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Family-Based Investigation of the Genetics and Epigenetics of Obesity in Qatar

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Family-Based Investigation of the Genetics and Epigenetics of Obesity in Qatar Family-Based Investigation of the Genetics and Epigenetics of Obesity in Qatar Mashael Nedham A J Alshafai A Thesis Submitted for the Degree of Doctor of Philosophy Department of Genomics of Common Disease School of Public Health Imperial College London July 2015 1 Abstract Abstract Single nucleotide polymorphisms (SNPs), copy number variations (CNVs) and DNA methylation patterns play a role in the susceptibility to obesity. Despite the alarming figures of obesity in the Arab world, the genetics of obesity remain understudied in Arabs. Here, I recruited ten multigenerational Qatari families segregating obesity, and generated genome-wide SNP genotyping, whole genome sequencing and genome-wide methylation profiling data using Illumina platforms to investigate the role of rare mutations, CNVs, and DNA methylation patterns in the susceptibility to obesity. For the identification of obesity mutations, I first identified candidate obesity regions through linkage and run of homozygosity analyses, and then investigated these regions to detect potential deleterious mutations. These analyses highlighted putative rare variants for obesity risk at PCSK1, NMUR2, CLOCK and RETSAT. The functional impact of the PCSK1 mutation on obesity was previously demonstrated while for the other candidates further work is needed to confirm their impact. For the identification of common obesity CNVs, I performed a genome-wide CNV association analysis with BMI and identified a common duplication of ~5.6kb on 19p13.3 that associates with higher BMI. Moreover, I investigated large (≥500kb) rare CNVs and identified a ~618kb deletion on 16p11.2 in the most extremely obese subject in my samples, which confirms the contribution of the previously reported 16p11.2 deletions to severe obesity beyond European populations. For the identification of DNA methylation changes in obesity, I attempted to replicate known associations with BMI from large EWASs. I replicated the associations at ABCG1 (P-value=6.3X10-3) and CPT1A (P-value=8.7X10-5) and compared the effects observed to the TwinsUK cohort through a meta- analysis. I observed low heterogeneity between the two studies, and that increased the associations at ABCG1 (P-value=2.5x10-13) and CPT1A (P-value=1.9x10-15). In conclusion, the work represents the first genetic and epigenetic study of obesity in an Arab population. I replicated known genetic and epigenetic obesity susceptibility loci and also discovered novel potential loci. 2 Table of Contents Table of Contents Abstract ......................................................................................................................................................... 2 Table of Contents .......................................................................................................................................... 3 List of Figures ................................................................................................................................................ 7 List of Tables ................................................................................................................................................. 9 Acknowledgements ..................................................................................................................................... 10 Declaration of Originality ............................................................................................................................ 11 Copyright Declaration ................................................................................................................................. 12 Publications, Presentations and Awards ..................................................................................................... 13 Abbreviations .............................................................................................................................................. 15 Preface ........................................................................................................................................................ 19 1.1 Epidemic of Obesity .......................................................................................................................... 21 1.2 Obesity in Qatar ................................................................................................................................ 21 1.3 Physiology of Obesity ........................................................................................................................ 23 1.4 Heritability of Obesity ....................................................................................................................... 26 1.5 Genetic Basis of Obesity.................................................................................................................... 27 1.5.1 Monogenic Forms of Obesity ..................................................................................................... 27 1.5.1.1 The Role of Leptin and Leptin Receptor in Obesity ............................................................ 27 1.5.1.2 The Role of other Leptin-Melanocortin Pathway Genes in Obesity ................................... 29 1.5.2 Syndromic Forms of Obesity ...................................................................................................... 32 1.5.3 Polygenic Form of Obesity ......................................................................................................... 32 1.5.3.1 Linkage Studies on Obesity ................................................................................................. 33 1.5.3.2 Candidate Gene Association Studies on Obesity ................................................................ 34 1.5.3.3 Genome-Wide Association Studies (GWASs) on Obesity ................................................... 35 1.7 The Role of Rare Mutations in the Development of Obesity ............................................................ 42 1.7.1 Detection Methods of Rare Mutations ...................................................................................... 42 1.7.2 Rare Mutations and Obesity ...................................................................................................... 44 1.8 The Role of Copy Number Variations (CNVs) in the Development of Obesity ................................. 44 1.8.1 Mechanisms of CNV Formation ................................................................................................. 45 1.8.2 Methods of CNV Detection ........................................................................................................ 46 1.8.3 Copy Number Variations and Obesity ........................................................................................ 48 3 Table of Contents 1.9 The Role of DNA Methylation Patterns in the Development of Obesity .......................................... 50 1.9.1 Formation Mechanisms of DNA Methylation Patterns .............................................................. 51 1.9.2 Detection Methods of DNA Methylation Patterns .................................................................... 52 1.9.3 DNA Methylation Patterns and Obesity ..................................................................................... 53 1.9.3.1 Candidate Gene Methylation Studies on Obesity ............................................................... 54 1.9.3.2 Genome-Wide Methylation Studies on Obesity ................................................................. 55 1.10 Aims................................................................................................................................................. 58 2. Materials and Methods ........................................................................................................................... 60 2.1 Ethical Approval of the Study ............................................................................................................ 60 2.2 Selection of Study Subjects ............................................................................................................... 60 2.3 Samples Collection ............................................................................................................................ 60 2.4 Phenotypic Data Collection ............................................................................................................... 60 2.5 Extraction of Genomic DNA .............................................................................................................. 64 2.6 Generation of Genomic Data ............................................................................................................ 64 2.6.1 Genome-Wide SNP Genotyping using the HumanOmni2.5-8 Beadchip ................................... 65 2.6.2 Whole Genome Sequencing (WGS) from Paired-End Reads ..................................................... 67 2.6.3 Genome-Wide Methylation Profiling using Infinium HumanMethylation450 BeadChip .......... 68 2.7 Additional Genomic Data Sets .......................................................................................................... 71 2.7.1 Data for 108 Qatari Genomes .................................................................................................... 71 2.7.2 Data from Adult Obesity and Childhood Obesity Case-Control Cohorts ................................... 71 2.7.3 Data from the Saudi Extreme Obesity and Mental Retardation Case-Control Sample Set ....... 71 2.7.4 Data from Qatari Families with T2D ..........................................................................................
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