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Claire Hastie Thesis Hastie, Claire E. (2011) Discovering common genetic variants for hypertension using an extreme case-control strategy. PhD thesis. http://theses.gla.ac.uk/2423/ Copyright and moral rights for this thesis are retained by the author A copy can be downloaded for personal non-commercial research or study, without prior permission or charge This thesis cannot be reproduced or quoted extensively from without first obtaining permission in writing from the Author The content must not be changed in any way or sold commercially in any format or medium without the formal permission of the Author When referring to this work, full bibliographic details including the author, title, awarding institution and date of the thesis must be given. Glasgow Theses Service http://theses.gla.ac.uk/ [email protected] Discovering Common Genetic Variants for Hypertension Using an Extreme Case-control Strategy Claire E. Hastie, M.Sc. This being a thesis submitted for the degree of Doctor of Philosophy (Ph.D.) in the Faculty of Medicine, University of Glasgow October 2010 BHF Glasgow Cardiovascular Research Centre Institute of Cardiovascular and Medical Sciences College of Medical, Veterinary, and Life Sciences University of Glasgow © C.E. Hastie 2010 Declaration I declare that this thesis has been written entirely by myself and is a record of research performed by myself with the exception of discovery cohort genotyping (Dr Wai K. Lee, Dr Anna Maria Di Blasio, Stewart Laing, and Dr Davide Gentilini), genotyping and association analysis of replication cohorts (undertaken by investigators from each cohort, respectively), and analysis of data from the BRIGHT (Dr Sandosh Padmanabhan), GRECO and HERCULES clinical functional cohorts (undertaken by investigators from each cohort, respectively). This work has not been submitted previously for a higher degree and was carried out under the supervision of Professor Anna F. Dominiczak and Professor Jill P. Pell. Claire E. Hastie Acknowledgements Firstly, I would like to thank my supervisors, Professor Anna Dominiczak and Professor Jill Pell, for their support and guidance. They are both wonderful role models and have provided me with many exciting opportunities over the last four years. Dr Sandosh Padmanabhan, although advisor in name, has always been much more than that. I would not have been able to complete this project without extensive training and advice from him. I also wish to thank Dr Wai Kwong Lee for his patience in helping me to understand the genotyping process. Cristina Menni has been a great source of practical and emotional help through the most difficult stages of this project. Special thanks to all of my colleagues who selflessly gave up their time to view cluster plots; Adyani Md Redzuan, Aiste Monkeviciute, Angela Bradshaw, Annika Delles, Alan Parker, Caline Koh-Tan, Carolyn Haggerty, Chiara Taurino, David Carty, Elisabeth Beattie, Emily Ord, Fernando Martinez Garcia, Jenny Greig, Jennifer McLachlan, Jim Mcculloch, John McClure, Kirsten Douglas, Laura Graham, Laura Denby, Laura Paul, Lorraine Work, Ruth Mackenzie, Samantha Alvarez-Madrazo, Sandra MacDonald, Teresa, Ulf Neisius, Wendy Crawford, Weiling Sarah Li. Finally, I cannot express enough my gratitude towards my parents, brother, and husband for their constant encouragement. 3 Contents Declaration………………………………………………………………………………….2 Acknowledgements…………………………………………………………………………3 Contents……………………………………………………………………………………..4 List of Figures………………………………………………………………………………7 List of Tables………………………………………………………………………………..9 List of Abbreviations, Acronyms & Symbols……………………………………………..10 Publications and Oral Presentations...……………………………………………………..16 Summary…………………………………………………………………………………..19 1 Introduction..................................................................................................................22 1.1 Cardiovascular disease.........................................................................................23 1.2 Human essential hypertension .............................................................................27 1.2.1 Causation of hypertension............................................................................28 1.3 Genetic factors in hypertension............................................................................30 1.3.1 Evidence of genetic determinants of blood pressure regulation and hypertension.................................................................................................30 1.3.2 Monogenic forms of hypertension...............................................................34 1.3.3 Linkage studies.............................................................................................36 1.3.4 Association studies.......................................................................................38 1.3.5 Candidate gene studies.................................................................................40 1.4 Genome-wide association studies........................................................................40 1.4.1 Subject ascertainment/ phenotyping ............................................................42 1.4.2 Phenotypic enrichment for genetic effects...................................................42 1.4.3 Population stratification...............................................................................44 1.4.4 Solutions to population stratification...........................................................45 1.4.5 Common Disease Common Variant Hypothesis .........................................47 1.4.6 Significance thresholds for GWAS..............................................................50 1.4.7 Statistical power...........................................................................................51 1.4.8 Replication ...................................................................................................54 1.4.9 GWAS of hypertension and blood pressure.................................................56 1.4.9.1 Wellcome Trust Case Control Consortium (WTCCC)............................58 1.4.9.2 Global Blood Pressure Genetics (Global BPgen) Consortium ................64 1.4.9.3 Cohorts for Heart and Aging Research in Genome Epidemiology (CHARGE) Consortium...........................................................................65 1.4.9.4 Potential candidate genes for blood pressure regulation identified by Global BPgen and/or CHARGE...............................................................71 1.5 Aims.....................................................................................................................72 2 Materials and methods .................................................................................................73 2.1 Description of samples.........................................................................................74 2.1.1 Nordic Diltiazem study (NORDIL) .............................................................74 2.1.2 Malmö Diet and Cancer Study (MDC)........................................................75 2.1.3 Use of hypercontrols....................................................................................75 2.1.4 Case inclusion criteria..................................................................................76 2.1.5 Control inclusion and exclusion criteria ......................................................76 2.2 Software ...............................................................................................................76 2.2.1 DNA extraction and genotyping ..................................................................78 2.2.2 PLINK..........................................................................................................78 2.2.3 Haploview....................................................................................................79 2.2.4 EIGENSTRAT.............................................................................................80 2.3 Statistical analysis................................................................................................81 2.3.1 Power calculations .......................................................................................81 4 2.3.2 Summary of phenotypic data .......................................................................83 2.3.3 Reformatting of Illumina output files ..........................................................83 2.3.4 Quality control .............................................................................................85 2.3.5 Assessment of population stratification.......................................................85 2.3.6 Association...................................................................................................86 2.3.7 Examination of cluster plots ........................................................................86 2.3.8 Meta-analysis ...............................................................................................87 2.3.9 Annotation of top hits ..................................................................................91 2.3.10 Clinical functional studies............................................................................95 3 Genome-wide association study in extremes of blood pressure distribution...............97 3.1 Sample quality control .........................................................................................98 3.1.1 Specification of gender ................................................................................98 3.1.2 Cryptic relatedness.......................................................................................98
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