GENET archive


[genet-news] PATENTS & REGULATION: U.S. government says genes should not be eligible for patents

                                  PART 1

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SOURCE:  The New York Times, USA

AUTHOR:  Andrew Pollak


DATE:    29.10.2010

SUMMARY: "Reversing a longstanding policy, the federal government said on Friday that human and other genes should not be eligible for patents because they are part of nature. The new position could have a huge impact on medicine and on the biotechnology industry. The new position was declared in a friend-of-the-court brief filed by the Department of Justice late Friday in a case involving two human genes linked to breast and ovarian cancer."

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Reversing a longstanding policy, the federal government said on Friday that human and other genes should not be eligible for patents because they are part of nature. The new position could have a huge impact on medicine and on the biotechnology industry.

The new position was declared in a friend-of-the-court brief filed by the Department of Justice late Friday in a case involving two human genes linked to breast and ovarian cancer.

?We acknowledge that this conclusion is contrary to the longstanding practice of the Patent and Trademark Office, as well as the practice of the National Institutes of Health and other government agencies that have in the past sought and obtained patents for isolated genomic DNA,? the brief said.

It is not clear if the position in the legal brief, which appears to have been the result of discussions among various government agencies, will be put into effect by the Patent Office.

If it were, it is likely to draw protests from some biotechnology companies that say such patents are vital to the development of diagnostic tests, drugs and the emerging field of personalized medicine, in which drugs are tailored for individual patients based on their genes.

?It?s major when the United States, in a filing, reverses decades of policies on an issue that everyone has been focused on for so long,? said Edward Reines, a patent attorney who represents biotechnology companies.

The issue of gene patents has long been a controversial and emotional one. Opponents say that genes are products of nature, not inventions, and should be the common heritage of mankind. They say that locking up basic genetic information in patents actually impedes medical progress. Proponents say genes isolated from the body are chemicals that are different from those found in the body and therefore are eligible for patents.

The Patent and Trademark Office has sided with the proponents and has issued thousands of patents on genes of various organisms, including on an estimated 20 percent of human genes.

But in its brief, the government said it now believed that the mere isolation of a gene, without further alteration or manipulation, does not change its nature.

?The chemical structure of native human genes is a product of nature, and it is no less a product of nature when that structure is ?isolated? from its natural environment than are cotton fibers that have been separated from cotton seeds or coal that has been extracted from the earth,? the brief said.

However, the government suggested such a change would have limited impact on the biotechnology industry because man-made manipulations of DNA, like methods to create genetically modified crops or gene therapies, could still be patented. Dr. James P. Evans, a professor of genetics and medicine at the University of North Carolina, who headed a government advisory task force on gene patents, called the government?s brief ?a bit of a landmark, kind of a line in the sand.?

He said that although gene patents had been issued for decades, the patentability of genes had never been examined in court.

That changed when the American Civil Liberties Union and the Public Patent Foundation organized various individuals, medical researchers and societies to file a lawsuit challenging patents held by Myriad Genetics and the University of Utah Research Foundation. The patents cover two genes, BRCA1 and BRCA2, and the over $3,000 analysis Myriad performs on the genes to see if women carry mutations that predispose them to breast and ovarian cancers.

In a surprise ruling in March, Judge Robert W. Sweet of the United States District Court in Manhattan ruled the patents invalid. He said that genes were important for the information they convey, and in that sense, an isolated gene was not really different from a gene in the body. The government said that that ruling prompted it to re-evaluate its policy.

Myriad and the University of Utah have appealed.

Saying that the questions in the case were ?of great importance to the national economy, to medical science and to the public health,? the Justice Department filed an amicus brief that sided with neither party. While the government took the plaintiffs? side on the issue of isolated DNA, it sided with Myriad on patentability of manipulated DNA.

Myriad and the plaintiffs did not comment on the government?s brief by deadline for this article.

Mr. Reines, the attorney, who is with the firm of Weil Gotshal & Manges and is not involved in the main part of the Myriad case, said he thought the Patent Office opposed the new position but was overruled by other agencies. A hint is that no lawyer from the Patent Office was listed on the brief.

                                  PART 2

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SOURCE:  Singularity Hub, USA

AUTHOR:  Drew Halley


DATE:    11.08.2010

SUMMARY: "Here?s a disconcerting thought: for the past thirty years, genes have been patentable. And we?re not just talking genetically modified corn ? your genes, pretty much as they exist in your body, can and have been patented. The US government reports over three million gene patent applications have been filed so far; over 40,000 patents are held on sections of the human genome, covering roughly 20% of our genes."

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The Who Owns You film is being directed by Taylor Roesch, and co-produced by Roesch and Koepsell. They are wrapping up filming this summer, and hope to have a final cut ready for festival submissions in the fall. Special thanks to Dr. Koepsell for taking time to speak with us.

Gene patenting is coming under ethical and legal scrutiny

Here?s a disconcerting thought: for the past thirty years, genes have been patentable. And we?re not just talking genetically modified corn ? your genes, pretty much as they exist in your body, can and have been patented. The US government reports over three million gene patent applications have been filed so far; over 40,000 patents are held on sections of the human genome, covering roughly 20% of our genes.

Upset? You?re not alone. Critics argue that the patents stifle potential research into disease, keep new treatments off the market, and bring in serious money to Big Pharma ? all by exercising property claims that shouldn?t exist. After all, genes aren?t inventions, which are patentable ? they?re discoveries, which aren?t. As Luigi Palombi noted recently at the Open Science Summit, ?You can?t patent Mount Everest; why can you patent a gene?? Here, we review the history of genetic law, the current state of affairs, and interview David Koepsell, an attorney and author of a recent book on gene patenting, Who Owns You? The Corporate Gold Rush To Patent Your Genes.

The ACLU has been waging a legal war against gene patenting, and some forward progress has been made. A few months back, a major (and unexpected) victory against gene patenting came when a district judge struck down patent claims by Myriad Genetics. Back in 1998, Myriad patented several genes of the BRCA family; mutations along these genes increase susceptibility to breast and ovarian cancer. The patents gave Myriad proprietary rights over diagnostic tests for the mutations ? tests they sold for over $3,000 each.

On March 29, 2010, District Judge Robert W. Sweet invalidated seven of the BRCA patents owned by Myriad. The decision shocked supporters and critics alike, and Myriad has appealed the decision. What remains to be seen is whether it will reach and survive a federal court, and thereby become precedent to strike down further gene patents owned by biotech companies.

So how are genes patentable in the first place? Parts of your body have actually been patented for over a century. Adrenalin was patented in 1906; insulin was patented in 1923. The argument for chemical patents was basically that isolated and purified forms of the naturally occurring molecules are more medically valuable than the forms floating around in your bloodstream. A comparable logic is what allows the FDA to outlaw DMT ? a chemical also produced within your body, but which acts as a powerful hallucinogenic in its concentrated form.

But gene patents got their big start in 1980 in the case of Diamond v. Chakrabarty. A GE engineer developed a bacterium capable of breaking down crude oil, and filed a patent for it. After a series of rulings and appeals, the case landed in the Supreme Court. On June 16, 1980, the court ruled in GE?s favor, and the first living organism was patented in the United States. The key distinction in the Diamond case was that the bacterium was man-made, and therefore constituted an invention.

Human gene patenting works on the logic that if a patent applicant has ?isolated and purified? genetic material, it constitutes an invention on their part ? even if the strand is identical to the DNA sequence found in nature. Proponents of gene patenting (i.e. generally, the companies or their patent lawyers) argue that patent protection is essential to retaining strong investment in genetic research, which speeds up progress in the field. It?s true that patents are important to the biomedical industry?s ability to attract capital ? Myriad stock took a nose dive after the Supreme Count shot down their BRCA patents. But the claim that a world without gene patents would stifle genetic research (or even make it unprofitable) seems overstated at best, and disingenuous at worst.

For years, the logic of purification and isolation has held up legally as a justification for human gene patenting ? that?s what made the Myriad case such a landmark decision. We recently interviewed Dr. David Koepsell, both a J.D. and a Ph.D. in Philosophy, about the fallout from Myriad, the ethics of gene patenting, and intellectual property. Koepsell is an author and educator whose work centers on how ethics and public policy are shaped in emerging science and technology. His book Who Owns You? is currently being adapted into a documentary film, including interviews with experts like James Watson and Tim Hubbard. Check out the preview:

Q: After the Myriad case, a large number of commentators reported being surprised at the outcome. I saw headlines with adjectives like ?jaw-dropping? and ?shocking?. Can you give us an idea of why the outcome was so unexpected?

It was surprising to people like me because we didn?t expect the court to do the right thing. The courts have been making the wrong decision on isolated and purified genes now for some time ? for decades. Ever since the case in which the Supreme Court said purified and isolated adrenalin was patentable. So the Patent and Trademark Office (PTO) has been granting patents pretty routinely to isolated and purified chemical compounds, as well as isolated and ?purified? (I use that term loosely) genetic sequences. So it was really quite surprising, and for me heartening, that the court in this case (a district court) saw through this notion of isolation and purification as somehow warranting a product claim.

For a lot of the patent community, it was jaw-dropping because suddenly somebody punctured the balloon, and basically said the party?s over if that becomes the law of the land. Of course, as we know, the PTO is not going to enforce this district court?s decision, and they are under no obligation to. It?ll take a long time before it makes its way up to the Supreme Court and is upheld, and there?s a fair amount of question whether that will happen.

Dr. David Koepsell, author of Who Owns You?

Q: What do you expect to come of the Myriad results? Will that case set a precedent for dismantling other genetic patents?

I?ve already seen a lot of Intellectual Property (IP) professionals recommending workarounds. Instead of trying to patent the isolated genes, they?re suggesting more utility claims or process claims, which is good. One of the problems with the precedent in gene patenting is that you?ve had what I call a gold rush. It?s like a land rush: you basically squat on a territory and wait for someone to come along to make it worthwhile for you to sell it. That?s not really pro-innovative. And new drugs haven?t been developed for the most part as a result of these claims.

Recently, somebody developed a very promising vaccine that is going to go into human trials for breast cancer. That vaccine was developed with public funds, not with a patent on the breast cancer genes but despite it. Meanwhile, Myriad is making 300 million in profits per year off their breast cancer gene patent and they haven?t used it. The amount of money that went into this vaccine was only 1.5 million. Myriad could have taken a very small portion of their exorbitant profits and put it into research to develop a vaccine. But there?s no incentive in this land claim on the gene for them to do so. They can make much more money simply reaping this monopolistic pricing over the diagnostic test without having to do any beneficial research into making new drugs.

I think this case will hopefully compel a lot more investigation into real cures and treatments, and less of this sort of squatting. Even if it doesn?t go on to become precedent, if it isn?t upheld later. I think it is sort of a warning shot across the bow. You?re better off trying to come up with something useful and make new products as opposed to simply squatting on these sequences.

Q: It also seems like it?s brought genetic patenting into the public consciousness.

It has, yes. Most people I talk to still don?t understand it, and don?t know what?s going on. But there is certainly a lot more awareness, especially in the breast cancer community, which is a significant community, about what patents are on these genes and how they?re affecting research and the cost of their treatments.

Q: How do you feel about patenting synthetic life forms ? wholly man-made genomes?

I wrote in my book [Who Owns You?] that that?s a legitimate thing to do. The point of patents is that if you create something new that doesn?t otherwise exist in nature, you?ve invented something. The patent system is set up to reward that sort of thing. On the other hand, if you grant those patents too far upstream ? and this is a practical consideration ? you really can impede innovation. So while I think it?s legally legitimate to get patents on synthetic genes, genes that don?t otherwise exist, I think it?s really imperative to have some sort of practical limit beyond which we don?t patent. You?re not going to want somebody to have a patent on a codon. That?s too far upstream, obviously. So how far downstream is it legitimate?

I think the industry has to figure out where it makes sense for them to draw a line. I think groups like the Biobricks Foundation, who are trying to build these standard parts, are doing the right thing. A repository of standard parts that is in the public domain makes sense from an engineering standpoint. If these tiny little parts can be put together in new ways that are inventive, and you get a patent on that final product, you leave open the possibility for innovators to play around with those parts. I think Biobricks is an excellent example of how the industry is heading off the problem with patenting that can develop if patent attorneys have their way.

Q: Defendants of genetic patents argue that without strong patent protection, capital investment will dry up and research progress will slow. I imagine you disagree ? why?

I completely disagree. Especially in pharmaceuticals (and that?s what they?re talking about) the patent system is encouraging people to shoot for blockbusters. Those are the patents that are going to make you a lot of money, and increase your share price. So these blockbuster drugs are costing hundreds of millions of dollars, and most of that is not in R&D. Most of it comes in the marketing. There?s no evidence that they couldn?t develop useful, marketable drugs if they concentrated less on blockbusters, and more on drugs that fill a useful niche in the medical market. Instead, because the value of IP portfolios to corporations, we?re encouraging a very narrow search for baldness cures, ED drugs, etc. ? drugs that are going to be marketable to a wide swath of the public instead of people who are suffering from a certain medical condition.

And in fact, history shows this is true. Aspirin is a very profitable drug, even though it went off patent long ago. There are millions of drugs whose the patents have expired that are still profitable, that have well made up for the investment in their R&D. There were actually periods of time in places like Europe, up until the mid-70?s, where you couldn?t get a patent on a chemical product itself. The pharmaceutical companies were making money, magically enough, by making drugs that served a market niche that people bought. The market demand drove the price instead of a monopolistic price structure. The evidence doesn?t bear out that contention [that gene patents are necessary to development] and I trust the free market to be able to come up with solutions.

Q: Where do you see genetic research going over the next few decades?

I personally think synthetic biology is going to be the next big field. Nanotech seems interesting, but there?s so many technical hurdles involved that I think everybody?s realizing you?ve got to use some of nature?s own innovative store of nanotechnology, and use them to do the sort of things we wanted to do with nanotech. Cataloguing the storehouse of usable biological parts and functions is going to be a huge scientific venture for the next ten years or so. Moving that into some innovative new products is where a lot of investment is going to be put, and where we?re going to see some of the promises we held in store for nanotechnology at one time.

                                  PART 3

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SOURCE:  Patentdocs, USA

AUTHOR:  Kevin E. Noonan


DATE:    28.10.2010

SUMMARY: "Myriad Genetics filed its appellant?s brief in Association of Molecular Pathology v. U.S. Patent and Trademark Office last Friday [...] This is the first step in an appeal that awaits a large number of anticipated amicus briefs and appellees? briefs from plaintiffs (supported by the American Civil Liberties Union and the Public Patent Foundation)."

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Myriad Genetics filed its appellant?s brief in Association of Molecular Pathology v. U.S. Patent and Trademark Office last Friday, joined by the Directors of the University of Utah Research Foundation (Lorris Betz, Roger Boyer, Jack Brittain, Arnold B. Combe, Raymond Gesteland, James U. Jensen, John Kendall Morris, Thomas Parks, David W. Pershing, and Michael K. Young). This is the first step in an appeal that awaits a large number of anticipated amicus briefs and appellees? briefs from plaintiffs (supported by the American Civil Liberties Union and the Public Patent Foundation). There are also rumors that the Government will weigh in, but it is unclear whether it will be in favor or in opposition to the verdict below.

Myriad?s brief begins with an attack on the plaintiffs? standing to bring the lawsuit, something expressly litigated during the District Court case (see ?Round One Goes to the ACLU?). Myriad lost below, but has a chance to win reversal on this procedural issue. Under this scenario, should Myriad prevail, the Federal Circuit would not reach the merits of the District Court?s decision that isolated human DNA is not patent-eligible subject matter. This would make it more likely that a certiorari petition would be limited to the procedural question, thus delaying any reconsideration of the patent-eligibility questions. In view of the fact that the patents-in-suit expire between December, 2014 and March, 2017, any delay in a final resolution of the case on the merits works in Myriad?s favor.

Myriad attacks both the District Court?s conclusion that the plaintiffs had standing as well as the way the Court applied the relevant jurisdictional test. Citing Medimmune, Inc. v. Genentech, Inc., 549 U.S. 118, 127 (2007), Myriad argues that the District Court erred in misapplying the ?all the circumstances? test, because plaintiffs had failed to show ?that there is a substantial controversy, between parties having adverse legal interests, of sufficient immediacy and reality to warrant the issuance of a declaratory judgment? (unless otherwise noted, all emphases are as set forth in the brief). Myriad cites as error the District Court?s application of the test in view of its assertion that, after Medimmune, ?there is now an ease of achieving declaratory judgment jurisdiction,? reminding the Court that it has held that ?a lowered bar does not mean no bar at all.? Hewlett-Packard Co. v. Acceleron, LLC, 587 F.3d 1358, 1361-62 (Fed. Cir. 2009). Contrary to this precedent, Myriad
  argues that ?[t]he court?s application of the ?all the circumstances? test eliminated any meaningful threshold for declaratory judgment jurisdiction by allowing any plaintiff with ?the ability and desire? to infringe . . . the right to challenge the patent?s validity based solely on subjective fears of suit.? Myriad and the plaintiffs ?do not have ?adverse legal interests,?? Myriad argues, because none of the plaintiffs have alleged that (recently) Myriad had any contact with any of them concerning the patents-in-suit nor did any of the plaintiffs ?inform[] Myriad about their ?ability and desire? to infringe? these patents. Plaintiffs did not allege any ?affirmative act? by Myriad, which the brief states is required under post-Medimmune Federal Circuit precedent, citing SanDisk Corp. v. STMicroelectronics, Inc., 480 F.3d 1372, 1380-81 (Fed. Cir. 2007). The brief analogizes the situation to the one in Prasco, LLC v. Medicis Pharm. Corp., 537 F.3d 1329, 1339 (Fed. Cir. 2008),
  where ?the totality of the circumstances analysis in the instant case is that which has not occurred.? The District Court skirted this jurisdictional requirement, according to Myriad, by holding that such a requirement (for ?a specific, affirmative act directed towards the plaintiff?) would be contrary to the ?all the circumstances? test. This decision was erroneous, Myriad argues, as being contrary to Federal Circuit (SanDisk) and Supreme Court (MedImmune) precedent (on the grounds that the Supreme Court found the ?touchstone? of an ?adverse legal interest? to be ?threatened [patent] enforcement action?). The brief also argues that the District Court?s finding that the plaintiffs had standing is contrary to the Federal Circuit?s decision in Hewlett-Packard Co. that ?a communication from a patent owner to another party, merely identifying its patent and the other party?s product line, without more, cannot establish adverse legal interests between the parties, let alone the 
 existence of a ?definite and concrete? dispute.?

The brief also assails the District Court?s decision insofar as it was grounded in the plaintiffs? ?subjective perceptions? of an apprehension of suit. Specifically, Myriad objects to the claim that ?it is widely understood within the research community that Myriad has taken the position that any BRCA1/2 related activity infringes its patents and that Myriad will assert its patent rights against parties engaged in such activity,? calling it ?rumor and innuendo.? ?The mere existence of a potentially adverse patent does not cause an injury nor create an imminent risk of an injury,? Myriad argues, citing Prasco, and goes on to say that, post-MedImmune, ?the law does ?not hold that a patent can always be challenged whenever it appears to pose a risk of infringement,?? citing Innovative Therapies, Inc. v. Kinetic Concepts, Inc., 599 F.3d 1377, 1382 (Fed. Cir. 2010). Instead of such chimerical fears and apprehensions, Myriad argues that case law demands that ?a ?controversy must be
  based on a real and immediate injury or threat of future injury that is caused by the defendants -- an objective standard that cannot be met by a purely subjective or speculative fear of future harm,?? citing Prasco.

Myriad also argues that the plaintiffs failed the second prong of the MedImmune test, that the controversy must be ?real, imminent, and traceable to defendants,? again citing Prasco, because Myriad had taken ?no action towards plaintiffs threatening suit.? The only actual ?specific affirmative acts? Myriad had taken had been letters and other ?communications? with three of the plaintiffs Drs. Kazazian, Ganguly, and Ostrer ?from May 1998 to June 1999,? as well as ?an alleged exchange of phone calls between some [unidentified] Myriad employee and Dr. Matloff in 2005.? The passage of time is sufficient, Myriad argues, to rob any controversy of ?sufficient immediacy and reality,? citing MedImmune. According to Myriad, the District Court ?dismissed? the ?staleness? of this conduct by attributing a requirement for greater immediacy with the ?now-defunct ?apprehension of suit? test.? Not so, according to Myriad, since an ?apprehension of suit? is properly one of the ?totality of the
  circumstances? that courts should consider in making jurisdictional determinations. (Although Myriad supports this position with pre-MedImmune Federal Circuit precedent, thereby weakening its impact.) Drawing an analogy with laches, Myriad argues that ?a patentee?s ten-year silence presumptively extinguishes any reasonably objective fear of suit.? Myriad also brings to the Court?s attention some interesting behavior by the plaintiffs (whether at the ACLU or PubPat?s instigation is unknown), whereby Dr. Matloff contacted an unidentified Myriad employee in 2005 by telephone ?regarding ?whether it was permissible for [Yale Laboratory] to perform genetic screening of BRCA genes.?? Fortunately, the District Court did not rely upon this purported incident in its jurisdictional decision-making, since as Myriad points out, to do so would permit ?anyone [to] manufacture jurisdiction by initiating phone calls or letters to a patentee; the patentee would be left with an untenable choi
 ce -- grant permission to infringe or face a declaratory-judgment suit.?

Similarly unavailing to plaintiffs in satisfying this second prong of the jurisdictional test were ?ten-year-old litigation and licensing activities,? according to the brief. The District Court used evidence of these activities to find that Myriad had engaged in a ?continuing course of [litigious] conduct over a period of several years.? True or not, Myriad argues that the Court ?fails to explain how such aged conduct created a ?substantially immediate? controversy with plaintiffs.? Specifically, neither of the two patent cases cited by the District Court in support of its conclusion were against any of the plaintiffs here, and although Myriad concedes that the Court has held that ?prior litigation is a circumstance to be considered in assessing the totality of circumstances,? the Court has also held that ?the fact that [patentee] had filed infringement suits against other parties for other products does not, in the absence of any act directed toward [plaintiff], meet the min
 imum standard discussed in MedImmune,? citing Innovative Therapies, 599 F.3d at 1382. Under this standard, neither the prior litigations nor licensing efforts -- amounting to ?a single 1998 letter sent to nonparty Dr. Nayfield? -- satisfy the jurisdictional standard, contrasting the situation here with cases where the Federal Circuit has held prior litigation conduct to support declaratory judgment jurisdiction (including Hewlett-Packard Co.; Sony Elecs., Inc. v. Guardian Media Techs., Ltd., 497 F.3d 1271, 1285 (Fed. Cir. 2007); and SanDisk Corp.).

Myriad finishes this portion of its brief by arguing that the District Court?s jurisdictional decision was outside the proper scope of Article III of the Constitution by providing an advisory opinion. The Declaratory Judgment Act was intended to provide a party ?with ?an equal start in the race to the court house, not a headstart,?? citing Kerotest Mfg. Co. v. C-O-Two Fire-29-Equip. Co., 342 U.S. 180, 185 (1952), and in the absence of any ?suggestion of infringement by anyone for over a decade,? a headstart is precisely what plaintiffs have sought (and, unfortunately for Myriad, obtained). Myriad characterizes the case for what indeed it is: ?[i]n sum, this is a manufactured controversy with recruited plaintiffs having no dispute with Myriad beyond a desire to assist two public-advocacy groups? effort to use the courts to dictate public policy on DNA patents. That sort of ?abstract? dispute is not enough for declaratory-judgment jurisdiction. Aetna Life Ins. Co. v. Haworth, 3
 00 U.S. 227, 240 (1937).

Turning to the substance, Myriad makes what are now well-known arguments for the patentability of human (and indeed any) DNA. New to the argument is the citation of Bilski v. Kappos for the proposition that the Supreme Court continues to recognize that Congress has ?plainly contemplated that the patent laws would be given wide scope,? citing Diamond v. Chakrabarty, 447 U.S. 303, 308 (1980), and that ?[t]his breadth ?ensure[s] that ?ingenuity should receive a liberal encouragement,?? Bilski v. Kappos, 130 S. Ct. 3218, 3225 (2010) (quoting, through Chakrabarty, 5 Writings of Thomas Jefferson 75-76 (H. Washington ed. 1871)). Isolated DNA is ?unquestionably? a ?composition of matter,? or, in the alternative, ?a new and useful improvement? on naturally occurring DNA. The brief cites the U.S. Patent and Trademark Office?s 2001 Utility Examination Guidelines for the proposition that isolated human DNA (?a gene?) ?is a chemical compound and is patentable if all the statutory requirem
 ents are met.? The brief also cites 35 U.S.C. § 103(b) as evidence that Congress has given its imprimatur to patenting isolated human DNA (specifically, wherein § 103(b)(3)(A)(i) specifies that ?nucleotide sequences? would be a category of ?patenting starting compositions? encompassed by the statute. Myriad draws an analogy to how the Supreme Court majority considered the effects of 35 U.S.C. § 273(a)(3) on the question of whether a ?business method? was patentable in Bilski v. Kappos:

In Bilski, the Supreme Court concluded that § 273(a)(3) and its definition of ?method? as including ?a method of doing or conducting business? demonstrated that Congress did not view business methods as categorically ineligible for patenting. 130 S. Ct. at 3228-29. Section 103(b) similarly confirms that Congress viewed ?nucleotide sequences? as appropriate subjects for patents; at minimum, it shows that Congress knows how to legislate in this area. Accord 141 Cong. Rec. S15220, S15222 (Oct. 17, 1995) (statement of Sen. Hatch) (?[t]he U.S. patent on the starting materials -- typically a new DNA molecule, a genetically altered host cell, or a vector -- can prevent others from using them in the United States in any way?).

The brief also argues that isolated DNA does not fall within the three recognized exceptions to broad patent eligibility, ?laws of nature, physical phenomena, and abstract ideas.? The brief sets forth an extensive argument that Supreme Court precedent does not contain a ?categorical? prohibition of patenting ?products of nature.? This section includes an explication of the commonly-cited precedents (American Wood-Paper Co. v. Fibre Disintegrating Co., 90 U.S. 566 (1874) (cellulose); Cochrane v. Badische Anilin & Soda Fabrik, 111 U.S. 293 (1884) (alizarine dye); American Fruit Growers, Inc. v. Brogdex Co., 283 U.S. 1 (1931) (borax-coated oranges); Funk Bros. Seed Co. v. Kalo Inoculant Co., 333 U.S. 127, 130 (1948) (mixed bacterial cultures); In re Kratz, 592 F.2d 1169, 1174 (C.C.P.A. 1979) (2-methyl-2-pentenoic acid); In re Bergstrom, 427 F.2d 1394, 1401 (C.C.P.A. 1970) (prosaglandins); and Chakrabarty), distinguishing those cases the District Court used to support its decisio
 n (because inter alia the precedent was based not on categorical patent-ineligibility but on unpatentability for obviousness, etc.) and arguing that the District Court had misread this precedent. Specifically, the brief argues that the Chakrabarty decision did not impose a requirement that to be patent-eligible a composition of matter must have ?markedly different characteristics,? making essentially a textual argument regarding how the Supreme Court set forth the applicable precedent. ??Markedly different? is a fine term for judges to use when describing the particular facts of a particular case, as in Chakrabarty, but it surely was not meant as a legal standard to govern all future cases decided under the statute,? Myriad argues. This is particularly egregious error when a court, as the District Court here, uses such a ?dubious standard? to ?dismiss[] all the factual showings about the substantial differences between isolated BRCA DNA molecules and native DNA [by] concludi
 ng as a matter of law that the isolated molecules were not ?markedly different.?? Myriad performs a similar deconstruction of the decision in Funk Bros., arguing that that decision was based not on patent-ineligibility but on lack of ?invention,? today known as obviousness. (Cleverly, the brief turns Judge Dyk?s dissent in Intervet Inc. v. Merial Ltd. to its advantage, arguing that the unpatentability of ?the leaves of a plant? is founded not on patent ineligibility but on lack of novelty or obviousness.)

The District Court?s decision that isolated human DNA was not patent-eligible ?gave insufficient respect to the PTO?s contrary determination, as well as to a long line of authority from this Court, its predecessor, and other respected jurists, holding that molecules that are newly isolated from natural products and useful are eligible for patents.? Even the Supreme Court properly defers to Congress to make these types of changes in longstanding practice Myriad argues, citing J.E.M. Ag Supply, Inc. v. Pioneer Hi-Bred International, Inc., 534 U.S. 124 (2001), and Bilski. The brief distinguishes the prudent application of judicial restraint by the Supreme Court in J.E.M. Ag Supply with the District Court ?dismissing out of hand? their arguments concerning the high degree of ?public reliance? on the patent-eligibility of isolated human DNA. (In a footnote, the brief recites the statistics that ?[o]ver the past 29 years, the PTO has issued some 2,645 patents with claims to ?isolat
 ed DNA,? and over 50,000 patents containing at least one claim directed to a nucleic acid sequence, including those derived from humans, other animals, plants, bacteria, and so on). As a result:

[B]y refusing to give any consideration to this historical practice, and the significant industries built up in reliance thereon, the district court disregarded almost 100 years of precedent, dating back at least to Judge Learned Hand?s opinion in Parke-Davis & Co. v. H.K. Mulford Co., 189 F. 95 (S.D.N.Y. 1911), aff?d, 196 F. 496 (2d Cir. 1912). In the face of this consistent and long-followed view of § 101?s scope, plaintiffs? arguments are better addressed to Congress, not to the courts. The Supreme Court has long held that courts ?should not read into the patent laws limitations and conditions which the legislature has not expressed.? United States v. Dubilier Condenser Corp., 289 U.S. 178, 199 (1933).

The isolated BRCA1 and 2 genes are patent-eligible as claimed because the claims are directed at ?a nonnaturally occurring manufacture or composition of matter? -- ?a product of human ingenuity ?having a distinctive name, character and use?? as required by Chakrabarty that ?exist only because of the ?human ingenuity? [exercised] in discovering and isolating them.?

And of course the brief alerts the Court to the deleterious consequences of ?a sweeping exception to patent eligibility for ?products of nature? on ?truly ?new? and ?useful? discoveries, like pharmaceuticals derived from natural sources.? Here, Myriad distinguishes the isolated BRCA 1 and BRCA 2 genes as being ?unavailable? to scientists for any use, including the ?detection and treatment of breast and other cancers.? Even the District Court acknowledged that the isolated BRCA 1 and 2 genes had utility, a utility that the brief notes was ?not available to the public? until the invention claimed in the patents-in-suit.

This section of the brief ends with Myriad?s argument that the District Court improperly granted summary judgment because there remain questions of fact regarding ?whether the characteristics of isolated DNA are ?markedly? different from those of native DNA? because ?the meaning of ?markedly different? has never been developed in case law, [and thus] the court improperly viewed itself as free to draw the ?legal? conclusion that ?none of the structural and functional differences . . . between native BRCA DNA and the isolated BRCA DNA claimed in the patents-in-suit render the claimed DNA ?markedly different.??

Finally, the brief addresses the patent eligibility of Myriad?s method claims, which the District Court decided were patent-ineligible under the Federal Circuit?s ?machine-or-transformation? (MoT) test from In re Bilski. Here, Myriad argues that the claims, properly construed, encompass a transformation step sufficient to satisfy the MoT test. The brief notes that the Supreme Court, in holding that the MoT test was ?useful? but not exclusive, specifically cited ?advanced diagnostic medical techniques? as types of methods where innovation might be differentially harmed by an overly restrictive patent eligibility standard. The brief notes that, even under the arguably more limited patent eligibility regime of the Federal Circuit?s MoT test, the Court found patent-eligible the method claimed in Prometheus Laboratories, Inc. v. Mayo Collaborative Services, 581 F.3d 1336 (Fed. Cir. 2009), certiorari granted, judgment vacated, and remanded, 130 S. Ct. 3543 (2010). In that case, the
  Court found transformative steps for assaying blood for the presence of thiopurine or its metabolites, since these steps involved physical or chemical transformations of levels that ?cannot be determined by mere inspection.? Similarly, Myriad argues, its claimed methods involve ?extracting, processing and analyzing a human tissue or blood sample using ?nucleotide sequences,? which are molecules.? (Myriad further argues that its claims ?show an even stronger claim to patent-eligibility [because] the BRCA sequences were not known prior to Myriad?s invention[, whereas] in Prometheus, by contrast, the method claims? transformative step involved the detection of old, known metabolites.) The District Court improperly ?read out? these ?critical elements? of the claims, considering only those elements that were (in the District Court?s view) ?directed only to the abstract mental processes of ?comparing? or ?analyzing? gene sequences.? The District Court?s error was in not consideri
 ng the claims as a whole; ?it is ?inappropriate to dissect the claims into old and new elements and then to ignore the presence of the old elements in the analysis,?? citing Diamond v. Diehr, 450 U.S. 175 (1981). Rather than being mere ?data gathering steps,? as the District Court characterized them, Myriad argues that the sequencing steps are the transformative steps that satisfy the requirements for patent-eligibility. (This argument illustrates the subjectivity introduced into the patent-eligibility determination by concepts like ?(mere) data gathering steps? and ?insignificant post-solution activity.?) The problem is the failure of the District Court to construe the claims: ?[u]nder a proper claim construction, the claims require the transformation of a human sample, and the transformation of the specific BRCA molecules in that sample,? according to Myriad, illustrating the point with claim 1 of U.S. Patent 5,709,999:

1. A method for detecting a germline alteration in a BRCA1 gene, said alteration selected from the group consisting of the alterations set forth in Tables 12A, 14, 18 or 19 in a human which comprises analyzing a sequence of a BRCA1 gene or BRCA1 RNA from a human sample or analyzing a sequence of BRCA1 cDNA made from mRNA from said human sample with the proviso that said germline alteration is not a deletion of 4 nucleotides corresponding to base numbers 4184-4187 of SEQ ID NO:1.

Myriad argues that, properly construed, this claim requires the steps of ?first, in order to analyze the BRCA1 gene, RNA or a BRCA1 cDNA made from mRNA of the human sample, the sample must be transformed[: t]he BRCA1 gene and mRNA are within the patient?s body and must be isolated from a patient?s tissue sample in order to be sequenced.? Myriad?s brief recites what this entails: ?the cells of the tissue sample must be broken open, and a sample of the DNA or RNA extracted. . . . Sequencing is accomplished using a diagnostic probe or primer to hybridize to the target DNA or RNA extracted from the sample to initiate a sequencing reaction.? The brief then sets forth the second step: ?the DNA or RNA of the tissue sample is transformed when a primer or probe is used to bind to and ?hybridize? the DNA or RNA isolated from the human sample; a new ?hybrid? DNA/DNA or DNA/RNA compound is formed, allowing its sequence to be analyzed.? As a consequence of these steps, Myriad argues, ?the
  original human sample is no longer the same human sample, and the DNA and mRNA obtained from that sample are no longer the same DNA and mRNA from the original sample.? Myriad draws the conclusion that ?[t]his is transformative under Supreme Court precedent,? citing Gottschalk v. Benson, 409 U.S. 63, 70 (1972); Diamond v. Diehr; and Parker v. Flook. Myriad characterizes these transformations as being ?central to the purpose of the claim -- detecting ?germline mutations in the BRCA1 gene and their use in the diagnosis of predisposition to breast and ovarian cancer.?? A similar analysis yields the same conclusion for all the other method claims at issue.

The brief then discusses the basis for the District Court?s error -- construing ?the term ?sequence? in the method claims as mere information (i.e., letters from the alphabet), rather than as a physical molecule.? This error was based on using what the Court considered the ?plain meaning? of the term ?sequence? devoid of any consideration of the disclosure of the specifications of the patents-in-suit, contrary to the mandates of Phillips v. AWH Corp., 415 F.3d 1303, 1313 (Fed. Cir. 2005) (en banc), Myriad argues, supporting its construction of the claim term ?sequence? to mean the molecule rather than ?mere words on a page? with citations to the specifications. And the brief also cites the District Court?s invalidation of a method of screening claim (claim 20 of U. S. Patent 5,747,282):

20. A method for screening potential cancer therapeutics which comprises: growing a transformed eukaryotic host cell containing an altered BRCA1 gene causing cancer in the presence of a compound suspected of being a cancer therapeutic, growing said transformed eukaryotic host cell in the absence of said compound, determining the rate of growth of said host cell in the presence of said compound and the rate of growth of said host cell in the absence of said compound and comparing the growth rate of said host cells, wherein a slower rate of growth of said host cell in the presence of said compound is indicative of a cancer therapeutic.

The brief specifically criticizes the District Court?s reliance on ?the essence of the claim? (which is not the proper approach for construing a claim), which gave the Court ?license? (according to Myriad) to ?entirely ignore the ?arguably? transformative steps . . . involv[ing] administering a substance to a cell in the expectation that the substance will slow [the cell?s] growth. If that is not transformative, nothing ever could be,? Myriad asserts. Citing the Supreme Court?s reasoning in Bilski:

Under the plain statutory language, these methods are ?new and useful process[es]? (again, their utility is stipulated), and these extraordinarily useful (indeed, lifesaving) methods are not mere ?concepts,? or ?unpatentable abstract idea[s],? as was the method of hedging ruled ineligible in Bilski, 130 S. Ct. at 3231. They are very real ways of diagnosing and treating cancers. They are patent-eligible because patent protection is in accord with the ?larger object of securing patents for valuable inventions without transgressing the public domain.? Id. at 3227. Patents representative of this ?Information Age,? id., should not be invalidated because they involve the use of information.

Finally, in a sentence, Myriad dismisses the ?alternative, constitutional arguments? raised by plaintiffs (and used by the District Court to deny motions to dismiss for standing and then discarded when the Court reached the merits), and termed the First Amendment arguments as ?frivolous . . . because these patent claims do not impede speech or thought; they are, as shown above, new and useful compositions and methods critical to the ongoing fight against one of the most insidious diseases known to man.?

Amicus briefs in support of Myriad or neither party are due tomorrow.

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