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DNA Sequencing - Technologies, Markets and Companies

DUBLIN, Feb. 12, 2014 /PRNewswire/ --

Research and Markets

(

http://www.researchandmarkets.com/research/l54sxm/dna_sequencing

) has announced the addition of Jain PharmaBiotech's new report

"DNA Sequencing - Technologies, Markets and Companies"

to their offering.


(Logo: http://photos.prnewswire.com/prnh/20130307/600769)

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 2013 is described with estimates for 2018 and 2023. Various methods and factors on which market estimates depend are described briefly. Markets are tabulated according to geographical areas as well as applications. Small sequencers form the basis of SWOT (strengths, weaknesses, opportunities, threats) analysis. Several marketing strategies have been outlined.



The report includes profiles of 111 companies involved in sequencing and their 115 collaborations. The report text is supplementd by 38 tables, 13 figures and 350 selected references to the literature.


Key Topics Covered:



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


Chromosome sequences


Telomeres


Mitochondrial DNA


Genes


The genetic code


Gene expression


The human genome


ENCODE


The exome


The epigenome


Human Epigenome Atlas


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


Validation of NGS data


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


GS-FLEX system (Roche/454)


Background of sequencing technology


454 sequencing


IBS sequencing technology


Illumina Genome Analyzer System


MiSeqDx


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


Non-PCR based sequencing


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


Nanopore-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


MALBAC for single cell DNA sequencing


Single cell sequencing of uncultured microbes


Single-sperm sequencing


Thermosequencing


Whole genome sequencing for haplotyping


Mitochondrial exome sequencing


ImmunoSEQ technology


Future prospects of next generation sequencing


Devices for NGS


Reduction of errors in NGS


Artifactual mutations during the sample preparation process


Duplex sequencing



3. Role of Bioinformatics in Sequencing


Introduction


Growth of the sequencing database


Sequencing data storage


Bioinformatics challenges of new sequencing technology


DNA libraries for NGS


Bioinformatic tools for analysis of genomic sequencing data


Software for DNA sequencing


Software from academic and open sources


Commercial software for sequencing


ChIA-PET tool for analysis with paired-end tag sequencing


Compressive genomics


Detection of CNVs and gene duplications


Detection of SVs in massively parallel sequencing data


Differential expression analysis for sequence count data


Expression profiling without genome sequence information


Ion Reporter Software


Opal platform


VAAST


knoSYSTM100


Accessing DNA sequence information


Analysis of genomic variation by sequencing of large populations


Analysis of rare variants in NGS studies


Human gene connectome


Funding of research for interpretation of sequencing data


Future challenges for managing sequencing data



4. 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 sequencer


Third generation small sequencers


Genometrica? desk top sequencer


Illumina's MiSeq sequencer


Roche/454 GS Junior System


Life Technologies' Benchtop Ion Proton Sequencer


Oxford Nanopore's MinION system


The ideal small sequencer


SWOT analysis of small sequencers


Concluding remarks on SWOT analysis



5. Sequencing for Research


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


Identifying protein-coding genes in genomic sequences


mRNA sequencing


Mutation rate measured by direct sequencing


Protein-protein interactome network mapping


Sequencing for the study of microchimerism


Sequencing for the study of CNVs


CNVnator


GS-FLX sequencing for simultaneous detection of mutations and CNVs


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


Saudi Arabian human genome program


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


Hominin genome


Future prospects of human genome sequencing


Sequencing genomes of non-human primates


Sequencing of chimpanzee genome


Sequencing of macaque genome


Sequencing of gorilla genome


Sequencing genomes of other organisms


Species biodiversity study by the Canadian Centre for DNA Barcoding


Ant genome


Bat genome


Body louse genome


Camel genome


Dog genome


Frog genome


Goat genome


Mouse genome


Tibetan antelope genome


Turkey genome


Water flea genome


Whale genome


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


NIH funding for interpreting sequence variants in the human genome


NIH to fund studies of gene-environmental interactions in human diseases


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


Protection of privacy of participants in 100 Genomes project


Concluding remarks


Human Variome Project


Academic centers conducting research on sequencing


The New York Genome Center


Important academic collaborations


Scientific manpower for sequencing


Large-scale genomic sequencing projects at Joint Genome Institute



6. Applications of Sequencing in Healthcare


Introduction


Applications of sequencing in molecular diagnostics


Guidelines for use of sequencing for diagnosis


HLA sequencing for patient stratification


Next generation sequencing for detection of solid organ transplant rejection


Next generation sequencing for forensic diagnosis


Companies developing sequence-based molecular diagnostics


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


Exosome sequencing


Gaining insights into mutational processes


High throughput sequencing for anticancer drug discovery


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 for identification of FGFR gene fusions in cancer


Sequencing single cells to study evolution of cancer


Sequencing for assessing resistance to anticancer therapy


Sequencing of brain tumors


Sequencing for genetic alterations in gliomas


Sequencing for genetic alterations in medulloblastoma


Sequencing of breast cancer


BRCA mutations


Circulating nucleic acids as biomarkers of cancer


Deep sequencing of miRNA for signatures of invasiveness


NGS reveals heterogeneity of breast cancer


Sequencing of breast cancer metastases


Triple negative breast cancer


Whole genome sequencing in breast cancer


Sequencing of colorectal cancer


Sequencing of head and neck cancer


NGS for detection of HPV sequences in carcinoma of oropharynx


Sequencing of hematological malignancies


Myelodysplastic syndromes


Acute myeloid leukemia


Acute promyelocytic leukemia


Chronic myelomonocytic leukemia


Hairy-cell leukemia


Sequencing in chronic neutrophilic leukemia and atypical CML


Sequencing in hepatocellular carcinoma


Sequencing of melanoma


Sequencing of ovarian cancer


Sequencing of prostate cancer


Identification of mutations in prostate cancer by exome sequencing


Future prospects and challenges of NGS applications in oncology


Sequencing in genetic disorders


Approaches to sequencing in genetic disorders


High-throughput sequencing in Undiagnosed Disease Program at NIH


Sequencing of maternal plasma for detection of fetal aneuploidy


Sequencing for study of transposons


Sequencing genomes of the newborn to screen for genetic disorders


Study of rare variants in pinpointing disease-causing genes


Whole exome sequencing for diagnosis of Mendelian disorders


Whole genome sequencing for diagnosis of genetic disorders


Whole genome sequencing of a human fetus from maternal plasma


Genetic disorders investigated by sequencing


CHARGE syndrome


DiGeorge syndrome


Discovery of the gene for Miller syndrome


Discovery of the gene for Kabuki syndrome


Familial combined hypolipidemia


Familial thoracic aortic aneurysm


Hereditary blindness


Proteus syndrome


Syndrome of hypogonadotropic hypogonadism, ataxia, and dementia


Whole-exome sequencing in Bartter syndrome


X-linked disorder due to N-terminal acetyltransferase deficiency


Sequencing for HLA typing


High-throughput HLA genotyping with deep sequencing


Sequencing for study of the human immune system


Sequencing for investigating drug-virome interactions in organ transplants


Sequencing in neurological and psychiatric disorders


Sequencing in Alzheimer disease


Sequencing in Parkinson disease


Sequencing in Huntington's disease


Sequencing in Wilson's disease


Sequencing for mutations in familial amyotrophic lateral sclerosis


Sequencing of whole genome in Charcot-Marie-Tooth disease


Sequencing in muscular dystrophy


Sequencing in acute brain injury due to hemorrhage


Sequencing for mutations associated with autism spectrum disorders


Sequencing for diagnosis of intellectual disability


Sequencing in neurodevelopmental disorders


NGS for identifying mutations in RNA gene


Sequencing in attention-deficit/hyperactivity disorder


Sequencing in schizophrenia and bipolar disorder


Sequencing in cardiovascular disorders


Inherited cardiomyopathies


Sequencing genomes of microbes


DNA sequencing for study of bacterial epidemics


Role of sequencing in cholera epidemics


Role of sequencing in epidemic of Shiga toxin-producing E. coli


Role of whole genome sequencing in identification of C. difficile


Sequencing study of Salmonella emergence in Sub-Saharan Africa


Sequencing of ancient specimes from past epidemics


Human Microbiome Project


Pyrosequencing of microbial flora in leg ulcers


Sequencing the human gut microbiome for new immunomodulatory molecules


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 fungal genomes


Sequencing for detection of drug resistance in Plasmodium falciparum


Sequencing of human salivary microbiome


Sequencing in the management of HIV/AIDS


Sequencing plus immunological analyses to study HIV evolution


NGS for studying neuroAIDS


Surveillance of drug resistance in HIV-infected individuals


Sequencing in the management of HBV


Sequencing in the management of HCV


Sequencing genome of Lassa fever virus


Sequencing genome of a rhabdovirus associated with acute hemorrhagic fever


Surveillance of H1N1 influenza A virus using resequencing arrays


Whole-genome sequencing for investigation of MRSA outbreaks


Role of sequencing in tracking a hospital infection of Klebsiella pneumoniae


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


Whole exome sequencing and personalized disease risk


Personal Genome Project


Role of sequencing in personalized cancer management


Standardization of sequencing for personalized medicine


Future of sequencing and personalized medicine


Current status and future prospects of clinical applications of NGS


Challenges for clinical applications of NGS


Rare Diseases Genomes Project


Ethical aspects of sequencing



7. 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 markets


Sequencing markets according to applications


Sequencing markets according to therapeutic areas


Marketing potential for sequencers


Challenges to developing market for sequencers


Recommendations



8. Companies Involved in Sequencing


Introduction


Major players in sequencing


Profiles of companies involved in sequencing


Collaborations



9. 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 3-1: Software programs for sequencing from open sources


Table 3-2: Companies providing DNA sequencing software


Table 4-1: Comparison of a generation I and generation II sequencers


Table 4-2: Similarities and differences between second generation sequencers


Table 4-3: SWOT of ABI 310


Table 4-4: SWOT of IBS sequencing


Table 4-5: SWOT of NABsys' Hybridization-Assisted Nanopore Sequencing


Table 4-6: SWOT of 4300 DNA Analysis System Li-Cor


Table 4-7: SWOT of Genometrica


Table 4-8: SWOT of Polonator


Table 4-9: SWOT of GS FLEX Junior


Table 4-10: SWOT of Oxford Nanopore's MinION system


Table 4-11: SWOT of Ion Torrent Personal Genome Machine


Table 4-12: SWOT of Pacific BioSciences' single-molecule real-time sequencing


Table 4-13: SWOT of Illumina's miSeq


Table 4-14: SWOT of QIAGEN's GeneReader sequencer


Table 4-15: SWOT of GnuBio's microfluidics-based sequencing system


Table 5-1: Number of genes in organisms with fully sequenced genomes


Table 5-2: Approved medical sequencing projects


Table 5-3: Academic centers conducting research on DNA sequencing


Table 5-4: Distribution of scientific manpower for sequencing


Table 6-1: Companies involved in application of sequencing in molecular diagnostics


Table 7-1: Marketed next generation sequencers


Table 7-2: De novo sequencing vs resequencing markets


Table 7-3: Global markets for sequencing services according to geographical regions


Table 7-4: Global markets for sequencing services according to applications


Table 7-5: Sequencing markets according to therapeutic areas


Table 7-6: Global markets for sequencers from 2013 to 2023


Table 8-1: Companies developing sequencing technologies and instruments


Table 8-2: Companies that provide sequencing services


Table 8-3: Companies that provide bioinformatics support for sequencing


Table 8-4: Major players in sequencing


Table 8-5: 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: Nanopore-based sequence-specific detection of DNA


Figure 2-9: Single molecule, realtime DNA sequencing


Figure 2-10: A scheme of thermosequencing platform


Figure 6-1: Role of sequencing in the development of personalized medicine


Figure 7-1: Cost of sequencing per genome


Figure 7-2: Global markets for sequencing services according to applications



Author



Professor K. K. Jain is a neurologist/neurosurgeon by training and has been working in the biotechnology/biopharmaceuticals industry for several years. He received graduate training in both Europe and USA, has held academic positions in several countries and is a Fellow of the Faculty of Pharmaceutical Medicine of the Royal Colleges of UK. Currently he is a consultant at Jain PharmaBiotech. Prof. Jain is the author of 415 publications including 16 books (2 as editor) and 48 special reports, which have covered important areas in biotechnology, gene therapy and biopharmaceuticals.



For more information visit

http://www.researchandmarkets.com/research/l54sxm/dna_sequencing



Source: Jain PharmaBiotech

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