DNA sequencing: technologies, markets and companies

Table of Contents

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 PRISMR 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' sR 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