Table of Contents
CHAPTER ONE: EXECUTIVE SUMMARY
- What is a SNP?
- Applications
- The Market
- Competitive Analysis
- Challenges
- Scope and Methodology
CHAPTER TWO: INTRODUCTION
- Background
- SNP Analysis Methods
- Amplification
- Allele discrimination / assay reaction mechanism
- Single Nucleotide Addition; Pyrosequencing
- Assay Format
- Detection Method
- Scope and Methodology
- Definitions
- DNA Microarray
- Genome-Wide Association
- Linkage Analysis
- Mass Spectrometry
- Single-Nucleotide Polymorphism (SNP)
CHAPTER THREE: APPLICATIONS
- Life Science Research
- Pharmacogenetics / Pharmacogenomics
- Case Study #1 -- SNPs in Gene for P-glycoprotein Affect Antidepressant
Response
- Case Study #2 - Celera Studying SNPs Associated With Heart Disease
- Case Study #3 - Synonymous SNPs Alter mRNA Splicing with Obesity
- Case Study #4 - University of Ottawa Heart Institute (UOHI) Coronary
Artery
- Disease Research
CHAPTER FOUR: INDUSTRY AND REGULATORY TRENDS
- Industry Trends
- Consolidation Occurring in Array and Life Science Markets
- FDA Involvement Making Drug Industry More Comfortable
- Acceptance of SNP Analysis, Pharmacogenetics Reached Tipping Point
- Core Labs Becoming Established Paradigm
- Technology Trends
- Increased Multiplexing Expands Applications
- End-Users Attracted to Larger-Scale SNP Platforms
- Complexity of Biological Systems Requires Multiple Techniques
- Miniaturization of Equipment and Instruments
- Regulatory Trends
- Introduction
- 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"
- August 2007 - FDA Updates Labeling of Warfarin (Coumadin)
- December 2007 - EGAPP Reviews Use of CYP450 Genetic Testing For SSRIs
CHAPTER FIVE: PRODUCTS
- Affymetrix
- Overview of Affymetrix Products
- Hardware
- Applied Biosystems
- Overview of Applied Biosystems Products
- Assays and Reagent
- Instruments
- Beckman Coulter
- CombiMatrix
- febit
- GE Healthcare
- Illumina
- Hardware
- Microarrays
- LI-COR Biosciences (Lincoln, NE)
- Roche Applied Science
- Sequenom
- Services
- Agencourt Biosciences
- DNAPrint Genomics
- Polymorphic DNA Technologies
- Software
- Applied Biosystems
- Premier Biosoft
- Public Tools
CHAPTER SIX: CONSORTIA, GOVERNMENT INVOLVEMENT, DEALS
- Consortia, Collaborative Projects
- The Cancer Genome Atlas (TCGA) Pilot Project
- Cancer Sequencing Project
- Critical Path Institute
- DNA Polymorphism Discovery Resource
- Genetic Association Information Network (GAIN)
- Genotype-To-Phenotype Database (GEN2PHEN)
- International HapMap Project
- Introduction & Background
- Rationale for HapMap Approach
- Process for Producing HapMap
- Populations Included in HapMap
- Measures Taken to Protect Donors' Privacy
- Laboratories and Technologies Involved in HapMap
- Practical Use of the HapMap Data
- MicroArray Quality Control (MAQC) Project
- NIH Roadmap
- NIH Roadmap for Medical Research
- Pharmacogenetics Research Network (PGRN)
- NIH Involvement, Funding for SNPs and Sequencing
- Funding for Sequencing Projects Affecting SNP Market
- Continued Rapid Growth in Sequence Production
- Funding and Consortia for Sequencing
- NHGRI Funds Large-Scale Sequencing Centers, 2006
- Competitive Activity
CHAPTER SEVEN: MARKET DATA AND COMPETITIVE ANALYSIS
- Historical
- Illumina as Bellwether for SNP Analysis Market
- Applied Biosystems as Bellwether for RT-PCR Products
- Forecast
- Assumptions
- SNP Revenues by Region
- SNP Revenues by Product
- Competitive Analysis
CHAPTER EIGHT: CORPORATE PROFILES
- Affymetrix
- Applied Biosystems
- Illumina
CHAPTER NINE: CHALLENGES AND STRATEGIC RECOMMENDATIONS
- Challenges
- Cheaper Sequencing Creates Competition for SNP Analysis Platforms
- Market Is Dominated by a Small Number of Suppliers
- Issues Arise With Use of Public Databases
- Data Management Requirements Limit Large-Scale Technologies
- Diagnostic Market Holds Obstacles For New Innovations
- Backlash Against Rush Into Genetic Testing, DTC Marketing
- Standard Processes for SNP Experiments Still Not Established
- Shortcomings in Sample Preparation and Handling Hinder Success
- Privacy Concerns Pose Threat to Broad Technology Adoption
- Strategic Recommendations
TABLE OF EXHIBITS
CHAPTER ONE: EXECUTIVE SUMMARY
- Figure-1-1: SNP Analysis Market 2007-2013
- Figure 1-2: Growth Rate in SNP Analysis Revenues 2008-2013
CHAPTER TWO: INTRODUCTION
- Table 2-1 Adelle-Specific Invasive Cleavage
- Table 2-2 Adelle-Specific Ligation
- Table 2-1 Allele-Specific Primer Extension
- Table 2-4 Single Base Primer Extension
CHAPTER FOUR: INDUSTRY AND REGULATORY TRENDS
- Table 4-1: Critical Path Opportunities List
CHAPTER FIVE: PRODUCTS
- Figure 5-1: Taq Man Assay
- Figure 5-2: SOLID System Average Throughput Progress
- Figure 5-3: SNPstream Method
- Figure 5-4: Roche SimpleProbe System
- Figure 5-5: Roche HybProbe System
- Table 5-1 Products in the SNP Analysis Market
- Table 5-2 Public SNP Tools and Resources (Tool, Website)
CHAPTER SIX: CONSORTIA, GOVERNMENT INVOLVEMENT, DEALS
- Figure 6-1: Domains of Genomes Sequenced by Year (Archaea, Bacteria,
Eukaryota) Major Sequencing Centers, Jan 2008
- Figure 6-5: Top Funding Agencies, DNA Sequencing, 2008
- Figure 6-4: Major Sequencing Centers and Percent of Sequencing Projects
(WORLD, GENOSCOPE, BMC, Sanger, WashU, BROAD, JCVI, JGI), Jan 2008
- Figure 6-5: Top Funding Agencies, DNA Sequencing, 2008 ($M)
- Figure 6-6: Human Genome Project Funding, DOE& NIH ' 90-‘03
- Figure 6-7: Areas Funding Genome Sequencing, Jan 2008 (Medical,
Evolutionary, Agricultural, Environmental, Biotechnology)
- Table 6-5: Large-Scale Sequencing Centers, NHGRI Funding, 2004-2006
- Figure 6-8: Top Genome Sequencing Countries, Jan. 2008 (# projects)
- Figure 6-9: SNP Analysis Related Deals (Companies, Date, Details of Deal)
- Figure 6-10: SNP: NHGRI Funded Large-Scale Sequencing Ctrs, ‘07
- Table 6-6: SNP Analysis-Related Deals (Companies, Date, Details of Deal)
CHAPTER SEVEN: MARKET DATA AND COMPETITIVE ANALYSIS
- Figure 7-1: Illumina Quarterly Revenues, 2001-2007 ($M)
- Figure 7-2: Applied Biosystems Revenues in Real Time PCR/Applied Genomics
- Table-7-1: Forecasted Revenues in the SNP Analysis Market
- Figure-7-3: Forecasted Revenues in the SNP Analysis Market
- Table 7-2: Growth Rate in SNP Analysis Tools Market, 2008-2013
- Figure 7-4: Growth Rate in SNP Analysis Tools Market, 2008-2013
- Figure 7-5: SNP Analysis Revenues by Region (North America, Europe, Rest
of World)
- Table 7-3: SNP Analysis Revenues by Region (North America, Europe, Rest of
World)
- Figure 7-6 SNP Market by Product Segment (Instruments, Consumables,
Software & Services)
- Table 7-4: SNP Market by Segment (Instruments, Consumables, Software &
Services)
- Table 7-5: Revenues Among the Top Companies in SNP Analysis (Illumina,
Affymetrix, Applied Biosystems, Other)
- Figure 7-7: SNP Analysis Market Share, 2007
CHAPTER EIGHT: CORPORATE PROFILES
- Figure 8-1: Affymetrix' Revenues by Product Type, 2004 - 2007
- Figure 8-2: Illumina BeadStation Installed Base, 2004-2006
CHAPTER NINE: CHALLENGES AND STRATEGIC RECOMMENDATIONS
- Figure 9-1: Estimated Decrease in Screening Price
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