分子診斷：技術・市場・企業

Abstract

Benefits of this report

• This report has evolved during the past 14 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 279 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 87 tables and 15 figures.

Who should read this report?

• Chief executive officers of molecular diagnostic companies.
• Business development executives of pharmaceutical and biotechnology companies.
• Executives of companies involved in developing integration of diagnosis and treatment as well as those interested in personalized medicine.
• Officers of genomic and proteomic companies interested in diagnostic technologies.
• Research scientists involved in application of molecular diagnostic technologies.
• Planners of healthcare services.

Summary

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

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

The number of companies involved in molecular diagnostics has increased remarkably during the past few years. More than 500 companies have been identified to be involved in developing molecular diagnostics and 277 of these are profiled in the report along with tabulation of 604 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 2008 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.

Table of Contents

part 1

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
• Genome 24
• DNA 24
• DNA polymerases 25
• Restriction endonucleases 25
• DNA methylation 25
• RNA 26
• RNA polymerases 26
• MicroRNAs 27
• DNA transcription 27
• Chromosomes 27
• Telomeres 28
• Mitochondrial DNA 28
• Genes 29
• The genetic code 29
• Gene expression 29
• DNA sequences 30
• Junk DNA 30
• Single nucleotide polymorphisms 30
• Genotype and haplotypes 31
• Replication of the DNA helix 31
• Proteins 32
• Proteomics 32
• Monoclonal antibodies 32
• Aptamers 32
• Basics of molecular diagnostics 33
• Tracking DNA: the Southern blot 33
• Pulsed-field gel electrophoresis 34
• DNA Probes 34
• The polymerase chain reaction 34
• Basic Principles of PCR 34
• Target selection 35
• Detection of amplified DNA 35
• Limitations of PCR 36
• Impact of human genome project on molecular diagnostics 36
• Genetic variations in the human genome 37
• Insertions and deletions in the human genome 37
• Large scale variation in human genome 38
• Variation in copy number in the human genome 38
• Structural variations in the human genome 38
• Mapping and sequencing of structural variation from human genomes 39
• 1000 Genomes Project 40
• Human Variome Project 40
• 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
• Long and accurate PCR 52
• Real-time PCR systems 52
• Dyes used in real-time PCR 53
• Commercially available real-time PCR systems 53
• LightCycler PCR system 54
• LightUp probes based on real-time PCR 54
• Applications of real-time PCR 54
• Limitations of real-time PCR 55
• Improving the reliability of low level DNA analysis by real-time PCR 55
• Guidelines for real-time quantitative PCR 56
• Future applications of real-time Q-PCR 56
• Reverse transcriptase (RT)-PCR 56
• Standardized reverse transcriptase PCR 57
• Single cell PCR 58
• LATE-PCR 58
• Cold-PCR 58
• AmpliGrid-System 58
• Digital PCR 59
• Combined PCR-ELISA 59
• Monitoring of gene amplification in molecular diagnostics 60
• Non-PCR nucleic acid amplification methods 60
• Linked Linear Amplification 60
• Transcription mediated amplification 61
• Rapid analysis of gene expression 61
• WAVE nucleic acid fragment analysis system 61
• DNA probes with conjugated minor groove binder 62
• Rolling circle amplification technology 62
• Gene-based diagnostics through RCAT 64
• RCAT-immunodiagnostics 64
• RCAT-biochips 65
• RCAT-pharmacogenomics 65
• Circle-to-circle amplification 65
• Ramification amplification method 65
• Single Primer Isothermal Amplification 66
• Isothermal reaction for amplification of oligonucleotides 66
• ICAN (Isothermal and Chimeric primer-initiated Amplification of Nucleic Acids) 66
• Technologies for signal amplification 67
• 3 DNA dendrimer signal amplification 67
• Hybridization signal amplification method 68
• Signal mediated amplification of RNA technology 69
• Invader assays 69
• Hybrid Capture technology 71
• Branched DNA test 72
• Tyramide signal amplification 72
• Non-enzymatic signal amplification technologies 72
• Direct molecular analysis without amplification 73
• Direct detection of dsDNA 74
• Multiplex assays 75
• Fluorescent in situ hybridization 75
• Modifications of FISH 77
• Direct visual in situ hybridization 77
• Direct labeled Satellite FISH probes 77
• Comparative genomic hybridization 78
• Primed in situ labeling 78
• Interphase FISH 78
• FISH with telomere-specific probes 78
• Multicolor FISH 79
• Automation of FISH 79
• Companies involved in FISH diagnostics 79
• RNA diagnostics 80
• Branched-chain DNA assay for measurement of RNA 81
• Cycling probe technology 82
• Linear RNA amplification 82
• Solid Phase Transcription Chain Reaction 82
• Nucleic acid sequence-based amplification 82
• Q Beta replicase system 85
• Non-isotopic RNase cleavage assay 85
• Invader RNA assays 85
• Visualization of mRNA expression in vivo 85
• MicroRNA diagnostics 86
• Real-time PCR for expression profiling of miRNAs 86
• Microarray vs quantitative PCR foro measuring miRNAs 86
• Use of LNA to explore miRNA 87
• Nuclease Protection Assay to measure miRNA expression 87
• Microarrays for analysis of miRNA gene expression 87
• Modification of in situ hybridization for detection of miRNAs 88
• Whole genome amplification 89
• Companies that provide technologies for whole genome amplification 89
• QIAGEN' s Repli-G system 89
• GenomePlex™ Whole Genome Amplification 90
• DNA sequencing 90
• Companies involved in sequencing 92
• Applications of next generation sequencing in molecular diagnostics 92
• Genome-wide approach for chromatin mapping 93
• Mitochondrial sequencing 93
• Identification of unknown DNA sequences 93
• Optical mapping 94
• Gene expression analysis 94
• Gene expression profiling on whole blood samples 95
• Gene expression patterns of white blood cells 95
• Gene expression profiling based on alternative RNA splicing 96
• MAUI (MicroArray User Interface) hybridization 96
• Monitoring in vivo gene expression by molecular imaging 97
• Serial analysis of gene expression (SAGE) 97
• Single-cell gene expression analysis 97
• T cell receptor expression analysis 98
• Tangerine"! expression profiling 98
• Whole genome expression array 98
• Ziplex"! system 99
• Companies involved in gene expression analysis 99
• Peptide nucleic acid technology 100
• Use of PNA with fluorescence in situ hybridization 101
• PNA and PCR 101
• Use of PNA with biosensors 102
• PNA-based PD-loop technology 102
• PNA-DNA hybrid quadruplexes 103
• Companies Involved in PNA Diagnostics 103
• Locked nucleic acids 103
• Electrochemical detection of DNA 104
• Mediated nucleic acid oxidation 104
• Detection of hybridized nucleic acid with cyclic voltametry 105
• Electrochemical detection based on Toshiba' s CMOS technology 105
• Concluding remarks on electrochemical DNA detection 106
• Scorpions"! technology 106
• The Scorpions reaction 106
• Applications of Scorpion 107

3. Biochips, Biosenors, and Molecular Labels 109

• Introduction to biochip technology 109
• Applications of biochips in diagnostics 109
• GeneChip 110
• GeneChip Human Genome Arrays 111
• AmpliChip CYP450 111
• Electronic detection of nucleic acids on microarrays 111
• Strand displacement amplification on a biochip 112
• Rolling circle amplification on DNA microarrays 112
• Fast PCR biochip 112
• Multiplex microarray-enhanced PCR for DNA analysis 112
• Multiplexed Molecular Profiling 113
• Universal DNA microarray combining PCR and ligase detection reaction 113
• Genomewide association scans 114
• Whole genome chips/microarrays 114
• Transposon insertion site profiling chip 115
• Standardizing the microarrays 115
• Companies involved in developing biochip technology for diagnostics 116
• Future of biochip technology for molecular diagnostics 117
• Microfluidic chips 117
• Fish-on-chip 118
• Lab-on-a-chip 118
• LabCD 118
• Micronics' microfluidic technology 119
• Microfluidic automated DNA analysis using PCR 119
• Microfluidic chips integrated with PET 119
• Companies developing microfluidic technologies 119
• Biosensor technologies 120
• Classification of biosensor technologies 121
• DNA-based biosensors 122
• DNA hybridization biosensor chips 122
• PCR-free DNA biosensor 122
• DNA based biosensor to detects metallic ions 122
• Genetically engineered B lymphocytes 123
• Biosensors immunoassays 123
• PNA (peptide nucleic acid)-based biosensors 124
• Protein-based biosensors 124
• Antibody biosensors 124
• Cell-based biosensors (cytosensors) 124
• Multicell biosensors 125
• Microbial biosensors 125
• Optical biosensors 126
• Surface plasmon resonance technology 126
• Label-free optical biosensor 127
• Microsensors using with nano/microelectronic communications technology 127
• Electrochemical sensors 127
• Enzyme electrodes for biosensing 127
• Conductometric sensors 128
• Electrochemical genosensors 128
• Electrochemical nanobiosensor 128
• Bioelectronic sensors 129
• Phototransistor biochip biosensor 129
• Ribozyme-based sensors 129
• RiboReporters 130
• Concluding remarks and future prospects of biosensor technology 130
• Companies developing biosensors for molecular diagnostics 131
• Molecular labels and detection 132
• Detection technologies for molecular labels 133
• Fluorescence and chemiluminescence 133
• Molecular beacons 135
• The Green fluorescent protein 136
• Multiophoton detection radioimmunoassay 136
• Multi-pixel photon counter 137
• Enzyme labels and detection by fluorescence 137
• Phase-sensitive flow cytometry 137
• Microtransponder-based DNA diagnostics 138
• Laboratory Multiple Analyte Profile 139
• Multiple labels 139
• Protein-DNA chimeras for detection of small numbers of molecules 140
• Single molecule detection 140
• Atomic force microscopy 140
• Capillary electrophoresis 140
• Confocal laser scanning 140
• Spectrally resolved fluorescence lifetime imaging microscopy 141
• Molecular imaging 141
• Basic research in molecular imaging 142
• Devices for molecular imaging 142
• Molecular imaging in clinical practice 142
• Challenges and future prospects of molecular imaging 143
• Companies involved in molecular imaging 143
• Nanobiotechnology for molecular diagnostics 143
• Magnetic nanoparticles 145
• Gold nanoparticles 145
• Quantum dot technology 146
• Nanotechnology on a chip 147
• Nanogen' s NanoChip 147
• Fullerene photodetectors for chemiluminescence detection on microfluidic chip 148
• Diagnostics based on nanopore technology 148
• Nanosensors 148
• Quartz nanobalance biosensor 148
• PEBBLE nanosensors 149
• Nanosensors for glucose monitoring 149
• Cantilever arrays 149
• Resonance Light Scattering technology 150
• DNA nanomachines for molecular diagnostics 150
• Nanobarcodes technology for molecular diagnostics 151
• Qdot nanobarcode for multiplexed gene expression profiling 151
• Role of nanobiotechnology in improving molecular diagnostics 152
• Companies involved in nanomolecular diagnostics 152
• Concluding remarks about nanodiagnostics 154
• Future prospects of nanodiagnostics 155

4. Proteomic Technologies for Molecular Diagnostics 157

• Introduction 157
• Proteomic technologies 157
• Biomarkers of disease 157
• Proteomic tools for biomarkers 157
• Search for biomarkers in body fluids 158
• Captamers with proximity extension assay for proteins 158
• Cyclical amplification of proteins 158
• Detection of misfolded proteins by ELISA with exponential signal amplification 159
• Diagnostics based on designed repeat proteins 159
• Differential Peptide Display 159
• Light-switching excimer probes 160
• MALDI-TOF Mass Spectrometry 160
• Molecular beacon aptamer 161
• Molecular beacon assay 161
• Proteomic patterns 161
• Protein biochip technologies 163
• ProteinChip 163
• LabChip for protein analysis 164
• TRINECTIN proteome chip 164
• Protein chips for antigen-antibody interactions molecular diagnostics 165
• Microfluidic devices for proteomics-based diagnostics 165
• Nanotechnology-based protein biochips/microarrays 165
• Nanoparticle protein chip 166
• Protein nanobiochip 166
• Protein biochips based on fluorescence planar wave guide technology 166
• New developments in protein chips/microarrays 167
• Antibody microarrays 167
• Aptamer-based protein biochip 167
• Multiplexed Protein Profiling on Microarrays 168
• Proteomic pattern analysis 168
• Single molecule array 168
• Viral protein chip 169
• Commercial development of protein chips for molecular diagnostics 169
• Proteome Identification Kit 170
• Laser capture microdissection (LCM) 171
• LCM technology 171
• Applications of LCM in molecular diagnostics 171
• Proteomic diagnosis of CNS disorders 172
• Cerebrospinal fluids tests based on proteomics 172
• Urine tests for CNS disorders based on proteins in urine 173
• Diagnosis of CNS disorders by examination of proteins in the blood 173
• Diagnosis of CNS disorders by examination of proteins in tears 174
• Role of proteomics in the diagnosis of Alzheimer' s disease 174
• Role of proteomics in the diagnosis of Creutzfeldt-Jakob disease 175
• Future prospects of use of proteomics for diagnosis of CNS disorders 175
• Concluding remarks on the use of proteomics in diagnostics 175

5. Molecular Diagnosis of Genetic Disorders 177

• Introduction 177
• Cytogenetics 178
• FISH with probes to the telomeres 178
• Single copy FISH probes 178
• Comparative genomic hybridization 179
• Use of biochips in genetic disorders 179
• Representational oligonucleotide microarray analysis 180
• SignatureChipR-based diagnostics for cytogenetic abnormalities 180
• Diagnosis of genomic rearrangements by multiplex PCR 180
• Quantitative fluorescent PCR 180
• Mutation detection technologies 181
• PCR-based methods for mutation detection 182
• Cleavase Fragment Length Polymorphism 182
• Direct dideoxy DNA sequencing 182
• Digital Genetic Analysis (DGA) 182
• Fluorescence-based directed termination PCR 183
• Heteroduplex analysis 183
• Restriction fragment length polymorphism 184
• Single-stranded conformation polymorphism (SSCP) analysis 184
• TaqMan real-time PCR 184
• Non-PCR methods for mutation detection 185
• Arrayed primer extension 185
• BEAMing (beads, emulsion, amplification, and magnetics) 185
• ELISA-protein truncation test 185
• Enzymatic mutation detection 186
• Specific anchor nucleotide incorporation 186
• Conversion analysis for mutation detection 186
• Biochip technologies for mutation detection 187
• Combination of FISH and gene chips 187
• Haplotype Specific Extraction 188
• Technologies for SNP analysis 188
• DNA sequencing 189
• Electrochemical DNA probes 189
• Use of NanoChip for detection of SNPs 190
• Single base extension-tag array 190
• Laboratory Multiple Analyte Profile 190
• SNP genotyping with gold nanoparticle probes 191
• PCR-CTPP (confronting two-pair primers) 191
• Peptide nucleic acid probes for SNP detection 191
• SNP genotyping on a genome-wide amplified DOP-PCR template 191
• Pyrosequencing 192
• Reversed enzyme activity DNA interrogation test 192
• Smart amplification process version 2 193
• Zinc finger proteins 193
• UCAN method (Takara Biomedical) 193
• Biochip and microarray-based detection of SNPs 194
• SNP genotyping by MassARRAY 194
• Electronic dot blot assay 194
• Biochip combining BeadArray and ZipCode technologies 195
• SNP-IT primer-extension technology 195
• OmniScan SNP genotyping 195
• Affymetrix SNP genotyping array 196
• Concluding remarks on SNP genotyping 196
• Limitations of SNP in genetic testing 196
• Haplotyping versus SNP genotyping 197
• Determination of copy number variations 197
• Companies involved in developing technologies/products for SNP analysis 197
• Prenatal DNA diagnosis 199
• Amniocentesis 199
• Chorionic villus sampling 199
• Separating fetal cells in maternal blood for genetic diagnosis 199
• Antenatal screening for Down' s syndrome 200
• Fetal DNA in maternal blood 200
• Molecular methods for prenatal diagnosis 201
• FISH for prenatal diagnosis 201
• PCR for prenatal diagnosis 201
• Plasma DNA sequencing to detect fetal chromosomal aneuploidies 202
• In vivo gene expression analysis of the living human fetus 202
• Noninvasive prenatal diagnosis of monogenic diseases 202
• Digital relative mutation dosage 203
• Massively parallel plasma DNA sequencing 203
• Applications of prenatal diagnosis 203
• Diagnosis of congenital infections 204
• Diagnosis of eclampsia 205
• Use of transrenal DNA for prenatal testing 205
• Preimplantation genetic diagnosis 205
• Technologies for preimplantation genetic diagnosis (PGD) 206
• PCR for preimplantation genetic diagnosis 206
• FISH for preimplantation genetic diagnosis 206
• Microarrays for preimplantation genetic diagnosis 207
• Conditions detected by preimplantation genetic diagnosis 207
• The future of preimplantation genetic diagnosis 207
• Companies involved in prenatal/preimplantation diagnosis 208
• Cystic fibrosis 209
• Detection of CFTR gene mutations 209
• CFTR technologies of various companies 210
• Genzyme' s CF gene sequencing 210
• CF Plus™ Tag-It Cystic Fibrosis Kit 211
• Asuragen' s bead array test 211
• The Ambry CF Test 212
• Biochip for CF diagnosis 212
• MassARRAYR system for high-throughput CFTR testing 212
• Serum proteomic signature for CF using antibody microarrays 213
• Guidelines for genetic screening for CF 213
• Congenital adrenal hyperplasia 213
• Primary immunodeficiencies 214
• Hematological disorders 215
• Hemoglobinopathies 215
• Sickle cell anemia 215
• Thalassemia 215
• Paroxysmal nocturnal hemoglobinuria 216
• Hemophilia 216
• Hereditary hemochromatosis 216
• Polycystic kidney disease 217
• Hereditary metabolic disorders 217
• Lesch-Nyhan Syndrome 217
• Gaucher' s Disease 218
• Acute Intermittent Porphyria 218
• Phenylketonuria 218
• Hereditary periodic fever 219
• Achondroplasia 219
• Molecular diagnosis of cardiovascular disorders 219
• Coronary Heart Disease 220
• Cardiomyopathy 221
• Familial Hypertrophic Cardiomyopathy 221
• Idiopathic dilated cardiomyopathy 221
• Cardiac Arrhythmias 221
• Long Q-T Syndrome 222
• Familial atrial fibrillation 222
• Idiopathic ventricular fibrillation 222
• Congestive heart failure 222
• Hypertension 223
• Disturbances of blood lipids 223
• Familial dyslipoproteinemias 223
• Hypercholesterolemia 224
• Thrombotic disorders 224
• Factor V Leiden mutation 224
• Pulmonary embolism 225
• Molecular diagnosis of eye diseases 225
• Molecular diagnosis of retinitis pigmentosa 225
• Genetic screening for glaucoma 226
• Role of molecular diagnostics in rheumatoid arthritis 226
• Molecular diagnosis of neurogenetic disorders 227
• Alzheimer' s disease 228
• Down syndrome 229
• Parkinson' s disease 229
• Spinal muscular atrophy 230
• Duchenne and Becker muscular dystrophy 230
• Triple repeat disorders 230
• Huntington disease 231
• Fragile X syndrome 232
• Charcot-Marie Tooth disease 232
• Hereditary neuropathy with liability to pressure palsies 232
• eNOS gene polymorphisms as predictor of cerebral aneurysm rupture 233
• Mitochondrial disorders affecting the nervous system 233
• Genetic testing for disease predisposition 234
• Direct-to-consumer genetic tests 234

6. Molecular Diagnosis of Infections 237

• Introduction 237
• Molecular techniques for the diagnosis of infections 237
• Antibody-enhanced microplate hybridization assays 238
• Biosensors for detection of microorganisms 238
• Ibis T5000"! Biosensor System 238
• DNA enzyme immunoassay 239
• DNA biochip/microarray in diagnosis of infections 239
• DNA-based typing methods 240
• Restriction fragment length polymorphism analysis 240
• Ribotyping 240
• Random amplified polymorphic DNA 240
• Combinatorial DNA melting assay 240
• Electrochemical detection of pathogens 241
• NASBA for detection of microorganisms 241
• Optical Mapping 241
• PCR-based multiplex rapid detection of sepsis 242
• LightCyclerR SeptiFast Test 242
• VYOOR Sepsis Test 242
• Two-step quantitative reverse-transcription PCR for bacterial diagnostics 242
• Ligase chain reaction 243
• Metagenomic pyrosequencing 243
• Multiplex PCR for detection of infections 244
• Dual priming oligonucleotide for multiplex PCR 245
• Nucleic acid probes 245
• Neutrophil CD11b expression as a diagnostic marker 245
• PNA-FISH for diagnosis of infections 246
• Rupture event scanning 246
• Real-time single-molecule imaging of virus particles 246
• Single-strand conformational polymorphism 246
• SmartGene platform for identifying pathogens based on genetic sequences 247
• Tessera array technology 247
• Applications, advantages and limitations of molecular diagnostics 247
• Molecular diagnostics versus other microbial detection technologies 247
• Advantages of nucleic acid-based diagnostics in infections 248
• Drawbacks of nucleic acid-based diagnostics in infections 248
• Nanotechnology for detection of infectious agents 249
• Bacterial and fungal infections 249
• Mycobacterium tuberculosis 251
• Conventional diagnosis of tuberculosis 251
• Microscopic Observation Drug Susceptible Assay for tuberculosis 251
• Molecular diagnostics for tuberculosis 252
• Combined tuberculin testing and ELISpotPLUS assay 253
• Biomarkers for tuberculosis 254
• Diagnosis of drug-resistant M. tuberculosis infection 254
• Cost-effectiveness of PCR in tuberculosis screening 255
• Other mycobacteria 255
• Chlamydial infections 255
• Neisseria gonorrhoeae 257
• Bacteria associated with bacterial vaginosis 257
• Streptococcal infections 257
• Group B Streptococci 257
• Streptococcus pyogenes and Streptococcus dysgalactiae 258
• Pseudomonas aeruginosa 258
• Helicobacter pylori 259
• Lyme disease 259
• Mycoplasmas 260
• Fungal infections 260
• Viral infections 261
• HIV/AIDS 262
• Diagnosis of HIV 262
• Neonatal screening of infants of HIV-positive mothers 263
• Screening of cadaveric tissue donors 263
• Detection of HIV provirus 263
• Resolution of indeterminate Western blot 263
• Global Surveillance of HIV-1 genetic variations 264
• Genotyping for drug-resistance in HIV 264
• Phenotyping as predictor of drug susceptibility/resistance in HIV 265
• Tests used for quantification of HIV 266
• Conclusions about HIV genotyping 266
• Hepatitis viruses 267
• Hepatitis A virus 267
• Hepatitis B virus 268
• Hepatitis C virus 268
• Detection and quantification of HCV RNA 269
• Quantification of HCV RNA levels as a guide to antiviral therapy 270
• Electrochemical DNA chip for diagnosis of HCV 270
• HCV Genotyping as a guide to therapy 270
• Enteroviruses 271
• Adenoviruses 272
• Rhinoviruses 272
• Herpes viruses 272
• Herpes simplex virus 272
• Genital and neonatal herpes simplex 273
• Human cytomegalovirus infections 273
• Epstein-Barr virus 273
• Human papilloma virus 274
• Molecular diagnostics for HPV 274
• Detection of encephalitis viruses 275
• West Nile and St. Louis encephalitis 275
• Venezuelan equine encephalitis virus 275
• Protozoal infections 276
• Amebiasis 276
• Cryptosporidium parvum 276
• Malaria 276
• Neurocysticercosis 277
• Pneumocystis carinii 277
• Toxoplasmosis 277
• Infections of various systems 278
• CNS infections 278
• Molecular diagnosis in bacterial meningitis 278
• Molecular diagnosis in herpes simplex encephalitis 278
• Diagnosis of transmissible spongiform encephalopathies 279
• Molecular diagnosis of respiratory viruses 280
• SARS-associated coronavirus 280
• Influenza viruses 281
• Avian influenza 283
• Swine influenza 286
• Gastrointestinal infections 287
• Periodontal infections 288
• Diagnosis of urinary infections by a biosensor 289
• Role of molecular diagnostics in septicemia 290
• Limitations and needs of diagnostics for infections 290
• Differentiation between live and antibiotic-killed bacteria 291
• Cell-based methods for identifying pathogenic microorganisms 291
• Cell-based virus assays 291
• Cell-based detection of host response to infection 292
• Role of molecular diagnostics in hospital acquired infections 292
• Detection of hospital-acquired bacterial infections 292
• Detection of methicillin-resistant S. aureus 292
• Detection of vancomycin-resistant enterococci 293
• Detection of hospital-acquired C. difficile 293
• Bacterial genome sequencing in antimicrobial resistance 294
• Detection of hospital-acquired viral infections 294
• Molecular diagnosis of BK virus 294
• Diagnosis of hospital-acquired rotavirus gastroenteritis 295
• Molecular diagnostics and the microbiome 295
• Human Microbiome Project 295
• Application of metagenomics to study of the microbiome 296
• MicroBiome Analysis Center 296
• Concluding remarks and future prospects of diagnosis of infections 297
• Rapid point-of-care diagnosis of infection 297
• Diagnosis of viruses using protein fingerprinting 299
• QIAplex PCR multiplex technology 299
• Companies involved in molecular diagnosis of infectious diseases 300

7. Molecular Diagnosis of Cancer 303

• Introduction 303
• Cancer Genetics 303
• Oncogenes 303
• Tumor Suppressor Genes 304
• p53 305
• p16 305
• Viruses and cancer 306
• Conventional cancer diagnosis 306
• Molecular techniques for cancer diagnosis 307
• Genome analysis at the molecular level 309
• Mutation detection at molecular level 309
• Expression profiling of tumor cells sorted by flow cytometry 309
• MicroRNA expression profiling to classify human cancers 310
• Biomarkers in cancer 310
• Sequencing-based approaches for detection of cancer biomarkers 311
• eTag assay system for cancer biomarkers 311
• HAAH as a biomarker for cancer 312
• Methods for detection of DNA methylation 312
• Circulating nucleosomes in serum of cancer patients 314
• LigAmp for detection of gene mutations in cancer 314
• Mitochondrial DNA as a cancer biomarker 315
• Molecular fingerprinting of cancer 315
• Fluorescent in situ hybridization 316
• Genetic analysis of cancer 316
• Comparative genomic hybridization in cancer diagnostics 316
• Loss of heterozygosity 316
• Digital karyotyping 317
• Gene expression profiles predict chromosomal instability in tumors 317
• PCR Techniques 318
• Realtime quantitative PCR for diagnosis of cancer 318
• Cold-PCR 318
• Monoclonal antibodies for diagnosis of cancer 319
• Combined immunological and nucleic acid tests 320
• Combination of MAbs and RT-PCR 320
• Immunobead RT-PCR 320
• Assays for determining susceptibility to cancer 320
• Gene expression profiling in cancer 321
• Microarrays for gene expression profiling in cancer 321
• Serial analysis of gene expression (SAGE) 322
• Suppression subtractive hybridization 322
• Measurement of telomerase activity 322
• Survivin and molecular diagnosis of cancer 323
• Detection of cancer cells in blood of patients with solid tumors 324
• Epithelial aggregate separation and isolation 325
• DNA tags for finding genes expressed in cancer 325
• Oncoproteins as biomarkers for cancer 325
• HER-2/neu oncoprotein 325
• Proteomic technologies for the molecular diagnosis of cancer 326
• Laser capture microdissection in oncology 326
• Proteomic technologies for tumor markers 326
• Automated image analysis of nuclear protein distribution 327
• Affibodies as contrast agents for imaging in cancer 327
• Layered expression scanning 328
• Aptamer-based technology for protein signatures of cancer cells 328
• Aptamers for combined diagnosis and therapeutics of cancer 329
• Biochip/microarrays for cancer diagnosis 329
• Role of DNA microarrays in gene expression profiling 330
• Biochip detection of FHIT gene 330
• Nanotechnology for early detection of cancer 330
• Quantum dots for early detection of cancer 331
• Magnetic nanoparticle probes 331
• Detection of nanoparticle self assembly in tumors by MRI 331
• Molecular imaging of cancer 331
• PET for in vivo molecular diagnosis of cancer 331
• Xenon-enhanced MRI 332
• Optical systems for in vivo molecular imaging of cancer 332
• Recombinant antibodies as a novel approach to cancer diagnosis 333
• Detection of micrometastases 333
• Molecular diagnosis of cancers of various organs 334
• Brain tumors 334
• Molecular diagnostic methods for brain tumors 334
• Glioblastoma multiforme 334
• Circulating microvesicles as biomarkers of glioblastoma 335
• Combination of neuroimaging and DNA microarray analysis in GBM 335
• Medulloblastoma 336
• Oligodendroglioma 336
• Advantages and limitations of molecular diagnosis of brain tumors 336
• Breast cancer 337
• Breast cancer genes 337
• Molecular diagnostic tests for breast cancer 338
• Mouse ESC-based assays to evaluate mutations in BRCA2 340
• Genomic profiles of breast cancer 340
• Role of molecular diagnostics in management of breast cancer 341
• Tests for prognosis of breast cancer 344
• Prediction of recurrence in breast cancer for personalizing therapy 346
• Cervical cancer 347
• Colorectal cancer 348
• Diagnosis of hereditary nonpolyposis colorectal cancer 348
• Detection of familial adenomatous polyposis coli 349
• Diagnosis of colorectal cancer from DNA in stools 349
• Detection of circulating tumor cells in colorectal cancer 349
• Minimally invasive screening for colorectal cancer 350
• Guanylyl cyclase C tests for colorectal cancer 350
• Early diagnosis of colorectal cancer from blood samples 350
• Head and neck cancer 351
• Hematological malignancies 351
• Chromosome translocations 351
• Flow cytometry in diagnosis of leukemia 351
• Gene chip technology 352
• Laboratory assessment of leukemia 352
• Molecular probes 353
• Minimal residual disease 353
• Screening of gene mutations in chronic myeloproliferative diseases 354
• Lung cancer 354
• Melanoma 356
• Ovarian cancer 357
• Mutation of genes 357
• Relevance of genetic testing to management of ovarian cancer 357
• Serum biomarkers for early detection of ovarian cancer 358
• Biomarkers of ovarian cancer 358
• Concluding remarks on testing for ovarian cancer 359
• Pancreatic cancer 359
• Prostate cancer 359
• Gene expression analysis of prostate cancer by microarrays 360
• Huntingtin Interacting Protein 1 360
• Integrative genomic and proteomic profiling of prostate cancer 360
• LCM for diagnosis of prostate cancer 361
• PCA3 gene detection in urine 361
• PCR assay for assessing silencing of protein cadherin 13 gene 362
• Prostate biopsy for detection of prostatic intraepithelial neoplasia 362
• Screening of multiple SNPs for risk of prostate cancer 362
• Semen testing for prostate cancer biomarkers 363
• Serum-protein fingerprinting in prostate cancer 363
• Thyroid cancer 364
• Gene expression biomarkers of thyroid cancer 364
• Multiple endocrine neoplasia type 2B as risk factor for thyroid cancer 365
• miRNA expression profiling in thyroid cancer 365
• Urinary bladder cancer 365
• Role of molecular diagnostics in the management of cancer 366
• Risk assessment and prevention of cancer 366
• Role of molecular diagnosis in the design of future cancer therapies 366
• Molecular classification of cancer 367
• Determination of cancer prognosis 367
• Prognosis by tumor classification 367
• Prognosis by cancer gene expression 367
• Selection of anticancer drugs based on molecular diagnosis 368
• Integrated genome-wide analysis of cancer for diagnosis and therapy 368
• Personalized therapy for cancer patients 369
• Pharmacogenetics and cancer therapy 369
• Molecular diagnostics as an aid to selection of cancer therapy 369
• Drug resistance in cancer 370
• Role of organizatons in molecular diagnosis of cancer 370
• Role of NCI in molecular diagnosis of cancer 370
• Molecular profiling of cancer 371
• Cancer Genome Atlas 371
• Cancer Genetic Markers of Susceptibility Project 372
• Support for future research in molecular diagnosis of cancer 372
• Role of the International Cancer Genome Consortium 372
• Future prospects of molecular diagnosis of cancer 373
• Companies involved in molecular diagnosis of cancer 374

8. Molecular Diagnostics in Biopharmaceutical Industry & Healthcare 379

• Introduction 379
• Molecular diagnostics in biopharmaceutical industry 379
• Molecular diagnostic technologies and drug discovery 379
• Molecular diagnostics and pharmacogenetics 380
• Molecular toxicology 381
• Gene expression studies 382
• Toxicogenomics 382
• Toxicoproteomics 383
• Mitochondrial assays 384
• MetaChip 384
• Molecular diagnostics and pharmacogenomics 385
• Applications molecular diagnostics in gene therapy 386
• Use of PCR to study biodistribution of gene therapy vector 386
• PCR for verification of the transcription of DNA 386
• In situ PCR for direct quantification of gene transfer into cells 387
• Detection of retroviruses by reverse transcriptase (RT)-PCR 387
• Assessment of safety issues of gene transfer 387
• Quantitative PCR for monitoring the effectiveness of gene therapy 387
• Use of FISH for analysis of adeno-associated viral vector integration 387
• Monitoring of gene expression by green fluorescent protein 388
• Detection of microbial contamination in biopharmaceutical manufacturing 388
• Role of PCR in detecting contamination of biopharmaceuticals 388
• Contamination of biopharmaceuticals with prions 388
• DNA tagging for control and tracing of drug distribution channels 389
• Molecular diagnostics for organ transplantation 389
• Tissue typing 389
• Commercial products for transplant molecular diagnostics 390
• Post-cardiac transplant patient monitoring for rejection 392
• Blood Transfusion Screening 393
• Molecular tests for screening of blood supply for viruses 394
• Commercial molecular diagnostic technologies for blood screening 394
• Bridge Amplification Technology 395
• COBAS AmpliScreen HCV and HIV Assays 395
• INACTINE 395
• NucliSens Extractor system 396
• Pall' s enhanced Bacteria Detection System 396
• PCR combined with algorithm method 397
• Prions detection in human blood 397
• PRISMR automated system 397
• Procleix HIV-1/HCV Assay 398
• West Nile virus detection in human blood 398
• Limitations of molecular diagnostics for blood screening 398
• Molecular epidemiology 399
• Molecular epidemiology of genetic diseases 400
• Monogenic versus polygenic disorders 400
• Critical issues facing genetic epidemiology 400
• Molecular epidemiology of infectious diseases 400
• Methods and purposes 400
• Emerging infections 401
• Human vs. non-human infections 402
• Genetics and susceptibility to infectious disease 402
• Molecular epidemiology of cancer 402
• Molecular epidemiology of p53 gene mutations 403
• Molecular epidemiology of link between virus and cancer 403
• Molecular epidemiology and cancer prevention 403
• SNPs and molecular epidemiology 403
• Molecular diagnostics for identification of food-borne pathogens 404
• Introduction 404
• Molecular diagnostic methods used in food-borne infections 404
• Limitations of use of molecular probes in food analysis 405
• Optical biosensor for detection of Listeria-contaminated foods 406
• Companies with technologies for food pathogen detection 406
• Transmissible spongiform encephalopathies (TSEs) 407
• Molecular diagnosis of TSEs 407
• Companies involved in developing molecular diagnostics for TSEs 410
• Detection of genetically modified organisms in food 411
• Molecular diagnostics for detection of doping in sports 412
• Screening of synthetic glucocorticosteroids in human urine 412
• Detection of gene doping 412
• Role of molecular diagnostics in future healthcare 413
• Translation of genomic research into genetic testing for healthcare 413
• Molecular diagnostics and disease management 414
• Role of genetic biomarkers in disease management 414
• Role of molecular diagnostics in personalized medicine 414
• Integrated healthcare 415
• Screening 415
• Early diagnosis 415
• Prevention 415
• Therapy based on molecular diagnosis 416
• Monitoring of therapy 416
• Advantages and limitations of integrated healthcare 416
• Commercially available systems for integrated healthcare 417
• Combination of diagnostics and therapeutics 417
• Companies combining diagnostics and therapeutics 417
• Point-of-care diagnosis 418
• Technologies for point-of-care diagnosis 419
• Biochips for point-of-care diagnosis 420
• Companies developing point-of-care diagnosis 421
• Advantages versus disadvantages of point-of-care diagnosis 423
• The impact of molecular diagnostics on clinical laboratory practice 424

9. Molecular Diagnostics in Forensic Medicine and Biological Warfare 425

• Application of molecular diagnostics in forensic medicine 425
• Technologies 425
• Extraction of DNA from forensic samples 425
• Mitochondrial DNA (mtDNA) analysis 426
• Polymorphic Alu insertions 426
• Single Nucleotide Polymorphisms (SNP) analysis 427
• Short tandem repeat (STR) 427
• Fluorescent detection systems 428
• ABO genotyping 428
• DNA analysis for identification of ancient or historical specimens 428
• Applications 428
• Applications in criminology 429
• Identification of remains of military personnel 430
• Identification of remains of victims of mass disasters 430
• Parentage testing 431
• Gender determination 432
• Companies developing molecular diagnostics for forensic science 433
• Molecular detection of biological warfare agents 434
• Introduction to biological warfare agents 434
• Role of PCR in the diagnosis of biological warfare agents 435
• Multiplex PCR microarray assay to detect bioterror pathogens in blood 435
• Laboratory diagnosis of Anthrax 436
• Challenges in diagnosis of biological warfare agents 436
• US government efforts for detection of biological warfare agents 437
• The US Army Medical Research Institute of Infectious Diseases 437
• Homeland Security Advance Research Projects Agency 438
• Commercial development of diagnostic devices for biological agents 438
• Companies developing diagnostic devices for biological agents 438
• Biodefence microarray 441
• Identification of genetic markers of individual pathogens 441
• Microbial Identification System based on OptiChip"! 442
• Hand-Held Advanced Nucleic Acid Analyzer 442
• Nanogen' s portable detection device 442
• Nanode Array Sensor Microchips 443
• MicroChemLab 443
• BioThreat Alert Test Strip 443
• Benchtop living cell biosensor 444
• BioForce NanoArray sensor technology 444
• QTL handheld biosensor 444
• Analyte 2000 biosensor 445
• Airborne bacterial spore detection technology 445
• Destruction and detection of anthrax by lysin 445
• Biosensor based on mass spectrometry of microorganisms' s RNA 445
• Bead ARray Counter 446
• ProteinChip-based detection of bioterroism agents 446
• TIGER biosensor 446
• The PathAlert™ Detection System 447
• VereThreat"! 447
• Concluding remarks about biodefense applications of diagnostics 447

10. References 449

Tables

• Table 1 1: Landmarks in development of molecular technology and its application to diagnosis 23
• Table 1 2: Applications of molecular diagnostics 42
• Table 2 1: Companies with products for nucleic acid isolation 51
• Table 2 2: Some commercially available real-time PCR systems 53
• Table 2 3: Applications of real-time PCR 55
• Table 2 4: A selection of companies with commercially available FISH diagnostics 80
• Table 2 5: Selected companies with RNA diagnostic tests 81
• Table 2 6: Companies involved in whole genome amplification 89
• Table 2 7: Companies involved in sequencers 92
• Table 2 8: Comparison of methods of identification of unknown DNA sequences 93
• Table 2 9: Classification of methods of gene expression analysis 94
• Table 2 10: A selection of companies with gene expression technologies 99
• Table 2 11: Companies involved in developing PNA diagnostics 103
• Table 3 1: Applications of biochip technology in relation to molecular diagnostics 109
• Table 3 2: Companies developing whole genome chips/microarrays 115
• Table 3 3: Companies involved in biochips for molecular diagnostics 116
• Table 3 4: Companies developing microfluidic technologies 120
• Table 3 5: Biosensor technologies with potential applications in molecular diagnostics 121
• Table 3 6: Important applications of biosensors 131
• Table 3 7: Companies involved in application of biosensors in molecular diagnostics 131
• Table 3 8: Selected labels for nucleic acid detection 133
• Table 3 9: Selected companies with fluorescence and chemiluminescence products 134
• Table 3 10: Companies involved in molecular beacon manufacture and research 136
• Table 3 11: Companies involved in developing molecular imaging 143
• Table 3 12: Nanotechnologies with potential applications in molecular diagnostics 144
• Table 3 13: Companies developing nanomolecular diagnostics 152
• Table 4 1: Applications of protein biochips/microarrays 163
• Table 4 2: Companies involved in developing diagnostic applications of protein biochips 169
• Table 4 3: Disease-specific proteins in the cerebrospinal fluid of patients 172
• Table 5 1: Mutation detection technologies 181
• Table 5 2: Technologies for SNP analysis 188
• Table 5 3: A sampling of companies involved in technologies for SNP genotyping 197
• Table 5 4: Application of preimplantation genetic diagnosis in monogenic disorders 207
• Table 5 5: Companies involved in prenatal/preimplantation diagnostics 208
• Table 5 6: CFTR genotyping in cystic fibrosis - companies and technologies 210
• Table 5 7: X-linked immunodeficiency disorders 214
• Table 5 8: Genes that cause cardiovascular diseases 220
• Table 5 9: Available molecular diagnostics for neurogenetic diseases 227
• Table 5 10: Companies offering genetic screening tests directly to consumers 235
• Table 6 1: Molecular techniques for the diagnosis of infections 237
• Table 6 2: Bacteria and fungi that can be detected by recombinant DNA tests 250
• Table 6 3: Viruses that can be detected by recombinant DNA methods 261
• Table 6 4: Companies with molecular diagnostics for avian influenza virus H5N1 283
• Table 6 5: Companies developing POC tests for the diagnosis of infections 298
• Table 6 6: Selected companies involved in molecular diagnosis of infections 300
• Table 7 1: Estimated new cases of cancer in the US at most involved organs - 2008 303
• Table 7 2: Tumor suppressor genes, their chromosomal location, function, and associated tumors 304
• Table 7 3: Viruses linked to human cancer 306
• Table 7 4: A classification of molecular diagnostic methods in cancer 308
• Table 7 5: Desirable characteristics of biomarkers for cancer 310
• Table 7 6: Approved monoclonal antibodies for cancer diagnosis 320
• Table 7 7: Methods for comparison of gene-expression profilling in tumor specimens 321
• Table 7 8: Impact of in vivo molecular imaging of cancer on oncology practice 333
• Table 7 9: Companies developing cancer molecular diagnostics 374
• Table 8 1: Applications of molecular diagnostics in the biopharmaceutical industry 379
• Table 8 2: Molecular diagnostic technologies for drug discovery 380
• Table 8 3: Molecular diagnostic technologies used for pharmacogenetic studies 380
• Table 8 4: Companies with novel molecular toxicology technologies 381
• Table 8 5: Applications of molecular diagnostics in gene therapy 386
• Table 8 6: Companies involved in transplant molecular diagnostics 391
• Table 8 7: Companies involved in molecular diagnostics of blood transfusions 394
• Table 8 8: Pathogenic bacteria in food and targets for molecular diagnostic probes 405
• Table 8 9: Companies involved in molecular diagnostics for food-borne infections 406
• Table 8 10: Testing for harmful prions in brain tissue from dead cattle 408
• Table 8 11: Companies involved in developing molecular diagnostics for TSEs 411
• Table 8 12: Companies combining molecular diagnostics and therapeutics 417
• Table 8 13: Applications of point-of-care diagnosis 419
• Table 8 14: Companies developing point-of-care diagnostic tests 422
• Table 9 1: Forensic and legal applications of molecular diagnostics. 428
• Table 9 2: Molecular technologies used for forensic applications 433
• Table 9 3: Classification of biological and chemical agents used as weapons of mass destruction 434
• Table 9 4: Biological warfare agents that can be identified by PCR methods 435
• Table 9 5: Companies developing detection devices for biological warfare agents 439

Figures

• Figure 1 1: Relation of molecular diagnostics to other technologies 43
• Figure 2 1: Rolling circle amplification technology 63
• Figure 2 2: A schematic view of the Invader operating system 71
• Figure 2 3: Principle of fluorescent in situ hybridization 75
• Figure 2 4: Repli-G system of Qiagen 90
• Figure 2 5: DNA sequencing process 91
• Figure 2 6: Electrochemical detection of DNA 105
• Figure 2 7: Elements of a Scorpions primer 106
• Figure 3 1: Affymetrix GeneChip technology 110
• Figure 3 2: Basic principle of a biosensor 121
• Figure 3 3: Surface plasmon resonance (SPR) technology 126
• Figure 6 1: Use of DNA chips in diagnosing microbial infections 239
• Figure 6 2: High throughput DNA pyrosequencing for pathogen discovery 244

Part 2

11. Ethics, Patents and Regulatory issues 11

• Introduction 11
• Ethical concerns about genetic diagnosis 11
• Ethical guidelines for molecular diagnostics 12
• Ethical and regulatory aspects of direct-to-consumer genetic services 13
• Genetic testing for susceptibility to adult-onset cancer 15
• Ethics of preimplantation genetic diagnosis 15
• Preimplantation genetic diagnosis to screen for hereditary diseases 15
• PGD to test for susceptibiliy to cancer 16
• PGD and stem cells 16
• Genetic research on stored tissues 17
• Informed consent in clinical trials of in vitro devices 17
• Concluding remarks about ethical issues 17
• Insurance underwriting and gene tests 18
• Should genetic information be available to health insurers? 18
• A need for the re-examination of current views 19
• Genetic Information Nondiscrimination Act of US 19
• Patents for molecular diagnostics 19
• PCR patents 19
• Patenting DNA sequences 19
• US policy on gene patenting relevant to molecular diagnostics 20
• The impact of disease gene patents on molecular diagnostics 21
• Licensing problems associated with genetic testing 21
• Role of the WHO in genetic testing standards 21
• Regulatory issues in the US 22
• Regulation of IVD by the FDA 22
• FDA guidance for IVDs to detect pathogens 23
• Regulation of in vivo diagnostics by the FDA 24
• Regulation of analytic-specific reagents 24
• Regulatory aspects of FISH 24
• FDA' s Microarray Quality Control 25
• Regulation of genetic testing 25
• Role of the FDA in genetic testing 25
• Genetic testing of rare disorders 26
• Quality control of molecular diagnostic laboratory procedures 26
• Assessment of diagnostic accuracy 27
• Sensitivity and specificity 27
• Documentation of diagnostic accuracy 28
• Discovery of incidental findings on genetic screening 28
• Regulatory issues concerning blood and plasma products 29
• Quality control of point-of-care tests 29
• FDA and point-of-care diagnosis 29
• Evaluation of companion diagnostics/therapeutic for cancer 30
• FDA regulation of multivariate index assays 30
• United States Diagnostics Standards 31
• Assay Migration Studies for In Vitro Diagnostic Devices 32
• Regulation of in vitro diagnostics in the EU 32
• EU regulations for testing of blood products 33
• Regulation of genetic testing in EU 33
• Evaluation of diagnostic laboratory tests in the UK 33
• Pre-implantation genetic diagnosis in the UK 34

12. Markets for Molecular Diagnostics 35

• Introduction 35
• Methods for study of molecular diagnostic markets 35
• The overall market for diagnostic technologies 36
• Molecular diagnostic markets according to technologies 36
• Marketing strategies according to technologies 37
• Nucleic acid isolation market 37
• Market for PCR-based tests 37
• DNA sequencing market 37
• Cytogenetic market 38
• Market for FISH technologies 38
• Biochip/microarray market 38
• Biosensor market 39
• Nanobiotechnology for molecular diagnostics 39
• Markets for gene expression technologies 39
• Reagents and other disposable laboratory materials 39
• Market for immunochemistry diagnostic 39
• Markets for tissue diagnostics 40
• Molecular diagnostic markets according to therapeutic areas 40
• Genetic disorders 41
• Prenatal testing 42
• Cancer 42
• Potential markets for cancer diagnosis according to type of cancer 43
• Infectious diseases 43
• Sexually transmitted diseases 44
• Hospital-acquired infections 44
• Testing for HIV drug resistance 46
• Potential markets for avian influenza diagnostics 46
• Cardiovascular diseases 46
• Neurological disorders 46
• Food testing 47
• Screening of blood for transfusion 47
• Tissue typing for transplantation 47
• Marketing opportunities according to geographic areas 47
• Unmet needs in molecular diagnostics 48
• Major market trends 49
• Decentralization of molecular diagnostics 49
• Point-of-care testing 49
• Development of personalized medicine 50
• Cost of sequencing the human genome 50
• Cost of genotyping 50
• Development of low-cost tests 51
• Simplification of test procedures 51
• Increasing role of proteomics in clinical diagnostics 52
• Forensic and legal applications 52
• Marketing strategies 52
• Role of alliances in commercialization of molecular diagnostics 53
• Acquisitions vs collaborations 53
• Analysis of collaborations in molecular diagnostics 55
• Licensing of the technologies 56
• Strategies related to laboratory facilities and technologies 56
• Strategies relevant to the healthcare system 57
• Cost-Benefit studies 57
• Genetic susceptibility testing 57
• Preventive medicine strategies 58
• Targeting treatable and common diseases 58
• Information/education 58
• Physician education 58
• Patient education 59
• European diagnostic information platform 59
• Regulatory strategies 60
• Merger of in vitro and in vivo diagnostics 60
• Integration of diagnostics with therapeutics 60
• Diagnostic applications in clinical trials 61
• Prospects for development of new technologies 61
• Drivers for the development of molecular diagnostics 61
• Factors slowing the development of molecular diagnostics 61
• Government support of research relevant to molecular diagnostics 62
• Cost of sequencing the human genome 62
• European projects for improving molecular diagnostics 64
• European Consortium for developing new DNA analysis tools 64
• EU project for improvement of IVD tools procedures 65
• Genetic knowledge parks in the UK 65
• Molecular diagnostic opportunities in defense against bioterrorism 65
• Molecular diagnostics for food safety 66
• POC diagnostics for the developing countries 66

13. Companies involved in molecular diagnostics 67

• Introduction 67
• Major players in molecular diagnostics 67
• Profiles of selected companies 68
• Collaborations 407

Tables

• Table 12 1: Share of in vitro diagnostics in the global diagnostic market 2008-2018 36
• Table 12 2: Molecular diagnostics markets according to technologies from 2008-2018 36
• Table 12 3: Molecular diagnostics markets according to applications 2008-2018 40
• Table 12 4: Markets in 2008 for tests to screen healthy persons for genetic disorders 41
• Table 12 5: Markets in 2008 for molecular diagnostic tests for cancer 42
• Table 12 6: Molecular diagnostic markets for selected cancers 2008-2018 43
• Table 12 7: Markets value in 2008 for molecular diagnostic screening for infections 44
• Table 12 8: Future markets for HAI diagnostics 2008-2013 45
• Table 12 9: Molecular diagnostic markets according to geographical areas 2008-2018 47
• Table 12 10: Marketing strategies for molecular diagnostics 52
• Table 12 11: Takeovers of molecular diagnostic companies 53
• Table 12 12: Advantages of the integration of diagnostics with therapeutics 60
• Table 13 1: Top ten players in molecular diagnostics 67
• Table 13 2: Collaborations of companies in molecular diagnostics 407

Figures

• Figure 12 1: Unmet needs in applications of molecular diagnostics 48
• Figure 12 2: Proportion of various areas in molecular diagnostic collaborations 56