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Advanced Bioinformatics, DTU Genes and Patents. Jens Viktor Nørgaard, NsGene A/S. Who am I. Msc in forestry, KVL (RAU, Royal Agricultural University) Phd in genetics & biochemistry, KVL 10 years of academic research, University of Copenhagen Patent consultant since 1998

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Advanced bioinformatics dtu genes and patents

Advanced Bioinformatics, DTUGenes and Patents

Jens Viktor Nørgaard,

NsGene A/S


Who am i
Who am I

  • Msc in forestry, KVL (RAU, Royal Agricultural University)

  • Phd in genetics & biochemistry, KVL

  • 10 years of academic research, University of Copenhagen

  • Patent consultant since 1998

  • European Patent Attorney 2003

  • Director of IPR (Intellectual Property Rights), NsGene A/S

  • jvn@nsgene.dk

  • www.nsgene.com


What is a patent attorney
What is a patent attorney?

  • 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
What does a patent attorney do

  • 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
Links

  • Training of Danish patent attorneys (Certified Danish Patent Attorney): http://www.difi.dk/

  • How to become a European Patent Attorney: http://www.european-patent-office.org/epo/pubs/pat_attorney/pdf/patbro_e.pdf


Agenda
Agenda

  • What is a patent

  • Patentability basics

    • Novelty, inventive step & other criteria

  • Claims

  • Break

  • Timelines

  • Patents as information source

  • Ethics and patent law

  • Searching for patent information

  • Searching for patented genes


Patents

Patents?

What is a patent?????


What is a patent
What is a Patent?

  • Which rights arise from a granted patent?


Patents i
Patents I

  • 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 patentee any right to exploit the invention


Patents ii
Patents II

  • Agreement between inventor and society

    • Inventor gets a time-limited monopoly

    • Society gets a description of the invention

  • Patenting forces publication

    • Stimulates exchange of information

    • Stimulates research and development

  • Alternative to patents

    • Secrecy



Patentability requirements1
Patentability Requirements

  • Novelty

  • Inventive step

  • Clarity

  • Conciseness

  • Enablement

  • Sufficiency of disclosure

  • Utility

  • Industrial applicability

  • Exceptions to patentability



Novelty1
Novelty

  • 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

  • Compounds can be made available by

    • 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)

a cup

a cup

a cup

a cup

a cup

Patent Application

a cup with a handle (novel)

a 15 cm tall cup (novel)

a cup adapted to hold coffee

(non-novel)

a red cup (novel)

a container for liquid (not novel)

The Concept of Novelty


The concept of novelty1

State of the art

cells secrete a protein with activity X

the protein with acivity X can be purified from organism Y using method Z

protein with sequence ...

peptide with sequence: ypskpdnpgedapaedmaryysalrhyinlitrqry (NPY)

conservative substitutions can be made in NPY

Patent application

an isolated protein with sequence ... having activity X

an isolated protein with sequence ... having activity X

glycosylated protein with sequence ...

peptide with sequence: ypskpdnpgeeapaedmaryysalrhyinlitrqry

peptide with sequence: ypskpdnpgeeapaedmaryysalrhyinlitrqry

The Concept of Novelty


The concept of novelty2

State of the art

gene X was cloned using primers A and B

genes 1 to N can be used for treating diseases 1 to N

gene x promotes cell division

Patent application

gene X having sequence ...........

gene 5 for treatment of obesity......

use of gene x as a growth factor

The Concept of Novelty


Inventive step non obviousness

Inventive StepNon-obviousness


Inventive step non obviousness1
Inventive Step/Non-obviousness

  • Inventive step/”non-obviousness”

    • 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

      • 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 obviousness2
Inventive Step/Non-obviousness

  • Complex arguments

  • Room for creativeness

  • Large differences between major patent autorities: EP, JP, US:

  • New sequence (new compound, new structure)

    • 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)

a cup

a cup

a cup

a cup

a cup

Patent application

a cup with a handle (inventive?)

a 15 cm tall cup (inventive?)

a cup adapted to hold coffee

(non-novel)

a red cup (inventive?)

a container for liquid (not novel)

The Concept of Inventive Step


The concept of inventive step1

State of the art

cells secrete a protein with activity X

the protein with acivity X can be purified from organism Y using method Z

protein with sequence ...

peptide with sequence: ypskpdnpgedapaedmaryysalrhyinlitrqry (NPY)

conservative substitutions can be made in NPY

Patent application

an isolated protein with sequence ... having activity X

an isolated protein with sequence ... having activity X

glycosylated protein with sequence ...

peptide with sequence: ypskpdnpgeeapaedmaryysalrhyinlitrqry

peptide with sequence: ypskpdnpgeeapaedmaryysalrhyinlitrqry

The Concept of Inventive Step


The concept of inventive step2

State of the art

gene X was cloned using primers A and B

genes 1 to N can be used for treating diseases 1 to N

gene x promotes cell division

an EST annotated as having homology to an enzyme with activity Y

Patent application

gene X having sequence ...........

gene 5 for treatment of obesity......

use of gene x as a growth factor

isolated and purified protein having sequence X and enzyme activity Y

The Concept of Inventive Step



Clarity sufficiency enablement
Clarity, Sufficiency, Enablement

  • ”Quality requirements”

    • 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
Clarity, Conciseness

  • The claims must be clear and concise

  • Results in many definitions:

    • Sequence homology

    • Alignment

    • Hybridisation

    • High stringency

    • Receptor binding


Sufficiency written description
Sufficiency, Written Description

  • 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
Utility

  • Industrial applicability/”utility”

    • 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 claims1
Patent Claims

  • 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
Rights arising from Patent I

  • Productpatent – forbid others to:

    • make, use, offer for sale, sell, import

  • Claims

    • 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
Rights arising from Patent II

  • Method patent – forbid others to

    • 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
Claim Types, Product

  • Nucleic acid

  • Polypeptide

  • Antibody

  • Expression vector

  • Screening assay (kit)

  • Array

  • Pharmaceutical composition

  • Cells

  • Data carrier


Claim types methods
Claim Types, Methods

  • Method of treatment (of disorder)

  • Medical use (any therapeutic use)

  • Second medical use (disease specific therapeutic use)

  • Method of preparing compound/protein

  • Method of identifying modulator of activity

  • Method of isolating compound/protein/gene


Timelines

Timelines

The Typical Life of an International Application


Pct patent application process
PCT Patent Application Process

PUBLICATION OF PCT APPLICATION

PRELIMINARY EXAMINATION

FILING NATIONAL OR REGIONAL APPLICATIONS

PRIORITY PATENT APPLICATION

FILING AN UPDATED PCT APLICATION

THE INVENTION

NOVELTY SEARCH

0

12

16

18

28

30

MONTHS


Patenting process
Patenting Process

THE INVENTION

PRIORITY PATENT APPLICATION

  • First filing– timing

  • Early filing –

    • Easier to get novelty

    • Enablement, sufficiency, utility?

  • Later filing –

    • More time to prove function (of a gene or protein)

    • Longer patent term (evergreening of Pharmaceutical products)


  • Patenting process1

    0

    12

    16

    18

    28

    30

    Patenting Process

    FILING AN UPDATED PCT APPLICATION

    • 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 October, 2006, 133 countries)


    Patenting process2

    0

    12

    16

    18

    28

    30

    Patenting Process

    NOVELTY SEARCH

    • Novelty search (database search)

    • Identification and classification of publications (patent applications and scientific papers)

    • Possibility to evaluate the fate of the patent application


    Patenting process3

    0

    12

    16

    18

    28

    30

    Patenting Process

    PUBLICATION

    • Publication of the application 18 months from first filing


    Patenting process4

    0

    12

    16

    18

    28

    30

    Patenting Process

    PRELIMINARY EXAMINATION

    • 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 process5

    0

    12

    16

    18

    28

    30

    Patenting Process

    NATIONAL, REGIONAL APPLICATIONS

    • Entry into national phase (US, JP, CA, AU etc) or regional phase (Europe, Eurasia, Africa).

      • Selection of countries

      • Geographic strategy

      • Language - translations

      • Costs


    Patenting process6

    0

    12

    16

    18

    28

    30

    Patenting Process

    NATIONAL PHASE

    • 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

    Patents and Applications as Information Source

    How to Read a Patent Application


    Patent applications layout i
    Patent Applications Layout I

    • 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
    Layout II

    • Examples

      • Materials & methods, results, rarely any discussion

    • Claims

      • Main claims and independent claims

    • Drawings

      • Always at the end of the application

    • Sequence listing

      • Amino acid and nucleotide sequences

      • Made according to special formal requirements


    International pct applications
    International (PCT) Applications

    • APPLICATIONS!! NOT PATENTS

    • Filed locally (e.g. Denmark)

    • Treated and published centrally (WIPO, EPO, USPTO, PRV, JPO).

    • Covers 133 countries (holes in South America and the Arab world)



    Pct applications
    PCT-applications

    • Filed, searched, published, examined

    • Timeline: priority year, published after 18 months, PCT phase ends after 2½ years

    • Example: WO0212514.pdf


    Us applications patents
    US-applications/Patents

    • US-applications published at 18 months

      • Long numbers, US20020098547 A1 (Tornoe et al)

    • US-patents, published at issue

      • Granted patents

      • Short numbers, fx US 6,555,674 (Tornoe et al)




    Ep patents
    EP-patents

    • Applications published at 18 months

    • Most are published as PCT applications (WO number)

    • Published as B1 publication at grant




    Ethics and patent law1
    Ethics and Patent Law

    • Why ethics?

    • Controversial issues:

      • Patents on life (Harvard Onco-mouse)

      • Plant patents

      • Human genes

      • Stem cells

      • Human embryos (cryopreserved embryos)

      • Breast cancer diagnostics (brca genes)

      • Computer programs

    • ”Non-controversial” issues:

      • Patents on weapons

      • Patents on nuclear power plants/weapons

      • Patents on chain-saws

      • Industrial fishing equipment


    For against patents on genes
    For & Against Patents on Genes

    • 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
    Ethics

    • Allegation: claims are way too broad

      • Cover all uses (product claims)

      • Gene claims should be restricted to use (Biotechnology directive as implented in France and Germany)

      • Stops research

    • My answer: gene claims should have same scope as all other claims

      • 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:

      • 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
    Human Gene Patent Applications

    • 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



    Finding patent information for free1
    Finding Patent Information – for Free

    • 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, 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 free2
    Finding Patent Information – for Free

    • 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 pdf-file


    Downloading patent documents for free
    Downloading Patent Documents for Free

    • pdf’s of US patents: www.freepatentsonline.com

    • pdf’s of European patents and applications (since 2004): https://publications.european-patent-office.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_QjzKLN4i3dAHJgFjGpvqRqCKOcAFvfV-P_NxU_QD9gtzQiHJHRUUA43OWZA!!/delta/base64xml/L3dJdyEvUUd3QndNQSEvNElVRS82XzBfOUc!


    Finding patent information
    Finding Patent Information

    • 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
    Limitations of NCBI Blast

    • 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))