Reportlinker Adds Molecular Diagnostics - Technologies, Markets and Companies

Jun 03, 2010, 12:20 ET from Reportlinker

NEW YORK, June 3 /PRNewswire/ -- announces that a new market research report is available in its catalogue:

Molecular Diagnostics - Technologies, Markets and Companies

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 291 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.


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 291 of these are profiled in the report along with tabulation of 648 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.


0. Executive Summary 21

1. Introduction 23

Definitions and scope of the subject 23

Historical evolution of molecular diagnostics 23

Molecular biology relevant to molecular diagnostics 24

DNA 24

DNA polymerases 24

Restriction endonucleases 25

DNA methylation 25

RNA 26

RNA polymerases 26

Non-coding RNAs 26

DNA transcription 27

Chromosomes 27

Telomeres 28

Mitochondrial DNA 28

Genes 29

The genetic code 29

Gene expression 29

The human genome 30

Variations in the human genome 30

Variations in DNA sequences 30

Single nucleotide polymorphisms 31

Genotype and haplotypes 31

Complex chromosomal rearrangements 31

Insertions and deletions in the human genome 31

Large scale variation in human genome 32

Variation in copy number in the human genome 33

Structural variations in the human genome 34

Replication of the DNA helix 34

Proteins 35

Proteomics 35

Monoclonal antibodies 36

Aptamers 36

Basics of molecular diagnostics 36

Tracking DNA: the Southern blot 36

Pulsed-field gel electrophoresis 37

DNA Probes 37

The polymerase chain reaction 38

Basic Principles of PCR 38

Target selection 38

Detection of amplified DNA 38

Impact of human genome project on molecular diagnostics 39

Mapping and sequencing of structural variation from human genomes 39

1000 Genomes Project 40

Human Variome Project 41

Systems biology approach to molecular diagnostics 41

Biomarkers 42

Applications of molecular diagnostics 42

2. Molecular Diagnostic Technologies 45

Introduction 45

DNA extraction 45

Transrenal DNA 45

Sample preparation 46

Pressure Cycling Technology 46

Membrane immobilization of nucleic acids 46

Automation of sample preparation in molecular diagnostics 47

ABI PRISM 6700 Automated Nucleic Acid Workstation 47

BioRobot technology 47

COBAS AmpliPrep System 47

GENESIS FE500 Workcell 47

GeneMole 48

PCR BioCube 48

QIAsymphony 48

Tigris instrument system 48

Techniques for sample preparation that are suitable for automation 49

Xtra Amp Genomic DNA Extraction 49

Extraction of DNA from paraffin sections 49

Dynabead technology 49

Pressure Cycling Technology 50

SamPrep 50

Use of magnetic particles for automation in genome analysis 50

Companies involved in nucleic acid isolation 51

Novel PCR methods 52

Addressing limitations of PCR 52

Real-time PCR systems 52

Dyes used in real-time PCR 53

Commercially available real-time PCR systems 54

LightCycler PCR system 54

LightUp probes based on real-time PCR 55

READ™ real-time PCR 55

Applications of real-time PCR 55

Limitations of real-time PCR 56

Improving the reliability of low level DNA analysis by real-time PCR 56

Guidelines for real-time quantitative PCR 56

Future applications of real-time Q-PCR 57

Reverse transcriptase (RT)-PCR 57

Standardized reverse transcriptase PCR 58

Single cell PCR 58



AmpliGrid-System 60

Digital PCR 60

Emulsion PCR 61

Long and accurate PCR 61

Combined PCR-ELISA 61

Monitoring of gene amplification in molecular diagnostics 62

Non-PCR nucleic acid amplification methods 62

Linked Linear Amplification 62

Multiplex Ligation-Dependent Probe Amplification 63

Transcription mediated amplification 63

Rapid analysis of gene expression 63

WAVE nucleic acid fragment analysis system 63

DNA probes with conjugated minor groove binder 64

Rolling circle amplification technology 64

Gene-based diagnostics through RCAT 66

RCAT-immunodiagnostics 66

RCAT-pharmacogenomics 67

Circle-to-circle amplification 67

Ramification amplification method 67

Single Primer Isothermal Amplification 68

Isothermal reaction for amplification of oligonucleotides 68

ICAN (Isothermal and Chimeric primer-initiated Amplification of Nucleic Acids) 68

Technologies for signal amplification 69

3 DNA dendrimer signal amplification 69

Hybridization signal amplification method 70

Signal mediated amplification of RNA technology 71

Invader assays 71

Hybrid Capture technology 72

Branched DNA test 73

Tyramide signal amplification 74

Non-enzymatic signal amplification technologies 74

Direct molecular analysis without amplification 75

Trilogy™ Platform 75

Direct detection of dsDNA 76

Multiplex assays 76

Fluorescent in situ hybridization 76

Modifications of FISH 78

Direct visual in situ hybridization 78

Direct labeled Satellite FISH probes 79

Comparative genomic hybridization 79

Primed in situ labeling 79

Interphase FISH 80

FISH with telomere-specific probes 80

Multicolor FISH 80

Automation of FISH 81

Companies involved in FISH diagnostics 81

RNA diagnostics 82

Branched-chain DNA assay for measurement of RNA 83

Cycling probe technology 84

Invader RNA assays 84

Linear RNA amplification 84

Non-isotopic RNase cleavage assay 85

Nucleic acid sequence-based amplification 85

Q Beta replicase system 87

Solid Phase Transcription Chain Reaction 87

Transcriptome analysis 87

Visualization of mRNA expression in vivo 88

MicroRNA diagnostics 88

Real-time PCR for expression profiling of miRNAs 88

Microarray vs quantitative PCR foro measuring miRNAs 89

Use of LNA to explore miRNA 89

Nuclease Protection Assay to measure miRNA expression 90

Microarrays for analysis of miRNA gene expression 90

Modification of in situ hybridization for detection of miRNAs 91

Whole genome amplification 91

Companies that provide technologies for whole genome amplification 91

QIAGEN's Repli-G system 92

GenomePlex? Whole Genome Amplification 92

DNA sequencing 93

Companies involved in sequencing 94

Applications of next generation sequencing in molecular diagnostics 95

Genome-wide approach for chromatin mapping 95

Mitochondrial sequencing 96

Identification of unknown DNA sequences 96

Optical mapping 96

Gene expression analysis 97

Gene expression profiling on whole blood samples 98

Gene expression patterns of white blood cells 98

Gene expression profiling based on alternative RNA splicing 99

MAUI (MicroArray User Interface) hybridization 99

Monitoring in vivo gene expression by molecular imaging 99

Serial analysis of gene expression (SAGE) 100

Single-cell gene expression analysis 100

T cell receptor expression analysis 100

Tangerine™ expression profiling 101

Whole genome expression array 101

Ziplex™ system 102

Companies involved in gene expression analysis 102

Peptide nucleic acid technology 103

Use of PNA with fluorescence in situ hybridization 103

PNA and PCR 104

Use of PNA with biosensors 105

PNA-based PD-loop technology 105

PNA-DNA hybrid quadruplexes 105

Companies involved in PNA diagnostics 106

Locked nucleic acids 106

Zip Nucleic Acids 107

Electrochemical detection of DNA 107

Mediated nucleic acid oxidation 108

Detection of hybridized nucleic acid with cyclic voltametry 108

Electrochemical detection based on Toshiba's CMOS technology 109

Concluding remarks on electrochemical DNA detection 109

Bead-based assay platforms 109

Scorpions™ technology 110

The Scorpions reaction 110

Applications of Scorpions 111

3. Biochips, Biosensors, and Molecular Labels 113

Introduction to biochip technology 113

Applications of biochips in diagnostics 113

GeneChip 114

GeneChip Human Genome Arrays 115

AmpliChip CYP450 115

Electronic detection of nucleic acids on microarrays 115

Microchip capillary electrophoresis 116

Strand displacement amplification on a biochip 116

Rolling circle amplification on microarrays 116

LiquiChip-RCAT 116

Fast PCR biochip 117

Multiplex microarray-enhanced PCR for DNA analysis 117

Multiplexed Molecular Profiling 117

Universal DNA microarray combining PCR and ligase detection reaction 118

Genomewide association scans 118

Whole genome chips/microarrays 119

Transposon insertion site profiling chip 119

Standardizing the microarrays 120

Companies involved in developing biochip technology for diagnostics 120

Future of biochip technology for molecular diagnostics 121

Microfluidic chips 122

Fish-on-chip 122

Lab-on-a-chip 122

LabCD 123

Micronics' microfluidic technology 123

Microfluidic automated DNA analysis using PCR 123

Microfluidic chips integrated with RCAT 123

Microfluidic chips integrated with PET 124

Companies developing microfluidic technologies 124

Biosensor technologies 125

Classification of biosensor technologies 126

DNA-based biosensors 126

DNA hybridization biosensor chips 127

PCR-free DNA biosensor 127

DNA based biosensor to detects metallic ions 127

Genetically engineered B lymphocytes 127

Biosensors immunoassays 128

PNA (peptide nucleic acid)-based biosensors 128

Protein-based biosensors 128

Antibody biosensors 128

Cell-based biosensors (cytosensors) 129

Multicell biosensors 129

Microbial biosensors 130

Optical biosensors 130

Surface plasmon resonance technology 130

Label-free optical biosensor 131

Microsensors using with nano/microelectronic communications technology 131

Electrochemical sensors 132

Enzyme electrodes for biosensing 132

Conductometric sensors 132

Electrochemical genosensors 132

Electrochemical nanobiosensor 133

Bioelectronic sensors 133

Phototransistor biochip biosensor 134

Ribozyme-based sensors 134

RiboReporters 134

Concluding remarks and future prospects of biosensor technology 135

Companies developing biosensors for molecular diagnostics 136

Molecular labels and detection 137

Detection technologies for molecular labels 137

Fluorescence and chemiluminescence 138

Fluorescence technologies for label detection 138

Companies with fluorescence and chemiluminescence products 139

Molecular beacons 140

The Green fluorescent protein 141

Multiophoton detection radioimmunoassay 141

Multi-pixel photon counter 142

Enzyme labels and detection by fluorescence 142

Phase-sensitive flow cytometry 142

Microtransponder-based DNA diagnostics 143

Laboratory Multiple Analyte Profile 144

Multiple labels 144

Protein-DNA chimeras for detection of small numbers of molecules 145

Single molecule detection 145

Atomic force microscopy 145

Capillary electrophoresis 145

Confocal laser scanning 145

Spectrally resolved fluorescence lifetime imaging microscopy 146

Molecular imaging 146

Basic research in molecular imaging 147

Devices for molecular imaging 147

Molecular imaging in clinical practice 147

Challenges and future prospects of molecular imaging 148

Companies involved in molecular imaging 148

Nanobiotechnology for molecular diagnostics 148

Magnetic nanoparticles 149

Gold nanoparticles 150

Quantum dot technology 150

Nanotechnology on a chip 152

Nanogen's NanoChip 152

Fullerene photodetectors for chemiluminescence detection on microfluidic chip 152

Diagnostics based on nanopore technology 153

Nanosensors 153

Detection of cocaine molecules by nanoparticle-labeled aptasensors 153

Nanosensors for glucose monitoring 154

PEBBLE nanosensors 154

Quartz nanobalance biosensor 154

Cantilever arrays 154

Resonance Light Scattering technology 155

DNA nanomachines for molecular diagnostics 156

Nanobarcodes technology for molecular diagnostics 156

Qdot nanobarcode for multiplexed gene expression profiling 156

Role of nanobiotechnology in improving molecular diagnostics 157

Companies involved in nanomolecular diagnostics 157

Concluding remarks about nanodiagnostics 160

Future prospects of nanodiagnostics 160

4. Proteomic Technologies for Molecular Diagnostics 163

Introduction 163

Proteomic technologies 163

Biomarkers of disease 163

Proteomic tools for biomarkers 163

Search for biomarkers in body fluids 164

Captamers with proximity extension assay for proteins 164

Cyclical amplification of proteins 164

Detection of misfolded proteins by ELISA with exponential signal amplification 165

Diagnostics based on designed repeat proteins 165

Differential Peptide Display 165

Light-switching excimer probes 166

MALDI-TOF Mass Spectrometry 166

Molecular beacon aptamer 167

Molecular beacon assay 167

Proteomic patterns 167

Real-time PCR for protein quantification 169

Protein biochip technologies 169

ProteinChip 170

LabChip for protein analysis 171

TRINECTIN proteome chip 171

Protein chips for antigen-antibody interactions molecular diagnostics 171

Microfluidic devices for proteomics-based diagnostics 172

Nanotechnology-based protein biochips/microarrays 172

Nanoparticle protein chip 172

Protein nanobiochip 172

Protein biochips based on fluorescence planar wave guide technology 173

New developments in protein chips/microarrays 173

Antibody microarrays 174

Aptamer-based protein biochip 174

Multiplexed Protein Profiling on Microarrays 174

Proteomic pattern analysis 175

Single molecule array 175

Viral protein chip 175

Commercial development of protein chips for molecular diagnostics 176

Proteome Identification Kit 177

Laser capture microdissection (LCM) 177

LCM technology 177

Applications of LCM in molecular diagnostics 178

Proteomic diagnosis of CNS disorders 178

Cerebrospinal fluids tests based on proteomics 178

Urine tests for CNS disorders based on proteins in urine 179

Diagnosis of CNS disorders by examination of proteins in the blood 179

Diagnosis of CNS disorders by examination of proteins in tears 180

Role of proteomics in the diagnosis of Alzheimer's disease 181

Role of proteomics in the diagnosis of Creutzfeldt-Jakob disease 181

Future prospects of use of proteomics for diagnosis of CNS disorders 181

Concluding remarks on the use of proteomics in diagnostics 181

5. Molecular Diagnosis of Genetic Disorders 183

Introduction 183

Cytogenetics 184

FISH with probes to the telomeres 184

Single copy FISH probes 184

Comparative genomic hybridization 185

Use of biochips in genetic disorders 185

Representational oligonucleotide microarray analysis 186

SignatureChip®-based diagnostics for cytogenetic abnormalities 186

Diagnosis of genomic rearrangements by multiplex PCR 186

Quantitative fluorescent PCR 186

Mutation detection technologies 187

PCR-based methods for mutation detection 188

Cleavase Fragment Length Polymorphism 188

Direct dideoxy DNA sequencing 188

Digital Genetic Analysis (DGA) 188

Fluorescence-based directed termination PCR 189

Heteroduplex analysis 189

Restriction fragment length polymorphism 190

Single-stranded conformation polymorphism (SSCP) analysis 190

TaqMan real-time PCR 191

Non-PCR methods for mutation detection 191

Arrayed primer extension 191

BEAMing (beads, emulsion, amplification, and magnetics) 191

ELISA-protein truncation test 192

Enzymatic mutation detection 192

Specific anchor nucleotide incorporation 192

Conversion analysis for mutation detection 193

Biochip technologies for mutation detection 193

Combination of FISH and gene chips 193

Haplotype Specific Extraction 194

Technologies for SNP analysis 194

DNA sequencing 195

Electrochemical DNA probes 196

Use of NanoChip for detection of SNPs 196

Single base extension-tag array 196

Laboratory Multiple Analyte Profile 196

SNP genotyping with gold nanoparticle probes 197

PCR-CTPP (confronting two-pair primers) 197

Peptide nucleic acid probes for SNP detection 197

SNP genotyping on a genome-wide amplified DOP-PCR template 198

Pyrosequencing 198

Reversed enzyme activity DNA interrogation test 199

Smart amplification process version 2 199

Zinc finger proteins 200

UCAN method (Takara Biomedical) 200

Biochip and microarray-based detection of SNPs 200

SNP genotyping by MassARRAY 200

Electronic dot blot assay 200

Biochip combining BeadArray and ZipCode technologies 201

SNP-IT primer-extension technology 201

OmniScan SNP genotyping 202

Affymetrix SNP genotyping array 202

Concluding remarks on SNP genotyping 202

Limitations of SNP in genetic testing 202

Haplotyping versus SNP genotyping 203

Companies involved in developing technologies/products for SNP analysis 203

Role of copy number variations in genetic diagnostic testing 204

CNVs in various diseases 205

CNVs in genetic epilepsy syndromes 205

CNVs associated with schizophrenia 205

CNVs associated with autism 205

Methods for determination of CNVs 206

Wellcome Trust Case Control Consortium CNV typing array 206

Study of rare variants in pinpointing disease-causing genes 207

Prenatal DNA diagnosis 207

Amniocentesis 208

Chorionic villus sampling 208

Separating fetal cells in maternal blood for genetic diagnosis 208

Antenatal screening for Down's syndrome 208

Fetal DNA in maternal blood 209

Molecular methods for prenatal diagnosis 210

aCGH for prenatal diagnosis 210

BAC HD Scan test 210

FISH for prenatal diagnosis 210

PCR for prenatal diagnosis 210

Plasma DNA sequencing to detect fetal chromosomal aneuploidies 211

In vivo gene expression analysis of the living human fetus 211

Noninvasive prenatal diagnosis of monogenic diseases 212

Digital relative mutation dosage 212

Massively parallel plasma DNA sequencing 212

Applications of prenatal diagnosis 212

Diagnosis of congenital infections 213

Diagnosis of eclampsia 214

Use of transrenal DNA for prenatal testing 214

Preimplantation genetic diagnosis 214

Technologies for preimplantation genetic diagnosis (PGD) 215

PCR for preimplantation genetic diagnosis 215

FISH for preimplantation genetic diagnosis 215

Microarrays for preimplantation genetic diagnosis 216

Conditions detected by preimplantation genetic diagnosis 216

The future of preimplantation genetic diagnosis 216

Companies involved in prenatal/preimplantation diagnosis 217

Cystic fibrosis 218

Detection of CFTR gene mutations 218

CFTR technologies of various companies 219

Genzyme's CF gene sequencing 220

CF Plus? Tag-It Cystic Fibrosis Kit 220

Asuragen's bead array test 220

The Ambry CF Test 221

Biochip for CF diagnosis 221

Identification of CF variants by PCR/Oligonucleotide Ligation Assay 221

SensiGene (SEQUENOM) CF carrier screening test 222

Serum proteomic signature for CF using antibody microarrays 222

Guidelines for genetic screening for CF 222

Congenital adrenal hyperplasia 222

Primary immunodeficiencies 223

Hematological disorders 224

Hemoglobinopathies 224

Sickle cell anemia 224

Thalassemia 225

Paroxysmal nocturnal hemoglobinuria 225

Hemophilia 225

Hereditary hemochromatosis 226

Polycystic kidney disease 226

Hereditary metabolic disorders 226

Lesch-Nyhan Syndrome 226

Gaucher's Disease 227

Acute Intermittent Porphyria 227

Phenylketonuria 227

Hereditary periodic fever 228

Achondroplasia 228

Molecular diagnosis of cardiovascular disorders 228

Coronary Heart Disease 229

Cardiomyopathy 230

Familial Hypertrophic Cardiomyopathy 230

Idiopathic dilated cardiomyopathy 230

Cardiac Arrhythmias 231

Long Q-T Syndrome 231

Familial atrial fibrillation 231

Idiopathic ventricular fibrillation 231

Congestive heart failure 232

Hypertension 232

Disturbances of blood lipids 232

Familial dyslipoproteinemias 232

Hypercholesterolemia 233

Thrombotic disorders 233

Factor V Leiden mutation 233

Pulmonary embolism 234

Molecular diagnosis of eye diseases 234

Molecular diagnosis of retinitis pigmentosa 234

Genetic screening for glaucoma 235

Role of molecular diagnostics in rheumatoid arthritis 235

Molecular diagnosis of neurogenetic disorders 236

Alzheimer's disease 237

Charcot-Marie Tooth disease 238

Down syndrome 238

Duchenne and Becker muscular dystrophy 239

eNOS gene polymorphisms as predictor of cerebral aneurysm rupture 239

Fragile X syndrome 240

Huntington disease 240

Hereditary neuropathy with liability to pressure palsies 241

Mitochondrial disorders affecting the nervous system 241

Parkinson's disease 242

Pompe's disease 243

Spinal muscular atrophy 243

Triple repeat disorders 243

Genetic testing for disease predisposition 243

Direct-to-consumer genetic tests 244

6. Molecular Diagnosis of Infections 247

Introduction 247

Molecular techniques for the diagnosis of infections 247

Antibody-enhanced microplate hybridization assays 248

Bacteriophage-based methods for detection of bacteria 248

Biosensors for detection of microorganisms 249

Ibis T5000™ Biosensor System 249

DNA enzyme immunoassay 249

DNA biochip/microarray in diagnosis of infections 249

DNA-based typing methods 250

Restriction fragment length polymorphism analysis 250

Ribotyping 251

Random amplified polymorphic DNA 251

Combinatorial DNA melting assay 251

Electrochemical detection of pathogens 251

Ligase chain reaction 252

Mass spectrometry for microbial identification 252

Metagenomic pyrosequencing 252

Multiplex PCR for detection of infections 253

LightCycler® SeptiFast Test 254

VYOO® Sepsis Test 254

Dual priming oligonucleotide for multiplex PCR 254

NASBA for detection of microorganisms 255

Nucleic acid probes 255

Neutrophil CD11b expression as a diagnostic marker 255

Optical Mapping 256

PNA-FISH for diagnosis of infections 256

Quantitative reverse-transcription PCR for bacterial diagnostics 256

Rupture event scanning 257

Real-time single-molecule imaging of virus particles 257

Single-strand conformational polymorphism 257

SmartGene platform for identifying pathogens based on genetic sequences 257

Tessera array technology 257

Applications, advantages and limitations of molecular diagnostics 258

Molecular diagnostics versus other microbial detection technologies 258

Advantages of nucleic acid-based diagnostics in infections 258

Drawbacks of nucleic acid-based diagnostics in infections 259

Nanotechnology for detection of infectious agents 259

Bacterial and fungal infections 260

Mycobacterium tuberculosis 262

Conventional diagnosis of tuberculosis 262

Microscopic Observation Drug Susceptible Assay for tuberculosis 262

Molecular diagnostics for tuberculosis 263

Combined tuberculin testing and ELISpotPLUS assay 264

Biomarkers for tuberculosis 265

Diagnosis of drug-resistant M. tuberculosis infection 265

Cost-effectiveness of PCR in tuberculosis screening 266

Other mycobacteria 266

Chlamydial infections 266

Neisseria gonorrhoeae 268

Bacteria associated with bacterial vaginosis 268

Streptococcal infections 268

Group B Streptococci 268

Streptococcus pyogenes and Streptococcus dysgalactiae 269

Pseudomonas aeruginosa 269

Helicobacter pylori 270

Lyme disease 270

Mycoplasmas 271

Fungal infections 271

Viral infections 272


Diagnosis of HIV 273

Neonatal screening of infants of HIV-positive mothers 274

Screening of cadaveric tissue donors 274

Detection of HIV provirus 274

Resolution of indeterminate Western blot 274

Global Surveillance of HIV-1 genetic variations 275

Genotyping for drug-resistance in HIV 275

Phenotyping as predictor of drug susceptibility/resistance in HIV 276

Tests used for quantification of HIV 277

Conclusions about HIV genotyping 277

Hepatitis viruses 278

Hepatitis A virus 278

Hepatitis B virus 279

Hepatitis C virus 279

Detection and quantification of HCV RNA 280

Quantification of HCV RNA levels as a guide to antiviral therapy 281

Electrochemical DNA chip for diagnosis of HCV 281

HCV Genotyping as a guide to therapy 281

Enteroviruses 282

Adenoviruses 283

Rhinoviruses 283

Herpes viruses 283

Herpes simplex virus 283

Genital and neonatal herpes simplex 284

Human cytomegalovirus infections 284

Epstein-Barr virus 284

Human papilloma virus 285

Molecular diagnostics for HPV 285

Detection of encephalitis viruses 286

West Nile and St. Louis encephalitis 286

Venezuelan equine encephalitis virus 287

Protozoal infections 287

Amebiasis 287

Cryptosporidium parvum 287

Malaria 287

Neurocysticercosis 288

Pneumocystis carinii 288

Toxoplasmosis 289

Infections of various systems 289

CNS infections 289

Molecular diagnosis in bacterial meningitis 289

Molecular diagnosis in herpes simplex encephalitis 289

Diagnosis of transmissible spongiform encephalopathies 290

Molecular diagnosis of respiratory viruses 291

SARS-associated coronavirus 291

Influenza viruses 293

Avian influenza 294

H1N1 influenza 298

Gastrointestinal infections 300

Periodontal infections 301

Diagnosis of urinary infections by a biosensor 302

Role of molecular diagnostics in septicemia 302

Limitations and needs of diagnostics for infections 303

Differentiation between live and antibiotic-killed bacteria 304

Cell-based methods for identifying pathogenic microorganisms 304

Cell-based virus assays 304

Cell-based detection of host response to infection 304

Role of molecular diagnostics in hospital acquired infections 305

Detection of hospital-acquired bacterial infections 305

Detection of methicillin-resistant S. aureus 305

Detection of vancomycin-resistant enterococci 306

Detection of hospital-acquired C. difficile 306

Bacterial genome sequencing in antimicrobial resistance 307

Detection of hospital-acquired viral infections 307

Molecular diagnosis of BK virus 307

Diagnosis of hospital-acquired rotavirus gastroenteritis 308

Molecular diagnostics and the microbiome 308

Human Microbiome Project 308

Application of metagenomics to study of the microbiome 309

MicroBiome Analysis Center 309

Concluding remarks and future prospects of diagnosis of infections 310

Rapid point-of-care diagnosis of infection 310

Diagnosis of viruses using protein fingerprinting 312

QIAplex PCR multiplex technology 313

Companies involved in molecular diagnosis of infectious diseases 313

7. Molecular Diagnosis of Cancer 317

Introduction 317

Cancer genomics 317

Cancer genes 318

Oncogenes 318

Tumor Suppressor Genes 318

p53 319

p16 320

CNVs in cancer 320

Viruses and cancer 321

Detecting viral agents in cancer 321

Conventional cancer diagnosis 322

Molecular techniques for cancer diagnosis 323

Genome analysis at the molecular level 324

Mutation detection at molecular level 325

Expression profiling of tumor cells sorted by flow cytometry 325

MicroRNA expression profiling for cancer diagnostics 325

Biomarkers in cancer 326

Circulating nucleosomes in serum of cancer patients 327

Detection of DNA methylation 327

eTag assay system for cancer biomarkers 329

HAAH as a biomarker for cancer 329

LigAmp for detection of gene mutations in cancer 330

Mitochondrial DNA as a cancer biomarker 330

Oncoproteins as biomarkers for cancer 330

Sequencing-based approaches for detection of cancer biomarkers 331

Molecular fingerprinting of cancer 331

Fluorescent in situ hybridization 332

Genetic analysis of cancer 332

Comparative genomic hybridization in cancer diagnostics 332

Loss of heterozygosity 333

Digital karyotyping 333

Gene expression profiles predict chromosomal instability in tumors 333

PCR Techniques 334

Realtime quantitative PCR for diagnosis of cancer 334

Cold-PCR 335

Antibody-based diagnosis of cancer 335

Monoclonal antibodies for diagnosis of cancer 335

Recombinant antibodies as a novel approach to cancer diagnosis 335

Combined immunological and nucleic acid tests 336

Combination of MAbs and RT-PCR 336

Immunobead RT-PCR 336

Assays for determining susceptibility to cancer 336

Gene expression profiling in cancer 336

Microarrays for gene expression profiling in cancer 337

Serial analysis of gene expression (SAGE) 337

DNA tags for finding genes expressed in cancer 338

Suppression subtractive hybridization 338

Measurement of telomerase activity 338

Detection of cancer cells in blood of patients with solid tumors 339

Epithelial aggregate separation and isolation 340

Proteomic technologies for the molecular diagnosis of cancer 341

Proteomic technologies for tumor biomarkers 341

Affibodies as contrast agents for imaging in cancer 341

Aptamer-based technology for protein signatures of cancer cells 342

Aptamers for combined diagnosis and therapeutics of cancer 342

Automated image analysis of nuclear protein distribution 343

Laser capture microdissection in oncology 343

Layered expression scanning 344

Membrane-type serine protease-1 344

Survivin and molecular diagnosis of cancer 344

Biochip/microarrays for cancer diagnosis 344

Role of DNA microarrays in gene expression profiling 345

Biochip detection of FHIT gene 346

Nanobiotechnology for early detection of cancer 346

Detection of nanoparticle self assembly in tumors by MRI 346

Differentiation between normal and cancer cells by nanosensors 346

Magnetic nanoparticle probes 347

Quantum dots for early detection of cancer 347

Molecular imaging of cancer 348

In vivo tumor illumination by adenoviral-GFP 348

PET for in vivo molecular diagnosis of cancer 348

Xenon-enhanced MRI 349

Optical systems for in vivo molecular imaging of cancer 349

Detection of micrometastases 349

Molecular diagnosis of cancers of various organs 350

Brain tumors 350

Molecular diagnostic methods for brain tumors 350

Glioblastoma multiforme 351

Circulating microvesicles as biomarkers of glioblastoma 351

Combination of neuroimaging and DNA microarray analysis in GBM 351

Medulloblastoma 352

Multigene predictor of outcome in GBM 352

Oligodendroglioma 352

Advantages and limitations of molecular diagnosis of brain tumors 353

Breast cancer 353

Breast cancer genes 354

Circulating nucleic acid biomarkers of breast cancer 355

Molecular diagnostic tests for breast cancer 355

Mouse ESC-based assays to evaluate mutations in BRCA2 357

Genomic profiles of breast cancer 358

Role of molecular diagnostics in management of breast cancer 359

Tests for prognosis of breast cancer 363

Prediction of recurrence in breast cancer for personalizing therapy 364

Cervical cancer 366

Colorectal cancer 367

Detection of familial adenomatous polyposis coli 367

Detection of CRC at precancerous state 367

Detection of circulating tumor cells in colorectal cancer 367

Diagnosis of hereditary nonpolyposis colorectal cancer 368

Diagnosis of colorectal cancer from DNA in stools 368

Early diagnosis of colorectal cancer from blood samples 369

Guanylyl cyclase C tests for colorectal cancer 369

Minimally invasive screening for colorectal cancer 369

Gastric cancer 370

Head and neck cancer 370

Nanobiochip sensor technique for analysis of oral cancer biomarkers 370

ProteinChip for diagnosis of head and neck cancer 371

Hematological malignancies 371

Chromosome translocations 371

Flow cytometry in diagnosis of leukemia 371

Gene chip technology 371

Laboratory assessment of leukemia 372

Molecular probes 373

Minimal residual disease 373

Screening of gene mutations in chronic myeloproliferative diseases 374

Lung cancer 374

Melanoma 376

Ovarian cancer 376

Mutation of genes 377

Relevance of genetic testing to management of ovarian cancer 377

Serum biomarkers for early detection of ovarian cancer 378

Biomarkers of ovarian cancer 378

Concluding remarks on testing for ovarian cancer 378

Pancreatic cancer 379

Prostate cancer 379

Early detection of prostate cancer recurrence by nanotechnology 380

Gene expression analysis of prostate cancer 380

Huntingtin Interacting Protein 1 380

Integrative genomic and proteomic profiling of prostate cancer 381

LCM for diagnosis of prostate cancer 381

PCA3 gene detection in urine 381

PCR assay for assessing silencing of protein cadherin 13 gene 382

Prostate biopsy for detection of prostatic intraepithelial neoplasia 382

Screening of multiple SNPs for risk of prostate cancer 383

Semen testing for prostate cancer biomarkers 383

Serum-protein fingerprint

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