Round One Goes to the ACLU

Association of Molecular Pathology v. U.S. Patent and Trademark Office

    By Kevin E. Noonan --

Not surprisingly, Judge Robert W. Sweet of the Southern District of New York ruled in favor of the plaintiffs today in Association of Molecular Pathology v. U.S. Patent and Trademark Office, granting partial summary judgment that the claims of several patents on BRCA1 were invalid as encompassing non-statutory subject matter.  In an extensive, 156-page opinion (which will be analyzed more thoroughly in a later post), the District Court entered a narrow ruling that was damaging to the University of Utah and its licensee Myriad Genetics, but not as far-reaching as plaintiffs and their backers, the American Civil Liberties Union and the Public Patent Foundation, undoubtedly hoped.

The Court granted summary judgment on the composition of matter claims, based on its (mis)reading of 19th century Supreme Court precedent as well as several old "product of nature" cases from several district courts and regional circuit Courts of Appeal.  (Ironically, the District Court disregarded the teachings of Learned Hand in this same court, Judge Learned Hand's opinion in Parke-Davis & Co. v. H.K. Mulford Co., 189 F.2d 95 (2d. Cir. 1911)).  The method claims were found invalid under the Federal Circuit's "machine or transformation" test from In re Bilski.  The Supreme Court will rule on the Federal Circuit's decision and adoption of this test (representing another rigid rule like the many the Court has overturned or has voiced its disapproval of), making this portion of the opinion of questionable longevity.

As a reminder, the following U.S. Patents were at issue in this litigation:  U.S. Patent  Nos. 5,747,282; 5,837,492; 5,693,473; 5,709,999; 5,710,001; 5,753,441; and 6,033,857.  They are assigned to Myriad Genetics, the University of Utah Research Foundation, and the National Institutes of Health (the '282, '001 and '441 patents); Myriad Genetics, Centre de Recherche du Chul, and the Japanese Cancer Institute (the '473 and 999 patents); and Myriad Genetics, Endo Recherche, HCS R&D Ltd. Partnership, and the University of Pennsylvania (the '492 and '857 patents).  All but the '492 and '857 patents claim priority to an application filed August 12, 1994; all but the '473 patent (December 2014) and the '857 patent (March 2017) will expire (upon timely payment of maintenance fees) in 2015.

The following claims have (for now) been invalidated:

For the '282 patent:

1.  An isolated DNA coding for a BRCA1 polypeptide, said polypeptide having the amino acid sequence set forth in SEQ ID NO:2.

5.  An isolated DNA having at least 15 nucleotides of the DNA of claim 1.

6.  An isolated DNA having at least 15 nucleotides of the DNA of claim 2.

7.  An isolated DNA selected from the group consisting of:
    (a)  a DNA having the nucleotide sequence set forth in SEQ ID NO:1 having T at nucleotide position 4056;
    (b)  a DNA having the nucleotide sequence set forth in SEQ ID NO:1 having an extra C at nucleotide position 5385;
    (c)  a DNA having the nucleotide sequence set forth in SEQ ID NO: 1 having G at nucleotide position 5443; and, (d) a DNA having the nucleotide sequence set forth in SEQ ID NO:1 having 11 base pairs at nucleotide positions 189-199 deleted.

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.

For the '492 patent:

1.  An isolated DNA molecule coding for a BRCA2 polypeptide, said DNA molecule comprising a nucleic acid sequence encoding the amino acid sequence set forth in SEQ ID NO:2.

6.  An isolated DNA molecule coding for a mutated form of the BRCA2 polypeptide set forth in SEQ ID NO:2, wherein said mutated form of the BRCA2 polypeptide is associated with susceptibility to cancer.

7.  The isolated DNA molecule of claim 6, wherein the DNA molecule comprises a mutated nucleotide sequence set forth in SEQ ID NO:1.

For the '473 patent:

1.  An isolated DNA comprising an altered BRCA1 DNA having at least one of the alterations set forth in Tables 12A, 14, 18 or 19 with the proviso that the alteration is not a deletion of four nucleotides corresponding to base numbers 4184-4187 in SEQ. ID. NO:1.

For the '999 patent:

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.

For the '001 patent:

1.  A method for screening a tumor sample from a human subject for a somatic alteration in a BRCA1 gene in said tumor which comprises gene comparing a first sequence selected form the group consisting of a BRCA1 gene from said tumor sample, BRCA1 RNA from said tumor sample and BRCA1 cDNA made from mRNA from said tumor sample with a second sequence selected from the group consisting of BRCA1 gene from a nontumor sample of said subject, BRCA1 RNA from said nontumor sample and BRCA1 cDNA made from mRNA from said nontumor sample, wherein a difference in the sequence of the BRCA1 gene, BRCA1 RNA or BRCA1 cDNA from said tumor sample from the sequence of the BRCA1 gene, BRCA1 RNA or BRCA1 cDNA from said nontumor sample indicates a somatic alteration in the BRCA1 gene in said tumor sample.

For the '441 patent:

1.  A method for screening germline of a human subject for an alteration of a BRCA1 gene which comprises comparing germline sequence of a BRCA1 gene or BRCA1 RNA from a tissue sample from said subject or a sequence of BRCA1 cDNA made from mRNA from said sample with germline sequences of wild-type BRCA1 gene, wild-type BRCA1 RNA or wild-type BRCA1 cDNA, wherein a difference in the sequence of the BRCA1 gene, BRCA1 RNA or BRCA1 cDNA of the subject from wild-type indicates an alteration in the BRCA1 gene in said subject.

And for the '857 patent:

1.  A method for identifying a mutant BRCA2 nucleotide sequence in a suspected mutant BRCA2 allele which comprises comparing the nucleotide sequence of the suspected mutant BRCA2 allele with the wild-type BRCA2 nucleotide sequence, wherein a difference between the suspected mutant and the wild-type sequences identifies a mutant BRCA2 nucleotide sequence.

2.  A method for diagnosing a predisposition for breast cancer in a human subject which comprises comparing the germline sequence of the BRCA2 gene or the sequence of its mRNA in a tissue sample from said subject with the germline sequence of the wild-type BRCA2 gene or the sequence of its mRNA, wherein an alteration in the germline sequence of the BRCA2 gene or the sequence of its mRNA of the subject indicates a predisposition to said cancer.

Fortunately, the District Court ignored plaintiffs' invitation to rule on several constitutional issues of questionable provenance (see "The USPTO Asks out of Gene Patenting Case (Again)"), dismissing the claims against the U.S. Patent and Trademark Office.  Invoking the principle of constitutional avoidance, i.e., that "federal courts should, where possible, avoid reaching constitutional questions (Allstate Ins. Co. v. Serio, 261 F.3d 143,149-150 (2d Cir. 2001) and Spector Motor Serv. Inc. v. McLaughlin, 323 U.S. 101 (1944)), the Court answered plaintiffs' argument that deciding as it did would not reach the question of whether the Patent Office was improperly granting patents on  genes by saying:

[A] decision by the Federal Circuit or the Supreme Court affirming the holding set forth above would apply to both the issued patents as well as patent applications and would be binding on all patent holders and applicants, as well as the USPTO.

We can only hope not.

As the District Court predicts, however, this case is now headed to the Federal Circuit, which may benefit from amici curiae briefs from those stakeholders, such as major patent bar groups, universities and others, who sat on the sidelines during the District Court case.  The dangers and negative consequences of a ban on gene patenting have been set out before and won't be repeated here.  That doesn't make the outcome any less dangerous, or the consequences any less threatening to the biotechnology industry or our society.

For information regarding this and other related topics, please see:

• "Debating Gene Patents - Round Four," February 10, 2010
• "Newsweek = Newspeak on Gene Patenting," February 8, 2010
• "Everybody Knows -- The Boston Globe Weighs in on Gene Patenting," February 1, 2010
• "The USPTO Asks out of Gene Patenting Case (Again)," January 19, 2010
• "Top Stories of 2009: #4 to #1," January 4, 2010
• "Gene Patenting: Australian Potpourri," December 28, 2009
• "Science Progress Article Examines Impact of Gene Patents on Research," December 21, 2009
• "Gene Patenting Debate Continues - Round Three," December 17, 2009
• "BRCA Patent Suit to Continue in Southern District of New York," November 2, 2009
• "Empirical Research Fails to Support Gene Patenting Ban," October 22, 2009
• "The Tragedy of a Bad Idea," August 25, 2009
• "Gene Patenting Debate Continues - Round Two," August 4, 2009
• "The Unwanted Consequences of Banning Gene Patenting," June 16, 2009
• "Falsehoods, Distortions and Outright Lies in the Gene Patenting Debate," June 15, 2009
• "Gene Patenting Debate Continues," June 9, 2009
• "Association for Molecular Pathology v. U.S. Patent and Trademark Office," May 17, 2009
• "Court Report: Special Edition," May 13, 2009

Comments

[Paul]

This is excellent news! James Watson co-discoverer of DNA was opposed to such patents and when NIH overruled him he left, or was forced out, in 1992. As the judge correctly notes these are products of nature not intellectual products. Now we are in the absurd position of being able to cheaply and rapidly sequence a persons entire genome. Is every single nucleotide polymorphism found in the individual by the testing company open to being patented. It is to my mind akin to buying a microscope and then claiming a patent on whatever components of life I find there. What about, again as the judge noted, the problem with stifling scientific advance by not being able to openly study the gene in question. I would go one further and say that no DNA sequence whether created artificially or found through sequencing may be patented. Quite often these sequences end up in self replicating or potentially self replicating organisms. There is an interesting story http://healthjournalclub.blogspot.com/2010/03/astonishing-court-case-of-becky-mcclain.html of a microbiologist who is claiming she was inadvertently infected by a genetically engineered virus. The company however, is refusing to release the sequence of the virus in question. Well what if that virus or a future one turned out to be contagious? Can you even place a patent on a computer virus? How much more foolish to claim there is patent protection on a virus that might someday be able to kill you. At the very least, requests by health practitioners or public health officials should over rule patent claims, whether a sequenced part of a genome or one made from scratch. Glad to see this ruling, gene patents hinder scientific advance and were absurd and offensive from the start.

Paul
http://healthjournalclub.blogspot.com/

[Geoff Karny]

The judge's 101 rationale is based on dicta in the Chakrabarty case that he raises to the level of a new test for patentability. He quotes the following language: "the patentee has produced a new bacterium with markedly different characteristics from any found in nature and one having the potential for significant utility." He then finds that the isolated DNA is not "markedly different" from "native DNA" because, although isolated, it is still a physical carrier of biological information, like the genes found in the body. Of course, all chemicals, in fact all matter, embodies information. A novel laboratory-synthesized drug is the sum of its atomic, molecular, and chemical properties, which properties are ultimately governed by universal scientific laws; i.e., information. Under the court's rationale, the drug would be a product of nature. Even if one were to accept the "markedly different" rationale, the claimed isolated DNA is markedly different from the genes in the human body. The ones in the body are useless for predicting a risk for breast or ovarian cancer. It was only when the inventors found and isolated the mutant genes could there be a test for risk of breast or ovarian cancer. The court overlooked the very simple fact that, but for the actions of the inventors, the test would not exist. If this isn't a "markedly different" situation, I don't know what is.

[Jesse]

Genes are not intellectual property. They may perhaps require proprietary techniques to isolate, but once discovered must be keep unencumbered.

What's the argument again in favor of patenting? In order to provide a profit incentive to isolate them in the first place? Any other reason?

[James Katt]

Hurray!

A Circuit Court of Appeal recently killed another parent on a biological discovery (the NF-Kappa-Beta protein) stating the patent was a “wish” but not an invention.

This ruling is another kill on biological patents which are “discoveries” but not inventions.

PATENTS ARE FOR INVENTIONS. If you can’t show that it is an invention, then you can’t patent it. Period. Wishful thinking aside.

A discovery is NOT an invention. It is the uncovering of fact.

Discovering the moon doesn't make the moon patentable. Invent the rocket to go to the moon. Then you can patent the invention of the rocket.

There is no invention when it comes to discovering a fact of nature - e.g. genes or proteins, etc. Invent something like a drug that can interact with the gene. Then you get to patent that invention. But the gene or protein, itself, is not patentable.

This ruling returns us to sanity.

[Prior Art]

[slaps forehead, looks down, and shakes head in disbelief]

Judge Sweet is not an unreasonable judge, nor an idiot, so I'm wondering if there's some politics behind the decision. Perhaps Judge Sweet (Carter appointee) felt the need to rule in favor of plaintiffs knowing that CAFC will reverse his decision.

[Baltazar]

Dear Kevin,

I can't imagine CAFC not reversing the SDNY decision. There is too much precedent that must be overturned to affirm the SDNY decision. An affirmance would be too drastic a change in the industry.

[Mpls Mark]

This could be just the vehicle for the Supreme Court to rule that natural products and other molecules isolated from nature are indeed patentable subject matter. At the very least, one hopes that higher courts would distinguish between cDNA/expression vectors and naturally occurring sequences.

[CNS]

Paul,
Your question demonstrates a fundamental lack of understanding of what patents are even about. If the company filed a patent on its genetically engineered virus, then the sequence would be published. Keeping things like sequences secret are exactly what the patent system incentives AGAINST. Patent rights are granted by the government in exchange for full, enabling disclosure of the invention. So your question doesn't even make sense. I won't even touch the inane question about whether a computer virus is patentable.

[EG]

Kevin,

As I told you, Judge Sweet's ruling is inane and contrary to In re Bergy (which he quotes from extensively but misrepresents) and Chakrabarty v. Diamond. At the very least, there's enough of a factual dispute here to deny plaintiff's motion for summary judgment. I hope (and pray) the Federal Circuit torches this ruling. If they don't, we may need to consider a new line work, as logic and legal precedent will obviously mean nothing.

[Geoff Karny]

The plaintiffs and their ACLU attorneys have wrapped themselves in the mantle of scientific freedom and women’s health, but the suit is ultimately about money. The molecular pathologists want to be able to offer the tests themselves for a fee. The opinion is replete with references to people charging much less than Myriad charges. Of course they can. Myriad invested substantial amounts of time, money and effort to commercialize the technology. Once the tests have been developed and proven, it’s easy for someone else to take a free ride. That’s why the friendly street corner vendor is able to offer Avatar for a dollar.

The judge cited a study by Mildred Cho which found that 53% of surveyed laboratory directors decided not to develop a new clinical test because of a gene patent or license and 67% believed that gene patents decreased their ability to conduct research. He did not cite the article where it was published, which is Journal of Molecular Diagnostics, Vol. 5, No. 1, February, 2003, pgs. 3-8. A closer examination of the article shows that the respondents simply did not want to pay to license the patented tests. One of the respondents even acknowledged this by stating, “People shouldn’t be complaining that they can’t run tests. They should just pay.”

[Wawa]

I am amazed by the ignorance of some comments about the current patent law. Leave ideology outside the court!

[6]

" A closer examination of the article shows that the respondents simply did not want to pay to license the patented tests."

How much $$$ are we talking about? A couple thousand, ten thousand, hundred thousand, or a million+? According to Kev it is perfectly reasonable to charge a man dying of some rare genetic disorder over a million dollars a year (iirc) to provide him with drugs.

OKAAAAAAY.

[Skeptical]

Looks like the symbol behind the banner of "Patent Docs" at the top of the page will have to be replaced.

[Sean]

Mpls Mark,

But what is cDNA? Just another "medium" of the same information in the same language. Why else would these patents claim every form of the sequence information - gene to cDNA to mRNA. Because the patentees know they would have to claim all forms of the sequence otherwise their patents are worthless. It's the same thing!

[Kevin E. Noonan]

All:

Thanks for carrying on the discussion in my absence.

My views, and the bases for those views are well known, so I'm not going to rehash them here - look at earlier posts for details. I think the opinion on the compositions of matter was wrongly decided, because I don't think there is a basis for a "products of nature" exception to patent eligibility (laws of nature, like gravity, are another matter). The reasoning is simple - if there is a chemical in a leaf in a tree in a forest, I think there is value in providing an incentive for investors to support the scientist who discovers the chemical, isolates it, characterizes it and all the other people who then commercialize it. I don't think a patent is a gold star or a pat on the head - it isn't a reward that must be earned, it is a tool to provide incentives to commercialize. And that's all it is.

The method claims were invalidated under the Federal Circuit's Bilski test, which might not last the week, so I wouldn't be gloating over that part of the decision just yet.

Most importantly, the constitutional claims were dismissed, which means that, unless appealed, this is one, lonely district court decision with zero precedential value. So despite the ACLU's press release, the only patent claims that are invalid today that were not invalid yesterday are the 11 claims at issue in this case. Provides a good reason for Myriad not to appeal, and let the anti-gene patenting crowd strike down these patents one at a time. Have fun.

And as for you, 6, only you could make $3,000 into a million - you must work for the government. On Nurse Jackie the other night, she responded to the information from a patient's insurance carrier that the patient had $3,000 in coverage per day that the patient "had already gone through that in IV fluids." $3,000 for a test that will tell you whether you have a 95% chance of getting cancer seems cost-effective in comparison.

Thanks for the comments. Carry on.

[anonymous]

Kevin wrote, "The method claims were invalidated under the Federal Circuit's Bilski test, which might not last the week, so I wouldn't be gloating over that part of the decision just yet."

No doubt. I wonder whether the District Court wanted to pass this hot potato before the Supreme Court tossed the machine-transformation test out and wrecked a large portion of its analysis/work.

[TF]

The ruling's gene composition of matter argument fails to make a proper distinction between DNA functioning within a cell (which may indeed be an "embodiment of [non-patentable] laws of nature," as the ruling states) and an isolated section of that DNA (i.e., a gene) which is a product of man and therefore patentable.

As for the method patent arguments, the ruling seems to go too far in reducing a very complicated method to non-patentable mental processes ("analysis" and "comparison").

The Supreme Court will have a say later this year on the method aspect of the argument in any case.

And by the way, at this point Sweet's ruling is binding only in parts of New York state.

[6]

"And as for you, 6, only you could make $3,000 into a million"

Easy there cupcake, 3000$ per test for women with breast cancer isn't the same thing as licensing the patent to labs to do their research, which was the topic under discussion I do believe.

If all we're talking about is a mere 3000$ that a frakin director of a lab didn't want to pay then fine, I concede the issue.

Somehow I suppose that a realistic number would be closer to 50-500k at a minimum for what they wanted to do.

And remember, I wasn't the one that implied 1 mil was reasonable. I don't mean to bludgeon you with that all that much Kev, your views are your views, and you're entitled to them. Most of the time you're pretty reasonable. Perhaps you were just shooting the sht on that particular day.

You guys discussing the "bindingness" of this decision are ignoring a more important point, the persuasiveness of the arguments made before this court.

[Kevin E. Noonan]

Dear 6:

"Cupcake" - I didn't know you cared.

As for persuasiveness, these arguments were persuasive before this judge on these claims of these patents. Any other challenge will (most likely) be to another judge on other claims of other patents. We'll see how that goes down.

Take care, 6. Thanks for the comment.

[7]

You can read my published law review article on why gene patents should inspire legislative reform at : http://omnilegalgroup.com/publications.html

[wholesale clothing]

If all we're talking about is a mere 3000$ that a frakin director of a lab didn't want to pay then fine, I concede the issue.

Somehow I suppose that a realistic number would be closer to 50-500k at a minimum for what they wanted to do.

[clothing stores]

If the company filed a patent on its genetically engineered virus, then the sequence would be published. Keeping things like sequences secret are exactly what the patent system incentives AGAINST. Patent rights are granted by the government in exchange for full, enabling disclosure of the invention. So your question doesn't even make sense