Download Genes and IPR

Bioinformatics and Gene Discovery
Center for Biological Sequence Analysis, DTU, June 12,
2007
Jens Viktor Nørgaard,
Symphogen A/S
Agenda
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Commercials
What is a patent
Patentability basics
• Novelty, inventive step & other criteria
Claims
Inventors
Timelines
Patents as information source
Searching for patent information
Ethics and patent law
Who am I
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MSc in Forestry, PhD in Genetics & Biochemistry (Royal
Agricultural University, now University of Copenhagen)
10 years of academic research, University of Copenhagen
Patent consultant since 1998
European Patent Attorney 2003
Director of IPR, Symphogen AS
Previously: NsGene (Biotech), Hoiberg (Patent Attorneys)
What is a patent attorney?
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Represents clients/employer before patent authorities
No authorisation requirements in Denmark
Authorisation required in a number of countries: United
Kingdom, Germany, France, United States, Japan, EPO
(European Patent Office)
Qualifications (European patent attorney):
• Scientific degree; MSc, PhD or equivalent
• Linguistic skills, writing & speaking
• Business attitude
• Patent training > 3 years
• Pass a qualifying exam
What does a patent attorney do
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Writing patent applications
Preparing legal documents
Monitoring dead-lines
Searching for and analysing technical information
Providing legal opinions on patent issues
Preparing and filing responses to patent authorities
Training of scientists/clients/students/trainees
Strategic advice/planning to Universities and Corporations
License negotiations and agreements
Links
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Training of Danish patent attorneys (Certified
Danish Patent Attorney): http://www.difi.dk/
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How to become a European Patent Attorney:
http://www.european-patentoffice.org/epo/pubs/pat_attorney/pdf/patbro_
e.pdf
Patents?
What is a patent?????
What is a Patent?
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Which rights arise from a granted patent?
Patents I
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A patent application - ”paid-for publication”,
source of information
A granted patent – a legal document defining
an injunction right & a right to claim damages
A patent does not give the owner any right to
exploit the invention
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Determined by other’s patents and by legislation
Patents II
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Agreement between inventor and society
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Patenting forces publication
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Inventor gets a time-limited monopoly
Society gets a description of the invention
Stimulates exchange of information
Stimulates research and development
Alternative to patents
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Secrecy
Patentability Requirements
Patentability Requirements
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Novelty
Inventive step
Clarity
Conciseness
Enablement
Sufficiency of disclosure
Utility
Industrial applicability
Exceptions to patentability
Novelty
Novelty
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Novelty = not available to the public on the date of
filing
Available = made available to the public without any
confidentiality barriers
A compound (including proteins and genes) is not
known merely because it is found in nature (e.g. an
mRNA in a cell, a protein in a plant)
Compounds can be made available by
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decribing the structure of the compound (structural formula
or sequence)
describing a method of producing/synthesising
describing a method of isolating/purifying the compound
The Concept of Novelty
State of the Art (known)
1. a cup
Patent Application
1. a cup with a handle (novel)
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a cup
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a 15 cm tall cup (novel)
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a cup
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a cup
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a red cup (novel)
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a cup
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a container for liquid (not
novel)
a cup adapted to hold coffee
(non-novel)
The Concept of Novelty
State of the art
1. cells secrete a protein with
activity X
2. the protein with acivity X can
be purified from organism Y
using method Z
3. protein with sequence ...
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peptide with sequence:
ypskpdnpgedapaedmaryysalr
hyinlitrqry (NPY)
conservative substitutions
can be made in NPY
Patent application
1. an isolated protein with
sequence ... having activity X
2. an isolated protein with
sequence ... having activity X
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glycosylated protein with
sequence ...
peptide with sequence:
ypskpdnpgeeapaedmaryysalr
hyinlitrqry
peptide with sequence:
ypskpdnpgeeapaedmaryysalr
hyinlitrqry
The Concept of Novelty
State of the art
1. gene X was cloned using
primers A and B
2. genes 1 to N can be
used for treating
diseases 1 to N
3. gene x promotes cell
division
Patent application
1. gene X having sequence
...........
2. gene 5 for treatment of
obesity......
3. use of gene x as a
growth factor
Inventive Step
Non-obviousness
Inventive Step/Non-obviousness
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Inventive step/”non-obviousness”
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Difference between prior art and invention must be of a
certain ”size”
No patents for trivial inventions
Patents promote technical progress, not stand-still
Non-obvious for the person skilled in the art
Person skilled in the art
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Fictitious person
Not a Nobel prize winner
Average skills
Knows everything (all languages) but is conservative, does not
go against established prejudice, does not try to enter
unpredictable areaas nor take uncalculable risks
Inventive Step/Non-obviousness
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Complex arguments
Room for creativeness
Large differences between major patent autorities: EP,
JP, US:
New sequence (new compound, new structure)
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US – any new stucture is non-obvious
JP – a significant and unexpected effect must be associated
with the new structure, or undue difficulty in obtaining new
sequence
EP – was the sequence difficult to make? any unexpected
technical effects associated with the new sequence? was it
obvious to try and see?
The Concept of Inventive Step
State of the art (known)
1. a cup
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Patent application
1. a cup with a handle
(inventive?)
a cup
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a cup
a 15 cm tall cup (inventive?)
a cup adapted to hold coffee
(non-novel)
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5.
a cup
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a red cup (inventive?)
5.
a container for liquid (not
novel)
a cup
The Concept of Inventive Step
State of the art
1. cells secrete a protein with
activity X
2. the protein with acivity X can
be purified from organism Y
using method Z
3. protein with sequence ...
4.
5.
peptide with sequence:
ypskpdnpgedapaedmaryysalr
hyinlitrqry (NPY)
conservative substitutions
can be made in NPY
Patent application
1. an isolated protein with
sequence ... having activity X
2. an isolated protein with
sequence ... having activity X
3.
4.
5.
glycosylated protein with
sequence ...
peptide with sequence:
ypskpdnpgeeapaedmaryysalr
hyinlitrqry
peptide with sequence:
ypskpdnpgeeapaedmaryysalr
hyinlitrqry
The Concept of Inventive Step
State of the art
1. gene X was cloned using
primers A and B
2. genes 1 to N can be used for
treating diseases 1 to N
3. gene x promotes cell division
4. an EST annotated as having
homology to an enzyme with
activity Y
Patent application
1. gene X having sequence
...........
2. gene 5 for treatment of
obesity......
3. use of gene x as a growth
factor
4. isolated and purified protein
having sequence X and
enzyme activity Y
Clarity, Sufficiency, Enablement,
Utility
Clarity, Sufficiency, Enablement
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”Quality requirements”
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No short cuts by trying to keep part of the
invention secret
No short cuts by filing too early – before invention
is complete
Legal certainty (possible for 3rd party to determine
scope of claims)
Clarity, Conciseness
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The claims must be clear and concise
Results in many definitions:
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Sequence homology
Binding specificity
Competition for antigen/epitope
Binding affinities
Alignment
Hybridisation
High stringency
Sufficiency, Written Description
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Description must be sufficient
Sufficiency – when the skilled person can carry out
the invention – don’t try to leave anything out
Also a question of credibility
Written description – you must show that you were in
possession of the invention upon filing – do not file
before you completed the invention
Utility
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Industrial applicability/”utility”
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USA – credible, substantial and specific utility (a
use for the invention) – high hurdle, used by the
Patent Office to refuse trivial or premature
applications
EPO – the industrial applicability of a sequence
must be given in the application (Biotekdirektivet)
– low hurdle
Patent Claims
Patent Claims
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The claim defines the invention
The claim must satisfy the patentability requirements
The description may only be used to interpret the
features of the claims
Rights arising from Patent I
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Productpatent – forbid others to:
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make, use, offer for sale, sell, import
Claims
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1. An isolated polypeptide comprising the amino acid
sequence of SEQ ID No. 2, or a biologically active sequence
variant having at least 70% sequence identity to SEQ ID No.
2.
2. A pharmaceutical composition comprising protein X.
3. An expression vector comprising a sequence coding for
protein X.
Rights arising from Patent II
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Method patent – forbid others to
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Use the method
Method of manufacture also protects the products
Claims:
1. Use of protein X for the preparation of a pharmaceutical
composition.
2. Use of protein X for the preparation of a medicament for the
treatment of disease Y.
3. A method for identifying a compound with activity X,
comprising testing the compound in screening assay Y.
4. A method of producing protein X, comprising culturing a host
cell transfected with vector Y and recovering protein X from
the culture medium.
Claim Types, Product
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Nucleic acid
Polypeptide
Antibody
Expression vector
Screening assay (kit)
Array
Pharmaceutical composition
Cells
Data carrier
Claim Types, Methods
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Method of treatment (of disorder)
Medical use (any therapeutic use)
Second medical use (disease specific therapeutic use)
Diagnostic use
Method of preparing compound/protein
Method of identifying modulator of activity
Method of isolating compound/protein/gene
Inventors
Why??
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European Patent Convention (Art 60)
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The right to a European Patent belongs to the
inventor or his successor in title.
US-statute
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Applications are filed in the name of the inventors
Inventorship is required to be accurate
Who is an inventor
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Not an award for good work!
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No justice at all!
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Inventorship is conception
Conception
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”the formation in the mind of the inventor of a
definite and permanent idea of the complete and
operative invention”
Conception is more than a goal
Must include how to make and use without undue
experimentation
Reduction to practise (=testing an invention
conceived by another) does not make you an inventor
Is the mental part of the invention, not the
constructive part
Joint inventions
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Joint conceivers are joint inventors
Do not need to work together
Do not need to make the same type or
amount of work
Do not need to contribute to every claim
Timelines
The Typical Life of an International
Application
PCT Patent Application Process
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12
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28
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MONTHS
Patenting Process
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First filing– timing
Early filing –
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Easier to get novelty
Enablement, sufficiency, utility?
Later filing –
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More time to prove function (of a gene or protein)
Longer patent term (evergreening of Pharmaceutical
products)
Patenting Process
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Filing of updated PCT-application
Filed within 12 months of the first filing
Claims priority from the earlier filing => prior art is
anything published before the priority date
One single application in one language can give
patents in 130+ countries (1 May, 2007, 137
countries)
Patenting Process
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Novelty search (database search)
Identification and classification of publications (patent
applications and scientific papers)
Possibility to evaluate the fate of the patent
application
Patenting Process
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Publication of the application 18 months from first
filing
Patenting Process
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Preliminary examination –
• A possibility to evaluate the patentability
• Dialog with examiner at EPO or PRV (Swedish
PTO); written procedure, but possibilty for
interview
International preliminary report on patentability
• Report on the patentability
• Preliminary, so not binding on national authorities
Patenting Process
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Entry into national phase (US, JP, CA, AU, IN, CN, etc)
or regional phase (Europe, Eurasia, Africa).
• Selection of countries
• Geographic strategy
• Language - translations
• Costs
Patenting Process
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The application is adjusted to national law
Patent grant/refusal
Possibility for opposition from third parties
Can be maintained up to 20 years from PCT filing
date
Patents and Applications
as Information Source
How to Read a Patent Application
Patent Applications Layout I
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Frontpage
• Bibliographic information
Background of the invention
• Corresponds to introduction
Summary of the invention
• Copy of the indpendent claims, perhaps arguments
Brief description of the drawings
• Figure legends
Detailed description
• Definitions, description of alternatives, variations, uses
• Supports sub-claims, fall-back positions, enablement, how to
make and use the invention
Layout II
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Examples
• Materials & methods, results, rarely any discussion
Claims
• Main claims and independent claims
Drawings (not Figures!)
• Always at the end of the application
Sequence listing
• Amino acid and nucleotide sequences
• Made according to special formal requirements
International (PCT) Applications
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APPLICATIONS!! NOT PATENTS
Filed locally (e.g. Denmark)
Treated and published centrally (WIPO, EPO, USPTO,
PRV, JPO).
Potentially covers 137 countries (holes in South
America and the Arab world)
PCT Countries
PCT-applications
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Filed, searched, published, examined
Timeline: priority year, published after 18
months, PCT phase ends after 2½ years
Example: WO 2006/007853 (Symphogen)
PCT application
US-applications/Patents
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US-applications published at 18 months
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Long numbers, US2007020279 A1 (Johnson et al)
US-patents, published at issue
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Granted patents
Short numbers, fx US 5,824,307 (Johnson et al)
US-patent
US-application
EP-patents
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Applications published at 18 months
Most are published as PCT applications (WO number)
Published as B1 publication at grant
Granted European patent
Finding Patent Information
for Free
Finding Patent Information – for Free
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espacenet
• Link: http://ep.espacenet.com
• Simple search functions
• Abstract from the application
• OCR text available for English, French and German language
applications
• Publication as pdf-file – full document/page by page
USPTO
• Link: http://www.uspto.gov/patft/index.html
• Simple and advanced search tools
• Patent number search
• Free text search
• OCR text available
• Publication available in Tiff format, page by page
Finding Patent Information – for Free
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Patentscope (WIPO)
• Link: http://www.wipo.int/pctdb/en/
• Advanced, simple, or structured search functions
• Abstract from the application
• OCR text available for English, French and German
language applications
• Publication as pdf-file
• Other documents (priority documents etc) as pdffile
Downloading Patent Documents for
Free
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pdf’s of European patents and applications (since
2004): https://publications.european-patentoffice.org/PublicationServer/search.jsp
pdf’s of PCT applications from Patentscope (WIPO):
http://www.wipo.int/pctdb/en/
pdf’s of PCT applications file inspection at EPO:
http://www.epoline.org/portal/public/!ut/p/kcxml/04_
Sj9SPykssy0xPLMnMz0vM0Y_QjzKLN4i3dAHJgFjGpvq
RqCKOcAFvfVP_NxU_QD9gtzQiHJHRUUA43OWZA!!/delta/base64xm
l/L3dJdyEvUUd3QndNQSEvNElVRS82XzBfOUc!
Finding Patent Information
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Blast searches in patent database at NCBI:
http://www.ncbi.nlm.nih.gov/BLAST/
Example:
Find US patents covering persephin:
http://www.ncbi.nlm.nih.gov/entrez/viewer.fcgi?db=protein&val
=2935710
• Copy sequence
• Paste into NCBI Blast (pat)
http://www.ncbi.nlm.nih.gov/BLAST/
• Searching.....
• Copy patent number
• Go to http://www.uspto.gov/patft/index.html
• Go to Patent Number Search
• Paste number - search
Limitations of NCBI Blast
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Accession policy appears inconsistent / random
Only a small fraction of patented sequences are found at NCBI
Alternatives:
• Search for gene names
• Commercial sequence databases (Chemical Abstracts
Registry, PCT-gen (WIPO), DGene (Derwent))
Ethics and Patent Law
Ethics and Patent Law
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Why ethics?
Controversial issues:
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Patents on life (Dolly the Sheep, Harvard Onco-mouse)
Plant patents
Human genes
Stem cells
Human embryos (cryopreserved embryos)
Breast cancer diagnostics (brca genes)
Computer programs
Ethics and patent law
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”Non-controversial” issues:
• Patents on weapons
• Patents on nuclear power plants/weapons
• Patents on chain-saws
• Industrial fishing equipment
Greenpeace
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Greenpeace believes the EPO is abusing patent law
for the benefit of the few multinational giants that
control the genetic engineering industry.
Over 150 patents on human and animal genes and
over 50 patents on seeds have been granted by the
EPO since it started applying the EU Patents Directive
in 1999.
Greenpeace opposes the wording of the EU Patents
Directive and calls for a re-negotiation of the Directive
at the EU level.
Greenpeace opposes patents on life. The sell-out of
biological diversity and intellectual property rights
that restrict access to plant genetic resources must
stop. (source: Greenpeace Web-site)
Greenpeace reports
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http://www.greenpeace.org/raw/content/inter
national/press/reports/greenpeace-patentson-life-in.pdf
http://www.greenpeace.org/international/pres
s/reports/the-true-cost-of-gene-patents
For & Against Patents on Genes
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Not novel – but novel in isolated (=available) form
Not invented by the inventor – but isolated by the
inventor
Isolation is no invention – but the isolated gene can
solve a technical problem and has utility
Immoral to patent life – why? – living creatures
(animals, plants, microorganisms) have been
regarded as goods for centuries
Patenting genes is contrary to development – mere
allegation, do not confuse patent applications with
valid patents
Ethics
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Allegation: gene claims are way too broad
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My answer: gene claims should have same scope as all other
claims
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Cover all uses (product claims)
Gene claims should be restricted to use (Biotechnology directive as
implented in France and Germany)
Stops research
Traditional compound claims cover all uses
Why should gene patent stop development and research while
patents in other fields enhance research?
Again: do not confuse patent applications with valid granted claims
Part of the problem:
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Backlog of human gene patent applications results in uncertainty
Sequence non-obviousness in the US
USPTO grants invalid patents
Very limited research exemption in the US
Human Gene Patent Applications
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The result of high-througput sequencing
Genes predicted with software
No biological data
Limited expression data (rarely quantitative)
Long list of genes (several 1000)
Laundry list of possible functions
Laundry list of possible uses
• Diagnostics
• Therapeutics
• Screening
Good Hunting!