Molecular Diagnostics - Technologies, Markets and Companies
NEW YORK, Nov. 30, 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=prnewswire&utm_medium=pr&utm_campaign=In_Vitro_Diagnostic
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 704 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 2010 according to technologies, applications and geographical regions. Forecasts are made up to 2020. 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.
MOLECULAR DIAGNOSTICS 1
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 50
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 52
GENESIS FE500 Workcell 53
GeneMole 53
PCR BioCube 53
QIAsymphony 53
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 54
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 58
Digital PCR 59
Emulsion PCR 59
ExCyto PCR 60
Long and accurate PCR 60
Multiplex PCR 60
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 63
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 65
Guidelines for real-time qPCR 66
Future applications of real-time qPCR 66
Reverse transcriptase (RT)-PCR 67
Standardized reverse transcriptase PCR 67
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 75
Single Primer Isothermal Amplification 76
Transcription mediated amplification 76
WAVE nucleic acid fragment analysis system 76
Technologies for signal amplification 77
3 DNA dendrimer signal amplification 77
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 89
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
Solid Phase Transcription Chain Reaction 96
Transcriptome analysis 96
Visualization of mRNA expression in vivo 97
MicroRNA diagnostics 97
Real-time PCR for expression profiling of miRNAs 97
Microarray vs quantitative PCR for measuring miRNAs 98
Use of LNA to explore miRNA 98
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 100
QIAGEN's Repli-G system 101
GenomePlex? Whole Genome Amplification 101
DNA sequencing 102
Companies involved in sequencing 103
Applications of next generation sequencing in molecular diagnostics 104
Companies developing sequencing for molecular diagnostics 105
Genome-wide approach for chromatin mapping 106
Mitochondrial sequencing 106
Identification of unknown DNA sequences 106
Optical mapping 107
Gene expression analysis 107
Gene expression profiling on whole blood samples 108
Gene expression patterns of white blood cells 108
Gene expression profiling based on alternative RNA splicing 109
MAUI (MicroArray User Interface) hybridization 109
Monitoring in vivo gene expression by molecular imaging 110
Serial analysis of gene expression (SAGE) 110
Single-cell gene expression analysis 110
T cell receptor expression analysis 111
Tangerine™ expression profiling 111
Whole genome expression array 112
Ziplex™ system 112
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 115
PNA-based PD-loop technology 116
PNA-DNA hybrid quadruplexes 116
Companies involved in PNA diagnostics 116
Locked nucleic acids 117
Zip Nucleic Acids 117
Electrochemical detection of DNA 118
Mediated nucleic acid oxidation 118
Detection of hybridized nucleic acid with cyclic voltametry 119
Electrochemical detection based on Toshiba's CMOS technology 119
Concluding remarks on electrochemical DNA detection 119
Bead-based assay platforms 120
Scorpions™ technology 121
The Scorpions reaction 121
Applications of Scorpions 121
Nucleic acid lateral flow molecular diagnostics 122
3. Biochips, Biosensors, and Molecular Labels 123
Introduction to biochip technology 123
Applications of biochips in diagnostics 123
GeneChip 124
GeneChip Human Genome Arrays 125
AmpliChip CYP450 125
Electronic detection of nucleic acids on microarrays 125
Microchip capillary electrophoresis 126
Strand displacement amplification on a biochip 126
Rolling circle amplification on microarrays 126
LiquiChip-RCAT 126
Fast PCR biochip 127
Multiplex microarray-enhanced PCR for DNA analysis 127
Multiplexed Molecular Profiling 127
Universal DNA microarray combining PCR and ligase detection reaction 128
Genomewide association scans 128
Whole genome chips/microarrays 129
Transposon insertion site profiling chip 129
Standardizing the microarrays 130
Companies involved in developing biochip technology for diagnostics 130
Future of biochip technology for molecular diagnostics 131
Microfluidic chips 132
Fish-on-chip 132
Lab-on-a-chip 132
LabCD 133
Micronics' microfluidic technology 133
Microfluidic chips/arrays using PCR 133
Microfluidic automated DNA analysis using PCR 133
Digital PCR Array 133
Digital PCR on a SlipChip 134
Microfluidic chips integrated with RCAT 134
Microfluidic chips integrated with PET 134
Companies developing microfluidic technologies 135
Biosensor technologies 135
Classification of biosensor technologies 136
DNA-based biosensors 137
DNA hybridization biosensor chips 137
PCR-free DNA biosensor 137
DNA based biosensor to detects metallic ions 138
Genetically engineered B lymphocytes 138
Biosensors immunoassays 138
PNA (peptide nucleic acid)-based biosensors 139
Protein-based biosensors 139
Antibody biosensors 139
Cell-based biosensors (cytosensors) 139
Multicell biosensors 140
Microbial biosensors 140
Optical biosensors 141
Surface plasmon resonance technology 141
Label-free optical biosensor 142
Microsensors using with nano/microelectronic communications technology 142
Electrochemical sensors 142
Enzyme electrodes for biosensing 142
Conductometric sensors 143
Electrochemical genosensors 143
Electrochemical nanobiosensor 143
Bioelectronic sensors 144
Phototransistor biochip biosensor 144
Ribozyme-based sensors 144
RiboReporters 145
Concluding remarks and future prospects of biosensor technology 145
Companies developing biosensors for molecular diagnostics 146
Molecular labels and detection 147
Detection technologies for molecular labels 148
Fluorescence and chemiluminescence 148
Fluorescence technologies for label detection 149
Companies with fluorescence and chemiluminescence products 149
Molecular beacons 150
The Green fluorescent protein 151
Multiophoton detection radioimmunoassay 152
Multi-pixel photon counter 152
Enzyme labels and detection by fluorescence 152
Phase-sensitive flow cytometry 153
Microtransponder-based DNA diagnostics 153
Laboratory Multiple Analyte Profile 154
Multiple labels 154
Protein-DNA chimeras for detection of small numbers of molecules 155
Single molecule detection 155
Atomic force microscopy 156
Capillary electrophoresis 156
Confocal laser scanning 156
nCounter Analysis System 156
Spectrally resolved fluorescence lifetime imaging microscopy 157
Molecular imaging 157
Basic research in molecular imaging 158
Devices for molecular imaging 158
Molecular imaging in clinical practice 158
Challenges and future prospects of molecular imaging 159
Companies involved in molecular imaging 159
Nanobiotechnology for molecular diagnostics 159
Magnetic nanoparticles 160
Gold nanoparticles 161
Quantum dot technology 162
Nanotechnology on a chip 163
Nanogen's NanoChip 163
Fullerene photodetectors for chemiluminescence detection on microfluidic chip 163
Diagnostics based on nanopore technology 164
Nanosensors 164
Detection of cocaine molecules by nanoparticle-labeled aptasensors 164
Nanosensors for glucose monitoring 165
PEBBLE nanosensors 165
Quartz nanobalance biosensor 165
Cantilever arrays 165
Resonance Light Scattering technology 166
DNA nanomachines for molecular diagnostics 167
Nanobarcodes technology for molecular diagnostics 167
Qdot nanobarcode for multiplexed gene expression profiling 167
Role of nanobiotechnology in improving molecular diagnostics 168
Companies involved in nanomolecular diagnostics 168
Concluding remarks about nanodiagnostics 171
Future prospects of nanodiagnostics 171
4. Proteomic Technologies for Molecular Diagnostics 173
Introduction 173
Proteomic technologies 173
Biomarkers of disease 173
Proteomic tools for biomarkers 173
Search for biomarkers in body fluids 174
Captamers with proximity extension assay for proteins 174
Cyclical amplification of proteins 174
Detection of misfolded proteins by ELISA with exponential signal amplification 175
Diagnostics based on designed repeat proteins 175
Differential Peptide Display 175
Light-switching excimer probes 176
MALDI-TOF MS 176
Molecular beacon aptamer 177
Molecular beacon assay 177
Proteomic patterns 178
Real-time PCR for protein quantification 178
Protein biochip technologies 179
ProteinChip 180
LabChip for protein analysis 180
TRINECTIN proteome chip 181
Protein chips for antigen-antibody interactions molecular diagnostics 181
Microfluidic devices for proteomics-based diagnostics 181
Nanotechnology-based protein biochips/microarrays 182
Nanoparticle protein chip 182
Protein nanobiochip 182
Protein biochips based on fluorescence planar wave guide technology 182
New developments in protein chips/microarrays 183
Antibody microarrays 183
Aptamer-based protein biochip 184
Multiplexed Protein Profiling on Microarrays 184
Proteomic pattern analysis 184
Single molecule array 185
Viral protein chip 185
Commercial development of protein chips for molecular diagnostics 185
Proteome Identification Kit 187
Laser capture microdissection (LCM) 187
LCM technology 187
Applications of LCM in molecular diagnostics 188
Proteomic diagnosis of CNS disorders 188
Cerebrospinal fluids tests based on proteomics 188
Urine tests for CNS disorders based on proteins in urine 189
Diagnosis of CNS disorders by examination of proteins in the blood 189
Diagnosis of CNS disorders by examination of proteins in tears 190
Role of proteomics in the diagnosis of Alzheimer's disease 190
Role of proteomics in the diagnosis of Creutzfeldt-Jakob disease 191
Future prospects of use of proteomics for diagnosis of CNS disorders 191
Concluding remarks on the use of proteomics in diagnostics 191
5. Molecular Diagnosis of Genetic Disorders 193
Introduction 193
Cytogenetics 194
FISH with probes to the telomeres 194
Single copy FISH probes 194
Comparative genomic hybridization 195
Use of biochips in genetic disorders 195
Representational oligonucleotide microarray analysis 196
SignatureChip®-based diagnostics for cytogenetic abnormalities 196
Diagnosis of genomic rearrangements by multiplex PCR 196
Quantitative fluorescent PCR 196
Mutation detection technologies 197
PCR-based methods for mutation detection 198
Cleavase Fragment Length Polymorphism 198
Direct dideoxy DNA sequencing 198
Digital Genetic Analysis (DGA) 198
Fluorescence-based directed termination PCR 199
Fluorescence melting curve analysis for multiplex mutation detection 199
Heteroduplex analysis 200
Restriction fragment length polymorphism 200
Single-stranded conformation polymorphism (SSCP) analysis 200
TaqMan real-time PCR 201
Non-PCR methods for mutation detection 201
Arrayed primer extension 201
BEAMing (beads, emulsion, amplification, and magnetics) 202
ELISA-protein truncation test 202
Enzymatic mutation detection 202
Specific anchor nucleotide incorporation 203
Conversion analysis for mutation detection 203
Biochip technologies for mutation detection 203
Combination of FISH and gene chips 204
Haplotype Specific Extraction 204
Technologies for SNP analysis 204
DNA sequencing 205
Electrochemical DNA probes 206
Use of NanoChip for detection of SNPs 206
Single base extension-tag array 206
Laboratory Multiple Analyte Profile 207
SNP genotyping with gold nanoparticle probes 207
PCR-CTPP (confronting two-pair primers) 207
Peptide nucleic acid probes for SNP detection 208
SNP genotyping on a genome-wide amplified DOP-PCR template 208
Pyrosequencing 208
Reversed enzyme activity DNA interrogation test 209
Smart amplification process version 2 210
Zinc finger proteins 210
UCAN method (Takara Biomedical) 210
Biochip and microarray-based detection of SNPs 210
SNP genotyping by MassARRAY 210
Electronic dot blot assay 211
Biochip combining BeadArray and ZipCode technologies 211
SNP-IT primer-extension technology 211
OmniScan SNP genotyping 212
Affymetrix SNP genotyping array 212
Concluding remarks on SNP genotyping 212
Limitations of SNP in genetic testing 213
Haplotyping versus SNP genotyping 213
Nanofluidics technology for high throughput SNP genotyping 213
Companies involved in developing technologies/products for SNP analysis 214
Role of copy number variations in genetic diagnostic testing 215
CNVs in various diseases 215
CNVs in genetic epilepsy syndromes 215
CNVs associated with schizophrenia 216
Methods for determination of CNVs 216
Digital array for CNV detection 217
Wellcome Trust Case Control Consortium CNV typing array 217
CNVer algorithm for CNV detection 217
Study of rare variants in pinpointing disease-causing genes 218
Prenatal DNA diagnosis 218
Amniocentesis 219
Chorionic villus sampling 219
Separating fetal cells in maternal blood for genetic diagnosis 219
Antenatal screening for Down's syndrome 219
Fetal DNA in maternal blood 220
Molecular methods for prenatal diagnosis 221
aCGH for prenatal diagnosis 221
BAC HD Scan test 221
FISH for prenatal diagnosis 221
PCR for prenatal diagnosis 221
Plasma DNA sequencing to detect fetal chromosomal aneuploidies 222
In vivo gene expression analysis of the living human fetus 222
Noninvasive prenatal diagnosis of monogenic diseases 223
Digital relative mutation dosage 223
Massively parallel plasma DNA sequencing 223
Applications of prenatal diagnosis 223
Diagnosis of congenital infections 224
Diagnosis of congenital CMV 225
Diagnosis of eclampsia 225
Use of transrenal DNA for prenatal testing 225
Preimplantation genetic diagnosis 225
Technologies for preimplantation genetic diagnosis (PGD) 226
PCR for preimplantation genetic diagnosis 226
FISH for preimplantation genetic diagnosis 226
Microarrays for preimplantation genetic diagnosis 227
Conditions detected by preimplantation genetic diagnosis 227
The future of preimplantation genetic diagnosis 228
Companies involved in prenatal/preimplantation diagnosis 228
Cystic fibrosis 229
Detection of CFTR gene mutations 230
CFTR technologies of various companies 230
Genzyme's CF gene sequencing 231
CF Plus? Tag-It Cystic Fibrosis Kit 231
Asuragen's bead array test 232
The Ambry CF Test 232
Biochip for CF diagnosis 232
Identification of CF variants by PCR/Oligonucleotide Ligation Assay 233
SensiGene (SEQUENOM) CF carrier screening test 233
Serum proteomic signature for CF using antibody microarrays 233
Guidelines for genetic screening for CF 233
Congenital adrenal hyperplasia 234
Primary immunodeficiencies 234
Hematological disorders 235
Hemoglobinopathies 235
Sickle cell anemia 236
Thalassemia 236
Paroxysmal nocturnal hemoglobinuria 236
Hemophilia 237
Hereditary hemochromatosis 237
Polycystic kidney disease 237
Hereditary metabolic disorders 238
Lesch-Nyhan Syndrome 238
Gaucher's Disease 238
Acute Intermittent Porphyria 239
Phenylketonuria 239
Hereditary periodic fever 239
Achondroplasia 240
Molecular diagnosis of cardiovascular disorders 240
Coronary heart disease 241
Genomics of coronary heart disease 241
Cardiomyopathy 242
Familial Hypertrophic Cardiomyopathy 242
Idiopathic dilated cardiomyopathy 242
Cardiac Arrhythmias 242
Long Q-T Syndrome 243
Familial atrial fibrillation 243
Idiopathic ventricular fibrillation 243
Congestive heart failure 243
Hypertension 244
Disturbances of blood lipids 244
Familial dyslipoproteinemias 244
Hypercholesterolemia 245
Thrombotic disorders 245
Factor V Leiden mutation 245
Pulmonary embolism 246
Hereditary thrombophilia 246
Companies developing molecular diagnostics for cardiovascular disorders 246
Molecular diagnosis of eye diseases 247
Molecular diagnosis of retinitis pigmentosa 247
Genetic screening for glaucoma 248
Role of molecular diagnostics in rheumatoid arthritis 248
Molecular diagnosis of neurogenetic disorders 249
Alzheimer's disease 250
Autism spectrum disorders 251
CNVs associated with autism 251
Charcot-Marie Tooth disease 252
Down syndrome 252
Duchenne and Becker muscular dystrophy 253
eNOS gene polymorphisms as predictor of cerebral aneurysm rupture 253
Fragile X syndrome 254
Huntington disease 254
Hereditary neuropathy with liability to pressure palsies 255
Mitochondrial disorders affecting the nervous system 255
Parkinson's disease 256
Pompe's disease 257
Spinal muscular atrophy 257
Triple repeat disorders 257
Genetic testing for disease predisposition 257
Direct-to-consumer genetic tests 258
6. Molecular Diagnosis of Infections 261
Introduction 261
Molecular techniques for the diagnosis of infections 261
Antibody-enhanced microplate hybridization assays 262
Bacteriophage-based methods for detection of bacteria 262
Biosensors for detection of microorganisms 263
Ibis T5000™ Biosensor System 263
DNA enzyme immunoassay 263
DNA biochip/microarray in diagnosis of infections 263
DNA-based typing methods 264
Restriction fragment length polymorphism analysis 264
Ribotyping 265
Random amplified polymorphic DNA 265
Combinatorial DNA melting assay 265
Electrochemical detection of pathogens 265
FISH for detection of infections 266
Helicase-dependent isothermal amplification for rapid detection of pathogens 266
High resolution melt analysis for diagnosis of infections 266
Ligase chain reaction 266
Mass spectrometry for microbial identification 267
Metagenomic pyrosequencing 267
Multiplex PCR for detection of infections 268
Dual priming oligonucleotide for multiplex PCR 269
LightCycler® SeptiFast Test 269
Multiplex amplified nominal tandem repeat analysis 270
VYOO® Sepsis Test 270
NASBA for detection of microorganisms 270
Nucleic acid probes 270
Neutrophil CD11b expression as a diagnostic marker 271
Optical Mapping 271
PNA-FISH for diagnosis of infections 271
QuantiFERON® technology for pre-molecular diagnosis of infections 272
Quantitative reverse-transcription PCR for bacterial diagnostics 272
Rupture event scanning 272
Real-time single-molecule imaging of virus particles 273
Single-strand conformational polymorphism 273
SmartGene platform for identifying pathogens based on genetic sequences 273
Tessera array technology 273
Unyvero Solution 274
Applications, advantages and limitations of molecular diagnostics 274
Molecular diagnostics versus other microbial detection technologies 274
Advantages of nucleic acid-based diagnostics in infections 274
Drawbacks of nucleic acid-based diagnostics in infections 275
Nanotechnology for detection of infectious agents 275
Bacterial and fungal infections 276
Mycobacterium tuberculosis 277
Conventional diagnosis of tuberculosis 278
Microscopic Observation Drug Susceptible Assay for tuberculosis 278
Molecular diagnostics for tuberculosis 278
Combined tuberculin testing and ELISpotPLUS assay 280
Biomarkers for tuberculosis 280
Diagnosis of drug-resistant M. tuberculosis infection 281
Xpert MTB/RIF automated molecular test for MTB 281
Diagnosis of other mycobacteria 282
Chlamydial infections 282
Neisseria gonorrhoeae 284
Bacteria associated with bacterial vaginosis 284
Streptococcal infections 284
Group B Streptococci 284
Streptococcus pyogenes and Streptococcus dysgalactiae 285
Pseudomonas aeruginosa 285
Helicobacter pylori 286
Lyme disease 286
Mycoplasmas 287
Fungal infections 287
Aspergillus 288
Candida species 288
Viral infections 289
HIV/AIDS 289
Diagnosis of HIV 290
Detection of HIV provirus 291
Global Surveillance of HIV-1 genetic variations 291
Genotyping for drug-resistance in HIV 291
Neonatal screening of infants of HIV-positive mothers 292
Phenotyping as predictor of drug susceptibility/resistance in HIV 292
Point-of-care testing for HIV 293
Resolution of indeterminate Western blot 294
Screening of cadaveric tissue donors 294
Tests used for quantification of HIV 294
Conclusions about HIV diagnostics 295
Hepatitis viruses 295
Hepatitis A virus 296
Hepatitis B virus 296
Hepatitis C virus 297
Detection and quantification of HCV RNA 297
Quantification of HCV RNA levels as a guide to antiviral therapy 298
Electrochemical DNA chip for diagnosis of HCV 298
HCV Genotyping as a guide to therapy 298
Enteroviruses 299
Adenoviruses 300
Rhinoviruses 300
Herpes viruses 300
Herpes simplex virus 300
Genital and neonatal herpes simplex 301
Human cytomegalovirus infections 301
Epstein-Barr virus 302
Human papilloma virus 302
Molecular diagnostics for HPV 302
Detection of encephalitis viruses 303
West Nile and St. Louis encephalitis 303
Venezuelan equine encephalitis virus 304
Detection of noroviruses 304
Protozoal infections 304
Amebiasis 304
Cryptosporidium parvum 305
Leishmaniasis 305
Malaria 305
Neurocysticercosis 306
Pneumocystis carinii 306
Toxoplasmosis 306
Infections of various systems 307
CNS infections 307
Molecular diagnosis in bacterial meningitis 307
Molecular diagnosis in herpes simplex encephalitis 307
Diagnosis of transmissible spongiform encephalopathies 308
Molecular diagnosis of respiratory viruses 309
SARS-associated coronavirus 309
Influenza viruses 310
Avian influenza 312
H1N1 influenza 316
Gastrointestinal infections 318
Periodontal infections 319
Diagnosis of urinary infections by a biosensor 320
Role of molecular diagnostics in septicemia 320
Limitations and needs of diagnostics for infections 321
Differentiation between live and antibiotic-killed bacteria 322
Cell-based methods for identifying pathogenic microorganisms 322
Cell-based virus assays 322
Cell-based detection of host response to infection 322
Role of molecular diagnostics in hospital acquired infections 323
Detection of hospital-acquired bacterial infections 323
Detection of methicillin-resistant S. aureus 323
Detection of vancomycin-resistant enterococci 324
Detection of hospital-acquired C. difficile 324
Bacterial genome sequencing in antimicrobial resistance 325
Detection of hospital-acquired viral infections 325
Molecular diagnosis of BK virus 325
Diagnosis of hospital-acquired rotavirus gastroenteritis 326
Molecular diagnostics and the microbiome 326
Human Microbiome Project326
Application of metagenomics to study of the microbiome 327
MicroBiome Analysis Center 327
Concluding remarks and future prospects of diagnosis of infections 328
Rapid point-of-care diagnosis of infection 328
Diagnosis of viruses using protein fingerprinting 331
QIAplex PCR multiplex technology 331
Companies involved in molecular diagnosis of infectious diseases 331
7. Molecular Diagnosis of Cancer 335
Introduction 335
Cancer genomics 335
Cancer genes 336
Oncogenes 336
Tumor Suppressor Genes 336
p53 337
p16 338
CNVs in cancer 338
Allele-specific copy number analysis of tumors 339
Viruses and cancer 339
Detecting viral agents in cancer 340
Conventional cancer diagnosis 341
Molecular techniques for cancer diagnosis 341
Genome analysis at the molecular level 343
Mutation detection at molecular level 343
Expression profiling of tumor cells sorted by flow cytometry 344
MicroRNA expression profiling for cancer diagnostics 344
Biomarkers in cancer 344
Circulating nucleosomes in serum of cancer patients 345
Detection of DNA methylation 345
eTag assay system for cancer biomarkers 347
HAAH as a biomarker for cancer 348
LigAmp for detection of gene mutations in cancer 348
Mitochondrial DNA as a cancer biomarker 348
Oncoproteins as biomarkers for cancer 349
Sequencing-based approaches for detection of cancer biomarkers 349
Molecular fingerprinting of cancer 350
Fluorescent in situ hybridization 350
Genetic analysis of cancer 351
Comparative genomic hybridization in cancer diagnostics 351
Loss of heterozygosity 351
Digital karyotyping 351
Gene expression profiles predict chromosomal instability in tumors 352
PCR Techniques 352
Realtime quantitative PCR for diagnosis of cancer 353
Cold-PCR 353
Antibody-based diagnosis of cancer 353
Monoclonal antibodies for diagnosis of cancer 353
Recombinant antibodies as a novel approach to cancer diagnosis 354
Combined immunological and nucleic acid tests 354
Combination of MAbs and RT-PCR 354
Immunobead RT-PCR 354
Assays for determining susceptibility to cancer 355
Gene expression profiling in cancer 355
Microarrays for gene expression profiling in cancer 356
Serial analysis of gene expression (SAGE) 356
DNA tags for finding genes expressed in cancer 356
Suppression subtractive hybridization 357
Measurement of telomerase activity 357
Detection of circulating tumor cells in blood 358
Biochips/microfluidics for detection of CTCs 358
CellSearch 359
CellTracks® AutoPrep® System 359
CTCscope system for detection of CTCs 359
CTChip™ 359
Fiber-optic array scanning technology 359
Lab-on-chip for the isolation and detection of CTCs 360
MagSweeper 360
Future prospects of detection of cancer cells in blood 360
Epithelial aggregate separation and isolation 361
Proteomic technologies for the molecular diagnosis of cancer 361
Proteomic technologies for tumor biomarkers 361
Affibodies as contrast agents for imaging in cancer 362
Aptamer-based technology for protein signatures of cancer cells 362
Aptamer probes for in vivo diagnosis of cancer 362
Aptamers for combined diagnosis and therapeutics of cancer 363
Automated image analysis of nuclear protein distribution 363
Laser capture microdissection in oncology 364
Layered expression scanning 364
Membrane-type serine protease-1 364
Survivin and molecular diagnosis of cancer 365
Biochip/microarrays for cancer diagnosis 365
Role of DNA microarrays in gene expression profiling 366
Biochip detection of FHIT gene 366
Nanobiotechnology for early detection of cancer 366
Detection of nanoparticle self assembly in tumors by MRI 367
Differentiation between normal and cancer cells by nanosensors 367
Magnetic nanoparticle probes 367
Quantum dots for early detection of cancer 367
Molecular imaging of cancer 368
In vivo tumor illumination by adenoviral-GFP 368
PET for in vivo molecular diagnosis of cancer 369
Radiolabeled peptide-based targeting probes for cancer imaging 369
Xenon-enhanced MRI 369
Optical systems for in vivo molecular imaging of cancer 369
Detection of micrometastases 370
Molecular diagnosis of cancers of various organs 370
Brain tumors 371
Molecular diagnostic methods for brain tumors 371
Glioblastoma multiforme 371
Circulating microvesicles as biomarkers of glioblastoma 372
Combination of neur
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