DNA Sequencing Equipment and Services Markets

Table of Contents

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)