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DNA Sequencing - Technologies, Markets and Companies

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

Research and Markets



) 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 polymerases

Restriction endonucleases

DNA methylation


RNA polymerases

Non-coding RNAs

DNA transcription


Chromosome sequences


Mitochondrial DNA


The genetic code

Gene expression

The human genome


The exome

The epigenome

Human Epigenome Atlas

Variations in the human genome

Variations in DNA sequences

Single nucleotide polymorphisms


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


Retrotransposon capture sequencing

Mapping and sequencing of structural variation from human genomes

Impact of sequencing on healthcare

2. DNA Sequencing Technologies


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


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


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


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



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


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


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


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


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


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


8. Companies Involved in Sequencing


Major players in sequencing

Profiles of companies involved in sequencing


9. References


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


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


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


Source: Jain PharmaBiotech

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