Cytogenomics

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Front Matter
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Contents
Contributors
Contributors_2021_Cytogenomics
Chapter-1---A-definition-for-cytogenomics---Which-also-may-be_2021_Cytogenom
	1 A definition for cytogenomics - Which also may be called chromosomics
		From cytogenetics to cytogenomics
		A definition of cytogenomics
		Conclusion
		References
SECTION 1 Technical aspects
	Chapter-2---Overview-of-currently-available-approaches-used-i_2021_Cytogenom
		Overview of currently available approaches used in cytogenomics
			What is cytogenomics?
			Cytogenomic approaches
				Before the word “genetics” was defined
				Cytogenetics
				Molecular genetics
				Molecular cytogenetics
				Epigenetics
			Conclusion
			References
	Chapter-3---Cytogenetics_2021_Cytogenomics
		Cytogenetics
			What is cytogenetics?
			A short history of cytogenetics
			Material and methods in cytogenetics
				Material applied in cytogenetics
				Cytogenetic methods
			Advantages and restrictions
			Applications
				Human genetic diagnostics
				Cytogenetic-based research
			Conclusion
			References
	Chapter-4---Molecular-cytogenetics_2021_Cytogenomics
		Molecular cytogenetics
			What is molecular cytogenetics?
			Probes applied in molecular cytogenetics and how to get them
				Locus-specific probes
				Repetitive probes
				Partial chromosome paints
				Whole chromosome paints
				Whole genome
			Probe-sets applied in molecular cytogenetics
			Different resolutions in molecular cytogenetics
			Cytogenomic applications of molecular cytogenetics
			Conclusion
			References
	Chapter-5---Molecular-combing-solutions-to-characterize-replica_2021_Cytogen
		Molecular combing solutions to characterize replication kinetics and genome rearrangements
			Introduction
			Basic studies on DNA replication
			Replication kinetic studies by molecular combing
			Replication kinetic studies in locus-specific manner
			Genomic Morse Code (GMC) and its applications
			GMC designs for CNV studies
			GMC designs for sequence-specific alterations
			GMC design for gene editing studies
			Conclusion
			References
	Chapter-6---Molecular-karyotyping_2021_Cytogenomics
		Molecular karyotyping
			Background
			Advantages and restrictions
			Material applied in molecular karyotyping
			Microarrays in molecular karyotyping
			Applications
				Molecular karyotyping approach in human genetic diagnostics
				Molecular karyotyping approach in cytogenomic research
			Conclusion
			References
	Chapter-7---Sequencing-approaches_2021_Cytogenomics
		Sequencing approaches
			Introduction
			The first generation
				Maxam and Gilbert’s chemical cleavage
				Sanger sequencing
				Further advances in Sanger sequencing
			The second generation
				Pyrosequencing
				Polony sequencing
				The Applied Biosystem SOLiD platform
				Ion torrents pH measurements with semiconductors
				Illumina’s sequence-by-synthesis approach
				Complete genomics/BGI combinatorial probe anchor synthesis
			Third generation
				Single-molecule real-time sequencing
				Nanopore sequencing
			Fourth generation
			Complementary methods
				Single-cell sequencing
				Optical mapping
				Sequencing by hybridization
			Summary and conclusion
			References
	Chapter-8---Next-generation-cytogenomics--High-resolution-struct_2021_Cytoge
		Next-generation cytogenomics: High-resolution structural variation detection by optical genome mapping
			Introduction
			Introduction to Optical Genome Mapping
				General principle
				Structural and copy number variation detection
				Data visualization, filtering, and reviewing
			Applications in constitutional cytogenetics
				Prenatal cytogenetics
				Postnatal cytogenetics
					Benchmarking against clinical testing
					Resolving unsolved cases
					Research studies on microdeletion and microduplication syndromes
					Repeat expansion/contraction disorders
			Applications in hematological malignancies
				Clinical benchmark studies
				Novel SV identification
			Application in solid tumors
			Concluding remarks
			References
	Chapter-9---Application-of-CRISPR-Cas9-to-visualize-defined-geno_2021_Cytoge
		Application of CRISPR/Cas9 to visualize defined genomic sequences in fixed chromosomes and nuclei
			Introduction
			Application of CRISPR-FISH
			Funding information
			References
	Chapter-10---Approaches-for-studying-epigenetic-aspects-of-th_2021_Cytogenom
		Approaches for studying epigenetic aspects of the human genome
			Introduction
			Analysis of DNA methylation
				Principles of DNA methylation analysis
				Global DNA methylation
					Luminometric methylation assay
						Applications of LUMA
					Cytosine extension assay
						Applications of cytosine extension assay
					Bisulfite PCR of LINE-1 and Alu repetitive DNA elements
						Applications of bisulfite PCR of LINE-1 and Alu repetitive DNA elements
					Enzyme-linked immunosorbent assay
						Applications of ELISA-based analysis
					Liquid chromatography-tandem mass spectrometry
						Applications of LC-MS/MS
				Genome-wide DNA methylation
					Bisulfite conversion-based microarray
						Applications of bisulfite conversion-based microarray analysis
				Gene-specific methylation
					PCR-based approaches
						Applications of PCR-based approaches
					Sequencing-based approaches
						Applications of sequencing-based approaches
					Mass spectrometry-based approaches
						Applications of mass spectrometry-based approaches
				Summary for methylated DNA detection
			Analysis of histone modifications
				Western blot
					Applications of Western blot
				Immunofluorescence assay
					Applications of ELISA/immunofluorescence assay
					Applications of γ -H2AX immunofluorescence assay
				Chromatin immunoprecipitation assay
					Applications of ChIP assay
				Mass spectrometry assay
					Applications of mass spectrometry assay
				Summary for histone modifications
			Higher-order chromatin structure analysis
				Chromatin remodeling
				3D nucleus organization and epigenetic regulation
					Applications of FISH and chromosome conformation capture
					Summary for 3D nucleus organization and epigenetic regulation
			Analysis of noncoding RNAs
				Real-time quantitative reverse transcription PCR
					In situ hybridization
					MiRNA microarray profiling
					MiRNA sequencing
					Summary for noncoding RNAs
			Messenger RNA sequencing
			Concluding remarks
			Acknowledgment
			References
SECTION 2 Current cytogenomic research
	Chapter-11---Chromoanagenesis-phenomena-and-their-formation-_2021_Cytogenomi
		Chromoanagenesis phenomena and their formation mechanisms
			Introduction
			An overview of chromoanagenesis phenomena: Definitions and hallmarks
				Chromothripsis
				Chromoplexy
				Chromoanasynthesis
			Mechanisms for chromoanagenesis occurrence
				The micronucleus-mediated model
				The chromatin bridge model
			Factors promoting the emergence of chromoanagenesis
			Conclusion
			References
	Chapter-12---3D-cytogenomics--Structural-variation-in-the-thre_2021_Cytogeno
		3D cytogenomics: Structural variation in the three-dimensional genome
			Introduction
			3D genome: Hierarchical organization of genetic information in the nucleus
			Topologically associating domains
			Techniques to detect chromatin interactions in the nuclear space
			Features of a Hi-C map
			Position effects and TADs
				Intra-TAD structural variants
				Inter-TAD structural variants: Enhancer hijacking
			SVs detection in the 3D genome
			Clinical application and future perspectives
			References
	Chapter-13---Multilayer-organization-of-chromosomes_2021_Cytogenomics
		Multilayer organization of chromosomes
			Introduction
			Experimental approaches to study the internal structure of mitotic chromosomes
			Chromatin plates in aqueous solution
			Self-organization of multilayer chromatin
			Stacked thin layers explain the morphology of bands and chromosome rearrangements
				Cytogenetic map and genome sequence
				Chromosome bands
				Thin bands
				Band splitting
				Replication bands
				Sister chromatid exchanges
				Chromosome translocations
				The topological organization of DNA is preserved in fixed chromosomes
			Functional implications of multilayered chromosomes
				Planar chromatin in interphase
				Chromosome bands in interphase
				Topologically associating domains
				Gene expression
				DNA replication
				DNA repair
			Concluding remarks
			References
	Chapter-14---Nuclear-architecture_2021_Cytogenomics
		Nuclear architecture
			Background
			Short history of nucleomics
				1888 to 1950s
				1950s to 1980s
				1980s to present
			Present insights into nuclear architecture
			Conclusion
			References
	Chapter-15---Nuclear-stability-in-early-embryo--Chromosomal-_2021_Cytogenomi
		Nuclear stability in early embryo. Chromosomal aberrations
			Introduction
			The nucleus of the zygote
				Zygotes and blastomeres
				Primary differentiation and blastocyst formation
			Chromosomal abnormalities
				Methods of karyotype analysis
				Chromosomal abnormalities in early embryogenesis
				Genomic imprinting
				Chromosomal mosaicism
				Chromothripsis
			Conclusion
			Acknowledgments
			References
	Chapter-16---Cytogenomic-landscape-of-the-human-brain_2021_Cytogenomics
		Cytogenomic landscape of the human brain
			Introduction to molecular neurocytogenetics/neurocytogenomics
			Cytogenomic variation in the human brain: Neuronal diversity versus disease
				Cyto(onto)genomic variations in the unaffected brain
				Neurocytogenomic variations and brain diseases
			Chromosomal organization in the human brain: Is there a postgenomic perspective?
			Pathway-based analysis of neurocytogenomic landscape
			Concluding remarks: What is and what should be
				What is
				What should be
				Acknowledgments
			References
	Chapter-17---Interchromosomal-interactions-with-meaning-for-_2021_Cytogenomi
		Interchromosomal interactions with meaning for disease
			Background
			Methods used in interchromosomal nucleomics
			Insights from two own studies
				Manvelyan et al. (2009) and Othman et al. (2012)
				Maass et al. (2018)
			Outlook
			References
	Chapter-18---Shaping-of-genome-by-long-noncoding-RNAs_2021_Cytogenomics
		Shaping of genome by long noncoding RNAs
			Introduction
			Technologies to determine genome-wide RNA-chromatin interactions
				Chromatin isolation by RNA purification (ChIRP), followed by high-throughput sequencing (ChIRP-seq)
				Capture hybridization analysis of RNA targets
				Proximity ligation-based methods like RADICL-seq
			Nuclear lncRNAs that recruit chromatin modifiers
			Nuclear lncRNAs that promote long-range chromatin interactions
			Interchromosomal interactions via subnuclear structures
			Breast cancer-specific lncRNAs regulate a long-range chromatin interaction
			Conclusion
			Acknowledgments
			References
	Chapter-19---Repetitive-elements--heteromorphisms--and-copy-n_2021_Cytogenom
		Repetitive elements, heteromorphisms, and copy number variants
			Background
			Types of polymorphic DNA
				Phenotypically visible polymorphisms
				Single nucleotide polymorphisms
				Microsatellites
				Small-scale insertions/inversions/deletions/duplications
				Minisatellites
				Small-scale repetitive elements
				Submicroscopic copy number variants (CNVs)
				Chromosomal heteromorphisms
				Euchromatic variants
				Chromosomal and whole genomic variants
			Insights and conclusions
			References
	Chapter-20---Epigenetics_2021_Cytogenomics
		Epigenetics
			Introduction
			Epigenetic regulation and chromatin organization
				Epigenetic landscape during development
			The maternal and the paternal genomes are functionally disparate in higher mammals
			Disturbances of the subcortical maternal complex
				The imprinted regions in 11p15.5 as an example of the interaction between local chromatin regulation and local chromatin or ...
			Conclusion and outlook
			References
Subject Index
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