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Molecular Diagnostics - Technologies, Markets and Companies Product Image

Molecular Diagnostics - Technologies, Markets and Companies

  • ID: 39070
  • November 2014
  • Region: Global
  • 1125 Pages
  • Jain PharmaBiotech

This report describes and evaluates the molecular diagnostics technologies that will play an important role in practice of medicine, public health, pharmaceutical industry, forensics and biological warfare in the 21st century. This includes several polymerase chain reaction (PCR)-based technologies, fluorescent in situ hybridization (FISH), peptide nucleic acids (PNA), electrochemical detection of DNA, 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 a considerable interest in developing rapid diagnostic methods for for point-of-care and biowarfare agents such as anthrax.

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Part 1

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
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
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
Cooperative primer
ARMS-PCR
CAST-PCR
Combined PCR-ELISA
Convection PCR
Digital 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
MNAzyme qPCR
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
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
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
Companies involved in sequencing
Applications of next generation sequencing in molecular diagnostics
Companies developing sequencing for molecular diagnostics
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
Concluding remarks on electrochemical DNA detection
Bead-based assay platforms
Scorpions™ technology
The Scorpions reaction
Applications of Scorpions
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 biosensor
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 prospects 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
Basic research in molecular imaging
Devices for molecular imaging
Molecular imaging in clinical practice
Challenges and future prospects of molecular imaging
Companies involved in molecular imaging
Nanobiotechnology for molecular diagnostics
Magnetic nanoparticles
Gold nanoparticles
Immunoliposome-PCR
Quantum dot technology
Nanotechnology on a chip
NanoChip® Electronic Microarray
Fullerene photodetectors for chemiluminescence detection on microfluidic chip
Diagnostics based on nanopore technology
Nanosensors
Detection of cocaine molecules by nanoparticle-labeled aptasensors
Nanosensors for glucose monitoring
PEBBLE nanosensors
Quartz nanobalance biosensor
Cantilever arrays
Resonance Light Scattering technology
DNA nanomachines for molecular diagnostics
Nanobarcodes technology for molecular diagnostics
Qdot nanobarcode for multiplexed gene expression profiling
Role of nanobiotechnology in improving molecular diagnostics
Companies involved in nanomolecular diagnostics
Concluding remarks about nanodiagnostics
Future prospects 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
Protein biochips based on fluorescence planar wave guide technology
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 prospects 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
Single base extension-tag array
Laboratory Multiple Analyte Profile
SNP genotyping with gold nanoparticle probes
PCR-CTPP (confronting two-pair primers)
PCR using one primer amplification of PCR-CTPP products
Peptide nucleic acid probes for SNP detection
SNP genotyping on a genome-wide amplified DOP-PCR template
Pyrosequencing
Reversed enzyme activity DNA interrogation test
Smart amplification process version 2
Zinc finger proteins
UCAN method (Takara Biomedical)
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
OmniScan 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
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
Tests on fetal DNA in maternal blood
Sequencing-based methods for prenatal diagnosis from maternal DNA
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
Preimplantation genetic diagnosis
Technologies for preimplantation genetic diagnosis (PGD)
PCR for preimplantation genetic diagnosis
FISH for preimplantation genetic diagnosis
Microarrays for preimplantation genetic diagnosis
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
Genzyme's CF gene sequencing
HerediT™ (SEQUENOM) CF carrier screening test
Identification of CF variants by PCR/Oligonucleotide Ligation Assay
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

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
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
Multiplex PCR for detection of infections
PCR electrospray ionization mass spectrometry
Metagenomic pyrosequencing
Dual priming oligonucleotide for multiplex PCR
Multiplex amplified nominal tandem repeat analysis
Tests for sepsis
LightCycler® SeptiFast Test
NanoDx™
SeptiCyte Triage assay
SepsiTest™
VYOO® Sepsis Test
Nanopore-based diagnosis of infections
NASBA for detection of microorganisms
Nucleic acid probes
Neutrophil CD11b expression as a diagnostic marker
Optical Mapping
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
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 testing and ELISpot PLUS assay
Microscopic Observation Drug Susceptible Assay for tuberculosis
Molecular diagnostics for tuberculosis
Biomarker-based tests for tuberculosis
Blood-based gene expression test for detecting TB
Diagnosis of TB in a POC setting
Diagnosis of drug-resistant MTB infection
GeneXpert MTB/RIF (eXpert) automated molecular test for MTB
Diagnosis of other mycobacteria
Leprosy and M. leprae
Chlamydial infections
Neisseria gonorrhoeae
Bacteria associated with bacterial vaginosis
Streptococcal infections
Group B Streptococci
Group A Streptococcus and Streptococcus dysgalactiae
Pseudomonas aeruginosa
Helicobacter pylori
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
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
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
Respiratory syndromes associated with coronavirus
Influenza viruses
Avian influenza H5N1
Avian influenza H7N9
H1N1 influenza
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
Differentiation between live and antibiotic-killed bacteria
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 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 to study of the microbiome
MicroBiome Analysis Center
Concluding remarks and future prospects 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
Genome analysis at the molecular level
Mutation detection by sequencing
Quality control of NGS in oncology
Expression profiling of tumor cells sorted by flow cytometry
MicroRNA expression profiling for cancer diagnostics
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
Mitochondrial DNA as a cancer biomarker
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
Detection of circulating tumor cells in blood
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
Future prospects 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 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 origin in cancers of unknown primary
Molecular diagnosis of cancers of various organs
Brain tumors
Molecular diagnostic methods for brain tumors
Glioblastoma multiforme
Circulating microvesicles as biomarkers of glioblastoma
Circulating tumor cells in glioblastoma
Combination of neuroimaging and DNA microarray analysis in GBM
Medulloblastoma
Multigene predictor of outcome in GBM
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
Microchimerism and breast cancer
Molecular diagnostic tests for breast cancer
Mouse ESC-based assays to evaluate mutations in BRCA2
Genomic profiles of breast cancer
Role of molecular diagnostics in management of breast cancer
Tests for prognosis 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
Early diagnosis of CRC from blood samples
Guanylyl cyclase C tests for CRC
Minimally invasive screening 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
Molecular subtyping of lung cancer
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
Early detection of prostate cancer recurrence by nanotechnology
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
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
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
Personalized therapy for cancer patients
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
Cancer Genetic Markers of Susceptibility Project
Support for future research in molecular diagnosis of cancer
Role of the International Cancer Genome Consortium
Future prospects 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
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
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
Technologies for point-of-care diagnosis
Biochips for POC diagnosis
Advantages versus disadvantages of 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
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
Single Nucleotide Polymorphisms (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 sequencing
Table 2-8: Companies involved in application of sequencing in molecular diagnostics
Table 2-9: Comparison of methods of identification of unknown DNA sequences
Table 2-10: Classification of methods of gene expression analysis
Table 2-11: A selection of companies with gene expression technologies
Table 2-12: Companies involved in developing PNA diagnostics
Table 2-13: Companies with bead-based diagnostic assay platforms
Table 2-14: 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 avian influenza virus H5N1
Table 7-7: Companies with molecular diagnostics for influenza virus H1N1
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 - 2013
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 profilling in tumor specimens
Table 8-8: Important cancer tests based on gene signatures
Table 8-9: Impact of in vivo molecular imaging of cancer on oncology practice
Table 8-10: Molecular diagnostic tests for breast cancer
Table 8-11: 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 detection devices for biological warfare agents

Figures
Figure 1-1: Relation of molecular diagnostics to other technologies
Figure 2-1: MNAzyme qPCR
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 biosensor1
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

Part 2

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 diagnosis
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
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
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
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
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 developing 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 2013-2023
Table 13-2: Molecular diagnostics markets according to technologies from 2013-2023
Table 13-3: PCR market 2013-2023
Table 13-4: Molecular diagnostics markets according to applications 2013-2023
Table 13-5: Markets in 2013 for tests to screen healthy persons for genetic disorders
Table 13-6: Markets in 2013 for molecular diagnostic screening tests for cancer
Table 13-7: Molecular diagnostic markets for selected cancers 2013-2023
Table 13-8: Markets value in 2013 for molecular diagnostic screening for infections
Table 13-9: Future markets for molecular diagnosis of infections 2014-2018
Table 13-10: Future markets for HAI diagnostics 2014-2018
Table 13-11: Growth of markets relevant to personalized medicine 2013-2023
Table 13-12: Molecular diagnostic markets according to geographical areas 2013-2023
Table 13-13: Molecular diagnostic markets according to home-brew and approved tests
Table 13-14: Marketing strategies for molecular diagnostics
Table 13-15: Acquisitions of molecular diagnostic companies
Table 13-16: 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

Professor K. K. Jain is a neurologist/neurosurgeon by training and has been working in the biotechnology/biopharmaceuticals industry for several years. He received graduate training in both Europe and USA, has held academic positions in several countries and is a Fellow of the Faculty of Pharmaceutical Medicine of the Royal Colleges of UK. Currently he is a consultant at Jain PharmaBiotech. Prof. Jain is the author of 415 publications including 16 books (2 as editor) and 48 special reports, which have covered important areas in biotechnology, gene therapy and biopharmaceuticals.

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