Next Generation Sequencing for Life Science R&D: Advancing to the $1,000 Genome

Table of Contents

• Executive Summary

1. Overview of the Genome Sequencing Market for R&D

• 1.1 Overview of Current and Next-Generation Genome Sequencing for R&D
  • Figure 1. The Next-Generation Genome Sequencing Market Landscape
  • 1.1.2 Genome Sequencing Equipment Systems
    • Current Sanger-based CE Sequencing Systems
    • Next-Generation Sequencing Systems (Commercial)
    • Next-Generation Sequencing Systems (In Development)
  • 1.1.3 Bioinformatics Software
    • Table 1. Sequencer Vendor Provided Software (Source, NG Seq. Platform, Name)
    • Table 2. Selected Commercial Software (Source, Name, Comment)
    • Table 3. Selected Open Source Short-Read Assembly Software (Source, Name, Comment)
  • 1.1.4 Genome Sequencing Organizations
    • Academic Genome Sequencing Centers
    • Academic/ Government Core Labs
    • Commercial Service Providers
  • 1.1.5 IT Infrastructure and Applications
    • IT Infrastructure Vendors and Solutions
  • 1.1.6 Others
• 1.2 Next-Gen. Genome Sequencing Applications & Projects for R&D
  • 1.2.1 Academic Life Science Applications
  • 1.2.2 Pharma/ Biotech Drug Discovery R&D
  • 1.2.3 Clinical Diagnostic Applications and Projects
  • 1.2.4 Public Health Applications
  • 1.2.5 Emerging ' Consumer Genomics' Applications
  • 1.2.6 Agricultural/ Veterinary Applications
  • 1.2.7 Environmental (Metagenomics) Applications
  • 1.2.8 Other Related Applications

2. Next-Gen. Genome Sequencing Technology Developments

• 2.1 Government and Private Next-Generation DNA Sequencing Initiatives
  • 2.1.1 The NIH' s 2004 Proposal for Sequencing the Genome for $1,000
    • Table 4. Next-Generation Sequencing Tech. Grants Awarded by NHGRI 2004-2007 (Grant Year, Grant Goal, Organization, Next-Gen.Sequencing Technology Development Grants, Grant Amount, Term (Yr), Teams)
  • 2.1.2 The $10 Million Archon X PRIZE for Genomics
    • Table 5. Competing Teams for the X PRIZE for Genomics
• 2.2 Developing Technologies for the Next Five-Years and Beyond
  • 2.2.1 Near-Term Time Line Goal
  • 2.2.2 $1,000 Genome Time Line Goal
• 2.3 Sequencing Technologies for the $100,000 Genome
  • Sample Preparation
  • Sequencing
  • Image Analysis
  • 2.3.1 Roche/ 454 Life Sciences, Inc. GS FLX and XLR
    • Massively Parallel Sequencing by Synthesis (Pyrosequencing)
    • Figure 2. Roche/ 454 GS FLX DNA Sequencer
  • 2.3.2 Illumina, Inc. Genome Analyzer II - Sequencing by Synthesis
    • Figure 3. Illumina Genome Analyzer
  • 2.3.3 Applied Biosystems Inc. SOLiD - Polony Sequencing by Ligation
    • Figure 4. The ABI SOLiD Sequencing
  • 2.3.4 Danaher Motion Polonator G.007 - Open Source Polony Sequencing System
    • Figure 5. The Danaher-Church Polonator G.007
  • 2.3.5 Helicos BioSciences Inc. HeliScope - Single-Molecule Sequencing
    • Figure 6. Helicos HeliScope Sequencer
• 2.4 Sequencing Technologies for $1,000 Genome
  • 2.4.1 Pacific BioSciences, Inc. Real Time Single-Molecule Sequencing
    • Figure 7. Simultaneous & Continuous Excitation & Detection in a ZMW
  • 2.4.2 ZS Genetics Direct Electron Microscope Sequencing
    • Figure 8. Overview of the ZSG Sequencing Process

3. Key Alliances, M&As and IP

• 3.1 Summary of Key Alliances and M&As
  • 3.1.1 Definitions of Alliance and M&A Deal Types
    • M&As
    • Development and Supplier Partnerships
    • IP Licensing Agreements
  • 3.1.2 Highlights of Key Alliances and M&As
    • Table 6. Summary of Key Alliances and M&As, Mar/2005 to Jun/2008
  • 3.1.3 Data Tables for Alliances and M&As
    • Table 7. Key Alliances and M&As Jan to Jun 2008 (Date, Technology, Alliance Type, Buyer, Seller, Comment)
• 3.2 IP, Business Development and Challenges
  • 3.2.1 Summary of Key Patents Involving Sequencing Technologies
    • Table 11. NGS Related US Patents Issued to Orgs., 2007 to May/2008
  • 3.2.2 The Business Value of IP
    • Table 12. Key Acquisitions in Next-Generation Sequencing. (Acquirer, Target Company, Comment, Value $M)
  • 3.2.3 IP Challenges

4. The Market and Outlook for Next-Generation Genome Sequencing

• 4.1 The Total Worldwide Market Size, 2007-2012
  • Figure 9. Total Next-Gen. Sequencing Tools & Service Market 2007-2012
  • Table 13. Total Next-Gen. Sequencing Tools & Service Market 2007-2012
• 4.2 Market Size by Products & Services
  • 4.2.1 Methodology and Definitions
  • 4.2.2 Next-Gen. Sequencing Tools & Service Market By Product & Service Segments
    • Figure 10. Next-Gen. Sequencing Tools & Service Market By Product & Service Segments2007-2012
    • Table 14. Next-Gen. Sequencing Tools & Service Market By Product & Service Segments 2007-2012
  • 4.2.3 Next-Gen. Sequencing Tools & Service Market By Product & Service Segment Shares, 2008 & 2012
    • Figure 11. Next-Gen. Sequencing Tools & Service Market By Product & Service Segment Shares, 2008 & 2012
    • Table 15. WW Market by Major Segments & Shares, 2008 & 2012
    • Figure 12. Next-Gen. Sequencing Tools & Service Market By Application Segments
    • Table 16. Next-Gen. Sequencing Tools & Service Market By Application Segments
• 4.3 Market by Customer Segments
  • Table 17. Next-Gen. Sequencing Tools & Service Market By Customer Segments
  • Figure 13. Next-Gen. Sequencing Tools & Service Market By Customer Segments
• 4.4 Market by WW Regions
  • Figure 14. Next-Gen. Sequencing Tools & Service Market By WW Regions
  • Table 18. Next-Gen. Sequencing Tools & Service Market By WW Regions

5. Activities of the Firms Offering Next-Generation Genome Sequencing Products & Services

• 5.1 NG Seq. Commercial Equipment
  • 5.1.1 - 5.1.4 (Total 4 companies)
    • A. Contact Information
    • B. Key Business Facts
    • C. Company Overview, Technology and Key Products
    • D. Alliances, Strategy, Mergers and Acquisitions
    • E. Patents, Milestones, Funding, and Other Findings
• 5.2 NG Seq. Equipment Developers
  • 5.2.1 - 5.2.4 (Total 4 compnies)
    • Same as above-mentioned research items
• 5.3 Consumer Genomics Services
  • 5.3.1 - 5.3.4 (Total 4 companies)
    • Same as above-mentioned research items
• 5.4Contract Genomic Research Services
  • 5.4.1 - 5.4.4 (Total 4 companies)
    • Same as above-mentioned research items
• 5.5 Software
  • 5.5.1 (Total one company)
    • Same as above-mentioned research items

6. Conclusions and New Business Opportunities

• 6.1 Likely Next-Gen. Genome Sequencing Success and Failure Factors
  • 6.1.1 The Human Genome Project Cost $3.5 Billion and 13 Years Effort
  • 6.1.2 Advances in Technology Enable Emerging Next-Gen. Sequencers.
  • 6.1.3 Government Technology Initiative - The $100, 000 and $1,000 Genomes
  • 6.1.4 Private Technology Initiative - The X PRIZE for Genomics Fosters Race to Reach the $10,000 Genome
  • 6.1.5 Key M&As Enabled Commercial Next-Gen. Sequencing Platforms
  • 6.1.6 Barriers to Market Entry Are Getting More Challenging
  • 6.1.7 Next-Generation Sequencers Output Enormous Amounts of Data
  • 6.1.8 Consumers Want Their Personal Genomes
  • 6.1.9 Known Individuals are Getting Their Genomes Sequenced
  • 6.1.10 Government Regulators Jump In
• 6.2 Review of the Hot Development Areas in Next-Generation Genome Sequencing
  • 6.2.1 Next-Generation Sequencing Systems May Replace CE Sequencing and Enable New Applications
    • Table 19. Applications Unique to Next-Generation Sequencers
  • 6.2.2 Automated Sample Preparation
  • 6.2.3 Microarray Capture Method Front-end for Targeted Sequencing
• 6.3 Large-Scale International Sequencing Projects Use Next-Generation Sequencing
  • 6.3.1 Scientists Want to Sequence 100,000' s of Humans to Enable Personal Medicine
  • 6.3.2 The 1,000 Genomes Project
  • 6.3.3 Human Microbiome Project
  • 6.3.4 The Cancer Genome Atlas (US)
  • 6.3.5 The Wellcome Trust Sanger Institute' s Cancer Genome Project
  • 6.3.6 The Yanhuang Project
• 6.4 Next-Generation Genome Sequencing Business Opportunities or Implications
  • 6.4.1 Opportunities or Implications for the US
    • Table 20. Opportunities or Implications for the US (Region, Opportunity Area, Comment)
  • 6.4.2 Opportunities or Implications for Europe
    • Table 21. Opportunities or Implications for Europe (Region, Opportunity Area, Comment)
  • 6.4.3 Opportunities or Implications for Japan and Asia (Region, Opportunity Area, Comment)

7. Appendix

• 7.1 Glossary
• 7.2 Key Genome Sequencing Centers