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

Genetic Technology is one of the closest-watched areas in healthcare and in the past two years Kalorama Information has published major studies on different aspects of this market. This Kalorama Information Bundle consists of four major reports in biotech equipment:

  • DNA Sequencing Equipment Markets: Markets, Forecasts, Sequencer Product Reviews and Company Profiles
  • SNP Genotyping Markets: Single base pair mutations that occur at a specific site in the DNA sequence, the most common type of genetic variation between human beings. Because they are responsible for over 80% of the variation between two individuals, SNPs are ideal for the task of hunting for correlations between genotype and behavior or quality exhibited by a living organism.
  • Gene Expression Profiling Markets (Coverage of Gene Expression in Biomarkers, Pharmacogenetics / Pharmacogenomics, Infectious Disease Research, Cancer Diagnostics and Prognostics, and Diagnosis and Prognosis of Other Diseases
  • Analytical Chip/BioChip Markets (Includes Lab on a Chip, DNA/Gene, Protein, and other Microarrays)
These reports, the result of Kalorama's biotech analyst Justin Saek's and Kenneth Krul's investigation into the biotech markets.


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

  • 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

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