Table of Contents
CHAPTER ONE: EXECUTIVE SUMMARY
- Introduction and Summary
- Background and Definitions
- Alternative Splicing; Splice Variant Microarrays
- Cap Analysis of Gene Expression (CAGE)
- Comparative Genomic Hybridization (CGH)
- ChIP-on-chip
- DNA Microarrays
- Gene Trapping
- Methylation, Other Epigenetic Analysis
- MicroRNA
- Real-time PCR (RT-PCR)
- RNAse Protection Assays
- Serial Analysis of Gene Expression (SAGE)
- Tissue Arrays / Microarrays
- Transcript Analysis with Affinity Capture (TRAC)
CHAPTER TWO: APPLICATIONS
- Biomarkers
- Pharmacogenetics / Pharmacogenomics
- Cancer Diagnosis, Prognosis, Sub-Classification
- Breast Cancer
- Esophageal Cancer
- Head and Neck Cancer
- Kidney Cancer
- Leukemia
- Lung Cancer
- Lymphoma
- Oral Cancer
- Ovarian Cancer
- Prostate Cancer
- Pancreatic Cancer
- Multiple, General
- Infectious Disease Research
- Diagnostic / Prognostic Technologies and Applications
- Agendia
- DakoCytomation
- ChondroGene
- Genomic Health
- Oncotype DX
- Gleevec, Sprycel
- Velcade
CHAPTER THREE: INDUSTRY, TECHNOLOGY, AND REGULATORY TRENDS
- Industry Trends
- Gene Expression Profiling Becoming Established Tool
- Various Types of Small RNA Gaining Importance
- Gene Expression Analysis Moves Gradually into Diagnostics
- Quality Control of RNA Samples Becoming Standard Process
- Technology Trends
- New Technologies Entering Gene Expression Analysis Market
- Questions Remain Regarding Housekeeping and Reference Genes
- Probe Length Still Varying Greatly Between Vendors
- Amplification Remains Key Aspect of Experiments
- Sample Preparation Becoming High Priority
- Regulatory Trends
- March 2004 - Critical Path Initiative
- March 2005 - “Guidance for Industry - Pharmacogenomic Data
Submissions”
- April 2005 - “Drug-Diagnostic Co-Development Concept Paper”
- March 2006 - Critical Path Opportunities List
- November 2006 - “Recommendations for the Generation and Submission
of Genomic Data”
- August 2007 - “Pharmacogenomic Data Submissions - Companion
Guidance”
CHAPTER FOUR: PRODUCTS AND SERVICES FOR RESEARCH APPLICATIONS
- Research Products
- Affymetrix
- Overview
- Hardware
- Microarrays
- Agilent Technologies
- Overview
- Hardware
- Microarrays
- Applied Biosystems
- Expression Array System
- TaqMan Gene Expression Assays
- Ambion (an Applied Biosystems Business)
- Beckman Coulter
- GenomeLab GeXP Genetic Analysis System
- GenomeLab GeXP Rat MultitoxPlex Panel
- Biomek 3000-ArrayPLEX
- Bio-Rad
- Aurum Total RNA Kits
- BioOdyssey Calligrapher MiniArrayer
- VersArray ChipWriter Pro
- Experion Automated Electrophoresis System
- Experion Automated Electrophoresis System
- Experion Priming Station, Experion Vortex Station
- Biosearch Technologies
- CAL Fluor Dyes, Quasar Dyes, Black Hole Quencher Dyes
- Combimatrix
- Overview
- CustomArray Synthesizer
- Epicentre Biotechnologies
- ArrayPure Nano-scale RNA Purification Kit
- MessageBOOSTER cDNA Synthesis Kit for qPCR
- TargetAmp aRNA Amplification Kits
- Exiqon
- febit
- Illumina
- DASL Assay Focused Arrays Genome-Wide Expression BeadChips
- Kreatech Biotechnology
- Marligen Biotechnologies
- Multiplex Transcription Factor Assays
- Panomics
- QuantiGene 2.0 Reagent System
- Roche Applied Science
- Stratagene (Agilent)
- SideStep and SideStep II Products and Kits
- Products - Selected List
- Next-Generation Sequencers
- Diagnostic, Prognostic, Theranostic Products
- Software and Services
- Althea Technologies
- Inflammation:
- Cancer:
- Tox and Specialty:
- Gene Logic Ocimum
- Genomatix Software GmbH
- ChipInspector
- BiblioSphere Pathway Edition
- Iconix Biosciences
CHAPTER FIVE: CONSORTIA, INITIATIVES, STANDARDIZATION, DEALS
- Critical Path Institute
- External RNA Controls Consortium (ERCC)
- MicroArray Quality Control (MAQC) Project
- Minimum Information About a Microarray Experiment (MIAME)
- NIH Roadmap for Medical Research
- Institutional Clinical and Translational Science Awards (CTSA' s) Program
(October 2005)
- Toxicogenomics Research Consortium
- Other Experiments to Assess Comparability, Reproducibility
- Case study #1
- Case Study #2
- Case Study #3
- Case study #4
- Case Study #5
- Deals
CHAPTER SIX: MARKET ANALYSIS
- Historical
- Affymetrix as Bellwether for Microarray Segment
- Applied Biosystems as Bellwether for qRT-PCR Segment
- Forecasts
- Assumptions
- Competitive Analysis
- Corporate Profiles
- Affymetrix
- Number of Employees
- Estimated 2006 Gene Expression Revenues
- Agilent Technologies
- Number of Employees
- Estimated 2006 Gene Expression Revenues
- Estimated 2006 Life Sciences and Chemical Analysis Group Revenues
- Applied Biosystems
- Number of Employees
- Estimated 2006 Gene Expression Revenues
- Beckman Coulter
- Number of Employees
- Estimated 2006 Gene Expression Revenues
- Combimatrix
- Number of Employees
- 2006 Revenues
- Illumina
- Number of Employees
- 2006 Revenues
- Roche Applied Science
- Number of Employees
- Estimated 2006 Gene Expression Revenues
CHAPTER SEVEN: CHALLENGES & STRATEGIC RECOMMENDATIONS
- Challenges
- Next-Generation Sequencers Create Wild Card
- Affymetrix Dominance Decreasing But Still Significant
- Market Complicated by New Gene Expression & Regulation Analysis Products
- Pharmaceutical Industry Tightening Budgets, Scrutinizing Technologies
- Regulations for Diagnostics Still Shaking Out
- RT-PCR Competing Strongly with Microarrays
- SNP Analysis and Copy Number Variation Easier and Popular
- Growth Threatened by Industrialization, Commoditization
- Resistance Towards Diagnostics Using Multiple Markers
- Data Analysis and Management Still Hindering End-Users
- Multiplexing Limitations of Real Time Quantitative PCR
- Longer-Term Prospects Threatened by Proteomics, Metabolomics
- Strategic Recommendations
- Diversify Into Multiple Aspects, Applications
- Partner With Market Leaders
- Provide Software Tools for Comparison Across Platforms, Techniques
- Investigate Intellectual Property and Licensing Possibilities
LIST OF EXHIBITS
CHAPTER TWO: APPLICATIONS
- Table 2-1: Areas Using Gene Expression Profiles in Infectious Disease
Research
CHAPTER THREE: INDUSTRY, TECHNOLOGY, AND REGULATORY TRENDS
- Table 3-1: Critical Path Opportunities List (March 2006)
CHAPTER FOUR: PRODUCTS AND SERVICES FOR RESEARCH APPLICATIONS
- Table 4-1: Selected Gene Expression Analysis Products
- Table 4-2: Selected List of Next-Generation Sequencer Products and
Technologies
- Table 4-3: Selected List of Next-Generation Sequencer Products and
Technologies
- Table 4-4: Selected List of Software Products Available for the Gene
Expression Analysis Market
CHAPTER FIVE: CONSORTIA, INITIATIVES, STANDARDIZATION, DEALS
- Table 5-1: Selected Deals Taking Place in the Gene Expression Analysis
Market
CHAPTER SIX: MARKET ANALYSIS
- Figure 6-1: Revenues for Microarrays, Instruments, and Reagents (2001-
2007)
- Figure 6-2: Revenues for Microarrays, Instruments, and Reagents with
Trendlines (2004- 2007)
- Figure 6-3: Revenues for Real-Time PCR/Applied Genomics (2001-2007)
- Table 6-1: Forcasted Revenues in the Gene Expression Market (2006-2012)
- Figure 6-4: Forecasted Revenues in the Gene Expression Analysis Market
(2006-2012)
- Table 6-2: Growth Rates Forecast (2006-2012)
- Figure 6-5: Growth Rates Forecast Chart (2006-2012)
- Table 6-3: Gene Expression Product Revenues Regional Breakdown and Trend
2006
- Figure 6-6: Gene Expression Product Revenues Regional Market Share 2006
- Table 6-4: Regional Shares of Affymetrix' s Overall Revenues (2001-2006)
- Figure 6-7: Trending in the Regional Share of Affymetrix' s Overall
Revenues (2001-2006)
- Table 6-5: Estimated Revenues and Market Shares for the Top Vendors in the
Gene Expression Analysis
- Figure 6-8: Estimated Market Shares for the Top Vendors in the Gene
Expression Analysis Chart
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