Cytogenetics - technologies,markets and companies -





Published: July 2014 | Pages: 231 | Format: PDF

 Summary 

 This report deals with cytogenetics in a broader sense rather than the classical use mainly to describe the chromosome structure and identify abnormalities related to disease. In the age of molecular biology, it is also referred to as molecular cytogenetics. Historical landmarks in the evolution of cytogenetics are reviewed since the first images of chromosomes were made in 1879. The scope of cytogenetics includes several technologies besides fluorescence in situ hybridization (FISH), comparative genomic hybridization (CGH), and multicolor FISH. Molecular cytogenetics includes application of nanobiotechnology, microarrays, real-time polymerase chain reaction (PCR), in vivo imaging, and single molecule detection. Bioinformatics is described briefly as it plays an important role in analyzing data from many of these technologies. 

 FISH remains the single most important technology in cytogenetics. Several innovations are described of which the most important are single copy FISH, in vivo FISH (imaging of nucleic acids in living cells) and nanotechnology-based FISH. The unique character of peptide nucleic acid (PNA) allows these probes to hybridize to target nucleic acid molecules more rapidly and with higher affinity and specificity compared with DNA probes. PNA-FISH is more suited for rapid diagnosis of infections. RNA-FISH and locked nucleic acids (LNAs), are also described. 

 Microarray/biochip-based technologies for cytogenetics promise to speed up detection of chromosome aberrations now examined by FISH. Other important genomic technologies are whole genome expression array and direct molecular analysis without amplification. Analysis of single-cell gene expression promises a more precise understanding of human disease pathogenesis and has important diagnostic applications. Optical Mapping can survey entire human genomes for insertions/deletions, which account for a significantly greater proportion of genetic variation between closely-related genomes as compared to single nucleotide polymorphisms (SNPs), and are a major cause of gene defects. 

 Technologies encompassed within molecular imaging include optical imaging, magnetic resonance imaging (MRI) and nuclear medicine techniques. Positron emission tomography (PET) is the most sensitive and specific technique for imaging molecular pathways in vivo in humans. Cytogenetics can be refined by application of cytogenetics at single molecule level. Nanotechnology has facilitated the development of technology for single molecule imaging. Atomic force microscope (AFM) has become a well-established technique for imaging single biomolecules under physiological conditions. The scanning probe microscope (SPM) system is emerging as an increasingly important tool for non-intrusive interrogation of biomolecular systems in vitro and have been applied to improve FISH. Another example of application of nanobiotechnology is QD (quantum dot)-FISH probes, which can detect down to the single molecule level. 

 There are connections between cytogenetics and biomarkers of genetic disorders as well as cancer. Biomarkers are very important for molecular diagnostics. Not only are molecular diagnostic technologies used for discovery of biomarkers, biomarkers are the basis of several diagnostics. As a means to understand pathomechanism of disease and as links between diagnostics and therapeutics, biomarkers are playing a role in development of personalized medicine. Application of cytogenetics extend beyond genetic disorder and cancer to diagnosis of several other diseases. Other important applications are drug discovery, and development of personalized medicine. 

 The chapter on markets provides a global perspective of the cytogenetics business in the major markets: US, Western Europe (including France, Germany, Italy, Spain, and the UK), and Japan. The total figures for the market are also broken out according to the technologies and major disease areas in which they are applied. Markets figure are given for the year 2013 and estimates are made for the years 2018 and 2023. Advantages and limitations of various technologies have been pointed out throughout the report but this chapter includes SWOT (Strengths, Weaknesses, Opportunities and Threats) analysis of some of the competing technologies including the following: conventional FISH, innovative FISH technologies, PCR-based assays, and single molecule imaging. Unfulfilled needs in cytogenetics market are depicted graphically. Among various technologies, FISH is most advanced and less opportunities for further development than single molecule detection, which is in infancy and has more future potential. 

 The report includes summary profiles of 67 companies relevant to cytogenetics along with their 74 collaborations. Companies developing innovative technologies as well as those supplying equipment/services/reagents are identified.The report text is supplemented with 27 Tables and 9 figures. Selected 200 references are included in the bibliography. 

 0. Executive Summary  

  

 1. Introduction 

 Definitions 

 Historical evolution of cytogenetics 

 Scope of cytogenetics 

 Molecular cytogenetics 

 Basics of molecular biology relevant to cytogenetics 

 DNA 

 RNA 

 DNA transcription 

 Chromosomes 

 Mitochondrial DNA 

 Genes 

 The genetic code 

 Gene expression 

 The human genome 

 Variations in the human genome 

 Variations in DNA sequences 

 Single nucleotide polymorphisms 

 Copy number variations in the human genome 

 Genotype and haplotypes 

 Complex chromosomal rearrangements 

 Insertions and deletions in the human genome 

 Large scale variation in human genome 

 Structural variations in the human genome 

 Replication of the DNA helix 

 Transposons 

 Mapping and sequencing of structural variation from human genomes  

  

 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 

 Automation of FISH 

 Chromogenic in situ hybridization (CISH) 

 Direct visual in situ hybridization 

 Direct labeled Satellite FISH probes 

 Fiber FISH 

 FISH with telomere-specific probes 

 High-throughput quantitative FISH 

 In vivo FISH 

 Interphase FISH 

 Intron chromosomal expression FISH 

 Multicolor FISH 

 Multicolor chromosome banding 

 Oligonucleotide FISH 

 peT-FISH- 

 Primed in situ labeling 

 RNA-FISH 

 Single copy FISH probes 

 Use of peptide nucleic acid with FISH 

 Use of locked nucleic acids with FISH 

 Applications of FISH 

 Companies involved in FISH diagnostics  

  

 4. Genomic Technologies relevant to Cytogenetics 

 Introduction 

 Microarrays/biochips for cytogenetics 

 Microarrays vs karyotyping 

 Tissue microarrays 

 Chromosome copy number analysis 

 Combination of FISH and gene chips 

 Combination of CGH+SNP microarrays 

 SignatureChip® 

 Molecular Combing 

 High density oligonucleotide arrays 

 Next Generation Screening® 

 Comparative genomic hybridization 

 Array-based comparative genomic hybridization 

 aCGH vs karyotyping 

 Comparison of array CGH and multipoint FISH 

 Combined use of tissue microarrays and aCGH 

 Single-cell array CGH 

 Regulatory requirements for array CGH 

 Future prospects of aCGH 

 Whole genome expression microarrays 

 Life Technologies Expression Array System 

 Arrayit's® H25K 

 CytoScan® HD Array 

 Optical Mapping 

 Single cell cytogenetics 

 Single cell PCR 

 LATE-PCR 

 AmpliGrid-System 

 Digital Counting 

 Analysis of single-cell gene expression 

 Fluorescent in situ RNA sequencing 

 Application of single cell cytogenetics in preimplantation genetic testing 

 Direct molecular analysis without amplification  

  

 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 

 Single Molecule Array 

 PCR systems for single molecule detection 

 Real-time PCR 

 Digital PCR 

 Emulsion PCR 

 Rolling circle amplification technology 

 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 

 Use of AFM for microdissection of chromosomes 

 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 

 Screening 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 

 Application of cytogenetics in epilepsy 

 Neuropsychiatric disorders in children 

 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 aCGH in oncology 

 Cytogenetics of tumor cells in body fluids 

 Cytogenetics and microRNAs 

 FISH on paraffin-embedded tissues 

 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 

 SNPs and cytogenetics 

 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 

 Cytogenetics of acute myeloid 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 

 aCGH-based strategies for targeting cancer pathways 

 Allele-specific inhibition 

 Prognostic and therapeutic significance of gene amplifications 

 RNAi-based approach for leukemia 

 Significance of double minutes 

 Online resources for cancer cytogenetics 

 The Cancer Genome Atlas 

 Concluding remarks on cancer cytogenetics  

  

 10. Cytogenetics Markets 

 Introduction 

 Methods for study of cytogenetic markets 

 Cytogenetic markets according to technologies 

 Market for FISH technologies 

 Array CGH markets 

 Sorting the markets of overlapping technologies 

 Markets for cytogenetics according to therapeutic areas 

 Geographical distribution of markets for cytogenetics 

 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: WHO classification of myelodysplastic syndromes 

 Table 9-2: Fusion genes in in malignant bone and soft tissue tumors 

 Table 9-3: Fusion genes in adenocarcinoma of the thyroid 

 Table 10-1: Cytogenetic markets according to technologies from 2013-2023 

 Table 10-2: Market size for cytogenetics according to applications 2013-2023 

 Table 10-3: Global cytogenetics markets 2013-2023 

 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 aCGH 

 Table 10-8: 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 2018 

 Figure 10-2: Distribution of applications of cytogenetics in the year 2023 

 Figure 10-3: Unfulfilled needs in cytogenetics according to technologies 

 Figure 10-4: Unfulfilled needs in cytogenetics according to areas of application