Variants in the ATP-binding cassette transporter (ABCA7), apolipoprotein E ϵ4,and the risk of late-onset Alzheimer disease in African Americans

Abstract

Importance: Genetic variants associated with susceptibility to late-onset Alzheimer disease are known for individuals of European ancestry, but whether the same or different variants account for the genetic risk of Alzheimer disease in African American individuals is unknown. Identification of disease-associated variants helps identify targets for genetic testing, prevention, and treatment.

Objective: To identify genetic loci associated with late-onset Alzheimer disease in African Americans.

Design, setting, and participants: The Alzheimer Disease Genetics Consortium (ADGC) assembled multiple data sets representing a total of 5896 African Americans (1968 case participants, 3928 control participants) 60 years or older that were collected between 1989 and 2011 at multiple sites. The association of Alzheimer disease with genotyped and imputed single-nucleotide polymorphisms (SNPs) was assessed in case-control and in family-based data sets. Results from individual data sets were combined to perform an inverse variance-weighted meta-analysis, first with genome-wide analyses and subsequently with gene-based tests for previously reported loci.

Main outcomes and measures: Presence of Alzheimer disease according to standardized criteria.

Results: Genome-wide significance in fully adjusted models (sex, age, APOE genotype, population stratification) was observed for a SNP in ABCA7 (rs115550680, allele = G; frequency, 0.09 cases and 0.06 controls; odds ratio [OR], 1.79 [95% CI, 1.47-2.12]; P = 2.2 × 10(-9)), which is in linkage disequilibrium with SNPs previously associated with Alzheimer disease in Europeans (0.8 < D' < 0.9). The effect size for the SNP in ABCA7 was comparable with that of the APOE ϵ4-determining SNP rs429358 (allele = C; frequency, 0.30 cases and 0.18 controls; OR, 2.31 [95% CI, 2.19-2.42]; P = 5.5 × 10(-47)). Several loci previously associated with Alzheimer disease but not reaching significance in genome-wide analyses were replicated in gene-based analyses accounting for linkage disequilibrium between markers and correcting for number of tests performed per gene (CR1, BIN1, EPHA1, CD33; 0.0005 < empirical P < .001).

Conclusions and relevance: In this meta-analysis of data from African American participants, Alzheimer disease was significantly associated with variants in ABCA7 and with other genes that have been associated with Alzheimer disease in individuals of European ancestry. Replication and functional validation of this finding is needed before this information is used in clinical settings.

Figure 1

Linkage Disequilibrium Pattern of Single-Nucleotide Polymorphisms in ABCA7 Based on the HapMap Reference Sample (African Americans in the Southwest USA) and NCBI36/hg18 Genome Build Black arrows indicate single-nucleotide polymorphisms (SNPs) previously reported to be associated with Alzheimer disease in whites^, (the top hit reported by Hollingworth et al [rs3752228] may have changed if the entire cohort had been genotyped in stages 2 and 3). Pink arrow indicates the location of rs115550680 associated with Alzheimer disease in the present study.The SNPs shown in blue are not represented in HapMap. Kb indicates kilobase.

Figure 2

Regional Association Plot of the ABCA7 Region (±100 Kilobases) in the African American Sample and the White Sample Described in Naj et al Based on the GRCh37/hg19 Genome Build Dashed black line indicates the threshold typically applied in genome-wide association studies for genome-wide significance (P ≤ 5 × 10^–8).