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Validation of the PARVA C.392A<T Variant in a South African Family

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Validation of the PARVA C.392A<T Variant in a South African Family Validation of the PARVA c.392A>T variant in a South African family with severe Arrhythmogenic Right Ventricular Cardiomyopathy Stephen Kamuli Thesis presented for the Degree of MASTER OF SCIENCE In the Department of Medicine UniversityUNIVERSITY OF of CAPE Cape TOWN Town Supervisor: Dr Gasnat Shaboodien Co-supervisor: Professor Bongani Mayosi August 2016 i The copyright of this thesis vests in the author. No quotation from it or information derived from it is to be published without full acknowledgement of the source. The thesis is to be used for private study or non- commercial research purposes only. Published by the University of Cape Town (UCT) in terms of the non-exclusive license granted to UCT by the author. University of Cape Town DECLARATION I, …Stephen Kamuli………………, hereby declare that the work on which this dissertation/thesis is based is my original work (except where acknowledgements indicate otherwise) and that neither the whole work nor any part of it has been, is being, or is to be submitted for another degree in this or any other university. I empower the university to reproduce for the purpose of research either the whole or any portion of the contents in any manner whatsoever. Signature: signature removed Date: 18 August 2016 ii TABLE OF CONTENTS TABLE OF CONTENTS ...................................................................................................................................... I ABSTRACT ..................................................................................................................................................... III ACKNOWLEDGEMENTS ................................................................................................................................. V LIST OF FIGURES ........................................................................................................................................... VI LIST OF TABLES ............................................................................................................................................ VII LIST OF ABBREVIATIONS AND SYMBOLS .................................................................................................... VIII CHAPTER 1: INTRODUCTION ......................................................................................................................... 1 1.1. Structure and function of the heart ................................................................................................... 1 1.2. Cardiomyopathy ................................................................................................................................. 2 1.2.1 Dilated Cardiomyopathy (DCM) ................................................................................................... 3 1.2.2 Arrhythmogenic Right Ventricular Cardiomyopathy (ARVC) ....................................................... 6 1.2.3. Hypertrophic Cardiomyopathy (HCM) ........................................................................................ 9 1.2.4. Restrictive Cardiomyopathy (RCM) ........................................................................................... 11 1.3. Molecular genetics of cardiomyopathy ........................................................................................... 12 1.3.1 DCM............................................................................................................................................ 13 1.3.2 ARVC ........................................................................................................................................... 17 1.3.3 HCM ........................................................................................................................................... 20 1.3.4 RCM ............................................................................................................................................ 23 1.4 Work leading to this thesis ............................................................................................................... 24 1.5. Hypothesis ........................................................................................................................................ 25 1.6. Aims.................................................................................................................................................. 25 CHAPTER 2: CANDIDATE GENE ANALYSIS OF PARVA .................................................................................. 26 2.1. Introduction ..................................................................................................................................... 26 2.2. Aims.................................................................................................................................................. 30 2.3. Methods ........................................................................................................................................... 30 2.3.1. ACM 8 Family ............................................................................................................................ 30 2.3.2 Cardiomyopathy Cohort ............................................................................................................. 31 2.3.3 Normal controls ......................................................................................................................... 32 2.3.4. DNA extraction .......................................................................................................................... 32 2.3.5. DNA quality control ................................................................................................................... 32 2.3.6 Polymerase Chain Reaction ....................................................................................................... 34 I 2.3.7. HRM analysis ............................................................................................................................. 37 2.3.8 Sanger sequencing ..................................................................................................................... 40 2.3.9 Bioinformatic Tools/ Public Genome Browsers/Databases ....................................................... 42 2.4. Results .............................................................................................................................................. 42 2.4.1. ACM 8 family screen ................................................................................................................. 42 2.4.2. Cardiomyopathy cohort screen ................................................................................................ 44 2.4.3 Variant functional analysis ......................................................................................................... 44 2.4.4 Population screening ................................................................................................................. 45 2.5. Discussion ......................................................................................................................................... 47 Chapter 3: WHOLE EXOME SEQUENCING OF ACM 8 .................................................................................. 49 3.1. Introduction ..................................................................................................................................... 49 3.2 Aim .................................................................................................................................................... 49 3.3 Methods ............................................................................................................................................ 50 3.3.1 Sample library preparation ........................................................................................................ 50 3.3.2 Library quality control ................................................................................................................ 50 3.3.3 Data Analysis .............................................................................................................................. 51 3.3.4 Variant filtering .......................................................................................................................... 51 3.3.5 Bioinformatic Tools/ Public Genome Browsers/Databases ....................................................... 52 3.3.6. Validation of potentially disease-causing variants ................................................................... 52 3.4. Results .............................................................................................................................................. 53 3.4.1. Variant filtering for the known cardiac genes .......................................................................... 53 3.4.2 Identification of the PKP2 c.1162C>T founder mutation ........................................................... 57 3.4.3 Segregation of the PKP2 c.1162C>T founder mutation ............................................................. 58 3.5 Discussion .......................................................................................................................................... 61 Chapter 4: CONCLUSION ............................................................................................................................. 65 REFERENCES ................................................................................................................................................ 66 APPENDICES
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