Investigation and assessment of copy number variation in Age-related Macular Degeneration

© 2013 Dr.Stuart CantsilierisAge-related Macular Degeneration (AMD) is a common form of irreversible vision loss in Western populations. AMD is classified as a complex multi-factorial disease and is associated with both genetic and environmental exposures. Despite intensive research efforts, the etiology of AMD remains incompletely understood. At the time of writing this thesis, AMD has been reported to be associated with 19 genetic loci, however, this has been reported to explain between 15-65% of the total genetic contribution to disease. Therefore a considerable amount of the “missing heritability” of AMD remains undiscovered. Now that we have reached the post-GWAS era of AMD studies, there is a need to examine genetic variants that to date have been technically challenging to analyse. This includes the study of rare/private variants, and copy number variation. This thesis will focus on the analysis of copy number variation (CNV) and the contribution of CNVs to AMD susceptibility. This doctoral work addresses some of the challenges involved for genotyping CNVs in association studies and applies several strategies to ensure reliable copy number typing. Using methods based on the Multiplex Ligation-dependent Amplification (MLPA) technique, the importance of ensuring reliable copy number measurement data is demonstrated. Additionally, I address potential outside influences such as differential bias, and implement statistical models that specifically take into account measurement error when performing tests for association. This thesis provides further evidence for the contribution of CNVs to the “missing heritability” of AMD. These studies represent a candidate gene approach, predominantly focusing on the genes associated with complement regulation and activation. However, as demonstrated recently, several other biological pathways have been implicated in the etiology of AMD including lipid metabolism, angiogenesis and extracellular matrix degradation. Future studies of CNVs in AMD cohorts will likely benefit from a genome-wide analysis, potentially implementing next generation sequencing approaches to facilitate a better understanding of the overall contribution of CNVs to AMD susceptibility