Reportlinker Adds Molecular Diagnostics - Technologies, Markets and Companies
NEW YORK, Dec. 21, 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 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 90 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 291 of these are profiled in the report along with tabulation of 650 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 2018. 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.
PART 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
Copy number variations in the human genome 33
Genotype and haplotypes 34
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 36
Replication of the DNA helix 37
Transposons 37
Proteins 37
Proteomics 38
Monoclonal antibodies 38
Aptamers 38
Basics of molecular diagnostics 39
Tracking DNA: the Southern blot 39
Pulsed-field gel electrophoresis 39
DNA Probes 40
The polymerase chain reaction 40
Basic Principles of PCR 40
Target selection 41
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
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
Fluorescent in situ hybridization 80
FISH technique 81
Applications of FISH 82
Modifications of FISH 82
Direct visual in situ hybridization 83
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 85
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 for 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
GenomePlexO 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
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
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
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
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
Methods for determination of CNVs 209
Digital array for CNV detection 210
Wellcome Trust Case Control Consortium CNV typing array 210
CNVer algorithm for CNV detection 210
Study of rare variants in pinpointing disease-causing genes 211
Prenatal DNA diagnosis 211
Amniocentesis 211
Chorionic villus sampling 212
Separating fetal cells in maternal blood for genetic diagnosis 212
Antenatal screening for Down's syndrome 212
Fetal DNA in maternal blood 213
Molecular methods for prenatal diagnosis 213
aCGH for prenatal diagnosis 213
BAC HD Scan test 214
FISH for prenatal diagnosis 214
PCR for prenatal diagnosis 214
Plasma DNA sequencing to detect fetal chromosomal aneuploidies 215
In vivo gene expression analysis of the living human fetus 215
Noninvasive prenatal diagnosis of monogenic diseases 215
Digital relative mutation dosage 216
Massively parallel plasma DNA sequencing 216
Applications of prenatal diagnosis 216
Diagnosis of congenital infections 217
Diagnosis of eclampsia 217
Use of transrenal DNA for prenatal testing 218
Preimplantation genetic diagnosis 218
Technologies for preimplantation genetic diagnosis (PGD) 218
PCR for preimplantation genetic diagnosis 218
FISH for preimplantation genetic diagnosis 219
Microarrays for preimplantation genetic diagnosis 219
Conditions detected by preimplantation genetic diagnosis 220
The future of preimplantation genetic diagnosis 220
Companies involved in prenatal/preimplantation diagnosis 221
Cystic fibrosis 222
Detection of CFTR gene mutations 222
CFTR technologies of various companies 222
Genzyme's CF gene sequencing 223
CF PlusO Tag-It Cystic Fibrosis Kit 224
Asuragen's bead array test 224
The Ambry CF Test 225
Biochip for CF diagnosis 225
Identification of CF variants by PCR/Oligonucleotide Ligation Assay 225
SensiGene (SEQUENOM) CF carrier screening test 225
Serum proteomic signature for CF using antibody microarrays 226
Guidelines for genetic screening for CF 226
Congenital adrenal hyperplasia 226
Primary immunodeficiencies 227
Hematological disorders 228
Hemoglobinopathies 228
Sickle cell anemia 228
Thalassemia 228
Paroxysmal nocturnal hemoglobinuria 229
Hemophilia 229
Hereditary hemochromatosis 229
Polycystic kidney disease 230
Hereditary metabolic disorders 230
Lesch-Nyhan Syndrome 230
Gaucher's Disease 231
Acute Intermittent Porphyria 231
Phenylketonuria 231
Hereditary periodic fever 232
Achondroplasia 232
Molecular diagnosis of cardiovascular disorders 232
Coronary Heart Disease 233
Cardiomyopathy 234
Familial Hypertrophic Cardiomyopathy 234
Idiopathic dilated cardiomyopathy 234
Cardiac Arrhythmias 234
Long Q-T Syndrome 234
Familial atrial fibrillation 235
Idiopathic ventricular fibrillation 235
Congestive heart failure 235
Hypertension 236
Disturbances of blood lipids 236
Familial dyslipoproteinemias 236
Hypercholesterolemia 236
Thrombotic disorders 237
Factor V Leiden mutation 237
Pulmonary embolism 238
Molecular diagnosis of eye diseases 238
Molecular diagnosis of retinitis pigmentosa 238
Genetic screening for glaucoma 239
Role of molecular diagnostics in rheumatoid arthritis 239
Molecular diagnosis of neurogenetic disorders 240
Alzheimer's disease 241
Autism spectrum disorders 241
CNVs associated with autism 242
Charcot-Marie Tooth disease 243
Down syndrome 243
Duchenne and Becker muscular dystrophy 244
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
FISH for detection of infections 256
High resolution melt analysis for diagnosis of infections 256
Ligase chain reaction 256
Mass spectrometry for microbial identification 256
Metagenomic pyrosequencing 257
Multiplex PCR for detection of infections 258
Dual priming oligonucleotide for multiplex PCR 259
LightCycler® SeptiFast Test 259
Multiplex amplified nominal tandem repeat analysis 260
VYOO® Sepsis Test 260
NASBA for detection of microorganisms 260
Nucleic acid probes 260
Neutrophil CD11b expression as a diagnostic marker 260
Optical Mapping 261
PNA-FISH for diagnosis of infections 261
Quantitative reverse-transcription PCR for bacterial diagnostics 262
Rupture event scanning 262
Real-time single-molecule imaging of virus particles 262
Single-strand conformational polymorphism 262
SmartGene platform for identifying pathogens based on genetic sequences 262
Tessera array technology 263
Applications, advantages and limitations of molecular diagnostics 263
Molecular diagnostics versus other microbial detection technologies 263
Advantages of nucleic acid-based diagnostics in infections 264
Drawbacks of nucleic acid-based diagnostics in infections 264
Nanotechnology for detection of infectious agents 265
Bacterial and fungal infections 265
Mycobacterium tuberculosis 267
Conventional diagnosis of tuberculosis 267
Microscopic Observation Drug Susceptible Assay for tuberculosis 267
Molecular diagnostics for tuberculosis 268
Combined tuberculin testing and ELISpotPLUS assay 269
Biomarkers for tuberculosis 270
Diagnosis of drug-resistant M. tuberculosis infection 270
Xpert MTB/RIF automated molecular test for MTB 271
Diagnosis of other mycobacteria 271
Chlamydial infections 272
Neisseria gonorrhoeae 273
Bacteria associated with bacterial vaginosis 274
Streptococcal infections 274
Group B Streptococci 274
Streptococcus pyogenes and Streptococcus dysgalactiae 274
Pseudomonas aeruginosa 275
Helicobacter pylori 275
Lyme disease 275
Mycoplasmas 276
Fungal infections 277
Aspergillus 277
Candida species 277
Viral infections 278
HIV/AIDS 279
Diagnosis of HIV 279
Neonatal screening of infants of HIV-positive mothers 280
Screening of cadaveric tissue donors 280
Detection of HIV provirus 280
Resolution of indeterminate Western blot 280
Global Surveillance of HIV-1 genetic variations 281
Genotyping for drug-resistance in HIV 281
Phenotyping as predictor of drug susceptibility/resistance in HIV 282
Tests used for quantification of HIV 283
Conclusions about HIV genotyping 283
Hepatitis viruses 284
Hepatitis A virus 284
Hepatitis B virus 285
Hepatitis C virus 285
Detection and quantification of HCV RNA 286
Quantification of HCV RNA levels as a guide to antiviral therapy 287
Electrochemical DNA chip for diagnosis of HCV 287
HCV Genotyping as a guide to therapy 287
Enteroviruses 288
Adenoviruses 289
Rhinoviruses 289
Herpes viruses 289
Herpes simplex virus 289
Genital and neonatal herpes simplex 290
Human cytomegalovirus infections 290
Epstein-Barr virus 290
Human papilloma virus 291
Molecular diagnostics for HPV 291
Detection of encephalitis viruses 292
West Nile and St. Louis encephalitis 292
Venezuelan equine encephalitis virus 293
Protozoal infections 293
Amebiasis 293
Cryptosporidium parvum 293
Malaria 293
Neurocysticercosis 294
Pneumocystis carinii 294
Toxoplasmosis 295
Infections of various systems 295
CNS infections 295
Molecular diagnosis in bacterial meningitis 295
Molecular diagnosis in herpes simplex encephalitis 295
Diagnosis of transmissible spongiform encephalopathies 296
Molecular diagnosis of respiratory viruses 297
SARS-associated coronavirus 297
Influenza viruses 299
Avian influenza 300
H1N1 influenza 304
Gastrointestinal infections 306
Periodontal infections 307
Diagnosis of urinary infections by a biosensor 308
Role of molecular diagnostics in septicemia 308
Limitations and needs of diagnostics for infections 309
Differentiation between live and antibiotic-killed bacteria 310
Cell-based methods for identifying pathogenic microorganisms 310
Cell-based virus assays 310
Cell-based detection of host response to infection 310
Role of molecular diagnostics in hospital acquired infections 311
Detection of hospital-acquired bacterial infections 311
Detection of methicillin-resistant S. aureus 311
Detection of vancomycin-resistant enterococci 312
Detection of hospital-acquired C. difficile 312
Bacterial genome sequencing in antimicrobial resistance 313
Detection of hospital-acquired viral infections 313
Molecular diagnosis of BK virus 313
Diagnosis of hospital-acquired rotavirus gastroenteritis 314
Molecular diagnostics and the microbiome 314
Human Microbiome Project 314
Application of metagenomics to study of the microbiome 315
MicroBiome Analysis Center 315
Concluding remarks and future prospects of diagnosis of infections 316
Rapid point-of-care diagnosis of infection 316
Diagnosis of viruses using protein fingerprinting 318
QIAplex PCR multiplex technology 319
Companies involved in molecular diagnosis of infectious diseases 319
7. Molecular Diagnosis of Cancer 323
Introduction 323
Cancer genomics 323
Cancer genes 324
Oncogenes 324
Tumor Suppressor Genes 324
p53 325
p16 326
CNVs in cancer 326
Allele-specific copy number analysis of tumors 327
Viruses and cancer 327
Detecting viral agents in cancer 328
Conventional cancer diagnosis 329
Molecular techniques for cancer diagnosis 329
Genome analysis at the molecular level 331
Mutation detection at molecular level 331
Expression profiling of tumor cells sorted by flow cytometry 332
MicroRNA expression profiling for cancer diagnostics 332
Biomarkers in cancer 332
Circulating nucleosomes in serum of cancer patients 333
Detection of DNA methylation 333
eTag assay system for cancer biomarkers 335
HAAH as a biomarker for cancer 336
LigAmp for detection of gene mutations in cancer 336
Mitochondrial DNA as a cancer biomarker 336
Oncoproteins as biomarkers for cancer 337
Sequencing-based approaches for detection of cancer biomarkers 337
Molecular fingerprinting of cancer 338
Fluorescent in situ hybridization 338
Genetic analysis of cancer 339
Comparative genomic hybridization in cancer diagnostics 339
Loss of heterozygosity 339
Digital karyotyping 340
Gene expression profiles predict chromosomal instability in tumors 340
PCR Techniques 340
Realtime quantitative PCR for diagnosis of cancer 341
Cold-PCR 341
Antibody-based diagnosis of cancer 341
Monoclonal antibodies for diagnosis of cancer 341
Recombinant antibodies as a novel approach to cancer diagnosis 342
Combined immunological and nucleic acid tests 342
Combination of MAbs and RT-PCR 342
Immunobead RT-PCR 342
Assays for determining susceptibility to cancer 343
Gene expression profiling in cancer 343
Microarrays for gene expression profiling in cancer 344
Serial analysis of gene expression (SAGE) 344
DNA tags for finding genes expressed in cancer 344
Suppression subtractive hybridization 345
Measurement of telomerase activity 345
Detection of circulating tumor cells in blood 346
Biochips/microfluidics for detection of CTCs 346
CellTracks® AutoPrep® System 347
CTCscope system for detection of CTCs 347
Fiber-optic array scanning technology 347
MagSweeper 348
Future prospects of detection of cancer cells in blood 348
Epithelial aggregate separation and isolation 348
Proteomic technologies for the molecular diagnosis of cancer 348
Proteomic technologies for tumor biomarkers 349
Affibodies as contrast agents for imaging in cancer 349
Aptamer-based technology for protein signatures of cancer cells 349
Aptamers for combined diagnosis and therapeutics of cancer 350
Automated image analysis of nuclear protein distribution 350
Laser capture microdissection in oncology 351
Layered expression scanning 351
Membrane-type serine protease-1 352
Survivin and molecular diagnosis of cancer 352
Biochip/microarrays for cancer diagnosis 352
Role of DNA microarrays in gene expression profiling 353
Biochip detection of FHIT gene 353
Nanobiotechnology for early detection of cancer 354
Detection of nanoparticle self assembly in tumors by MRI 354
Differentiation between normal and cancer cells by nanosensors 354
Magnetic nanoparticle probes 354
Quantum dots for early detection of cancer 355
Molecular imaging of cancer 356
In vivo tumor illumination by adenoviral-GFP 356
PET for in vivo molecular diagnosis of cancer 356
Xenon-enhanced MRI 356
Optical systems for in vivo molecular imaging of cancer 357
Detection of micrometastases 357
Molecular diagnosis of cancers of various organs 357
Brain tumors 358
Molecular diagnostic methods for brain tumors 358
Glioblastoma multiforme 358
Circulating microvesicles as biomarkers of glioblastoma 359
Combination of neuroimaging and DNA microarray analysis in GBM 359
Medulloblastoma 360
Multigene predictor of outcome in GBM 360
Oligodendroglioma 360
Advantages and limitations of molecular diagnosis of brain tumors 360
Breast cancer 361
Breast cancer genes 361
Circulating nucleic acid biomarkers of breast cancer 362
Molecular diagnostic tests for breast cancer 363
Mouse ESC-based assays to evaluate mutations in BRCA2 365
Genomic profiles of breast cancer 366
Role of molecular diagnostics in management of breast cancer 366
Tests for prognosis of breast cancer 370
Prediction of recurrence in breast cancer for personalizing therapy 372
Cervical cancer 373
Colorectal ca
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