 | Dudley J.T. Exploring personal genomics / J.T.Dudley, K.J.Karczewski. - Oxford: Oxford University Press, 2013. xi, 243 p., [8] p. of plates: ill. (some col.), maps. - Ind.: p.242-243. - ISBN 978-0-19-964448-3
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Foreword ...................................................... vii
George M. Church
Introduction ................................................... ix
Acknowledgments ................................................ xi
Part I
1 A gentle introduction to genomics ............................ 3
1.1 Introduction ............................................ 3
1.2 What is a genome? ....................................... 3
1.3 How does a genome work? ................................. 8
1.4 Gene regulation: when and where a gene is expressed .... 11
1.5 The human epigenome .................................... 13
1.6 Replication and reproduction ........................... 14
1.7 Genetic variation ...................................... 16
2 Practical and ethical considerations in personal genomics ... 24
2.1 Considerations when obtaining personal genomic
information ............................................ 24
2.2 Limitations of personal genomics ....................... 25
2.3 Risks of personal genomics ............................. 30
2.4 Summary ................................................ 33
3 Getting started with personal genomics ...................... 34
3.1 Obtaining personal genomic information ................. 34
3.2 From DNA to "raw" data ................................. 36
3.3 Working with personal genomic data ..................... 47
3.4 Conclusion ............................................. 50
4 Visualizing personal genomics ............................... 52
4.1 Introduction ........................................... 52
4.2 Tabular views .......................................... 53
4.3 Ideograms .............................................. 57
4.4 Genome browsers ........................................ 61
4.5 Visual quantitative assessment ......................... 67
4.6 Integrative visualizations ............................. 71
4.7 Conclusion ............................................. 74
5 Ancestry and genealogy ...................................... 76
5.1 The genetics of human ancestry ......................... 76
5.2 Global genetic similarity .............................. 78
5.3 Genetic similarity between individuals ................. 86
5.4 Identity by descent .................................... 89
5.5 Familial lineages ...................................... 92
5.6 Genetic anthropology and ancient human DNA ............. 95
5.7 Conclusions ............................................ 98
6 Genetic trait associations ................................. 100
6.1 Introduction .......................................... 100
6.2 Discovery of genetic trait associations ............... 100
6.3 Genetic disease associations .......................... 111
6.4 Application and interpretation of genetic
associations .......................................... 117
6.5 Quantitative trait inference .......................... 135
6.6 Summary ............................................... 137
7 Pharmacogenomics ........................................... 139
7.1 What is pharmacogenomics? ............................. 139
7.2 Mapping common pharmacogenomic variants ............... 142
7.3 Major applications of pharmacogenomics ................ 146
7.4 Assessment of rare variants in PD/PK genes ............ 149
7.5 Variation in pharmacogenomic pathways ................. 155
7.6 Conclusion ............................................ 158
Part II
8 Personal genomics and the environment ...................... 163
8.1 Introduction .......................................... 163
8.2 Nutritional genomics .................................. 164
8.3 Environmental toxins .................................. 167
8.4 Metagenomics and infectious disease ................... 174
8.5 Identifying personal genetic risk modifiers ........... 174
8.6 Summary ............................................... 178
9 From DNA to physiology ..................................... 181
9.1 Introduction .......................................... 181
9.2 Bridging DNA and physiology through gene regulation ... 182
9.3 Creating personal genomic eQTL profiles ............... 184
9.4 Personal genomic eQTL enrichment analysis ............. 187
9.5 Functional assessment of personal genomic regulatory
variants .............................................. 193
9.6 Linking to further aspects of physiology .............. 195
9.7 Summary ............................................... 197
10 Rare and novel variants .................................... 199
10.1 General challenges .................................... 200
10.2 Compound heterozygosity ............................... 202
10.3 Evolutionary conservation ............................. 204
10.4 Rare variants in coding regions ....................... 208
10.5 Rare variants in non-coding regions ................... 211
10.6 Practical application of rare variant assessment
tools ................................................. 213
10.7 Further challenges .................................... 218
11 Structural variation ....................................... 221
11.1 Copy number variation ................................. 223
11.2 More complex events (insertions, inversions,
translocations) ....................................... 225
11.3 Challenges ............................................ 228
Conclusion ................................................. 232
Glossary ...................................................... 233
Index ......................................................... 241
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