DNA sequencing

Content

• 0 Executive Summary
• 1 DNA sequencing Technologies
  • Introduction
  • Technologies
    • DNA extraction and sample preparation
      • Selective immobilization of nucleic acids onto magnetic microparticles
      • Electrophoresis-based method
      • Pressure Cycling Technology
      • Targeted and hybridization-based DNA capture
    • Sanger-sequencing technology
      • Dye-terminator sequencing
      • Large-scale sequencing
      • Automated DNA-sequencing
      • Enhancements of Sanger-sequencing
    • Limitations of current sequencing methods and measures to remedy them
      • High-throughput paired end transcriptome sequencing
    • ABI PRISM® 310 Genetic Analyzer
    • Emerging sequencing technologies
    • Second generation sequencers
      • 4300 DNA analyzer
      • Apollo 100
      • "Color blind" approach to DNA sequencing
      • Cyclic array sequencing
      • CEQ™ 8000
      • Electron microscope-based DNA sequencing
      • Genometrica™ sequencer
      • IBS sequencing technology
      • Illumina Genome Analyzer System
      • MegaBACE 500
      • Multiplex amplification of human DNA sequences
      • Nanoscale Sanger
      • Polonator sequencer
      • Pyrosequencing
      • RainStorm™ microdroplet technology
      • Sequential DEXAS
      • Sequencing-by-synthesis
    • Microarray-based emerging DNA sequencing technologies
      • High-throughput array-based resequencing
      • Sequencing by hybridization
      • SOLiD-System based ChIP-Sequencing
    • Microarray-based whole genome sequencing
      • Arrayit's® H25K
      • Human exome microarrays
      • Optical Mapping
    • Next generation sequencing vs microarrays for expression profiling
    • Third generation sequencing
      • SOLiD 3 System
      • Detection of single molecules for sequencing
      • Direct observation of nucleotide incorporation
      • Helicos™ Genetic Analysis System
      • Molecular Combing
      • Nanopore sequencing
      • DNA sequence by use of nanoparticles
      • Zero-mode waveguide nanostructure arrays
  • Role of bioinformatics in sequencing
    • Bioinformatics challenges of new sequencing technology
    • Bioinformatic tools for analysis of genomic sequencing data
      • Detection of CNVs and gene duplications
      • Sequencing data storage
      • Sequencing analysis tools at academic organizations
      • Commercially available software for DNA sequencing
  • Academic centers conducting research on sequencing
• 2 Applications of sequencing
  • Introduction
  • Applications in basic research
    • Identifying protein-coding genes in genomic sequences
    • Mutation rate measured by direct sequencing
    • Mapping and sequencing of structural variation from human genomes
    • Personal genome sequencing
    • Sequencing genomes of other organisms
    • Sequencing genomes of non-human primates
    • Sequencing genome of microbes
      • Sequencing for mapping genomic variation in Mycobacterium ulcerans
      • Sequencing for mapping genetic interactions in bacteria
  • Applications in drug discovery and development
    • Resequencing
    • RNA profiling
    • Transcriptome sequencing for mRNA Expression
    • RNA splice variants
  • NHGRI's sequencing initiatives
    • Approved medical sequencing projects
  • 1000 Genomes Project
    • HapMap catalog as a foundation
    • Role of SOLiD™ System in 1000 Genomes Project
    • Conclusion of pilot studies
  • Human Variome Project
  • Applications in clinically relevant areas
    • Genetic disorders
    • Cancer research
      • Assessment of sequencing technologies for analyzing tumor DNA
      • Cancer Genome Atlas
      • Detection of cancer biomarkers
      • Paired-end sequencing
      • Sequencing of complex human cancer genomes
      • Sequencing mitochondrial DNA to identify cancer biomarkers
    • Management of HIV/AIDS
  • Future prospects of next generation sequencing
    • Devices for next generation sequencing
    • Next generation sequencing for population targeted sequencing studies
    • Applications of next generation sequencing in molecular diagnostics
• 3 Comparative Analysis of Sequencing Technologies
  • General findings of the study
    • Sanger versus second generation marketed sequencers
  • Third generation large sequencers
    • SOLiD3 versus competing large sequencers
  • The ideal small sequencer
  • SWOT analysis of small sequencers
  • Concluding remarks on SWOT analysis
• 4 Markets for Sequencers
  • Introduction
  • Methods used for estimation of sequencer markets
  • Currently marketed sequencers
  • Academic and research markets for sequencing
  • Factors affecting future development of sequencing markets
    • Future needs and support of research
    • Reducing the cost of human genome sequencing
      • US Government-supported research on sequencing
      • Genome X Prize Foundation
      • Innovations to reduce cost of whole genome sequencing
      • Commercial prospects of low cost genome sequencing
    • Genome sequencing for personalized medicine
    • The global sequencing market
  • Marketing potential for sequencers
  • Challenges to developing market for sequencers
  • Recommendations
• 5 Companies Involved in Sequencing
  • Introduction
  • Profiles of companies
  • Collaborations
• 6 References
• Tables
  • Table 1-1: Historical landmarks in DNA sequencing
  • Table 1-2: ChIP detection platforms for sequencing
  • Table 1-3: Companies developing whole genome chips/microarrays
  • Table 1-4: Companies providing DNA sequencing software
  • Table 1-5: Academic centers conducting research on DNA sequencing
  • Table 2-1: Approved medical sequencing projects
  • Table 3-1: Comparison of a generation I and generation II sequencers
  • Table 3-2: SWOT of ABI 310
  • Table 3-3: SWOT of IBS sequencing
  • Table 3-4: SWOT of Hybridization-Assisted Nanopore Sequencing
  • Table 3-5: SWOT of 4300 DNA Analysis System Li-Cor
  • Table 3-6: SWOT of Genometrica
  • Table 3-7: SWOT of Polonator
  • Table 4-1: Marketed next generation sequencers
  • Table 4-2: De novo sequencing vs resequencing markets
  • Table 4-3: Global markets for sequencers according to geographical regions
  • Table 4-4: Global markets for sequencers according to applications
  • Table 5-1: Companies involved in sequencing
  • Table 5-2: Selected collaborations for DNA sequencing
• Figures
  • Figure 1-1: DNA sequencing process
  • Figure 1-2: Workflow of Genome Sequenser FLX system
  • Figure 1-3: Sequencing by ligation
  • Figure 1-4: Construction of SOLiD fragment library using DNA enrichment by ChIP
  • Figure 1-5: Single molecule, realtime DNA sequencing
  • Figure 4-1: Global markets for sequencers according to applications