[June 07, 2010] Reportlinker Adds DNA Sequencing - Technologies, Markets and Companies Tweet NEW YORK, June 7, 2010 /PRNewswire via COMTEX/ -- Reportlinker.com announces that a new market research report is available in its catalogue: DNA Sequencing - technologies,markets and companies http://www.reportlinker.com/p0203540/DNA-Sequencing---technologiesmarkets-and-companies.html 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 2009 is described with estimates for 2014 and 2019. 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 54 companies involved in sequencing and their 47 collaborations. The report text is supplemented by 27 tables, 7 figures and 150 selected references to the literature. TABLE OF CONTENTS 0.Executive Summary11 1.Introduction13 Definition and scope of sequencing13 Historical aspects of sequencing13 Basics of molecular biology14 DNA14 DNA polymerases14 Restriction endonucleases14 DNA methylation15 RNA15 RNA polymerases16 Non-coding RNAs16 DNA transcription16 Chromosomes16 Telomeres17 Mitochondrial DNA17 Genes18 The genetic code18 Gene expression18 The human genome19 Variations in the human genome19 Variations in DNA sequences20 Single nucleotide polymorphisms20 Complex chromosomal rearrangements21 Insertions and deletions in the human genome21 Large scale variation in human genome22 Variation in copy number in the human genome22 Structural variations in the human genome23 Mapping and sequencing of structural variation from human genomes24 Impact of sequencing on healthcare24 2.DNA Sequencing Technologies27 Introduction27 DNA extraction and sample preparation28 Electrophoresis-based method28 Microfluidics-based extraction and sample preparation29 Pressure Cycling Technology29 Selective immobilization of nucleic acids onto magnetic microparticles29 Targeted and hybridization-based DNA capture30 Sanger-sequencing technology30 Dye-terminator sequencing31 Large-scale sequencing31 Automated DNA-sequencing31 Enhancements of Sanger-sequencing31 ABI PRISM(R) 310 Genetic Analyzer32 Limitations of current sequencing methods and measures to remedy them32 High-throughput paired end transcriptome sequencing33 Emerging sequencing technologies33 Chemical DNA sequencing33 Second generation sequencers34 4300 DNA analyzer34 Apollo 10035 Applied Biosystems 3500 series Genetic Analyzer35 "Color blind" approach to DNA sequencing36 Cyclic array sequencing36 CEQ(TM) 800036 DeepCAGE sequencing36 Electron microscope-based DNA sequencing37 Genometrica- sequencer37 GS-FLEX system (Roche/454)38 IBS sequencing technology41 Illumina Genome Analyzer System41 Ion Torrent's sequencing technology42 MegaBACE 50043 Microdroplet-based PCR for large-scale targeted sequencing.43 Multiplex amplification of human DNA sequences43 Nanoscale sequencing44 Polonator sequencer44 RainStorm(TM) microdroplet technology45 Sequential DEXAS45 SOLiD system: sequencing by ligation46 PCR-based DNA sequencing technologies46 Digital PCR47 Emulsion PCR47 Bridge amplification PCR system48 Dual primer emulsion PCR48 Nucleic acid sequence-based amplification48 Microarray-based DNA sequencing technologies48 Arrayit's(R) H25K49 High-throughput array-based resequencing49 Human exome microarrays49 Optical Mapping50 Sequencing by hybridization51 SOLiD-System based ChIP-Sequencing51 Companies developing whole genome chips/microarrays52 Next generation sequencing vs microarrays for gene expression profiling52 Third generation sequencing53 SOLiD4 System53 SOLiD PI System54 Detection of single molecules for sequencing54 DNA sequence by use of nanoparticles55 Helicos(TM) Genetic Analysis System56 Molecular Combing56 Nanopore sequencing57 PNA-based single-molecule detection of specific DNA sequences57 Sequencing-by-synthesis for single-molecule sequencing58 Single molecule DNA sequencing by use of carbon nanotubes58 Single molecule sequencing using Qdot nanocrystals59 Single-molecule DNA sequencing in a sTOP chip nanowell60 Single-molecule real-time sequencing60 Single cell DNA sequencing61 Role of bioinformatics in sequencing62 Growth of the sequencing database62 Data storage62 Bioinformatics challenges of new sequencing technology62 Bioinformatic tools for analysis of genomic sequencing data63 Commercially available software for DNA sequencing64 ChIA-PET tool for analysis with paired-end tag sequencing65 Detection of CNVs and gene duplications65 Sequencing data storage65 Sequencing analysis tools at academic organizations66 Accessing DNA sequence information66 3.Comparative Analysis of Sequencing Technologies69 General findings of the study69 Sanger versus second generation marketed sequencers69 Common features and differences among second generation sequencers69 Third generation large sequencers70 SOLiD4 versus competing large sequencers70 Illumina's HiSeq 200071 The ideal small sequencer72 SWOT analysis of small sequencers72 Concluding remarks on SWOT analysis74 4.Research Applications of sequencing75 Introduction75 Applications in basic research75 ChIA-PET technology for 3D study of the genome75 ChIP-Seq for study of gene expression in embryonic stem cells76 Chromatin profiling by direct DNA sequencing76 Epigenetic modifications analyzed by next generation sequencing76 Genome sequencing with combinatorial probe anchor ligation76 GS-FLX sequencing for simultaneous detection of mutation and CNV77 Identifying protein-coding genes in genomic sequences77 mRNA sequencing78 Mutation rate measured by direct sequencing78 Sequencing the transcriptomes of stem cells79 Synthetic sequence in a bacterial cell79 Sequencing of human genomes80 Whole genome sequencing80 Whole genome resequencing80 Personal genome sequencing80 Missing human genome sequences81 Role of sequencing in identification of human remains81 Sequence map of the human pan-genome81 Sequencing of African genomes82 Sequencing mitochondrial genome82 Sequencing of ancient genomes82 Sequencing genomes of other organisms83 Sequencing of the mouse genome83 Sequencing of the dog genome84 Sequencing of the frog genome84 Sequencing genomes of non-human primates85 Applications in drug discovery and development86 Resequencing86 RNA profiling86 Transcriptome sequencing for mRNA Expression87 RNA splice variants88 NHGRI's sequencing initiatives88 Approved medical sequencing projects89 1000 Genomes Project89 HapMap catalog as a foundation90 Role of SOLiD(TM) System in 1000 Genomes Project90 Concluding remarks91 Human Variome Project91 Academic centers conducting research on sequencing91 5.Applications of Sequencing in Healthcare95 Introduction95 Applications of sequencing in molecular diagnostics95 Cancer95 Assessment of sequencing technologies for analyzing tumor DNA95 Cancer Genome Atlas96 Detection of cancer biomarkers96 Discovery of biomarkers for personalizing cancer treatment97 Discovery of amplified cancer genes98 Digital proteomics for cancer profiling98 Epigenome profiling98 Insights into mutational processes98 Paired-end sequencing99 RNA-Seq to study cancer transcriptome100 Sequencing cancer cell lines100 Sequencing in acute myeloid leukemia100 Sequencing brain tumors101 Sequencing in breast cancer101 Sequencing of complex human cancer genomes102 Sequencing mitochondrial DNA to identify cancer biomarkers102 Sequencing to guide cancer management102 Genetic disorders103 Array-based whole-exome sequencing in Bartter syndrome103 DNA sequencing of maternal plasma103 Exome sequencing for discovery of the gene for Miller syndrome104 Whole genome sequencing in Charcot-Marie-Tooth disease104 Sequencing in Huntington's disease105 Sequencing genomes of the newborn to screen for genetic disorders105 Study of rare variants in pinpointing disease-causing genes106 Sequencing genomes of microbes106 DNA sequencing for study of bacterial epidemics107 Next generation sequencing for antibacterial drug discovery107 Sequencing for mapping genomic variation in Mycobacterium ulcerans108 Sequencing for mapping genetic interactions in bacteria108 Sequencing in the management of HIV/AIDS108 Sequencing genome of Lassa fever virus109 Future prospects of next generation sequencing109 Devices for next generation sequencing109 COLD-PCR and sequencing109 Next generation sequencing for population targeted sequencing studies110 Next generation sequencing and drug design111 Next-generation sequencing in aging research111 Applications of next generation sequencing in molecular diagnostics111 Next generation sequencing and personalized medicine112 6.Markets for Sequencers113 Introduction113 Methods used for estimation of sequencer markets113 Currently marketed sequencers113 Academic and research markets for sequencing113 Factors affecting future development of sequencing markets114 Future needs and support of research114 Bioinformatics in relation to sequencing114 Reducing the cost of human genome sequencing115 US Government-supported research on sequencing115 Genome X Prize Foundation117 Innovations to reduce cost of whole genome sequencing117 Commercial prospects of low cost genome sequencing117 Genome sequencing suitable for personalized medicine118 The global sequencing market118 Marketing potential for sequencers119 Challenges to developing market for sequencers120 Recommendations121 7.Companies Involved in Sequencing123 Introduction123 Collaborations186 8.References189 Tables Table 1 1: Historical landmarks in DNA sequencing13 Table 1 2: Genetic variations in the human genome20 Table 2 1: ChIP detection platforms for sequencing52 Table 2 2: Companies developing whole genome chips/microarrays52 Table 2 3: Systems for single molecule sequencing55 Table 2 4: Companies providing DNA sequencing software64 Table 3 1: Comparison of a generation I and generation II sequencers69 Table 3 2: Similarities and differences between second generation sequencers70 Table 3 3: SWOT of ABI 31072 Table 3 4: SWOT of IBS sequencing72 Table 3 5: SWOT of NABsys' Hybridization-Assisted Nanopore Sequencing72 Table 3 6: SWOT of 4300 DNA Analysis System Li-Cor73 Table 3 7: SWOT of Genometrica73 Table 3 8: SWOT of Polonator73 Table 3 9: SWOT of GS FLEX Junior73 Table 3 10: SWOT of Oxford Nanopore Technologies' nanopore DNA sequencing73 Table 3 11: SWOT of Ion Torrent(TM) non-optical sequencer74 Table 3 12: SWOT of Pacific BioSciences' single-molecule real-time sequencing74 Table 4 1: Approved medical sequencing projects89 Table 4 2: Academic centers conducting research on DNA sequencing92 Table 6 1: Marketed next generation sequencers113 Table 6 2: De novo sequencing vs resequencing markets114 Table 6 3: Global markets for sequencing services according to geographical regions119 Table 6 4: Global markets for sequencing services according to applications119 Table 6 5: Global markets for sequencers120 Table 7 1: Companies involved in sequencing123 Table 7 2: Selected collaborations for DNA sequencing186 Figures Figure 2 1: DNA sequencing process28 Figure 2 2: Watson-Crick base pairing34 Figure 2 3: Workflow of Genome Sequenser FLX system40 Figure 2 4: Sequencing by ligation46 Figure 2 5: Construction of SOLiD fragment library using DNA enrichment by ChIP52 Figure 2 6: Single molecule, realtime DNA sequencing60 Figure 6 1: Global markets for sequencing services according to applications119 To order this report: Biotechnology Industry: DNA Sequencing - technologies,markets and companies More Market Research Report Check our Company Profile, SWOT and Revenue Analysis! 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