Patents in the Postgenomic Era: Proprietary Drug Targets and Therapies

Table of Contents

Chapter 1: Executive Summary

Chapter 2: Trends in Postgenomic Biotechnology

• Biomedical Innovation in the Postgenomic Era
• The Role of Patents in the Biomedical Industry
• Post-Genomic Technologies
• Functional Genomics
• Pharmacogenomics
• Transcriptomics
• Proteomics
• Glycomics
• Metabolomics
• Other Omics
• Established and Emerging Therapies
• Small Molecules
• Protein-Based Biotherapies
• Nucleic Acid-Based Biotherapies
• Gene Therapy
• Antisense Including RNA Interference
• Molecular Diagnostics

Chapter 3: Patent Law, Procedures, and Biomedical Inventions

• What is a Patent?
• Patents Confer an Exclusionary Right
• Patents Do Not Confer Ownership of Products
• Patents and Property Rights
• Patents and Monopolies
• Consideration for Grant
• Patents Require International Cooperation
• The Paris Convention
• The European Patent Convention
• GATT-TRIPs
• Recent Developments
• Patents are Time-Limited
• What can be Patented?
• Novelty
• The Inventive Step
• Effect of Unpublished Prior Applications
• Industrial Application
• Exceptions to Patentability
• Patents in the Postgenomic Era
• US Utility Patents
• Patent Costs
• The Patent Document
• Inventors and Assignees
• "First-to-Invent"
• Provisional Applications
• The American Inventors Protection Act
• Novelty Requirement
• Non-Obviousness Requirement
• Recent Growth in Patenting
• Grace Periods
• Post-Issue Challenges to Patent Validity
• EPO Opposition Procedure
• US Reexamination Procedures
• Proposals for Post-Grant Review
• Patenting Chemical Compounds
• Patenting Pharmaceuticals
• Overview
• First Pharmaceutical Use
• Second Pharmaceutical Use
• Other Aspects of Pharmaceutical Patenting
• Patenting Natural Products
• Patenting Microbiological Inventions
• Patent Infringement
• Overview
• Remedies for Infringement
• Patent Litigation in the US
• Litigation Costs
• Doctrine of Equivalents
• Research Use of an Invention
• Patent Litigation in Europe

Chapter 4: Patenting of Genes and Proteins

• Introduction
• Patenting of Genes
• Background on Genes
• The Drive Toward Patenting
• Protection Afforded by Patent Law
• Growth in DNA-related Patenting
• Patenting of Proteins
• Background on Proteins
• Structural Initiatives
• The Drive Toward Patenting
• Patents in the Postgenomic Era
• Protection Afforded by Patent Law
• Regulatory Developments Relevant to Genes
• Tightening Patentability Requirements
• Areas of Controversy
• Patenting of ESTs
• Patenting DNA Sequence Variations
• Regulatory Developments Relevant to Proteins
• Patenting of 3-D Structures 4--12
• Areas of Controversy
• Computational Prediction of Function
• Broadly Interpreted Patents 4--15
• Patent Claims and Risk of Litigation
• Solutions to the Patent Thicket Problem
• Issues Raised by Exclusive Licensing

Chapter 5: Analysis of US Patents 1990 -- 2005

• Patent Activity Survey: Aims and Methodology
• Overview of Therapy Areas
• Cancer
• CNS Therapy
• Metabolism/Cardiology
• Infection/Immunology
• Patent Activity in Major Drug Target Classes
• GPCRs
• Enzymes
• Kinases
• Phosphatases
• Proteases
• ATPases and ABC Transporters
• Monamine Oxidases
• Glycoenzymes/Glycobiology
• Ion Channels
• Nuclear Receptors
• Cytokines and Chemokines
• Patent Activity in Gene Therapy
• Patent Activity in RNA Interference
• Patent Activity in Pharmacogenomics
• Summary of Patent Activity Survey
• Analysis of Patents by Filing and Publication Year
• Analysis of Patent Maintenance
• Analysis of Patents by US Classification
• Patents in the Postgenomic Era

Chapter 6: Patent Competitive Intelligence

• Mining Patents for Competitive Intelligence
• Patent Searching
• Internet-Based Patent Resources
• Computational Patent Mapping
• Indicators of Patent Quality
• Patent Citations Weights
• Length of Life and Spatial Weights
• Composite Index of Patent Quality
• Competitive Analysis of Biopatents Survey
• Most Prolific Assignees
• Most Frequently Cited Patents

TABLE OF EXHIBITS

• Exhibit 3.1 Legal Definitions of Patentable Inventions
• Exhibit 5.1 Biopatents Search Syntax (Using Delphion)
• Exhibit 5.2 Biopatents Dataset by Target/Technology
• Exhibit 5.3 Patent Activity Analysis for GPCRs
• Exhibit 5.4 US Patents on Novel Target Proteins (n=23)
• Exhibit 5.5 Patent Activity Analysis for Kinases
• Exhibit 5.6 Patent Activity Analysis for Phosphatases
• Exhibit 5.7 Patent Activity Analysis for Proteases
• Exhibit 5.8 Patent Activity Analysis for ATPases
• Exhibit 5.9 Patent Activity Analysis for ABC Transporters
• Exhibit 5.10 Patent Activity Analysis for MAOs
• Exhibit 5.11 Patent Activity Analysis for Glycobiology
• Exhibit 5.12 Patent Activity Analysis for Ion Channels
• Exhibit 5.13 Patent Activity Analysis for Nuclear Receptors
• Exhibit 5.14 Patent Activity Analysis for Cytokines and Chemokines
• Exhibit 5.15 Patent Activity Analysis for Gene Therapy
• Exhibit 5.16 Patent Activity Analysis for RNAi
• Exhibit 5.17 Patent Activity Analysis for Pharmacogenomics
• Exhibit 5.18 Activity Analysis for All Patents
• Exhibit 5.19 Proportion of Mainly Methodological Patents in Each Group
• Exhibit 5.20 Proportion of Therapy-oriented Patents in Each Group
• Exhibit 5.21 Proportion of Therapy-oriented Tatents Disclosing One or More Novel Target Proteins
• Exhibit 5.22 Proportion of Therapy-oriented Patents Reporting One or More Novel Target Sequences
• Exhibit 5.23 Proportion of Therapy-oriented Patents Disclosing One or More Novel Peptides
• Exhibit 5.24 Proportion of Patents Describing Therapy with One or More Novel Small Molecules
• Exhibit 5.25 Proportion of Therapy-oriented Patents Focusing on Cancer
• Exhibit 5.26 Proportion of Therapy-oriented Patents Docusing on CNS Disorders
• Exhibit 5.27 Proportion of Therapy-oriented Patents Focusing on Metabolism and/or Cardiology
• Exhibit 5.28 Proportion of Therapy-oriented Patents Focusing on Infection and/or Immunology
• Exhibit 5.29 Proportion of Therapy-oriented Patents Describing Diagnostics and/or Biomarkers 5--37
• Exhibit 5.30 Percent Published Patent Applications by Group
• Exhibit 5.31 Numbers of Mainly Methodological Patents in Each Group
• Exhibit 5.32 Numbers of Therapy-oriented Patents in Each Group
• Exhibit 5.33 Numbers of Patents Disclosing One or More Novel Target Proteins
• Exhibit 5.34 Numbers of Patents Reporting One or More Novel Target Sequences
• Exhibit 5.35 Numbers of Patents Disclosing One or More Novel Peptides
• Exhibit 5.36 Numbers of Patents Describing Therapy with One or More Novel Small Molecules
• Exhibit 5.37 Numbers of Patents Focusing on Cancer
• Exhibit 5.38 Numbers of Patents Focusing on CNS Disorders
• Exhibit 5.39 Numbers of Patents Focusing on Metabolism and/or Cardiology
• Exhibit 5.40 Numbers of Patents Focusing on Infection and/or Immunology
• Exhibit 5.41 Numbers of Patents Describing Diagnostics and/or Biomarkers
• Exhibit 5.42 Numbers of Published Patent Applications by Group
• Exhibit 5.43 US Patents and Published Applications, 1990-2005
• Exhibit 5.44 Analysis of US Applications and Patents by Filing and Publication Year: ABC Transporters (103)
• Exhibit 5.45 Analysis of US Applications and Patents by Filing and Publication Year: ATPases (556)
• Exhibit 5.46 Analysis of US Applications and Patents by Filing and Publication Year: Cytokines and Chemokines (836)
• Exhibit 5.47 Analysis of US Applications and Patents by Filing and Publication Year: Gene Therapy (423)
• Exhibit 5.48 Analysis of US Applications and Patents by Filing and Publication Year: Glycobiology (390)
• Exhibit 5.49 Analysis of US Applications and Patents by Filing and Publication Year: G-Protein Coupled Receptors (1,097)
• Exhibit 5.50 Analysis of US Applications and Patents by Filing and Publication Year: Ion Channels (852)
• Exhibit 5.51 Analysis of US Applications and Patents by Filing and Publication Year: Monoamine Oxidase Inhibitors (273)
• Exhibit 5.52 Analysis of US Applications and Patents by Filing and Publication Year: Nuclear Receptors (453)
• Exhibit 5.53 Analysis of US Applications and Patents by Filing and Publication Year: Protein Kinases (1,559)
• Exhibit 5.54 Analysis of US Applications and Patents by Filing and Publication Year: Pharmacogenomics (1,122)
• Exhibit 5.55 Analysis of US Applications and Patents by Filing and Publication Year: Phosphatases (800)
• Exhibit 5.56 Analysis of US Applications and Patents by Filing and Publication Year: Proteases (1,396)
• Exhibit 5.57 Analysis of US Applications and Patents by Filing and Publication Year: RNA Interference (824)
• Exhibit 5.58 Comparison of 15-Year Patenting Activity in Biopatents with Mechanical Engineering and Software
• Exhibit 5.59 Patent Shares 1990--2005 for Biopatents, Mechanical Engineering, and Software
• Exhibit 5.60 Patent Shares 1990--2005 for Biopatents and Technologies
• Exhibit 5.61 Patent Shares 1990--2005 for Biopatents Applications and Categories
• Exhibit 5.62 Biopatents Publication Rates 1990--2005 by Category and Application
• Exhibit 5.63 Analysis of Patent Maintenance
• Exhibit 5.64 Analysis of Patents by US Classification
• Exhibit 6.1 Analysis of US Patents by Top 20 Assignees
• Exhibit 6.2 Analysis of Most Frequently Cited US Patents