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Background: Amyloid β (Aβ) peptides are the products of the catalytic processing of the Aβ precursor protein (APP) by the β-secretase, BACE1 and the γ-secretase complex. Impairment of the Aβ production/clearance balance is the major pathophysiological hypothesis in Alzheimer's disease. Plasma Aβ levels are easy to measure in large numbers and therefore can be used as an endophenotype to study the genetics of Aβ and its relevance to AD. Methods: We performed genome-wide association studies (GWAS) of plasma Aβ1-40, Aβ1-42 and Aβ1-42/Aβ1-40 ratio in 12,369 non-demented participants across 8 studies, using genetic data imputed on the 1000 Genomes phase 1 version 3 reference panel. To gain further insight, we performed LD-score regression analysis of plasma Aβ-42 and Aβ-40 levels using previously published GWAS of AD and other related traits, and pathway analyses. Results: We identified 21 variants reaching genome-wide significance across two loci. The most significant locus spanned the APOE gene, with significant associations with plasma Aβ42 levels (p = 9.01×10-13) and plasma Aβ42/Aβ40 ratio (p = 6.46×10-20). The second locus was located on chromosome 11, near the BACE1 gene (p = 2.56×10-8). We also observed suggestive evidence of association (p < 1×10-5) around genes involved in Aβ metabolism including APP and PSEN2. Conclusion: Using plasma Aβ40 and Aβ42 levels, this GWAS was able to identify relevant and central actors of the APP metabolism in AD. Overall, this study strengthens the utility of plasma Aβ levels both as an endophenotype and a biomarker.

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