Exploring Personal Genomics

By Joel Dudley and Konrad Karczewski. Released January 2013.

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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 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 and undergraduate 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.

Sample Chapter available here: Chapter 7: Pharmacogenomics

1.1 Introduction
1.2 What is a genome?
1.3 How does a genome work?
1.4 Gene regulation: when and where a gene is expressed
1.5 The human epigenome
1.6 Replication and reproduction
1.7 Genetic variation
2.1 Considerations when obtaining personal genomic information
2.2 Limitations of personal genomics
2.3 Risks of personal genomics
2.4 Summary
3.1 Obtaining personal genomic information
3.2 From DNA to "raw" data
3.3 Working with personal genomic data
3.4 Conclusion
4.1 Introduction
4.2 Tabular views
4.3 Ideograms
4.4 Genome browsers
4.5 Visual quantitative assessment
4.6 Integrative visualizations
4.7 Conclusion
5.1 The genetics of human ancestry
5.2 Global genetic similarity
5.3 Genetic similarity between individuals
5.4 Identity by descent
5.5 Familial lineages
5.6 Genetic anthropology and ancient human DNA
5.7 Conclusions
6.1 Introduction
6.2 Discovery of genetic trait associations
6.3 Genetic disease associations
6.4 Application and interpretation of genetic associations
6.5 Quantitative trait inference
6.6 Summary
7.1 What is pharmacogenomics?
7.2 Mapping common pharmacogenomic variants
7.3 Major applications of pharmacogenomics
7.4 Assessment of rare variants in PD/PK genes
7.5 Variation in pharmacogenomic pathways
7.6 Conclusion
8.1 Introduction
8.2 Nutritional genomics
8.3 Environmental toxins
8.4 Metagenomics and infectious disease
8.5 Identifying personal genetic risk modifiers
8.6 Summary
9.1 Introduction
9.2 Bridging DNA and physiology through gene regulation
9.3 Creating personal genomic eQTL profiles
9.4 Personal genomic eQTL enrichment analysis
9.5 Functional assessment of personal genomic regulatory variants
9.6 Linking to further aspects of physiology
9.7 Summary
10.1 General challenges
10.2 Compound heterozygosity
10.3 Evolutionary conservation
10.4 Rare variants in coding regions
10.5 Rare variants in non-coding regions
10.6 Practical application of rare variant assessment tools
10.7 Further challenges
11.1 Copy number variation
11.2 More complex events (insertions, inversions, translocations)
11.3 Challenges

Analysis tools

  • Mapping pipeline for personal genomics data: STORMSeq
  • Browser-based interpretation software: Interpretome
  • Educational resources

  • Calculating OR, RR, and LR (courtesy of Alex Morgan).
    • Note: This reference tool is provided as-is and is for educational purposes only.
  • pgEd
  • Joel T. Dudley

    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

    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.