DNA Sequencing: Emerging Technologies and Applications

Table of Contents

Chapter- 1: SUMMARY

• SUMMARY TABLE GLOBAL VALUE OF DNA SEQUENCING, BY END USE APPLICATION, THROUGH 2013 ($ MILLIONS)
• SUMMARY FIGURE GLOBAL VALUE OF DNA SEQUENCING, BY END USE APPLICATION, 2006-2013 ($ MILLIONS)

Chapter- 1: SUMMARY

• SUMMARY TABLE GLOBAL VALUE OF DNA SEQUENCING, BY END USE APPLICATION, THROUGH 2013 ($ MILLIONS)
• SUMMARY FIGURE GLOBAL VALUE OF DNA SEQUENCING, BY END USE APPLICATION, 2006-2013 ($ MILLIONS)

Chapter- 2: OVERVIEW

• INTRODUCTION
• DNA SEQUENCING TECHNOLOGIES COVERED IN THIS REPORT
  • TABLE 1 SCOPE OF THIS REPORT
• MARKET POTENTIAL OF DNA SEQUENCING PRODUCTS
  • TABLE 2 GLOBAL VALUE OF DNA SEQUENCING, BY END USE APPLICATION, THROUGH 2013 ($ MILLIONS)
  • TABLE 3 DNA SEQUENCING KEY GROWTH DRIVING FORCES
• SEQUENCING INDUSTRY GROWTH ..... (CONTINUED)
• SEQUENCING PRODUCTS
• SEQUENCING PRODUCT LIFE CYCLE STATUS
  • TABLE 4 LIFE CYCLE STATUS OF NEXT GENERATION SEQUENCING PLATFORMS
• COMMERCIAL STATUS
• SEQUENCING INDUSTRY
  • TABLE 5 COMPANY POSITIONING BY SEQUENCING TECHNOLOGY

Chapter- 3: DNA SEQUENCING TECHNOLOGIES

• GENETIC ANALYSIS
  • FIGURE 1 DNA, MRNA AND GENETIC VARIATION
• GENETIC ANALYSIS (CONTINUED)
  • TABLE 6 SCOPE OF KEY GENETIC ANALYSIS TECHNOLOGIES
• HISTORY OF DNA SEQUENCING
  • TABLE 7 GENETIC ANALYSIS HISTORY
  • TABLE 7 (CONTINUED)
• HISTORY OF DNA SEQUENCING (CONTINUED)
• HISTORY OF DNA SEQUENCING (CONTINUED)
  • FIGURE 2 SEQUENCING THROUGHPUT TREND
  • FIGURE 3 HUMAN GENOME SEQUENCING COST TREND
  • FIGURE 4 $1,000 GENOME PRODUCT SPACE
• OVERVIEW OF SEQUENCING TECHNOLOGIES
  • FIGURE 5 KEY DNA SEQUENCING TECHNOLOGIES
• OVERVIEW OF SEQUENCING ..... (CONTINUED)
• SEQUENCING WORKFLOW 23
  • FIGURE 6 DNA SEQUENCING PLATFORM WORKFLOW STEPS
• SEQUENCING WORKFLOW (CONTINUED)
• SANGER SEQUENCING
• SANGER SEQUENCING TECHNOLOGY
  • FIGURE 7 DDNTP CHEMICAL STRUCTURE
  • FIGURE 8 SANGER SEQUENCING WORKFLOW
• Sanger Sequencing Technology (Continued)
• SANGER SEQUENCING COSTS
  • FIGURE 9 COST BREAKDOWN FOR SEQUENCING A SINGLE HUMAN GENOME, USING 2005 SANGER SEQUENCER TECHNOLOGY (%)
  • TABLE 8 LIMITATIONS OF SANGER SEQUENCING TECHNOLOGY
  • TABLE 9 IMPROVEMENTS IN SANGER SEQUENCING TECHNOLOGY
• NEXT GENERATION SEQUENCING TECHNOLOGIES
  • FIGURE 10 NEXT GENERATION SEQUENCING TECHNOLOGIES
  • TABLE 10 COMMERCIAL IN-VITRO AMPLIFICATION NGS TECHNOLOGIES
  • FIGURE 11 SCHEMATIC COMPARISON OF SBS AND SBL SEQUENCING PLATFORMS
  • FIGURE 12 SEQUENCING BY SYNTHESIS: REVERSIBLE TERMINATOR REACTION
• PYROSEQUENCING BY SYNTHESIS
  • FIGURE 13 SEQUENCING BY SYNTHESIS: PYROSEQUENCING REACTION
• SEQUENCING BY LIGATION
• Sample Preparation
• Sequencing Reaction
  • FIGURE 14 SCHEMATIC OF SOLID SEQUENCING BY LIGATION
• Cycle 1
• Cycle 2
• Cycles 3 to 5
• Decoding
  • FIGURE 15 DECODING SOLID COLOR DATA
• SINGLE MOLECULE SEQUENCING
• Single Molecule Sequencing by Synthesis
  • FIGURE 16 SINGLE MOLECULE SEQUENCING BY SYNTHESIS
• Nanopore Sequencing
• Nanopore Sequencing (Continued)
  • FIGURE 17 NANOPORE SEQUENCING WORKFLOW AND TECHNOLOGY APPROACHES
• SEQUENCING TECHNOLOGY PLATFORMS COMPARED
  • TABLE 11 KEY PERFORMANCE METRICS FOR SEQUENCING TECHNOLOGIES
  • TABLE 12 COMPARISON OF SELECTED DNA SEQUENCING PLATFORMS
• Sequencing Technology Platforms ..... (Continued)
• SEQUENCING PRODUCT LIFE CYCLE
  • TABLE 13 LIFE CYCLE OF DNA SEQUENCING TECHNOLOGIES
• SEQUENCING INSTRUMENT CUMULATIVE INSTALLED BASE
  • FIGURE 18 GLOBAL CUMULATIVE INSTALLED BASE OF DNA SEQUENCERS, THROUGH 2008 (%)
• FUTURE PERFORMANCE OF NEXT GENERATION SEQUENCERS
  • TABLE 14 FUTURE PERFORMANCE OF NEXT GENERATION SEQUENCING PLATFORMS
• SEQUENCE READ LENGTH
  • TABLE 15 READ LENGTHS FOR SELECTED SEQUENCING PLATFORMS
• SEQUENCER PERFORMANCE SPACE
  • FIGURE 19 SEQUENCING COMPETITIVE MARKET SPACE
• END USER SWITCHING
• PAIRED END READS
  • TABLE 16 STRENGTHS AND LIMITATIONS OF PAIRED END READS
• DNA POLYMERASES
• TECHNOLOGY CHALLENGES FOR NGS PLATFORMS
  • TABLE 17 TECHNOLOGY CHALLENGES FOR NEXT GENERATION SEQUENCING
• Technology Challenges for ..... (Continued)
• DNA SEQUENCING APPLICATIONS
• INTRODUCTION
• RESEARCH AND DRUG DISCOVERY APPLICATIONS
• INTRODUCTION
  • TABLE 18 SEQUENCING APPLICATIONS
  • TABLE 19 DE NOVO VERSUS RE-SEQUENCING REQUIREMENTS
• DE NOVO WHOLE GENOME SEQUENCING
• De Novo Human Whole Genome Sequencing
• De Novo Microbial Whole Genome Sequencing
  • TABLE 20 CASE STUDY: NEANDERTHAL DNA SEQUENCING
• RESEQUENCING
• Whole Genome Resequencing (Genome-wide Association Studies or Loci Discovery)
  • FIGURE 20 SINGLE SEQUENCER, WHOLE GENOME THROUGHPUT TRENDS 1975-2015
• Targeted Resequencing
• TAG SEQUENCING: NGS AND MICROARRAYS SEEK SAME APPLICATIONS SPACE
  • TABLE 21 EMERGING GENETIC ANALYSIS APPLICATIONS
• Chromatin Immunoprecipitation Applications
  • TABLE 22 COMPARISON OF SEQUENCING WITH MICROARRAYS FOR CHIP APPLICATIONS
• Gene Expression Analysis
  • TABLE 23 NEXT GENERATION SEQUENCING VERSUS MICROARRAYS IN THE GENE EXPRESSION ANALYSIS SPACE
• DNA Methylation Analysis
• DNA Mutation Studies
• Complementary Sequencing and Microarray Platforms Drive Market Growth
• DIAGNOSTICS AND DRUG DISCOVERY
• Diagnostics and Drug Discovery (Continued)
• PERSONAL GENOMICS
  • FIGURE 21 GENETIC ANALYSIS COST/INFORMATION CONTENT TRENDS

Chapter- 4: DNA SEQUENCING INITIATIVES

• INTRODUCTION
• NHGRI $100,000 GENOME AND $1,000 GENOME PROJECTS
  • TABLE 24 NHGRI GRANTS FOR NEXT GENERATION SEQUENCING TO COMMERCIAL ENTITIES, 2004-2007 ($ MILLION)
  • FIGURE 22 NHGRI $100,000 AND $1,000 GENOME PROJECT CUMULATIVE FUNDING BY TECHNOLOGY, 2004-2007 ($98.7 MILLION) (%)
  • FIGURE 23 NHGRI ANNUAL FUNDING BY TECHNOLOGY, 2004-2007
  • FIGURE 24 NHGRI FUNDING OF $100,000 AND $1,000 PROGRAMS, 2004-2007
• GENOMICS PROJECTS OVERVIEW AND STATUS
  • TABLE 25 IMPORTANT SEQUENCING RESEARCH INITIATIVES
  • TABLE 25 (CONTINUED)
• GENOME SEQUENCING PROJECTS
• FUNCTIONAL GENOMICS IN NORWAY II
• PERSONAL GENOME PROJECT
• ARCHON X PRIZE IN GENOMICS
• MEDICAL SEQUENCING PROJECTS
• MAPPED AUTOSOMAL MENDELIAN DISORDERS
• ALLELIC SPECTRUM IN COMMON DISEASE PROGRAM
• CLINSEQ
• CANCER SEQUENCING PROJECTS
• TUMOR SEQUENCING PROJECT (TSP)
• THE CANCER GENOME ATLAS
• MICROBIAL SEQUENCING PROJECTS
• HUMAN MICROBIOME PROJECT
• MICROBIAL GENOME SEQUENCING PROJECT
• MARINE MICROBIAL GENOME SEQUENCING PROJECT
• FUNGAL GENOME INITIATIVE
• PATHOGEN SEQUENCING PROGRAM
• GENOMIC ENCYCLOPEDIA OF BACTERIA AND ARCHAEA (GEBA)
• METAGENOMICS OF THE HUMAN INTESTINAL TRACT (METAHIT)
• GUT MICROBIOME INITIATIVE
• GENOME VARIATION PROJECTS
• 1,000 GENOMES PROJECT
• RESEQUENCING TECHNOLOGY PROGRAM.
• HUMAN GENOME STRUCTURAL VARIATION PROJECT
• YANHUANG PROJECT
• AGRICULTURAL GENOMICS
• NATIONAL PLANT GENOME INITIATIVE
• EPIGENOMICS SEQUENCING PROJECTS
• ROADMAP EPIGENOMICS PROGRAM
• ENCYCLOPEDIA OF DNA ELEMENTS (ENCODE)
• IMPACT OF SEQUENCING PROJECTS
  • FIGURE 26 GROWTH IN BASE PAIRS DEPOSITIED IN GENBANK, 1986-2006

Chapter- 5: DNA SEQUENCING INDUSTRY STRUCTURE

• INDUSTRY STRUCTURE ANALYSIS
  • FIGURE 27 DNA SEQUENCING INDUSTRY STRUCTURE, 1995-2005
• INDUSTRY STRUCTURE ANALYSIS (CONTINUED)
  • FIGURE 28 DNA SEQUENCING INDUSTRY STRUCTURE, POST 2005
  • TABLE 26 DNA SEQUENCING INDUSTRY TRANSITION
• THE ROLE OF EARLY ADAPTORS
• SEQUENCING INSTRUMENT COMPETITOR POSITIONING
  • TABLE 27 COMPANY POSITIONING BY SEQUENCING TECHNOLOGY
• SEQUENCING INSTRUMENT ..... (CONTINUED)
• SEQUENCING INSTRUMENT ..... (CONTINUED)
• COMPETITOR MARKET SHARES
  • FIGURE 29 2008 ESTIMATED COMPETITOR MARKET SHARE: SEQUENCING INSTRUMENTS AND REAGENTS (TOTAL MARKET: $862.4 MILLION) (%)
  • FIGURE 30 2008 ESTIMATED COMPETITOR MARKET SHARE: SANGER SEQUENCING INSTRUMENTS AND REAGENTS (TOTAL MARKET: $557.1 MILLION) (%)
  • FIGURE 31 2008 ESTIMATED COMPETITOR MARKET SHARE: NEXT GENERATION SEQUENCING INSTRUMENTS AND REAGENTS (TOTAL MARKET $305.3 MILLION) (%)
• INDUSTRY ACQUISITIONS AND STRATEGIC ALLIANCES
  • TABLE 28 SEQUENCING INDUSTRY ACQUISITIONS, 2006-2008
• INDUSTRY ACQUISITIONS AND .....(CONTINUED)
  • TABLE 29 SEQUENCING INDUSTRY STRATEGIC ALLIANCES, 2005-2008
• REAGENTS SUPPLY ALLIANCES
• PERSONAL GENOMICS MARKET SEGMENT
  • TABLE 30 PERSONAL GENOMICS KEY COMPETITORS
  • TABLE 31 PERSONAL GENOMICS COMPETITOR STRATEGIES
• PERSONAL GENOMICS MARKET SEGMENT (CONTINUED)
  • FIGURE 32 PERSONAL GENOMICS COMPETITIVE POSITIONING
• DNA SEQUENCING END USERS
  • TABLE 32 DNA SEQUENCING END USER MARKET SEGMENTS
• MAJOR SEQUENCING CENTERS
  • TABLE 33 MAJOR SEQUENCING CENTERS
• Major Sequencing Centers (Continued)
  • FIGURE 33 MAJOR SEQUENCING CENTER' S SHARE OF THE GENOME SEQUENCING PROJECTS MARKET, 2008 (%)
  • FIGURE 34 WASHINGTON UNIVERSITY ADOPTION OF NEXT GENERATION SEQUENCERS, 2007 AND 2008
• LARGE CORE SEQUENCING CENTERS
  • TABLE 34 EXAMPLES OF LARGE CORE SEQUENCING CENTERS
• SMALL TO MID-SIZE LABORATORIES
• SEQUENCING SERVICE LABORATORIES
• Sequencing Service Laboratories (Continued)

Chapter- 6: DNA SEQUENCING MARKETS

• GROWTH DRIVING FORCES
  • TABLE 35 DNA SEQUENCING KEY GROWTH DRIVING FORCES
• GROWTH DRIVING FORCES (CONTINUED)
  • FIGURE 35 2008 SEQUENCING FUNDING BY AGENCY (%)
• GROWTH DRIVING FORCES (CONTINUED)
  • FIGURE 36 EUKARYOTIC SEQUENCING PARADIGM
• GENETIC ANALYSIS MARKETS
• Genetic Analysis Markets (Continued)
  • TABLE 36 GLOBAL VALUE OF GENETIC ANALYSIS MARKET, BY ANALYSIS TYPE, THROUGH 2013 ($ MILLIONS)
  • FIGURE 37 SNP GENOTYPING MARKET
• DNA SEQUENCING PRODUCTS MARKETS
• DNA SEQUENCING MARKETS BY PRODUCT TYPE
  • TABLE 37 GLOBAL VALUE OF DNA SEQUENCING MARKET, BY PRODUCT TYPE, THROUGH 2013 ($ MILLIONS)
• DNA SEQUENCING MARKETS BY SANGER AND NEXT GENERATION FORMATS
• DNA Sequencing Markets by Sanger ..... (Continued)
  • TABLE 38 GLOBAL VALUE OF DNA SEQUENCING INSTRUMENTS, BY SANGER AND NEXT GENERATION FORMATS, THROUGH 2013 ($ MILLIONS)
  • TABLE 39 GLOBAL VALUE OF DNA SEQUENCING CONSUMABLES MARKET, BY SANGER AND NEXT GENERATION FORMATS, THROUGH 2013 ($ MILLIONS)
• DNA SEQUENCING MARKETS BY END USER
  • TABLE 40 GLOBAL VALUE OF DNA SEQUENCING, BY CUSTOMER, THROUGH 2013 ($ MILLIONS)
• DNA Sequencing Markets by ..... (Continued)
  • TABLE 41 GLOBAL VALUE OF SANGER SEQUENCING, BY CUSTOMER, THROUGH 2013 ($ MILLIONS)
  • TABLE 42 GLOBAL VALUE OF NEXT GENERATION SEQUENCING, BY CUSTOMER, THROUGH 2013 ($ MILLIONS)
• DNA SEQUENCING MARKETS BY TECHNOLOGY
  • TABLE 43 GLOBAL VALUE OF DNA SEQUENCING MARKET, BY TECHNOLOGY, THROUGH 2013 ($ MILLIONS)
• DNA SEQUENCING MARKETS BY END USER APPLICATION
  • TABLE 44 GLOBAL VALUE OF DNA SEQUENCING, BY END USE APPLICATION, THROUGH 2013 ($ MILLIONS)
• Research and Drug Discovery and Development
• Forensic and Human ID
• Bacterial Genomics
• Agricultural Genomics
• Clinical Diagnostics
• Personal Genomics
• Personal Genomics (Continued)
• Other
  • TABLE 45 GLOBAL VALUE OF NEXT GENERATION SEQUENCING, BY END USE APPLICATION, THROUGH 2013 ($ MILLIONS) 152
• Other (Continued)
  • TABLE 46 GLOBAL VALUE OF SANGER SEQUENCING, BY END-USE APPLICATION, THROUGH 2013 ($ MILLIONS)
• DNA SEQUENCING MARKETS BY GENOME TYPE
  • TABLE 47 GLOBAL VALUE OF SEQUENCING, BY GENOME, THROUGH 2013 ($ MILLIONS)
• DNA SEQUENCING MARKETS BY ANALYSIS TYPE
  • TABLE 48 GLOBAL VALUE OF DNA SEQUENCING, BY ANALYSIS TYPE, THROUGH 2013 ($ MILLIONS)
  • TABLE 49 GLOBAL VALUE OF NEXT GENERATION SEQUENCING, BY ANALYSIS TYPE, THROUGH 2013 ($ MILLIONS)
  • TABLE 50 GLOBAL VALUE OF SANGER SEQUENCING, BY ANALYSIS TYPE, THROUGH 2013 ($ MILLIONS)
• DNA SEQUENCING MARKETS BY GEOGRAPHY
  • TABLE 51 GLOBAL VALUE OF DNA SEQUENCING PRODUCTS, BY GEOGRAPHICAL MARKET, THROUGH 2013 ($ MILLIONS)
  • TABLE 52 GLOBAL VALUE OF SANGER SEQUENCING PRODUCTS, BY GEOGRAPHICAL MARKET, THROUGH 2013 ($ MILLIONS)
  • TABLE 53 GLOBAL VALUE OF NEXT GENERATION SEQUENCING PRODUCTS, BY GEOGRAPHICAL MARKET, THROUGH 2013 ($ MILLIONS)
• DNA Sequencing Markets by Geography (Continued)

Chapter- 7: DNA SEQUENCING PATENT STATUS

• RECENT PATENT ACTIVITY IN NEXT GENERATION DNA SEQUENCING
  • TABLE 54 RECENT ACTIVITY IN NEXT GENERATION SEQUENCING PATENTS
  • TABLE 54 (CONTINUED)
• SEQUENCING BY SYNTHESIS
• SINGLE MOLECULE SEQUENCING
• NANOPORE SEQUENCING
• POLONY SEQUENCING
• NUCLEOTIDE MODIFICATIONS AND ANALOGS
• DNA POLYMERASES
• PAIRED END INVENTIONS
• OTHER METHODS
• PATENT POSITION OF SEQUENCING COMPETITORS
  • FIGURE 38 WORLDWIDE SEQUENCING PATENT APPLICATIONS BY COMPANY, 2001 TO PRESENT
• TECHNOLOGY DISTRIBUTION OF NEXT GENERATION SEQUENCING PATENTS
  • FIGURE 39 WORLDWIDE NEXT GENERATION SEQUENCING PATENT APPLICATIONS, BY TECHNOLOGY, 2001-2008 (NUMBER OF PATENT APPLICATIONS)
• GEOGRAPHICAL DISTRIBUTION OF SEQUENCING-RELATED PATENTS 171
  • FIGURE 40 WORLDWIDE SEQUENCING-RELATED PATENT APPLICATIONS, BY GEOGRAPHY, 2001-2008 (NUMBER OF PATENT APPLICATIONS)
• SEQUENCING LITIGATION STATUS
  • TABLE 55 SEQUENCING IP LITIGATION STATUS
• AFFYMETRIX VERSUS ILLUMINA
• APPLIED BIOSYSTEMS VERSUS SOLEXA
• BECKMAN COULTER VERSUS APPLIED BIOSYSTEMS
• ENZO BIOCHEM VERSUS CALTECH/ABI
• INTELLECTUAL PROPERTY POSITION OF SELECTED SEQUENCING COMPANIES
• APPLIED BIOSYSTEMS
• LI-COR BIOSCIENCES
• HELICOS BIOSCIENCES
• ILLUMINA
• INTELLIGENT BIOSYSTEMS
• PACIFIC BIOSCIENCES
• VISIGEN BIOTECHNOLOGIES

Chapter- 8: COMPANY PROFILES

• 23ANDME
• AFFYMETRIX INC.
• AGILENT TECHNOLOGIES, INC.
• APPLIED BIOSYSTEMS
• APPLIED BIOSYSTEMS (CONTINUED)
• BASE4INNOVATION LTD.
• BECKMAN COULTER
• BIONANOMATRIX
• CARTESIAN GRIDSPEED
• CLINICAL DATA CORPORATION (COGENICS DIVISION)
• COMPLETE GENOMICS, INC.
• DANAHER MOTION
• DECODEME
• DELTADOT LTD.
• EUROFINS MEDIGENOMIX GMBH
• EXPRESSION ANALYSIS, INC.
• FASTERIS SA
• FOUNDATION FOR APPLIED MOLECULAR EVOLUTION
• GATC BIOTECH AG
• GE HEALTHCARE
• GENOME CORP.
• GENOME DIAGNOSTICS B.V
• GENOME DIAGNOSTICS, INC.
• GENOMEQUEST
• GENOVOXX GMBH
• HELICOS BIOSCIENCES CORPORATION
• HELICOS BIOSCIENCES CORPORATION (CONTINUED)
• HELICOS BIOSCIENCES CORPORATION (CONTINUED)
• HELICOS BIOSCIENCES CORPORATION (CONTINUED)
• HELIX HEALTH
• ILLUMINA, INC.
• ILLUMINA, INC. (CONTINUED)
• ILLUMINA, INC.
• ILLUMINA, INC. (CONTINUED)
• INTERNA GENOMICS BV
• INVITROGEN
• INVITROGEN (CONTINUED)
• IP GENESIS INC.
• KNOME, INC.
• LASERGEN, INC.
• LI-COR BIOSCIENCES
• LIGHTSPEED GENOMICS
• LINGVITAE AS
• MICROCHIP BIOTECHNOLOGIES, INC.
• MWG BIOTECH AG
• NABSYS, INC.
• NAVIGENICS
• NANOPHOTONICS BIOSCIENCES INC.
• NETWORK BIOSYSTEMS
• PACIFIC BIOSCIENCES
• POPULATION GENETICS TECHNOLOGIES, LTD.
• POPULATION GENETICS (CONTINUED)
• REVEO INC.
• ROCHE LIFE SCIENCES
• ROCHE LIFE SCIENCES (CONTINUED)
• SEIRAD, INC.
• SEQUENOM
• SEQUENOM (CONTINUED)
• SEQWRIGHT
• SMARTGENE
• SORENSON GENOMICS
• U.S. GENOMICS
• VICGENE BIOTECHNOLOGY
• VISIGEN BIOTECHNOLOGIES, INC.
• X-PRIZE FOUNDATION
• ZS GENETICS
• ZS GENETICS (CONTINUED)