Reportlinker Adds Molecular Diagnostics - Technologies, Markets and Companies

NEW YORK, Nov. 9, 2010 /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

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 296 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 92 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 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 296 of these are profiled in the report along with tabulation of 667 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 2009 according to technologies, applications and geographical regions. Forecasts are made up to 2019. 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

Genotype and haplotypes 34

Complex chromosomal rearrangements . 35

Insertions and deletions in the human genome 34

Large scale variation in human genome . 36

Variation in copy number in the human genome . 33

Structural variations in the human genome .. 36

Replication of the DNA helix .. 36

Transposons 37

Proteins .. 37

Proteomics . 38

Monoclonal antibodies 38

Aptamers 38

Basics of molecular diagnostics .. 38

Tracking DNA: the Southern blot 39

Pulsed-field gel electrophoresis 39

DNA Probes 39

The polymerase chain reaction 40

Basic Principles of PCR . 40

Target selection . 40

Detection of amplified DNA . 41

Impact of human genome project on molecular diagnostics . 41

Mapping and sequencing of structural variation from human genomes . 42

1000 Genomes Project .. 42

Human Variome Project .. 43

Role of bioinformatics in molecular diagnostics .. 44

Systems biology approach to molecular diagnostics . 44

Biomarkers 45

Applications of molecular diagnostics .. 45

2. Molecular Diagnostic Technologies . 47

Introduction . 47

DNA sample collection and extraction .. 47

Blood samples .. 47

Buccal swabs and saliva . 47

Urine samples for transrenal DNA .. 48

Manual vs automated DNA extraction 48

Sample preparation .. 49

Pressure Cycling Technology 49

Membrane immobilization of nucleic acids . 49

Automation of sample preparation in molecular diagnostics . 50

ABI PRISM 6700 Automated Nucleic Acid Workstation . 50

BioRobot technology 50

COBAS AmpliPrep System . 50 - 5 -

GENESIS FE500 Workcell .. 50

GeneMole 51

PCR BioCube . 51

QIAsymphony 51

Tigris instrument system .. 51

Techniques for sample preparation that are suitable for automation 52

Xtra Amp Genomic DNA Extraction .. 52

Extraction of DNA from paraffin sections 52

Dynabead technology .. 52

Pressure Cycling Technology . 52

SamPrep .. 53

Use of magnetic particles for automation in genome analysis 53

Companies involved in nucleic acid isolation 54

Novel PCR methods 55

Addressing limitations of PCR .. 55

CAST-PCR .. 55

Combined PCR-ELISA . 55

Digital PCR . 56

Emulsion PCR 56

ExCyto PCR 57

Long and accurate PCR .. 57

Real-time PCR systems .. 57

Dyes used in real-time PCR 58

Commercially available real-time PCR systems 59

LightCycler PCR system .. 59

LightUp probes based on real-time PCR . 60

READ™ real-time PCR method .. 60

ViiA™ 7 real-time PCR system .. 60

Applications of real-time PCR . 60

Limitations of real-time PCR .. 61

Improving the reliability of low level DNA analysis by real-time PCR . 61

Guidelines for real-time quantitative PCR .. 62

Future applications of real-time Q-PCR .. 62

Reverse transcriptase (RT)-PCR .. 62

Standardized reverse transcriptase PCR . 63

Single cell PCR.. 64

LATE-PCR . 64

COLD-PCR 64

AmpliGrid-System . 65

Post-PCR genotyping methods . 65

High-resolution melt analysis 66

Monitoring of gene amplification in molecular diagnostics 66

Non-PCR nucleic acid amplification methods 66

Linked Linear Amplification 66

Multiplex Ligation-Dependent Probe Amplification . 67

Transcription mediated amplification . 67

Rapid analysis of gene expression .. 67

WAVE nucleic acid fragment analysis system .. 68

DNA probes with conjugated minor groove binder . 68

Rolling circle amplification technology 69

Gene-based diagnostics through RCAT 70

RCAT-immunodiagnostics 70

RCAT-pharmacogenomics .. 71

Circle-to-circle amplification .. 71

Ramification amplification method .. 71

Single Primer Isothermal Amplification . 72

Isothermal reaction for amplification of oligonucleotides . 72

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

Technologies for signal amplification 73

3 DNA dendrimer signal amplification 73

Hybridization signal amplification method 74

Signal mediated amplification of RNA technology .. 75

Invader assays . 75

Hybrid Capture technology 77

Branched DNA test .. 77

Tyramide signal amplification .. 78

Non-enzymatic signal amplification technologies 78

Direct molecular analysis without amplification . 79

Trilogy™ Platform 79

Direct detection of dsDNA . 80

Multiplex assays . 80 - 6 -

Fluorescent in situ hybridization . 80

Modifications of FISH .. 82

Direct visual in situ hybridization 82

Direct labeled Satellite FISH probes 83

Comparative genomic hybridization 83

Primed in situ labeling 83

Interphase FISH .. 84

FISH with telomere-specific probes 84

Multicolor FISH . 84

Automation of FISH . 85

Companies involved in FISH diagnostics 85

RNA diagnostics .. 86

Branched-chain DNA assay for measurement of RNA 87

Cycling probe technology .. 87

Invader RNA assays 87

Linear RNA amplification 88

Non-isotopic RNase cleavage assay 88

Nucleic acid sequence-based amplification .. 88

Q Beta replicase system 90

RNAScope .. 90

Solid Phase Transcription Chain Reaction . 91

Transcriptome analysis .. 91

Visualization of mRNA expression in vivo . 91

MicroRNA diagnostics . 92

Real-time PCR for expression profiling of miRNAs 92

Microarray vs quantitative PCR foro measuring miRNAs 92

Use of LNA to explore miRNA . 93

Nuclease Protection Assay to measure miRNA expression . 93

Microarrays for analysis of miRNA gene expression 93

Modification of in situ hybridization for detection of miRNAs 94

Whole genome amplification . 94

Companies that provide technologies for whole genome amplification . 95

QIAGEN's Repli-G system 95

GenomePlex? Whole Genome Amplification . 96

DNA sequencing .. 96

Companies involved in sequencing . 97

Applications of next generation sequencing in molecular diagnostics .. 99

Genome-wide approach for chromatin mapping .. 100

Mitochondrial sequencing 100

Identification of unknown DNA sequences . 100

Optical mapping 101

Gene expression analysis . 101

Gene expression profiling on whole blood samples . 102

Gene expression patterns of white blood cells .. 102

Gene expression profiling based on alternative RNA splicing 103

MAUI (MicroArray User Interface) hybridization .. 103

Monitoring in vivo gene expression by molecular imaging 103

Serial analysis of gene expression (SAGE) . 104

Single-cell gene expression analysis 104

T cell receptor expression analysis .. 105

Tangerine™ expression profiling .. 105

Whole genome expression array .. 105

Ziplex™ system . 106

Companies involved in gene expression analysis . 106

Peptide nucleic acid technology 107

Use of PNA with fluorescence in situ hybridization .. 108

PNA and PCR .. 108

Use of PNA with biosensors 109

PNA-based PD-loop technology . 109

PNA-DNA hybrid quadruplexes .. 110

Companies involved in PNA diagnostics .. 110

Locked nucleic acids .. 110

Zip Nucleic Acids .. 111

Electrochemical detection of DNA 112

Mediated nucleic acid oxidation . 112

Detection of hybridized nucleic acid with cyclic voltametry .. 113

Electrochemical detection based on Toshiba's CMOS technology. 113

Concluding remarks on electrochemical DNA detection . 113

Bead-based assay platforms .. 113

Scorpions™ technology . 114

The Scorpions reaction 114 - 7 -

Applications of Scorpions 115

3. Biochips, Biosensors, and Molecular Labels . 117

Introduction to biochip technology . 117

Applications of biochips in diagnostics . 117

GeneChip . 118

GeneChip Human Genome Arrays . 119

AmpliChip CYP450 .. 119

Electronic detection of nucleic acids on microarrays 119

Microchip capillary electrophoresis .. 120

Strand displacement amplification on a biochip 120

Rolling circle amplification on microarrays . 120

LiquiChip-RCAT 120

Fast PCR biochip 121

Multiplex microarray-enhanced PCR for DNA analysis 121

Multiplexed Molecular Profiling .. 121

Universal DNA microarray combining PCR and ligase detection reaction .. 122

Genomewide association scans . 122

Whole genome chips/microarrays. 123

Transposon insertion site profiling chip .. 123

Standardizing the microarrays .. 124

Companies involved in developing biochip technology for diagnostics .. 124

Future of biochip technology for molecular diagnostics.. 125

Microfluidic chips . 126

Fish-on-chip 126

Lab-on-a-chip . 126

LabCD .. 127

Micronics' microfluidic technology. 127

Microfluidic chips/arrays using PCR . 127

Microfluidic automated DNA analysis using PCR 127

Digital PCR Array 127

Digital PCR on a SlipChip . 128

Microfluidic chips integrated with RCAT .. 128

Microfluidic chips integrated with PET . 128

Companies developing microfluidic technologies . 129

Biosensor technologies . 129

Classification of biosensor technologies .. 130

DNA-based biosensors . 131

DNA hybridization biosensor chips . 131

PCR-free DNA biosensor 131

DNA based biosensor to detects metallic ions 132

Genetically engineered B lymphocytes 132

Biosensors immunoassays .. 132

PNA (peptide nucleic acid)-based biosensors 133

Protein-based biosensors 133

Antibody biosensors . 133

Cell-based biosensors (cytosensors) 133

Multicell biosensors 134

Microbial biosensors .. 134

Optical biosensors . 135

Surface plasmon resonance technology 135

Label-free optical biosensor . 136

Microsensors using with nano/microelectronic communications technology . 136

Electrochemical sensors .. 136

Enzyme electrodes for biosensing . 136

Conductometric sensors 137

Electrochemical genosensors .. 137

Electrochemical nanobiosensor .. 137

Bioelectronic sensors 138

Phototransistor biochip biosensor . 138

Ribozyme-based sensors . 138

RiboReporters .. 139

Concluding remarks and future prospects of biosensor technology 139

Companies developing biosensors for molecular diagnostics 140

Molecular labels and detection.. 141

Detection technologies for molecular labels .. 142

Fluorescence and chemiluminescence . 142

Fluorescence technologies for label detection . 143

Companies with fluorescence and chemiluminescence products .. 143

Molecular beacons . 144

The Green fluorescent protein .. 145 - 8 -

Multiophoton detection radioimmunoassay 146

Multi-pixel photon counter . 146

Enzyme labels and detection by fluorescence .. 146

Phase-sensitive flow cytometry . 147

Microtransponder-based DNA diagnostics .. 147

Laboratory Multiple Analyte Profile .. 148

Multiple labels 148

Protein-DNA chimeras for detection of small numbers of molecules .. 149

Single molecule detection 149

Atomic force microscopy . 150

Capillary electrophoresis . 150

Confocal laser scanning .. 150

Spectrally resolved fluorescence lifetime imaging microscopy . 150

Molecular imaging .. 151

Basic research in molecular imaging 151

Devices for molecular imaging .. 152

Molecular imaging in clinical practice .. 152

Challenges and future prospects of molecular imaging .. 152

Companies involved in molecular imaging . 152

Nanobiotechnology for molecular diagnostics 153

Magnetic nanoparticles 154

Gold nanoparticles 154

Quantum dot technology . 155

Nanotechnology on a chip .. 156

Nanogen's NanoChip 157

Fullerene photodetectors for chemiluminescence detection on microfluidic chip . 157

Diagnostics based on nanopore technology .. 157

Nanosensors .. 157

Detection of cocaine molecules by nanoparticle-labeled aptasensors .. 158

Nanosensors for glucose monitoring . 158

PEBBLE nanosensors . 158

Quartz nanobalance biosensor 159

Cantilever arrays .. 159

Resonance Light Scattering technology .. 159

DNA nanomachines for molecular diagnostics .. 160

Nanobarcodes technology for molecular diagnostics .. 160

Qdot nanobarcode for multiplexed gene expression profiling .. 161

Role of nanobiotechnology in improving molecular diagnostics 161

Companies involved in nanomolecular diagnostics .. 162

Concluding remarks about nanodiagnostics .. 164

Future prospects of nanodiagnostics 165

4. Proteomic Technologies for Molecular Diagnostics .. 167

Introduction .. 167

Proteomic technologies 167

Biomarkers of disease . 167

Proteomic tools for biomarkers .. 167

Search for biomarkers in body fluids. 168

Captamers with proximity extension assay for proteins . 168

Cyclical amplification of proteins .. 168

Detection of misfolded proteins by ELISA with exponential signal amplification . 169

Diagnostics based on designed repeat proteins 169

Differential Peptide Display 169

Light-switching excimer probes . 170

MALDI-TOF MS .. 170

Molecular beacon aptamer . 171

Molecular beacon assay .. 171

Proteomic patterns 172

Real-time PCR for protein quantification . 172

Protein biochip technologies .. 173

ProteinChip . 174

LabChip for protein analysis .. 174

TRINECTIN proteome chip .. 175

Protein chips for antigen-antibody interactions molecular diagnostics .. 175

Microfluidic devices for proteomics-based diagnostics 175

Nanotechnology-based protein biochips/microarrays . 176

Nanoparticle protein chip . 176

Protein nanobiochip 176

Protein biochips based on fluorescence planar wave guide technology .. 176

New developments in protein chips/microarrays . 177

Antibody microarrays 177 - 9 -

Aptamer-based protein biochip .. 178

Multiplexed Protein Profiling on Microarrays 178

Proteomic pattern analysis .. 178

Single molecule array 179

Viral protein chip 179

Commercial development of protein chips for molecular diagnostics . 179

Proteome Identification Kit . 181

Laser capture microdissection (LCM) . 181

LCM technology . 181

Applications of LCM in molecular diagnostics 182

Proteomic diagnosis of CNS disorders 182

Cerebrospinal fluids tests based on proteomics 182

Urine tests for CNS disorders based on proteins in urine .. 183

Diagnosis of CNS disorders by examination of proteins in the blood.. 183

Diagnosis of CNS disorders by examination of proteins in tears .. 184

Role of proteomics in the diagnosis of Alzheimer's disease .. 184

Role of proteomics in the diagnosis of Creutzfeldt-Jakob disease 185

Future prospects of use of proteomics for diagnosis of CNS disorders .. 185

Concluding remarks on the use of proteomics in diagnostics . 185

5. Molecular Diagnosis of Genetic Disorders . 187

Introduction .. 187

Cytogenetics .. 188

FISH with probes to the telomeres .. 188

Single copy FISH probes . 188

Comparative genomic hybridization . 189

Use of biochips in genetic disorders 189

Representational oligonucleotide microarray analysis . 190

SignatureChip®-based diagnostics for cytogenetic abnormalities 190

Diagnosis of genomic rearrangements by multiplex PCR . 190

Quantitative fluorescent PCR . 190

Mutation detection technologies .. 191

PCR-based methods for mutation detection .. 192

Cleavase Fragment Length Polymorphism .. 192

Direct dideoxy DNA sequencing . 192

Digital Genetic Analysis (DGA) 192

Fluorescence-based directed termination PCR 193

Heteroduplex analysis .. 193

Restriction fragment length polymorphism . 194

Single-stranded conformation polymorphism (SSCP) analysis .. 194

TaqMan real-time PCR .. 195

Non-PCR methods for mutation detection .. 195

Arrayed primer extension . 195

BEAMing (beads, emulsion, amplification, and magnetics) . 195

ELISA-protein truncation test . 196

Enzymatic mutation detection . 196

Specific anchor nucleotide incorporation . 196

Conversion analysis for mutation detection 197

Biochip technologies for mutation detection .. 197

Combination of FISH and gene chips 197

Haplotype Specific Extraction . 198

Technologies for SNP analysis .. 198

DNA sequencing 199

Electrochemical DNA probes .. 200

Use of NanoChip for detection of SNPs . 200

Single base extension-tag array 200

Laboratory Multiple Analyte Profile .. 200

SNP genotyping with gold nanoparticle probes . 201

PCR-CTPP (confronting two-pair primers) .. 201

Peptide nucleic acid probes for SNP detection .. 201

SNP genotyping on a genome-wide amplified DOP-PCR template .. 202

Pyrosequencing . 202

Reversed enzyme activity DNA interrogation test 203

Smart amplification process version 2 203

Zinc finger proteins .. 204

UCAN method (Takara Biomedical) .. 204

Biochip and microarray-based detection of SNPs . 204

SNP genotyping by MassARRAY 204

Electronic dot blot assay . 204

Biochip combining BeadArray and ZipCode technologies .. 205

SNP-IT primer-extension technology .. 205 - 10 -

OmniScan SNP genotyping . 206

Affymetrix SNP genotyping array . 206

Concluding remarks on SNP genotyping . 206

Limitations of SNP in genetic testing 206

Haplotyping versus SNP genotyping 207

Companies involved in developing technologies/products for SNP analysis . 207

Role of copy number variations in genetic diagnostic testing 208

CNVs in various diseases 209

CNVs in genetic epilepsy syndromes . 209

CNVs associated with schizophrenia . 209

CNVs associated with autism .. 209

Methods for determination of CNVs . 210

Digital array for CNV detection .. 210

Wellcome Trust Case Control Consortium CNV typing array .. 211

CNVer algorithm for CNV detection 211

Study of rare variants in pinpointing disease-causing genes 211

Prenatal DNA diagnosis 212

Amniocentesis 212

Chorionic villus sampling . 212

Separating fetal cells in maternal blood for genetic diagnosis . 213

Antenatal screening for Down's syndrome . 213

Fetal DNA in maternal blood .. 213

Molecular methods for prenatal diagnosis .. 214

aCGH for prenatal diagnosis 214

BAC HD Scan test .. 214

FISH for prenatal diagnosis . 215

PCR for prenatal diagnosis .. 215

Plasma DNA sequencing to detect fetal chromosomal aneuploidies . 215

In vivo gene expression analysis of the living human fetus .. 216

Noninvasive prenatal diagnosis of monogenic diseases . 216

Digital relative mutation dosage . 216

Massively parallel plasma DNA sequencing . 217

Applications of prenatal diagnosis 217

Diagnosis of congenital infections . 218

Diagnosis of eclampsia 218

Use of transrenal DNA for prenatal testing 219

Preimplantation genetic diagnosis .. 219

Technologies for preimplantation genetic diagnosis (PGD) 219

PCR for preimplantation genetic diagnosis .. 219

FISH for preimplantation genetic diagnosis . 220

Microarrays for preimplantation genetic diagnosis 220

Conditions detected by preimplantation genetic diagnosis 221

The future of preimplantation genetic diagnosis .. 221

Companies involved in prenatal/preimplantation diagnosis .. 222

Cystic fibrosis 223

Detection of CFTR gene mutations .. 223

CFTR technologies of various companies 223

Genzyme's CF gene sequencing . 224

CF Plus? Tag-It Cystic Fibrosis Kit 225

Asuragen's bead array test .. 225

The Ambry CF Test . 225

Biochip for CF diagnosis 226

Identification of CF variants by PCR/Oligonucleotide Ligation Assay 226

SensiGene (SEQUENOM) CF carrier screening test 226

Serum proteomic signature for CF using antibody microarrays . 227

Guidelines for genetic screening for CF .. 227

Congenital adrenal hyperplasia . 227

Primary immunodeficiencies .. 228

Hematological disorders .. 229

Hemoglobinopathies . 229

Sickle cell anemia .. 229

Thalassemia . 229

Paroxysmal nocturnal hemoglobinuria.. 230

Hemophilia .. 230

Hereditary hemochromatosis . 230

Polycystic kidney disease 231

Hereditary metabolic disorders . 231

Lesch-Nyhan Syndrome .. 231

Gaucher's Disease . 232

Acute Intermittent Porphyria . 232

Phenylketonuria . 232 - 11 -

Hereditary periodic fever. 233

Achondroplasia . 233

Molecular diagnosis of cardiovascular disorders .. 233

Coronary Heart Disease .. 234

Cardiomyopathy 235

Familial Hypertrophic Cardiomyopathy . 235

Idiopathic dilated cardiomyopathy . 235

Cardiac Arrhythmias . 235

Long Q-T Syndrome .. 235

Familial atrial fibrillation 236

Idiopathic ventricular fibrillation . 236

Congestive heart failure .. 236

Hypertension .. 237

Disturbances of blood lipids 237

Familial dyslipoproteinemias 237

Hypercholesterolemia 237

Thrombotic disorders 238

Factor V Leiden mutation . 238

Pulmonary embolism . 239

Molecular diagnosis of eye diseases .. 239

Molecular diagnosis of retinitis pigmentosa 239

Genetic screening for glaucoma 240

Role of molecular diagnostics in rheumatoid arthritis 240

Molecular diagnosis of neurogenetic disorders . 241

Alzheimer's disease .. 242

Charcot-Marie Tooth disease . 242

Down syndrome . 243

Duchenne and Becker muscular dystrophy 243

eNOS gene polymorphisms as predictor of cerebral aneurysm rupture . 244

Fragile X syndrome .. 245

Huntington disease .. 245

Hereditary neuropathy with liability to pressure palsies . 246

Mitochondrial disorders affecting the nervous system 246

Parkinson's disease .. 246

Pompe's disease 247

Spinal muscular atrophy . 248

Triple repeat disorders . 248

Genetic testing for disease predisposition .. 248

Direct-to-consumer genetic tests . 249

6. Molecular Diagnosis of Infections . 251

Introduction .. 251

Molecular techniques for the diagnosis of infections . 251

Antibody-enhanced microplate hybridization assays .. 252

Bacteriophage-based methods for detection of bacteria 252

Biosensors for detection of microorganisms .. 253

Ibis T5000™ Biosensor System .. 253

DNA enzyme immunoassay 253

DNA biochip/microarray in diagnosis of infections .. 253

DNA-based typing methods 254

Restriction fragment length polymorphism analysis . 254

Ribotyping 255

Random amplified polymorphic DNA . 255

Combinatorial DNA melting assay.. 255

Electrochemical detection of pathogens . 255

High resolution melt analysis for diagnosis of infections 256

Ligase chain reaction 256

Mass spectrometry for microbial identification . 256

Metagenomic pyrosequencing 256

Multiplex PCR for detection of infections . 258

Dual priming oligonucleotide for multiplex PCR . 258

LightCycler® SeptiFast Test 258

Multiplex amplified nominal tandem repeat analysis 259

VYOO® Sepsis Test 259

NASBA for detection of microorganisms . 259

Nucleic acid probes .. 260

Neutrophil CD11b expression as a diagnostic marker . 260

Optical Mapping . 260

PNA-FISH for diagnosis of infections 260

Quantitative reverse-transcription PCR for bacterial diagnostics . 261

Rupture event scanning .. 261 - 12 -

Real-time single-molecule imaging of virus particles . 261

Single-strand conformational polymorphism . 262

SmartGene platform for identifying pathogens based on genetic sequences .. 262

Tessera array technology 262

Applications, advantages and limitations of molecular diagnostics . 262

Molecular diagnostics versus other microbial detection technologies . 262

Advantages of nucleic acid-based diagnostics in infections .. 263

Drawbacks of nucleic acid-based diagnostics in infections 263

Nanotechnology for detection of infectious agents .. 264

Bacterial and fungal infections . 264

Mycobacterium tuberculosis .. 266

Conventional diagnosis of tuberculosis . 266

Microscopic Observation Drug Susceptible Assay for tuberculosis 266

Molecular diagnostics for tuberculosis .. 267

Combined tuberculin testing and ELISpotPLUS assay .. 268

Biomarkers for tuberculosis . 269

Diagnosis of drug-resistant M. tuberculosis infection 269

Xpert MTB/RIF automated molecular test for MTB 270

Diagnosis of other mycobacteria 270

Chlamydial infections 271

Neisseria gonorrhoeae . 272

Bacteria associated with bacterial vaginosis .. 273

Streptococcal infections .. 273

Group B Streptococci . 273

Streptococcus pyogenes and Streptococcus dysgalactiae .. 273

Pseudomonas aeruginosa 274

Helicobacter pylori 274

Lyme disease . 274

Mycoplasmas .. 275

Fungal infections 276

Aspergillus 276

Candida species .. 276

Viral infections .. 277

HIV/AIDS . 278

Diagnosis of HIV . 278

Neonatal screening of infants of HIV-positive mothers 279

Screening of cadaveric tissue donors 279

Detection of HIV provirus . 279

Resolution of indeterminate Western blot 279

Global Surveillance of HIV-1 genetic variations . 280

Genotyping for drug-resistance in HIV . 280

Phenotyping as predictor of drug susceptibility/resistance in HIV 281

Tests used for quantification of HIV .. 282

Conclusions about HIV genotyping 282

Hepatitis viruses 283

Hepatitis A virus . 283

Hepatitis B virus . 284

Hepatitis C virus . 284

Detection and quantification of HCV RNA. 285

Quantification of HCV RNA levels as a guide to antiviral therapy . 286

Electrochemical DNA chip for diagnosis of HCV . 286

HCV Genotyping as a guide to therapy . 286

Enteroviruses . 287

Adenoviruses .. 288

Rhinoviruses .. 288

Herpes viruses 288

Herpes simplex virus . 288

Genital and neonatal herpes simplex 289

Human cytomegalovirus infections 289

Epstein-Barr virus .. 289

Human papilloma virus 290

Molecular diagnostics for HPV . 290

Detection of encephalitis viruses .. 291

West Nile and St. Louis encephalitis . 291

Venezuelan equine encephalitis virus 292

Protozoal infections 292

Amebiasis 292

Cryptosporidium parvum. 292

Malaria . 292

Neurocysticercosis 293

Pneumocystis carinii . 293 - 13 -

Toxoplasmosis 294

Infections of various systems 294

CNS infections 294

Molecular diagnosis in bacterial meningitis . 294

Molecular diagnosis in herpes simplex encephalitis .. 294

Diagnosis of transmissible spongiform encephalopathies 295

Molecular diagnosis of respiratory viruses . 296

SARS-associated coronavirus .. 296

Influenza viruses 298

Avian influenza 299

H1N1 influenza 303

Gastrointestinal infections .. 305

Periodontal infections .. 306

Diagnosis of urinary infections by a biosensor .. 307

Role of molecular diagnostics in septicemia .. 307

Limitations and needs of diagnostics for infections 308

Differentiation between live and antibiotic-killed bacteria . 309

Cell-based methods for identifying pathogenic microorganisms .. 309

Cell-based virus assays . 309

Cell-based detection of host response to infection 309

Role of molecular diagnostics in hospital acquired infections 310

Detection of hospital-acquired bacterial infections .. 310

Detection of methicillin-resistant S. aureus 310

Detection of vancomycin-resistant enterococci .. 311

Detection of hospital-acquired C. difficile. 311

Bacterial genome sequencing in antimicrobial resistance 312

Detection of hospital-acquired viral infections .. 312

Molecular diagnosis of BK virus .. 312

Diagnosis of hospital-acquired rotavirus gastroenteritis.. 313

Molecular diagnostics and the microbiome . 313

Human Microbiome Project . 313

Application of metagenomics to study of the microbiome . 314

MicroBiome Analysis Center .. 314

Concluding remarks and future prospects of diagnosis of infections . 315

Rapid point-of-care diagnosis of infection .. 315

Diagnosis of viruses using protein fingerprinting . 317

QIAplex PCR multiplex technology 318

Companies involved in molecular diagnosis of infectious diseases . 318

7. Molecular Diagnosis of Cancer 321

Introduction .. 321

Cancer genomics .. 321

Cancer genes . 322

Oncogenes .. 322

Tumor Suppressor Genes 322

p53 . 323

p16 . 324

CNVs in cancer .. 324

Allele-specific copy number analysis of tumors . 325

Viruses and cancer 325

Detecting viral agents in cancer . 326

Conventional cancer diagnosis .. 327

Molecular techniques for cancer diagnosis.. 327

Genome analysis at the molecular level . 329

Mutation detection at molecular level . 329

Expression profiling of tumor cells sorted by flow cytometry 330

MicroRNA expression profiling for cancer diagnostics . 330

Biomarkers in cancer 330

Circulating nucleosomes in serum of cancer patients .. 331

Detection of DNA methylation . 331

eTag assay system for cancer biomarkers .. 333

HAAH as a biomarker for cancer 334

LigAmp for detection of gene mutations in cancer 334

Mitochondrial DNA as a cancer biomarker 334

Oncoproteins as biomarkers for cancer 335

Sequencing-based approaches for detection of cancer biomarkers .. 335

Molecular fingerprinting of cancer 336

Fluorescent in situ hybridization 336

Genetic analysis of cancer .. 337

Comparative genomic hybridization in cancer diagnostics .. 337

Loss of heterozygosity .. 337 - 14 -

Digital karyotyping . 338

Gene expression profiles predict chromosomal instability in tumors 338

PCR Techniques . 338

Realtime quantitative PCR for diagnosis of cancer 339

Cold-PCR .. 339

Antibody-based diagnosis of cancer . 339

Monoclonal antibodies for diagnosis of cancer 339

Recombinant antibodies as a novel approach to cancer diagnosis 340

Combined immunological and nucleic acid tests .. 340

Combination of MAbs and RT-PCR . 340

Immunobead RT-PCR 340

Assays for determining susceptibility to cancer 341

Gene expression profiling in cancer . 341

Microarrays for gene expression profiling in cancer.. 342

Serial analysis of gene expression (SAGE) .. 342

DNA tags for finding genes expressed in cancer 342

Suppression subtractive hybridization .. 343

Measurement of telomerase activity 343

Detection of circulating tumor cells in blood . 344

Biochips/microfluidics for detection of CTCs 344

CellTracks® AutoPrep® System 345

CTCscope system for detection of CTCs .. 345

Fiber-optic array scanning technology .. 345

MagSweeper 346

Future prospects of detection of cancer cells in blood . 346

Epithelial aggregate separation and isolation 346

Proteomic technologies for the molecular diagnosis of cancer . 346

Proteomic technologies for tumor biomarkers 347

Affibodies as contrast agents for imaging in cancer . 347

Aptamer-based technology for protein signatures of cancer cells . 347

Aptamers for combined diagnosis and therapeutics of cancer 348

Automated image analysis of nuclear protein distribution .. 348

Laser capture microdissection in oncology .. 349

Layered expression scanning .. 349

Membrane-type serine protease-1 . 350

Survivin and molecular diagnosis of cancer 350

Biochip/microarrays for cancer diagnosis .. 350

Role of DNA microarrays in gene expression profiling . 351

Biochip detection of FHIT gene .. 351

Nanobiotechnology for early detection of cancer . 352

Detection of nanoparticle self assembly in tumors by MRI . 3

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