Gene Expression
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
TABLE OF CONTENTSCHAPTER 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 EXHIBITSCHAPTER 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
DNA SEQUENCING MARKETS
CHAPTER ONE: Executive Summary
- DNA Sequencing Applications
- Types of Samples
- Market Trends
- Scope and Methodology
CHAPTER TWO: Introduction
- Background
- DNA Sequencing Applications
- Types of Samples
- DNA Sequencing Strategies
- DNA Sequencing Chemistries and Techniques
- Sanger Sequencing
- Single Nucleotide Addition; Pyrosequencing
- Cyclic Reversible Terminators
CHAPTER THREE: Sequencer Market Trends and
- Funding Trends
- Market Trends
- Market Fragmenting Into Multiple Applications, Products
- Synergies Appearing Between Companies’ Products
- Microbes and Metagenomics Gaining Importance
- Various Disruptive Technologies Rapidly Appearing On Market
- Miniaturization of Sanger and CE Technology
- Paired-End Techniques, Increasing Read-Lengths Expanding Applications
- Development of Multiplexing Approaches Extends Market
- SNP and Other Experiments Moving to Sequencing for Higher Detail
- Continued Rapid Growth in Sequence Production
- Funding Trends
- Funding and Consortia for Sequencing
- The Cancer Genome Atlas Pilot Project
- Cancer Sequencing Project
- FUGE - Functional Genomics in Norway
- NSF / USDA Microbial Genome Sequencing Program
- OTHER FUNDING
CHAPTER FOUR: DNA Sequencer Products
- 454 Life Sciences (Branford, CT) / Roche
- Genome Sequencer 20
- Genome Sequencer FLX.
- Applied Biosystems (Foster City, CA)
- ABI Prism 310 Genetic Analyzer
- ABI Prism 3100-Avant Genetic Analyzer
- Applied Biosystems 3100 Genetic Analyzer
- Applied Biosystems 3130 Genetic Analyzer
- Applied Biosystems 3130xl Genetic Analyzer
- Applied Biosystems 3730 DNA Analyzer
- Applied Biosystems 3730xl DNA Analyzer
- SOLiD (early access)
- Beckman Coulter
- CEQ 8000; CEQ 8800
- GE Healthcare
- MegaBACE 500.
- MegaBACE 750
- MegaBACE 1000
- MegaBACE 1500
- MegaBACE 4000
- Illumina / Solexa
- LI-COR Biosciences (Lincoln, NE)
CHAPTER FIVE: Market Data
CHAPTER SIX: Competitive Analysis
- Features and Strengths of Next-Generation Sequencers
- 454 Life Sciences - Strengths / Advantages
- 454 Life Sciences - Weaknesses / Disadvantages
- Applied Biosystems SOLiD - Strength / Advantages
- Applied Biosystems SOLiD - Weaknesses / Disadvantages
- Illumina Genome Analyzer - Strength / Advantages
- Illumina Genome Analyzer - Weaknesses / Disadvantages
CHAPTER SEVEN: Intellectual Property and Litigation
- Affymetrix Wins Patent Infringement Case Against Illumina
- Applied Biosystems and Amersham plc (GE Healthcare) Settle Sequencing Patent Litigation
- Applied Biosystems Sues Solexa and Former Chief Patent Counsel
- Beckman Coulter and Applied Biosystems Settle Outstanding Legal Disputes
- Cepheid and Idaho Technology Settle Dispute Over PCR Patents
- Enzo Biochem Disputes CalTech Sequencing Patents
- Huang v. CalTech
CHAPTER EIGHT: Deals
CHAPTER NINE: Corporate Profiles
- 454 Life Sciences (Branford, CT) / Roche
- Applied Biosystems (Foster City, CA)
- Beckman Coulter (Fullerton, CA)
- GE Healthcare Life Sciences (Little Chalfont, UK)
- Helicos Biosciences (Cambridge, MA)
- Illumina / Solexa
- Intelligent Bio-Systems (Waltham, MA)
- LI-COR Biosciences (Lincoln, NE)
- NABsys (Providence, RI)
CHAPTER TEN: Technologies Under Development
- NHGRI Funds Next Generation of Sequencing Technologies
- 454 Life Sciences Corp
- “Massively Parallel High Throughput, Low Cost Sequencing”
- “454 Life Sciences Massively Parallel System DNA Sequencing”
- Agencourt Personal Genomics [Applied Biosystems]
- “Bead-based Polony Sequencing”
- Arizona State University, Tempe
- “Multiplexed Reactive Sequencing of DNA”
- Baylor College of Medicine, Human Genome Sequencing Ctr
- “Ultrafast SBS Method for Large-Scale Human Resequencing”
- Columbia University
- “An Integrated System for DNA Sequencing by Synthesis”
- Harvard University, Rowland Institute; moved to Boston Univ.
- “Ultra-fast Nanopore Readout Platform for Designed DNA's”
- LI-COR Inc.
- “Single-Molecule DNA Sequencing Using Charge-Switch dNTPs”
- Microchip Biotechnologies Inc
- “Microbead INtegrated DNA Sequencer (MINDS) System”
- Stanford University
- “High-Throughput, Single-Molecule DNA Sequencing”
- Stanford Genome Technology Center
- “Pyrosequencing Array for DNA Sequencing”
- University of Gainesville, Florida
- “DNA Sequencing Using Nanopores”
- “Polymerases for Sequencing by Synthesis”
- Second Group of Grants, $1000 Genome
- Arizona State University, Tempe
- “Molecular Reading Head for Single-Molecule DNA Sequencing”
- Oak Ridge National Laboratory
- “Experimental R&D for Rapid Sequencing Nanotechnology”
- “Computational R&D for Rapid Sequencing Nanotechnology”
- Stanford University
- “Single Molecule Nucleic Acid Detection with Nanopipettes”
- University of British Columbia, Vancouver
- “Nanopores for Trans-Membrane Bio-Molecule Detection”
- University of Maine, Orono
- “High-speed Nanopore Gene Sequencing”
- University of North Carolina, Chapel Hill
- “Nanotechnology for the Structural Interrogation of DNA”
- NHGRI Expands Effort to Revolutionize Sequencing Technologies
- Agencourt Personal Genomics [Applied Biosystems]
- “Bead-Based Polony Sequencing (Supplemental)”
- Network Biosystems
- “$100,000 Genome Using Integrated Microfluidic CE”
- The State University of New York, Stony Brook (SUNY)
- “Ultra High Throughput DNA Sequencing System Based on 2D Monolith
- Multi-Capillary Arrays and Nanoliter Reaction Volume”
- Columbia University
- “Modulating Nucleotide Size in DNA for Detection by Nanopore”
- Duke University
- “Droplet-Based Digital Microfluidic Genome Sequencing”
- Harvard University
- “Electronic Sequencing in Nanopores”
- Nanofluidics
- “Real-Time Multiplex Single-Molecule DNA Sequencing”
- New York University
- “Haplotype Sequencing Via Single Molecule Hybridization”
- Oxford University and The Scripps Research Institute
- “Single-Molecule DNA Sequencing with Engineered Nanopores”
- University of California, San Diego
- “Massively Parallel Cloning and Sequencing of DNA”
- University of Illinois at Urbana-Champaign
- “Sequencing a DNA Molecule Using a Synthetic Nanopore”
- VisiGen Biotechnologies
- “Real-Time DNA Sequencing”
- “NHGRI Aims to Make DNA Sequencing Faster, More Cost Effective”,
- “Fabrication of Universal DNA Nanoarrays for Sequencing by Hybridization”
- Boston University
- “High-Throughput DNA Sequencing Using Design Polymers and Nanopore Arrays”
- Case Western Reserve University
- “Large-Scale Nanopore Arrays for DNA Sequencing”
- General Electric Global Research
- “Closed Complex Single Molecule Sequencing”
- Helicos Biosciences
- “High Accuracy Single Molecule DNA Sequencing by Synthesis”
- Lehigh University
- “Force Spectroscopy Platform for Label Free Genome Sequencing”
- University of California, San Diego
- “Genome Sequencing by Ligation Using Nano-Arrays of Single DNA Molecules”
- University of North Carolina, Chapel Hill
- “Nanoscale Fluidic Technologies for Rapidly Sequencing Single DNA Molecules”
- University of Washington, Seattle
- “Engineering MspA for Nanopore Sequencing”
- Baylor College of Medicine, HGS
- “Ultrafast SBS Method for Large-Scale Human Resequencing”
- Intelligent Bio-Systems
- “High-Throughput DNA Sequencing by Synthesis Platform”
- Other Microfluidics and Lab-on-a-Chip
CHAPTER ELEVEN: Challenges and Strategic
- RecommendationS
- Market Challenges
- Saturation, Technology Advances Threaten Market Growth
- Next-Generation Vendors Contending With 454’s Head-Start
- Rapid Changes, Multiple Variables Creating Unpredictable Market
- Labs Hesitant to Invest in Unproven Technologies
- Segments Resisting Change Where Long Read-Lengths Key
- New Technologies Create Data Management Issues
- Recent Acquisitions Make Tougher Environment for New Entrants
- Strategic Recommendations
- Increase Products’ Value Through Software Tools
- Explore Demand in Expanding Industry Segments
- Address Niche Markets Resulting From Fragmentation
- Increase Value by Combining with Complementary Content
- Establish Early Connections With End-Users
- Balance Risks by Diversifying Applications
- Move Towards Diagnostic Environment Requires Partnering
table of exhibits
CHAPTER ONE: Executive Summary
- Table 1-1: DNA Sequencer Equipment Revenues 1999-2006
- Figure 1-1: Trending in the DNA Sequencer Equipment Market 2006-2012
Chapter three: Sequencer Market Trends and Funding Trensd
- Figure 3-1: Distribution of Archaeal and Bacterial Genome Projects, Q1 2007
- (JGI, TIGR, J Venter, World)
- Figure 3-2: Phylogenetic Distribution of Bacterial Genome Projects, Q1 '07
- Figure 3-3: Number of Completely Sequenced Genomes (Published vs
- Unpublished) 1999 through Q1 2007
- Figure 3-4: Distribution of Number of Projects Among Major Sequencing Centers Q1 2007
- Figure 3-5: Funding by the Top Agencies in DNA Sequencing
- Figure 3-6: U.S. Funding for the Human Genome Project DOE vs NIH 1990-2003
- Figure 3-7: Distribution of the Number of Bacterial Sequencing Projects by Area of Focus (Agriculture/Food, Biomedical, Biotech, Environmental, Evolutionary)
- Table 3-1: FUGE Funding Recipients
- Table 3-2 Large-Scale Sequencing Centers NHGRI Funding, 2007
- Figure 3-8: NHGRI Funding of Large-Scale Sequencing Centers by Organization 2004-2006 (cumulative)
- Figure 3-9: NHGRI Funding of Large-Scale Sequencing Centers by Organization 2007 Figure 3-10: Broad Institute Organizational Structure
- Table 3-3: NSF Plant Genome Research Project Recent Funding Awards (Title Start Date, Expiration Date, PI, Organizatino, Funding Amount) Table 3-4: NSF / USDA Microbial Genome Sequencing Program Recent
- Funding Awards (Title, Start Date, Expiration Date, PI, Organization, Funding Amount)
Chapter four: DNA Sequencer Products
- Table 4-1: Key Products and Technologies Currently on the Market by Company (Company, Product/ Technology, Comments)
Chapter five: Market Data
- Table 5-1: DNA Sequencer Equipment Revenues 1999-2006
- Table 5-2: DNA Sequencer Equipment Revenues 2006-2012
- Figure 5-1 DNA Sequencer Market, Market Share by Industry, 2006
- Figure 5-2: Trending in the DNA Sequencer Equipment Market 1999-2006
- Figure 5-3: ABI’s Quarterly Overall Sequencing Revenues 2001 to 2006
- Figure 5-4: ABI’s Quarterly Overall Sequencing Revenues Q3 2005 to Q4 2006
- Figure 5-5: Estimated Forecasted Price of Sequencing a Genome 1990-2030
- Figure 5-6: Trending in the DNA Sequencer Equipment Market, 2006-2012
Chapter SIX: Competitive Analysis
- Table 6-1: Revenues and Market Shares of Leading DNA Sequencer System
- Suppliers, 2006 (Company, Market Share, Revenues, Trend)
- Figure 6-1: Market Shares, DNA Sequencer Systems, 2006
- Table 6-2: Comparison of Next-Generation Sequencer System Features (Reads,
- Read Length, Number of Samples at Once, BP Output, Cost Comparison with Sanger/ CE, Consumable Cost per Run)
chapter seven: Intellectual Property and Litigation
- Table 7-1: Selected Sequencing-Related Patents Assigned or Licensed to Applied
- Biosystems (Assignee, Title, Patent #)
Chapter eight: Deals
- Table 8-1: Notable Deals in Recent Years (Companies, Date, Details
Chapter ten: Technologies Under Development
- Table 10-1: First Set of NHGRI “$100,000 Genome” Grant Awardees
- October 2004 (Awardee, Title, Amount, Term)
- Table 10-2: First Set of NHGRI “$1,000 Genome” Grant Awardees
- October 2004 (Awardee, Title, Amount, Term)
- Table 10-3: Second Set of NHGRI “$100,000 Genome” Grant Awardees
- August 2005 (Awardee, Title, Amount, Term)
- Table 10-4: Second Set of NHGRI “$1,000 Genome” Grant Awardees
- August 2005 (Awardee, Title, Amount, Term)
- Table 10-5: Latest Set of NHGRI “$1,000 Genome” Grant Awardees
- October 2006 (Awardee, Title, Amount, Term)
- Table 10-6: Latest Set of NHGRI “$100,000 Genome” Grant Awardees
- October 2006 (Awardee, Title, Amount, Term)
- Table 10-7: Selected Group s Workingon Microfluidics for DNA Sequencing
- Applications (Number of Channels, Read Length, Time)
CHAPTER ONE: Executive Summary
- Background
- Scope and Methodology
- Size and Growth of Market
- Analytical Microchips Market
- Analytical Chips for DNA/Gene Microarrays
- Analytical Chips for Protein Microarrays
- Analytical Chips for Microbiology Microarrays
- Analytical Chips for Tissue Microarrays
- Analytical Chips for Cell Microarrays
- Analytical Process Microchips
- Key Occurances in the Analytical Chip Market
CHAPTER TWO: Introduction
- Background
- Early Analytical Chip Products
- New Chip Applications
CHAPTER THREE: DNA/Gene Biochips
- Microbiology Microarrays
- DNA/Gene Microarrays
- DNA/Gene Microarray Production
- Gene and Clone Selection
- DNA/Gene Microarray Applications
- Genotyping
- Gene Expression Measurement
- DNA/Gene Microarray Informatics
- Microbiology Arrays
- Microbiology Array Technology
- Microbiology Microarray Applications
- Drug/Vaccine Discovery and Development
- Microbiology Microarray Commercialization
CHAPTER FOUR: Protein Microarrays
- Background
- Protein Array Applications
- Drug Discovery and Development
- Clinical Diagnostics
- Protein Microarray Commercialization
CHAPTER FIVE: Cell and Tissue Microarray
- Cell Microarray Technology
- Cell Microarray Applications
- Transcriptional Regulation
- Drug Discovery and Development
- Cell Microarray Commercialization
- Tissue Microarrays
- Tissue Microarray Technology
- Tissue Microarray Commercialization
CHAPTER SIX: Process Microchips: Lab-On-A-Chip Technology
- Overview
- Microchip Technology
- LOC Applications
CHAPTER SEVEN: Company Profiles
- Overview
- Accelr8 Technology Corporation
- Affymetrix, Inc.
- Agilent Technologies, Inc.
- Ambion, Inc.
- Bio-Rad Laboratories
- Caliper Life Sciences
- Invitrogen Corporation
- Nanogen, Inc.
- NimbleGen Systems, Inc.
- TeleChem International, Inc.
CHAPTER EIGHT: Market Analysis
- DNA/Gene Microarrays
- Protein Microarrays
- Cell Microarrays
- Tissue Microarrays
- Microbiology Microarrays
CHAPTER NINE: Conclusions and Strategic Implications
- First Conclusion
- Second Conclusion
- Third Conclusion
- Fourth Conclusion
- Fifth Conclusion
- Sixth Conclusion
- Seventh Conclusion
- Eighth Conclusion
- Ninth Conclusion
APPENDIX
table of exhibits
Executive Summary
Figure 1-1: The Market Potential for Analytical Microchips in the United States: 2007 - 2017
Table 1-1 : Estimated Market Potential for United States Market for Analytic Microchips: 2007 - 2017 by Application (DNA/Gene, Protein, Cell, Tissue, Microbiology, Process)
Figure 1-2 : Growth in the United States Market Potential for DNA/Gene Microarray Products: 2007 - 2017
Figure 1-3 : Growth in the United States Market for Protein Microarray Products: 2007 - 2017
Figure 1-4 : Growth in the United States Market for Microbiological Microarray Products: 2007 - 2017
Figure 1-5: Growth in the United States Market for Tissue Microarray Products: 2007 - 2017
Figure 1-6 : Growth in the United States Market for Cell Microarray Products: 2007 - 2017
Figure 1-7 : Growth in the United States Market for Process Microchip Products: 2007 - 2017
ChAPTER THREE: DNA/Gene and Microbiology Microarrays
- Table 3-1:Selected Genomics Databases
CHAPTER FOUR: Protein Microarrays
- Table 4-1: Key Competitors in Antibody and Protein Microarray Technology
- Cell and Tissue Microarray
CHAPTER FIVE: Cell and Tissue Microarray
- Table 5-1: Key Competitors in Cell and Tissue Microarray Technology
- Process Microchips: Lab-On-A-Chip Technology
CHAPTER SIX: Process Microchips: Lab-On-A-Chip Technology
- Table 6-1: Advantages and Disadvantages of LOC Technology
- Table 6-2: Key Competitors in Cell Process Microchip (LOC) Technology
CHAPTER EIGHT: Market Analysis
- Table 8-1: Historic and Projected United States Market Potential for Analytical Microarrays: 2007-2017
- Table 8-2 Historic and Projected United States Market Potential for DNA/Gene Microarrays: 2007-2017
- Figure 8-2 Trends in the Historic and Projected United States Market Potential for DNA/Gene Microarrays: 2007-2017
- Table 8-3 Historic and Projected United States Market Potential for Protein Microarrays: 2007-2017
- Figure 8-3: Trends in the Historic and Projected United States Market Potential for Protein Microarrays: 2007-2017
- Table 8-4: Historic and Projected United States Market Potential for Cell Microarrays: 2007-2017
- Figure 8-4: Trends in the Historic and Projected United States Market Potential for Cell Microarrays: 2007-2017
- Table 8-5: Historic and Projected United States Market Potential for Tissue Microarrays: 2007-2017
- Figure 8-5 Trends in the Historic and Projected United States Market Potential for Tissue Microarrays: 2007-2017
- Table 8-6: Historic and Projected United States Market Potential for Microbiology Microarrays: 2007-2017
- Figure 8-6: Trends in the Historic and Projected United States Market Potential for Microbiology Microarrays: 2007-2017
- Table 8-7: Historic and Projected United States Market Potential for Process Microchips: 2007-2017
- Figure 8-7: Trends in the Historic and Projected United States Market Potential for Process Microchips: 2007-2017 229
