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Wan, Yize Isalina (2011) Genetic Epidemiology of Atopy and Asthma

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Wan, Yize Isalina (2011) Genetic Epidemiology of Atopy and Asthma Wan, Yize Isalina (2011) Genetic epidemiology of atopy and asthma. PhD thesis, University of Nottingham. Access from the University of Nottingham repository: http://eprints.nottingham.ac.uk/12224/1/Print_YWan_ThesisFinal_Oct2011.pdf Copyright and reuse: The Nottingham ePrints service makes this work by researchers of the University of Nottingham available open access under the following conditions. · Copyright and all moral rights to the version of the paper presented here belong to the individual author(s) and/or other copyright owners. · To the extent reasonable and practicable the material made available in Nottingham ePrints has been checked for eligibility before being made available. · Copies of full items can be used for personal research or study, educational, or not- for-profit purposes without prior permission or charge provided that the authors, title and full bibliographic details are credited, a hyperlink and/or URL is given for the original metadata page and the content is not changed in any way. · Quotations or similar reproductions must be sufficiently acknowledged. Please see our full end user licence at: http://eprints.nottingham.ac.uk/end_user_agreement.pdf A note on versions: The version presented here may differ from the published version or from the version of record. If you wish to cite this item you are advised to consult the publisher’s version. Please see the repository url above for details on accessing the published version and note that access may require a subscription. For more information, please contact [email protected] Genetic Epidemiology of Atopy and Asthma By Yize I Wan, BMedsci. (Hons) Thesis submitted to the University of Nottingham for the degree of Doctor of Philosophy May 2011 To my family, with all my love Contents ABSTRACT ..........................................................................................................................I ACKNOWLEDGEMENTS ................................................................................................ II ABBREVIATIONS ............................................................................................................III PUBLICATIONS RELEVANT TO THESIS .................................................................... IV CHAPTER 1 ........................................................................................................................ 1 GENERAL INTRODUCTION ............................................................................................ 1 1.1 ALLERGIC DISEASE ................................................................................................... 1 1.1.1 Definition ............................................................................................................. 1 1.1.2 Epidemiology ....................................................................................................... 1 1.1.3 Pathogenesis ........................................................................................................ 1 1.1.4 Allergens .............................................................................................................. 4 1.1.5 Atopy ................................................................................................................... 6 1.1.6 Clinical Manifestations of Allergic Disease........................................................... 7 1.1.7 Management ...................................................................................................... 10 1.1.8 Susceptibility to Disease ..................................................................................... 12 1.2 GENETICS OF COMPLEX DISEASE ................................................................................ 15 1.2.1 Statistical Approaches ........................................................................................ 15 1.2.2 Linkage Analysis ................................................................................................ 16 1.2.2 Association Analysis ........................................................................................... 17 1.2.3 Genome-Wide Association (GWA) Studies .......................................................... 18 1.3 GENETICS OF ALLERGIC DISEASE ................................................................................ 20 1.3.1 Genetic Studies of Allergic Disease..................................................................... 20 1.3.2 Genome–Wide Linkage (GWL) Studies ............................................................... 20 1.3.3 Meta-Analysis of GWL Studies ............................................................................ 24 1.3.4 Candidate Gene Studies ...................................................................................... 25 1.3.5 GWA Studies ...................................................................................................... 27 1.3.6 Gene-Gene Interactions ...................................................................................... 29 1.3.7 Gene-Environment Interactions .......................................................................... 29 1.4 THE „MISSING HERITABILITY‟ COMPONENT................................................................. 31 1.4.1 Deficiencies in Previous Studies ......................................................................... 31 1.4.2 Next-Generation Sequencing (NGS) .................................................................... 33 1.5 SUMMARY .................................................................................................................. 35 1.6 PROJECT AIMS ............................................................................................................ 37 CHAPTER 2 ...................................................................................................................... 38 MATERIALS AND METHODS ....................................................................................... 38 2.1 STUDY POPULATIONS AND PHENOTYPING .................................................................... 38 2.1.1 Atopy Analyses ................................................................................................... 38 2.1.2 Asthma Analyses ................................................................................................ 43 2.2 GENOTYPING AND SEQUENCING .................................................................................. 48 2.2.1 Genome-Wide SNP Genotyping .......................................................................... 48 2.2.2 Direct SNP Genotyping (Atopy Analyses)............................................................ 52 2.2.3 Targeted Re-sequencing (Asthma Analyses) ........................................................ 54 2.2.4 Dye Terminator Sequencing................................................................................ 54 2.3 BIOINFORMATICS........................................................................................................ 56 2.3.1 Online Resources ............................................................................................... 56 2.3.2 Genetics Analysis Software ................................................................................. 57 2.4 STATISTICAL ANALYSES ............................................................................................. 58 2.4.1 Principal Components Analysis (PCA) ................................................................ 58 2.4.2 Association Testing ............................................................................................ 58 2.4.3 Test Inflation ...................................................................................................... 60 2.4.4 Statistical Power ................................................................................................ 61 2.4.5 Meta-Analysis .................................................................................................... 61 2.4.6 Linkage Disequilibrium (LD) .............................................................................. 61 2.4.7 Imputation.......................................................................................................... 62 2.4.8 Significance Testing ........................................................................................... 63 2.5 CELLULAR AND MOLECULAR TECHNIQUES .................................................................. 64 2.5.1 Cell Culture ....................................................................................................... 64 2.5.2 Molecular Biology Methods ................................................................................ 66 2.6 INDIVIDUAL CONTRIBUTIONS AND COLLABORATIONS .................................................. 72 CHAPTER 3 ...................................................................................................................... 73 GENOME-WIDE ASSOCIATION STUDY TO IDENTIFY NOVEL ATOPY SUSCEPTIBILITY LOCI ................................................................................................. 73 3.1 INTRODUCTION ........................................................................................................... 73 3.2 AIM ........................................................................................................................... 74 3.3 METHODS .................................................................................................................. 75 3.3.1 Study Populations..............................................................................................
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