DNA sequencing

Technologies, Markets and Companies

Product Code JAI00042
Publication Date January 2012
Publisher Jain PharmaBiotech
Product Type Report
Pages 297
ISBN Number not applicable
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DNA sequencing

Technologies, Markets and Companies

Summary

This report briefly reviews basics of human genome variations, development of sequencing technologies, and their applications. Current large and small sequencers are described as well as companies developing them. Various applications of sequencing are described including those for genetics, medical diagnostics, drug discovery and cancer. Next generation sequencing technologies, both second and third generations, are reviewed. Companies developing software for analysis of sequencing data are also included. Selected academic institutes conducting research in sequencing are also listed.

Current market is mostly for research applications and future markets will be other applications related to healthcare. The value of DNA sequencer market in 2011 is described with estimates for 2016 and 2021. Various methods and factors on which market estimates depend are described briefly. Small sequencers form the basis of SWOT (strengths, weaknesses, opportunities, threats) analysis. Several marketing strategies have been outlined.

The report includes profiles of 90 companies involved in sequencing and their 90 collaborations. The report text is supplementd by 32 tables, 10 figures and 240 selected references to the literature.

Contents

  • 0. Executive Summary
  • 1. Introduction
    • Definition and scope of sequencing
    • Historical aspects of sequencing
    • Basics of molecular biology
    • DNA
    • DNA polymerases
    • Restriction endonucleases
    • DNA methylation
    • RNA
    • RNA polymerases
    • Non-coding RNAs
    • DNA transcription
    • Chromosomes
    • Telomeres
    • Mitochondrial DNA
    • Genes
    • The genetic code
    • Gene expression
    • The human genome
    • Variations in the human genome
    • Variations in DNA sequences
    • Single nucleotide polymorphisms
    • Haplotyping
    • Complex chromosomal rearrangements
    • Insertions and deletions in the human genome
    • Large scale variation in human genome
    • Variation in copy number in the human genome
    • Structural variations in the human genome
    • Transposons
    • Retrotransposon capture sequencing
    • Mapping and sequencing of structural variation from human genomes
    • Impact of sequencing on healthcare
  • 2. DNA Sequencing Technologies
    • Introduction
    • DNA extraction and sample preparation
    • Apollo 300 System for next generation sequencing
    • Electrophoresis-based method
    • Ion OneTouch System
    • Microfluidics-based extraction and sample preparation
    • Pressure Cycling Technology
    • Selective immobilization of nucleic acids onto magnetic microparticles
    • Targeted and hybridization-based DNA capture
    • Sanger-sequencing technology
    • Dye-terminator sequencing
    • Large-scale sequencing
    • Automated DNA-sequencing
    • Enhancements of Sanger-sequencing
    • ABI PRISM® 310 Genetic Analyzer
    • Life Technologies' 3500 Dx genetic analyzer
    • Limitations of sequencing methods and measures to remedy them
    • High-throughput paired end transcriptome sequencing
    • Long vs short read lengths
    • Emerging sequencing technologies
    • Chemical DNA sequencing
    • Second generation sequencers
    • 4300 DNA analyzer
    • Apollo 100
    • Applied Biosystems 3500 series Genetic Analyzer
    • "Color blind" approach to DNA sequencing
    • Cyclic array sequencing
    • CEQ™ 8000
    • DeepCAGE sequencing
    • Electron microscope-based DNA sequencing
    • Genometrica sequencer
    • GS-FLEX system (Roche/454)
    • Background of sequencing technology
    • 454 sequencing
    • GS Junior System
    • IBS sequencing technology
    • Illumina Genome Analyzer System
    • Ion Torrent's sequencing technology
    • MegaBACE 500
    • Microdroplet-based PCR for large-scale targeted sequencing.
    • Millikan sequencing
    • Multiplex amplification of human DNA sequences
    • Nanoscale sequencing
    • Polonator sequencer
    • RainStorm™ microdroplet technology
    • Sequential DEXAS
    • SOLiD system: sequencing by ligation
    • PCR-based DNA sequencing technologies
    • Bridge amplification PCR system
    • COLD-PCR and sequencing
    • Digital PCR
    • Dual primer emulsion PCR
    • Emulsion PCR
    • Multiplex PCR
    • Nucleic acid sequence-based amplification
    • Microarray-based DNA sequencing technologies
    • Arrayit's® H25K
    • High-throughput array-based resequencing
    • Human exome microarrays
    • Sequencing by hybridization
    • SOLiD-System based ChIP-Sequencing
    • Companies developing whole genome chips/microarrays
    • Next generation sequencing vs microarrays for gene expression profiling
    • Third generation sequencing
    • SOLiD4 System
    • SOLiD PI System
    • Detection of single molecules for sequencing
    • DNA sequence by use of nanoparticles
    • Denaturation mapping of DNA in nanofluidic channels
    • Helicos™ Genetic Analysis System
    • Molecular Combing
    • Nanopore sequencing
    • Optical Mapping
    • PNA-based single-molecule detection of specific DNA sequences
    • Sequencing-by-synthesis for single-molecule sequencing
    • Single molecule DNA sequencing by use of carbon nanotubes
    • Single molecule sequencing using Qdot nanocrystals
    • Single-molecule DNA sequencing in a sTOP chip nanowell
    • Single-molecule real-time sequencing
    • Single cell DNA sequencing
    • Haplotyping for whole genome sequencing
    • ImmunoSEQ technology
    • Role of bioinformatics in sequencing
    • Growth of the sequencing database
    • Data storage
    • Bioinformatics challenges of new sequencing technology
    • Bioinformatic tools for analysis of genomic sequencing data
    • Commercially available software for DNA sequencing
    • ChIA-PET tool for analysis with paired-end tag sequencing
    • Detection of CNVs and gene duplications
    • Differential expression analysis for sequence count data
    • Expression profiling without genome sequence information
    • VAAST
    • Sequencing data storage
    • Sequencing analysis tools at academic organizations
    • Accessing DNA sequence information
    • Analysis of genomic variation by sequencing of large populations
    • Fund of research into interpretation of sequencing data
    • Future challenges for managing sequencing data
  • 3. Comparative Analysis of Sequencing Technologies
    • General findings of the study
    • Sanger versus second generation marketed sequencers
    • Common features and differences among second generation sequencers
    • Third generation large sequencers
    • SOLiD4 versus competing large sequencers
    • Illumina's HiSeq and MiSeq sequencers
    • Life Technologies' Benchtop Ion Proton™ Sequencer
    • The ideal small sequencer
    • SWOT analysis of small sequencers
    • Concluding remarks on SWOT analysis
  • 4. Research Applications of Sequencing
    • Introduction
    • Applications in basic research
    • ChIA-PET technology for 3D study of the genome
    • ChIP-Seq for study of gene expression
    • Chromatin profiling by direct DNA sequencing
    • Discovery of immunoglobulin gene by pyrosequencing
    • Epigenetic modifications analyzed by next generation sequencing
    • Exome sequencing for study of human variation
    • Genome sequencing with combinatorial probe anchor ligation
    • GS-FLX sequencing for simultaneous detection of mutation and CNV
    • Identifying protein-coding genes in genomic sequences
    • mRNA sequencing
    • Mutation rate measured by direct sequencing
    • Protein-protein interactome network mapping
    • Sequencing the transcriptomes of stem cells
    • Sequencing and synthetic biology
    • Synthetic sequence in a bacterial cell
    • Functional synthetic proteins
    • Sequencing of human genomes
    • Whole genome sequencing
    • Whole-genome sequencing of methylome
    • Whole genome resequencing
    • Personal genome sequencing
    • Sequencing 1000 human genomes
    • Missing human genome sequences
    • Role of sequencing in identification of human remains
    • Sequence map of the human pan-genome
    • Sequencing of African genomes
    • Sequencing of Korean genomes
    • Sequencing mitochondrial genome
    • Sequencing of ancient genomes
    • Saqqaq genome
    • Neandertal genome
    • Future prospects of human genome sequencing
    • Sequencing genomes of non-human primates
    • Sequencing genomes of other organisms
    • Sequencing of the mouse genome
    • Sequencing of the dog genome
    • Sequencing the turkey genome
    • Sequencing of the frog genome
    • Sequencing the genome of body louse
    • Sequencing of the ant genome
    • Sequencing of the genome of water flea
    • Applications in drug discovery and development
    • Resequencing
    • RNA profiling
    • Transcriptome sequencing for mRNA Expression
    • RNA splice variants
    • Quantitative selection of aptamers through sequencing
    • Sequencing projects supported by US Government
    • NHGRI's sequencing initiatives
    • JGI's Community Sequencing Program
    • Approved medical sequencing projects
    • 1000 Genomes Project
    • Findings of some studies of the 1000 genomes project
    • HapMap catalog as a foundation
    • Role of SOLiD™ System in 1000 Genomes Project
    • Concluding remarks
    • Human Variome Project
    • Academic centers conducting research on sequencing
    • Important academic collaborations
    • Scientific manpower for sequencing
    • Large-scale genomic sequencing projects at Joint Genome Institute
  • 5. Applications of Sequencing in Healthcare
    • Introduction
    • Applications of sequencing in molecular diagnostics
    • Next generation sequencing for detection of solid organ transplant rejection
    • Applications of sequencing in oncology
    • A project to assess sequencing technologies for tumor DNA
    • Amplicon sequencing in cancer
    • Cancer Genome Atlas
    • Detection of cancer biomarkers
    • Sequencing mitochondrial DNA to identify cancer biomarkers
    • Biomarkers for personalizing cancer treatment
    • Digital proteomics for cancer profiling
    • Epigenome profiling
    • Gaining insights into mutational processes
    • Multiplexed cancer gene mutation analysis
    • NGS-based molecular profiling of cancer in FFPE specimens
    • Paired-end sequencing
    • Pathology tissue-ChIP
    • RNA-Seq to study cancer transcriptome
    • Sequencing cancer cell lines
    • Sequencing for studying chromothripsis in cancer
    • Sequencing of complex human cancer genomes
    • Sequencing single cells to study evolution of cancer
    • Sequencing for assessing resistance to anticancer therapy
    • Sequencing in various types of malignancies
    • Brain tumors
    • Breast cancer
    • Hematological malignancies
    • Hepatocellular carcinoma
    • Melanoma
    • Ovarian cancer
    • Prostate cancer
    • Sequencing in genetic disorders
    • Array-based whole-exome sequencing in Bartter syndrome
    • Detection of X-linked disorder due to N-terminal acetyltransferase deficiency
    • DNA sequencing of maternal plasma for detection of fetal aneuploidy
    • Exome sequencing for genetic disorders
    • Discovery of the gene for Miller syndrome
    • Discovery of the gene for Kabuki syndrome
    • Familial combined hypolipidemia
    • Familial thoracic aortic aneurysm
    • Proteus syndrome
    • Sequencing for study of transposons
    • Sequencing of whole genome in Charcot-Marie-Tooth disease
    • Sequencing in muscular dystrophy
    • Sequencing in Huntington's disease
    • Sequencing genomes of the newborn to screen for genetic disorders
    • Study of rare variants in pinpointing disease-causing genes
    • Whole genome sequencing for diagnosis of genetic disorders
    • Sequencing for HLA typing
    • Sequencing for study of the human immune system
    • Sequencing in neurological disorders
    • Sequencing for mutations associated with autism spectrum disorders
    • Sequencing in attention-deficit/hyperactivity disorder
    • Sequencing genomes of microbes
    • DNA sequencing for study of bacterial epidemics
    • Human Microbiome Project
    • Pyrosequencing of microbial flora in leg ulcers
    • Sequencing of gut microbes in obesity
    • Sequencing for mapping genomic variation in Mycobacterium ulcerans
    • Sequencing for mapping genetic interactions in bacteria
    • Sequencing for study of antibiotic resistance in bacteria
    • Sequencing of DNA from single cells of bacteria
    • Sequencing of the Candida genome
    • Sequencing of human salivary microbiome
    • Sequencing in the management of HIV/AIDS
    • Sequencing in the management of HBV
    • Sequencing in the management of HCV
    • Sequencing genome of Lassa fever virus
    • Surveillance of H1N1 influenza A virus using resequencing arrays
    • Population targeted sequencing studies
    • Sequencing in aging research
    • Next generation sequencing and pharmaceutical industry
    • Next generation sequencing and drug design and discovery
    • Next generation sequencing and drug safety
    • Next generation sequencing for antibacterial therapeutic discovery
    • Applications of human transcriptome array in clinical trials
    • Role of sequencing in personalized medicine
    • Whole genome sequencing and personalized medicine
    • Role of sequencing in personalized cancer management
    • Standardization of sequencing for personalized medicine
    • Future of sequencing and personalized medicine
    • Future prospects of next generation sequencing
    • Devices for next generation sequencing
    • Clinical applications of NGS
  • 6. 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
    • Bioinformatics in relation to sequencing
    • Reducing the cost of human genome sequencing
    • US Government-supported research on sequencing
    • Contribution of American Recovery and Reinvestment Act
    • Genome X Prize Foundation
    • Innovations to reduce cost of whole genome sequencing
    • Commercial aspects of low cost genome sequencing
    • Genome sequencing suitable for personalized medicine
    • The global sequencing market
    • Marketing potential for sequencers
    • Challenges to developing market for sequencers
    • Recommendations
  • 7. Companies Involved in Sequencing
    • Introduction
    • Collaborations
  • 8. References
  • Tables
    • Table 1 1: Historical landmarks in DNA sequencing
    • Table 1 2: Genetic variations in the human genome
    • Table 2 1: ChIP detection platforms for sequencing
    • Table 2 2: Companies developing whole genome chips/microarrays
    • Table 2 3: Systems for single molecule sequencing
    • Table 2 4: Companies providing DNA sequencing software
    • Table 3 1: Comparison of a generation I and generation II sequencers
    • Table 3 2: Similarities and differences between second generation sequencers
    • Table 3 3: SWOT of ABI 310
    • Table 3 4: SWOT of IBS sequencing
    • Table 3 5: SWOT of NABsys' Hybridization-Assisted Nanopore Sequencing
    • Table 3 6: SWOT of 4300 DNA Analysis System Li-Cor
    • Table 3 7: SWOT of Genometrica
    • Table 3 8: SWOT of Polonator
    • Table 3 9: SWOT of GS FLEX Junior
    • Table 3 10: SWOT of Oxford Nanopore Technologies' nanopore DNA sequencing
    • Table 3 11: SWOT of Ion Torrent™ Personal Genome Machine
    • Table 3 12: SWOT of Pacific BioSciences' single-molecule real-time sequencing
    • Table 4 1: Number of genes in organisms with fully sequenced genomes
    • Table 4 2: Approved medical sequencing projects
    • Table 4 3: Academic centers conducting research on DNA sequencing
    • Table 4 4: Distribution of scientific manpower for sequencing
    • Table 5 1: Companies involved in application of sequencing in molecular diagnostics
    • Table 6 1: Marketed next generation sequencers
    • Table 6 2: De novo sequencing vs resequencing markets
    • Table 6 3: Global markets for sequencing services according to geographical regions
    • Table 6 4: Global markets for sequencing services according to applications
    • Table 6 5: Global markets for sequencers from 2011 to 2021
    • Table 7 1: Companies developing sequencing technologies and instruments
    • Table 7 2: Companies that provide sequencing services
    • Table 7 3: Companies that provide bioinformatics support for sequencing
    • Table 7 4: Selected collaborations for DNA sequencing
  • Figures
    • Figure 2 1: DNA sequencing process
    • Figure 2 2: Comparison of traditional sequencing and next generation sequencing
    • Figure 2 3: Watson-Crick base pairing
    • Figure 2 4: Genome Sequencer FLX system(Roche/454)
    • Figure 2 5: Workflow of Genome Sequenser FLX system
    • Figure 2 6: Sequencing by ligation
    • Figure 2 7: Construction of SOLiD fragment library using DNA enrichment by ChIP
    • Figure 2 8: Single molecule, realtime DNA sequencing
    • Figure 5 1: Role of sequencing in the development of personalized medicine
    • Figure 6 1: Global markets for sequencing services according to applications