Principles of Genetics and Molecular Epidemiology

Foreword
	References
Preface
Acknowledgements
Contents
Contributors
1: Principles of Modern Epidemiology and Public Health
	Introduction
	Life-Course Epidemiology
		Principles of Life-Course Research
			Development over Time
			Time and Place
			Timing
			Linked Lives
			Free Will or Agency
		Challenges for Life-Course Epidemiology
	Translational Epidemiology
	Postmodern Epidemiology
		Need for a Refocus on Postmodern Epidemiology
		Analysis Levels to be Considered in Postmodern Epidemiology
		Postmodern Epidemiology Perspective
	Final Considerations
	References
2: Molecular Tools for Modern Epidemiology: From the Concepts to Clinical Applications
	Introduction
	PCR
		Types of PCR
			Multiplex PCR
			Real-Time PCR
			Reverse Transcription PCR
			Digital PCR
			Lamp
	Principles of Karyotyping
	FISH
	Microarray
	Immunoassays
		Enzyme-Linked Immunosorbent Assay (ELISA)
		Direct ELISA (Antigen-Coated Plate, Screening Antibody)
		Indirect ELISA (Antigen-Coated Plate; Screening Antigen/Antibody)
		Sandwich ELISA (Antibody-Coated Plate; Screening Antigen)
		Competitive ELISA (Screening Antibody)
		New Methods
		Clinical Significance
		Western Blot
		Multiplex Western Blot (MWB)
		Capillary Electrophoresis (CE) and Capillary Western Blotting (CWB)
		Microfluidic Western Blotting
		Single-Cell Western Blotting
		Dot Blot
		Far-Western Blotting
		Clinical Significance
	Flow Cytometry
		Clinical Applications
		Phenotypic Characterization of Blood Cells
		Intracellular Antigen Expression
		Characterization of Antigen-Specific Responses
		Cell Cycle Analysis
		Apoptosis
	Proteomics
		Studying the Proteome
	Concluding Remarks
	References
3: Genomic Tools in Clinical Epidemiology
	Introduction
	NGS in the Study of Relevant SNVs and SNPs for Epidemiological Surveillance
	Implication of NGS Technologies on the Control of SARS-CoV-2 Pandemic
	The Influence of Genomic Tools on the Management of Helicobacter pylori Infection
	General Applications of NGS Technologies in Oncology Practices
	Advances on the Pathogenesis and Treatment Knowledge of Rheumatoid Arthritis by Using NGS
	Concluding Remarks
	References
4: Epigenetics in Epidemiology
	Introduction
	Epigenetic Process
	Epigenetic Technology Analysis
	Overview of Bioinformatic Analysis of Epigenome
	Epigenetic Biomarkers
		Epigenetics in Pharmacology
	Conclusions
	References
5: Principles of Clinical Transcriptomics and Splicing
	Introduction
	The Leap From Classic Gene Expression Studies to Transcriptomics
	General Overview of Transcriptomic Technologies
		SAGE-Derived Sequencing Technologies
		Microarrays
		RNA-seq
		Bulk Transcriptomics Profiling and Single-Cell Transcriptomics
	Splicing and Alternative Splicing
		Implications of Alternative Splicing in Clinics
	Applications of Transcriptomics in Clinical Disease
	Concluding Remarks
	References
6: Proteomics Principles and Clinical Applications
	Introduction
	Proteome
	Proteomics
		Proteomics Databases and Tools
		Proteomics Technologies
	Proteomics in Health and Disease
		Proteomics for the Diagnosis of Neurodegenerative Diseases
			Alzheimer’s Disease (AD) and Related Dementias Diagnosis
			Proteomic Studies in Parkinson’s Disease
			Huntington’s Disease
		Cancer
		Mitochondria and Proteomics
			Proteomics of Infectious Diseases
				Viral Infections
				Bacterial Infections
				Parasitic Infections
		Aging, Frailty, and Skeletal Muscle Wasting
	Conclusions
	References
7: Metabolomics: From Scientific Research to the Clinical Diagnosis
	Introduction
	The “Omics Science” in Human Health
	Toward Personalized Medicine
		Predictive Technologies in Human Diseases
	How to Implement Clinical Analysis Through Metabolomics
		Instrumentation in the Metabolomic Clinic
	Mass Spectral Library and Bioinformatics
	Conclusions
	References
8: Microscopy Principles in the Diagnosis of Epidemic Diseases
	Introduction
		Brief History of the Development of the Microscope
	Photonic Microscope
		The Use of Microscopy in the Life Sciences
		Generalities
		Components of the Photon Microscope
	Types of Photon Microscopes
		Bright-Field Microscope
		Dark-Field Microscope
		Phase Contrast Microscope
	Staining of Biological Samples, for Use in Different Types of Photon Microscopy
	The Use of the Photon Microscope in Clinical Diagnosis
		Microscopy as a Diagnostic Method
		The Use of the Photon Microscope in Histopathology for the Diagnosis of Diseases
		Diagnosis of Viral Infections
		Diagnosis of Bacterial Infections
		Diagnosis of Parasitic Infections
		Use of the Microscope in Examination of Urine Sediment
		Fluorescence Microscopy
			Fluorophores
			Excitation Spectrum
			The Fluorescence Microscope
			Confocal Microscopy
			Architecture of the Confocal Microscope
	Confocal Microscopy in Molecular Epidemiology: Clinical Applications and Further Directions
		Confocal Microscopy in Ophthalmology
		Confocal Microscopy in Dermatology
		Rare Diseases and Confocal Microscopy
	Electron Microscopy
		Wave Particle Duality
		Components of the TEM
		Sample Preparation
		The Role of the Electron Microscopy in Virus Diagnostic
			The Role of the TEM in Viral Gastrointestinal Diseases
				The Norovovirus
				The Rotavirus
				The Role of TEM in Viral Respiratory Diseases
					The Influenza Virus
			The Role of Electron Microscopy and the Last Pandemic
	Concluding Remarks
	References
9: Physiomics and Phenomics
	Physiomics
	Practical Applications of Physiomics
		Drug Research
		Organ Models
	“The Human Physiome Project”
	Phenomics
	Practical Applications of Phenomics
	Closing Remarks
	References
10: Digital Health and Physiomics
	Introduction
	Digital Health
	Wearables and Biosensors
	Social Media and Health
		Social Media in Healthcare
			Monitoring and Retrieval of Official Information
				Disease Detection
				Timely Estimates and Forecasts of Disease Incidence
			Situational Awareness During Emergency Response
		Communication Surveillance
			Global Awareness
			Reaction to Public Health Campaigns and Messages
	Applications
	Digital Health and Physiome
	Conclusion
	References
11: Principles of Imaging for Epidemiologists
	Introduction to Imaging Methods in Epidemiology
	Imaging Applications in Neurological and Psychiatric Research
		Illustrative Example: Population Imaging in Alzheimer’s Disease
	Imaging Applications in Cardiovascular Research
	Imaging Applications in Cardio-Metabolic Research
	Imaging Applications in Cancer Research
	Use of Imaging in Population-Based Epidemiological Studies
		Study of Health in Pomerania (SHIP)
		Cooperative Health Research in the Region Augsburg (KORA)
		Generation R
		Imaging Biobanks for Epidemiological Research
	Analysis of Imaging Data from Population-Based Studies
		Big Data Challenges
		Multivariate Analysis in Imaging
		Artificial Intelligence: Machine Learning and Deep Learning
		Bayesian Statistics in Imaging
	Limitations and Biases in Imaging Studies
		Anatomical and Incidental Findings
		Nonrepresentative Samples
		Establishing Causal Relationships
		Costs in Population Imaging
	Concluding Remarks
	References
12: Bioinformatics and Genomics for Epidemiologists
	Introduction: Bioinformatics Applied to Modern Epidemiology
	Applications of Bioinformatics in Modern Epidemiology
		The Need for Clinical Bioinformaticians in the Era of Big Data in Epidemiology
		Technical and Conceptual Limitations in Bioinformatics
	Genome-Wide Association Studies
		A Primer on GWAS and its Applications to Epidemiology
		How Is the GWAS Approach Applied to Epidemiology?
		Incorporating GWAS Findings into Epidemiology
		Analyzing GWAS Data
	Epigenome-Wide Association Studies
		Methods for Conducting EWAS
		Application of EWAS in Epidemiological Studies
	Polygenic Risk Scores
		Polygenic Risk Scores in Personalized Medicine
		First Approaches within the Estimation of GRS
		Determination of Genetic Risk Scores
		Limitations of Polygenic Risk Scores when Applied to a Real-World Scenario
	Perspectives for Bioinformatics and Genomics Using Systems Biology
	Conclusions
	References
13: Spatial Statistics and Health Sciences: Methods and Applications
	Introduction
		Descriptive Statistics
	Global and Local Spatial Autocorrelation
		Neighbours
		Spatial Weights
	Interpolation and Geostatistics
		Variogram
		Spatial Interpolation
			Inverse Distance Weight
			Kriging
	Linear Models for Spatial Data
		Spatial Lag Model
		Spatial Autoregressive and Spatial Error Models
		Inference with the Models
		Other Spatial Models
			Simultaneous Moving Average
		Geographically Weighted Regression
	Conclusion
	References
14: Principles of Network Models and Systems Epidemiology
	Introduction
	Systems Epidemiology
	Network Models
	Probabilistic Graphical Models (PGM)
	Neural Networks
	Social Network Analysis (SNA)
	Perspectives
	Conclusions
	References
15: Molecular Pharmacological Tools Applied to Epidemiology
	Introduction
		Drug Discovery
		Target Identification
		Validation of the Target
		Lead Identification
		Lead Optimization
	Clinical Trials
		Phase I
		Phase II
		Phase III
		Phase IV
	In Silico vs In vitro
	Sources of Pharmacologically Active Compounds
		Natural Products
		Quantitative Structure Relationship (QSAR)
		Docking
		Global Docking
		Network Pharmacology and Drug Repurposing
	Quantitative Systems Pharmacology
	Conclusions
	References
16: Systems Medicine Applied to Epidemiology
	Bioinformatic Tools for Medicine
	What Is Systems Biology?
	Principles of Network Biology
	Systems Medicine, a Novel Branch
	Applications of Systems Medicine to Clinical Research
	Future Directions and Conclusion
	References
17: Genomic Surveillance in Public Health
	Genomics in Public Health
	Genomic Tools for Epidemiological Surveillance
	Genomic and Molecular Research Tools
		Culture Methods for Virus
		Imaging
		High-Performance Sequencing
		Virus Outbreaks and Genomic Surveillance
	Bacterial Outbreaks and Genomic Surveillance
		Mycobacterium Tuberculosis
		Clostridium Perfringens
		Mycobacterium Leprae
	Genomic Surveillance over Other Infectious Diseases
	Chronic Diseases and Genomic Surveillance
		Cancer
		Neurodegenerative Diseases
		Cardiovascular Diseases
	Other Chronic Diseases
	Concluding Remarks
	References
Index