2 CONTENTS
I. ABSTRACT p.5
II. TABLE OF ABBREVIATIONS p.6
1. INTRODUCTION p.7
1.1. Oxygen Metabolism p.7
1.1.1. Oxygen Sensing Machinery p.7
1.1.2. Downstream Effectors p.9
1.2. Living At High Altitudes, The Hypoxic Stress p.10
1.3. Daghestani Populations p.13
1.3.1. Overview p.13
1.3.2. Preliminary Data p.14
1.3.3. Evidences for High Altitude Adaptation p.16
1.4. Proposed Approach p.17
1.4.1 General Idea p.17
1.4.2 Populations p.18
1.4.3 Candidate Genes p.19
1.4.4 Control Regions p.20
2. MATERIALS AND METHODS p.23
2.1. Ethical Consent p.23
2.2. Control Regions p.23
2.3. Primer Design And Standardization p.25
2.4. Whole Genome Amplification p.25
3
2.5. PCRs (Polymerase Chain Reactions) p.26
2.6 Illumina flow-cell platform p.26
2.7. Indexed re-sequencing p.29
2.8. Data Processing p.30
2.9. Coverage Analysis p.34
2.10. Quality Controls p.35
2.10.1. Discordance rate p.36
2.10.2. False Negative And False Positive Rates p.37
2.10.3. Further Filtering p.38
2.11. SNPs Calling and Analysis p.38
2.11.1. Summary Statistics p.39
2.11.2. Synonymous And Non Synonymous SNPs p.39
3. RESULTS p.41
3.1. Preliminary Results p.41
3.1.1. Existing Data p.41
3.1.2. DNA Quality p.41
3.2. Plate Design And PCRs Yields p.42
3.3. Whole Genome Amplifications p.45
3.4. Samples p.46
3.5. Sequencing Output p.47
3.6. Coverage p.48
3.7. Quality Controls p.53
3.8. SNPs Calling p.58
4
3.9. Downstream Analysis p.59
3.9.1. Summary Statistics p.59
3.9.2. SNPs Mapping p.60
4. DISCUSSION p.64
4.1. PCRs Yield And Coverage p.64
4.2. Quality Controls p.65
4.3. Demographic Events And Selective Sweeps p.66
4.4 SNPs Analysis p.67
5. PERSPECTIVES p.69
6. ACKNOWLEDGEMENTS p.71
7. APPENDICES p.72
Appendix 1 Ethical Approval Documents p.72
Appendix 2 Sample IDs And Ethnicity p.73
Appendix 3 Genes And Control Regions Coordinates p.76
Appendix 4 Primers Sequences p.80
Appendix 5 PCR Protocols p.86
Appendix 6 Unix Error Interpretation Table p.99
Appendix 7 Scripts p.100
8. BIBLIOGRAPHY p.124
9. SPECIAL THANKS p.128
10. CD Containing Supplementary Materials
