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DNA Sequencing - Technologies, Markets and Companies Description:

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 2015 is described with estimates for 2020 and 2025. 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 137 companies involved in sequencing and their 145 collaborations. The report text is supplementd by 42 tables, 21 figures and 500 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 Chromatin Chromosome sequences Telomeres Mitochondrial DNA Genes The genetic code Gene expression Genes and human diseases The human genome ENCODE The epigenome Epigenetics and epigenomics DNA methylation Human Epigenome Atlas Metagenomics 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 Paired end transcriptome sequencing to overcome short read lengths Long vs short read lengths Validation of NGS data Emerging sequencing technologies Chemical DNA sequencing Chemical affinity capture and massively parallel 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) Background of sequencing technology IBS sequencing technology Illumina Genome Analyzer System MiSeqDx NextSeq 500 desktop sequencer MiSeq FGx Ion Torrent's sequencing technology Ion S5 system 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 Sequencing by hybridization SOLiD-System based ChIP-Sequencing Companies developing whole genome chips/microarrays Next generation sequencing vs microarrays for gene expression profiling RNA sequencing RNA-seq vs microarrays Capture sequencing ChIP-Seq Strand specific RNA sequencing SHAPE-Seq Applications of RNA-seq Challenges for future development of RNA-seq Exome sequencing Limitations of exome sequencing Human exome microarrays WES vs WGS Third generation sequencing SOLiD4 System SOLiD PI System Helicos™ Genetic Analysis System Molecular Combing Nanotechnology-based sequencing DNA sequence by use of nanoparticles Denaturation mapping of DNA in nanofluidic channels Nanopore sequencing Sequencing through graphene nanopores Convex lens-induced nanoscale templating Detection of single molecules for sequencing Helicos™ Genetic Analysis System Molecular Combing Optical Mapping Nanopore-based single-molecule detection of specific DNA sequences Phasing through the sequencing of single molecules 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 molecule targeted sequencing using GenoCare™ Analyzer Single cell sequencing MALBAC for single cell DNA sequencing Microfluidic single-cell whole-transcriptome sequencing Single cell sequencing of uncultured microbes Single sperm sequencing Single cell RNA sequencing Future of single cell 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 Contamination in high throughput sequencing Duplex sequencing

3. Role of Bioinformatics in Sequencing Introduction Growth of the sequencing database Sequencing data storage Cloud computing for sequencing data Cloud computing facilities Bioinformatics challenges of new sequencing technology Construction of 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 CLC Cancer Research Workbench Compressive genomics Detection of CNVs and gene duplications Detection of SVs in massively parallel sequencing data Differential expression analysis for sequence count data DRAGEN™ Bio-IT Processor Expression profiling without genome sequence information Ingenuity® Variant Analysis™ Ion Reporter Software Opal platform VAAST Accessing DNA sequence information Clinical Genomicist Workspace for managing NGS-based clinical tests 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 desktop sequencers BGI’s BGISEQ-500 desk top sequencer Illumina's MiSeq sequencer Roche GS Junior System Life Technologies’ Benchtop Ion Proton™ Sequencer Oxford Nanopore’s MinION™ system The ideal desk-top sequencer SWOT analysis of small sequencers Concluding remarks on SWOT analysis of desktop sequencers 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 Mutation rate measured by direct sequencing Protein-protein interactome network mapping RNA sequencing

Applications of RNA sequencing Contribution of RNA structure to gene regulation revealed by RNA-Seq Molecular indexing for quantitative targeted RNA sequencing 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, stem cells and neurodegeneration Sequencing, stem cells and regeneration Sequencing and synthetic biology Synthetic sequence in a bacterial cell Synthesizing long DNA molecules 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 100,000 Genomes Project Saudi Arabian human genome program Genome of the Netherlands 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 Hominin genome Neandertal genome Anzick-1 genome Genome of the Kennewick Man Saqqaq genome Sequencing and controversies about origin of Native Americans Future prospects of genome sequencing for human ancestry Sequencing genomes of non-human primates Sequencing of chimpanzee genome Sequencing of macaque genome Sequencing of gorilla genome Sequence the genomes of vertebrate species Sequencing genomes of other organisms Species biodiversity study by the Canadian Centre for DNA Barcoding Ant genome Avian genomes Bat genome Body louse genome Camel genome Cat genome Dog genome Frog genome Goat genome Horse genome Ancient horse genome House fly Mosquito genome Mouse genome Tibetan antelope genome Turkey genome Water flea genome Whale genome Woolly mammoth genome

Sequencing studies of the human microbiome Human Microbiome Project Human virome Microbial codes to distinguish individuals Population targeted sequencing studies Transcriptome sequencing for mRNA expression RNA splice variants 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 Sequencing in space Academic centers conducting research on sequencing Important academic collaborations Manpower for sequencing New York Genome Center USTAR Center for Genetic Discovery US Government funding for research Joint Genome Institute NHGRI’s Clinical Sequencing Exploratory Research grants 6. Applications of Sequencing in Healthcare Introduction Applications of sequencing in molecular diagnostics Clinical exome sequencing ACE Clinical Exome test Diagnosis and screening of genetic disorders Cystic fibrosis screening using high-throughput NGS CNV sequencing for diagnosis of chromosomal disorders Genetic misdiagnosis due to limited population sequencing data Karyotyping based on NGS NGS for diagnosis of rare genetic disorders Role of WGS in screening of newborns Role of WGS in chromothripsis Single cell sequencing for PGD WGS for identification of genetic disorders in critically ill infants WGS for pre-implantation genetic diagnosis in IVF Guidelines for use of sequencing for diagnosis Incidental findings on clinical sequencing NGS for diagnosis of CNS infections NGS for detection of solid organ transplant rejection NGS for forensic diagnosis Companies developing sequence-based molecular diagnostics Sequencing in cardiovascular disorders Inherited cardiomyopathies Exome sequencing and mutations associated with risk of coronary heart disease Sequencing for study of the human immune system Sequencing for investigating drug-virome interactions in organ transplants Immune profiling using a synthetic human virome NGS-based HLA typing High-throughput HLA genotyping with deep sequencing Approaches to NGS-based HLA typing Applications of NGS-based HLA typing Applications of sequencing relevant to the human microbiome

Sequencing the gut microbiome for discovery of immunomodulators Sequencing of gut microbes in obesity Companies developing microbiome-based products Pharmaceutical applications of sequencing Drug discovery and development Resequencing RNA profiling Quantitative selection of aptamers through sequencing Next generation sequencing and drug safety Sequencing in aging research WGS for the study of supercentenarians Sequencing of APOE gene in centenarians 7. Applications of Sequencing in Oncology Introduction Sequencing technologies for cancer A project to assess sequencing technologies for tumor DNA A universal NGS-based oncology test system Amplicon sequencing in cancer ASCO guidelines for use of NGS to test cancer susceptibility Cancer Genome Atlas Catalog of cancer genes Detection of cancer biomarkers Sequencing mitochondrial DNA to identify cancer biomarkers Biomarkers for personalizing cancer treatment Digital proteomics for cancer profiling Discrepancies in cancer genome sequencing Epigenome profiling Exosome sequencing Gaining insights into mutational processes Multiple-gene sequencing panel to assess risk of hereditary cancer Multiplexed cancer gene mutation analysis NGS for enhancing verification rate of chromosomal structural rearrangements NGS-based molecular profiling of cancer in FFPE specimens Paired-end sequencing Pathology tissue-ChIP Quality control of NGS in oncology RNA-Seq to study cancer transcriptome Sequencing cancer cell lines Sequencing for studying somatic mutations in cancer Chromothripsis in cancer Microsatellite instability in cancer genome Somatically acquired genomic rearrangements in cancer Sequencing for identification of FGFR gene fusions in cancer Sequencing single cells to study evolution of cancer Sequencing circulating tumor cell genomes High throughput sequencing for anticancer drug discovery NGS for developing targeted cancer therapies Sequencing for assessing resistance to anticancer therapy Sequencing of tumors of various organs Brain tumors Sequencing for genetic alterations in gliomas Sequencing for genetic alterations in medulloblastoma 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 Colorectal cancer Gastric cancer

Head and neck cancer NGS for detection of HPV sequences in carcinoma of oropharynx Hematological malignancies Acute myeloid leukemia Acute promyelocytic leukemia Chronic myelomonocytic leukemia Hairy-cell leukemia Hematological cancer risk inferred from blood DNA sequence Myelodysplastic syndromes Sequencing in chronic neutrophilic leukemia and atypical CML Sequencing in hepatocellular carcinoma Lung cancer Sequencing of small cell lung cancer Melanoma Ovarian cancer Prostate cancer Identification of mutations in prostate cancer by exome sequencing Role of sequencing in liquid biopsy for prostate cancer patients Current status and future prospects of NGS applications in oncology Actionable Genome Consortium to guide NGS in clinical oncology Points to consider for germline findings in tumor-only sequencing 8. Sequencing in Genetic Disorders Introduction Approaches to sequencing in genetic disorders DNA sequencing for prenatal 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 Tandem repeat variability for detection of genetic factors in diseases Whole genome sequencing for diagnosis of genetic disorders Whole exome sequencing for diagnosis of genetic disorders WES and WGS in monogenic disorders Whole genome sequencing of a human fetus from maternal plasma Genetic disorders investigated by sequencing Bartter syndrome 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 ataxia Hereditary blindness Neurofibromatosis type 1 Noonan syndrome Proteus syndrome Syndrome of hypogonadotropic hypogonadism, ataxia, and dementia Syndrome of polyarthritis nodosa vasculopathy X-linked disorder due to N-terminal acetyltransferase deficiency Sequencing in mitochondrial disorders Chronic progressive external ophthalmoplegia Role of NGS in prevention of chromosome abnormalities & monogenic disorders 9. Sequencing in Neurological and Psychiatric Disorders Introduction Sequencing in Alzheimer disease Sequencing in Parkinson disease Sequencing in Huntington’s disease Sequencing in Wilson’s disease Sequencing in ataxias

Sequencing in epilepsy Epileptic encephalopathy Sequencing for mutations in familial amyotrophic lateral sclerosis Sequencing of whole genome in Charcot-Marie-Tooth disease Sequence-based detection of a variant of Lambert-Eaton syndrome Sequencing in muscular dystrophy Sequencing in acute brain injury due to hemorrhage Sequencing for mutations in autism spectrum disorders Sequencing for diagnosis of intellectual disability Sequencing in neurodevelopmental disorders NGS for identifying mutations in RNA gene Sequencing in Möbius syndrome Sequencing in attention-deficit/hyperactivity disorder Sequencing in schizophrenia and bipolar disorder Sequencing in drug addiction 10. Applications of sequencings in infections Introduction DNA sequencing for study of bacterial epidemics Sequencing of GAS genotype emm89 Genome sequencing of H. influenzae to identify population structure Role of sequencing in cholera epidemics Role of sequencing in epidemic of Shiga toxin-producing E. coli Sequencing study of emergence of M. tuberculosis in East Africa Sequencing study of Salmonella emergence in Sub-Saharan Africa Sequencing of ancient specimes from past epidemics Sequencing for tracking hospital acquired infections Sequencing for investigation of MRSA outbreaks Role of sequencing in tracking a hospital infection of K. pneumoniae Role of whole genome sequencing in identification of C. difficile Role of NGS in diagnosis of infectious agents causing meningitis & encephalitis Role of sequencing in the management of bacterial infections Pyrosequencing of microbial flora in leg ulcers Sequencing for mapping genomic variation in Mycobacterium ulcerans Sequencing in the management of antimicrobial drug resistance Maximum-depth sequencing Sequencing for study of antibiotic resistance in bacteria Sequencing for predicting the virulence of MRSA Sequencing for detection of drug resistance in Plasmodium falciparum WGS for diagnosis of drug-resistant M. tuberculosis Sequencing for investigation of food-borne infections Sequencing for mapping genetic interactions in bacteria Metagenomic sequencing of bacteria Sequencing of DNA from single cells of bacteria Sequencing of the fungal genomes Sequencing of human salivary microbiome Next generation sequencing for antibacterial therapeutic discovery High throughput sequencing for diagnosis of viral diseases Sequencing in the management of HIV/AIDS Long read sequencing for personalizing HIV therapy NGS for studying neuroAIDS Sequencing plus immunological analyses to study HIV evolution Surveillance of drug resistance in HIV-infected individuals Sequencing in the management of Ebola virus infection Sequencing in the management of HCV Sequencing for detection of a novel pegivirus associated with HCV Sequencing genomes of hemorrhagic fever viruses 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 Regulatory aspects of sequencing for diagnosis of infections 11. Role of Sequencing in Personalized Medicine

Introduction Technologies relevant to sequencing and personalized medicine Whole genome sequencing and personalized medicine Whole exome sequencing and personalized disease risk Large-scale deep sequencing of human genomes Personal Genome Project Role of sequencing in personalized cancer management Standardization of sequencing for personalized medicine Regulating genomic testing in the era of personalized medicine Future of sequencing and personalized medicine 12. Current Status and Future Prospects ACMG clinical laboratory standards for NGS Regulatory and quality control issues of sequencers Applications of NGS in clinical trials Human transcriptome array in clinical trials Challenges for clinical applications of NGS Direct-to-consumer WGS services Ethical aspects of sequencing Future trends in clinical sequencing Rare Diseases Genomes Project 13. 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 Cost of integrating WGS into clinical care 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 Global sequencing markets Global markets for sequencers Markets for sequencing services according to geographical regions Global sequencing markets according to applications Global sequencing markets according to therapeutic areas Market trends for NGS Needs of the clinical market for NGS Sequencers for the clinical market Challenges to developing market for sequencers Recommendations 14. Companies Involved in Sequencing Introduction Major players in sequencing Profiles of companies involved in sequencing Collaborations 15. 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 BGI’s BGISEQ-500 desktop sequencer Table 4-8: SWOT of Polonator Table 4-9: SWOT of Roche 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 MiSeqDx Table 4-14: SWOT of Illumina’s NextSeq 500 Table 4-15: SWOT of QIAGEN’s GeneReader™ sequencer Table 4-16: SWOT of Bio-Rad (formerly GnuBio’s) droplet-based sequencing system Table 4-17: SWOT of 10X Genomics’ GemCode 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 6-2: Companies developing microbiome-based products Table 12-1: Companies offering direct-to-consumer genome testing services Table 13-1: Marketed next generation sequencers Table 13-2: De novo sequencing vs resequencing markets Table 13-3: Global markets for sequencers from 2015 to 2025 Table 13-4: Global markets for sequencing services according to geographical regions Table 13-5: Global markets for sequencing services according to applications Table 13-6: Sequencing markets according to therapeutic areas from 2015 to 2025 Table 14-1: Companies developing sequencing technologies and instruments Table 14-2: Companies that provide sequencing services Table 14-3: Companies that provide bioinformatics support for sequencing Table 14-4: Major players in sequencing Table 14-5: Selected collaborations for DNA sequencing Figures Figure 2-1: DNA sequencing process Figure 2-2: Components of next generation sequencing Figure 2-3: Comparison of traditional sequencing and next generation sequencing Figure 2-4: Watson-Crick base pairing Figure 2-5: Genome Sequencer FLX system (Roche) Figure 2-6: Workflow of Genome Sequenser FLX system Figure 2-7: Sequencing by ligation Figure 2-8: Construction of SOLiD fragment library using DNA enrichment by ChIP Figure 2-9: RNA sequencing Figure 2-10: Nanopore-based sequence-specific detection of DNA Figure 2-11: DNA sequencing through a graphene nanopore Figure 2-12: Nanopore-based, single molecule, realtime DNA sequencing Figure 2-13: A scheme of thermosequencing platform Figure 2-14: Duplex sequencing Figure 3-1: Basic workflow of NGS libraries Figure 7-1: Comparison of conventional and high-throughput NGS workflows Figure 7-2: Procedure for sequencing of CTC exome Figure 8-1: Schematic view of role of WES ND WGS in diagnosis of monogenic disorders Figure 11-1: Role of sequencing in the development of personalized medicine Figure 13-1: Cost of sequencing per genome Figure 13-2: Global markets for sequencing services according to applications

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