The Outlook For The Biotech Sector In The Post-Genomic Era: Strategies for drug discovery, diagnostics and personalized medicine

Table of Contents

Executive Summary

• The Biotech sector in the post-genomic era

Chapter 1 Technology Overview

• Introduction to the post-genomic era
• Structural genomics
• Sequencing
  • Sequencing techniques
• Genotyping
  • SNPs
  • Techniques to identify, detect and validate SNPs
  • Association studies
  • SNP scoring
• Pharmacogenomics
• Key characteristics of the completed human genome
  • Protein expression
• Gene expression
  • Abnormal gene expression
  • Expression profiling
  • Proteomics
• Functional genomics
  • The gene-to-function approach
  • The function-to-gene approach
  • Limitations
  • Determining a gene function
• From the genome to the proteome
  • Post-translational modification
• Transcriptomics
• Glycomics
  • CBPs
• Proteomics
  • Protein functions and disease
• Structural proteomics
  • Protein structures
  • Mapping the human proteome
• Functional proteomics
  • Protein functions and interactions
• Proteins and diseases
• Cellomics
• Systems biology
• The search for disease markers
• Bioinformatics
  • Data management challenges
  • Bioinformatic software

Chapter 2 Drug Discovery

• Traditional and genomics-based drug discovery
  • Small molecule therapeutics
• Market drivers
  • The product pipeline gap
  • New and improved drug discovery technologies
• The drug discovery process
  • Target identification
  • Target validation
  • Lead generation/primary screening
  • Lead optimisation
• Limitations
• Functional genomics in drug discovery
• Proteomics in drug discovery
• Targeting protein expression
• Targeting protein interactions
• SNP scoring in drug discovery
• Increasing the efficiency of drug discovery
• Integrated use of technologies
  • Chemical genomics
• Target identification in the post-genomic era
  • Novel biological targets
• Targeting gene regulation
  • Gene switches
  • Apoptosis
• Target validation in the post-genomic era
• Role of functional genomics
  • Determining the precise functions of individual genes
  • Knockout mice
• Antisense inhibition assays
• Lead generation in the post-genomic era
  • Ultra-high throughput systems
• Lead optimisation in the post-genomic era
• Rational drug design in the post-genomic era
  • Structure-based drug design
  • Biological-modelling software
  • DNA sequence data
  • Combinatorial chemistry
• Prediction of safety and efficacy of drugs
  • Targeting signalling pathways inside the cell
• Managing bioinformatics information
  • Bioinformatic solutions
• Commercial exploitation of data
  • Informational genomics
  • The merging of bioinformatics and chemoinformatics
• Trends in genomics/proteomics databases
• Bio-simulation technologies
  • New bio-simulation in silico tools

Chapter 3 Development of Small Molecule Drugs and Biotherapies

• Traditional drug development
• Market drivers
• The drug development process
  • Preclinical stage
• Drug development in the post-genomic era
• Role of pharmacogenomics
  • SNP scoring
  • Preclinical testing
  • Segmented markets and revenue streams for pharmacogenomics-derived products
• Computer-based management solutions
• Drug delivery advancements
  • Delivery of biopharmaceuticals
  • Delivery of therapeutic proteins and peptides
• Directed molecular evolution
  • Non-random mutagenesis
  • Molecular breeding
• Drug development outsourcing industry
  • A full-service industry
  • Industry consolidation
• New and emerging biotherapies
• Protein therapy
  • Monoclonal antibodies
• Antisense therapy
  • Classes of antisense agents
  • Exploiting the technology's advantage
  • Effective drug delivery
• DNA vaccines and gene therapy
  • The challenge of translating sequence data into human vaccines
  • New applications for gene therapy
  • Customized gene therapy
• Glycotherapy
• Major therapy areas
• Infectious disease
• Cardiovascular disease
• Oncology

Chapter 4 Predictive Diagnostics

• Overview of the traditional IVD industry
  • Segmentation
• IVDs in the post-genomic era
• Predictive diagnostics and preventive medicine
• Predisposition tests
• Cancer
• Cardiovascular disease
• Early detection of disease
• Genomics and early detection of disease
  • Infectious disease
  • Cancer
• Proteomics and early detection of disease
  • Detection of pre-symptomatic disease
• The role of the homebrew market

Chapter 5 Theranostics

• Drug selection in the post-genomic era
• Theranostics and personalized medicine
• Theranostics and established drugs
• Gene-based theranostics and applications
  • Infectious disease
• Cancer
• Cardiovascular disease
• Other diseases
• Prediction of drug toxicity
  • Proteomics: the next frontier in theranostics
• Impact of bioinformatics
• Does theranostics improve outcomes?

Chapter 6 Company Profiles

• Introduction
• ACADIA Pharmaceuticals Inc
• Summary financial data
• Company overview
  • Genomic target discovery
• Platform drug discovery technologies
  • Applications of platform technologies
  • Drug discovery pipeline
• Collaborations
• Applera Corp (Celera Genomics business unit)
• Summary financial data
• Company overview
  • Applied Biosystems
  • Celera Genomics
  • Celera Diagnostics
  • The Celera Discovery System
  • Program to discover SNPs in genes
  • Drug discovery and development
• Collaborations
• ArQule Inc
• Summary financial data
• Company overview
  • Integrated drug discovery platform
  • AMAP Chemistry Operating System
• Drug discovery products and services
• Internal drug discovery program
• Collaborations
• Athersys Inc
• Summary financial data
• Company overview
• RAGE technology
  • Applications
• Collaborations
• Cellomics Inc
• Summary financial data
• Company overview
• Core cellomics competencies
  • Integrated product platform
  • Cellular screening products
  • Bioinformatics products
• Collaborations
• Cytogen Corp
• Summary financial data
• Company overview
• Systems biology approach
• Proteomics-based products ProChart protein pathway database
• Protein Arrays
• Collaborations
• DiagnoSwiss SA
• Summary financial data
• Company overview
  • Technology for rapid protein analysis
  • Microfluidics technology
  • Lab-on-a-chip systems
  • Immunoassays on microchip format
• Genaissance Pharmaceuticals Inc
• Summary financial data
• Company overview
• HAP technology platform
• Informatics technology platform
  • Applications of HAP technology
  • HAP drug discovery pipeline
• Collaborations
• Gene Logic Inc
• Summary financial data
• Company overview
• Gene expression technology
  • Gene expression databases
• Collaborations
  • Acquisition of TherImmune Research Corporation
• Keryx Biopharmaceuticals Inc
• Summary financial data
• Company overview
• KinAce drug discovery technology
  • Peptide conversion technology
  • Functional genomics program
  • KinAce drug discovery pipeline
• Lexicon Genetics Inc
• Summary financial data
• Company overview
• The Genome 5000 program
  • Gene knockout technology
  • OmniBank library and database
  • Drug discovery programs
  • Functional Genomics programs
• Collaborations
• Lynx Therapeutics Inc
• Summary financial data
• Company overview
  • Megaclone technology and applications
  • Proteomics technology and applications
  • Internal product development
• Collaborations
• Myriad Genetics Inc
• Summary financial data
• Company overview
  • An integrated proteomics platform
  • Genomic technologies
  • Predictive medicine products
  • Drug discovery pipeline
• Collaborations
• Neurogen Corporation
• Summary financial data
• Company overview
• Accelerated Intelligent Drug Discovery
  • Drug discovery pipeline
• Collaborations
• Orchid BioSciences Inc
• Summary financial data
• Company overview
  • SNP-IT SNP scoring technology
• Collaborations
• Rigel Pharmaceuticals Inc
• Summary financial data
• Company overview
  • Combinatorial biology platform
  • Proteomics program
  • Drug discovery portfolio
• Collaborations
• Rosetta Inpharmatics Inc (acquired by Merck & Co.)
• Summary financial data
• Company overview
  • Informational genomics platform
• Collaborations
• Sequenom Inc
• Summary financial data
• Company overview
  • MassARRAY genotyping technology
• Collaborations
• Synaptic Pharmaceutical Corp (acquired by Lundbeck)
• Summary financial data
• Company overview
• Merger with Lundbeck
  • SNAP drug discovery platform
• Collaborations
• Vertex Pharmaceuticals Inc
• Summary financial data
• Company overview
  • Chemogenomics platform
• Drug discovery technologies
  • Drug discovery pipeline
• Collaborations

Chapter 7 Conclusions Trends and Opportunities

• Post-genomic biotechnology is changing medicine
• Young companies are driving the changes
• The value of post-genomic science to the pharmaceutical industry
• Towards personalized and predictive medicine
  • Using pharmacogenomics throughout the drug lifecycle?
  • Issues preventing dissemination of personal genetic information
  • Benefits of orphan-drug status
  • Analysis of multiple gene and/or protein expression
• Drug discovery in transition
  • New targets for drug discovery
• Tackling the critical issue of productivity
  • Novel drug discovery technologies
  • Integration and collaboration are key
  • Is personalized medicine the answer to falling R&D productivity?
  • The potential of post-genomic science
  • Role of alliances in drug discovery
• Post-genomic outsourcing industry
• Business models in bioinformatics
  • In-house versus external investment
  • IT giants enter the life science market
  • Prominet failures
  • The limitations of only selling bioinformatics tools
  • Acquisitions
• IP issues in the post-genomic era
  • Mining the proteome
  • IP as a restrictor of development
  • Alternative approaches to overcome IP barriers
• Key trends in the pharmacogenomics industry until 2012

Chapter 8 Appendix

• Terms and abbreviations
• Index of companies/organisations included I n the report

List of Figures

• Figure 1.1: Types of data analysis involved in the identification of biological targets for drugs or diagnostics
• Figure 3.2: Using market-driven genotype screening to increase the revenue potential of pharmacogenomics-derived products
• Figure 7.3: Selected niche technologies and providers that are expected to impact on discovery and development of genomic-based drugs
• Figure 7.4: The link between personalized medicine and R&D productivity
• Figure 7.5: Key events and effects impacting the genomics industry until 2012

List of Tables

• Table 3.1: World pharmaceutical market by regions
• Table 3.2: World pharmaceutical market by therapeutic category
• Table 6.3: Summary financial data for ACADIA Pharmaceuticals Inc, 2000 2002
• Table 6.4: Summary financial data for Applera Corp, 2000 2002
• Table 6.5: Summary financial data for ArQule Inc, 2000 2002
• Table 6.6: Summary financial data for Athersys Inc
• Table 6.7: Summary financial data for Cellomics Inc
• Table 6.8: Summary financial data for Cytogen Corp, 2000 2002
• Table 6.9: Summary financial data for Genaissance Pharmaceuticals Inc, 2000 2002
• Table 6.10: Summary financial data for Gene Logic Inc, 2000 2002
• Table 6.11: Summary financial data for Keryx Biopharmaceuticals Inc, 2000 2002
• Table 6.12: Summary financial data for Lexicon Genetics Inc, 2000 2002
• Table 6.13: Summary financial data for Lynx Therapeutics Inc, 2000 2002
• Table 6.14: Summary financial data for Myriad Genetics Inc, 2000 2002
• Table 6.15: Summary financial data for Neurogen Corporation
• Table 6.16: Summary financial data for Orchid Biosciences Inc, 2000 2002
• Table 6.17: Summary financial data for Rigel Pharmaceuticals Inc, 2000 2002
• Table 6.18: Summary financial data for Rosetta Inpharmatics, 1998 2000
• Table 6.19: Summary financial data for Sequenom Inc, 2000 2002
• Table 6.20: Summary financial data for Synaptic Pharmaceutical Corp, 2000 2002
• Table 6.21: Summary financial data for Vertex Pharmaceuticals Inc, 2000 2002