DNA Sequencing - Technologies, Markets & Companies

Table of Contents

Part I: Technologies & Applications

0. Executive Summary 

1. Introduction 

• Definition and scope of sequencing 
• Historical aspects of sequencing 
• Basics of molecular biology 
• DNA  
• DNA polymerases 
• DNA helicases  
• Restriction endonucleases 
• 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  
• Next generation sequencers 
• 4300 DNA analyzer  
• Apollo 100  
• Life Technologies 3500 series Genetic Analyzer 
• 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  
• Next generation sequencing based on Lightning Terminators 
• MiSeq FGx 
• NovaSeq 6000 system  
• 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  
• SiMSen-seq for ultrasensitive detection of mutations  
• 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  
• In situ sequencing  
• 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 
• DNBseq technology 
• 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 
• Drop-seq for single cell sequencing  
• MALBAC for single cell DNA sequencing  
• Microfluidic single-cell whole-transcriptome sequencing 
• Optical-mapping and whole-genome sequencing of cells 
• Single cell sequencing of uncultured microbes  
• Single sperm sequencing 
• Single cell RNA sequencing  
• Single-cell combinatorial indexed sequencing 
• Single-stranded sequencing using microfluidic reactors  
• 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  
• Flye long-read assembly algorithm 
• 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 
• Barcoding of synapses in the brain 
• 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 
• Single-cell sequencing for study of cell lineage 
• Sequencing of human genomes 
• 100,000 Genomes Project 
• Genome of the Netherlands 
• Missing human genome sequences 
• Personal genome sequencing  
• Role of sequencing in identification of human remains 
• Saudi Arabian human genome program  
• Sequence map of the human pan-genome 
• Sequencing of African genomes 
• Sequencing of Korean genomes 
• Sequencing mitochondrial genome 
• Sequencing of ancient genomes 
• Ancient DNA evidence for genomic variations in South East Asia  
• Anzick-1 genome 
• Genome of the Kennewick Man 
• Hominin genome  
• Indus valley civilization and DNA sequencing  
• Neandertal genome 
• Saqqaq genome 
• Sequencing and controversies about origin of Native Americans 
• Whole genome sequencing  
• Whole-genome sequencing of methylome  
• Whole genome resequencing  
• 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 
• Single cell sequencing of the brain 
• 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  
• NGS-based molecular diagnosis at POC using mobile phone microscopy 
• 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 
• Sequencing for detection of germline cancer risk variants 
• 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 
• NGS to distinguish primary lung cancer from pulmonary metastases  
• 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 of NGS applications in oncology 
• Actionable Genome Consortium to guide NGS in clinical oncology 
• Guidelines for interpretation/reporting of sequence variants in cancer 
• Points to consider for germline findings in tumor-only sequencing 
• Translation of gene panel sequencing into routine cancer diagnosis 

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 
• WES in neurodevelopmental disorders 
• 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 
• Sequencing for diagnosis of viral diseases 
• High throughput sequencing for diagnosis of viral diseases  
• Sensitive metagenomic sequencing for detection of pathogenic human viruses  
• 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  
• Sequencing genomes of coronaviruses 
• Regulatory aspects of sequencing for diagnosis of infections 
• Future of pathogen sequencing 

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 
• Circulating cell-free DNA sequencing for personalized cancer therapy 
• Companies and cancer centers using sequencing for personalized oncology  
• 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 in the USA 
• International NGS standardization 
• 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 

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  

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: In situ sequencing 
Figure 2-11: Nanopore-based sequence-specific detection of DNA  
Figure 2-12: DNA sequencing through a graphene nanopore 
Figure 2-13: Nanopore-based, single molecule, realtime DNA sequencing 
Figure 2-14: Drop-seq single cell analysis  
Figure 2-15: A scheme of thermosequencing platform 
Figure 2-16: 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 7-3: Outline of a study to show current genetic testing and NGS cancer panel 
Figure 8-1: Schematic view of role of WES ND WGS in diagnosis of monogenic disorders 
Figure 10-1: Workflow for pathogen sequencing 
Figure 11-1: Role of sequencing in the development of personalized medicine 

Part II: Markets & Companies

13. Markets for Sequencing 

• 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 
• Cost of NGS 
• Genome X Prize Foundation 
• Innovations to reduce cost of whole genome sequencing  
• Commercial aspects of low-cost genome sequencing  
• NGS 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  
• NGS markets for cancer 
• NGS markets for genetic disorders 
• NGS markets for microbiome  
• 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 
• Top ten players in sequencing 
• Profiles of companies involved in sequencing 
• Collaborations 

15. References  

Tables

Table 13-1: Marketed next generation sequencers 
Table 13-2: De novo sequencing vs resequencing markets  
Table 13-3: Global markets for sequencers from 2020 to 2030 
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 2020 to 2030 
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: Top ten companies in sequencing  
Table 14-5: Selected collaborations for DNA sequencing 

Figures

Figure 13-1: Cost of sequencing per genome from 2001 to 2020 

Samples