Contents:

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 Companies involved in FISH diagnostics 4. Genomic Technologies relevant to Cytogenetics Introduction Whole genome chips/microarrays 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 array Optical Mapping Single cell cytogenetics Single cell PCR 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 Representational oligonucleotide microarray analysis SignatureChip®-based diagnostics for cytogenetic abnormalities Quantitative fluorescent PCR Detection of non-recurrent DNA rearrangements by aCGH Cytogenetics in prenatal diagnosis PCR for prenatal diagnosis of trisomy 21 FISH for prenatal diagnosis Concluding remarks and future prospects of prenatal diagnosis Cytogenetics in preimplantation genetic diagnosis Fluorescent PCR for PGD FISH for PGD Microarrays CGH 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 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 Determining of HER-2/neu oncogene 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: Companies developing whole genome chips/microarrays Table 4-2: Microarray/biochip-based technologies for cytogenetics Table 4-3: Chromosomal structural abnormalities detected by CGH 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 2007-2017 Table 10-2: Cytogenetic markets according to technologies from 2007-2017 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