Patent Docs

Conference & CLE Calendar

April 4, 2010

April
7, 2010 – First
Annual Board
Conference (U.S.
Patent and Trademark Office Board
of Patent
Appeals and Interferences) – Alexandria,
VA

April
7-10, 2010 – 25th
Annual
Intellectual Property Law Conference (American
Bar
Association Section of Intellectual Property Law) – Arlington,
VA

April
11-17, 2010 – Advanced
Patent Courses (Patent
Resources
Group) – Bonita
Springs, FL

April
14, 2010 – "Obviousness
Standard for Patents
Post-KSR: Strategies to Withstand USPTO
Obviousness Rejections and
Attacks on Patent Validity" (Strafford) – 1:00
– 2:30 PM (EST)

April
19-21, 2010 – Intellectual
Property Counsels
Committee (IPCC) Spring Conference & Meeting (Biotechnology
Industry
Organization) – New
Orleans,
LA

April
23-24, 2010 – 12th
Comprehensive PCT Seminar (Franklin Pierce Law Center &
World Intellectual Property
Organization) – Concord,
NH

April 27-28, 2010 – 4th
Annual Paragraph IV Disputes*** (American Conference
Institute) – New York, NY

April
27-28, 2010 – Corporate
IP Counsel Summit (World
Research
Group) – New
York, NY

April
29,
2010 – 26th
Annual Joint Patent Practice Seminar (Connecticut,
New
Jersey, New York, and Philadelphia Intellectual Property Law
Associations) – New York, NY

May
3-6, 2010 – 2010
BIO International Convention (Biotechnology
Industry Organization) – Chicago, IL

May
11, 2010 – Law
Symposium on Intellectual Property (George
Washington
University Law School, Howrey LLP & Cornerstone Research) –
Washington, DC

May
24-25,
2010 – Hatch-Waxman
Boot Camp*** (American
Conference
Institute) – San
Diego, CA

May
24-26, 2010 – Pharmaceutical
& Biotech Patent Litigation
Strategies*** (Pharma IQ) – London,
England

***Patent Docs is a media partner of this conference or CLE
“60 Minutes” Examines Gene Patenting Issue on Sunday, April 4th — Patent Docs Author Kevin Noonan to Appear on Program

April 2, 2010

On Sunday, April 4, 2010, the CBS news program "60 Minutes" will take a look at the
issue of gene patenting in a segment entitled "Patented Genes." According to the program's website,
the segment will examine the question of whether "companies [should] be
able to own human genes," and "the idea of biotech firms patenting
genes for profit" (a preview of the program and video clip can be found here) Patent Docs author Dr. Kevin Noonan, who
has written extensively on the issue, and who spoke with "60 Minutes" and CBS News correspondent Morley Safer late last fall, will be appearing on the program.

The
timing of the segment is perhaps appropriate given Monday's ruling by the District Court for the
Southern District of New York in Association of Molecular Pathology v. U.S.
Patent and Trademark Office. The District Court determined that the claims of several patents
directed to the BRCA1 and BRCA2 genes were invalid as encompassing
non-statutory subject matter (see
"Round
One Goes to the ACLU").

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

• "AMP v. USPTO: What the Parties Are Saying About the Decision," April 1, 2010
• "Caught in a Time Warp: The (In)validity of BRCA1 Oligonucleotide Claims," March 30, 2010
• "Round
One
Goes to the ACLU," March 29, 2010
•
"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
AMP v. USPTO: What the Parties Are Saying About the Decision

April 1, 2010

By
Donald Zuhn —

On
Monday, the District Court for the Southern District of New York ruled in favor
of the plaintiffs in Association of
Molecular Pathology v. U.S. Patent and Trademark Office, finding the claims
of several patents directed to the BRCA1 and BRCA2 genes invalid as
encompassing non-statutory subject matter (see
"Round One Goes to the ACLU"). So what are the parties saying about
Monday's decision?

The
originally named defendants in the case included the U.S. Patent and Trademark
Office, Myriad Genetics, and the Directors of the University of Utah Research
Foundation. The District Court's
dismissal of claims against the USPTO left Myriad Genetics and the University
of Utah Research Foundation as the remaining defendants.

While the University of Utah Research
Foundation has not issued a statement regarding the decision, Myriad Genetics
released a statement
on Tuesday in which the molecular diagnostic company announced that it will
appeal the decision to the Federal Circuit and "will continue to
vigorously defend this litigation."
Myriad President and CEO Peter Meldrum said that "[w]hile we are
disappointed that Judge Sweet did not follow prior judicial precedent or
Congress's intent that the Patent Act be broadly construed and applied, we are
very confident that the Court of Appeals for the Federal Circuit will reverse
this decision and uphold the patent claims being challenged in this
litigation." Mr. Meldrum
added that "[m]ore importantly, we do not believe that the final outcome
of this litigation will have a material impact on Myriad's operations due to
the patent protection afforded Myriad by its remaining patents." Myriad noted that while the District
Court invalidated 15 claims in seven BRCA patents that the company owns or
exclusively licenses, there are 164 remaining claims in those seven patents and
an additional 16 patents covering Myriad's BRCA tests that were not challenged
in the case.

Among
the organizational plaintiffs and their counsel, the Association for Molecular
Pathology, American College of Medical Genetics, American Society for Clinical
Pathology, American Civil Liberties Union (ACLU), and Public Patent Foundation
(PUBPAT) all issued statements regarding the decision (the College of American
Pathologists, Breast Cancer Action, and Boston Women's Health Book Collective
did not issue any statements on their respective websites).

In
its press release,
the ACLU noted that "[t]he precedent-setting ruling marks the first time a
court has found patents on genes unlawful and calls into question the validity
of patents now held on approximately 2,000 human genes." ACLU First
Amendment Working Group staff attorney Chris Hansen said the decision was
"a victory for the free flow of ideas in scientific research," adding
that "[t]he human genome, like the structure of blood, air or water, was
discovered, not created. There is
an endless amount of information on genes that begs for further discovery, and
gene patents put up unacceptable barriers to the free exchange of ideas." With respect to the USPTO's dismissal,
the ACLU asserted that "[t]he court found that it was unnecessary to reach
the First Amendment claims against the USPTO because it had already ruled in
favor of the plaintiffs." The
ACLU release also suggested that "[b]ecause the ACLU's lawsuit challenges the
whole notion of gene patenting, its outcome could have far-reaching effects
beyond the patents on the BRCA genes." ACLU Women's Rights Project staff attorney Sandra Park
predicted that the decision was "the beginning of the end to patents that
restrict women's access to their own genetic information and interfere with
their medical care."

In
a statement issued by PUBPAT,
Executive Director Daniel Ravicher said that "[t]he court correctly saw
that companies should not be able to own the rights to a piece of the human
genome." Mr. Ravicher added
that "[n]o one invented genes.
Inventions are specific tests or drugs, which can be patented, but genes
are not inventions."

The
Association for Molecular Pathology (AMP) applauded the decision in its release. AMP President Dr. Karen Mann called the
outcome "a landmark decision that has the potential to dramatically
improve patient access to genetic testing." Dr. Mann suggested that the decision would also be "a
boon to personalized medicine in the purest sense as nothing is more personal
than one's genetic makeup."
The AMP noted that it had adopted a Policy Statement on gene patenting in 2008 that "urged
an end to the practice of granting patents on single genes, sequences of the
genome or correlations between genetic variations and biological states,"
and "encouraged groups that currently hold gene patents, including higher
educational and research institutions, not to grant exclusive licenses to
access those patents." The
AMP release contends that the decision is a "significant step forward to
eliminating future DNA patents and calls into question the appropriateness of
those already in existence."

In
its statement, the
American College of Medical Genetics (ACMG) "celebrated the US District
Court ruling [on Monday] that genes are 'unpatentable.'" The group's release states that
"[t]he outcome of this case is likely to have far-reaching positive
implications for physicians, researchers and patients." ACMG executive director Dr. Michael
Watson contended that "[t]he invalidation of gene patents will allow
patients to get second opinions on test results, encourage quality improvement
of current testing, allow researchers to develop new and better methods of
testing and decrease costs of laboratory testing." ACMG President Dr. Bruce Korn added
that "[t]he successful outcome will pave the way towards genome-wide
testing, avoiding an obstacle course of patent protection of individual genes
that will prevent reporting of a complete set of results." The group's release notes that the ACMG was
the first professional medical association to establish a position against gene
patenting (which it did in 1999).

The
American Society for Clinical Pathology's (ASCP) release
"hailed" the District Court's decision. ASCP President Dr. Mark Stoler said the ruling "gives
patients the right to choose who will perform the test that determines whether
they are at greater risk for breast cancer — a right they never should have
been denied." He added that as
a result of the court's decision, "[w]e have won back our natural right to
own our own genes."
“Takings” by Congress and the Courts

April 1, 2010

By Kevin E. Noonan —

In a recent article in the journal Science, Sherry Knowles, the Chief Patent Counsel at GlaxoSmithKline, raises several interesting questions regarding the concept of "takings"
of property in the patent context. In a "Policy Forum" article entitled "Fixing the Legal Framework for Pharmaceutical Research," Ms. Knowles (at right) tackles two aspects of such takings regarding
branded drugs. First, she reviews
the provisions of the Hatch-Waxman Act that permit a generic drug maker to use
an innovator company's safety and efficacy data to support an Abbreviated New
Drug Application (ANDA) (calling these provisions of Hatch-Waxman the "forced
data-sharing requirement"). Second,
she reviews the effects of several Supreme Court and Federal Circuit cases
(including KSR International Co. v. Teleflex, Inc., In re Bilksi, and Ariad Pharmaceuticals, Inc. v. Eli Lilly and Co.) on the validity of patents and the consequences of
the retroactive application of these rulings on issued patents. In each case, Ms. Knowles suggests,
companies that have invested substantial sums in developing innovative drugs
should be entitled to recompense from the government when their data or their
patent protection is taken.

With regard to Hatch-Waxman, Ms. Knowles cites the
increased costs of bringing a new drug to market today (approximately $1.2 billion) and in
the early 1980's (approximately $230 million), the time when Hatch-Waxman was enacted. She also sets forth the
differences in timeframe that innovators and generic drug manufacturers are
burdened with. For the innovator,
this involves "10-15 years of pre-approval R&D after a patent
application is filed." In
return, an innovator can recoup up to five years of additional patent
protection, capped at 14 years after drug approval. The generic drug maker is constrained by a much shorter
period: an ANDA filer is
prohibited from using an innovator's safety and efficacy data for 5 years after
drug approval. Ms. Knowles
characterizes this period as a "political compromise" arrived at
during negotiations over the Hatch-Waxman Act, but one that was "without
substantial supporting economic analysis." "This period is vastly inadequate today," she says,
"and rarely covers the breakeven point for reimbursement of R&D
costs. Because of this, new drugs
are almost never developed without patent protection, which limits the number
of new drugs created (as not all useful drugs are patentable)."

In those instances where the Hatch-Waxman regime
forces an innovator drug company to share its "expensive clinical research
data" with a generic drug company, under circumstances where patent
protection does not keep the generic drug off the market, Ms. Knowles asks whether the consequent
loss of revenue is a "taking" under the Fifth Amendment? (While the takings clause of the Fifth
Amendment is restricted by its terms to takings by the government, the lines
between public and private takings have been blurred by the Supreme Court's
decision in Kelo v. City of New London, where the Court
held valid the taking of private property by a public entity for the benefit of
another private entity.) The
extent of the taking of private data under Hatch-Waxman having "increased
sixfold" over the past twenty years, Ms. Knowles asks whether an increase
in the data exclusivity period (which would mitigate the deleterious effects of
Hatch-Waxman on return of investment) would not be fair.

Ms. Knowles also criticizes the 14-year cap
limitation of Hatch-Waxman on patent term extension. She notes that patents on inventions such as the "Beerella"
(U.S. Patent No. 6,637,447) enjoy
a longer term than a patent on a metastatic breast cancer therapy (U.S. Patent
No. 6,713,485). This is
hardly a societally-useful outcome. Increasing the data exclusivity period would mitigate these deficiencies
of how Hatch-Waxman has been put into practice (in view of our 26 years of
experience with the Act and its consequences).

Turning to court decisions that may constitute a
taking, Ms. Knowles notes that "[a] patent application filed today on a
pharmaceutical innovation will not be used to defend a marker for about 15
years." Under these
circumstances, the state of the law over that time will have significant
effects on the capacity of the patent to protect the innovator drug
franchise. While Congress could
enact legislation changing the law, this is generally done prospectively, while
court decisions apply retrospectively. While both actions "change the rules of the game," court
decisions have a much more drastic effect, since they may "disrupt
well-settled expectations, which can affect the outcome of long-term business
decisions."

Ms. Knowles then discusses the changes in the law
occasioned by the KSR
(obviousness), Bilski (patentable
subject matter), and Ariad (written
description) cases. Each one of
these decisions (or the prospect of these decisions, since the piece was
written before the Federal Circuit decided Ariad en banc, and the Supreme Court has yet to decide Bilski)
has had the effect of reducing the certainty or expectation of patent
protection ex post facto. She then summarizes the effects of
retroactive application of these (and other) judicial decisions: "[t]hey can
facilitate the increase of challenges by
generic producers under Hatch-Waxman, . . . stop R&D investment decisions
that have already been made and could prevent a product from reaching the
market because of patentability issues." Ms. Knowles also mentions the potential to prevent R&D to take
place at all.

These effects
can constitute a taking, and the effects of such decisions should be analyzed
according to takings law:

An issued patent is property just like
a piece of land or a house (citing Consolidated
Fruit-Jar Co. v. Wright,
84 U.S. 92, 96 (1872) and Patlex Corp. v. Mossinghoff, 758 F.2d
594, 599 (Fed. Cir. 1985)). When a federal judicial decision
dramatically changes the law, such that a valid patent becomes invalid, has the
federal government taken private property in violation of the federal
Constitution? Application of the Fifth Amendment is not clearly limited to
legislative and executive action; nothing in its text bars extension of the takings
clause to judicial action.

"The time has come," Ms. Knowles
contends, "to rethink the right legal framework to promote and protect
investment in pharmaceutical research and development." This rethinking involves increasing the
term of data exclusivity under Hatch-Waxman from 5 to 14 years, and for
Congress to give appellate courts discretion to have a decision have
prospective effect only, should it overrule prior interpretation of patent
law. The benefit of these changes
would be to "substantially increase the number of drugs in the R&D
pipeline, which would greatly benefit patients and ultimately benefit generic
drug companies."

Before wags jump to mention that these changes
would also benefit pharmaceutical companies like GSK, it would be well to
consider where novel therapies will come from without companies with experience
in obtaining (and financing) regulatory approval of such drugs, protecting them
with patents, and having the business resources to bring such drugs to
market. It is certainly the case
that these companies are for-profit (it's capitalism, after all), but the costs
of R&D and regulatory approval, as well as scale-up, production, and
distribution are realities that cannot be ignored. It would be well to remember that, whatever other criticisms
may be raised against the pharmaceutical industry, there is no other way for
consumers to get new drugs. It is
also good to remember that innovation is not what generic drug companies do
(generally), and that without innovator biotechnology and pharmaceutical
companies, generic drug makers would have nothing to copy or sell.
Director Kappos Testifies before House Subcommittee Regarding USPTO Budget

March 31, 2010

By Sarah Fendrick —

On March 25, 2010, U.S. Patent and Trademark Office Director David Kappos appeared before the
House Subcommittee on Commerce, Justice, Sciences, and Related Agencies for the Committee on Appropriations to seek funds for FY 2011 to enable USPTO operations and
to fund a variety of Office initiatives and programs.

The current budget proposed
by the President requests $2.322 billion for the USPTO and projects USPTO fee
collections will generate $2.098 billion in FY 2011. According Director Kappos (at left), the deficit of $224 million
would be covered by an interim patent fee increase. Further proposals included in the budget include implementing
legislation to better align the cost of operating the UPSTO with the actual
cost of its services and emphasizing effective business tools. As set out in the Director's statement, the President's budget seeks to support a five-year plan
designed to:

1. Reduce the time to first Office action
on the merits to 10 months;

2. Reduce total average pendency for
patent applications to 20 months;

3. Reach a target patent inventory backlog
level of 10 months; and

4. Invest in IT infrastructure and tools
to achieve a 21st Century system
that permits end-to-end electronic processing in patent and trademark IT
systems.

In line with the President's
budget, the USPTO has set out of the following goals to facilitate end-to-end
processing within 12 months:

1. Initiate targeted hiring to recruit and hire 1,000
patent examiners (projected to be a net increase of 400 to 500) annually during
FY 2011 and FY 2012; and

2. Achieve efficiency improvements brought
about by re-engineering many USPTO management and operational systems.

To support the allotment of
funds to the USPTO, the Director presented a number of current USPTO initiatives
that were implemented to facilitate more effective processing of patent
applications.
Caught in a Time Warp: The (In)validity of BRCA1 Oligonucleotide Claims

March 30, 2010

By Kevin E. Noonan —

Albeit a bit anticlimactically, a study published
in the journal Genomics assesses the
patentability of one of the claims invalidated on Monday by Judge Robert W. Sweet
of the Southern District of New York in Association
of Molecular Pathology v. U.S. Patent and Trademark Office. The study is interesting in that
it illustrates the pitfalls in patents on oligonucleotides related to isolated
genes, filed at a time prior to the elucidation of the human genome by the
Human Genome Project. Most
relevant to the question of whether such claims are patentable are the many
revelations from the HGP that overturned settled dogma based on a
now-recognized unrealistic view of the randomness of genomic DNA sequences, as
illustrated by the results reported in this study.

The research was performed by Thomas B. Kepler,
from the Department of Biostatistics and Bioinformatics at Duke University, and
the Center for Computational Immunology; Colin Crossman, a lawyer and owner of
Memento Mori, LLC; and Robert Cook-Deegan from the Institute for Genome Science
and Policy and the Sanford School of Public Policy, Duke University (Kepler et al., "Metastasizing patent claims on BRCA1"). According to these authors, one of the
claims of U.S. Patent No. 5,747,282 seemed "exceptionally broad" — this is
claim 5 that depends on claim 1 (which is directed to an isolated DNA molecule
encoding a BRCA1 polypeptide):

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.

The authors estimate that "the human genome
contains over one million oligonucleotides covered by this claim," and
follow up this statement with the following calculations:

Accounting for bias in the usage of
amino acids as reported, for example, in [7],
the usage-weighted geometric mean codon
degeneracy per amino acid is 3.107. Therefore, the mean number of 15-mers
encoding a polypeptide of length 5 chosen at random from a vertebrate proteome
is 3.107⁵, about 290. There are 5,575
15-mers in BRCA1, so, if we consider all of the nucleotide sequences that
encode the BCRA1 protein, there are about 1.6 x 10⁶ 15-mers embodied by the
claim. There are 4¹⁵=1.07 x 10⁹ different 15-mers altogether,
so the probability that a 15-mer chosen at random will be covered by the claim
is p=1.6 x 10⁶ / 1.07 x 10⁹=0.0015 (roughly, 1 in 600
possible 15-mers). A typical human gene (before RNA editing) contains 10,000
bases, so, if human genes were random strings of nucleotides, one would expect
a human gene to contain an average of 15 15-mers claimed under the patent.

The predicted results of this analysis were found
in the study. The authors
analyzed the nucleotide sequence of human chromosome 1 looking for only a
subset of 15-mers encompassed by claim 5. ("Computing time" was minimized by excluding two of the six
degenerate codons for serine, leucine and arginine amino acids, a reduction said
to only "slightly underestimate the degree of redundancy and breadth of
claim 5.") The authors reported
finding 340,000 "matches" of the claimed sequences in the 250,000,000
nucleotides comprising chromosome 1.

The authors also examined 713 entries in GenBank
representing complete coding sequences for human mRNAs deposited in 1994,
reporting that 80% (568/713 contained at least one of the claimed 15-mers.

There is nothing incorrect about this
analysis; however, it benefits
from current knowledge and (in its implied conclusion of intentional
overreaching) neglects to consider the state of the genomics art on August
12,1994, the earliest priority date of the '282 patent. The calculation was much more simple
(or perhaps naïve) then: any
particular 15-mer was expected to occur once in every 1.07 x 10⁹
nucleotides, and thus in a completely random genome the size of the human
genome (haploid size of about 3 x 10⁹ nucleotides), to occur about 3
times; a 16-mer would be expected to occur four times less frequently,
etc. Thus, the results set forth
in this paper were almost completely unexpected when approached from the outlook
of the person of skill in the art in 1994.

As it turns out, the human genome (and most other
genomes) are much more inhomogeneous than expected, and the effects of evolution
and the relatedness of all organisms (as well as the conservation of motifs and
functional domains between species) were equally unexpected. Indeed, even the number of genes
encoded in the human genome turns out to be much smaller (2- to 3-fold fewer
genes) than was expected. As the
authors state: "human genes are not random strings [of nucleotides.]" Evident now, not so evident 16 years ago.

No one wants an invalid patent. The in
terrorem effect of such a patent is greatly exaggerated, particularly when
its invalidity is so easily demonstrated. Here, these claims, as well as similar claims in other patents, turn out
to be sufficiently overbroad as to be easily invalidated. It is unlikely that the University of
Utah, the National Institutes of Health, or Myriad Genetics (all owners of this
patent) wanted this result.

Nevertheless, the remainder of the paper discussed
the policy implications of this invalid claim. The authors correctly note that their results indicate that
claim 5 was anticipated by the 15-mers known in the prior art as exemplified by
the GenBank results. Thus, "[i]f
challenged by re-examination or in litigation, claim 5 may be deemed invalid
due to readily identifiable prior art covered by the claim." The paper cites U.S. Patent Examiner
James Martinell, examining a 1991 expressed sequence tag patent application,
for recognizing that certain 15-mers could be found in "many genes"
and that it was impossible using then-current computer technology to search all
known sequences for the 700,000 15-mers claimed in that patent. Perhaps for that reason, there is no
evidence in the prosecution history of the '282 patent that such a search was
ever performed.

Despite this strong evidence that claim 5 of the '282
patent is invalid (even before the District Court's decision yesterday), the paper
speculates on the scope and reach of the claim (including oligonucleotide
primers for performing the polymerase chain reaction). Regarding the effects of this claim
(and Myriad's patents) on basic research, the authors recognize what many
others have noted: no appreciable
effect (which belies the introductory sentence of this section that "[t]he effect of this claim on
research is very difficult to assess"):

A PubMed search for the term "BRCA1"
returned 7,107 articles. This suggests a large body of research on the gene has
been published in the technical literature. Myriad has not enforced its patents
against most research, with the exception of laboratories engaged in clinical
research that entailed giving test results to individuals beyond their home
institutions [11–13]. Any such research that
entailed analysis of DNA molecules containing BRCA1 sequences in the United
States very likely infringed this claim, however, so enforcement of this claim would
have substantial impact on research. (Claims to BRCA1 sequences are somewhat narrower
in other English-language jurisdictions such as Canada, Australia and New
Zealand, and a fortiori in Europe, where the claims that emerged from
opposition proceedings were dramatically narrowed.) There is a very narrow "research
exemption" from infringement liability in the United States under common
law, and a broader exemption for research that results in data contributed to
the government for a regulated medical product or service [14]. Since laboratory-developed
tests are not currently subject to Food and Drug Administration approval,
however, this exemption may not apply.

The
simplest conclusion about the effect of claim 5 and Myriad's other BRCA1
patents on research and clinical testing is that Myriad has only rarely
enforced its patents in research, has vigorously enforced its patents against
commercial genetic testing, and has selectively enforced its patents in
clinical research. It is also apparent that research on BRCA1 for the past 12
years has entailed massive pervasive infringement of this claim, even if the
claim's scope were restricted to BRCA1 research. Any such research in the United States was
thus undertaken under risk of infringement liability and its associated uncertainty. While
Myriad has stated publicly that it has not
enforced its patents against basic research [11,12,15],
it has not stated it will not do so in
the future, and therefore BRCA research in the
United States continues only with Myriad's indulgence.

The authors are correct that there is no exemption
from infringement liability for basic research, but they admit that Myriad has
not enforced (or attempted to enforce) the '282 patent against any basic
researchers. The absence of the
exemption may be the problem, not claim 5 of the '282 patent (in view of the
results of this research). Myriad's track record with regard to basic research is consistent with
its public statements that it would not enforce its patents against basic
research; there is very little else it can do. And after yesterday's decision, basic or clinical researchers or commercial
entities that practice the oligonucleotides recited in claim 5 no longer risk
infringement liability.
Round One Goes to the ACLU

March 29, 2010

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
False Patent Marking Bill Introduced in the House

March 29, 2010

By
Donald Zuhn —

On
Thursday, Rep. Darrell Issa (R-CA) introduced a bill in the House (H.R. 4954)
that would amend 35 U.S.C. § 292(b) to permit "[a] person who has suffered
a competitive injury as a result of a violation of this section may file a
civil action in a district court of the United States for recovery of damages
adequate to compensate for the injury." Currently, that section of Title 35 states that "[a]ny
person may sue for the penalty, in which event one-half shall go to the person
suing and the other to the use of the United States." Thus, the legislation introduced by
Rep. Issa (at right) would, if enacted, put an end to qui
tam (or whistleblower) suits for false patent marking.

While
the text of Rep. Issa's bill has not yet been made available on THOMAS.loc.gov, the draft bill appears to use essentially the same language as the
provision added to the Senate patent reform bill (S. 515) by Manager's
Amendment (see "Qui Tam Actions
in Senate Sights"). Both the Senate provision and Rep.
Issa's bill would "apply to all cases, without exception, pending on or
after the date of the enactment of this Act." The legislation would therefore impact the more than 150 qui tam lawsuits that have been filed since
the Federal Circuit's decision in Forest
Group, Inc. v. Bon Tool Co.
on December 28, 2009 (see "False
Patent Marking Resources"). At least sixteen of these qui tam suits have been filed against
biotech or pharma companies:

Promote Innovation LLC v. Sanofi-Aventis US
LLC, March 22
Simonian v. Allergan, Inc., March 9,
2010
Simonian v. Abbott Laboratories,
March 9, 2010
Simonian v. Amgen Inc., March 9, 2010
Simonian v. Baxter Healthcare Corp.,
March 9, 2010
Simonian v. Astellas Pharma US, Inc.,
March 9, 2010
Hollander v. Ortho-McNeil-Janssen
Pharmaceuticals, Inc., March 1, 2010
Simonian v. Merck & Co., Inc.,
February 25, 2010
Simonian v. Novartis Pharmaceuticals
Corp., February 25, 2010
Simonian v. Novartis Consumer Health,
Inc., February 24, 2010
Simonian v. Novartis Consumer Health,
Inc., February 24, 2010
Public Patent Foundation, Inc. v. Novartis
Consumer Health, Inc., February 24, 2010
O'Neill v. Roche Diagnostics Corp.,
February 23, 2010
Simonian v. Pfizer, Inc., February
23, 2010
Simonian v. Merial L.L.C., February
23, 2010
Hollander v. Ranbaxy Laboratories Inc.,
February 23, 2010

(see "Court Report," March 28,
2010; March 14, 2010;
March 7, 2010; March 1, 2010).

The House bill, which was co-sponsored by Rep. Rick Boucher (D-VA), Howard Coble
(R-NC), Steve
Cohen (D-TN), John Conyers, Jr. (D-MI), Trent Franks (R-AZ), Daniel Lungren
(R-CA), and Lamar Smith (R-TX), was referred to the House Judiciary Committee
after being introduced. Rep. Issa
and the seven co-sponsors are all members of the House Judiciary Committee, which is
responsible for crafting the House patent reform bill. On March 4, Chairman Conyers, Ranking
Member Smith, and Rep. Howard Berman (D-CA) and Zoe Lofgren (D-CA) released a
statement concerning the Senate Judiciary Committee's latest patent reform
effort (see "Chairman Leahy
Announces 'Tentative Agreement in Principle' on Patent Reform Bill"),
saying that: "With regard to
the proposed Senate Judiciary Committee language released today, we believe a
number of changes are essential before it could be considered by the House. We
are hopeful our Senate Judiciary colleagues will consider these changes as part
of their process." By
introducing H.R. 4954, and attempting to quickly and directly address the recent
surge in qui tam actions, the House
Judiciary Committee could be sending a message to Senate Judiciary Chairman
Patrick Leahy (D-VT) that enactment of more comprehensive patent reform legislation
is farther off than Chairman Leahy would like.

For
additional information regarding this topic, please see:

•
"PUBPAT Expresses 'Deep Concern' over Senate False Marking Provision,"
March 25, 2010
EPO Search Fees Set to Decrease on April 1, 2010

March 29, 2010

By Christopher P. Singer —

The U.S. Patent and Trademark Office sent out an e-mail alert on March 26,
2010 advising that it has been informed by the International Bureau of the
World Intellectual Property Organization (WIPO) that the European Patent Office
(EPO) will decrease its search fee when acting as the International Search
Authority (ISA). The fee change
will become effective on April 1, 2010. The EPO currently charges $2515 to act as the ISA. According to the e-mail announcement,
as of April 1, 2010 the EPO will charge $2485 to act the ISA. A revised PCT Fee Schedule will be made
available here.

Of course, April 1, 2010 also marks the effective
date of the more substantive changes to EPO rules, including revisions to divisional
application filing requirements, mandatory responses to EPO-issued search
reports and opinions, and additional requirements relating to amending
applications. A brief overview of
those three particular rule changes can be found here.
In re Arora (Fed. Cir. 2010)

March 28, 2010

    By
Donald Zuhn —

Earlier
this month, the Federal Circuit, in In re
Arora, affirmed a decision of the Board of Patent Appeals and Interferences
affirming the rejection of claims 11-16 of Appellant Arun Arora's application
as being obvious in view of U.S. Patent Nos. 6,978,286 and 5,934,273. Claims 11-16 of Dr. Arora's application
relate to a method for converting drug dosages to prevent overdose. Representative claim 11 recites:

11. A method for converting drug dosages to
prevent overdose, comprising the steps of:
    defining
a common medication reference range;
    assigning
dosages of first and second drugs to respective values within the common
medication reference range;
    prescribing
a particular dosage of the first drug;
    identifying
a value within the common medication reference range for the particular dosage;
and
    permitting
prescription fulfillment with a dosage of the second drug which corresponds
[to] the dosage of the first drug using the common medication reference range.

On
appeal, Dr. Arora argued that the '286 and '273 patents fail to disclose or
suggest the steps of "assigning dosages of first and second drugs to
respective values within the common medication reference range" or "permitting
prescription fulfillment with a dosage of the second drug which corresponds
[to] the dosage of the first drug using the common medication reference range."

In
an opinion issued per curiam, the
panel disagreed, stating that "substantial evidence supports the Board's
finding that the references teach those two limitations." In response to Dr. Arora's argument
that '286 patent "does not teach 'assigning dosages' of two different
drugs to values in the same reference range, i.e., the claimed 'common
medication reference range,'" the panel states that "[e]ven if [the
'286 patent] does not explicitly disclose conversion to a common reference
range, . . . the Board found that a person of ordinary skill in the art would
appreciate that dosages should be assigned to respective values in a common reference
range based on [the '273 patent's] teaching that equipotent doses of different
medications should be directly compared." In response to Dr. Arora's argument that the '273 patent "should
be understood as limited to the narrow teaching that a smaller amount of a drug
is needed when delivered via [the '273 patent's] inventive dry powder inhaler
instead of a metered dose inhaler," the panel states that "[i]t is
well-settled . . . that a prior art reference must be considered for all that
it teaches to those of ordinary skill in the art, not just the embodiments
disclosed therein," and that the '273 patent "teaches the broad
principle that different drugs are equipotent at different dosages." The panel therefore concluded that "[s]ubstantial
evidence supports the Board's findings regarding the teachings of [the '273
patent], and the Board did not err in concluding that a person of ordinary
skill in the art would apply those teachings to [the '286 patent] to convert
dosages of two different drugs into a 'common medication reference range,'"
and affirmed the Board's decision affirming the rejection of the claims.

In re Arora (Fed. Cir. 2010)
Nonprecedential
disposition
Panel:
Circuit Judges Gajarsa, Plager, and Dyk
Per curiam opinion

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