sure, but probably limited by Myriad. One still has to figure out how to implement that idea, and that is where '540 falls on its face. There is no way, at the time the patent was written, that one could use the very simple PCR methods therein to actually perform anueploidy analysis and do the very exacting counting that was required to have a statistically usable test. Every scientist I have talked to about this agrees, although it wouldn't be hard to find expert witnesses or amicae briefs that would suggest otherwise.

On another, more general, point you raised e,g, "But in view of the fact that anything short of reversing the District Court's decision below can be expected to reduce the likelihood that personalized medicine will become commercially viable in our lifetimes, it is important that they prevail." I would disagree. The large numbers of companies that entered into the NIPT space that is currently the subject of this article would suggest otherwise. It is clear that there is a lot of commercial value that will be pursued even with the current state of the patent environment. And I don't see any overly strong impediments to strong competition in this space of personalized medicine - especially given how much of the ip came from the Human Genome Project and how many non-profits (e.g. the J. Craig Venter Foundation) are engaged in this pursuit. But again, I am not a lawyer and I may have a naive viewpoint.

By the way, in the interests of full disclosure, I am long Sequenom stock, but I just wish they would stop spending massive amounts of money defending what I believe is a very weak patent.

Dear Fred:

Interesting perspective. From the legal point of view, I would have no issue invalidating the '540 patent on any of the grounds you raise, which is the traditional way to do it: the patent claims are not novel, are obvious, are inoperable, are not enabled, etc. I have no desire to preserve patents that objectively fail the many tests for patentability.

The problem here is that the judge invalidated the claims categorically - "these types of claims (no matter how novel, useful and non-obvious) cannot be patented." And she did so based on her subjective view that these claims (and their ilk) should not be patented.

As for the prediction, we are in an interesting time - lots of DNA information from the HGP but less (not zero) information about how to predict diseases or adverse drug reactions based on genotypes. Yes, there are lots of people in the space but because of the complexity of the task disclosure will become more and more of a problem - without a way to recompense the costs of not discovery but commercialization there will be incentives not to disclose. This may or may not come to pass, but we know the world with patents - more than a million women having been tested for the BRCA gene mutations, and those methods become freely available in about 2 years. In a future without patents, it is much harder to predict what will happen.

Thanks for the comment.

Dr. Noonan,

I believe that Abraham Lincoln had something to say about that.

(as would Congressmen Bayh and Dole)

Perhaps the next President will give more than one liners and empty platitudes to innovation.

"But in view of the fact that anything short of reversing the District Court's decision below can be expected to reduce the likelihood that personalized medicine will become commercially viable in our lifetimes, it is important that they prevail."

You know Kev, if it is that important to the commercial viability of such then congress can always be lobbied for an exception to the exceptions. It isn't like they're immune to evidence of failure in the marketplace because of no patent protection if that should occur here shortly.

Though frankly I'm a bit wary of your alleged foreseeing the sky falling in this area.

Kevin: "in view of the fact that anything short of reversing the District Court's decision below can be expected to reduce the likelihood that personalized medicine will become commercially viable in our lifetimes, it is important that they prevail."

I don't think even Kevin believes this. But maybe he believes it's a good sound bite in defense of his clients' interests so he repeats something similarly ominous every time a case turns up that might affect those interests.

The fact is that various forms of "personalized medicine" have been with us for a long, long time and as more (unpatentable) information is made available to doctors, more "personalized" treatment can be provided to patients. Of course, there's also the issue of what insurance companies, who currently function as middle-men/parasites in our healthcare system, will do with the information.

"From the legal point of view, I would have no issue invalidating the '540 patent on any of the grounds you raise, which is the traditional way to do it: the patent claims are not novel, are obvious, are inoperable, are not enabled, etc."

Then why do you insist on burying such an admission in the comments? As an "expert" on this subject, your views would be welcomed by the public -- you know, vast majority of non-patent owning people whose well-being you are allegedly so concerned about. If you this patent is obvious, non-enabled junk then you should be spreading the news because, if that's the case, then everyone will be paying more for whatever test falls within the scope of the junk claims than they otherwise would be.

"In view of the exquisitely subjective nature of the standards for patent eligibility enunciated by the Supreme Court (most recently in Mayo v. Prometheus)"

There was nothing "subjective" about the decision to declare the claims at issue in Prometheus ineligible. You do understand that now, don't you, Kevin?

Mayo was using its claims to prevent practitioners of the prior art from thinking about an inelgible fact. You can't use patents to protect facts (or any other ineligible subject matter). There's nothing "subjective" about that, unless you believe that one should be able to patent facts. And if you believe that, you should just come right out and say it rather than pretending you are making some "principled" argument about the reasoning in Prometheus.

A friendly reminder about what you wrote, Kevin, last August in a comment thread about this case:

"I agree that the patent eligibility of the claim will depend on whether detecting fetal DNA in maternal blood was "new" when the patent application was filed."

Subsequent interesting discussion here last November after the Judge Illston's decision:


That's fetal DNA detection in maternal blood, by one of the inventors, published in Lancet in 1989, 7 years before the patent at issue here was filed. This paper is mentioned in the background section of specification. Also this publication from the inventors in 1993:

http://link.springer.com/article/10.1007/BF00217445 "Prenatal sex determination from maternal peripheral blood using the polymerase chain reaction"

At the time of publication of those papers, it was already known that PCR would and could detect minute amounts of DNA. I haven't read these two papers to read all the details but at least one Ph.D. student wrote the following: "Lo et al. (1989) have demonstrated by PCR the existence of fetal cell-free DNA in maternal plasma ..." Perhaps that student misread the paper ...

Regardless, it boggles the mind that nobody in the field suggested checking whether some of that fetal DNA was cell-free around the time that those earlier papers were published. I would expect such an analysis would show up as a control in those papers circa 1989-1993. Very odd.

Thank you for this informative post.
I am wondering to what extent the patentability of Sequenom's method bears an analogy to extractive mining, an area where I have greater expertise.
There are some common leaching methods to extract minerals and metals, such as gold, from mine tailings. Each method involves several engineering steps, which are in themselves complex and can be discussed in isolation, but are combined in well known ways for the process.
Would the application of one such common method specifically to extract a different mineral from a different waste stream merit a patent - if nobody had previously thought to apply the method to extract that different mineral or metal?
I don't know if there is a general answer to my question. However I would much appreciate your thoughts on the relevance of the analogy to the Sequenom case, if you have time.
Thank you

Dear JN:

Thanks for supporting my position - there were ample ways to invalidate this claim under 102 instead of 101, and I think that would be the better way.

As for Prometheus, how they were trying to enforce the claim isn't the point - if you can find a practical standard that can be applied objectively (and not in the "we know it when we see it" sense) from Justice Breyer's decision, please let me know. As I see it, the lack of objective standard leads to a decision like the one in Ariosa.

As for the future of personalized medicine, we shall see - I have some faith in my fellow practitioners' ability to adapt to whatever nonsense the courts come up with.

The comments to this entry are closed.

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