Population Genomics in the Developing World
Concepts, Applications, and Challenges
- 1st Edition - November 10, 2024
- Editors: George P. Patrinos, Marlo Möller, Caitlin Uren
- Language: English
- Paperback ISBN:9 7 8 - 0 - 4 4 3 - 1 8 5 4 6 - 5
- eBook ISBN:9 7 8 - 0 - 4 4 3 - 1 8 5 4 7 - 2
Population Genomics in the Developing World: Concepts, Applications, and Challenges, a new volume in the Translational and Applied Genomics series, provides a comprehen… Read more
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Request a sales quotePopulation Genomics in the Developing World: Concepts, Applications, and Challenges, a new volume in the Translational and Applied Genomics series, provides a comprehensive, up-to-date summary of the field of population genomics in developing countries. This book equips students, researchers, and clinicians with the practical skills and approaches necessary to face the unique challenges and opportunities of practicing population genomics in developing countries. Following a brief foundational overview, more than a dozen authors working in developing nations share applied case studies from the field, including rationale, methods, analysis, and outcomes to reinforce understanding. Key themes across the country-specific chapters include efficient genetic data generation and effective computational and statistical tools to analyze population-level data. This book then discusses clinical interpretation of these data, from direct-to-consumer ancestry testing to translational and applied precision medicine. A final chapter considers the ethical aspects of conducting genomic research in developing countries.
- Addresses the unique opportunities to positively impact global health by practicing population genomics in developing countries
- Features applied case studies from genomic research in various developing nations, with clear instruction in research rationale, methods, tools, materials used, analysis, and outcomes
- Features international chapter authors and population genomics experts practicing in South Africa, Gabon, India, South America, Central America, and Honduras, among other locations
Human genetics and genomics researchers, practitioners of genomic medicine, healthcare professionals, sociologists, and individuals employed in international development, public health, health economics and regulatory bodies, students of biomedical and clinical sciences, Allied health professionals
- Title of Book
- Cover image
- Title page
- Table of Contents
- Copyright
- Contributors
- Chapter 1. Population genomics—The fundamentals
- The Hardy-Weinberg principle
- Why is the Hardy-Weinberg theorem important?
- Evolutionary implications of the Hardy-Weinberg theorem
- Quality control in genetic association studies
- Genetic counseling
- Evolutionary forces on populations
- Nonrandom mating
- Inbreeding
- Assortative mating
- Mutation
- Gene flow
- Genetic drift
- Bottleneck effect
- Founder effect
- Natural selection
- Stabilizing selection
- Directional selection
- Disruptive selection
- Linkage disequilibrium, haplotypes, and allele frequency patterns
- Meiosis and recombination
- Linkage disequilibrium and haplotypes
- Measuring linkage disequilibrium
- Factors influencing linkage disequilibrium
- Natural selection
- Genetic recombination
- Genetic drift
- Population growth
- Consanguinity
- Admixture
- Identity by descent (IBD) and identity by state (IBS)
- Applications of IBD in genetic studies
- Ancestral contributions, mtDNA, and Y-chromosome haplogroups
- What is ancestry?
- Genealogical ancestry
- Genetic ancestry
- Genetic similarity
- How is genetic ancestry investigated?
- How is genetic similarity investigated?
- Chapter 2. Why focus on population genomics in developing countries?
- Introduction
- The importance of population genomics in developing countries
- Evolutionary biology
- Genetic diversity
- Disease burden
- Precision medicine and pharmacogenomics
- Genomic research infrastructure
- The impact of population genomics on developing countries
- Conclusions
- Chapter 3. Contribution of large consortium studies to population genomics in the developing world: Examples from Africa and South Asia
- Introduction
- Large consortium studies have played a major role in assessing African diversity and population structure
- Resources generated from large consortium datasets
- Insights into the genetics of South Asians from large consortium studies
- Use of large consortia datasets for population genomics inferences—the promises and challenges
- Strategies to enable large consortium studies to support population genomics research
- Conclusions and future directions
- Chapter 4. Implementing genomics research in developing countries: Common challenges, and emerging solutions
- Introduction
- Community engagement in human genomics research: Where we've been and where we're going
- Common challenges for community-engaged genomics research
- Working with local researchers in developing countries: Getting started
- Equitable collaborations with researchers in developing countries
- Study designs for genomic research in developing countries
- Ongoing and emerging challenges to genomics research in developing countries
- Working during pandemics
- Genomic data access and secondary use
- Building genomics research capacity in developing countries
- Conclusions
- Chapter 5. Next-generation sequencing technologies: Implementation in developing countries
- Introduction
- Barriers to NGS access in developing countries
- Lack of infrastructure and high operating costs
- High cost of equipment and consumables—From sample collection to data generation and storage
- Lack of technical expertize
- Poor access to and representation on reference databases
- Limited or overly restrictive regulatory and ethical challenges
- Funding and research prioritization
- The way forward for NGS in LMICs—Potential solutions
- Investment in local infrastructure
- Capital expenditure investment
- Training programs
- Conclusion
- Chapter 6. Computational disease-risk prediction: Tools and statistical approaches
- Introduction
- Computational tools for genetic ancestry and population structure
- Computational genome-wide association studies
- Computational artificial intelligence approaches for PRS
- Origin of PRS
- Classification of current PRS methods
- Computing PRS
- Opportunities and challenges in computational artificial intelligence disease-scoring statistics
- Opportunities
- Genetic diversity and its impact on PRS development and clinical interpretation—an opportunity for advancement
- PRS predictive power in real-world clinical populations—potential challenges and possible next steps
- Conclusion
- Chapter 7. Genotype versus phenotype versus environment
- Introduction
- Genotype versus environment
- Phenotype
- The trap of the observable
- The clinical dilemma of missing traits within complex diseases
- Challenges in framing the genotype versus phenotype versus environment triad
- Proof of principle of viability of the triad within the proposed framework
- Pathology-supported genomics: Report overview
- Background introduction
- Case presentation
- Questionnaire based assessment of clinical characteristics to guide genetic testing and interpretation
- Genetic approach
- WES methodology
- Bioinformatics tools
- Results
- Recommendations from the results
- Notes on patient consent and clinical reporting
- Conclusion
- Disclosure
- Glossary
- List of abbreviation
- Chapter 8. Implementing population pharmacogenomics: Tailoring drug therapy for diverse populations
- Personalized medicine: “One size does not fit all”
- Pharmacogenomics: The right drug, to the right patent, at the right time
- The present landscape of pharmacogenomics: Necessity or luxury?
- Introducing population pharmacogenomics
- Pharmacogenomics across diverse populations
- Advancing population pharmacogenomics: Clinical impact and benefits
- Drug-gene interactions in cardiology, psychiatry, and oncology
- List of abbreviaitons
- Chapter 9. Direct-to-consumer (DTC) genetic testing and the population genomics industry
- What is direct-to-consumer (DTC) testing?
- What are the logistics behind a DTC test?
- DTC genetic tests currently available
- Nonhealth related DTC tests
- Health-related DTC tests
- Benefits of and opportunities related to DTC testing
- Increased accessibility and convenience
- Decreased cost
- Improved confidentiality
- Improved sense of connectedness, family, and community
- More control and independence
- Early detection, intervention, prevention and family planning
- Enlightening and educational
- For the greater good
- Increased involvement and experience
- Faster innovation and novelty
- Alleviate emotional turmoil
- Risks and controversies
- Privacy
- Inaccurate results
- Data erroneously being shared with others for an unintended purpose
- Data is compromised on websites where personal and genetic data was stored
- Lack of understanding regarding the DTC test privacy policy
- Technical limitations
- Cost
- Clinical utility and validity
- Risk for incorrect diagnosis
- Overutilization and interpretation
- Service provider-consumer relationship
- Community
- Emotional turmoil
- Potential for implementation in developing countries - is there a future?
- List of abbreviations
- Glossary
- Chapter 10. Clinical translation of genomics research in Africa—Mainstreaming medical ethics, equity, genetics education, and public engagement
- Introduction
- Informed consent comprehension and ethically appropriate consent models
- Genetic privacy, stigmatization, and discrimination
- Privacy protection vs. duty to warn of shared genetic risk
- Defining priorities for genomics research and medicine in Africa
- Governance of data sharing and access
- Knowledge translation: Commercialization, patents, and intellectual property rights
- Benefit sharing
- Feedback of genetic and genomic findings
- Actionability in the African context
- Feedback of individual genetic results and incidental findings
- Secondary findings in the African context
- The next frontier for ethical and equity-oriented genomics in Africa
- Building a critical mass of big data and genomics medicine workforce in Africa
- A social justice lens for genomics and health in Africa
- Public engagement for genomics medicine in Africa
- Chapter 11. The future of population genomics in developing countries
- Introduction
- Genetic diversity studies and new analysis approaches
- Disease surveillance and prevention
- Precision medicine and pharmacogenomics
- Genomic research consortia
- Ethical considerations and data privacy
- Investing in capacity and infrastructure development
- Bridging the healthcare gap: public health genomics and precision public health
- Conclusion
- Index
- No. of pages: 472
- Language: English
- Edition: 1
- Published: November 10, 2024
- Imprint: Academic Press
- Paperback ISBN: 9780443185465
- eBook ISBN: 9780443185472
GP
George P. Patrinos
George P. Patrinos is a Professor of Pharmacogenomics and Pharmaceutical Biotechnology in the University of Patras (Greece), Department of Pharmacy, and Head of Division of Pharmacology and Biosciences of the same department and holds adjunct Full Professorships at Erasmus MC, Faculty of Medicine, and Health Sciences, Rotterdam (the Netherlands), and the United Arab Emirates University, College of Medicine, Department of Genetics and Genomics, Al-Ain (UAE). Also, from 2018 until the end of 2024, he was Chair of the Global Genomic Medicine Collaborative (G2MC). He served 12.5 years as a full member and Greece’s National representative in the CHMP Pharmacogenomics Working Party of the European Medicines Agency (EMA). George has more than 340 publications in peer-reviewed scientific journals, some of them in leading scientific journals, such as The Lancet, Nature Genetics, Nature Reviews Genetic, Nucleic Acids Research, Genes & Development. He has also coauthored and coedited more than 15 textbooks, among which the renowned textbook Molecular Diagnostics, published by Academic Press, now in its 3rd edition, while he is the editor of Translational and Applied Genomics book series, published by Elsevier. Furthermore, he serves as the Editor-In-Chief of the prestigious Pharmacogenomics Journal (TPJ), published by Nature Publishing Group, Associate Editor, and member of the editorial board of several scientific journals, and advisory and evaluation committees. Apart from that, George is the main coorganizer of the Golden Helix Conferences, an international meeting series on Pharmacogenomics and Genomic Medicine with more than 50 conferences organized in more than 25 countries worldwide.
Affiliations and expertise
Department of Pharmacy, School of Health Sciences, University of Patras, Patras, Greece; Department of Genetics and Genomics, College of Medicine and Health Sciences, United Arab Emirates University, Al-Ain, United Arab Emirates; Zayed Center of Health Sciences, United Arab Emirates University, Al-Ain, United Arab EmiratesMM
Marlo Möller
Dr. Marlo Möller's primary research focuses on finding the genetic underpinnings of tuberculosis (TB). She developed an interest in this field at the beginning of her postgraduate degrees and continued this focus throughout her postdoctoral studies. She is currently an Associate Professor at Stellenbosch University, in Stellenbosch, South Africa. Her investigations into the genetic contribution of the human host to individual and population susceptibility to tuberculosis include tuberculous meningitis, tuberculosis resisters, the role of ancestry in tuberculosis disease, and primary immunodeficiencies. Dr. Möller's work leverages the complex ancestry of the admixed people in South Africa, specifically the unique genetic contribution from hunter–gatherer ancestry, to find novel genes and pathways involved in TB resistance and susceptibility.
Affiliations and expertise
SAMRC Centre for Tuberculosis Research, DSI/NRF Centre of Excellence for Biomedical TB Research, Division of Molecular Biology and Human Genetics, Department of Biomedical Sciences, Stellenbosch University; Associate Member, Centre for Bioinformatics and Computational Biology, Stellenbosch University, South AfricaCU
Caitlin Uren
Dr. Caitlin Uren currently works in the fields of human population genetics, bioinformatics, and communicable and noncommunicable diseases. Her initial research focused on identifying and characterizing genetic population structure in southern African human populations. This information was then used in the development of novel computational pipelines. In addition, she has been involved in the analysis of next-generation sequencing data with the goal to provide a molecular diagnosis to patients with suspected genetic disorders. She is currently involved in numerous projects that encompass data repositories, bioethics, bioinformatics, pharmacogenetics, and population genetics. As an early-career researcher, it is her goal to further the human genetics field in Africa and to teach and guide the next generation of scientists.
Affiliations and expertise
Post-Doctoral Fellow: Department of Biomedical Sciences and Associate Member: Centre for Bioinformatics and Computational BiologyDSI-NRF Centre of Excellence for Biomedical Tuberculosis Research, South African Medical Research Council Centre for Tuberculosis Research, Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health SciencesRead Population Genomics in the Developing World on ScienceDirect