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E-raamat: Exploring Personal Genomics

(Biomedical Informatics, Stanford University School of Medicine, USA), (Director of Informatics and Assistant Professor of Genetics and Genomics Sciences, Mount Sinai School of Medicine, USA)
  • Formaat: PDF+DRM
  • Ilmumisaeg: 04-Jan-2013
  • Kirjastus: Oxford University Press
  • Keel: eng
  • ISBN-13: 9780191663765
  • Formaat - PDF+DRM
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  • Formaat: PDF+DRM
  • Ilmumisaeg: 04-Jan-2013
  • Kirjastus: Oxford University Press
  • Keel: eng
  • ISBN-13: 9780191663765

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Rapid advances in high-throughput genome sequencing technologies foreshadow a near-future in which millions of individuals will gain affordable access to their complete genome sequence. This promises to offer unprecedented insights into the fundamental biological nature of ourselves and our species: where we came from, how we begin our lives, how we develop and grow, how we interact with our environment, how we get sick, how we get well, and how we age. Personal genomics is an essential component of the inevitable transition towards personalized health and medicine. As the medical establishment begins to explore and evaluate the role of personal genomics in health and medicine, both clinicians and patients alike will gain from becoming well versed in both the power and the pitfalls of personal genomic information. Furthermore, it is likely that all students of the biomedical sciences will soon be required to gain crucial understanding in the emerging field of personal genomics.

Exploring Personal Genomics provides a novel, inquiry-based approach to the understanding and interpretation of the practical, medical, physiological, and societal aspects of personal genomic information. The material is presented in two parts: the first provides readers of all backgrounds with a fundamental understanding of the biology of human genomes, information on how to obtain and understand digital representations of personal genomic data, tools and techniques for exploring the personal genomics of ancestry and genealogy, discovery and interpretation of genetic trait associations, and the role of personal genomics in drug response. The second part offers more advanced readers an understanding of the science, tools, and techniques for investigating interactions between a personal genome and the environment, connecting DNA to physiology, and assessing rare variants and structural variation.

This book aims to support undergraduate and graduate studies in medicine, genetics, molecular biology, and bioinformatics. Additionally, the design of the content is such that medical practitioners, professionals working in the biomedical sciences or related fields, and motivated lay individuals interested in exploring their personal genetic data should find it relevant and approachable.

Arvustused

The book is a remarkable demonstration of how, through cogent and thoughtful writing, two authors can indeed portray the content and texture of highly sophisticated science in a style enlightening for a very wide audience. * Bernard Dixon, The Biologist * Beneficiaries will include not only researchers, students and biomedical professionals but general readers and social scientists wanting to comprehend the personal and social implications of genomic information...an exceptional piece of authorship and publishing. * Dr Bernard Dixon OBE, The Biologist *

Foreword vii
George M. Church
Introduction ix
Acknowledgments xi
Part I
1 A gentle introduction to genomics
3(21)
1.1 Introduction
3(1)
1.2 What is a genome?
3(5)
1.3 How does a genome work?
8(3)
1.4 Gene regulation: when and where a gene is expressed
11(2)
1.5 The human epigenome
13(1)
1.6 Replication and reproduction
14(2)
1.7 Genetic variation
16(8)
2 Practical and ethical considerations in personal genomics
24(10)
2.1 Considerations when obtaining personal genomic information
24(1)
2.2 Limitations of personal genomics
25(5)
2.3 Risks of personal genomics
30(3)
2.4 Summary
33(1)
3 Getting started with personal genomics
34(18)
3.1 Obtaining personal genomic information
34(2)
3.2 From DNA to "raw" data
36(11)
3.3 Working with personal genomic data
47(3)
3.4 Conclusion
50(2)
4 Visualizing personal genomics
52(24)
4.1 Introduction
52(1)
4.2 Tabular views
53(4)
4.3 Ideograms
57(4)
4.4 Genome browsers
61(6)
4.5 Visual quantitative assessment
67(4)
4.6 Integrative visualizations
71(3)
4.7 Conclusion
74(2)
5 Ancestry and genealogy
76(24)
5.1 The genetics of human ancestry
76(2)
5.2 Global genetic similarity
78(8)
5.3 Genetic similarity between individuals
86(3)
5.4 Identity by descent
89(3)
5.5 Familial lineages
92(3)
5.6 Genetic anthropology and ancient human DNA
95(3)
5.7 Conclusions
98(2)
6 Genetic trait associations
100(39)
6.1 Introduction
100(1)
6.2 Discovery of genetic trait associations
100(11)
6.3 Genetic disease associations
111(6)
6.4 Application and interpretation of genetic associations
117(18)
6.5 Quantitative trait inference
135(2)
6.6 Summary
137(2)
7 Pharmacogenomics
139(24)
7.1 What is pharmacogenomics?
139(3)
7.2 Mapping common pharmacogenomic variants
142(4)
7.3 Major applications of pharmacogenomics
146(3)
7.4 Assessment of rare variants in PD/PK genes
149(6)
7.5 Variation in pharmacogenomic pathways
155(3)
7.6 Conclusion
158(5)
Part II
8 Personal genomics and the environment
163(18)
8.1 Introduction
163(1)
8.2 Nutritional genomics
164(3)
8.3 Environmental toxins
167(7)
8.4 Metagenomics and infectious disease
174(1)
8.5 Identifying personal genetic risk modifiers
174(4)
8.6 Summary
178(3)
9 From DNA to physiology
181(18)
9.1 Introduction
181(1)
9.2 Bridging DNA and physiology through gene regulation
182(2)
9.3 Creating personal genomic eQTL profiles
184(3)
9.4 Personal genomic eQTL enrichment analysis
187(6)
9.5 Functional assessment of personal genomic regulatory variants
193(2)
9.6 Linking to further aspects of physiology
195(2)
9.7 Summary
197(2)
10 Rare and novel variants
199(22)
10.1 General challenges
200(2)
10.2 Compound heterozygosity
202(2)
10.3 Evolutionary conservation
204(4)
10.4 Rare variants in coding regions
208(3)
10.5 Rare variants in non-coding regions
211(2)
10.6 Practical application of rare variant assessment tools
213(5)
10.7 Further challenges
218(3)
11 Structural variation
221(11)
11.1 Copy number variation
223(2)
11.2 More complex events (insertions, inversions, translocations)
225(3)
11.3 Challenges
228(4)
Conclusion 232(1)
Glossary 233(8)
Index 241
Joel T. Dudley is a veteran bioinformatics and genomics researcher with more than 10 years of professional experience studying the genomic basis of species evolution and human disease. He has published more than 35 peer-review research articles pertaining to personal genomics, genomic medicine, pharmacogenomics, drug discovery, bioinformatics, and evolutionary genomics. Joel is currently the Director of Bioinformatics and Assistant Professor of Genetics and Genomics Sciences at Mount Sinai School of Medicine in New York. Joel earned a B.S. in Microbiology from Arizona State University and a Ph.D. in Biomedical Informatics from Stanford University.

Konrad J. Karczewski is a genome scientist, bringing systems-level approaches to the study of human disease biology. He was involved with the pioneering course at Stanford University in Personalized Medicine and Genomics, where he led the development of a platform for personal genotype interpretation, the Interpretome. Konrad earned a B.A. in Molecular Biology from Princeton University and a M.S. in Biomedical Informatics from Stanford University, where he is working towards a Ph.D.