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Foreword | |
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Introduction | |
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Acknowledgments | |
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A gentle introduction to genomics | |
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Introduction | |
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What is a genome? | |
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How does a genome work? | |
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Gene regulation: when and where a gene is expressed | |
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The human epigenome | |
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Replication and reproduction | |
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Genetic variation | |
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Practical and ethical considerations in personal genomics | |
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Considerations when obtaining personal genomic information | |
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Limitations of personal genomics | |
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Risks of personal genomics | |
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Summary | |
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Getting started with personal genomics | |
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Obtaining personal genomic information | |
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From DNA to "raw" data | |
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Working with personal genomic data | |
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Conclusion | |
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Visualizing personal genomics | |
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Introduction | |
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Tabular views | |
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Ideograms | |
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Genome browsers | |
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Visual quantitative assessment | |
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Integrative visualizations | |
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Conclusion | |
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Ancestry and genealogy | |
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The generics of human ancestry | |
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Global genetic similarity | |
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Genetic similarity between individuals | |
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Identity by descent | |
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Familial lineages | |
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Genetic anthropology and ancient human DNA | |
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Conclusions | |
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Genetic trait associations | |
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Introduction | |
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Discovery of genetic trait associations | |
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Genetic disease associations | |
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Application and interpretation of genetic associations | |
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Quantitative trait inference | |
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Summary | |
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Pharmacogenomics | |
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What is pharmacogenomics? | |
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Mapping common pharmacogenomic variants | |
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Major applications of pharmacogenomics | |
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Assessment of rare variants in PD/PK genes | |
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Variation in pharmacogenomic pathways | |
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Conclusion | |
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Personal genomics and the environment | |
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Introduction | |
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Nutritional genomics | |
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Environmental toxins | |
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Metagenomics and infectious disease | |
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Identifying personal genetic risk modifiers | |
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Summary | |
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From DNA to physiology | |
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Introduction | |
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Bridging DNA and physiology through gene regulation | |
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Creating personal genomic eQTL profiles | |
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Personal genomic eQTL enrichment analysis | |
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Functional assessment of personal genomic regulatory variants | |
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Linking to further aspects of physiology | |
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Summary | |
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Rare and novel variants | |
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General challenges | |
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Compound heterozygosity | |
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Evolutionary conservation | |
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Rare variants in coding regions | |
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Rare variants in non-coding regions | |
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Practical application of rare variant assessment tools | |
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Further challenges | |
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Structural variation | |
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Copy number variation | |
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More complex events (insertions, inversions, translocations) | |
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Challenges | |
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Conclusion | |
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Glossary | |
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Index | |