Cytogenetics - Technologies, Markets and Companies

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Cytogenetics - technologies,markets and companies

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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 2011 and estimates are made for the years 2016 and 2021. 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 69 companies relevant to cytogenetics along with their 68 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.

Table of Contents

0. Executive Summary 11

1. Introduction 13

Definitions 13

Historical evolution of cytogenetics 13

Scope of cytogenetics 14

Molecular cytogenetics 15

Basics of molecular biology relevant to cytogenetics 15

DNA 15

RNA 16

DNA transcription 16

Chromosomes 16

Mitochondrial DNA 17

Genes 17

The genetic code 17

Gene expression 18

The human genome 18

Variations in the human genome 19

Variations in DNA sequences 19

Single nucleotide polymorphisms 19

Copy number variations in the human genome 19

Genotype and haplotypes 21

Complex chromosomal rearrangements 21

Insertions and deletions in the human genome 21

Large scale variation in human genome 22

Structural variations in the human genome 22

Replication of the DNA helix 23

Transposons 23

Mapping and sequencing of structural variation from human genomes 24

2. Technologies used for cytogenetics 25

Introduction 25

Quantitative fluorescent polymerase chain reaction 25

RNA interference and cytogenetics 26

RNA-induced transcriptional silencing complex 26

Single cell genetics by siRNA ablation 26

RNAi and cancer cytogenetics 27

Role of miRNAs in cancer cytogenetics 27

Preimplantation genetic diagnosis 27

Preimplantation genetic haplotyping 28

Bioinformatics and cytogenetics 28

FISH probe design software 28

LS-CAP algorithm 29

Distance-based clustering of CGH data 29

3. Fluorescent In Situ Hybridization 31

Introduction 31

Innovative FISH technologies 33

Direct visual in situ hybridization 33

Direct labeled Satellite FISH probes 33

Chromogenic in situ hybridization (CISH) 33

Primed in situ labeling 34

Interphase FISH 34

FISH with telomere-specific probes 35

High-throughput quantitative FISH 35

Multicolor FISH 36

Multicolor chromosome banding 36

Fiber FISH 36

Use of peptide nucleic acid with FISH 36

RNA-FISH 38

Use of locked nucleic acids with FISH 38

Automation of FISH 38

Single copy FISH probes 39

peT-FISH™ 39

In vivo FISH 40

Applications of FISH 40

Companies involved in FISH diagnostics 41

4. Genomic Technologies relevant to Cytogenetics 43

Introduction 43

Microarrays/biochips for cytogenetics 43

Tissue microarrays 43

Chromosome copy number analysis 43

Combination of FISH and gene chips 44

Combination of CGH+SNP microarrays 44

SignatureChip® 44

Molecular Combing 45

High density oligonucleotide arrays 45

Next Generation Screening® 46

Comparative genomic hybridization 46

Array-based comparative genomic hybridization 48

aCGH vs karyotyping 48

Comparison of array CGH and multipoint FISH 49

Combined use of tissue microarrays and aCGH 49

Single-cell array CGH 49

Regulatory requirements for array CGH 50

Future prospects of aCGH 50

Whole genome expression microarrays 51

Life Technologies Expression Array System 51

Arrayit's® H25K 52

Optical Mapping 52

Single cell cytogenetics 53

Single cell PCR 53

LATE-PCR 53

AmpliGrid-System 53

Digital Counting 53

Analysis of single-cell gene expression 54

Application of single cell cytogenetics in preimplantation genetic testing 54

Direct molecular analysis without amplification 55

5. Molecular Imaging & Single Molecular Detection 57

Molecular imaging 57

Companies involved in molecular imaging 57

Single molecule detection 58

Spectrally resolved fluorescence lifetime imaging microscopy 58

Single-molecule fluorescence resonance energy transfer 59

Confocal laser scanning 59

Single Molecule Array 59

PCR systems for single molecule detection 60

Real-time PCR 60

Digital PCR 60

Emulsion PCR 61

Rolling circle amplification technology 61

Microfluidic assay for protein expression at the single molecule level 61

Bioinformatic and single molecule detection 62

6. Role of Nanobiotechnology in Cytogenetics 63

Introduction 63

Nanobiology and the cell 63

Visualization on nanoscale 64

Application of AFM for biomolecular imaging 64

Future insights into biomolecular processes by AFM 64

Use of AFM for microdissection of chromosomes 65

Scanning probe microscopy 65

Near-field scanning optical microscopy 65

Multiple single-molecule fluorescence microscopy 66

Nanoscale scanning electron microscopy 66

Nanotechnology-based FISH 66

Study of chromosomes by atomic force microscopy 66

Quantum dot FISH 66

Nanobiotechnology for single molecule detection 67

Nanolaser spectroscopy for detection of cancer in single cells 68

Carbon nanotube transistors for genetic screening 68

Quantum-dots-FRET nanosensors for single molecule detection 69

3D single-molecular imaging by nanotechnology 69

Manipulation of DNA sequence by use of nanoparticles 69

Nanofluidic/nanoarray devices to detect a single molecule of DNA 69

Nanopore technology 70

Portable nanocantilever system for diagnosis 70

Nanobiosensors 71

7. Biomarkers and Cytogenetics 73

Introduction 73

Definitions 73

Biomarkers and cytogenetics 73

Cancer biomarkers 73

Technologies for detection of cancer biomarkers 74

Telomerase as a biomarker of cancer 74

Digital karyotyping for cancer biomarkers 74

Optical systems for in vivo molecular imaging of cancer 75

Circulating cancer cells in blood as biomarkers of cancer 75

Array CGH for biomarker discovery in cancer 76

Genetic biomarkers 76

8. Applications of Cytogenetics 77

Introduction 77

Applications of cytogenetics in research 77

Cytogenetics of embryonic stem cells 77

Genetic disorders 78

Technologies for diagnosis of genetic disorders 78

Cytogenetic microarrays for diagnosis of mental retardation 78

Detection of copy number variations in genetic disorders 79

Detection of non-recurrent DNA rearrangements by aCGH 79

Quantitative fluorescent PCR 80

Representational oligonucleotide microarray analysis 80

SignatureChip®-based diagnostics for cytogenetic abnormalities 80

Screening for cytogenetic abnormalities 81

Cytogenetics in prenatal diagnosis 81

aCGH for prenatal diagnosis 81

BAC HD Scan test 82

FISH for prenatal diagnosis 82

PCR for prenatal diagnosis of trisomy 21 82

Plasma DNA sequencing to detect fetal chromosomal aneuploidies 83

Concluding remarks and future prospects of prenatal diagnosis 83

Cytogenetics in preimplantation genetic diagnosis 84

Array CGH for PGD 84

Fluorescent PCR for PGD 84

FISH for PGD 85

PGD using whole genome amplification 85

Conditions detected by preimplantation cytogenetic diagnosis 86

The future of preimplantation genetic diagnosis 86

Disorders of the nervous system 87

Application of cytogenetics in epilepsy 87

Neuropsychiatric disorders in children 87

Cardiovascular disorders 88

Infections 88

PNA-FISH for diagnosis of infections 88

Diagnosis of bacterial infections at single molecule level 89

Detection of single virus particles 89

Role of cytogenetics in drug discovery and development 90

Role of cytogenetics in the development of personalized medicine 90

Relation of cytogenetics to personalized medicine 90

Cytomics as a basis for personalized medicine 91

Molecular imaging and personalized medicine 92

Cytogenetics for gender determination 92

Gender determination in competitive sport 92

Gender determination in forensic cases 93

Regulatory aspects of FISH 93

9. Cancer Cytogenetics 95

Cancer genetics 95

Cytogenetic abnormalities in cancer 95

Cytogenetic technologies for molecular diagnosis of cancer 95

Applications of aCGH in oncology 96

Cytogenetics of tumor cells in body fluids 97

Cytogenetics and microRNAs 97

Gene expression profiles predict chromosomal instability in tumors 97

Loss of heterozygosity 98

Molecular Combing for cancer diagnosis 98

Mutation detection at molecular level 99

Proteomic identification of oncogenic chromosomal translocation partners 99

Tissue microarrays for cancer diagnosis 100

Applications of cytogenetics in molecular diagnosis of cancer 100

Molecular cytogenetics in hematological malignancies 100

Chromosome translocations in leukemias 101

Cytogenetics diagnostics for leukemia 101

Detection of p53 deletions in chronic lymphocytic leukemia 102

Cytogenetics of lymphomas 102

Cytogenetics of myelodysplastic syndrome 103

Cytogenetics of plasma cell myeloma 104

Bladder cancer 104

Bone and soft tissue tumors 104

Brain tumors 105

Breast cancer 106

Chromosomal aberrations in breast carcinomas 106

FISH vs CISH and SISH for determining of HER-2/neu amplification 106

Genomic profiles of breast cancer 107

Colorectal cancer 107

Lung cancer 108

Ovarian cancer 109

aCGH analyses of cisplatin-resistant ovarian cancer cells 109

Prostate cancer 109

Renal cancer 110

Thyroid cancer 110

Cytogenetics-based anticancer strategies 111

aCGH-based strategies for targeting cancer pathways 111

Allele-specific inhibition 111

Prognostic and therapeutic significance of gene amplifications 111

RNAi-based approach for leukemia 112

Significance of double minutes 112

Online resources for cancer cytogenetics 112

The Cancer Genome Atlas 113

Concluding remarks on cancer cytogenetics 113

10. Cytogenetics Markets 115

Introduction 115

Methods for study of cytogenetic markets 115

Cytogenetic markets according to technologies 115

Market for FISH technologies 116

Array CGH markets 116

Sorting the markets of overlapping technologies 117

Markets for cytogenetics according to therapeutic areas 117

Geographical distribution of markets for cytogenetics 119

SWOT of competing technologies 119

Unfulfilled needs 120

Limitations of current technologies 122

Promising future developments in cytogenetics 122

Commercial aspects of genome sequencing technologies 122

Cost of genotyping 122

11. Companies 125

Profiles of companies 125

Collaborations 209

12. References 213

Tables

Table 1-1: Historical landmarks in the evolution of cytogenetics 13

Table 2-1: A classification of technologies used for cytogenetics 25

Table 3-1: Classification and scope of FISH and related technologies 32

Table 3-2: A selection of companies with FISH diagnostics 41

Table 4-1: Microarray/biochip-based technologies for cytogenetics 43

Table 4-2: Chromosomal structural abnormalities detected by CGH 46

Table 4-3: Companies developing whole genome chips/microarrays 51

Table 5-1: Companies involved in developing molecular imaging 57

Table 5-2: Technologies for single molecule detection 58

Table 6-1: Nanobiotechnologies for single molecule detection 68

Table 7-1: Types of cancer biomarkers relevant to cytogenetics 74

Table 8-1: Applications of cytogenetics 77

Table 8-2: Application of preimplantation cytogenetic diagnosis in monogenic disorders 86

Table 9-1: WHO classification of myelodysplastic syndromes 103

Table 9-2: Fusion genes in in malignant bone and soft tissue tumors 105

Table 9-3: Fusion genes in adenocarcinoma of the thyroid 110

Table 10-1: Cytogenetic markets according to technologies from 2011-2021 115

Table 10-2: Market size for cytogenetics according to applications 2011-2021 117

Table 10-3: Global cytogenetics markets 2011-2021 119

Table 10-4: SWOT of conventional FISH 119

Table 10-5: SWOT of innovative FISH technologies 119

Table 10-6: SWOT of PCR-based assays 120

Table 10-7: SWOT of aCGH 120

Table 10-8: SWOT of single molecule imaging 120

Table 11-1: Major suppliers of reagents/services/equipment for cytogenetics 125

Table 11-2: Major consumers of reagents 126

Table 11-3: Companies developing innovative technologies in cytogenetics 126

Table 11-4: Collaborations in cytogenetics 209

Figures

Figure 6-1: Scheme of a novel optical mRNA biosensor 71

Figure 8-1: Relation of various technologies to drug discovery and development 90

Figure 8-2: Relation of cytogenetics to personalized medicine 91

Figure 8-3: Relation of cytomics to personalized medicine 92

Figure 9-1: Basic scheme of genome-wide screening techniques for cancer 95

Figure 10-1: Distribution of applications of cytogenetics in the year 2016. 118

Figure 10-2: Distribution of applications of cytogenetics in the year 2021. 118

Figure 10-3: Unfulfilled needs in cytogenetics according to technologies 121

Figure 10-4: Unfulfilled needs in cytogenetics according to areas of application 121

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