Diagnostics and Gene Therapy for Human Genetic Disorders

Cover
Half Title
Title Page
Copyright Page
Table of Contents
Preface
Acknowledgments
Author Bio
1 Genetic Analysis
1.1 Introduction
1.2 Monogenic Traits
1.3 Linkage Analysis
1.3.1 Linkage
1.3.2 Linkage Analysis
1.3.3 Polymorphic DNA Markers
1.4 Linkage Disequilibrium
1.4.1 Linkage Disequilibrium at One Pair of Loci
1.4.2 Linkage Equilibrium
1.4.3 Linkage Disequilibrium at More Than Two Loci
1.4.4 Linkage Disequilibrium Within and Between Populations
1.4.5 Population Genetics of Linkage Disequilibrium
1.4.6 Applications of Linkage Disequilibrium
1.4.7 Linkage Disequilibrium and Human Genome
1.5 Mendelian Pedigree Patterns
1.5.1 Dominance and Recessiveness of Characters
1.5.2 Types of Mendelian Pedigree
1.6 Mendelian Pedigree Analysis
1.6.1 Pedigree Analysis
1.6.2 Patterns Indicating a Recessive Trait
1.6.2.1 Autosomal Recessive
1.6.3 Patterns Indicating a Dominant Trait
1.6.3.1 Autosomal Dominant Trait
1.6.4 X-Linked Recessive
1.6.5 X-Linked Dominant
1.6.6 Calculations for the Risk Allele By Pedigree Analysis
1.7 Allele Frequency Estimation
1.7.1 Determination of Allele Frequency
1.7.1.1 DNA Pooling
1.8 The Hardy-Weinberg Law
1.8.1 Infinitely Large Population
1.8.2 Random Mating
1.8.3 No Mutation
1.8.4 No Immigration
1.8.5 No Evolutionary Forces Affecting the Population
1.8.6 Conclusion
1.8.7 Circumstances in Which the Hardy-Weinberg Law Cannot Apply
1.9 Multifactorial Inheritance
1.9.1 Open Neural Tube Defects (ONTDs)
1.9.2 Hip Dysplasia
1.9.3 Height
1.9.4 Model for Multifactorial Inheritance
1.10 Heritability
1.10.1 Types of Heritability
1.10.2 Methods of Estimating the Heritability
1.10.3 Heritability and the Environmentability of a Trait
1.10.4 Misconceptions Or Misunderstandings On Heritability
1.10.5 Heritability of Human Height
1.10.6 Heritability and Human Behavior
1.10.7 Designs for Estimating the Heritability of Behavior
1.10.7.1 Twin Studies
1.10.7.2 Adoption Studies
1.10.7.3 Developmental Models
1.10.8 Candidate Genes for Studying Heritability
1.11 Polygenic Inheritance
1.11.1 Human Skin Colour
1.12 Haplotyping
1.12.1 The Importance of Haplotype Analysis
1.12.2 Methods of Haplotyping
1.12.2.1 Haplotyping for Pedigree
1.12.2.2 DNA Sample Based Haplotyping Methods
1.13 Conclusion
References
2 Genetic Variations in Human Beings
2.1 Introduction
2.2 The Origin of Human Beings
2.2.1 Out of Africa Theory and Supporting Evidence
2.2.2 Evidence From Population Genetics
2.3 Genetic Diversity Among Human Beings
2.3.1 The Salient Features of Human Genetic Diversity
2.3.1.1 From Genetic Research
2.3.1.2 Findings From Fossil Remains
2.3.1.3 Techniques for the Measurement of Genetic Diversity
2.4 Genetic Polymorphisms
2.4.1 Single Nucleotide Polymorphisms (SNPs)
2.4.1.1 Identification of SNPs
2.4.1.2 SNP Genotyping
2.4.1.3 SNP Frequency in Human Genome
2.4.1.4 SNP Based Genome Wide Association Studies (SNP-GWAS)
2.4.2 Short-Tandem-Repeat Polymorphisms (STRPs)
2.4.2.1 Minisatellite Repeat Sequences and Their Functions
2.4.2.2 Microsatellite Repeats
2.4.2.3 Alu Insertion Polymorphisms
2.4.2.4 Hypervariable Region Polymorphism of Mitochondrial DNA
2.4.2.5 Y Chromosome Polymorphisms
2.5 Immunogenic Polymorphisms
2.5.1 Polymorphism in Human Major Histocompatibility Complex (MHC)
2.5.2 Immune Polymorphism
2.5.3 Cytokine Polymorphism
2.5.3.1 Polymorphisms and Cytokine Signaling
2.6 Trans-Species Polymorphism
2.6.1 Trans-Species Polymorphism in Major Histo Compatibility (MHC) Genes
2.6.2 Trans-Species Polymorphism in Other Genes Related to the Immune System
2.7 Genetic Variations in Drug Metabolizing Enzymes
2.7.1 Cytochrome P-450
2.7.2 Glucose-6-Phosphate Dehydrogenase
2.7.3 N- Acetyltransferase Polymorphism
2.8 Methods of Genotyping
2.8.1 Human HapMap Project
2.8.2 Genome Wide Association Study
2.8.3 Next-Generation Sequencing Technologies for Genotyping
2.9 Single Stranded Conformational Polymorphism (SSCP)
2.9.1 SSCP Procedure
2.9.2 High Throughput Methods for SSCP
2.9.3 Applications
2.9.4 Limitations
2.9.5 Modifications of SSCP
2.10 Conclusion
References
3 Genetic Disorders
3.1 Introduction
3.2 Classification of Genetic Disorders
3.3 Chromosomal Disorders
3.3.1 Human Chromosomes
3.3.1.1 Human Chromosome 1
3.3.2 Chromosome Staining and Karyotype
3.3.3 Chromosomal Abnormalities
3.3.3.1 Factors Responsible for Chromosomal Abnormalities
3.3.3.2 Types of Chromosomal Abnormalities
3.4 Single Gene Disorders
3.4.1 Autosomal Dominant Disorders
3.4.1.1 Marfan Syndrome
3.4.2 Autosomal Recessive Disorders
3.4.2.1 Sickle Cell Disease
3.4.3 Sex-Linked Disorders
3.4.3.1 X-Inactivation
3.4.3.2 X-Linked Dominant Disorders
3.4.3.3 X-Linked Recessive Disorders
3.4.3.4 Y-Linked Disorders
3.5 Mitochondrial Disorders
3.5.1 Genetic Diseases Due to the Mitochondrial Genome
3.6 Multifactorial Disorders
3.7 Molecular Basis of Cancer
3.7.1 Cell Cycle Regulation and the Importance of Apoptosis
3.7.2 The P53 Gene and Cancer
3.7.3 Telomeres, Cell Immortalization, and Tumorigenesis
3.7.4 Genes Frequently Mutated During Cancer
3.7.4.1 Cellular Oncogenes
3.7.4.2 Tumor Suppressor Genes
3.7.4.3 DNA Damage Repair Genes
3.7.5 Mutations in DNA and Cancer
3.8 Gene Expression Analysis
3.8.1 Gene Expression Profiling of Lung Cancer
3.9 Hematopoietic Disorders
3.9.1 Techniques for Studying the Hematopoietic Disorders
3.10 Conclusion
References
4 Techniques for the Diagnosis of Genetic Disorders
4.1 Introduction
4.2 Molecular Approach
4.2.1 Nucleic Acid Isolation Methods
4.2.1.1 DNA Extraction From Buccal Swabs
4.2.1.2 DNA Extraction From a Hair Sample
4.2.1.3 Extraction of DNA From Urine Samples
4.2.1.4 DNA Extraction From a Blood Sample
4.2.2 Restriction Fragment Length Polymorphism
4.2.2.1 Role of RFLPs as Markers for the Identification of Genetic Disorder
4.2.2.2 RFLP Procedure
4.2.2.3 Applications of RFLP
4.2.3 Hybridization-Based Methods
4.2.3.1 Membrane-Based Methods
4.2.3.2 Array-Based Methods
4.2.4 Polymerase Chain Reaction-Based Techniques
4.2.4.1 Reverse Transcriptase PCR
4.2.4.2 Real-Time PCR
4.2.4.3 Allele-Specific Amplification (ASA) By Amplification Refractory Mutation System (ARMS) PCR
4.2.4.4 Multiplex PCR
4.2.4.5 Digital PCR
4.2.4.6 Nested PCR
4.2.4.7 Multiplex Ligation-Dependent Probe Amplification (MLPA)
4.2.5 Electrophoresis Based Methods
4.2.5.1 Confirmation Sensitive Gel Electrophoresis
4.2.5.2 Denaturation Gradient Gel Electrophoresis
4.2.5.3 Temporal Temperature Gradient Gel Electrophoresis (TTGE)
4.2.5.4 Single-Strand Conformational Polymorphism (SSCP)
4.2.6 DNA Typing and Testing
4.2.7 HLA Typing
4.3 Cytogenetic Techniques
4.3.1 Classical Cytogenetic Techniques
4.3.1.1 Specialized Staining Techniques
4.3.2 Molecular Cytogenetic Techniques
4.3.2.1 Fluorescent In Situ Hybridization (FISH)
4.3.2.2 Spectral Karyotyping (SKY)
4.3.2.3 Comparative Genomic Hybridization (CGH)
4.4 Prenatal Genetic Diagnosis
4.4.1 Amniocentesis
4.4.2 Chorionic Villus Sampling
4.4.3 Fetal Blood Sampling
4.4.4 Prenatal Diagnosis of Genetic Disorders
4.5 Denaturing High-Performance Liquid Chromatography
4.5.1 Applications
4.6 Conclusion
References
5 Diagnosis of Genetic Disorders
5.1 Introduction
5.2 The History of Molecular Diagnostics
5.2.1 Molecular Diagnostic Tests for the Detection of Changes in Genetic Composition
5.2.1.1 Nucleic Acid-Based Diagnostic Tests
5.2.1.2 Gene-Based Diagnostic Tests
5.3 Lab On a Chip
5.3.1 A Brief History of Lab On a Chip
5.3.2 Materials Used for the Development of LOCs
5.3.3 Operation of a Microfluidic Unit
5.3.4 Storage of Reagents On a LOC Device
5.3.5 Microfluidic Platforms Used as LOCs
5.3.5.1 Lateral Flow Tests
5.3.5.2 Linear-Actuated Devices
5.3.5.3 Centrifugal Microfluidic Devices
5.3.6 LOC Diagnostic Targets
5.3.7 Applications and Future Perspectives of LOC
5.4 Diagnosis of Genetic Disorders Associated With the Chromosomal Abnormalities
5.4.1 Down Syndrome
5.4.1.1 Symptoms
5.4.1.2 Etiology
5.4.1.3 Diagnosis
5.4.1.4 Treatment
5.4.2 Turner Syndrome
5.4.2.1 Symptoms
5.4.2.2 Etiology
5.4.2.3 Diagnosis
5.4.2.4 Treatment
5.4.3 Klinefelter Syndrome
5.4.3.1 Symptoms
5.4.3.2 Etiology
5.4.3.3 Diagnosis
5.4.3.4 Treatment
5.4.4 Huntington’s Disease
5.4.4.1 Symptoms
5.4.4.2 Etiology
5.4.4.3 Diagnosis
5.4.4.4 Treatment
5.4.5 Fragile X Syndrome
5.4.5.1 Symptoms
5.4.5.2 Etiology of Fragile X Syndrome
5.4.5.3 Disease Diagnosis
5.4.5.4 Treatment
5.4.6 Thalassemia
5.4.6.1 Symptoms
5.4.6.2 Etiology
5.4.6.3 Diagnosis
5.4.6.4 Treatment
5.4.7 Sickle Cell Disease
5.4.7.1 Symptoms
5.4.7.2 Etiology
5.4.7.3 Diagnosis
5.4.7.4 Treatment
5.4.8 Alzheimer’s Disease
5.4.8.1 Symptoms
5.4.8.2 Etiology
5.4.8.3 Diagnosis
5.4.8.4 Treatment
5.4.9 Schizophrenia
5.4.9.1 Symptoms
5.4.9.2 Etiology
5.4.9.3 Diagnosis
5.4.9.4 Treatment
5.4.10 Cystic Fibrosis
5.4.10.1 Symptoms
5.4.10.2 Etiology
5.4.10.3 Diagnosis
5.4.10.4 Treatment
5.4.11 Thrombophilia
5.4.11.1 Symptoms
5.4.11.2 Etiology
5.4.11.3 Diagnosis
5.4.11.4 Treatment
5.4.12 Tay Sachs Disease
5.4.12.1 Symptoms
5.4.12.2 Etiology
5.4.12.3 Diagnosis
5.4.12.4 Treatment
5.4.13 Muscular Dystrophy
5.4.13.1 Symptoms
5.4.13.2 Etiology
5.4.13.3 Diagnosis
5.4.13.4 Treatment
5.4.14 Ataxia
5.4.14.1 Symptoms
5.4.14.2 Etiology
5.4.14.3 Diagnosis
5.4.14.4 Treatment
5.5 Diagnosis of Rare Genetic Disorders
5.5.1 Emanuel Syndrome
5.5.1.1 Symptoms
5.5.1.2 Etiology
5.5.1.3 Diagnosis
5.5.1.4 Treatment
5.5.2 Cat Eye Syndrome
5.5.2.1 Symptoms
5.5.2.2 Etiology
5.5.2.3 Diagnosis
5.5.2.4 Treatment
5.5.3 Uniparental Disomy
5.5.3.1 Symptoms
5.5.3.2 Etiology
5.5.3.3 Diagnosis
5.5.3.4 Treatment
5.5.4 Jacobsen Syndrome
5.5.4.1 Symptoms
5.5.4.2 Etiology
5.5.4.3 Diagnosis
5.5.4.4 Treatment
5.5.5 Kleefstra Syndrome
5.5.5.1 Symptoms
5.5.5.2 Etiology
5.5.5.3 Diagnosis
5.5.5.4 Treatment
5.6 Conclusions
References
6 Gene Therapy
6.1 Introduction
6.2 Gene Therapy and Genetic Engineering
6.2.1 Gene Therapy
6.2.2 Gene Therapy and Hematopoietic Stem Cells
6.2.3 CAR-T Therapy
6.2.4 CRISPR/Cas9
6.2.4.1 CRISPR/Cas9 and Neurodegenerative Disorders
6.2.4.2 Limitations of CRISPR/Cas9
6.3 Therapeutic Nucleic Acids and Therapeutic Polynucleotides
6.3.1 DNA-Based Therapeutics
6.3.1.1 Plasmids
6.3.1.2 Oligonucleotides for Antisense and Antigene Applications
6.3.1.3 DNA Aptamers
6.3.1.4 DNAzymes
6.3.2 RNA Based Therapeutics
6.3.2.1 RNA Aptamers
6.3.2.2 RNA Decoys
6.3.2.3 Ribozymes
6.3.2.4 Small Interfering RNAs
6.3.2.5 MicroRNA (MiRNA)
6.3.2.6 Circular RNA (CircRNA)
6.4 Therapeutic Polynucleotides
6.4.1 DNA Vaccines
6.5 Therapeutic Genes and Their Role in Cancer Therapy
6.5.1 HSV-Thymidine Kinase
6.5.2 Cytosine Deaminase
6.5.3 Cytochrome P450 2B1
6.5.4 Suicide Genes
6.5.5 Gene Therapy Directed Apoptosis and Cell Control
6.5.5.1 P53
6.5.5.2 E2F-1
6.5.6 Cytokine Genes
6.5.7 Costimulatory Genes
6.5.8 Tumor-Associated Antigen Genes
6.6 Gene Knockin and Gene Knockout
6.6.1 Gene Targeting
6.6.2 Gene Knockin
6.6.2.1 Knockin Editing
6.6.3 Gene Knockout
6.6.3.1 Conditional Gene Knockout
6.6.3.2 Other Applications of Gene Knockout
6.6.3.3 Limitations
6.7 Methods of Gene Delivery
6.7.1 Physical Methods
6.7.1.1 Microinjection
6.7.1.2 Particle Bombardment
6.7.1.3 Electroporation
6.7.1.4 Sonoporation
6.7.1.5 Magnetofection
6.7.1.6 Hydroporation
6.7.1.7 Photoporation
6.7.2 Viral Vector-Based Gene Delivery Systems
6.7.2.1 Retroviral Vectors
6.7.2.2 Adenoviral Vectors
6.7.2.3 Adeno-Associated Viral Vectors
6.7.2.4 Herpes Simplex Viral Vectors
6.7.2.5 Other Viral Vectors
6.7.3 Non-Viral Based Gene Delivery Systems
6.7.3.1 Naked DNA Delivery Systems
6.7.3.2 Polymeric Gene Delivery Systems
6.7.3.3 Liposomal Delivery Systems
6.8 Conclusions
References
7 Applications of Gene Therapy
7.1 Introduction
7.2 Applications of Gene Therapy
7.2.1 Prevention of Irradiation Damage to Salivary Glands
7.2.2 Autoimmune Disorders
7.2.2.1 Gene Therapy for Autoimmune Disorders
7.2.2.2 Gene Therapy for Grave’s Disease and Lupus Disease
7.2.2.3 Sjogren’s Syndrome
7.2.2.4 Pre-Clinical and Clinical Studies
7.2.3 Systemic Protein Deficiencies
7.2.4 Spinal Disorders
7.2.5 Gene Therapy for Cancer
7.2.5.1 Immunotherapy
7.2.5.2 Oncolytic Virotherapy
7.2.5.3 Gene Transfer
7.2.6 Gene Therapy for Eye Diseases
7.2.7 Gene Therapy for Cardiovascular Disorders
7.2.7.1 Gene Therapy for Coronary Artery Disease
7.2.7.2 Gene Therapy for Heart Failure
7.2.7.3 Gene Therapy for Vein Graft Stenosis
7.2.8 Gene Therapy for Neuro Degenerative Disorders
7.2.8.1 Gene Therapy for Neurodegenerative Disorders in Model Organisms
7.2.9 Gene Therapy and Dermatological Disorders
7.3 Difficulties With Gene Therapy
7.4 Conclusion
References
8 Applications of Molecular Diagnostics
8.1 Introduction
8.2 Applications of Diagnostics in Testing for Rare Genetic Disorders
8.2.1 Targeted Sequencing Panel
8.2.2 Whole Exome Sequencing
8.2.3 Whole Genome Sequencing
8.3 Applications of Diagnostics in Pharmacogenetics and Pharmacogenomics
8.3.1 Commercially Available Pharmacogenetic and Pharmacogenomics Tests
8.3.2 Clinical Significance of Pharmacogenetics and Pharmacogenomics
8.3.2.1 Cancer
8.3.2.2 Cardiology
8.3.2.3 Psychiatry
8.4 Applications of Diagnostics in Personalized Medicine
8.4.1 SNP Genotyping and Personalized Medicine
8.5 Applications of Diagnostics in Family Risk Assessment
8.6 Applications of Diagnostics in Transplantation
8.6.1 Role of Short-Term Repeats in Organ Transplantation
8.7 Applications of Diagnostics in Epigenetics
8.7.1 Mechanisms of Epigenetic Changes
8.7.1.1 DNA Methylation
8.7.1.2 Histone Modification
8.7.1.3 Non-Coding RNAs
8.7.2 Epigenetic Biomarkers
8.7.3 Epigenetics Based Tests Performed in Clinical Laboratories
8.8 Applications of Diagnostics in Forensic Sciences
8.8.1 Methods in Forensic Sciences for Identification of Humans
8.8.1.1 Autosomal STR Profiling
8.8.1.2 Y-Chromosome Analysis
8.8.1.3 Mitochondrial DNA
8.8.1.4 Autosomal SNPs
8.8.1.5 Biomarkers in Forensics
8.9 Conclusion
References
9 Case Studies
9.1 Introduction
9.2 Factors Responsible for the Occurrence of Genetic Disorders
9.3 Genetic Testing
9.4 Case Studies
9.4.1 Huntington’s Disease
9.4.2 Down Syndrome
9.4.3 Fragile X Syndrome
9.4.4 Duplication of Chromosomes and Trisomy
9.4.5 Chromosomal Abnormalities and Heteromorphism in Couples Leading to Recurrent Abortions
9.4.6 Congenital Anomalies in Newborn Infants
9.4.7 Tree Man Syndrome
9.4.8 Emanuel Syndrome
9.4.9 Jacobsen Syndrome
9.4.9.1 Case Study
9.4.10 Uniparental Disomy and Chediak-Higashi Syndrome
9.4.10.1 Case Study
9.5 Conclusion
References
Glossary
Index