Key Genetic Technologies Market Research Bundle (SNPs, Gene Expression Profiling, DNA Sequencing and Analytical Chips)

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
    • MammaPrint
  • DakoCytomation
    • Hercep-Test
  • ChondroGene
    • Sentinel Technology
  • 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)
    • mirVana miRNA Bioarrays
  • 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
    • Geniom One
  • Illumina
    • DASL Assay Focused Arrays Genome-Wide Expression BeadChips
  • Kreatech Biotechnology
    • miRACULS miRNA Kit
  • Marligen Biotechnologies
    • Multiplex Transcription Factor Assays
  • Panomics
    • QuantiGene 2.0 Reagent System
  • Roche Applied Science
    • LightCycler 480 System
  • Stratagene (Agilent)
    • Stratagene
  • 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
    • DrugMatrix

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 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

  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
  • Illumina Genome Analyzer
  
  
• LI-COR Biosciences (Lincoln, NE)
  • 4300

CHAPTER FIVE: Market Data

• Revenues and Forecast

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

• Glossary

table of exhibits