Admixture mapping reveals the association between Native American ancestry at 3q13.11 and reduced risk of Alzheimer\u2019s disease in Caribbean Hispanics

Andréa R V R Horimoto,Timothy A Thornton,Diane Xue,Elizabeth E Blue

doi:10.1186/s13195-021-00866-9

Andréa R V R Horimoto, Timothy A Thornton + Show 2 more

Open Access

https://doi.org/10.1186/s13195-021-00866-9

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Abstract

BackgroundGenetic studies have primarily been conducted in European ancestry populations, identifying dozens of loci associated with late-onset Alzheimer’s disease (AD). However, much of AD’s heritability remains unexplained; as the prevalence of AD varies across populations, the genetic architecture of the disease may also vary by population with the presence of novel variants or loci.MethodsWe conducted genome-wide analyses of AD in a sample of 2565 Caribbean Hispanics to better understand the genetic contribution to AD in this population. Statistical analysis included both admixture mapping and association testing. Evidence for differential gene expression within regions of interest was collected from independent transcriptomic studies comparing AD cases and controls in samples with primarily European ancestry.ResultsOur genome-wide association study of AD identified no loci reaching genome-wide significance. However, a genome-wide admixture mapping analysis that tests for association between a haplotype’s ancestral origin and AD status detected a genome-wide significant association with chromosome 3q13.11 (103.7–107.7Mb, P = 8.76E−07), driven by a protective effect conferred by the Native American ancestry (OR = 0.58, 95%CI = 0.47−0.73). Within this region, two variants were significantly associated with AD after accounting for the number of independent tests (rs12494162, P = 2.33E−06; rs1731642, P = 6.36E−05). The significant admixture mapping signal is composed of 15 haplotype blocks spanning 5 protein-coding genes (ALCAM, BBX, CBLB, CCDC54, CD47) and four brain-derived topologically associated domains, and includes markers significantly associated with the expression of ALCAM, BBX, CBLB, and CD47 in the brain. ALCAM and BBX were also significantly differentially expressed in the brain between AD cases and controls with European ancestry.ConclusionThese results provide multiethnic evidence for a relationship between AD and multiple genes at 3q13.11 and illustrate the utility of leveraging genetic ancestry diversity via admixture mapping for new insights into AD.

Highlights

Genetic studies have primarily been conducted in European ancestry populations, identifying dozens of loci associated with late-onset Alzheimer’s disease (AD)
Much less is known about AD genetics across diverse populations, and in particular African Americans and Hispanic/Latino Americans who have increased risk of AD compared to European Americans [9,10,11]
Caribbean Hispanics, despite being more likely to be diagnosed with AD [80, 81], have been underrepresented in AD genetics studies [82]

Summary

Introduction

Genetic studies have primarily been conducted in European ancestry populations, identifying dozens of loci associated with late-onset Alzheimer’s disease (AD). The APOE ε4 allele is the strongest common genetic risk factor for AD [4, 5], dozens of loci have been associated with AD via genome-wide association studies (GWAS) [6, 7]. Unlike widely used GWAS approaches that treat genetic ancestry differences as potential confounders in the analysis, admixture mapping leverages genetic ancestry differences [12,13,14,15]. Admixture mapping is most powerful when both disease risk and trait-locus allele frequencies differ across groups, and it can be viewed as a complement to GWAS [17, 18]

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