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Molecular Diagnostics - Technologies, Markets and Companies

  • ID: 4748144
  • Report
  • 1078 Pages
  • Jain PharmaBiotech
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This report describes and evaluates the molecular diagnostics technologies that will play an important role in the 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, sequencing, mitochondrial 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 considerable interest in developing rapid diagnostic methods for point-of-care and biowarfare agents such as anthrax.

The number of companies involved in molecular diagnostics has increased remarkably during the past few years. More than 1,000 companies have been identified to be involved in developing molecular diagnostics and 268 of these are profiled in the report along with tabulation of 657 collaborations. Despite the strict regulation, most of the development of 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 2018 according to technologies, applications and geographical regions. Forecasts are made up to 2028. 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 was the first commercial report on this topic and published as "DNA Diagnostics" in 1995 by PJB Publications, UK. A new edition in 1997 "Molecular Diagnostics I" as well as the next edition, "Molecular Diagnostics II" in 1999, were published by Decision Resources Inc, USA. All three versions of the reports were well received and sold widely. The report has been rewritten several times since then.

Benefits of this report

  • This report has evolved during the past 24 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 268 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 101 tables and 16 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.
Note: Product cover images may vary from those shown
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Part I: Technologies & Applications

0. Executive Summary  

1. Introduction
Definitions and scope of the subject  
Historical evolution of molecular diagnostics
Molecular biology relevant to molecular diagnostics
DNA
DNA polymerases  
Restriction endonucleases  
RNA
RNA polymerases  
Non-coding RNAs  
DNA transcription
Chromosomes
Chromatin  
Telomeres
Mitochondrial DNA
Genes
The genetic code
Gene expression
The human genome
ENCODE  
Variations in the human genome
Variations in DNA sequences  
Single nucleotide polymorphisms  
Haplotyping
Copy number variations in the human genome
Genotype and haplotypes
Genomic imprinting
Insertions and deletions in the human genome
Complex chromosomal rearrangements
Large scale variation in human genome
Structural variations in the human genome  
Replication of the DNA helix
Transposons
Epigenetics/epigenomics
DNA methylation
Proteins  
Proteomics  
Monoclonal antibodies  
Aptamers  
Basics of molecular diagnostics
Tracking DNA: the Southern blot
Pulsed-field gel electrophoresis  
DNA Probes
The polymerase chain reaction  
Basic Principles of PCR
Target selection  
Detection of amplified DNA
Impact of human genome project on molecular diagnostics  
Mapping and sequencing of structural variation from human genomes
1000 Genomes Project
Human Variome Project
Role of bioinformatics in molecular diagnostics
Systems biology approach to molecular diagnostics  
Synthetic biology and molecular diagnostics
Biomarkers  
Applications of molecular diagnostics  

2. Molecular Diagnostic Technologies
Introduction  
DNA sample collection and extraction  
Blood samples
Buccal swabs and saliva  
Dried blood spots
Formalin-fixed, paraffin-embedded tissues  
Manual vs automated DNA extraction
Urine samples for transrenal DNA  
Sample preparation
Pressure Cycling Technology
Membrane immobilization of nucleic acids
Automation of sample preparation in molecular diagnostics  
ABI PRISM 6700 Automated Nucleic Acid Workstation  
BioRobot technology
COBAS AmpliPrep System
GENESIS FE500 Workcell  
GeneMole  
PCR BioCube
QIAsymphony  
Tigris instrument system  
Techniques for sample preparation suitable for automation
Xtra Amp Genomic DNA Extraction  
Extraction of DNA from paraffin sections  
Dynabead technology  
SamPrep  
Use of magnetic particles for automation in genome analysis  
Companies involved in nucleic acid isolation  
Labeling and detection of nucleic acids  
Novel PCR methods  
Addressing limitations of PCR  
ARMS-PCR  
CAST-PCR
Combined PCR-ELISA
Convection PCR
Co-Dx PCR  
Digital PCR  
Dumbbell PCR
Emulsion PCR  
ExCyto PCR
Fast PCR
Immuno PCR
Long and accurate PCR
Multiplex PCR  
Overlap extension PCR
Real-time PCR systems
Dyes used in real-time PCR  
Target-specific fluorogenic probes for monitoring real-time PCR  
Applications of real-time PCR  
Limitations of real-time PCR
Quantitative PCR for accurate low level DNA analysis.
qPCR for quantification of mtDNA  
Real-time qPCR for measuring the length of telomeres  
Guidelines for real-time qPCR
Future applications of real-time qPCR  
Commercially available real-time PCR systems  
Life Technologies’ Real-Time PCR systems
LightCycler PCR system
LightUp probes based on real-time PCR
PlexPCR based on PlexZyme technology
READ™ real-time PCR method  
StellARray™ technology
Reverse hybridization PCR assays  
Reverse transcriptase (RT)-PCR
Standardized reverse transcriptase PCR
Single cell PCR.
LATE-PCR
COLD-PCR  
AmpliGrid-System
Solar thermal PCR system monitored by Smartphone
Ultrafast photonic PCR  
DNA melt analysis  
High-resolution DNA melt analysis for genotyping  
PCR device for DNA melt analysis in space  
Monitoring of gene amplification in molecular diagnostics  
Non-PCR nucleic acid amplification methods
DNA probes with conjugated minor groove binder  
DNAble
Dynamic Flux Amplification
Isothermal nucleic acid amplifications
Isothermal reaction for amplification of oligonucleotides  
Isothermal and chimeric primer-initiated amplification of nucleic acids.
Loop-mediated amplification
Single Primer Isothermal Amplification  
Strand Invasion Based Amplification  
Linked Linear Amplification  
Multiplex Ligation-Dependent Probe Amplification  
Rapid analysis of gene expression  
Recombinase polymerase amplification
Rolling circle amplification technology
Gene-based diagnostics through RCAT
RCAT-immunodiagnostics
RCAT-pharmacogenomics  
Circle-to-circle amplification
Ramification amplification method  
Transcription mediated amplification  
WAVE nucleic acid fragment analysis system
Technologies for signal amplification
3 DNA dendrimer signal amplification
Hybridization signal amplification method
Signal mediated amplification of RNA technology
Invader assays  
Hybrid Capture technology  
Branched DNA test
Tyramide signal amplification  
Non-enzymatic signal amplification technologies  
Non-PCR methods for molecular diagnosis  
Direct molecular analysis without amplification  
Trilogy™ Platform
Direct detection of dsDNA  
Multiplex assays  
Fluorescent in situ hybridization  
FISH technique  
Applications of FISH
Modifications of FISH  
Direct visual in situ hybridization
Direct labeled Satellite FISH probes
Comparative genomic hybridization  
Primed in situ labeling  
Interphase FISH  
FISH with telomere-specific probes  
Multicolor FISH  
Simultaneous Ultrasensitive Subpopulation staining/Hybridization In situ
Automation of FISH  
Companies involved in FISH diagnostics
RNA diagnostics
RNA isolation from tissue samples  
Commercially available tests for mRNA detection and quantitation
Branched-chain DNA assay for measurement of RNA  
Cycling probe technology  
Invader RNA assays
Linear RNA amplification
Non-isotopic RNase cleavage assay  
Nucleic acid sequence-based amplification  
Q Beta replicase system
RNAScope
RNA expression profiling
Visualization of mRNA expression in vivo
Solid Phase Transcription Chain Reaction  
Transcriptome analysis
MicroRNA diagnostics
Microarray vs quantitative PCR for measuring miRNAs
Microarrays for analysis of miRNA gene expression
miR-TRAP to identify miRNA targets in vivo  
Modification of in situ hybridization for detection of miRNAs
Nuclease Protection Assay to measure miRNA expression
Real-time PCR for expression profiling of miRNAs  
Use of LNA to explore miRNA  
Whole genome amplification  
Companies that provide technologies for whole genome amplification
QIAGEN’s Repli-G system
GenomePlex Whole Genome Amplification
DNA sequencing
Applications of next generation sequencing in molecular diagnostics  
Companies developing sequencing for molecular diagnostics
Molecular diagnostics and sequencing in space  
Genome-wide approach for chromatin mapping  
Mitochondrial sequencing  
Identification of unknown DNA sequences
Mitochondrial exome sequencing
Optical mapping
Gene expression analysis
Gene expression profiling on whole blood samples
Gene expression patterns of white blood cells  
Gene expression profiling based on alternative RNA splicing  
MAUI (MicroArray User Interface) hybridization
Monitoring in vivo gene expression by molecular imaging
Serial analysis of gene expression (SAGE)
Single-cell gene expression analysis
T cell receptor expression analysis
Tangerine™ expression profiling  
Whole genome expression array  
Ziplex™ system
Companies involved in gene expression analysis  
Peptide nucleic acid technology
Use of PNA with fluorescence in situ hybridization  
PNA and PCR
Use of PNA with biosensors
PNA-based PD-loop technology  
PNA-DNA hybrid quadruplexes
Companies involved in PNA diagnostics
Locked nucleic acids  
Zip Nucleic Acids  
Electrochemical detection of DNA  
Mediated nucleic acid oxidation  
Detection of hybridized nucleic acid with cyclic voltametry  
Electrochemical detection based on Toshiba’s CMOS technology.
Electrochemical detection of DNA for POC
Concluding remarks on electrochemical DNA detection
Bead-based assay platforms  
Amplification Refractory Mutation System
Nucleic acid lateral flow molecular diagnostics  
Omics-based tests

3. Biochips, Biosensors, and Nanobiotechnology  
Introduction to biochip technology  
Applications of biochips in diagnostics  
GeneChip  
GeneChip Human Genome Arrays
AmpliChip CYP450
Electronic detection of nucleic acids on microarrays  
Microchip capillary electrophoresis
Strand displacement amplification on a biochip  
Rolling circle amplification on microarrays
LiquiChip-RCAT
Fast PCR biochip  
Multiplex microarray-enhanced PCR for DNA analysis
Multiplexed Molecular Profiling
Universal DNA microarray combining PCR and ligase detection reaction  
Genomewide association scans  
Whole genome chips/microarrays.
Transposon insertion site profiling chip
Standardizing the microarrays
Companies involved in developing biochip technology for diagnostics
Future of biochip technology for molecular diagnostics
Microfluidic chips
Fish-on-chip  
Lab-on-a-chip  
LabCD  
Micronics' microfluidic technology.
Microfluidic chips/arrays using PCR  
Microfluidic automated DNA analysis using PCR  
Digital PCR Array  
Digital PCR on a SlipChip
Microfluidic chips integrated with RCAT
Microfluidic chips integrated with PET
Companies developing microfluidic technologies  
Biosensor technologies  
Classification of biosensor technologies
DNA-based biosensors  
DNA hybridization biosensor chips
PCR-free DNA biosensors
DNA based biosensor to detects metallic ions
Genetically engineered B lymphocytes  
Biosensors immunoassays
PNA (peptide nucleic acid)-based biosensors
Protein-based biosensors  
Antibody biosensors
Cell-based biosensors (cytosensors)
Multicell biosensors
Microbial biosensors  
Optical biosensors  
Surface plasmon resonance technology
Label-free optical biosensor  
Microsensors using with nano/microelectronic communications technology  
Electrochemical sensors  
Enzyme electrodes for biosensing
Conductometric sensors
Electrochemical genosensors  
Electrochemical nanobiosensor
Electrochemical microRNA biosensor
Phototransistor biochip biosensor
Ribozyme-based sensors
RiboReporters
Concluding remarks and future of biosensor technology  
Companies developing biosensors for molecular diagnostics  
Molecular labels and detection.
Detection technologies for molecular labels
Fluorescence and chemiluminescence
Fluorescence technologies for label detection  
Companies with fluorescence and chemiluminescence products  
Molecular beacons  
The Green fluorescent protein
Multiophoton detection radioimmunoassay  
Multi-pixel photon counter  
Enzyme labels and detection by fluorescence  
Phase-sensitive flow cytometry  
Microtransponder-based DNA diagnostics  
Laboratory Multiple Analyte Profile
Multiple labels
Protein-DNA chimeras for detection of small numbers of molecules  
Single molecule detection  
Atomic force microscopy
Capillary electrophoresis
Confocal laser scanning  
Time domain optical imaging technology
nCounter Analysis System
Spectrally resolved fluorescence lifetime imaging microscopy  
Molecular imaging
Technologies for molecular imaging  
Positron emission tomography  
Magnetic resonance imaging  
Optoacoustic imaging  
Computer tomography
Hyperpolarized diazirines for in vivo biomolecular imaging
Basic research in molecular imaging
Devices for molecular imaging
Molecular imaging in clinical practice  
Companies involved in molecular imaging
Nanobiotechnology for molecular diagnostics
Cantilever arrays
Diagnostics based on nanopore technology
DNA nanomachines for molecular diagnostics  
Exosome-based molecular diagnostics  
Fullerene photodetectors for chemiluminescence detection on microfluidic chip  
Gold nanoparticles
Immunoliposome-PCR  
Magnetic nanoparticles
Nanotechnology on a chip
NanoChip® Electronic Microarray
Nanobarcodes technology for molecular diagnostics
Nanosensors
Detection of cocaine molecules by nanoparticle-labeled aptasensors  
Nanosensors for glucose monitoring  
PEBBLE nanosensors
Quartz nanobalance biosensor  
DNA nanoswitch-linked immunosorbent assay
Quantum dot technology
Qdot nanobarcode for multiplexed gene expression profiling.
Resonance Light Scattering technology
Role of nanobiotechnology in improving molecular diagnostics
Companies involved in nanomolecular diagnostics  
Concluding remarks about nanodiagnostics
Future of nanodiagnostics

4. Proteomic Technologies for Molecular Diagnostics
Introduction  
Proteomic technologies
Biomarkers of disease  
Proteomic tools for biomarkers
Search for biomarkers in body fluids
Captamers with proximity extension assay for proteins
Cyclical amplification of proteins  
Detection of misfolded proteins by ELISA with exponential signal amplification  
Detection of proteins by Western blot
Diagnostics based on designed repeat proteins  
Differential Peptide Display
Light-switching excimer probes  
MALDI-TOF MS  
Molecular beacon aptamer  
Molecular beacon assay  
Proteomic patterns
Real-time PCR for protein quantification  
Protein biochip technologies  
ProteinChip
LabChip for protein analysis  
TRINECTIN proteome chip
Protein chips for antigen-antibody interactions molecular diagnostics
Microfluidic devices for proteomics-based diagnostics
Nanotechnology-based protein biochips/microarrays  
Nanoparticle protein chip
Protein nanobiochip
New developments in protein chips/microarrays  
Antibody microarrays  
Aptamer-based protein biochip
Multiplexed Protein Profiling on Microarrays  
Proteomic pattern analysis
Single molecule array  
Viral protein chip  
Commercial development of protein chips for molecular diagnostics
Proteome Identification Kit  
Laser capture microdissection (LCM)
LCM technology
Applications of LCM in molecular diagnostics
Proteomic diagnosis of CNS disorders  
Cerebrospinal fluids tests based on proteomics  
Urine tests for CNS disorders based on proteins in urine
Diagnosis of CNS disorders by examination of proteins in the blood
Diagnosis of CNS disorders by examination of proteins in tears  
Role of proteomics in the diagnosis of Alzheimer's disease  
Role of proteomics in the diagnosis of Creutzfeldt-Jakob disease  
Future of use of proteomics for diagnosis of CNS disorders  
Concluding remarks on the use of proteomics in diagnostics

5. Molecular Diagnosis of Genetic Disorders
Introduction  
Cytogenetics  
FISH with probes to the telomeres
Single copy FISH probes
Comparative genomic hybridization  
Use of biochips in genetic disorders
Representational oligonucleotide microarray analysis  
Diagnosis of genomic rearrangements by multiplex PCR
Quantitative fluorescent PCR
Mutation detection technologies  
PCR-based methods for mutation detection
Cleavase Fragment Length Polymorphism  
Direct dideoxy DNA sequencing  
Digital Genetic Analysis (DGA)  
Fluorescence-based directed termination PCR
Fluorescence melting curve analysis for multiplex mutation detection  
Heteroduplex analysis
Restriction fragment length polymorphism
Single-stranded conformation polymorphism (SSCP) analysis
TaqMan real-time PCR
Non-PCR methods for mutation detection  
Arrayed primer extension
BEAMing (beads, emulsion, amplification, and magnetics)  
ELISA-protein truncation test
Enzymatic mutation detection
Specific anchor nucleotide incorporation  
Conversion analysis for mutation detection  
Biochip technologies for mutation detection
Combination of FISH and gene chips
Haplotype Specific Extraction
Use of biosensors for detection of mutations
Technologies for SNP analysis
Acoustic detection of DNA conformation in genetic assays combined with PCR
DNA sequencing  
Electrochemical DNA probes  
Use of NanoChip for detection of SNPs
Laboratory Multiple Analyte Profile
Pathway enrichment and network analysis of GWAS
PCR-CTPP (confronting two-pair primers)  
PCR using one primer amplification of PCR-CTPP products
Peptide nucleic acid probes for SNP detection  
Pyrosequencing
Reversed enzyme activity DNA interrogation test
Single base extension-tag array
Smart amplification process version 2  
SNP genotyping on a genome-wide amplified DOP-PCR template
SNP genotyping with gold nanoparticle probes
UCAN method (Takara Biomedical)
Zinc finger proteins  
Biochip and microarray-based detection of SNPs
SNP genotyping by MassARRAY
Electronic dot blot assay
Biochip combining BeadArray and ZipCode technologies
SNP-IT primer-extension technology  
SNaPshot® Multiplex System for SNP genotyping  
Affymetrix SNP genotyping array
Concluding remarks on SNP genotyping  
Limitations of SNP in genetic testing
Haplotyping versus SNP genotyping
Nanofluidics technology for high throughput SNP genotyping
Companies involved in developing technologies/products for SNP analysis  
Role of copy number variations in genetic diagnostic testing  
CNVs in various diseases  
CNVs in genetic epilepsy syndromes  
CNVs associated with schizophrenia  
Methods for determination of CNVs  
Digital array for CNV detection
Wellcome Trust Case Control Consortium CNV typing array  
CNVer algorithm for CNV detection  
CNVnator for discovery of CNVs and genotyping
Study of rare variants in pinpointing disease-causing genes  
Chromothripsis and congenital abnormalities  
Role of whole genome sequencing in screening of newborns  
Prenatal DNA diagnosis
Invasive prenatal diagnostic procedures
Amniocentesis  
Chorionic villus sampling  
Molecular methods for prenatal diagnosis  
aCGH for prenatal diagnosis
BAC HD Scan test
FISH for prenatal diagnosis  
PCR for prenatal diagnosis
In vivo gene expression analysis of the living human fetus
Non-invasive prenatal molecular diagnostic procedures  
Fetal cells separation from maternal blood for genetic diagnosis
Digital relative mutation dosage in maternal plasma  
Prenatal testing based on transrenal DNA from urine
Reflex DNA screening protocol  
Tests for preterm birth  
Tests on fetal DNA in maternal blood  
Sequencing-based methods for prenatal diagnosis from maternal DNA  
cfDNA testing vs routine screening in first trimester of pregnancy
Noninvasive WGS of the fetus
Directed DNA analysis of maternal blood  
Applications of prenatal diagnosis  
Antenatal screening for Down's syndrome  
Diagnosis of congenital infections  
Diagnosis of eclampsia  
Identification of cancers in pregnant women during NIPT
Preimplantation genetic diagnosis
Technologies for preimplantation genetic diagnosis  
PCR for preimplantation genetic diagnosis  
FISH for preimplantation genetic diagnosis
Microarrays for preimplantation genetic diagnosis
Whole genome sequencing for PGD
Conditions detected by preimplantation genetic diagnosis
The future of preimplantation genetic diagnosis
Companies involved in prenatal/preimplantation diagnosis  
Cystic fibrosis  
Detection of CFTR gene mutations
CFTR technologies of various companies
Asuragen's bead array test
Ambry CF Test  
Biochip for CF diagnosis
CF Plus Tag-It Cystic Fibrosis Kit  
HerediT™ (SEQUENOM) CF carrier screening test  
Identification of CF variants by PCR/Oligonucleotide Ligation Assay
LabCorp's CF gene sequencing  
MiSeqDx sequencing-based CF assays
Serum proteomic signature for CF using antibody microarrays  
Guidelines for genetic screening for CF
Congenital adrenal hyperplasia  
Primary immunodeficiencies  
Hematological disorders  
Hemoglobinopathies
Sickle cell anemia
Thalassemia
Paroxysmal nocturnal hemoglobinuria
Hemophilia  
Hereditary hemochromatosis
Polycystic kidney disease  
Hereditary metabolic disorders  
Lesch-Nyhan Syndrome  
Gaucher’s Disease  
Acute Intermittent Porphyria
Phenylketonuria
Hereditary periodic fever.
Achondroplasia  
Molecular diagnosis of eye diseases  
Molecular diagnosis of retinitis pigmentosa  
Genetic screening for glaucoma
Role of molecular diagnostics in rheumatoid arthritis  
Molecular diagnosis of neurogenetic disorders  
Alzheimer's disease  
Autism spectrum disorders  
CNVs associated with autism  
Charcot-Marie Tooth disease
Down syndrome
Duchenne and Becker muscular dystrophy  
eNOS gene polymorphisms as predictor of cerebral aneurysm rupture  
Fragile X syndrome  
Huntington disease  
Hereditary neuropathy with liability to pressure palsies
Mitochondrial disorders affecting the nervous system
Parkinson’s disease  
Pompe’s disease  
Spinal muscular atrophy
Triple repeat disorders  
Genetic testing for disease predisposition
Direct-to-consumer genetic tests
Genetic diagnosis in patients with previously undiagnosed disease  

6. Molecular diagnosis of cardiovascular disorders
Introduction  
Coronary heart disease  
Genomics of coronary heart disease
Diagnosis of coronary artery disease based on gene expression
Cardiomyopathy
Hypertrophic cardiomyopathy  
Idiopathic dilated cardiomyopathy  
Cardiac arrhythmias  
Genetic tests for cardiac arrhythmias
Long Q-T syndrome  
Familial atrial fibrillation
Idiopathic ventricular fibrillation
Congestive heart failure
Hypertension
Disturbances of blood lipids
Familial dyslipoproteinemias  
Hypercholesterolemia
Thrombotic disorders
Factor V Leiden mutation  
Pulmonary embolism  
Hereditary thrombophilia  
Molecular diagnostics for monitoring heart transplant rejection
AlloMap® molecular expression testing.
Commercial molecular diagnostics for cardiovascular disorders  

7. Molecular Diagnosis of Infections
Introduction  
Molecular techniques for the diagnosis of infections
Antibody-enhanced microplate hybridization assays
Bacteriophage-based methods for detection of bacteria  
Biochips/microarrays for detection of microorganisms  
Lawrence Livermore Microbial Detection Array  
Biosensors for detection of microorganisms
Ibis T5000™ Biosensor System
Molecular Mirroring Technology
DNA enzyme immunoassay
DNA biochip/microarray in diagnosis of infections  
DNA-based typing methods
Restriction fragment length polymorphism analysis
Ribotyping
Random amplified polymorphic DNA  
Combinatorial DNA melting assay
Electrochemical detection of pathogens  
Field Activated Sample Treatment (FAST)
FISH for detection of infections  
hemoFISH assay
Helicase-dependent isothermal amplification for rapid detection of pathogens
High resolution melt analysis for diagnosis of infections  
Immunomagnetic cell capture
Ligase chain reaction  
MRI for diagnosis of infections
Multiplex PCR for detection of infections  
Metagenomic pyrosequencing  
Dual priming oligonucleotide for multiplex PCR
Multiplex amplified nominal tandem repeat analysis  
Nanopore-based diagnosis of infections  
NASBA for detection of microorganisms  
Nucleic acid probes  
Neutrophil CD11b expression as a diagnostic marker  
Optical Mapping
PCR electrospray ionization mass spectrometry
PNA-FISH for diagnosis of infections
Proteomic technologies for diagnosis of infections  
Mass spectrometry for microbial identification  
QuantiFERON® technology for pre-molecular diagnosis of infections  
Quantitative reverse-transcription PCR for bacterial diagnostics
Rapid electrochemical diagnosis of infections
Rupture event scanning  
Real-time single-molecule imaging of virus particles
Single-strand conformational polymorphism  
SmartGene platform for identifying pathogens based on genetic sequences  
Tessera array technology  
Tests for sepsis  
LightCycler® SeptiFast Test
NanoDx™
Next-generation sequencing assay to detect cell-free microbial DNA
SeptiCyte Triage assay  
SepsiTest™  
VYOO® Sepsis Test
Unyvero Solution
Applications, advantages and limitations of molecular diagnostics  
Molecular diagnostics versus other microbial detection technologies
Advantages of nucleic acid-based diagnostics in infections  
Drawbacks of nucleic acid-based diagnostics in infections
Nanotechnology for detection of infectious agents  
Bacterial infections  
Mycobacterium tuberculosis  
Conventional diagnosis of tuberculosis  
Combined tuberculin skin testing and ELISpot
PLUS assay
Microscopic Observation Drug Susceptible Assay for tuberculosis  
Molecular diagnostics for tuberculosis
Diagnosis of TB in a POC setting
Diagnosis of drug-resistant MTB infection
Gene expression blood test for detecting TB
GeneXpert MTB/RIF (eXpert) automated molecular test for MTB
QuantiFERON-TB Gold test
Transcriptional signatures in active vs asymptomatic tuberculosis
Diagnosis of other mycobacteria  
Leprosy and M. leprae
Bacteria associated with bacterial vaginosis
Chlamydial infections
Neisseria gonorrhoeae  
Trichomonas vaginalis  
Streptococcal infections  
Group B Streptococci
Group A Streptococcus and Streptococcus dysgalactiae
Pseudomonas aeruginosa  
Helicobacter pylori
Vibrio Cholerae  
Lyme disease  
Mycoplasmas
Fungal infections
PCR-based tests for fungal infections  
DNA barcode marker for fungi
DNA sequencing for fungal infections  
MALDI-TOF MS for diagnosis of fungal infections  
Aspergillus  
Candida species
Viral infections
Carbon nanotubes-based detection of viruses  
Sensitive metagenomic sequencing for detection of pathogenic human viruses  
Simultaneous testing of multiple viruses by VirScan
FDA-approved molecular diagnostics for viral infections  
HIV/AIDS  
Diagnosis of HIV
Detection of HIV provirus
Global Surveillance of HIV-1 genetic variations
Genotyping for drug-resistance in HIV
Neonatal screening of infants of HIV-positive mothers
Phenotyping as predictor of drug susceptibility/resistance in HIV  
POC testing for HIV
PCR for resolution of indeterminate Western blot  
Screening of cadaveric tissue donors
Tests used for quantification of HIV
Conclusions about HIV diagnostics  
Hepatitis viruses  
Hepatitis A virus
Hepatitis B virus
Hepatitis C virus
Detection and quantification of HCV RNA
Quantification of HCV RNA levels as a guide to antiviral therapy
Electrochemical DNA chip for diagnosis of HCV
HCV Genotyping as a guide to therapy
Hepatitis E
Enteroviruses  
Adenoviruses
Rhinoviruses
Herpes viruses
Herpes simplex virus
Genital and neonatal herpes simplex
Human cytomegalovirus infections  
Epstein-Barr virus
Human papilloma virus
Molecular diagnostics for HPV
Detection of encephalitis viruses  
West Nile and St. Louis encephalitis  
Venezuelan equine encephalitis virus
Detection of noroviruses
Detection of dengue virus
Detection of Ebola virus  
Detection of Zika virus  
Protozoal infections
Amebiasis
Cryptosporidium parvum.
Leishmaniasis  
Malaria
Neurocysticercosis
Pneumocystis carinii
Toxoplasmosis
Infections of various systems  
CNS infections
Molecular diagnosis in bacterial meningitis
Molecular diagnosis in herpes simplex encephalitis  
Diagnosis of transmissible spongiform encephalopathies  
Molecular diagnosis of respiratory viruses
Avian influenza H7N9  
H1N1 influenza
Influenza viruses  
Avian influenza H5N1  
Respiratory syndromes associated with coronavirus  
Gastrointestinal infections
Periodontal infections
Diagnosis of urinary infections by a biosensor  
Role of molecular diagnosis in sexually transmitted infections  
Role of molecular diagnostics in septicemia
Limitations and needs of diagnostics for infections
Cell-based methods for identifying pathogenic microorganisms  
Cell-based virus assays  
Cell-based detection of host response to infection
Role of molecular diagnostics in hospital acquired infections  
Molecular diagnostics for detection of drug resistance in infections
Detection of hospital-acquired bacterial infections  
Detection of methicillin-resistant S. aureus  
Whole-genome sequencing for investigation of MRSA outbreaks
Detection of carbapenemase-producing Gram-negative bacteria
Detection of vancomycin-resistant enterococci  
Detection of hospital-acquired C. difficile
Integrated device for rapid detection of organisms associated HAI  
Bacterial genome sequencing in antimicrobial resistance  
Detection of hospital-acquired viral infections  
Molecular diagnosis of BK virus
Diagnosis of hospital-acquired rotavirus gastroenteritis
Molecular diagnostics and the microbiome  
Human Microbiome Project  
Application of metagenomics for study of the microbiome
MicroBiome Analysis Center  
Concluding remarks and future of diagnosis of infections  
Rapid point-of-care diagnosis of infections  
Diagnosis of viruses using protein fingerprinting  
QIAplex PCR multiplex technology  
Role of PCR vs sequencing for diagnosis of infections  
Companies involved in molecular diagnosis of infectious diseases  

8. Molecular Diagnosis of Cancer  
Introduction  
Cancer genomics  
Cancer genes  
Oncogenes  
Tumor Suppressor Genes  
BRCA mutations  
p53
p16
CNVs in cancer  
Allele-specific copy number analysis of tumors
Viruses and cancer
Detecting viral agents in cancer  
Conventional cancer diagnosis
Molecular techniques for cancer diagnosis.
Exosome-based molecular diagnosis of cancer
Expression profiling of tumor cells sorted by flow cytometry  
MicroRNA expression profiling for cancer diagnostics  
Genome analysis at the molecular level  
Mutation detection by sequencing  
Quality control of NGS in oncology
Biomarkers in cancer  
Circulating nucleic acids as potential biomarkers of cancer
Circulating nucleosomes in serum of cancer patients
Detection of DNA methylation
eTag assay system for cancer biomarkers  
HAAH as a biomarker for cancer
LigAmp for detection of gene mutations in cancer
Methylscape biomarker of cancer  
Mitochondrial DNA as a cancer biomarker.
NIPT for detecting biomarkers of gynecological cancers
Oncoproteins as biomarkers for cancer  
Sequencing-based approaches for detection of cancer biomarkers
Molecular fingerprinting of cancer  
Fluorescent in situ hybridization
Genetic analysis of cancer
Comparative genomic hybridization in cancer diagnostics
Loss of heterozygosity
Digital karyotyping  
Gene expression profiles predict chromosomal instability in tumors
PCR Techniques
Cold-PCR
Real-time qPCR for diagnosis of cancer  
Real-time PCR with myT™ Primer reagents  
Antibody-based diagnosis of cancer  
Monoclonal antibodies for diagnosis of cancer
Recombinant antibodies as a novel approach to cancer diagnosis  
Combined immunological and nucleic acid tests
Combination of MAbs and RT-PCR
Immunobead RT-PCR  
Assays for determining susceptibility to cancer  
Gene expression profiling in cancer  
Microarrays for gene expression profiling in cancer
Serial analysis of gene expression (SAGE)  
Suppression subtractive hybridization  
Cancer tests based on gene expression profiling
Measurement of telomerase activity
Liquid biopsy for detection of circulating tumor cells and cfDNA in body fluids
ApoStream for POC detection of CTCs  
BEAMing technology for quantification of circulating tumor DNA  
CEE (cell enrichment and extraction) technology
CellSearch
CellTracks® AutoPrep® System
CTCscope system for detection of CTCs
CTChip™  
CTC sorting by acoustic waves  
Detection of circulating tumor DNA
Droplet digital PCR for examination of cell free plasma DNA in cancer  
DNA nanospheres for isolation of CTCs  
Fiber-optic array scanning technology  
Herringbone-chip for detection of CTCs  
IsoFlux System
Lab-on-chip for the isolation and detection of CTCs
MagSweeper  
Nano-Velcro to capture CTCs for diagnosis of cancer
NanoFlares for detection of CTCs  
Companies developing tests for detection of CTCs
Future of detection of cancer cells in blood
Epithelial aggregate separation and isolation
Proteomic technologies for the molecular diagnosis of cancer  
Proteomic technologies for tumor biomarkers
Affibodies as contrast agents for imaging in cancer
Aptamer-based technology for protein signatures of cancer cells
Aptamer probes for in vivo diagnosis of cancer
Aptamers for combined diagnosis and therapeutics of cancer
Automated image analysis of nuclear protein distribution
Laser capture microdissection in oncology  
Layered expression scanning  
Membrane-type serine protease-1
Survivin and molecular diagnosis of cancer  
Biochip/microarrays for cancer diagnosis  
Role of DNA microarrays in gene expression profiling  
Biochip detection of FHIT gene
Multiplexed single-cell analysis of FFPE cancer tissue samples
Nanobiotechnology for early detection of cancer  
Detection of nanoparticle self assembly in tumors by MRI  
Differentiation between normal and cancer cells by nanosensors
Magnetic nanoparticle probes
Quantum dots for early detection of cancer  
Molecular imaging of cancer  
In vivo imaging of single cancer cells
In vivo molecular imaging of cancer  
In vivo tumor illumination by adenoviral-GFP
PET for in vivo molecular diagnosis of cancer  
Radiolabeled peptide-based targeting probes for cancer imaging
Xenon-enhanced MRI  
Detection of micrometastases  
Detection of cancer stem cells
Detection of origin in cancers of unknown primary
Molecular diagnosis of cancers of various organs  
Brain tumors
Molecular diagnostic methods for brain tumors
Glioblastoma  
Circulating microvesicles as biomarkers of glioblastoma
Circulating tumor cells in glioblastoma
Combination of neuroimaging and microarray analysis in glioblastoma  
Medulloblastoma
Multigene predictor of outcome in glioblastoma  
Oligodendroglioma  
Advantages and limitations of molecular diagnosis of brain tumors  
Breast cancer  
Breast cancer genes  
Circulating tumor cells and nucleic acid biomarkers of breast cancer
Genomic profiles of breast cancer
Imaging biopsy specimens as alternative to histological examination
Microchimerism and breast cancer  
Molecular diagnostic tests for breast cancer
Molecular diagnostics for management of breast cancer
Mouse ESC-based assays to evaluate mutations in BRCA2
One step mucleic acid amplification assay for breast sentinel nodes  
Prognostic testing for of breast cancer
Prediction of recurrence in breast cancer for personalizing therapy  
Cervical cancer  
Colorectal cancer
ColoVantage CRC test  
Detection of familial adenomatous polyposis coli
Detection of CRC at precancerous state
Detection of circulating tumor cells in CRC
Diagnosis of hereditary nonpolyposis CRC  
Diagnosis of CRC from DNA in stools
Droplet Digital™ PCR for detection of KRAS Mutations
Early diagnosis of CRC from blood samples  
Guanylyl cyclase C-based tests for CRC
Multitarget stool DNA testing for CRC screening  
Gastric cancer
Head and neck cancer  
Nanobiochip sensor technique for analysis of oral cancer biomarkers
ProteinChip for diagnosis of head and neck cancer  
Hematological malignancies  
Chromosome translocations
Flow cytometry in diagnosis of leukemia  
Gene chip technology  
Hairy-cell leukemia
Laboratory assessment of leukemia
Molecular probes
Minimal residual disease  
Molecular diagnosis in myelodysplastic syndromes  
Screening of gene mutations in chronic myeloproliferative diseases.
Lung cancer  
Biomarkers of immune response in lung cancer  
Early diagnosis of lung cancer.
Gene abnormalities in lung cancer
Liquid biopsy based on CTCs in lung cancer  
Methylation profiling of lung cancer
Molecular subtyping of lung cancer  
Prediction of efficacy of chemotherapy
Melanoma
Ovarian cancer  
Mutation of genes
Relevance of genetic testing to management of ovarian cancer
Serum biomarkers for early detection of ovarian cancer
Biomarkers of ovarian cancer
Concluding remarks on testing for ovarian cancer
Pancreatic cancer
Proteomic techniques for diagnosis of pancreatic cancer  
Detection of KRAS mutations in pancreatic cancer
Prostate cancer  
Identification of genetic risks for prostate cancer  
Gene expression analysis of prostate cancer
Huntingtin Interacting Protein 1  
Integrative genomic and proteomic profiling of prostate cancer  
LCM for diagnosis of prostate cancer
Liquid biopsy for prostate cancer patients  
Mitomic™ prostate test  
Nanotechnology for early detection of recurrence of prostate cancer
PCA3 gene detection in urine  
PCR assay for assessing silencing of protein cadherin 13 gene  
Prolaris test  
Prostate biopsy for detection of prostatic intraepithelial neoplasia
Prostate Core Mitomic Test™  
Prostat Health Index
Screening of multiple SNPs for risk of prostate cancer
Semen testing for prostate cancer biomarkers  
Serum-protein fingerprinting in prostate cancer  
Tissue-based epigenetic test for prostate cancer
Thyroid cancer
Afirma gene expression classifier for inconclusive thyroid biopsies.
Gene expression biomarkers of thyroid cancer  
Multiple endocrine neoplasia type 2B as risk factor for thyroid cancer  
miRNA expression profiling in thyroid cancer  
Urinary bladder cancer
Role of molecular diagnostics in the management of cancer
Risk assessment and prevention of cancer  
Role of molecular diagnosis in the design of future cancer therapies
Molecular classification of cancer
Determination of cancer prognosis
Prognosis by tumor classification  
Prognosis by cancer gene expression
Selection of anticancer drugs based on molecular diagnosis  
Integrated genome-wide analysis of cancer for diagnosis and therapy  
Role of molecular diagnostics in personalized therapy for cancer  
Personalized diagnosis of cancer  
Pharmacogenetics and cancer therapy  
Molecular diagnostics as an aid to selection of cancer therapy
Drug resistance in cancer  
Role of organizations in molecular diagnosis of cancer  
Role of NCI in molecular diagnosis of cancer
Molecular profiling of cancer
Cancer Genome Atlas  
Support for future research in molecular diagnosis of cancer  
Role of the International Cancer Genome Consortium
Future of molecular diagnosis of cancer  
Companies involved in molecular diagnosis of cancer  

9. Molecular Diagnostics in Biopharmaceutical Industry & Healthcare
Introduction  
Molecular diagnostics in biopharmaceutical industry
Molecular diagnostic technologies and drug discovery
Molecular diagnostics and pharmacogenetics
Molecular toxicology
Gene expression studies for toxicology  
Toxicogenomics  
Toxicoproteomics  
Mitochondrial assays  
MetaChip/Datachip
Molecular diagnostics and pharmacogenomics
Molecular diagnostics and therapeutic drug monitoring
Applications molecular diagnostics in gene therapy  
Use of PCR to study biodistribution of gene therapy vectors
PCR for verification of the transcription of DNA
In situ PCR for direct quantification of gene transfer into cells.
Detection of retroviruses by reverse transcriptase (RT)-PCR
Assessment of safety issues of gene transfer  
Quantitative PCR for monitoring the effectiveness of gene therapy  
Use of FISH for analysis of adeno-associated viral vector integration
Monitoring of gene expression by green fluorescent protein  
Quality control of protein therapeutics and vaccines
Detection of microbial contamination in biopharmaceutical manufacturing
Role of PCR in detecting contamination  
Systems for rapid detection of contaminants  
Contamination of biopharmaceuticals with prions  
DNA tagging for control and tracing of drug distribution channels  
Molecular diagnostics for organ transplantation  
HLA typing  
Sequencing for HLA typing  
Commercial products for transplant molecular diagnostics
Post-cardiac transplant patient monitoring for rejection  
Application of molecular diagnostics in blood transfusion
Molecular diagnostics for testing transfusion compatibility
Transmission of infections in blood transfusion  
Molecular tests for screening of blood supply for viruses
Commercial molecular diagnostic technologies for blood screening
Bridge amplification technology  
COBAS AmpliScreen HCV and HIV Assays  
INACTINE  
NucliSens Extractor system  
Pall's enhanced Bacteria Detection System
PCR combined with algorithm method
Prions detection in human blood
PRISM® automated system
Procleix HIV-1/HCV Assay  
West Nile virus detection in human blood
Zika virus screening of US blood donors
Advantages and limitations of molecular diagnostics for blood screening
Molecular epidemiology
Molecular epidemiology of genetic diseases
Role of CNVs in study of genetic epidemiology  
Accumulation of CNVs with aging  
Monogenic versus polygenic disorders
Critical issues facing genetic epidemiology
Molecular epidemiology of infectious diseases  
Methods and purposes
Emerging infections
Human vs. non-human infections  
Genetics and susceptibility to infectious disease  
Molecular epidemiology of cancer
Molecular epidemiology of p53 gene mutations
Molecular epidemiology of link between virus and cancer
Molecular epidemiology and cancer prevention
SNPs and molecular epidemiology
Molecular diagnostics for identification of food-borne pathogens  
Introduction  
Molecular diagnostic methods used in food-borne infections  
Limitations of use of molecular probes in food analysis
Detection of Listeria-contaminated foods  
Optical biosensor for detection of Listeria
Real-time PCR for detection of Listeria
Sequencing for investigation of food-borne Listeria infections
Detection of Salmonella  
MicroSEQ® Salmonella Detection Kit
E. Coli detection
MicroSEQ® E. Coli Detection Kit
DuPont Bax system
MLG method for detection of multiple STEC strains
Detection of rare strains of E. Coli
Companies with technologies for food pathogen detection
Transmissible spongiform encephalopathies (TSEs)  
Basis of molecular diagnosis of prion diseases  
Molecular diagnosis of TSEs  
Companies involved in developing molecular diagnostics for TSEs
Detection of genetically modified food
Molecular diagnostics for detection of doping in sports
Screening of synthetic glucocorticosteroids in human urine
Detection of gene doping  
Role of molecular diagnostics in future healthcare  
Translation of genomic research into genetic testing for healthcare  
Molecular diagnostics and disease management
Role of genetic biomarkers in disease management  
Role of molecular diagnostics in personalized medicine
Integrated healthcare
Screening  
Early diagnosis
Prevention
Therapy based on molecular diagnosis
Monitoring of therapy  
Advantages and limitations of integrated healthcare  
Commercially available systems for integrated healthcare  
Combination of diagnostics and therapeutics
Companion diagnostics  
Companies involved in companion diagnostics  
Point-of-care diagnosis
Advantages versus disadvantages of POC diagnosis.
Technologies for point-of-care diagnosis  
Biochips for POC diagnosis
CRISPR for POC diagnosis  
Mobile detection of infections by microfluidic LAMP and smartphone  
Nanosensors for POC diagnosis
POC Diagnostic Initiative  
Paper-based POC diagnostic for infectious diseases
Synthetic biomarker-based POC diagnostic for cancer  
Future prospects of POC testing  
Companies developing POC diagnosis  
The impact of molecular diagnostics on clinical laboratory practice

10. Molecular Diagnostics in Forensic Medicine and Biological Warfare  
Application of molecular diagnostics in forensic medicine
Technologies
ABO genotyping  
DNA analysis for identification of ancient or historical specimens
DNA fingerprinting and short tandem repeats
DNA processing of forensic samples  
DNA profiles from fingerprints  
Fluorescent detection systems  
Genome wide association studies linking genes to facial features  
Mitochondrial DNA analysis  
Next generation sequencing for forensic diagnosis  
Pressure cycling technology for forensic applications
Polymorphic Alu insertions
SNP analysis  
Applications  
Applications in criminology
Identification of remains of military personnel  
Identification of remains of victims of mass disasters  
Parentage testing  
Gender determination  
Companies developing molecular diagnostics for forensic science
Molecular detection of biological warfare agents
Introduction to biological warfare agents  
Role of PCR in the diagnosis of biological warfare agents
Multiplex PCR microarray assay to detect bioterror pathogens in blood  
Laboratory diagnosis of Anthrax
Challenges in diagnosis of biological warfare agents
US government efforts for detection of biological warfare agents
The US Army Medical Research Institute of Infectious Diseases  
Homeland Security Advance Research Projects Agency  
Handheld Isothermal Silver Standard Sensor  
Hapten mediated display and pairing of rAbs for biothreat assays
Commercial development of diagnostic devices for biological agents.
Companies developing diagnostic devices for biological agents
Various devices for testing  
Airborne bacterial spore detection technology
Analyte 2000 biosensor
Bead ARray Counter  
Benchtop living cell biosensor
BioThreat Alert Test Strip
BioForce NanoArray sensor technology  
Biodefence microarray
Biosensor based on mass spectrometry of microorganisms's RNA
Destruction and detection of anthrax by lysin
Hand-Held Advanced Nucleic Acid Analyzer  
Identification of genetic markers of individual pathogens
Microbial Identification System based on OptiChip™  
MicroChemLab  
Nanode Array Sensor Microchips
ProteinChip-based detection of bioterroism agents  
QTL handheld biosensor
TIGER biosensor
The PathAlert Detection System
VereThreat™  
Concluding remarks about biodefense applications of diagnostics

11. References  

Tables
Table 1-1: Landmarks in development of molecular technology and its application to diagnosis
Table 1-2: Applications of molecular diagnostics  
Table 2-1: Companies with products for nucleic acid isolation  
Table 2-2: Applications of real-time PCR
Table 2-3: Some commercially available real-time PCR systems  
Table 2-4: A selection of companies with commercially available FISH diagnostics
Table 2-5: Selected companies with RNA diagnostic tests
Table 2-6: Companies involved in whole genome amplification  
Table 2-7: Companies involved in application of sequencing in molecular diagnostics
Table 2-8: Comparison of methods of identification of unknown DNA sequences  
Table 2-9: Classification of methods of gene expression analysis
Table 2-10: A selection of companies with gene expression technologies  
Table 2-11: Companies involved in developing PNA diagnostics
Table 2-12: Companies with bead-based diagnostic assay platforms  
Table 2-13: Companies developing nucleic acid lateral flow molecular diagnostics  
Table 3-1: Applications of biochip technology in relation to molecular diagnostics  
Table 3-2: Companies developing whole genome chips/microarrays
Table 3-3: Companies involved in biochips for molecular diagnostics  
Table 3-4: Companies developing microfluidic technologies
Table 3-5: Biosensor technologies with potential applications in molecular diagnostics
Table 3-6: Important applications of biosensors  
Table 3-7: Companies involved in application of biosensors in molecular diagnostics  
Table 3-8: Selected labels for nucleic acid detection
Table 3-9: Selected companies with fluorescence and chemiluminescence products
Table 3-10: Companies involved in molecular beacon manufacture and research
Table 3-11: Selected companies involved in molecular imaging
Table 3-12: Nanotechnologies with potential applications in molecular diagnostics
Table 3-13: Companies developing nanomolecular diagnostics  
Table 4-1: Applications of protein biochips/microarrays  
Table 4-2: Companies involved in developing diagnostic applications of protein biochips
Table 4-3: Disease-specific proteins in the cerebrospinal fluid of patients  
Table 5-1: Mutation detection technologies
Table 5-2: Technologies for SNP analysis  
Table 5-3: A sampling of companies involved in technologies for SNP genotyping  
Table 5-4: Application of preimplantation genetic diagnosis in monogenic disorders
Table 5-5: Companies involved in prenatal/preimplantation diagnostics  
Table 5-6: CFTR genotyping in cystic fibrosis − companies and technologies  
Table 5-7: X-linked immunodeficiency disorders  
Table 5-8: Available molecular diagnostics for neurogenetic diseases
Table 5-9: Companies offering genetic screening tests directly to consumers  
Table 6-1: Genes that cause cardiovascular diseases
Table 6-2: Molecular diagnostics for cardiovascular diseases: commercial development  
Table 7-1: Molecular techniques for the diagnosis of infections  
Table 7-2: Commercially available molecular diagnostics for sepsis  
Table 7-3: FDA-approved molecular diagnostics for various bacterial infections
Table 7-4: Commercially available molecular diagnostics for fungal infections
Table 7-5: FDA-approved molecular diagnostics for viral infections  
Table 7-6: Companies with molecular diagnostics for influenza virus H1N1
Table 7-7: Companies with molecular diagnostics for avian influenza virus H5N1
Table 7-8: Commercially available molecular diagnostics for C. difficile
Table 7-9: Companies developing POC tests for the diagnosis of infections
Table 7-10: Selected companies involved in molecular diagnosis of infections
Table 8-1: Estimated new cases of cancer in the US of most involved organs - 2017  
Table 8-2: Tumor suppressor genes, their chromosomal location, function, and associated tumors  
Table 8-3: Viruses linked to human cancer
Table 8-4: A classification of molecular diagnostic methods in cancer
Table 8-5: Desirable characteristics of biomarkers for cancer  
Table 8-6: Approved monoclonal antibodies for cancer diagnosis
Table 8-7: Methods for comparison of gene-expression profiling in tumor specimens
Table 8-8: Companies that have important cancer tests based on gene signatures  
Table 8-9: Companies developing technologies for detection of CTCs
Table 8-10: Impact of in vivo molecular imaging of cancer on oncology practice  
Table 8-11: Molecular diagnostic tests for breast cancer
Table 8-12: Companies developing cancer molecular diagnostics
Table 9-1: Applications of molecular diagnostics in the biopharmaceutical industry  
Table 9-2: Molecular diagnostic technologies for drug discovery  
Table 9-3: Molecular diagnostic technologies used for pharmacogenetic studies
Table 9-4: Companies with novel molecular toxicology technologies
Table 9-5: Applications of molecular diagnostics in gene therapy
Table 9-6: Companies involved in transplant molecular diagnostics  
Table 9-7: Companies involved in molecular diagnostics of blood transfusions
Table 9-8: Pathogenic bacteria in food and targets for molecular diagnostic probes  
Table 9-9: Companies involved in molecular diagnostics for food-borne infections
Table 9-10: Testing for harmful prions in brain tissue from dead cattle
Table 9-11: Companies involved in developing molecular diagnostics for TSEs  
Table 9-12: Companies involved in detection of genetically modified food
Table 9-13: Companies involved in companion diagnostics  
Table 9-14: Applications of point-of-care diagnosis  
Table 9-15: Companies developing point-of-care diagnostic tests  
Table 10-1: Forensic and legal applications of molecular diagnostics.
Table 10-2: Molecular technologies used for forensic applications  
Table 10-3: Biological and chemical agents used as weapons of mass destruction  
Table 10-4: Biological warfare agents that can be identified by PCR methods  
Table 10-5: Companies developing devices for detection of biological warfare agents

Figures
Figure 1-1: Relation of molecular diagnostics to other technologies  
Figure 2-1: PlexZyme technology for PlexPCR
Figure 2-2: Rolling circle amplification technology  
Figure 2-3: A schematic view of the Invader operating system  
Figure 2-4: Principle of fluorescent in situ hybridization  
Figure 2-5: Repli-G system of QIAGEN
Figure 2-6: DNA sequencing process  
Figure 2-7: Electrochemical detection of DNA  
Figure 2-8: Elements of a Scorpions primer  
Figure 3-1: Affymetrix GeneChip technology
Figure 3-2: Basic principle of a biosensor  
Figure 3-3: Surface plasmon resonance (SPR) technology
Figure 7-1: Use of DNA chips in diagnosing microbial infections
Figure 7-2: High throughput DNA pyrosequencing for pathogen discovery  
Figure 9-1: The mechanism of SHERLOCK for POC diagnosis

Part II: Regulations, Markets & Companies

12. Ethics, Patents and Regulatory issues
Introduction  
Ethical concerns about genetic diagnosis
Ethical guidelines for molecular diagnostics
Ethical aspects of use of WGS for newborn and prenatal screening
Ethical aspects of direct-to-consumer genetic services  
US public attitudes about genetic testing  
Opinion of European geneticists about DTC genetic testing  
Genetic testing for susceptibility to adult-onset cancer
Ethics of preimplantation genetic diagnosis
Preimplantation genetic diagnosis to screen for hereditary diseases  
PGD to test for susceptibiliy to cancer  
PGD and stem cells
Genetic research on stored tissues
Informed consent in clinical trials of in vitro devices
Concluding remarks about ethical issues
Insurance underwriting and gene tests
Should genetic information be available to health insurers?  
A need for the re-examination of current views
Genetic Information Nondiscrimination Act of US  
Impact of the US health care reform bill on genetic testing issues
Patents for molecular diagnostics  
PCR patents  
Patenting DNA sequences
US policy on gene patenting relevant to molecular diagnostics
The impact of disease gene patents on molecular diagnostics  
Licensing problems associated with genetic testing  
BRCA1 and BRCA2 gene patents  
Role of the WHO in genetic testing standards  
NIH's Genetic Testing Registry  
Regulatory issues in the US
Assay Migration Studies for In Vitro Diagnostic Devices  
Assessment of diagnostic accuracy
Sensitivity and specificity
Documentation of diagnostic accuracy
Discovery of incidental findings on genetic screening  
Evaluation of companion diagnostics/therapeutic for cancer  
FDA regulation of multivariate index assays  
FDA guidance for IVDs to detect pathogens
FDA guidelines for devices to detect and differentiate HPV  
FDA's Microarray Quality Control  
FDA and point-of-care diagnosis  
Genetic testing of rare disorders  
Guidelines for developing omics-based tests  
Shared responsibility on oversight of omics-based tests
Guidelines for use of sequencing for molecular diagnosis  
FDA oversight of next generation sequencing
Quality control of molecular diagnostic laboratory procedures  
Quality assurance of RNA expression profiling
Quality control of point-of-care tests  
Regulation of IVD by the FDA  
FDA guidance on research use and investigational use only IVDs
Regulation of in vitro companion diagnostics by the FDA
Regulation of in vivo diagnostics by the FDA  
Regulation of laboratory developed tests
Home-brew tests  
Laboratory-developed tests used by Medicare recipients  
Oversight of LDTs by the FDA
Alternative to FDA LDT guidance
Regulatory aspects of FISH
Regulation of genetic testing
Role of the FDA in genetic testing
Regulation of direct-to-consumer genetic testing
Need for regulatory oversight of DTC
Regulatory issues concerning blood and plasma products  
United States Diagnostics Standards  
Regulation of in vitro diagnostics in the EU
EU regulations for testing of blood products  
Regulation of genetic testing in EU
Evaluation of diagnostic laboratory tests in the UK
Pre-implantation genetic diagnosis in the UK

13. Markets for Molecular Diagnostics  
Introduction  
Methods for study of molecular diagnostic markets
The overall market for diagnostic technologies
Markets for in vitro diagnostics  
Molecular diagnostic markets according to technologies
Marketing strategies according to technologies  
Nucleic acid isolation market
Market for PCR-based tests
Markets for PCR instrumentation
Markets for real-time PCR and qRT-PCR
PCR market players
DNA sequencing market
Cost of NGS  
Cytogenetic market  
Market for FISH technologies  
Biochip/microarray market  
Biosensor market
Nanobiotechnology for molecular diagnostics
Markets for gene expression technologies
Reagents and other disposable laboratory materials
Market for immunochemistry diagnostic  
Markets for tissue diagnostics  
Molecular diagnostic markets according to therapeutic areas
Genetic disorders
Prenatal testing
Non-invasive prenatal testing
Cancer  
Potential markets for cancer diagnosis according to type of cancer  
Infectious diseases
Sexually transmitted diseases.
Hospital-acquired infections
Testing for HIV drug resistance
Potential markets for avian influenza diagnostics  
Cardiovascular diseases  
Neurological disorders  
Food testing  
Screening of blood for transfusion  
Tissue typing for transplantation  
Molecular diagnostic markets relevant to pharmaceutical industry
Molecular diagnosis and personalized medicine markets  
Growth of markets relevant to personalized medicine
Point-of-care market
Marketing opportunities according to geographic areas  
Unmet needs in molecular diagnostics
Major market trends  
Markets according to home-brew and FDA-approved tests  
Decentralization of molecular diagnostics  
Direct-to-consumers healthcare testing  
Point-of-care testing
Development of personalized medicine
Cost of sequencing the human genome
Cost of genotyping  
Marketing companion diagnostics for personalized medicine
Development of low-cost tests
Simplification of test procedures  
Increasing role of proteomics in clinical diagnostics  
Forensic and legal applications  
Veterinary molecular diagnostics  
Marketing strategies  
Role of alliances in commercialization of molecular diagnostics  
Acquisitions vs collaborations
Analysis of collaborations in molecular diagnostics  
Licensing of the technologies  
Strategies related to laboratory facilities and technologies  
Strategies relevant to the healthcare system
Cost-Benefit studies  
Genetic susceptibility testing  
Preventive medicine strategies
Targeting treatable and common diseases  
Information/education  
Physician education
Patient education  
European diagnostic information platform  
Regulatory strategies
Merger of in vitro and in vivo diagnostics  
Integration of diagnostics with therapeutics  
Diagnostic applications in clinical trials
Prospects for development of new technologies  
Drivers for the development of molecular diagnostics
Factors slowing the development of molecular diagnostics  
Cost of sequencing the human genome  
Challenges and future prospects for diagnostic applications of sequencing  
US organizations for advancing molecular diagnostic industry  
AdvaMedDx  
European projects for improving molecular diagnostics
European Consortium for developing new DNA analysis tools  
EU project for improvement of IVD tools procedures
Genetic knowledge parks in the UK
Molecular diagnostic opportunities in defense against bioterrorism
Molecular diagnostics for food safety  
POC diagnostics for the Asian countries  

14. Companies involved in molecular diagnostics
Introduction  
Major players in molecular diagnostics  
Profiles of selected companies
Collaborations  

Tables
Table 13-1: Share of in vitro diagnostics in the global diagnostic market 2018-2028  
Table 13-2: Molecular diagnostics markets according to technologies from 2018-2028
Table 13-3: PCR market 2018-2028
Table 13-4: Molecular diagnostics markets according to applications 2018-2028  
Table 13-5: Markets in 2018 for tests to screen healthy persons for genetic disorders  
Table 13-6: Markets in 2018 for molecular diagnostic screening tests for cancer  
Table 13-7: Molecular diagnostic markets for selected cancers 2018-2028  
Table 13-8: Markets value in 2018 for molecular diagnostic screening for infections
Table 13-9: Future markets for HAI diagnostics 2018-2028  
Table 13-10: Growth of markets relevant to personalized medicine 2018-2028
Table 13-11: Molecular diagnostic markets according to geographical areas 2018-2028
Table 13-12: Molecular diagnostic markets according to home-brew and approved tests  
Table 13-13: Marketing strategies for molecular diagnostics
Table 13-14: Acquisitions of molecular diagnostic companies  
Table 13-15: Advantages of the integration of diagnostics with therapeutics
Table 14-1: Top ten players in molecular diagnostics
Table 14-2: Collaborations of companies in molecular diagnostics  

Figures
Figure 13-1: Unmet needs in applications of molecular diagnostics  

Note: Product cover images may vary from those shown
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