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Molecular Diagnostics

December 30, 2011
By

NEW YORK , Dec. 29, 2011 /PRNewswire/ — Reportlinker.com announces that a new market research report is available in its catalogue:

Molecular Diagnostics – Technologies, Markets and Companies

http://www.reportlinker.com/p0203544/Molecular-Diagnostics—Technologies-Markets-and-Companies.html#utm_source=prnewswireutm_medium=prutm_campaign=In_Vitro_Diagnostic

Benefits of this report

-This report has evolved during the past 15 years, profiting from feedback by numerous readers and experts.

-The most comprehensive and up-to-date one-stop source of information on technical and commercial aspects of molecular diagnostics.

-Includes profiles of 313 companies, the largest number in any report on this topic.

-500 references, cited in the report are included in the bibliography.

-The text is supplemented by 97 tables and 15 figures.

Who should read this report?

-Chief executive officers of molecular diagnostic companies.

-Business development executives of pharmaceutical and biotechnology companies.

-Executives of companies involved in developing integration of diagnosis and treatment as well as those interested in personalized medicine.

-Officers of genomic and proteomic companies interested in diagnostic technologies.

-Research scientists involved in application of molecular diagnostic technologies.

-Planners of healthcare services.

Summary

This report describes and evaluates the molecular diagnostics technologies that will play an important role in practice of medicine, public health, pharmaceutical industry, forensics and biological warfare in the 21st century. This includes several polymerase chain reaction (PCR)-based technologies, fluorescent in situ hybridization (FISH), peptide nucleic acids (PNA), electrochemical detection of DNA, biochips, nanotechnology and proteomic technologies.

Initial applications of molecular diagnostics were mostly for infections but are now increasing in the areas of genetic disorders, preimplantation screening and cancer. Genetic screening tests, despite some restrictions is a promising area for future expansion of in vitro diagnostic market. Molecular diagnostics is being combined with therapeutics and forms an important component of integrated healthcare. Molecular diagnostic technologies are also involved in development of personalized medicine based on pharmacogenetics and pharmacogenomics. Currently, there has been a considerable interest in developing rapid diagnostic methods for for point-of-care and biowarfare agents such as anthrax.

The number of companies involved in molecular diagnostics has increased remarkably during the past few years. More than 500 companies have been identified to be involved in developing molecular diagnostics and 313 of these are profiled in the report along with tabulation of 707 collaborations. Despite the strict regulation, most of the development in molecular diagnostics has taken place in the United States , which has the largest number of companies.

The markets for molecular diagnostics technologies are difficult to estimate. Molecular diagnostics markets overlap with markets for non-molecular diagnostic technologies in the in vitro diagnostic market and are less well defined than those for pharmaceuticals. Molecular diagnostic markets are analyzed for 2011 according to technologies, applications and geographical regions. Forecasts are made up to 2021. A major portion of the molecular diagnostic market can be attributed to advances in genomics and proteomics. Biochip and nanobiotechnology are expected to make a significant contribution to the growth of molecular diagnostics.

This report was first published as DNA Diagnostics in 1995 by PJB Publications, UK. It was updated in 1997 as Molecular Diagnostics and the next edition, Molecular Diagnostics II, was published by Decision Resources Inc in 1999. All the three versions of the reports were well accepted and sold widely.The report has been rewritten several times since then.

Table of Contents

0. Executive Summary 23

1. Introduction 25

Definitions and scope of the subject 25

Historical evolution of molecular diagnostics 25

Molecular biology relevant to molecular diagnostics 26

DNA 26

DNA polymerases 26

Restriction endonucleases 27

DNA methylation 27

RNA 28

RNA polymerases 28

Non-coding RNAs 28

DNA transcription 29

Chromosomes 29

Telomeres 30

Mitochondrial DNA 30

Genes 31

The genetic code 31

Gene expression 31

The human genome 32

Variations in the human genome 32

Variations in DNA sequences 32

Single nucleotide polymorphisms 33

Haplotyping 33

Copy number variations in the human genome 34

Genotype and haplotypes 35

Insertions and deletions in the human genome 35

Complex chromosomal rearrangements 36

Large scale variation in human genome 36

Structural variations in the human genome 37

Replication of the DNA helix 37

Transposons 38

Proteins 38

Proteomics 38

Monoclonal antibodies 39

Aptamers 39

Basics of molecular diagnostics 39

Tracking DNA: the Southern blot 39

Pulsed-field gel electrophoresis 40

DNA Probes 40

The polymerase chain reaction 41

Basic Principles of PCR 41

Target selection 41

Detection of amplified DNA 41

Impact of human genome project on molecular diagnostics 42

Mapping and sequencing of structural variation from human genomes 43

1000 Genomes Project 43

Human Variome Project 44

Role of bioinformatics in molecular diagnostics 45

Systems biology approach to molecular diagnostics 45

Biomarkers 45

Applications of molecular diagnostics 46

2. Molecular Diagnostic Technologies 49

Introduction 49

DNA sample collection and extraction 49

Blood samples 49

Dried blood spots 49

Buccal swabs and saliva 50

Urine samples for transrenal DNA 50

Manual vs automated DNA extraction 51

Sample preparation 51

Pressure Cycling Technology 51

Membrane immobilization of nucleic acids 51

Automation of sample preparation in molecular diagnostics 52

ABI PRISM 6700 Automated Nucleic Acid Workstation 52

BioRobot technology 52

COBAS AmpliPrep System 53

GENESIS FE500 Workcell 53

GeneMole 53

PCR BioCube 53

QIAsymphony 54

Tigris instrument system 54

Techniques for sample preparation that are suitable for automation 54

Xtra Amp Genomic DNA Extraction 54

Extraction of DNA from paraffin sections 54

Dynabead technology 55

Pressure Cycling Technology 55

SamPrep 55

Use of magnetic particles for automation in genome analysis 55

Companies involved in nucleic acid isolation 56

Labeling and detection of nucleic acids 57

Novel PCR methods 57

Addressing limitations of PCR 57

CAST-PCR 58

Combined PCR-ELISA 58

Convection PCR 59

Digital PCR 59

Emulsion PCR 60

ExCyto PCR 60

Long and accurate PCR 60

Multiplex PCR 61

Real-time PCR systems 61

Dyes used in real-time PCR 62

Commercially available real-time PCR systems 62

LightCycler PCR system 63

LightUp probes based on real-time PCR 63

READ™ real-time PCR method 64

StellARray™ technology 64

7500 Fast Dx Real-Time PCR Instrument 64

Applications of real-time PCR 64

Limitations of real-time PCR 65

Quantitative PCR for accurate low level DNA analysis 65

qPCR for quantification of circulating mtDNA 66

Guidelines for real-time qPCR 66

Future applications of real-time qPCR 66

Reverse transcriptase (RT)-PCR 67

Standardized reverse transcriptase PCR 68

Single cell PCR 68

LATE-PCR 68

COLD-PCR 68

AmpliGrid-System 69

DNA melt analysis 70

High-resolution DNA melt analysis for genotyping 70

PCR device for DNA melt analysis in space 70

Monitoring of gene amplification in molecular diagnostics 70

Non-PCR nucleic acid amplification methods 71

DNA probes with conjugated minor groove binder 71

Dynamic Flux Amplification 71

Isothermal reaction for amplification of oligonucleotides 71

ICAN (Isothermal and Chimeric primer-initiated Amplification of Nucleic Acids) 72

Linked Linear Amplification 72

Multiplex Ligation-Dependent Probe Amplification 72

Rapid analysis of gene expression 73

Rolling circle amplification technology 73

Gene-based diagnostics through RCAT 74

RCAT-immunodiagnostics 75

RCAT-pharmacogenomics 75

Circle-to-circle amplification 75

Ramification amplification method 76

Single Primer Isothermal Amplification 76

Transcription mediated amplification 76

WAVE nucleic acid fragment analysis system 77

Technologies for signal amplification 77

3 DNA dendrimer signal amplification 78

Hybridization signal amplification method 78

Signal mediated amplification of RNA technology 79

Invader assays 80

Hybrid Capture technology 81

Branched DNA test 82

Tyramide signal amplification 82

Non-enzymatic signal amplification technologies 82

Direct molecular analysis without amplification 83

Trilogy™ Platform 83

Direct detection of dsDNA 84

Multiplex assays 85

Fluorescent in situ hybridization 85

FISH technique 86

Applications of FISH 86

Modifications of FISH 87

Direct visual in situ hybridization 87

Direct labeled Satellite FISH probes 87

Comparative genomic hybridization 88

Primed in situ labeling 88

Interphase FISH 88

FISH with telomere-specific probes 89

Multicolor FISH 89

Simultaneous Ultrasensitive Subpopulation staining/Hybridization In situ 90

Automation of FISH 90

Companies involved in FISH diagnostics 90

RNA diagnostics 91

RNA isolation from tissue samples 91

Commercially available tests for mRNA detection and quantitation 91

Branched-chain DNA assay for measurement of RNA 92

Cycling probe technology 92

Invader RNA assays 93

Linear RNA amplification 93

Non-isotopic RNase cleavage assay 93

Nucleic acid sequence-based amplification 94

Q Beta replicase system 96

RNAScope 96

RNA expression profiling 96

Visualization of mRNA expression in vivo 96

Solid Phase Transcription Chain Reaction 97

Transcriptome analysis 97

MicroRNA diagnostics 97

Real-time PCR for expression profiling of miRNAs 98

Microarray vs quantitative PCR for measuring miRNAs 98

Use of LNA to explore miRNA 99

Nuclease Protection Assay to measure miRNA expression 99

Microarrays for analysis of miRNA gene expression 99

Modification of in situ hybridization for detection of miRNAs 100

Whole genome amplification 100

Companies that provide technologies for whole genome amplification 101

QIAGEN’s Repli-G system 101

GenomePlexÔ Whole Genome Amplification 102

DNA sequencing 102

Companies involved in sequencing 103

Applications of next generation sequencing in molecular diagnostics 105

Companies developing sequencing for molecular diagnostics 105

Genome-wide approach for chromatin mapping 106

Mitochondrial sequencing 106

Identification of unknown DNA sequences 107

Optical mapping 107

Gene expression analysis 108

Gene expression profiling on whole blood samples 108

Gene expression patterns of white blood cells 109

Gene expression profiling based on alternative RNA splicing 109

MAUI (MicroArray User Interface) hybridization 110

Monitoring in vivo gene expression by molecular imaging 110

Serial analysis of gene expression (SAGE) 110

Single-cell gene expression analysis 111

T cell receptor expression analysis 111

Tangerine™ expression profiling 112

Whole genome expression array 112

Ziplex™ system 113

Companies involved in gene expression analysis 113

Peptide nucleic acid technology 114

Use of PNA with fluorescence in situ hybridization 114

PNA and PCR 115

Use of PNA with biosensors 116

PNA-based PD-loop technology 116

PNA-DNA hybrid quadruplexes 117

Companies involved in PNA diagnostics 117

Locked nucleic acids 117

Zip Nucleic Acids 118

Electrochemical detection of DNA 118

Mediated nucleic acid oxidation 119

Detection of hybridized nucleic acid with cyclic voltametry 119

Electrochemical detection based on Toshiba’s CMOS technology 120

Concluding remarks on electrochemical DNA detection 120

Bead-based assay platforms 120

Scorpions™ technology 121

The Scorpions reaction 121

Applications of Scorpions 122

Nucleic acid lateral flow molecular diagnostics 122

3. Biochips, Biosensors, and Molecular Labels 125

Introduction to biochip technology 125

Applications of biochips in diagnostics 125

GeneChip 126

GeneChip Human Genome Arrays 127

AmpliChip CYP450 127

Electronic detection of nucleic acids on microarrays 127

Microchip capillary electrophoresis 128

Strand displacement amplification on a biochip 128

Rolling circle amplification on microarrays 128

LiquiChip-RCAT 128

Fast PCR biochip 129

Multiplex microarray-enhanced PCR for DNA analysis 129

Multiplexed Molecular Profiling 129

Universal DNA microarray combining PCR and ligase detection reaction 130

Genomewide association scans 130

Whole genome chips/microarrays 131

Transposon insertion site profiling chip 131

Standardizing the microarrays 132

Companies involved in developing biochip technology for diagnostics 132

Future of biochip technology for molecular diagnostics 133

Microfluidic chips 134

Fish-on-chip 134

Lab-on-a-chip 134

LabCD 135

Micronics’ microfluidic technology 135

Microfluidic chips/arrays using PCR 135

Microfluidic automated DNA analysis using PCR 135

Digital PCR Array 135

Digital PCR on a SlipChip 136

Microfluidic chips integrated with RCAT 136

Microfluidic chips integrated with PET 136

Companies developing microfluidic technologies 137

Biosensor technologies 137

Classification of biosensor technologies 138

DNA-based biosensors 139

DNA hybridization biosensor chips 139

PCR-free DNA biosensor 139

DNA based biosensor to detects metallic ions 140

Genetically engineered B lymphocytes 140

Biosensors immunoassays 140

PNA (peptide nucleic acid)-based biosensors 141

Protein-based biosensors 141

Antibody biosensors 141

Cell-based biosensors (cytosensors) 141

Multicell biosensors 142

Microbial biosensors 142

Optical biosensors 143

Surface plasmon resonance technology 143

Label-free optical biosensor 144

Microsensors using with nano/microelectronic communications technology 144

Electrochemical sensors 144

Enzyme electrodes for biosensing 144

Conductometric sensors 145

Electrochemical genosensors 145

Electrochemical nanobiosensor 145

Bioelectronic sensors 146

Phototransistor biochip biosensor 146

Ribozyme-based sensors 146

RiboReporters 147

Concluding remarks and future prospects of biosensor technology 147

Companies developing biosensors for molecular diagnostics 148

Molecular labels and detection 149

Detection technologies for molecular labels 150

Fluorescence and chemiluminescence 150

Fluorescence technologies for label detection 151

Companies with fluorescence and chemiluminescence products 151

Molecular beacons 152

The Green fluorescent protein 153

Multiophoton detection radioimmunoassay 154

Multi-pixel photon counter 154

Enzyme labels and detection by fluorescence 154

Phase-sensitive flow cytometry 155

Microtransponder-based DNA diagnostics 155

Laboratory Multiple Analyte Profile 156

Multiple labels 156

Protein-DNA chimeras for detection of small numbers of molecules 157

Single molecule detection 157

Atomic force microscopy 158

Capillary electrophoresis 158

Confocal laser scanning 158

nCounter Analysis System 158

Spectrally resolved fluorescence lifetime imaging microscopy 159

Molecular imaging 159

Basic research in molecular imaging 160

Devices for molecular imaging 160

Molecular imaging in clinical practice 160

Challenges and future prospects of molecular imaging 161

Companies involved in molecular imaging 161

Nanobiotechnology for molecular diagnostics 161

Magnetic nanoparticles 162

Gold nanoparticles 163

Quantum dot technology 164

Nanotechnology on a chip 165

Nanogen’s NanoChip 165

Fullerene photodetectors for chemiluminescence detection on microfluidic chip 165

Diagnostics based on nanopore technology 166

Nanosensors 166

Detection of cocaine molecules by nanoparticle-labeled aptasensors 166

Nanosensors for glucose monitoring 167

PEBBLE nanosensors 167

Quartz nanobalance biosensor 167

Cantilever arrays 167

Resonance Light Scattering technology 168

DNA nanomachines for molecular diagnostics 169

Nanobarcodes technology for molecular diagnostics 169

Qdot nanobarcode for multiplexed gene expression profiling 169

Role of nanobiotechnology in improving molecular diagnostics 170

Companies involved in nanomolecular diagnostics 170

Concluding remarks about nanodiagnostics 173

Future prospects of nanodiagnostics 173

4. Proteomic Technologies for Molecular Diagnostics 175

Introduction 175

Proteomic technologies 175

Biomarkers of disease 175

Proteomic tools for biomarkers 175

Search for biomarkers in body fluids 176

Captamers with proximity extension assay for proteins 176

Cyclical amplification of proteins 176

Detection of misfolded proteins by ELISA with exponential signal amplification 177

Diagnostics based on designed repeat proteins 177

Differential Peptide Display 177

Light-switching excimer probes 178

MALDI-TOF MS 178

Molecular beacon aptamer 179

Molecular beacon assay 179

Proteomic patterns 180

Real-time PCR for protein quantification 180

Protein biochip technologies 181

ProteinChip 182

LabChip for protein analysis 182

TRINECTIN proteome chip 183

Protein chips for antigen-antibody interactions molecular diagnostics 183

Microfluidic devices for proteomics-based diagnostics 183

Nanotechnology-based protein biochips/microarrays 184

Nanoparticle protein chip 184

Protein nanobiochip 184

Protein biochips based on fluorescence planar wave guide technology 184

New developments in protein chips/microarrays 185

Antibody microarrays 185

Aptamer-based protein biochip 186

Multiplexed Protein Profiling on Microarrays 186

Proteomic pattern analysis 186

Single molecule array 187

Viral protein chip 187

Commercial development of protein chips for molecular diagnostics 187

Proteome Identification Kit 189

Laser capture microdissection (LCM) 189

LCM technology 189

Applications of LCM in molecular diagnostics 190

Proteomic diagnosis of CNS disorders 190

Cerebrospinal fluids tests based on proteomics 190

Urine tests for CNS disorders based on proteins in urine 191

Diagnosis of CNS disorders by examination of proteins in the blood 191

Diagnosis of CNS disorders by examination of proteins in tears 192

Role of proteomics in the diagnosis of Alzheimer’s disease 192

Role of proteomics in the diagnosis of Creutzfeldt-Jakob disease 193

Future prospects of use of proteomics for diagnosis of CNS disorders 193

Concluding remarks on the use of proteomics in diagnostics 193

5. Molecular Diagnosis of Genetic Disorders 195

Introduction 195

Cytogenetics 196

FISH with probes to the telomeres 196

Single copy FISH probes 196

Comparative genomic hybridization 197

Use of biochips in genetic disorders 197

Representational oligonucleotide microarray analysis 198

SignatureChip®-based diagnostics for cytogenetic abnormalities 198

Diagnosis of genomic rearrangements by multiplex PCR 198

Quantitative fluorescent PCR 198

Mutation detection technologies 199

PCR-based methods for mutation detection 200

Cleavase Fragment Length Polymorphism 200

Direct dideoxy DNA sequencing 200

Digital Genetic Analysis (DGA) 200

Fluorescence-based directed termination PCR 201

Fluorescence melting curve analysis for multiplex mutation detection 201

Heteroduplex analysis 202

Restriction fragment length polymorphism 202

Single-stranded conformation polymorphism (SSCP) analysis 202

TaqMan real-time PCR 203

Non-PCR methods for mutation detection 203

Arrayed primer extension 203

BEAMing (beads, emulsion, amplification, and magnetics) 204

ELISA-protein truncation test 204

Enzymatic mutation detection 204

Specific anchor nucleotide incorporation 205

Conversion analysis for mutation detection 205

Biochip technologies for mutation detection 205

Combination of FISH and gene chips 206

Haplotype Specific Extraction 206

Use of biosensors for detection of mutations 206

Technologies for SNP analysis 207

DNA sequencing 208

Electrochemical DNA probes 208

Use of NanoChip for detection of SNPs 209

Single base extension-tag array 209

Laboratory Multiple Analyte Profile 209

SNP genotyping with gold nanoparticle probes 210

PCR-CTPP (confronting two-pair primers) 210

Peptide nucleic acid probes for SNP detection 210

SNP genotyping on a genome-wide amplified DOP-PCR template 210

Pyrosequencing 211

Reversed enzyme activity DNA interrogation test 211

Smart amplification process version 2 212

Zinc finger proteins 212

UCAN method (Takara Biomedical) 212

Biochip and microarray-based detection of SNPs 213

SNP genotyping by MassARRAY 213

Electronic dot blot assay 213

Biochip combining BeadArray and ZipCode technologies 214

SNP-IT primer-extension technology 214

OmniScan SNP genotyping 214

Affymetrix SNP genotyping array 214

Concluding remarks on SNP genotyping 215

Limitations of SNP in genetic testing 215

Haplotyping versus SNP genotyping 216

Nanofluidics technology for high throughput SNP genotyping 216

Companies involved in developing technologies/products for SNP analysis 216

Role of copy number variations in genetic diagnostic testing 218

CNVs in various diseases 218

CNVs in genetic epilepsy syndromes 218

CNVs associated with schizophrenia 218

Methods for determination of CNVs 219

Digital array for CNV detection 219

Wellcome Trust Case Control Consortium CNV typing array 219

CNVer algorithm for CNV detection 219

Study of rare variants in pinpointing disease-causing genes 220

Prenatal DNA diagnosis 221

Amniocentesis 221

Chorionic villus sampling 221

Separating fetal cells in maternal blood for genetic diagnosis 221

Antenatal screening for Down’s syndrome 222

Fetal DNA in maternal blood 222

Molecular methods for prenatal diagnosis 223

aCGH for prenatal diagnosis 223

BAC HD Scan test 223

FISH for prenatal diagnosis 223

PCR for prenatal diagnosis 224

Plasma DNA sequencing to detect fetal chromosomal aneuploidies 224

In vivo gene expression analysis of the living human fetus 225

Noninvasive prenatal diagnosis of monogenic diseases 225

Digital relative mutation dosage 225

Massively parallel plasma DNA sequencing 225

Applications of prenatal diagnosis 226

Diagnosis of congenital infections 227

Diagnosis of congenital CMV 227

Diagnosis of eclampsia 227

Use of transrenal DNA for prenatal testing 227

Preimplantation genetic diagnosis 228

Technologies for preimplantation genetic diagnosis (PGD) 228

PCR for preimplantation genetic diagnosis 228

FISH for preimplantation genetic diagnosis 229

Microarrays for preimplantation genetic diagnosis 229

Conditions detected by preimplantation genetic diagnosis 229

The future of preimplantation genetic diagnosis 230

Companies involved in prenatal/preimplantation diagnosis 231

Cystic fibrosis 232

Detection of CFTR gene mutations 232

CFTR technologies of various companies 232

Genzyme’s CF gene sequencing 233

CF PlusÔ Tag-It Cystic Fibrosis Kit 234

Asuragen’s bead array test 234

The Ambry CF Test 235

Biochip for CF diagnosis 235

Identification of CF variants by PCR/Oligonucleotide Ligation Assay 235

SensiGene (SEQUENOM) CF carrier screening test 235

Serum proteomic signature for CF using antibody microarrays 236

Guidelines for genetic screening for CF 236

Congenital adrenal hyperplasia 236

Primary immunodeficiencies 237

Hematological disorders 238

Hemoglobinopathies 238

Sickle cell anemia 238

Thalassemia 238

Paroxysmal nocturnal hemoglobinuria 239

Hemophilia 239

Hereditary hemochromatosis 239

Polycystic kidney disease 240

Hereditary metabolic disorders 240

Lesch-Nyhan Syndrome 240

Gaucher’s Disease 241

Acute Intermittent Porphyria 241

Phenylketonuria 241

Hereditary periodic fever 242

Achondroplasia 242

Molecular diagnosis of cardiovascular disorders 242

Coronary heart disease 243

Genomics of coronary heart disease 244

Cardiomyopathy 244

Familial Hypertrophic Cardiomyopathy 244

Idiopathic dilated cardiomyopathy 245

Cardiac Arrhythmias 245

Long Q-T Syndrome 245

Familial atrial fibrillation 245

Idiopathic ventricular fibrillation 246

Congestive heart failure 246

Hypertension 246

Disturbances of blood lipids 247

Familial dyslipoproteinemias 247

Hypercholesterolemia 247

Thrombotic disorders 247

Factor V Leiden mutation 248

Pulmonary embolism 248

Hereditary thrombophilia 249

Companies developing molecular diagnostics for cardiovascular disorders 249

Molecular diagnosis of eye diseases 250

Molecular diagnosis of retinitis pigmentosa 250

Genetic screening for glaucoma 250

Role of molecular diagnostics in rheumatoid arthritis 251

Molecular diagnosis of neurogenetic disorders 251

Alzheimer’s disease 253

Autism spectrum disorders 253

CNVs associated with autism 253

Charcot- Marie Tooth disease 254

Down syndrome 255

Duchenne and Becker muscular dystrophy 255

eNOS gene polymorphisms as predictor of cerebral aneurysm rupture 256

Fragile X syndrome 256

Huntington disease 257

Hereditary neuropathy with liability to pressure palsies 257

Mitochondrial disorders affecting the nervous system 258

Parkinson’s disease 258

Pompe’s disease 259

Spinal muscular atrophy 259

Triple repeat disorders 259

Genetic testing for disease predisposition 260

Direct-to-consumer genetic tests 260

6. Molecular Diagnosis of Infections 263

Introduction 263

Molecular techniques for the diagnosis of infections 263

Antibody-enhanced microplate hybridization assays 264

Bacteriophage-based methods for detection of bacteria 264

Biosensors for detection of microorganisms 265

Ibis T5000™ Biosensor System 265

DNA enzyme immunoassay 265

DNA biochip/microarray in diagnosis of infections 265

DNA-based typing methods 266

Restriction fragment length polymorphism analysis 266

Ribotyping 267

Random amplified polymorphic DNA 267

Combinatorial DNA melting assay 267

Electrochemical detection of pathogens 267

FISH for detection of infections 268

Helicase-dependent isothermal amplification for rapid detection of pathogens 268

High resolution melt analysis for diagnosis of infections 268

Ligase chain reaction 268

Mass spectrometry for microbial identification 269

Metagenomic pyrosequencing 269

Multiplex PCR for detection of infections 270

Dual priming oligonucleotide for multiplex PCR 271

LightCycler® SeptiFast Test 271

Multiplex amplified nominal tandem repeat analysis 272

VYOO® Sepsis Test 272

NASBA for detection of microorganisms 272

Nucleic acid probes 272

Neutrophil CD11b expression as a diagnostic marker 273

Optical Mapping 273

PNA-FISH for diagnosis of infections 273

QuantiFERON® technology for pre-molecular diagnosis of infections 274

Quantitative reverse-transcription PCR for bacterial diagnostics 274

Rupture event scanning 274

Real-time single-molecule imaging of virus particles 275

Single-strand conformational polymorphism 275

SmartGene platform for identifying pathogens based on genetic sequences 275

Tessera array technology 275

Unyvero Solution 276

Applications, advantages and limitations of molecular diagnostics 276

Molecular diagnostics versus other microbial detection technologies 276

Advantages of nucleic acid-based diagnostics in infections 276

Drawbacks of nucleic acid-based diagnostics in infections 277

Nanotechnology for detection of infectious agents 277

Bacterial and fungal infections 278

Mycobacterium tuberculosis 279

Conventional diagnosis of tuberculosis 280

Microscopic Observation Drug Susceptible Assay for tuberculosis 280

Molecular diagnostics for tuberculosis 280

Combined tuberculin testing and ELISpotPLUS assay 282

Biomarkers for tuberculosis 282

Diagnosis of drug-resistant M. tuberculosis infection 283

Xpert MTB/RIF automated molecular test for MTB 283

Diagnosis of other mycobacteria 284

Chlamydial infections 284

Neisseria gonorrhoeae 286

Bacteria associated with bacterial vaginosis 286

Streptococcal infections 286

Group B Streptococci 286

Streptococcus pyogenes and Streptococcus dysgalactiae 287

Pseudomonas aeruginosa 287

Helicobacter pylori 288

Lyme disease 288

Mycoplasmas 289

Fungal infections 289

Aspergillus 290

Candida species 290

Viral infections 291

HIV/AIDS 291

Diagnosis of HIV 292

Detection of HIV provirus 293

Global Surveillance of HIV-1 genetic variations 293

Genotyping for drug-resistance in HIV 293

Neonatal screening of infants of HIV-positive mothers 294

Phenotyping as predictor of drug susceptibility/resistance in HIV 294

Point-of-care testing for HIV 295

Resolution of indeterminate Western blot 296

Screening of cadaveric tissue donors 296

Tests used for quantification of HIV 296

Conclusions about HIV diagnostics 297

Hepatitis viruses 297

Hepatitis A virus 298

Hepatitis B virus 298

Hepatitis C virus 299

Detection and quantification of HCV RNA 299

Quantification of HCV RNA levels as a guide to antiviral therapy 300

Electrochemical DNA chip for diagnosis of HCV 300

HCV Genotyping as a guide to therapy 300

Enteroviruses 301

Adenoviruses 302

Rhinoviruses 302

Herpes viruses 302

Herpes simplex virus 302

Genital and neonatal herpes simplex 303

Human cytomegalovirus infections 303

Epstein-Barr virus 304

Human papilloma virus 304

Molecular diagnostics for HPV 304

Detection of encephalitis viruses 305

West Nile and St. Louis encephalitis 305

Venezuelan equine encephalitis virus 306

Detection of noroviruses 306

Protozoal infections 306

Amebiasis 306

Cryptosporidium parvum 307

Leishmaniasis 307

Malaria 307

Neurocysticercosis 308

Pneumocystis carinii 308

Toxoplasmosis 308

Infections of various systems 309

CNS infections 309

Molecular diagnosis in bacterial meningitis 309

Molecular diagnosis in herpes simplex encephalitis 309

Diagnosis of transmissible spongiform encephalopathies 310

Molecular diagnosis of respiratory viruses 311

SARS-associated coronavirus 311

Influenza viruses 312

Avian influenza 314

H1N1 influenza 318

Gastrointestinal infections 320

Periodontal infections 321

Diagnosis of urinary infections by a biosensor 322

Role of molecular diagnostics in septicemia 322

Limitations and needs of diagnostics for infections 323

Differentiation between live and antibiotic-killed bacteria 324

Cell-based methods for identifying pathogenic microorganisms 324

Cell-based virus assays 324

Cell-based detection of host response to infection 324

Role of molecular diagnostics in hospital acquired infections 325

Detection of hospital-acquired bacterial infections 325

Detection of methicillin-resistant S. aureus 325

Detection of vancomycin-resistant enterococci 326

Detection of hospital-acquired C. difficile 326

Bacterial genome sequencing in antimicrobial resistance 327

Detection of hospital-acquired viral infections 327

Molecular diagnosis of BK virus 327

Diagnosis of hospital-acquired rotavirus gastroenteritis 328

Molecular diagnostics and the microbiome 328

Human Microbiome Project 328

Application of metagenomics to study of the microbiome 329

MicroBiome Analysis Center 329

Concluding remarks and future prospects of diagnosis of infections 330

Rapid point-of-care diagnosis of infection 330

Diagnosis of viruses using protein fingerprinting 333

QIAplex PCR multiplex technology 333

Companies involved in molecular diagnosis of infectious diseases 333

7. Molecular Diagnosis of Cancer 337

Introduction 337

Cancer genomics 337

Cancer genes 338

Oncogenes 338

Tumor Suppressor Genes 338

p53 339

p16 340

CNVs in cancer 340

Allele-specific copy number analysis of tumors 341

Viruses and cancer 341

Detecting viral agents in cancer 342

Conventional cancer diagnosis 343

Molecular techniques for cancer diagnosis 343

Genome analysis at the molecular level 345

Mutation detection at molecular level 345

Expression profiling of tumor cells sorted by flow cytometry 346

MicroRNA expression profiling for cancer diagnostics 346

Biomarkers in cancer 346

Circulating nucleosomes in serum of cancer patients 347

Detection of DNA methylation 347

eTag assay system for cancer biomarkers 349

HAAH as a biomarker for cancer 350

LigAmp for detection of gene mutations in cancer 350

Mitochondrial DNA as a cancer biomarker 350

Oncoproteins as biomarkers for cancer 351

Sequencing-based approaches for detection of cancer biomarkers 351

Molecular fingerprinting of cancer 352

Fluorescent in situ hybridization 352

Genetic analysis of cancer 353

Comparative genomic hybridization in cancer diagnostics 353

Loss of heterozygosity 353

Digital karyotyping 353

Gene expression profiles predict chromosomal instability in tumors 354

PCR Techniques 354

Realtime quantitative PCR for diagnosis of cancer 355

Cold-PCR 355

Antibody-based diagnosis of cancer 355

Monoclonal antibodies for diagnosis of cancer 355

Recombinant antibodies as a novel approach to cancer diagnosis 356

Combined immunological and nucleic acid tests 356

Combination of MAbs and RT-PCR 356

Immunobead RT-PCR 356

Assays for determining susceptibility to cancer 357

Gene expression profiling in cancer 357

Microarrays for gene expression profiling in cancer 358

Serial analysis of gene expression (SAGE) 358

DNA tags for finding genes expressed in cancer 358

Suppression subtractive hybridization 359

Measurement of telomerase activity 359

Detection of circulating tumor cells in blood 360

Biochips/microfluidics for detection of CTCs 360

CellSearch 361

CellTracks® AutoPrep® System 361

CTCscope system for detection of CTCs 361

CTChip™ 361

Fiber-optic array scanning technology 361

Lab-on-chip for the isolation and detection of CTCs 362

MagSweeper 362

Future prospects of detection of cancer cells in blood 362

Epithelial aggregate separation and isolation 363

Proteomic technologies for the molecular diagnosis of cancer 363

Proteomic technologies for tumor biomarkers 363

Affibodies as contrast agents for imaging in cancer 364

Aptamer-based technology for protein signatures of cancer cells 364

Aptamer probes for in vivo diagnosis of cancer 364

Aptamers for combined diagnosis and therapeutics of cancer 365

Automated image analysis of nuclear protein distribution 365

Laser capture microdissection in oncology 366

Layered expression scanning 366

Membrane-type serine protease-1 366

Survivin and molecular diagnosis of cancer 367

Biochip/microarrays for cancer diagnosis 367

Role of DNA microarrays in gene expression profiling 368

Biochip detection of FHIT gene 368

Nanobiotechnology for e

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CONTACT:
Nicolas Bombourg
Reportlinker
Email: nbo@reportlinker.com
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Article source: http://finance.yahoo.com/news/molecular-diagnostics-technologies-markets-companies-163900421.html

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