Omics Technologies for Clinical Diagnosis and Gene Therapy.

Format:

Book

Author/Creator:

Bakhtiar, Syeda Marriam.

Contributor:

Dilshad, Erum.

Language:

English

Subjects (All):

Gene therapy.

Genetic disorders.

Genetics--Research.

Genetics.

Human genetics.

Physical Description:

1 online resource (334 pages)

Edition:

1st ed.

Place of Publication:

Sharjah : Bentham Science Publishers, 2022.

Summary:

Genetic disorders have been the focus of scientists for a long time. The emergence of next-generation sequencing techniques has ushered a new era in genetics and several developments have occurred in human genetics. The scientific perspective has also been widened with omics technologies that allow researchers to analyze genetic sequences and their expression products. An integrated approach is being used not only for diagnosis but also for disease management and therapeutic purposes. This book highlights emerging areas of omics technology and its application in the diagnosis and management of human genetic disorders. The book covers three areas of research and implementation: 1) Diagnosis (covering conventional strategies to next-generation platforms). This section focuses on the role of in silico analysis, databases and multi-omics of single-cell which will help in designing better management strategies. 2) Disease Management and therapeutic interventions. This section starts with genetic counselling and progresses to more specific techniques such as pharmacogenomics and personalized medicine, gene editing techniques and their applications in gene therapies and regenerative medicine. 3) Case studies. This section discusses the applications and success of all the above-mentioned strategies on selected human disorders. This book serves as a handy reference for students and academics studying advanced omics techniques in biochemistry and molecular genetics as part of courses in life sciences, pharmacology and medicine.

Contents:

Cover

Title

Copyright

End User License Agreement

Contents

Foreword

Preface

List of Contributors

Next-Generation Technologies for Rare Inherited Disorders

Hira Kazmi1 and Muhammad Ilyas2,3,*

1. INTRODUCTION

1.1. Whole Genome/Exome Sequencing

1.2. Transcriptomics (RNA-Seq) of Rare Diseases

1.3. DNA Methylation (Methyl-Seq) in Rare Diseases

1.4. Long-Reads Sequencing for Rare Inherited Disorders

1.5. The International Rare Diseases Research Consortium

CONCLUSION AND RECOMMENDATIONS

CONSENT FOR PUBLICATION

CONFLICT OF INTEREST

ACKNOWLEDGEMENTS

REFERENCES

Genetic Testing for Rare Genetic Disorders

Muhammad Tariq1,*, Naveed Altaf Malik1, Ilyas Ahmad2, Syeda Seema Waseem and Shahid Mahmood Baig1

1.1. Genetic Testing and Its Scope

1.2. Screening and Diagnostic Testing

1.3. Why Genetic Testing?

2. TESTING TECHNOLOGIES

2.1. Detection of Targeted Allele Specific Mutation

2.2. Gene-specific Sanger Sequencing

2.3. Testing for Structural Variations

2.4. Genetic Testing in the NGS Era

3. INCIDENTAL FINDINGS

4. FUTURE PROSPECTS AND CHALLENGES

CONCLUDING REMARKS

Preimplantation, Prenatal, and Postnatal Diagnosis

Sadia Nawaz1,* and Humna Masood1

1.1. Preimplantation Genetic Diagnosis (PGD)

1.1.1. PGD and In vitro Diagnostic Procedures

1.1.2. Phases of PGD

1.1.3. Embryo Biopsy

1.1.4. Genetic Diagnostic Analysis

1.2. Prenatal Diagnosis (PND)

1.2.1. In Vivo Procedure of PND

1.2.2. Sampling of Fetus Cells

1.2.3. Genetic Diagnostic Analysis

1.3. Postnatal Diagnosis

1.3.1. Chromosomal Abnormalities

1.3.2. Monogenic (Mendelian) Diseases

1.3.3. Polygenic Diseases.

2. PREIMPLANTATION, PRENATAL, AND POSTNATAL DIAGNOSTIC TECHNIQUES

2.1. Array Comparative Genomic Hybridization (aCGH)

2.2. Fluorescence In Situ Hybridization (FISH)

2.3. Next Generation Sequencing (NGS)

2.4. Whole Genome Amplification (WGA)

3. PRENATAL AND POSTNATAL DIAGNOSTIC TECHNIQUES FOR CHROMOSOMAL ABNORMALITIES, MONOGENIC, AND POLYGENIC DISEASES

3.1. Methylation PCR

3.2. Amniocentesis

3.3. Karyotyping

3.4. Multiplex Ligation Dependent Probe Amplification (MLPA)

3.5. Restriction Fragment Length Polymorphism (RFLP)

3.6. Quantitative Fluorescence Polymerase Chain Reaction (QF-PCR)

3.7. Cell Free Fetal DNA Analysis

3.8. Chromosomal Microarray Analysis

3.9. Chorionic Villus Sampling

4. FUTURE CHALLENGES IN PREIMPLANTATION, PRENATAL AND POSTNATAL DIAGNOSIS

5. FUTURE PROSPECTS

Genetic Counseling in Inherited Disorders

Shumaila Zulfiqar1,2, Muhammad Tariq1,*, Naveed Altaf Malik1, Ayaz Khan1, Shafaq Ramzan1, Maria Iqbal1,3, Iram Anjum2 and Shahid Mahmood Baig1

2. POPULATION CARRIER SCREENING MECHANISM

2.1. Thalassemia a Case Study

3. RISK ESTIMATION

4. CLINICAL PRACTICES

5. ETHICAL ISSUES

6. FUTURE PROSPECTS

Genome-Wide Association Studies (GWAS)

Hafiza Noor Ul Ayan1,2 and Muhammad Tariq1,*

1.1. Rationale

2. BENEFITS OF GWAS

3. SUCCESS STORIES

3.1. Type 2 Diabetes

3.2. Autoimmune Diseases

3.3. Coronary Artery Disease (CAD)

4. LIMITATIONS OF GWAS

5. POST-GWAS ERA: PROSPECTS AND CHALLENGES

REFERENCES.

Regenerative Medicine

Hajra Qayyum1,* and Syeda Marriam Bakhtiar1

2. APPROACHES TO RM

2.1. Cell-based Therapy

2.1.1. Adult Stem Cells

2.1.2. Pluripotent Stem Cell-Based Cell Therapies

2.2. Biomaterials

2.3. Implantation of Scaffold Seeded with Cells

3. CLINICAL APPLICATIONS (CASE STUDIES)

3.1. Bladder and Urethra

3.2. Blood Vessels

3.3. Heart

3.4. Liver

3.5. Skin

3.6. Bone

3.7. Cartilage Tissue

4. CHALLENGES AND FUTURE PERSPECTIVES

4.1. Lack of Robust Lineage-Specific Differentiation Protocols

4.2. Tumorigenicity

4.3. Immune Rejection

4.4. Heterogeneity

Emerging OMICS and Genetic Disease

Muhammad Jawad Hassan1,*, Muhammad Faheem1 and Sabba Mehmood1

1. INTRODUCTION TO OMICS AND GENETIC DISEASE

2. ADVANCED TECHNIQUES IN "OMICS"

2.1. Emerging Omics Techniques: Genomics and Transcriptomics

2.1.1. Genomics

2.1.2. Transcriptomics

2.2. Emerging Omics Techniques: Proteomics and Metabolomics

2.2.1. Proteomics

2.2.2. Metabolomics

3. OMICS AND DIAGNOSIS OF GENETIC DISEASES

3.1. Back To The Future

3.2. Advances In Omics Technologies For Disease Diagnosis (examples)

3.3. Mendelian Disorders

3.4. Non-mendelian/common Disorders

4. OMICS DATABASES

5. OMICS: GENETIC DISEASE MANAGEMENT AND THERAPEUTICS

6. CHALLENGES AND OPPORTUNITIES

6.1. Reference Populations and Phenotyping

Integrated Bioinformatics and Computational Biology Approaches: Applications in Diagnosis and Therapeutics

Fatima Shahid1, Shifa Tariq Ashraf1, Hayeqa Shahwar Awan1, Amina Basheer1 and Amjad Ali1,*

1. INTRODUCTION.

1.1. Exploration of Disease-Associated Biomarkers

1.2. Computational Models as Tools to Identify Key Biomarkers

1.3. Annotation of Disease Associated Mutations

1.4. Identification of Epigenetic Drivers

2. ROLE OF SYSTEMS BIOINFORMATICS (NETWORK-BASED METHODS FOR HUMAN DISEASE GENE PREDICTION)

2.1. Systems Modelling and Simulation

2.2. Network-Based Diagnostics and Therapeutics

2.3. Tools/ Data Bases Used in Diagnosis and Treatment Regimens

2.4. Contribution of Bioinformatics in Cancer Diagnostics and Therapeutics

3. APPLICATION IN PRECISION MEDICINE AND PHARMACOGENOMICS

3.1. Pharmacogenomics and Pharmacogenetics in Personalized Medicine

3.2. Pharmacogenomics and Pharmacogenetics in Drug Development

3.3. Pharmacogenomics in Establishment of Drug Application Guidelines

4. REVERSE VACCINOLOGY-A PROGRESSIVE STEP TOWARDS THERAPEUTIC INNOVATION

Multi-omics Data Integration: Applications in Systems Genomics

Anam Naz1,*, Ammara Siddique2, Aqsa Ikram1, Bisma Rauff5, Huma Tariq3 and Sajjad Ahmed4

1.1. Advanced Techniques in "Omics"

1.2. Omics-Driven Targeted Therapy

1.3. Meta-omics

1.4. Transcriptomics

1.5. Single-Dimensional Transcriptomic Assessment versus Integrated Omics

1.6. Rewards of Integrated Omics

2. PATHWAY PROFILING USING SYSTEM GENOMICS

3. CATEGORIES OF PATHWAY PROFILING AND GENETIC NETWORK

3.1. Metabolic Pathway Profiling

3.2. Signaling Pathways Profiling

3.3. Networks for Protein-Protein Interaction

3.4. Gene Regulatory Networks

4. DESIGNING EXPERIMENTS FOR OMICS DATA INTEGRATION

4.1. Multi-Omics Data from Genome to Phenome: Integration in Systems Genomics

4.2. Software and Tools Used for Integration.

4.3. Multi-Omics Factor Analysis (MOFA)

4.4. MixOmics

4.5. Graph-based Clustering of Samples

4.6. Nonnegative Matrix Factorization (NMF)

4.7. Multi-Omics Data Integration (miodin)

4.8. Network-based Integration of Multi-omics Data (NetICS)

4.9. moCluster

4.10. Penalized Multivariate Analysis (PMA)

5. CHALLENGES

6. FUTURE ASPECTS

Single Cell Omics

Erum Dilshad1,*, Amna Naheed Khan1, Iqra Bashir1, Muhammad Maaz1, Maria Shabbir2 and Marriam Bakhtiar1

1.1. Single-cell genomics

Single-cell transcriptomics

1.3. Single-cell Proteomics

1.4. Single-cell Metabolomics

2. STRATEGIES FOR SINGLE-CELL ISOLATION

2.1. Fluorescence-Activated Cell Sorting (FACS)

2.2. Magnetic-activated Cell Sorting (MACS)

2.3. Laser Capture Micro-dissection (LCM)

2.4. Manual Cell Picking/micro-manipulation

2.5. Micro-fluidics

3. STRATEGIES FOR SINGLE-CELL SEQUENCING

3.1. Multiple Displacement Amplification

3.2. Multiple Annealing And Looping Based Amplification Cycles

3.3. PCR Based scRNA Sequencing

3.4. In vitro Transcription (IVT)-based Amplification

3.5. Mass Spectrometry

3.6. Single-cell multi-Omics

3.7. Multi-Omics Approaches: Challenges and Opportunities

4. STRATEGIES FOR MULTI-OMICS PROFILING OF SINGLE CELLS

4.1. Combined

4.2. Separate

4.3. Split

4.4. Convert

4.5. Predict

Pharmacogenomics

Shumaila Azam1, Sahar Fazal1,*, Attiya Kanwal2, Muhammad Saad Khan5, Narjis Khatoon1, Muneeba Ishtiaq1, RabbiahManzoor Malik1, 3, Sana Elahi1 and Fakhra Nazir1, 4

1.1. Application of Pharmacogenomics.

1.2. Translating Pharmacogenomics.

Notes:

Description based on publisher supplied metadata and other sources.

Other Format:

Print version: Bakhtiar, Syeda Marriam Omics Technologies for Clinical Diagnosis and Gene Therapy: Medical Applications in Human Genetics

ISBN:

9789815079517

9815079514

OCLC:

1350689299