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Genome‐wide association analyses identify genes modifying age‐at‐onset of Alzheimer’s disease
Author(s) -
Martin Eden R.,
Sun Shuming,
Slifer Susan H.,
Naj Adam C.,
Gao Xiaoyi R.,
Li YiJu
Publication year - 2020
Publication title -
alzheimer's and dementia
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 6.713
H-Index - 118
eISSN - 1552-5279
pISSN - 1552-5260
DOI - 10.1002/alz.046264
Subject(s) - imputation (statistics) , genome wide association study , genetic association , covariate , genotype , apolipoprotein e , population , cohort , disease , genetics , biology , 1000 genomes project , medicine , gene , missing data , single nucleotide polymorphism , statistics , mathematics , environmental health
Abstract Background Several studies have attempted to identify genes for age‐at‐onset (AAO) of dementia symptoms in Alzheimer’s disease (AD) through genome‐wide linkage (Daw et al. 1999, Li et al. 2002, Choi et al. 2011) and genome‐wide association studies (Kamboh et al. 2012, Naj et al. 2014). Naj et al. conducted a meta‐analysis of 14 datasets from the Alzheimer’s Disease Genetics Consortium (ADGC) with genotype imputation to HapMap2. Using an expanded set of ADGC cohorts, we re‐examined AAO using higher‐quality genome‐wide imputation data and pooled‐data analysis instead of meta‐analysis to identify novel genetic contributors to AAO of AD. Methods We combined data from 20 non‐Hispanic white prospective and case‐control ADGC datasets, excluding family‐based datasets. Genotype data were imputed to the Haplotype Reference Consortium (HRC) r1.1 reference panel using the Michigan Imputation Server and consistent quality control applied to each dataset, after which genotype data were merged across datasets using QCTOOL and GTOOL. We performed case‐only association analyses for log 10 (AAO) using multivariable linear regression with covariate adjustment for sex, cohort, and principal components capturing population substructure, and then conducted analyses conditioning on dosage of APOE ε4 alleles. Variants with P < 10 −5 from conditional analyses were re‐analyzed using linear mixed modeling treating cohort as a random effect. Results We used 9,228 AD cases, including 5,307 females (57.4%) with mean (SD) AAO of 74.2(7.7) years. In addition to the APOE region, which reached genome‐wide significance ( P < 5 × 10 −8 ), we observed strong novel associations with variants in NTM (encoding neurotrimin) on chr11q25 (rs117589002, P = 1.24 × 10 −7 ) and in an intergenic region on chr3p22.3 ( P min = 1.89 × 10 −7 ). Other AAO loci previously identified in the smaller ADGC dataset (Naj et al 2014) remained nominally significant. After adjusting for APOE ε4, thirty‐two regions showed suggestive association ( P < 10 −5 ), with chr3p22.3 and NTM remaining the top loci. Chromosome 11q25 includes a known AD linkage region (Blacker et al. 2003). In addition, NTM variation has been found to be correlated with cognitive function tests (Liu et al. 2007) and intelligence (Pan et al. 2010). Conclusions In an expanded ADGC dataset, we confirmed AAO associations in the APOE region and observed evidence for potential novel AD AAO loci including NTM .