SNP and Whole Genome Sequencing Market Research Bundle

 
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Published Apr 1, 2010 | 500 Pages | Pub ID: KLI2614026

This report combines two of Kalorama's latest research volumes DNA Sequencing and SNP Genotyping and Analysis Markets into one package, and includes a preface on the complementary/competitive use of SNP Analysis and whole-genome sequencing on topics and the impact of the results of GWAS on the market.
PREFACE: SNP and Sequencing in Personalized Medicine

Future of SNP Since The Latest GWAS Results: Kalorama Editors Interview Justin Saeks, Analyst and Author

DNA SEQUENCING MARKETS

TABLE OF CONTENTS
CHAPTER ONE: EXECUTIVE SUMMARY
  • Introduction, Background, & Definition
  • Introduction
    • A Period of Rapid Developments
    • Further Longer-Term Challenges
    • Rapid Growth Overall, But Intense Competition
    • Moving Into New Applications and Segments
    • Customers’ Research Models Evolving
    • Second-Generation Systems Getting Established
  • Background
    • Scope and Methodology
    • Applications and Definitions
    • Types of Samples
    • DNA Sequencing Strategies
    • DNA Sequencing Chemistries and Techniques
  • Sanger Sequencing
  • Reversible Terminators
  • Single Nucleotide Addition; Pyrosequencing
CHAPTER TWO: SEQUENCER MARKET TRENDS
  • Industry and Technology Trends
  • Continual Improvements Expand Next-Generation Market
  • Spread of Targeted Enrichment, Sequence-Capture Products and Services
  • Synergies Appearing Between Life Science Companies’ Products
  • SNP and Other Experiments Moving to Sequencing for Higher Detail
  • Market Fragmenting Into Multiple Applications, Products
  • Miniaturization of Sanger and CE Technology
  • Rise of Consumer Genomics, Genetic Testing
  • Genome Sequencing Trends
    • Continued Acceleration in Sequence Output
    • Phylogenetic Breakout of Genome Sequencing Projects
    • Technologies Used in Genome Projects
    • Types of Genome Projects in GOLD Database
    • Technologies Used in Genome Projects by Type of Project
    • Technologies Used in Genome Projects by Country
    • Countries Leading Genome Projects
    • Technologies Used in Genome Projects by Institution
    • Technologies Used in Genome Projects by Funding Organization
    • Technologies Used in Genome Projects by Domain
    • Phenotypes of Genomes Being Sequenced
    • Diseases / Conditions Associated With Genomes Being Sequenced
    • Phylogenetic Breakout of Eukaryotic Genome Projects
  • Funding Trends, Genome Centers, Consortia
    • Introduction
    • Major Sequencing Centers
    • Major Funding Sources
    • Annual Funding of Genome Projects by Organization
    • Funding Relevance of Bacterial Sequencing Projects
    • Funding Relevance of Non-Bacterial Genome Project
    • NHGRI Annual Funding, Budget, Periodic Strategic Planning
    • NHGRI Funds Large-Scale Sequencing Center
    • NHGRI White Paper #4: The Future of Genome Sequencing
    • The Cancer Genome Atlas Project
    • Cancer Sequencing Projec
    • FUGE - Functional Genomics in Norway
    • National Plant Genome Initiative
    • NSF / USDA Microbial Genome Sequencing Programs
    • Other Initiatives and Consortia
CHAPTER THREE: DNA SEQUENCER PRODUCTS
  • 454 Life Sciences (Branford, CT) / Roche
    • 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 3500 Genetic Analyzer
    • Applied Biosystems 3730 DNA Analyzer
    • Applied Biosystems 3730xl DNA Analyzer
    • SOLiD 3
  • Beckman Coulter
    • CEQ 8000; CEQ 8800
    • GenomeLab GeXP Genetic Analysis System
  • Dover Systems (Danaher Motion)
    • Polonator G.007
    • GE Healthcare
    • MegaBACE 500
    • MegaBACE 750
    • MegaBACE 1000
    • MegaBACE 1500
    • MegaBACE 4000
  • Helicos Biosciences
    • Helicos Genetic Analysis System
  • Illumina / Solexa
    • Illumina Genome Analyzer II
  • LI-COR Biosciences (Lincoln, NE)
    • 4300
  • Pacific Biosciences
    • SMRT Technology
CHAPTER FOUR: DNA SEQUENCER MARKET FORECAST
  • Revenues and Forecast
  • Current Market (01-08)
  • Forecasted Market: ABI as a Market Bellweather
  • Growth Indicators
CHAPTER FIVE: COMPETITIVE ANALYSIS OF SEQUENCER MARKET
  • Introduction
  • Next- and Next-Next-Generation Creating Turbulence
  • Capillary Electrophoresis Maintains Large Segment
  • Second-, Third-Generation Battle Still Up in the Air
  • DNA Sequencer Market Shares
  • Features and Strengths of Second-Generation Sequencers
    • 454 Life Sciences GS FLX - Strengths / Advantages
    • 454 Life Sciences GS FLX - Weaknesses / Disadvantages
    • Applied Biosystems SOLiD - Strength / Advantages
    • Applied Biosystems SOLiD - Weaknesses / Disadvantages
    • Illumina Genome Analyzer - Strength / Advantages
    • Illumina Genome Analyzer - Weaknesses / Disadvantages
CHAPTER SIX: INTELLECTUAL PROPERTY AND LITIGATION
  • Patent Interference Between Life Technologies and Pacific Biosciences
  • Helicos Appeals European Patent Office Decision on Illumina Patent
  • Illumina Files ‘841 Patent Infringement Suit Against Affymetrix
  • Affymetrix and Illumina Settle Case Over ‘243, ‘432, ‘531, ‘365, and ‘716
  • Applied Biosystems and Illumina Claims and Counter-claims Both Unsuccessful
  • Fluidigm and Applied Biosystems Agree to End Case
  • 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
  • Applied Biosystems and Amersham plc (GE Healthcare) Settle Sequencing Patent Litigation
CHAPTER SEVEN: DEALS
  • Significant DNA Sequencing Equipment Deals
CHAPTER EIGHT: CORPORATE PROFILES
  • 454 Life Sciences / Roche
  • Applied Biosystems / Life Technologies
  • Beckman Coulter (Fullerton, CA)
  • GE Healthcare Life Sciences
  • Helicos Biosciences
  • Illumina / Solexa
  • LI-COR Biosciences (Lincoln, NE)
CHAPTER NINE: TECHNOLOGIES UNDER DEVELOPMENT
  • Introduction
  • Human Microbiome Project Awards Funds for Technology Development, Data Analysis and Ethical Research
  • NHGRI Seeks DNA Sequencing Technologies Fit for Routine Laboratory and Medical Use, August 2008
  • Arizona State University, Tempe
    • “Sequencing by Recognition”
  • Harvard College
    • “Electronic Sequencing in Nanopores”
  • Oak Ridge National Laboratory / UT Battelle
    • “DNA Transport and Sequencing Through a Quadrupole Gate”
  • Princeton University
    • “Nanogap Detector (Arrays) Inside Nanofluidic Channel for Fast Real-Time DNA Sequencing”
  • University of Arkansas, Fayetteville
    • “Exploration of Solid-State Nanopore Reading Labeled Linear DNA Sequence”
  • University of California, San Diego
    • “Genome Sequencing by Natural DNA Synthesis on Amplified DNA Clones”
  • University of Pennsylvania, Philadelphia
    • “DNA Sequencing Using Nanopore-Nanoelectrode Devices for Sensing and Manipulation”
  • University of Pittsburgh
    • “DNA Sequencing at a Stretch”
  • Columbia University
    • “DNA Sequencing with Reversible dNTP and Cleavable Fluorescent ddNTP Terminators”
  • Foundation for Applied Molecular Evolution, Inc.
    • “Near Term Development of Reagents and Enzymes for Genome Sequencing”
  • Illumina
    • “Development of a 10Gb Pyrosequencer”
  • NHGRI Seeks to Advance Next Generation of Sequencing Technologies, August 2007
  • Arizona State University, Tempe
    • “Sequencing by Recognition”
  • Brown University
    • “Hybridization-assisted Nanopore DNA Sequencing”
  • Duke University
    • “Continuous Sequencing-by-Synthesis Based on a Digital Microfluidic Platform”
  • NABsys, Inc.
    • “Hybridization-assisted Nanopore Sequencing”
  • North Carolina State University, Raleigh
    • “Sequencing DNA by Transverse Electrical Measurements in Nanochannels”
  • UMDNJ-New Jersey Medical School
    • “Ribosome-based Single Molecule Method to Acquire Sequence Data from Genomes”
  • University of British Columbia, Vancouver
    • “Nanopore Array Force Spectroscopy Chip for Rapid Clinical Genotyping”
  • University of California, Irvine
    • “High Throughput Low Cost DNA Sequencing Using Probe Tip Arrays”
    Columbia University
    • “3'-O-Modified Nucleotide Reversible Terminators for Pyrosequencing”
    “An Integrated System for DNA Sequencing by Synthesis”
  • University of New Mexico School of Medicine, Albuquerque
    • “Polony Sequencing the Human Genome”
  • University of Wisconsin, Madison
    • “Sequence Acquisition from Mapped Single DNA Molecules”
  • “NHGRI Aims to Make DNA Sequencing Faster, More Cost Effective”, October 2006
  • Arizona State University
    • “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, HGSC
    • “Ultrafast SBS Method for Large-Scale Human Resequencing”
  • Intelligent Bio-Systems
    • “High-Throughput DNA Sequencing by Synthesis Platform”
  • NHGRI Expands Effort to Revolutionize Sequencing Technologies, August 2005
  • Agencourt Personal Genomics [Applied Biosystems / Life Technologies]
    • “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”
  • Pacific Biosciences (formerly 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 Funds Next Generation of Sequencing Technologies, October 2004
CHAPTER TEN: CHALLENGES AND STRATEGIC RECOMMENDATIONS
  • Market Challenges
    • Challenge #1
    • Challenge #2
    • Challenge #3
    • Challenge #3
    • Challenge #4
    • Challenge #5
    • Challenge $6
    • Challenge #7
  • Strategic Recommendations
    • Recommendation #1
    • Recommendation #2
    • Recommendation #3
    • Recommendation #4
    • Recommendation #5
    • Recommendation #6

LIST OF EXHIBITS

CHAPTER TWO: SEQUENCER MARKET TRENDS

  • Table 2-1: Completely Sequenced Genomes in GOLD, 1995-2008(Without Publication, With Publication)
  • Figure 2-1: Completely Sequenced Genomes in GOLD, 1999-2008
  • Table 2-2: Domains of Completed Genomes in GOLD by Year, 1995-2008 (Archaes’, Bacteria, Eukaryota’)
  • Figure 2-2: Domains of Completely Sequenced Genomes in GOLD by Year, 1999-2008 (Archaes’, Bacteria, Eukaryota’)
  • Table 2-3: Genome Projects in IMG by Domain, 2005-2008 (Cumulative)
  • Figure 2-3: Genome Projects in IMG by Domain, 2005-2008 (Cumulative)
  • Table 2-4: Phylogenetic Groups of Sequencing Projects in GOLD, 1998-2008 (Cumulative)
  • Figure 2-4: Phylogenetic Groups of Sequencing Projects in GOLD, 1998-2008 (Cumulative)
  • Table 2-5: Phylogenetic Distribution of Bacterial Genome Projects, Q1 2007
  • Figure 2-5: Phylogenetic Distribution, Bacterial Genome Projects, Q1 2007
  • Table 2-6: Phylogenetic Distribution of Bacterial Genome Projects, Q1 2009
  • Figure 2-6: Phylogenetic Distribution, Bacterial Genome Projects, Q1 2009
  • Table 2-7: Category / Phylogeny of Metagenomics Projects (Cumulative)
  • Figure 2-7: Category/Phylogeny of Metagenomics Projects in GOLD, 2008-2009 Cumulative
  • Table 2-8: Technology Used in Genome Projects, '95-Q1'09
  • Figure 2-8: Sequencer Technology Used in Genome Projects '95-Q1'09
  • Table 2-9: Types of Projects in GOLD, ‘95-Q1’09
  • Figure 2-9: Types of Projects in GOLD, ‘95-Q1’09 (Cumulative)
  • Table 2-10: Systems Used in Genome Projects by Type, '95-Q1'09 (Sanger, Illumina)
  • Table 2-11: Systems Used in Genome Projects by Type, '95-Q1'09
  • Table 2-12: Systems Used in Genome Projects by Type, '95-Q1'09 Figure 2-10: Systems Used in Genome Projects by Type, '95-Q1'09
  • Table 2-13: Systems Used in Genome Projects by Country, '95-Q1'09
  • Table 2-14: Systems Used in Genome Projects by Country, '95-Q1'09
  • Figure 2-11: Systems Used in Genome Projects by Country, '95-Q1'09
  • Table 2-15: Countries Leading Projects, '95-Q1'09
  • Figure 2-12: Countries Leading Projects, '95-Q1 '09
  • Table 2-16: Systems Used in Genome Projects by Institute, '95-Q1'09
  • Table 2-17: Systems Used in Genome Projects by Inst, '95-Q1'09 Figure 2-13: Systems Used in Genome Projects by Inst, '95-Q1'09
  • Table 2-18: Systems Used in Genome Projects by Funding Org., '95-Q1'09
  • Table 2-19: Systems Used in Genome Projects by Funding Organization, '95-Q1'09
  • Figure 2-14: Systems Used in Genome Projects by Funding Organization, '95-Q1'09
  • Table 2-20: System Used in Genome Projects by Domain, '95-Q1'09
  • Table 2-21: System Used in Genome Projects by Domain, '95-Q1'09
  • Table 2-22: System Used in Genome Projects by Domain, '95-Q1'09
  • Figure 2-15: Systems Used in Genome Projects by Domain, '95-Q1'09
  • Figure 2-16: Systems Used in Genome Projects by Domain, '95-Q1'09
  • Table 2-23: Phenotypes of Projects in GOLD, '95-Q1 '09
  • Figure 2-17: Phenotypes of Projects in GOLD, '95-Q1 '09
  • Table 2-24: Diseases/Conditions Associated with Projects, '95-Q1'09
  • Figure 2-18: Diseases/Conditions Associated with Projects, '95-Q1 '09
  • Table 2-25: Eukaryotic Genome Projects in GOLD, '07-09
  • Figure 2-19: Eukaryotic Genome Projects in GOLD, '07-'09 (Cumulative)
  • Table 2-26: Number of Genome Projects by Institute, '95- Q1 '09
  • Figure 2-20 Number of Genome Projects by Institute, '95- Q1 '09 Cumulative
  • Table 2-26 Funding Sources of Genome Projects, '95-Q1 '09
  • Figure 2-21: Funding Sources of Genome Projects, '95-Q1 '09
  • Table 2-26: Funding of Genome Projects by Organization, Q1'07-Q1'09
  • Figure 2-21: Funding of Genome Projects, 2007-2009 ($M)
  • Figure 2-22: Human Genome Project Funding, DOE & NIH '90-'03
  • Table 2-27: Relevance of Bacterial Sequencing Projects, '95 - Q1 '09, (Cumulative)
  • Figure 2-23: Relevance of Bacterial Sequencing Projects, '95- Q1 '09 (Cumulative)
  • Table 2-28: Relevance of Non-Bacterial Sequencing Project, '95 - Q1 '09, (Cumulative)
  • Figure 2-24: Relevance of Non-Bacterial Sequencing Projects, '95- Q1 '09 (Cumulative)
  • Table 2-29: NHGRI Budget by Year
  • Figure 2-25: NHGRI Budget by Year incl. ARRA, 2006-2010
  • Table 2-30: 2010 Estimated NHGRI Budget by Mechanism
  • Figure 2-26: 2010 Estimated NHGRI Budget by Mechanism (percent)
  • Table 2-31: NHGRI Budget by Activity, 2008-2010 (Medical Sequencing, Genomic Function, Technology Development, Computation Genomics, Large-scale Sequencing
  • Table 2-32: NHGRI Extramural Budget, 2006-2010
  • Figure 2-27: NHGRI Extramural Budget by Activity, 2008 Comparable
  • Figure 2-28: NHGRI Extramural Budget by Activity, 2009 Estimated
  • Figure 2-9: NHGRI Extramural Budget by Activity, 2010 Estimated
  • Table 2-33: NHGRI Budget by Mechanism (No. And Amount), FY 2008, FY 2009 and FY2010
  • Table 2-34: Large-Scale Sequencing Centers NHGRI Funding, 2004-2006
  • Figure 2-10: NHGRI Funded Large-Scale Sequencing Centers '04-'06
  • Table 2-34: Large-Scale Sequencing Centers NHGRI Funding by Year, 2007-2008
  • Figure 2-11: NHGRI Funded Large-Scale Sequencing Centers '07-'08
  • Figure 2-12: Broad Institute Organizational Structure
  • Table 2-35: FUGE Funding Recipients
  • Table 2-36: Plant Genome Comparative Sequencing Program (PGCSP) Awards, 2007-2008
  • Table 2-37: Plant Genome Research Program GEPR, TRMS, and TRPGR Awards, 2007
  • Table 2-38: Plant Genome Research Program GEPR, TRMS, and TRPGR Awards, 2008 (Institution, Title, Total Award, Duration)
  • Table 2-39: NSF / USDA Microbial Genome Sequencing Program Awards, 2007-2009
  • Table 2-40: Other Initiatives and Consortia Supporting Technology Development, 2009Table 2-41: Other Initiatives and Consortia Performing DNA Sequencing, 2009
  • Table 2-41: Other Initiatives and Consortia Performing DNA Sequencing, 2009
  • Table 2-41 (continued): Other Initiatives and Consortia Performing DNA Sequencing, 2009
CHAPTER THREE: PRODUCTS
  • Table 3-1: Key Systems and Technologies Currently in the Market (Company, Product, Comments)
CHAPTER FOUR: MARKETS
  • Table 4-1: Revenues, 2001-2008 DNA Sequencer Equipment
  • Table 4-2: Growth Rate, 2001-2008 DNA Sequencer Equipment
  • Figure 4-1: Revenues, DNA Sequencer Equipment Market, '01-'08
  • Figure 4-2: ABI Sequencing Revenues, Q3 2001 - Q3 2008
  • Figure 4-3: ABI Sequencing Revenues, Q4 2004 - Q3 2008
  • Figure 4-4: Cost of Sequencing a Genome
  • Table 4-3: 2008-2014 DNA Sequencer Equipment Market Forecast
  • Figure 4-5: DNA Sequencer Equipment Market Forecast, 2008-2014
  • Table 4-4: Growth Rate, 2008-2014 DNA Sequencer Equipment
  • Figure 4-6: Growth Rate, DNA Sequencers, 2008-2014
CHAPTER FIVE: COMPETITIVE ANALYSIS OF SEQUENCER MARKET
  • Table 5-1: Revenues & Market Shares, DNA Sequencer Systems, 2006 & 2008
  • Figure 5-1: Estimated DNA Sequencer Revenues by Company, 2006 & 2008
  • Table 5-2: Comparison of Second-Generation Sequencers, 2007
  • Table 5-3: Comparison of Second-Generation Sequencers, 2009
CHAPTER SIX: INTELLECTUAL PROPERTY AND LITIGATION
  • Table 6-1: Select Early Sequencing-Related Patents Assigned or Licensed to Life Technologies / Applied Biosystems
CHAPTER SEVEN: DEALS
  • Table 7-1: Significant Deals in the DNA Sequencing Equipment and Services Market
CHAPTER NINE: TECHNOLOGIES UNDER DEVELOPMENT
  • Table 9-1: NIH Human Microbiome Project Technology Development Awards, 2008
  • Table 9-2: NHGRI $1000 Genome Grant Awardees, August 2008
  • Table 9-3: NHGRI $100,000 Genome Grant Awardees, August 2008
  • Table 9-4: NHGRI $1000 Genome Grant Awardees, August 2007
  • Table 9-5: NHGRI $100,000 Genome Grant Awardees, August 2007
  • Table 9-6: NHGRI $1000 Genome Grant Awardees, October 2006
  • Table 9-7: NHGRI $100,000 Genome Grant Awardees, October 2006
  • Table 9-8: NHGRI $100,000 Genome Grant Awardees, August 2005
  • Table 9-9: NHGRI $1000 Genome Grant Awardees, August 2005
  • Table 9-10: NHGRI $100,000 Genome Grant Awardees, October 2004
  • Table 9-11: NHGRI $1000 Genome Grant Awardees, October 2004

SNP GENOTYPING AND ANALYSIS MARKETS


TABLE OF CONTENTS


CHAPTER ONE: EXECUTIVE SUMMARY
  • Introduction
  • Market
  • Trends
CHAPTER TWO: OVERVIEW
  • SNP Analysis Methods
    • Amplification
    • Allele Discrimination / Assay Reaction Mechanism
      • Allele-Specific Hybridization
      • Allele-Specific Invasive Cleavage
      • Allele-Specific Ligation
      • Allele-Specific Primer Extension
      • Allele-Specific Single Base Extension (Single Base Primer Extension)
      • Single Nucleotide Addition; Pyrosequencing
      • Assay Format
    • Detection Method
  • Definitions
    • DNA Microarray
    • Genome-Wide Association
    • Linkage Analysis
    • Mass Spectrometry
    • Single-Nucleotide Polymorphism (SNP)
  • Applications
    • Life Science Research
    • Pharmacogenetics / Pharmacogenomics
    • Agriculture / Breeding
  • Case Studies
    • 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
    • Case Study #5 - Development of Miniaturized Integrated SNP Genotyping Microsystems
CHAPTER THREE: INDUSTRY, TECHNOLOGY, REGULATORY TRENDS
  • Industry Trends
    • Period of Limbo While Funding and Content Materialize
    • Consolidation Occurring in Array and Life Science Markets
    • Drug and Diagnostics Industries More Comfortable
    • Broad Acceptance of SNP Analysis’ Value
    • Core Labs Becoming Established Paradigm
  • Technology Trends
  • Rapid Rate of Product Introductions
  • Increased Multiplexing Creates Improved Products
  • End-Users Attracted to Larger-Scale SNP Platforms
  • Complexity of Biological Systems Requires Multiple Techniques
  • Miniaturization of Equipment and Instruments
  • Regulatory Trends
    • Introduction
    • March 2004 - Critical Path Initiative
    • March 2005 - “Guidance for Industry - Pharmacogenomic Data Submissions”
    • March 2006 - Critical Path Opportunities
    • November 2006 - “Recommendations for the Generation and Submission of Genomic Data”
    • August 2007 - Pharmacogenomic Data Submissions — Companion Guidance
    • December 2007 - EGAPP Reviews Use of CYP450 Genetic Testing For SSRIs
    • NIH Limits Access to Data from GWAS
CHAPTER FOUR: PRODUCTS
  • Affymetrix
    • Overview
    • Systems
      • Axiom Genotyping Solution
      • GeneChip Scanner 3000 7G
      • GeneChip Scanner 3000 7G Plus Targeted Genotyping System
      • GeneTitan Multi-Channel (MC) Instrument
      • Array Station
    • Microarrays and Reagents
      • GeneChip Human Mapping 10K Array Xba 142 2.0 (GeneChip Mapping 10K 2.0 Array)
      • GeneChip Human Mapping 100K Set
      • Genome-Wide Human SNP Array 5.0
      • Genome-Wide Human SNP Array 6.0
      • Axiom Genome-Wide Human Array Plates, Reagent Kits
      • DMET Plus Premier Pack
    • GeneChip Universal Tag Arrays and Related Kits
      • Human 20K cSNP Kit
      • Human Immune-Inflammation 9K SNP Kit
      • Human MALD 3K SNP Kit
      • Bovine Mapping 10K SNP Kit
      • Bovine Mapping 25K SNP Kit
      • Rat Mapping 5K SNP Kit
  • Applied Biosystems (Life Technologies)
    • Overview
    • SNP Genotyping Systems and Kits
      • SNaPshot Multiplex System
      • SNPlex Genotyping System
    • TaqMan Genotyping Assays
      • Applied Biosystems’ TaqMan Genotyping Assay Strategy
      • TaqMan Sample-to-SNP Kits
      • VariantSEQr Resequencing System
      • TaqMan OpenArray Genotyping System
    • RT-PCR
      • 7900HT Fast Real-Time PCR System
    • Sequencers
      • 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 3
  • Beckman Coulter
    • CEQ 8000; CEQ 8800
    • GenomeLab SNPstream Genotyping Series
  • CombiMatrix
    • CustomArray Synthesizer
    • Geniom RT Analyzer
  • GE Healthcare
    • Overview
    • Reagents and Kits
    • SNP Genotyping Kits
    • Sequencers
      • MegaBACE 500
      • MegaBACE 750
      • MegaBACE 1000
      • MegaBACE 1500
      • MegaBACE 4000
  • Illumina
    • Overview
      • iScan
      • iScan SQ
      • BeadXpress Reader
      • Illumina Genome Analyzer IIx
    • Microarrays
      • Human1M-Duo BeadChip
      • Human1M-Quad BeadChip
  • LI-COR Biosciences
    • 4300
  • Roche Applied Science
    • LightCycler 480 System
    • HybProbe; SimpleProbe
  • Sequenom
    • iPLEX GOLD Assay
    • MassARRAY System
    • MassARRAY Compact 96
    • Selected SNP Genotyping Products & Technologies
CHAPTER FIVE: CONSORTIA, FUNDING, LITIGATION AND DEALS
  • Consortia, Initiatives
    • The Cancer Genome Atlas (TCGA) Project
    • Cancer Sequencing Project
    • Critical Path Institute (C-Path)
    • 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
    • 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)
    • Wellcome Trust Case-Control Consortium (WTCCC)
    • WTCCC2
    • Other Related Initiatives and Consortia
    • 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
  • Deals
  • Intellectual Property and Litigation
    • Patent Interference Between Life Technologies and Pacific Biosciences
    • Helicos Appeals European Patent Office Decision on Illumina Patent
    • Applied Biosystems and Illumina Claims and Counter-claims Both Unsuccessful
    • Fluidigm and Applied Biosystems Agree to End Case
    • 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
    • Applied Biosystems and Amersham plc (GE Healthcare)
    • Settle Sequencing Patent Litigation
CHAPTER SIX: MARKET ANALYSIS
  • Historical
  • Illumina as Bellwether for SNP Analysis Market
  • Applied Biosystems as Bellwether for RT-PCR Products
  • Forecast
  • Assumptions and Scope
  • Consumer SNP
  • Product Revenue
  • Competitive Analysis
CHAPTER SEVEN: CORPORATE PROFILES
  • Affymetrix
  • Applied Biosystems (ABI) (Life Technologies)
  • Illumina
CHAPTER EIGHT: CHALLENGES AND STRATEGIC RECOMMENDATIONS
  • Challenges
    • Challenge #1
    • Challenge #2
    • Challenge #3
    • Challenge #4
    • Challenge #5
    • Challenge #6
    • Challenge #7
    • Challenge #8
    • Challenge #9
    • Challenge #10
    • Challenge #11
    • Challenge #12
  • Strategic Recommendations
    • Recommendation #1
    • Recommendation #2
    • Recommendation #3
    • Recommendation #4
    • Recommendation #5
    • Recommendation #6
    • Recommendation #7
    • Recommendation #8

TABLE OF EXHIBITS


EXECUTIVE SUMMARY

  • Figure 1-1: SNP Analysis Market

CHAPTER THREE: INDUSTRY, TECHNOLOGY, REGULATORY TRENDS

  • Table 3-1 Critical Path Opportunities List

CHAPTER FOUR: PRODUCTS

  • Table 4-1: Axiom Genome-Wide Array Planes SNP Content

  • Figure 4-1: TaqMan Assay Strategy

  • Figure 4-2: Beckman Coulter’s SNPstream Assay Strategy

  • Table 4-2 Selected SNP Products and Technologies.

  • Figure 4-3 Simple ProbeSequenom

CHAPTER FIVE: CONSORTIA, FUNDING, LITIGATION AND DEALS

  • Table 5-1: Number of Individuals in Each Subset

  • Table 5-2: Composition of the DNA Polymorphism Discovery Resources

  • Figure 5-1: Companies’ Technologies Used in First Phase of HapMap

  • Table 5-3: Technologies Used in Phase 1 of HapMap

  • Table 5-4: SNP and Sequencing Related Initiatives and Consortia, 2009

  • Table 5-5: Completely Sequenced Genomes in GOLD, Jan 2009

  • Figure 5-2 Domains of Completely Sequenced Genomes in GOLD by Year, 1999-2008 and by Category (Archae, Bacteria, Eukaryota)

  • Figure 5-3 Number of Genome Projects by Inst., '95- Q1 '09 Cumulative

  • Figure 5-4 Domains of Sequenced Genomes in GOLD, Jan 2009

  • Table 5-6 Number of Genome Projects by Institution

  • Figure 5-5 Funding of Genome Projects, 2007-2009 ($M)

  • Table 5-7: Funding Sources of Genome Projects

  • Figure 5-6 Human Genome Project Funding, DOE & NIH '90-'03

  • Table 5-7: Countries Leading Projects, '95-Q1'09

  • Table 5-8: SNP Projects by Category

  • Table 5-9: Relevance of Non-Bacterial Sequencing Projects, '95 - Q1 '09, Cum.

  • Figure 5-7: Disease/Conditions Associated with Projects

  • Figure 5-8: NHGRI Budget by Year incl. ARRA, 2006-2010 ($M)

  • Table 5-10: 2010 Est. NHGRI Budget by Mechanism

  • Figure 5-9 2010 Est. NHGRI Budget by Mechanism

  • Figure 5-10 NHGRI Funded Large-Scale Sequencing Ctrs '07-'08

  • Table 5-11 SNP Related Deals, 2009

  • Table 5-12: SNP Related Patents

CHAPTER SIX: MARKET ANALYSIS

  • Figure 6-1: Illumina Total Quarterly Revenues, 2003-2009 ($M)

  • Figure 6-2: Applied Biosystems RT-PCR / Applied Genomics Revenues, 2001-2008 ($M)

  • Table 6-1: SNP Analysis Tools Market, 2008-2014 ($M)

  • Figure 6-3: SNP Analysis Tools Market Revenues, 2008-2014 ($M)

  • Table 6-4: Growth Rate for SNP Analysis Tools

  • Figure 6-4: SNP Analysis Tools Market Growth Rate, 2008-2014

  • Figure 6-5: SNP Tools Market by Region (North America, Europe, Japan, ROW)

  • Table 6-5: SNP Tools Market by Product (Consumable, System, Software/Service)

  • Figure 6-6: SNP Market by Product, 2008 (Systems, Services/Software,

    Consumables)

  • Table 6-6: SNP Analysis Market Shares, 2008 ($M)

  • Figure 6-7: SNP Analysis Tools Market Shares, 2008 ($M)

CHAPTER SEVEN: CORPORATE PROFILES

  • Figure 7-1: Affymetrix Revenues by Product Type, 2005 - 2009

  • Figure 7-2: Affymetrix Consumables Revenues by DNA v RNA

  • Figure 7-3: Illumina Revenues 2008-2009 by quarter

CHAPTER EIGHT: CHALLENGES AND STRATEGIC RECOMMENDATIONS

  • Figure 8-1: Cheaper Sequencing Impacts SNP Market

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