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Patenting Products of Nature:
Assoc. Molecular Pathol. v. U.S. PTO
Technology Transfer Tactics
Webinar
August 31, 2011
Kevin E. Noonan, Ph.D.
Outline of the Talk
 Introduction
 How did we get here?
 Gene patenting myths
 Patenting “products of nature”
 19th Century Supreme Court cases
 Brogdex, Funk Bros.
 Bergy and Chakrabarty
Outline of the Talk
 AMP v. US PTO (“the Myriad case”)
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Parties and interests
The claims: DNA and methods
The arguments
The court’s decision
CAFC opinion
 Consequences and Recommendations
 Alternatives to patent
 Effects of non-disclosure
 Policy and societal concerns
Introduction
How did we get here?
 Tremendous success of a technological age
 Biotechnology the beneficiary of strong
patent protection
 Biotechnology developed in university
setting – 1980 Bayh-Dole Act promotes
patenting
 But success breeds criticism – from variety
of sources
 These include political criticism from those
opposed to university patenting
5
Where is here?
 Politically-motivated groups in the arena:
ACLU and PubPat
 PubPat challenges variety of patents (not just
biotech); notable the WARF human ESC
patents
 General attitude that patents have become
too powerful and retard innovation (little
empirical support)
 Time ripe for Myriad challenge: in addition,
the “right” defendant, due to aggressive
patent enforcement tactics
6
Gene Patenting Myths
 The Ownership Myth
 Michael Crichton, ACLU
and “Who Owns You”
 The Information Myth
 “Physical Embodiment of Genetic Information”
 Information not what’s patented; “DNA is a
chemical compound, albeit a complex one”
Gene Patenting Myths
 The “Natural Product” Myth
 Isolated DNA not found in nature
 cDNA not found in nature
 Natural products not patent-ineligible
per se
 The “Inhibits Research” Myth
 The Anti-commons are not tragic
 Progress promoted by disclosure
 No evidence of research inhibition
Patenting “Products of Nature”
Is it possible?
 Widespread belief
that “products of
nature” cannot be
patented
 Little support in
binding precedent
 Some sporadic
support for both
sides of the
argument in lower
court cases
No binding precedent
 19th Century cases
 Wood Paper Patent Cases (1874)
 Cochrane v. Badische Anilin Soda Fabrik, (1874)
 20th century cases
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American Fruit Growers v. Brogdex (1931)
Funk Bros. Seed Co. v. Kalo Inoculant Co. (1948)
In re Bergy (1979)
Diamond v. Chakrabarty (1980)
Bilski v. Kappos (2010)
What does the law say?
20th century cases
Funk Bros. Seed Co. v. Kalo Inoculant Co.
(1948):
 Discovery of the fact that certain strains of each
species of these bacteria can be mixed without
harmful effect to the properties of either . . . is no
more than the discovery of some of the handiwork
of nature and hence is not patentable . . . The
combination of species produces no new bacteria,
no change in the six species of bacteria, and no
enlargement of the range of their utility . . . does
not improve in any way their natural functioning.
What does the law say?
20th century cases
Diamond v. Chakrabarty (1980):
 The laws of nature, physical phenomena, and
abstract ideas have been held not patentable . .
. Thus, a new mineral discovered in the earth or
a new plant found in the wild is not patentable
subject matter. Likewise, Einstein could not
patent his celebrated law that E=mc2; nor could
Newton have patented the law of gravity. Such
discoveries are "manifestations of . . . nature,
free to all men and reserved exclusively to
none."
What does the law say?
 Diamond v. Chakrabarty (1980)
 [R]espondent's micro-organism plainly qualifies as
patentable subject matter. His claim is not to a
hitherto unknown natural phenomenon, but to a
nonnaturally occurring manufacture or
composition of matter - a product of human
ingenuity "having a distinctive name, character
[and] use."
 Better way to state the proposition: mere
products of nature, unmodified by man, are not
patent-eligible (predominantly because they
are not novel)
What does the law say?
20th century cases
 In re Bergy (1979):
 Therefore, in case there is doubt as to whether
the examiner's product-of-nature rejection is still
an issue in this case, in the interest of judicial
economy we rule on it now . . . We hold that
Bergy's claim 5 clearly does not define a
product of nature.
 We were thinking of something preexisting and
merely plucked from the earth and claimed as
such, a far cry from a biologically pure culture
produced by great labor in a laboratory and so
claimed.
AMP v. USPTO (“Myriad”)
Myriad: The claims
 Two broad types of claims at issue: claims to
isolated DNA molecules, and diagnostic
method claims
 DNA claims recite “isolated” DNA encoding
specific amino acid sequences (cDNA)
 Also claims to oligonucleotide probes
 Method claims: methods of detecting mutation
or providing a diagnosis/risk assessment
 Method claims involve “comparing” mutant
sequence to normal sequence
17
Myriad: The claims
 Composition of matter claims covering
“isolated DNA” covering the BRCA 1 and
BRCA 2 genes. Claim 1 of US Patent
5,747,282 is representative of this class of
claims:
An isolated DNA coding for a BRCA1
polypeptide, said polypeptide having the amino
acid sequence set forth in SEQ ID NO:2.
18
Myriad: The claims
 Methods of detecting mutations in the BRCA
genes. Claim 1 of US Patent 5,709,999 is the
only claim in this class:
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
19
District Court Decision
 Judge Sweet agrees that DNA an
unpatentable “product of nature”
 DNA is “the physical embodiment of genetic
information”
 Distinguishes other types of “natural
products” (antibiotics, vitamins) on this basis
 Method claim invalid under Bilski
20
Federal Circuit Decision
 Oral argument April 4th; decision July
29th
 Three separate opinions, Judge Lourie
wrote the majority opinion
 Judge Moore concurred and Judge
Bryson concurred in part and dissented
in part
 Overall consensus on outcome for most
issues
 Important differences in approach
Federal Circuit Decision
 Consensus on:
 Standing (but for just one plaintiff)
 Patent-ineligibility of diagnostic method
claims
 Patent-eligibility of screening method
claims
 Patent-eligibility of composition of matter
claims to cDNA
Federal Circuit Decision
 Disagreement over patent-eligibility of
“isolated DNA” claims encompassing
genomic DNA and primers
 Also fundamental differences in
approach in “majority” opinion, but
agreement on decision in this case
 Judge Bryson dissenting indicates a
different approach
Federal Circuit: Majority
 Judge Lourie: “isolated DNA” patenteligible because it satisfies the Supreme
Court “test” from Funk Brothers and
Chakrabarty that a natural product can be
patented provided that there is “a change
in the claimed composition's identity
compared with what exists in nature” and
“that human intervention has given
‘markedly different,’ or ‘distinctive,
characteristics.
 Chemical changes in isolated DNA enough
Isolated DNA claims
 “Isolated DNA”
comes in two
forms: genomic
DNA and cDNA
 Significant
differences in
structure and
how isolated/
prepared
Is DNA a “product of nature”?
 Genomic DNA may
be
 But chemically
modified from
native state
 cDNA certainly is not
 Claims limited to
specific sequence
that does not exist
prior to human
intervention
Federal Circuit: Majority
 19th Century cases dismissed as being
based on novelty issues
 Many lower court decisions directed to
“products of nature” also dismissed as
precedent as not addressing
fundamental issue before court
 Funk Bros. and Chakrabarty primary
precedent
 In re Bergy also dismissed as being
non-precedential
Federal Circuit: Concurrence
 Judge Moore: DNA a polymer, like
nylon
 Isolated DNA not just purified from
nature
 Also reads precedent as requiring
alteration of natural product
 This rationale convincing for cDNA and
oligonucleotide fragments because do
not occur in nature – made by man
Federal Circuit: Concurrence
 “Isolated DNA” claims are a “closer
case”
 Not entirely convinced that isolation
effects sufficient change to satisfy
precedent
 But, not “drawing on a blank canvas” cannot ignore 30 years of PTO practice
and CAFC precedent (Amgen v. Chugai
etc.)
 Change in the law up to Congress
“Isolation” vs. “Purification”
 Both the majority opinion and Judge
Moore’s concurring opinion set up a
dichotomy
 “Isolated” DNA as claimed patenteligible because it has been chemically
transformed
 Thus, DNA has not “merely” been
isolated
 Implications for other biological
molecule-based inventions
Federal Circuit: Dissent
 Judge Bryson: “common sense”
conclusion that human DNA not patenteligible (including oligonucleotide primers)
 Applies the same Supreme Court
precedent, comes to the opposite
conclusion
 Concern seems to be negative effects on
whole genome sequencing
 Discounts PTO practice and deference to
Congress, citing DOJ position
DOJ amicus brief
 On the one hand, the brief argues that
manipulated DNA (cDNA, vectors,
oligonucleotides, etc.) are patent-eligible
because they show “the hand of man”
 On the other, isolated genomic DNA not patenteligible because it is not sufficiently changed
 Tries to “split the baby” by arguing on both
sides of the issue
 Genetic diagnostic methods also patentineligible, since merely a “natural phenomena”
 Not from the Department of Commerce or the
PTO and seemingly with little or no PTO input
Federal Circuit Decision
 Method claims: claims reciting merely
“analyzing” or “comparing” fail the
“machine-or-transformation” test
 Claims to screening methods do not,
since cell growth in presence of putative
BRCA inhibitor is transformative
Method claims
 Methods that “compare” and “correlate”
mutations in the BRCA genes with an
increased risk of breast or ovarian cancer.
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.
Claim 2 of US Patent 6,033,857
Federal Circuit Decision
 Standing: rejects standing for most
plaintiffs – no immediacy and reality
 One plaintiff (Dr. Ostrer) on record that
he will “immediately” provide testing
 This is sufficient for standing
 Recent controversy on whether the
predicate condition – Dr. Ostrer’s
capacity to begin immediate testing - still
met
Federal Circuit Decision
 Status: a few possibilities
 Petition for panel rehearing
 Petition for rehearing en banc
 Petition for writ of certiorari
 Both parties have grounds for filing
 Plaintiffs filed petition for rehearing on
August 25th
 Parties have 90 days to petition for
certiorari
Consequences and Recommendations
Consequences of CAFC decision
 For now, “gene patents” claim patenteligible subject matter
 Practically, consensus decision on gene
patent-eligibility for cDNA covers most
patents on genes
 Isolated genomic DNA claims less certain,
but less valuable
 Oligonucleotide claims more certain as
man-made manufactures
Consequences of PON ban
 Not a good thing for DNA patents, but not
the end of the world
 BUT, the philosophy not limited to DNA
claims
 The best biologic drugs will be as close as
possible to how they exist “in nature” – in
the body
 The better the drug, the less patent-eligible
it will be
 Can’t be the correct result
Proposition
 Bad analogies make bad law
 Isolated DNA is not a leaf (Judge Dyk),
or a mineral (DOJ brief) or information
(Judge Sweet) or an arm (Morley Safer)
 Consider these examples:
 Isolated chemical compound from crude oil
useful as a lubricant
 Isolated chemical compound from a plant
useful as a drug
 Isolated protein from an animal useful to
cure/ameliorate human disease
Consequences of CAFC decision
 Diagnostic method claims less certain
 Claims at issue flawed by claim language
 Interpreted to broadly encompass mere
comparison of germline and patient BRCA
gene sequences by inspection
 Claims do not recite affirmative steps for
obtaining sequence
 Myriad has many other claims that do
recite such steps
Consequences of CAFC decision
 Diagnostic method claims generally less
certain
 Supreme Court will consider question this
term in Mayo Labs v. Prometheus
 Slightly different question, since the
Prometheus case involves determination of
effective dose of administered drug
 Basis for Federal Circuit to find a
“transformation”
 Also implicates “practice of medicine”
Why should these claims be
patent-eligible?
 Only way to protect “correlation” discoveries –
basis for molecular diagnostics
 Promotes disclosure from academic/medical
scientists, and translation of information into
patentable technologies = innovation
 Alternatives – such as trade secret – greater
negative effects
 Risk of upsetting balanced approach to innovation
(academics do basic research, industry develops
commercial embodiments)
Possible Solutions
• Machine or transformation test remains
viable
• De-emphasize purely informational aspects
of claims; recite claims containing more
active steps (like “sequencing”)
• Recite method of treatment step relating to
diagnosis
 But this raises MuniAuction issues
• Will depend on Supreme Court decision in
Prometheus
Additional considerations
 Potential for a patent “thicket”
 Involves reagents for performing the assays
– need to license dozens/thousands of
genes correlated with disease
 Some efforts around this (patent pooling,
standard setting SNP consortium,
Navigenics “ASCAP” solution)
 Will get worse before it gets better,
particularly regarding personalized medicine
45
Unintended (?) Consequences
 No remedy for women
 Myriad patents expire in ~4-6 years
 Test availability depends on insurance
companies, not patents
 Financial impact on biotech industry
 Burrill Report
 http://www.patentdocs.org/2011/01/steve-burrill-makespredictions-for-the-biotech-industry-in-25th-annualreport.html
Unintended (?) Consequences
 Patent ineligibility promotes nondisclosure
 Non-disclosure contrary to academic
mission
 Academia (U.S. taxpayer) as
uncompensated corporate R&D
department (foreign and domestic)
Unintended (?) Consequences
 The future will be different from the
past – much more complicated
 Trade secret protection perpetual
(and biotech hard to reverse
engineer)
 “Natural product” patent ineligibility
extends to all medicinal chemistry
and biologic drugs
Thank you!
Kevin E. Noonan, Ph.D.
Partner [ ] 300 South Wacker Drive [ ] Chicago, Illinois 60606-6709
312-913-2145 direct [ ] 312-913-0001 main [ ] 312-913-0002 fax
[email protected] [ ] www.mbhb.com [ ] www.patentdocs.org