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Q&A: What is the Impact of Myriad Patent Rulings on IP Landscape for Protein Biomarker-Based Tests?


By Adam Bonislawski

Name: Geoff Karny
Position: Principal, Law Office of Geoffrey M. Karny
Background: Vice President, Intellectual Property, Gene Logic; Senior Patent Counsel, Novartis; Senior Intellectual Property Counsel, Genetic Therapy; Attorney, Office of Technology Assessment, United States Congress

Last month, the Court of Appeals for the Federal Circuit ruled on a number of Myriad Genetics' patents, overturning a previous district court ruling that had invalidated seven of the company's BRCA gene patents related to its BRACAnalysis test for breast and ovarian cancer risk (see PM sister publication PGx Reporter 08/03/2011).

The decision ruled that isolated gene sequences such as those used by Myriad in BRACAnalysis are not products of nature and are therefore patentable. However, the court ruled that a number of Myriad's patents related to the tests that involve "comparing" or "analyzing" DNA sequences are invalid because they involve "no transformative steps and cover only patent-ineligible abstract, mental steps."

While the decision focused only on Myriad's DNA-based tests, legal experts have suggested that it could impact the personalized medicine business more broadly.

Geoff Karny is an attorney specializing in life sciences patent law. He managed the patent departments of biotech firms Gene Logic and Genetic Therapy and was senior patent council for Novartis Pharmaceuticals. This week ProteoMonitor spoke to him about the potential impact of the Myriad case on protein biomarker work and IP issues surrounding protein biomarker tests more generally.

Below is an edited version of the interview, which reflects Karny's personal views and not the positions of his clients.

How relevant is the Myriad ruling handed down earlier this month to the protein biomarker space?

It's very relevant to protein biomarker tests. In theory, if one could challenge patents on isolated DNA, one could challenge patents on isolated proteins or novel proteins, [though] I don't think those challenges should prevail, just as they did not prevail in the Myriad case.

Where I think it gets more troublesome is in the methodology claims [portion of the ruling] where, coming back again to protein biomarkers, take the very simple case where protein X is associated with disease Y. The court said, in theory, that those kinds of claims are patentable, but depending on how the claim is written there could be problems. If you have steps like analyzing and comparing — and if those are essentially all that you have in the claim — apparently you're patenting an abstract idea, and you can't patent an abstract idea.

What you're going to see [in response] is claims written to include non-mental steps and non-abstract steps. One simple way to do this is simply to write the claim in terms of: "Obtain a sample. Assay the sample. Determine the result of the assay and compare it to some predetermined result and therefore conclude the person is likely to get the disease or not." One problem with that, though, is, as a patent lawyer you want to write the claims as broad as possible, because once you start adding a lot of steps that are frankly unnecessary, you're actually narrowing the claim.

The court ruled that isolated genes were patentable because isolated DNA molecules as claimed in Myriad's patents "do not exist in nature." Would that line of thinking apply in the same way to protein biomarkers?

I think it’s the same analysis, the same legal analysis. People might be able to argue a little bit against it by saying, "Well, OK, the DNA is in the chromosome, and now it's been isolated, and the protein is just floating around in there." But again, what you have to stop and step back and look at is [that] when you're talking about isolation [of a gene or protein], you're talking about a major change. It is transformative.

Let's take my favorite example of the Factor VIII gene [which codes for a glycoprotein procofactor used to treat hemophiliacs]. I may be a hemophiliac, and you may have the correctly occurring Factor VIII gene in your body. It doesn't do me any good there until I isolate that gene and put it in a lab and make Factor VIII that I can inject in myself. The normal Factor VIII in your body is useless to me as a hemophiliac. It's the isolation. But for the isolated protein, it doesn't do me any good. If I found it; I isolated it; it wasn't obvious, why shouldn't that be patentable? I would argue that [the Myriad] ruling clearly applies to proteins. Could some court do something different? Yes. Do I think the legal principal for genes is sound and should be applied to proteins? Yes.

What other cases might weigh on protein biomarker work?

Prometheus v. Mayo [in which a federal appeals court upheld patents held by Prometheus Laboratories for a method of administering a drug, measuring the drug's level in a patient, and then adjusting the dosage] is similar. It's not a protein biomarker. It's a drug. You administer the drug. You determine the level of the drug. And if it's at a certain level or less, then you make determination of the amount you need to subsequently administer to the subject. [It's] conceptually very applicable to protein biomarkers.

Another potential issue facing protein biomarker tests is that of competing tests aimed at the same indication that use overlapping panels of proteins. Because of the low number of multi-protein tests that have been commercialized so far, this hasn't really been a problem, but could it become an issue?

It depends very much on the particular patents and on the claims. How do you claim a collection of biomarkers? Generally, if these are known proteins, you're not going to patent the proteins, so it's generally the methodology — the method of predicting the likelihood of getting ovarian cancer comprising finding the following five biomarkers or whatever.

[A company] may be looking at five and [another company] may be looking at five different [proteins], or they maybe overlapping in three, it depends on the claims. I've written claims in terms of one or more, two or more, three or more [biomarkers], and so if there's an issue claim that says one or more of the following [proteins] and the other guys overlap by one, then there's going to be a problem.

The fundamental issue in this area for the patent lawyers is how do you claim a collection and protect your client. If your client has made an advance, if your client says, "I've found five biomarkers correlated with a disease," well what happens? Do you need all five? What happens if you claim five and somebody [else] only uses four? So, the biomarker area, whether it's proteins or genes, is very challenging in terms of patent protection because, again, how do you claim a collection and cover the proper scope of the invention? And from the other side, of course, the competitors are going to look at, "Is this claim valid or not? What was the technological contribution? Is the claim limited to that or does it go beyond that?"

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Is this more of a challenge for genetic or protein-based tests?

I guess it is a little bit [more of a problem with proteins] in the sense that somebody goes out and finds a gene, and they're the first to find it and show that it's new, useful, and non-obvious, they're entitled to the patent if it's isolated, based on not only the Myriad decision but on 30 years of court decisions. And maybe that's easier — company X has this gene and company Y has that gene. Whereas, when you're working with protein biomarkers, you are working with a collection [of proteins], and you are more likely to have overlap, and it's just going to depend on how that's claimed.

I've been told that some of the early patents for protein biomarker-based diagnostics were written very broadly to include a number of proteins the companies thought could be useful but weren't certain would be useful, and that it's unclear how well these patents will hold up if they're challenged down the road.

I think I would agree on that. You get into speculative areas, and it's problematic. In certain respects, in the patent area you can guess as long as you guess right. You don't have to necessarily reduce an invention to practice. The problem is that maybe some of this stuff is not going to hold up. Then the patents can get challenged for lack of enablement. If they simply don't work, then it lacks the requirement for utility.

So there are two issues. One is, do we have a number of, let's say, improperly granted or overly broad patents out there that are impeding the development of a particular technology? That's a problem, and that could be the case, but the system is self-correcting. This happens a lot. It's not going to be limited to protein biomarkers. This happens throughout technology, and the system is self-correcting because the patents get litigated, and then there's a very rigorous assessment of whether or not the claims meet the standards.

I can see that happening. I can see competing tests where there's some overlap, and then the question depends very much on what the patents are and what they say. You have to look at the claim language. What exactly does it say? What is covered? What is not covered? How is terminology defined in the specification? It's a very, very detailed and fact-specific analysis.

So far, most of these patent disputes seem to be playing out around gene-based tests. Do you expect there to be a rise in similar litigation regarding protein biomarkers as more protein-biomarker-based tests come to market?

Yes, I would expect it. I would think so.

Have topics you'd like to see covered in ProteoMonitor? Contact the editor at abonislawski [at] genomeweb [.] com.

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