Cytogenetics - technologies,markets and companies

Table of Contents

0. Executive Summary

1. Introduction

• Definitions
• Historical evolution of cytogenetics
• Scope of cytogenetics
• Molecular cytogenetics
• Basics of molecular biology relevant to cytogenetics
• Chromosomes
• Telomeres
• DNA sequences
• Single nucleotide polymorphisms
• Genotype and haplotypes
• Replication of the DNA helix

2. Technologies used for cytogenetics

• Introduction
• Quantitative fluorescent polymerase chain reaction
• RNA interference and cytogenetics
• RNA-induced transcriptional silencing complex
• Single cell genetics by siRNA ablation
• RNAi and cancer cytogenetics
• Role of miRNAs in cancer cytogenetics
• Preimplantation genetic diagnosis
• Preimplantation genetic haplotyping
• Bioinformatics and cytogenetics
• FISH probe design software
• LS-CAP algorithm
• Distance-based clustering of CGH data

3. Fluorescent In Situ Hybridization

• Introduction
• Innovative FISH technologies
• Direct visual in situ hybridization
• Direct labeled Satellite FISH probes
• Chromogenic in situ hybridization (CISH)
• Primed in situ labeling
• Interphase FISH
• FISH with telomere-specific probes
• High-throughput quantitative FISH
• Multicolor FISH
• Multicolor chromosome banding
• Fiber FISH
• Use of peptide nucleic acid with FISH
• RNA-FISH
• Use of locked nucleic acids with FISH
• Automation of FISH
• Single copy FISH probes
• peT-FISH™
• In vivo FISH
• Applications of FISH
• Companies involved in FISH diagnostics

4. Genomic Technologies relevant to Cytogenetics

• Introduction
• Microarrays/biochips for cytogenetics
• Tissue microarrays
• Chromosome copy number analysis
• Combination of FISH and gene chips
• SignatureChip®
• Molecular Combing
• High density oligonucleotide arrays
• Next Generation Screening®
• Comparative genomic hybridization
• Array-based comparative genomic hybridization
• Comparison of array CGH and multipoint FISH
• Combined use of tissue microarrays and array CGH
• Single-cell array CGH
• Regulatory requirements for array CGH
• Whole genome expression microarrays
• Life Technologies Expression Array System
• Arrayit' s® H25K
• Optical Mapping
• Single cell cytogenetics
• Single cell PCR
• LATE-PCR
• AmpliGrid-System
• Digital Counting
• Analysis of single-cell gene expression
• Direct molecular analysis without amplification
• Study of genetic variations other than SNPs
• Insertions and deletions in the human genome
• Large scale variation in human genome
• Variation in copy number in the human genome
• Structural variations in the human genome
• Mapping and sequencing of structural variation from human genomes

5. Molecular Imaging & Single Molecular Detection

• Molecular imaging
• Companies involved in molecular imaging
• Single molecule detection
• Spectrally resolved fluorescence lifetime imaging microscopy
• Single-molecule fluorescence resonance energy transfer
• Confocal laser scanning
• Real-time PCR systems
• Microfluidic assay for protein expression at the single molecule level
• Bioinformatic and single molecule detection

6. Role of Nanobiotechnology in Cytogenetics

• Introduction
• Nanobiology and the cell
• Visualization on nanoscale
• Application of AFM for biomolecular imaging
• Future insights into biomolecular processes by AFM
• Scanning probe microscopy
• Near-field scanning optical microscopy
• Multiple single-molecule fluorescence microscopy
• Nanoscale scanning electron microscopy
• Nanotechnology-based FISH
• Study of chromosomes by atomic force microscopy
• Quantum dot FISH
• Nanobiotechnology for single molecule detection
• Nanolaser spectroscopy for detection of cancer in single cells
• Carbon nanotube transistors for genetic screening
• Quantum-dots-FRET nanosensors for single molecule detection
• 3D single-molecular imaging by nanotechnology
• Manipulation of DNA sequence by use of nanoparticles
• Nanofluidic/nanoarray devices to detect a single molecule of DNA
• Nanopore technology
• Portable nanocantilever system for diagnosis
• Nanobiosensors

7. Biomarkers and Cytogenetics

• Introduction
• Definitions
• Biomarkers and cytogenetics
• Cancer biomarkers
• Technologies for detection of cancer biomarkers
• Telomerase as a biomarker of cancer
• Digital karyotyping for cancer biomarkers
• Optical systems for in vivo molecular imaging of cancer
• Circulating cancer cells in blood as biomarkers of cancer
• Array CGH for biomarker discovery in cancer
• Genetic biomarkers

8. Applications of Cytogenetics

• Introduction
• Applications of cytogenetics in research
• Cytogenetics of embryonic stem cells
• Genetic disorders
• Technologies for diagnosis of genetic disorders
• Cytogenetic microarrays for diagnosis of mental retardation
• Detection of copy number variations in genetic disorders
• Detection of non-recurrent DNA rearrangements by aCGH
• Quantitative fluorescent PCR
• Representational oligonucleotide microarray analysis
• SignatureChip®-based diagnostics for cytogenetic abnormalities
• Cytogenetics in prenatal diagnosis
• aCGH for prenatal diagnosis
• BAC HD Scan test
• FISH for prenatal diagnosis
• PCR for prenatal diagnosis of trisomy 21
• Plasma DNA sequencing to detect fetal chromosomal aneuploidies
• Concluding remarks and future prospects of prenatal diagnosis
• Cytogenetics in preimplantation genetic diagnosis
• Array CGH for PGD
• Fluorescent PCR for PGD
• FISH for PGD
• PGD using whole genome amplification
• Conditions detected by preimplantation cytogenetic diagnosis
• The future of preimplantation genetic diagnosis
• Disorders of the nervous system
• Cardiovascular disorders
• Infections
• PNA-FISH for diagnosis of infections
• Diagnosis of bacterial infections at single molecule level
• Detection of single virus particles
• Role of cytogenetics in drug discovery and development
• Role of cytogenetics in the development of personalized medicine
• Relation of cytogenetics to personalized medicine
• Cytomics as a basis for personalized medicine
• Molecular imaging and personalized medicine
• Cytogenetics for gender determination
• Gender determination in competitive sport
• Gender determination in forensic cases
• Regulatory aspects of FISH

9. Cancer Cytogenetics

• Cancer genetics
• Cytogenetic abnormalities in cancer
• Cytogenetic technologies for molecular diagnosis of cancer
• Applications of array CGH in oncology
• Cytogenetics of tumor cells in body fluids
• Gene expression profiles predict chromosomal instability in tumors
• Loss of heterozygosity
• Molecular Combing for cancer diagnosis
• Mutation detection at molecular level
• Proteomic identification of oncogenic chromosomal translocation partners
• Tissue microarrays for cancer diagnosis
• Applications of cytogenetics in molecular diagnosis of cancer
• Molecular cytogenetics in hematological malignancies
• Chromosome translocations in leukemias
• Cytogenetics diagnostics for leukemia
• Detection of p53 deletions in chronic lymphocytic leukemia
• Cytogenetics of lymphomas
• Cytogenetics of myelodysplastic syndrome
• Cytogenetics of plasma cell myeloma
• Bladder cancer
• Bone and soft tissue tumors
• Brain tumors
• Breast cancer
• Chromosomal aberrations in breast carcinomas
• FISH vs CISH and SISH for determining of HER-2/neu amplification
• Genomic profiles of breast cancer
• Colorectal cancer
• Lung cancer
• Ovarian cancer
• aCGH analyses of cisplatin-resistant ovarian cancer cells
• Prostate cancer
• Renal cancer
• Thyroid cancer
• Cytogenetics-based anticancer strategies
• Significance of double minutes
• Prognostic and therapeutic significance of gene amplifications
• Allele-specific inhibition
• RNAi-based approach for leukemia
• Online resources for cancer cytogenetics
• The Cancer Genome Atlas

10. Cytogenetics Markets

• Introduction
• Methods for study of cytogenetic markets
• The overall market for cytogenetics
• Cytogenetic markets according to technologies
• Market for FISH technologies
• Sorting the markets of overlapping technologies
• Markets for cytogenetics according to therapeutic areas
• SWOT of competing technologies
• Unfulfilled needs
• Limitations of current technologies
• Promising future developments in cytogenetics
• Commercial aspects of genome sequencing technologies
• Cost of genotyping

11. Companies

• Profiles of companies
• Collaborations

12. References

Tables

• Table 1 1: Historical landmarks in the evolution of cytogenetics
• Table 2 1: A classification of technologies used for cytogenetics
• Table 3 1: Classification and scope of FISH and related technologies
• Table 3 2: A selection of companies with FISH diagnostics
• Table 4 1: Microarray/biochip-based technologies for cytogenetics
• Table 4 2: Chromosomal structural abnormalities detected by CGH
• Table 4 3: Companies developing whole genome chips/microarrays
• Table 5 1: Companies involved in developing molecular imaging
• Table 5 2: Technologies for single molecule detection
• Table 6 1: Nanobiotechnologies for single molecule detection
• Table 7 1: Types of cancer biomarkers relevant to cytogenetics
• Table 8 1: Applications of cytogenetics
• Table 8 2: Application of preimplantation cytogenetic diagnosis in monogenic disorders
• Table 9 1: Fusion genes in in malignant bone and soft tissue tumors
• Table 9 2: Fusion genes in adenocarcinoma of the thyroid
• Table 10 1: Global cytogenetics markets 2008-2018
• Table 10 2: Cytogenetic markets according to technologies from 2008-2018
• Table 10 3: Market size for cytogenetics according to applications 2007-2017
• Table 10 4: SWOT of conventional FISH
• Table 10 5: SWOT of innovative FISH technologies
• Table 10 6: SWOT of PCR-based assays
• Table 10 7: SWOT of single molecule imaging
• Table 11 1: Major suppliers of reagents/services/equipment for cytogenetics
• Table 11 2: Major consumers of reagents
• Table 11 3: Companies developing innovative technologies in cytogenetics
• Table 11 4: Collaborations in cytogenetics

Figures

• Figure 6 1: Scheme of a novel optical mRNA biosensor
• Figure 8 1: Relation of various technologies to drug discovery and development
• Figure 8 2: Relation of cytogenetics to personalized medicine
• Figure 8 3: Relation of cytomics to personalized medicine
• Figure 9 1: Basic scheme of genome-wide screening techniques for cancer
• Figure 10 1: Distribution of applications of cytogenetics in the year 2012.
• Figure 10 2: Distribution of applications of cytogenetics in the year 2017.
• Figure 10 3: Unfulfilled needs in cytogenetics according to technologies
• Figure 10 4: Unfulfilled needs in cytogenetics according to areas of application