Molecular Diagnostics - Technologies, Markets and Companies

Table of Contents

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
• Impact of human genome project on molecular diagnostics 36
• Genetic variations in the human genome 36
• Insertions and deletions in the human genome 36
• Large scale variation in human genome 37
• Variation in copy number in the human genome 37
• Structural variations in the human genome 38
• Mapping and sequencing of structural variation from human genomes 39
• 1000 Genomes Project 39
• Human Variome Project 40
• Systems biology approach to molecular diagnostics 41
• Biomarkers 41
• Applications of molecular diagnostics 42

2. Molecular Diagnostic Technologies 45

• Introduction 45
• DNA extraction 45
• Transrenal DNA 45
• Sample preparation 46
• Pressure Cycling Technology 46
• Membrane immobilization of nucleic acids 46
• Automation of sample preparation in molecular diagnostics 47
• ABI PRISM 6700 Automated Nucleic Acid Workstation 47
• BioRobot technology 47
• COBAS AmpliPrep System 47
• GENESIS FE500 Workcell 47
• GeneMole 48
• PCR BioCube 48
• QIAsymphony 48
• Tigris instrument system 48
• Techniques for sample preparation that are suitable for automation 49
• Xtra Amp Genomic DNA Extraction 49
• Extraction of DNA from paraffin sections 49
• Dynabead technology 49
• Pressure Cycling Technology 50
• SamPrep 50
• Use of magnetic particles for automation in genome analysis 50
• Companies involved in nucleic acid isolation 51
• Novel PCR methods 52
• Addressing limitations of PCR 52
• Real-time PCR systems 52
• Dyes used in real-time PCR 53
• Commercially available real-time PCR systems 54
• LightCycler PCR system 54
• LightUp probes based on real-time PCR 55
• Applications of real-time PCR 55
• Limitations of real-time PCR 56
• Improving the reliability of low level DNA analysis by real-time PCR 56
• Guidelines for real-time quantitative PCR 56
• Future applications of real-time Q-PCR 57
• Reverse transcriptase (RT)-PCR 57
• Standardized reverse transcriptase PCR 58
• Single cell PCR 58
• LATE-PCR 58
• Cold-PCR 59
• AmpliGrid-System 59
• Digital PCR 59
• Long and accurate PCR 60
• Combined PCR-ELISA 60
• Monitoring of gene amplification in molecular diagnostics 61
• Non-PCR nucleic acid amplification methods 61
• Linked Linear Amplification 61
• Transcription mediated amplification 61
• Rapid analysis of gene expression 62
• WAVE nucleic acid fragment analysis system 62
• DNA probes with conjugated minor groove binder 63
• Rolling circle amplification technology 63
• Gene-based diagnostics through RCAT 64
• RCAT-immunodiagnostics 65
• RCAT-biochips 65
• RCAT-pharmacogenomics 65
• Circle-to-circle amplification 66
• Ramification amplification method 66
• Single Primer Isothermal Amplification 66
• Isothermal reaction for amplification of oligonucleotides 67
• ICAN (Isothermal and Chimeric primer-initiated Amplification of Nucleic Acids) 67
• 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 70
• 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
• Invader RNA assays 82
• Linear RNA amplification 82
• Non-isotopic RNase cleavage assay 83
• Nucleic acid sequence-based amplification 83
• Q Beta replicase system 85
• Solid Phase Transcription Chain Reaction 85
• Transcriptome analysis 85
• Visualization of mRNA expression in vivo 86
• MicroRNA diagnostics 86
• Real-time PCR for expression profiling of miRNAs 86
• Microarray vs quantitative PCR foro measuring miRNAs 87
• Use of LNA to explore miRNA 87
• Nuclease Protection Assay to measure miRNA expression 88
• Microarrays for analysis of miRNA gene expression 88
• Modification of in situ hybridization for detection of miRNAs 89
• Whole genome amplification 89
• Companies that provide technologies for whole genome amplification 89
• QIAGEN' s Repli-G system 90
• GenomePlex™ Whole Genome Amplification 90
• DNA sequencing 91
• Companies involved in sequencing 92
• Applications of next generation sequencing in molecular diagnostics 93
• Genome-wide approach for chromatin mapping 93
• Mitochondrial sequencing 93
• Identification of unknown DNA sequences 94
• Optical mapping 94
• Gene expression analysis 95
• Gene expression profiling on whole blood samples 95
• Gene expression patterns of white blood cells 96
• Gene expression profiling based on alternative RNA splicing 96
• MAUI (MicroArray User Interface) hybridization 97
• 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 99
• Ziplex"! system 99
• Companies involved in gene expression analysis 100
• Peptide nucleic acid technology 101
• Use of PNA with fluorescence in situ hybridization 101
• PNA and PCR 102
• Use of PNA with biosensors 102
• PNA-based PD-loop technology 103
• PNA-DNA hybrid quadruplexes 103
• Companies Involved in PNA Diagnostics 103
• Locked nucleic acids 104
• Electrochemical detection of DNA 104
• Mediated nucleic acid oxidation 105
• Detection of hybridized nucleic acid with cyclic voltametry 105
• Electrochemical detection based on Toshiba' s CMOS technology 106
• Concluding remarks on electrochemical DNA detection 106
• Scorpions"! technology 106
• The Scorpions reaction 106
• Applications of Scorpion 107

3. Biochips, Biosensors, 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
• Microchip capillary electrophoresis 112
• 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 113
• Multiplexed Molecular Profiling 113
• Universal DNA microarray combining PCR and ligase detection reaction 114
• 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 120
• 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 123
• 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
• Fluorescence technologies for label detection 134
• Companies with fluorescence and chemiluminescence products 134
• Molecular beacons 135
• The Green fluorescent protein 136
• Multiophoton detection radioimmunoassay 137
• Multi-pixel photon counter 137
• Enzyme labels and detection by fluorescence 137
• Phase-sensitive flow cytometry 138
• 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 141
• Capillary electrophoresis 141
• Confocal laser scanning 141
• Spectrally resolved fluorescence lifetime imaging microscopy 141
• Molecular imaging 142
• Basic research in molecular imaging 142
• Devices for molecular imaging 143
• Molecular imaging in clinical practice 143
• Challenges and future prospects of molecular imaging 143
• Companies involved in molecular imaging 143
• Nanobiotechnology for molecular diagnostics 144
• Magnetic nanoparticles 145
• Gold nanoparticles 146
• Quantum dot technology 146
• Nanotechnology on a chip 147
• Nanogen' s NanoChip 148
• Fullerene photodetectors for chemiluminescence detection on microfluidic chip 148
• Diagnostics based on nanopore technology 148
• Nanosensors 148
• Quartz nanobalance biosensor 149
• PEBBLE nanosensors 149
• Nanosensors for glucose monitoring 149
• Cantilever arrays 150
• Resonance Light Scattering technology 150
• DNA nanomachines for molecular diagnostics 151
• Nanobarcodes technology for molecular diagnostics 151
• Qdot nanobarcode for multiplexed gene expression profiling 152
• Role of nanobiotechnology in improving molecular diagnostics 152
• Companies involved in nanomolecular diagnostics 152
• Concluding remarks about nanodiagnostics 155
• 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
• Real-time PCR for protein quantification 163
• Protein biochip technologies 163
• ProteinChip 164
• LabChip for protein analysis 165
• TRINECTIN proteome chip 165
• Protein chips for antigen-antibody interactions molecular diagnostics 165
• Microfluidic devices for proteomics-based diagnostics 166
• Nanotechnology-based protein biochips/microarrays 166
• Nanoparticle protein chip 166
• Protein nanobiochip 166
• Protein biochips based on fluorescence planar wave guide technology 167
• New developments in protein chips/microarrays 167
• Antibody microarrays 168
• Aptamer-based protein biochip 168
• Multiplexed Protein Profiling on Microarrays 168
• Proteomic pattern analysis 169
• Single molecule array 169
• Viral protein chip 169
• Commercial development of protein chips for molecular diagnostics 170
• Proteome Identification Kit 171
• Laser capture microdissection (LCM) 171
• LCM technology 171
• Applications of LCM in molecular diagnostics 172
• 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 175
• 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
• aCGH for prenatal diagnosis 201
• BAC HD Scan test 201
• FISH for prenatal diagnosis 202
• PCR for prenatal diagnosis 202
• Plasma DNA sequencing to detect fetal chromosomal aneuploidies 202
• In vivo gene expression analysis of the living human fetus 203
• Noninvasive prenatal diagnosis of monogenic diseases 203
• Digital relative mutation dosage 203
• Massively parallel plasma DNA sequencing 203
• Applications of prenatal diagnosis 204
• Diagnosis of congenital infections 205
• Diagnosis of eclampsia 205
• Use of transrenal DNA for prenatal testing 205
• Preimplantation genetic diagnosis 206
• 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 208
• Companies involved in prenatal/preimplantation diagnosis 209
• Cystic fibrosis 209
• Detection of CFTR gene mutations 210
• CFTR technologies of various companies 210
• Genzyme' s CF gene sequencing 211
• CF Plus™ Tag-It Cystic Fibrosis Kit 211
• Asuragen' s bead array test 212
• The Ambry CF Test 212
• Biochip for CF diagnosis 212
• Identification of CF variants by PCR/Oligonucleotide Ligation Assay 213
• MassARRAYR system for high-throughput CFTR testing 213
• Serum proteomic signature for CF using antibody microarrays 213
• Guidelines for genetic screening for CF 213
• Congenital adrenal hyperplasia 214
• Primary immunodeficiencies 214
• Hematological disorders 215
• Hemoglobinopathies 215
• Sickle cell anemia 215
• Thalassemia 216
• Paroxysmal nocturnal hemoglobinuria 216
• Hemophilia 217
• Hereditary hemochromatosis 217
• Polycystic kidney disease 217
• Hereditary metabolic disorders 218
• Lesch-Nyhan Syndrome 218
• Gaucher' s Disease 218
• Acute Intermittent Porphyria 219
• Phenylketonuria 219
• Hereditary periodic fever 219
• Achondroplasia 219
• Molecular diagnosis of cardiovascular disorders 220
• Coronary Heart Disease 221
• Cardiomyopathy 221
• Familial Hypertrophic Cardiomyopathy 222
• Idiopathic dilated cardiomyopathy 222
• Cardiac Arrhythmias 222
• Long Q-T Syndrome 222
• Familial atrial fibrillation 223
• Idiopathic ventricular fibrillation 223
• Congestive heart failure 223
• Hypertension 223
• Disturbances of blood lipids 224
• Familial dyslipoproteinemias 224
• Hypercholesterolemia 224
• Thrombotic disorders 225
• Factor V Leiden mutation 225
• Pulmonary embolism 225
• Molecular diagnosis of eye diseases 226
• Molecular diagnosis of retinitis pigmentosa 226
• Genetic screening for glaucoma 226
• Role of molecular diagnostics in rheumatoid arthritis 227
• Molecular diagnosis of neurogenetic disorders 227
• Alzheimer' s disease 229
• Down syndrome 229
• Parkinson' s disease 230
• Spinal muscular atrophy 231
• Duchenne and Becker muscular dystrophy 231
• Triple repeat disorders 231
• Huntington disease 232
• Fragile X syndrome 232
• Charcot-Marie Tooth disease 233
• Hereditary neuropathy with liability to pressure palsies 233
• eNOS gene polymorphisms as predictor of cerebral aneurysm rupture 233
• Mitochondrial disorders affecting the nervous system 234
• Genetic testing for disease predisposition 234
• Direct-to-consumer genetic tests 235

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
• Ligase chain reaction 241
• Mass spectrometry for microbial identification 241
• Metagenomic pyrosequencing 241
• Multiplex PCR for detection of infections 243
• LightCyclerR SeptiFast Test 243
• VYOOR Sepsis Test 243
• Dual priming oligonucleotide for multiplex PCR 244
• NASBA for detection of microorganisms 244
• Nucleic acid probes 244
• Neutrophil CD11b expression as a diagnostic marker 245
• Optical Mapping 245
• PNA-FISH for diagnosis of infections 245
• Quantitative reverse-transcription PCR for bacterial diagnostics 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
• H1N1 influenza 286
• Gastrointestinal infections 288
• Periodontal infections 289
• Diagnosis of urinary infections by a biosensor 290
• Role of molecular diagnostics in septicemia 290
• Limitations and needs of diagnostics for infections 291
• Differentiation between live and antibiotic-killed bacteria 291
• Cell-based methods for identifying pathogenic microorganisms 292
• Cell-based virus assays 292
• Cell-based detection of host response to infection 292
• Role of molecular diagnostics in hospital acquired infections 292
• Detection of hospital-acquired bacterial infections 293
• Detection of methicillin-resistant S. aureus 293
• Detection of vancomycin-resistant enterococci 294
• Detection of hospital-acquired C. difficile 294
• Bacterial genome sequencing in antimicrobial resistance 294
• Detection of hospital-acquired viral infections 295
• Molecular diagnosis of BK virus 295
• Diagnosis of hospital-acquired rotavirus gastroenteritis 295
• Molecular diagnostics and the microbiome 296
• Human Microbiome Project 296
• Application of metagenomics to study of the microbiome 296
• MicroBiome Analysis Center 297
• Concluding remarks and future prospects of diagnosis of infections 297
• Rapid point-of-care diagnosis of infection 298
• Diagnosis of viruses using protein fingerprinting 300
• QIAplex PCR multiplex technology 300
• 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
• Detecting viral agents in cancer 306
• Conventional cancer diagnosis 307
• Molecular techniques for cancer diagnosis 308
• Genome analysis at the molecular level 309
• Mutation detection at molecular level 310
• Expression profiling of tumor cells sorted by flow cytometry 310
• MicroRNA expression profiling to classify human cancers 310
• Biomarkers in cancer 311
• Circulating nucleosomes in serum of cancer patients 311
• Detection of DNA methylation 312
• eTag assay system for cancer biomarkers 314
• HAAH as a biomarker for cancer 314
• LigAmp for detection of gene mutations in cancer 314
• Mitochondrial DNA as a cancer biomarker 315
• Oncoproteins as biomarkers for cancer 315
• Sequencing-based approaches for detection of cancer biomarkers 316
• Molecular fingerprinting of cancer 316
• Fluorescent in situ hybridization 317
• Genetic analysis of cancer 317
• Comparative genomic hybridization in cancer diagnostics 317
• Loss of heterozygosity 318
• Digital karyotyping 318
• Gene expression profiles predict chromosomal instability in tumors 318
• PCR Techniques 319
• Realtime quantitative PCR for diagnosis of cancer 319
• Cold-PCR 319
• Antibody-based diagnosis of cancer 320
• Monoclonal antibodies for diagnosis of cancer 320
• Recombinant antibodies as a novel approach to cancer diagnosis 320
• Combined immunological and nucleic acid tests 321
• Combination of MAbs and RT-PCR 321
• Immunobead RT-PCR 321
• Assays for determining susceptibility to cancer 321
• Gene expression profiling in cancer 321
• Microarrays for gene expression profiling in cancer 322
• Serial analysis of gene expression (SAGE) 322
• DNA tags for finding genes expressed in cancer 323
• Suppression subtractive hybridization 323
• Measurement of telomerase activity 323
• Detection of cancer cells in blood of patients with solid tumors 324
• Epithelial aggregate separation and isolation 325
• Proteomic technologies for the molecular diagnosis of cancer 326
• Proteomic technologies for tumor biomarkers 326
• Affibodies as contrast agents for imaging in cancer 326
• Aptamer-based technology for protein signatures of cancer cells 327
• Aptamers for combined diagnosis and therapeutics of cancer 327
• Automated image analysis of nuclear protein distribution 328
• Laser capture microdissection in oncology 328
• Layered expression scanning 329
• Survivin and molecular diagnosis of cancer 329
• Biochip/microarrays for cancer diagnosis 329
• Role of DNA microarrays in gene expression profiling 330
• Biochip detection of FHIT gene 330
• Nanobiotechnology for early detection of cancer 331
• Detection of nanoparticle self assembly in tumors by MRI 331
• Differentiation between normal and cancer cells by nanosensors 331
• Magnetic nanoparticle probes 331
• Quantum dots for early detection of cancer 332
• Molecular imaging of cancer 332
• In vivo tumor illumination by adenoviral-GFP 333
• PET for in vivo molecular diagnosis of cancer 333
• Xenon-enhanced MRI 333
• Optical systems for in vivo molecular imaging of cancer 333
• Detection of micrometastases 334
• Molecular diagnosis of cancers of various organs 334
• Brain tumors 335
• Molecular diagnostic methods for brain tumors 335
• Glioblastoma multiforme 335
• Circulating microvesicles as biomarkers of glioblastoma 336
• Combination of neuroimaging and DNA microarray analysis in GBM 336
• Medulloblastoma 337
• Oligodendroglioma 337
• Advantages and limitations of molecular diagnosis of brain tumors 337
• Breast cancer 337
• Breast cancer genes 338
• Molecular diagnostic tests for breast cancer 339
• Mouse ESC-based assays to evaluate mutations in BRCA2 341
• Genomic profiles of breast cancer 341
• Role of molecular diagnostics in management of breast cancer 342
• Tests for prognosis of breast cancer 346
• Prediction of recurrence in breast cancer for personalizing therapy 347
• Cervical cancer 349
• Colorectal cancer 349
• Diagnosis of hereditary nonpolyposis colorectal cancer 349
• Detection of familial adenomatous polyposis coli 350
• Diagnosis of colorectal cancer from DNA in stools 350
• Detection of circulating tumor cells in colorectal cancer 351
• Minimally invasive screening for colorectal cancer 351
• Guanylyl cyclase C tests for colorectal cancer 351
• Early diagnosis of colorectal cancer from blood samples 352
• Gastric cancer 352
• Head and neck cancer 352
• Hematological malignancies 353
• Chromosome translocations 353
• Flow cytometry in diagnosis of leukemia 353
• Gene chip technology 353
• Laboratory assessment of leukemia 354
• Molecular probes 355
• Minimal residual disease 355
• Screening of gene mutations in chronic myeloproliferative diseases 355
• Lung cancer 356
• Melanoma 358
• Ovarian cancer 358
• Mutation of genes 359
• Relevance of genetic testing to management of ovarian cancer 359
• Serum biomarkers for early detection of ovarian cancer 359
• Biomarkers of ovarian cancer 359
• Concluding remarks on testing for ovarian cancer 360
• Pancreatic cancer 360
• Prostate cancer 361
• Gene expression analysis of prostate cancer by microarrays 361
• Huntingtin Interacting Protein 1 362
• Integrative genomic and proteomic profiling of prostate cancer 362
• LCM for diagnosis of prostate cancer 362
• PCA3 gene detection in urine 363
• PCR assay for assessing silencing of protein cadherin 13 gene 363
• Prostate biopsy for detection of prostatic intraepithelial neoplasia 364
• Screening of multiple SNPs for risk of prostate cancer 364
• Semen testing for prostate cancer biomarkers 364
• Serum-protein fingerprinting in prostate cancer 365
• Thyroid cancer 365
• Gene expression biomarkers of thyroid cancer 366
• Multiple endocrine neoplasia type 2B as risk factor for thyroid cancer 366
• miRNA expression profiling in thyroid cancer 366
• Urinary bladder cancer 367
• Role of molecular diagnostics in the management of cancer 367
• Risk assessment and prevention of cancer 367
• Role of molecular diagnosis in the design of future cancer therapies 368
• Molecular classification of cancer 368
• Determination of cancer prognosis 369
• Prognosis by tumor classification 369
• Prognosis by cancer gene expression 369
• Selection of anticancer drugs based on molecular diagnosis 369
• Integrated genome-wide analysis of cancer for diagnosis and therapy 370
• Personalized therapy for cancer patients 370
• Pharmacogenetics and cancer therapy 370
• Molecular diagnostics as an aid to selection of cancer therapy 371
• Drug resistance in cancer 372
• Role of organizatons in molecular diagnosis of cancer 372
• Role of NCI in molecular diagnosis of cancer 372
• Molecular profiling of cancer 372
• Cancer Genome Atlas 373
• Cancer Genetic Markers of Susceptibility Project 373
• Support for future research in molecular diagnosis of cancer 374
• Role of the International Cancer Genome Consortium 374
• Future prospects of molecular diagnosis of cancer 375
• Companies involved in molecular diagnosis of cancer 375

8. Molecular Diagnostics in Biopharmaceutical Industry & Healthcare 381

• Introduction 381
• Molecular diagnostics in biopharmaceutical industry 381
• Molecular diagnostic technologies and drug discovery 381
• Molecular diagnostics and pharmacogenetics 382
• Molecular toxicology 383
• Gene expression studies 384
• Toxicogenomics 384
• Toxicoproteomics 385
• Mitochondrial assays 386
• MetaChip 386
• Molecular diagnostics and pharmacogenomics 387
• Applications molecular diagnostics in gene therapy 388
• Use of PCR to study biodistribution of gene therapy vectors 388
• PCR for verification of the transcription of DNA 389
• In situ PCR for direct quantification of gene transfer into cells 389
• Detection of retroviruses by reverse transcriptase (RT)-PCR 389
• Assessment of safety issues of gene transfer 389
• Quantitative PCR for monitoring the effectiveness of gene therapy 389
• Use of FISH for analysis of adeno-associated viral vector integration 389
• Monitoring of gene expression by green fluorescent protein 390
• Detection of microbial contamination in biopharmaceutical manufacturing 390
• Role of PCR in detecting contamination of biopharmaceuticals 390
• Contamination of biopharmaceuticals with prions 391
• DNA tagging for control and tracing of drug distribution channels 391
• Molecular diagnostics for organ transplantation 391
• Tissue typing 391
• Commercial products for transplant molecular diagnostics 393
• Post-cardiac transplant patient monitoring for rejection 395
• Blood Transfusion Screening 395
• Molecular tests for screening of blood supply for viruses 396
• Commercial molecular diagnostic technologies for blood screening 397
• Bridge Amplification Technology 398
• COBAS AmpliScreen HCV and HIV Assays 398
• INACTINE 398
• NucliSens Extractor system 398
• Pall' s enhanced Bacteria Detection System 399
• PCR combined with algorithm method 399
• Prions detection in human blood 400
• PRISMR automated system 400
• Procleix HIV-1/HCV Assay 400
• West Nile virus detection in human blood 401
• Limitations of molecular diagnostics for blood screening 401
• Molecular epidemiology 402
• Molecular epidemiology of genetic diseases 402
• Monogenic versus polygenic disorders 403
• Critical issues facing genetic epidemiology 403
• Molecular epidemiology of infectious diseases 403
• Methods and purposes 403
• Emerging infections 404
• Human vs. non-human infections 404
• Genetics and susceptibility to infectious disease 405
• Molecular epidemiology of cancer 405
• Molecular epidemiology of p53 gene mutations 406
• Molecular epidemiology of link between virus and cancer 406
• Molecular epidemiology and cancer prevention 406
• SNPs and molecular epidemiology 406
• Molecular diagnostics for identification of food-borne pathogens 406
• Introduction 406
• Molecular diagnostic methods used in food-borne infections 407
• Limitations of use of molecular probes in food analysis 408
• Optical biosensor for detection of Listeria-contaminated foods 408
• Companies with technologies for food pathogen detection 409
• Transmissible spongiform encephalopathies (TSEs) 410
• Molecular diagnosis of TSEs 410
• Companies involved in developing molecular diagnostics for TSEs 413
• Detection of genetically modified organisms in food 414
• Molecular diagnostics for detection of doping in sports 414
• Screening of synthetic glucocorticosteroids in human urine 415
• Detection of gene doping 415
• Role of molecular diagnostics in future healthcare 415
• Translation of genomic research into genetic testing for healthcare 416
• Molecular diagnostics and disease management 416
• Role of genetic biomarkers in disease management 417
• Role of molecular diagnostics in personalized medicine 417
• Integrated healthcare 417
• Screening 417
• Early diagnosis 418
• Prevention 418
• Therapy based on molecular diagnosis 418
• Monitoring of therapy 418
• Advantages and limitations of integrated healthcare 419
• Commercially available systems for integrated healthcare 419
• Combination of diagnostics and therapeutics 420
• Companies combining diagnostics and therapeutics 420
• Point-of-care diagnosis 421
• Technologies for point-of-care diagnosis 422
• Biochips for point-of-care diagnosis 423
• Companies developing point-of-care diagnosis 424
• Advantages versus disadvantages of point-of-care diagnosis 425
• The impact of molecular diagnostics on clinical laboratory practice 426

9. Molecular Diagnostics in Forensic Medicine and Biological Warfare 427

• Application of molecular diagnostics in forensic medicine 427
• Technologies 427
• Extraction of DNA from forensic samples 427
• Mitochondrial DNA (mtDNA) analysis 428
• Polymorphic Alu insertions 428
• Single Nucleotide Polymorphisms (SNP) analysis 429
• Short tandem repeat (STR) 429
• Fluorescent detection systems 430
• ABO genotyping 430
• DNA analysis for identification of ancient or historical specimens 430
• Applications 430
• Applications in criminology 431
• Identification of remains of military personnel 432
• Identification of remains of victims of mass disasters 432
• Parentage testing 433
• Gender determination 434
• Companies developing molecular diagnostics for forensic science 435
• Molecular detection of biological warfare agents 436
• Introduction to biological warfare agents 436
• Role of PCR in the diagnosis of biological warfare agents 437
• Multiplex PCR microarray assay to detect bioterror pathogens in blood 437
• Laboratory diagnosis of Anthrax 438
• Challenges in diagnosis of biological warfare agents 438
• US government efforts for detection of biological warfare agents 439
• The US Army Medical Research Institute of Infectious Diseases 439
• Homeland Security Advance Research Projects Agency 440
• Commercial development of diagnostic devices for biological agents 440
• Companies developing diagnostic devices for biological agents 440
• Biodefence microarray 443
• Identification of genetic markers of individual pathogens 443
• Microbial Identification System based on OptiChip"! 444
• Hand-Held Advanced Nucleic Acid Analyzer 444
• Nanogen' s portable detection device 444
• Nanode Array Sensor Microchips 445
• MicroChemLab 445
• BioThreat Alert Test Strip 445
• Benchtop living cell biosensor 446
• BioForce NanoArray sensor technology 446
• QTL handheld biosensor 446
• Analyte 2000 biosensor 447
• Airborne bacterial spore detection technology 447
• Destruction and detection of anthrax by lysin 447
• Biosensor based on mass spectrometry of microorganisms' s RNA 447
• Bead ARray Counter 448
• ProteinChip-based detection of bioterroism agents 448
• TIGER biosensor 448
• The PathAlert™ Detection System 449
• VereThreat"! 449
• Concluding remarks about biodefense applications of diagnostics 449

10. References 451

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 54
• 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 sequencing 92
• Table 2 8: Comparison of methods of identification of unknown DNA sequences 94
• Table 2 9: Classification of methods of gene expression analysis 95
• Table 2 10: A selection of companies with gene expression technologies 100
• 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: Selected companies involved in 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 170
• 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 198
• Table 5 4: Application of preimplantation genetic diagnosis in monogenic disorders 207
• Table 5 5: Companies involved in prenatal/preimplantation diagnostics 209
• 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 228
• 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 301
• 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 311
• Table 7 6: Approved monoclonal antibodies for cancer diagnosis 320
• Table 7 7: Methods for comparison of gene-expression profilling in tumor specimens 322
• Table 7 8: Impact of in vivo molecular imaging of cancer on oncology practice 334
• Table 7 9: Companies developing cancer molecular diagnostics 375
• Table 8 1: Applications of molecular diagnostics in the biopharmaceutical industry 381
• Table 8 2: Molecular diagnostic technologies for drug discovery 382
• Table 8 3: Molecular diagnostic technologies used for pharmacogenetic studies 382
• Table 8 4: Companies with novel molecular toxicology technologies 383
• Table 8 5: Applications of molecular diagnostics in gene therapy 388
• Table 8 6: Companies involved in transplant molecular diagnostics 393
• Table 8 7: Companies involved in molecular diagnostics of blood transfusions 397
• Table 8 8: Pathogenic bacteria in food and targets for molecular diagnostic probes 407
• Table 8 9: Companies involved in molecular diagnostics for food-borne infections 409
• Table 8 10: Testing for harmful prions in brain tissue from dead cattle 410
• Table 8 11: Companies involved in developing molecular diagnostics for TSEs 413
• Table 8 12: Companies combining molecular diagnostics and therapeutics 420
• Table 8 13: Applications of point-of-care diagnosis 421
• Table 8 14: Companies developing point-of-care diagnostic tests 424
• Table 9 1: Forensic and legal applications of molecular diagnostics. 430
• Table 9 2: Molecular technologies used for forensic applications 435
• Table 9 3: Classification of biological and chemical agents used as weapons of mass destruction 436
• Table 9 4: Biological warfare agents that can be identified by PCR methods 437
• Table 9 5: Companies developing detection devices for biological warfare agents 441

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 242

Part II: Markets & Companies

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 20
• 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
• Assay Migration Studies for In Vitro Diagnostic Devices 22
• Assessment of diagnostic accuracy 22
• Sensitivity and specificity 22
• Documentation of diagnostic accuracy 23
• Assessment of laboratory-developed tests used by Medicare recipients 24
• Discovery of incidental findings on genetic screening 25
• Evaluation of companion diagnostics/therapeutic for cancer 25
• FDA regulation of multivariate index assays 25
• FDA guidance for IVDs to detect pathogens 27
• FDA guidelines for devices to detect and differentiate HPV 27
• FDA' s Microarray Quality Control 28
• FDA and point-of-care diagnosis 28
• Genetic testing of rare disorders 29
• Quality control of molecular diagnostic laboratory procedures 29
• Quality control of point-of-care tests 30
• Regulation of IVD by the FDA 30
• Regulation of in vivo diagnostics by the FDA 31
• Regulation of analytic-specific reagents 32
• Regulatory aspects of FISH 32
• Regulation of genetic testing 32
• Role of the FDA in genetic testing 32
• Regulatory issues concerning blood and plasma products 33
• United States Diagnostics Standards 33
• Regulation of in vitro diagnostics in the EU 34
• EU regulations for testing of blood products 34
• Regulation of genetic testing in EU 34
• Evaluation of diagnostic laboratory tests in the UK 35
• Pre-implantation genetic diagnosis in the UK 35

12. Markets for Molecular Diagnostics 37

• Introduction 37
• Methods for study of molecular diagnostic markets 37
• The overall market for diagnostic technologies 38
• Molecular diagnostic markets according to technologies 38
• Marketing strategies according to technologies 39
• Nucleic acid isolation market 39
• Market for PCR-based tests 39
• DNA sequencing market 39
• Cytogenetic market 40
• Market for FISH technologies 40
• Biochip/microarray market 40
• Biosensor market 41
• Nanobiotechnology for molecular diagnostics 41
• Markets for gene expression technologies 41
• Reagents and other disposable laboratory materials 41
• Market for immunochemistry diagnostic 42
• Markets for tissue diagnostics 42
• Molecular diagnostic markets according to therapeutic areas 42
• Genetic disorders 43
• Prenatal testing 44
• Cancer 44
• Potential markets for cancer diagnosis according to type of cancer 45
• Infectious diseases 45
• Sexually transmitted diseases 46
• Hospital-acquired infections 47
• Testing for HIV drug resistance 48
• Potential markets for avian influenza diagnostics 48
• Cardiovascular diseases 48
• Neurological disorders 49
• Food testing 49
• Screening of blood for transfusion 49
• Tissue typing for transplantation 49
• Marketing opportunities according to geographic areas 49
• Unmet needs in molecular diagnostics 50
• Major market trends 51
• Markets according to home-brew and FDA-approved tests 51
• Decentralization of molecular diagnostics 52
• Point-of-care testing 52
• Development of personalized medicine 53
• Cost of sequencing the human genome 53
• Cost of genotyping 53
• Development of low-cost tests 54
• Simplification of test procedures 54
• Increasing role of proteomics in clinical diagnostics 55
• Forensic and legal applications 55
• Marketing strategies 55
• Role of alliances in commercialization of molecular diagnostics 56
• Acquisitions vs collaborations 56
• Analysis of collaborations in molecular diagnostics 59
• Licensing of the technologies 59
• Strategies related to laboratory facilities and technologies 60
• Strategies relevant to the healthcare system 60
• Cost-Benefit studies 60
• Genetic susceptibility testing 60
• Preventive medicine strategies 61
• Targeting treatable and common diseases 61
• Information/education 61
• Physician education 61
• Patient education 62
• European diagnostic information platform 63
• Regulatory strategies 63
• Merger of in vitro and in vivo diagnostics 63
• Integration of diagnostics with therapeutics 63
• Diagnostic applications in clinical trials 64
• Prospects for development of new technologies 64
• Drivers for the development of molecular diagnostics 64
• Factors slowing the development of molecular diagnostics 64
• Government support of research relevant to molecular diagnostics 65
• Cost of sequencing the human genome 65
• European projects for improving molecular diagnostics 67
• European Consortium for developing new DNA analysis tools 67
• EU project for improvement of IVD tools procedures 68
• Genetic knowledge parks in the UK 68
• Molecular diagnostic opportunities in defense against bioterrorism 68
• Molecular diagnostics for food safety 69
• POC diagnostics for the developing countries 69

13. Companies involved in molecular diagnostics 71

• Introduction 71
• Major players in molecular diagnostics 71
• Profiles of selected companies 72
• Collaborations 417

Tables

• Table 12 1: Share of in vitro diagnostics in the global diagnostic market 2008-2018 38
• Table 12 2: Molecular diagnostics markets according to technologies from 2008-2018 38
• Table 12 3: Molecular diagnostics markets according to applications 2008-2018 42
• Table 12 4: Markets in 2008 for tests to screen healthy persons for genetic disorders 43
• Table 12 5: Markets in 2008 for molecular diagnostic tests for cancer 44
• Table 12 6: Molecular diagnostic markets for selected cancers 2008-2018 45
• Table 12 7: Markets value in 2008 for molecular diagnostic screening for infections 46
• Table 12 8: Future markets for HAI diagnostics 2008-2013 47
• Table 12 9: Molecular diagnostic markets according to geographical areas 2008-2018 50
• Table 12 10: Molecular diagnostic markets according to home-brew and approved tests 51
• Table 12 11: Marketing strategies for molecular diagnostics 55
• Table 12 12: Takeovers of molecular diagnostic companies 56
• Table 12 13: Advantages of the integration of diagnostics with therapeutics 63
• Table 13 1: Top ten players in molecular diagnostics 71
• Table 13 2: Collaborations of companies in molecular diagnostics 417

Figures

• Figure 12 1: Unmet needs in applications of molecular diagnostics 51
• Figure 12 2: Proportion of various areas in molecular diagnostic collaborations 59