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Common Variants at MS4A4/MS4A6E, CD2AP, CD33 and EPHA1 Are Associated with Late-Onset Alzheimer’S Disease

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Common Variants at MS4A4/MS4A6E, CD2AP, CD33 and EPHA1 Are Associated with Late-Onset Alzheimer’S Disease LETTERS Common variants at MS4A4/MS4A6E, CD2AP, CD33 and EPHA1 are associated with late-onset Alzheimer’s disease The Alzheimer Disease Genetics Consortium (ADGC) performed from the association analyses of individual datasets and a joint a genome-wide association study of late-onset Alzheimer disease analysis approach in which genotype data from each study were using a three-stage design consisting of a discovery stage pooled. The latter method has improved power over the meta-analysis (stage 1) and two replication stages (stages 2 and 3). Both joint in the absence of between-study heterogeneity13 and has a more direct analysis and meta-analysis approaches were used. We obtained correction for confounding sampling bias14. We were limited to meta- genome-wide significant results at MS4A4A (rs4938933; stages 1 analysis for stage 3 analyses. −9 and 2, meta-analysis P (PM) = 1.7 × 10 , joint analysis P (PJ) = Because the cohorts were genotyped using different platforms, −9 −12 1.7 × 10 ; stages 1, 2 and 3, PM = 8.2 × 10 ), CD2AP we used imputation to generate a common set of 2,324,889 SNPs. −9 (rs9349407; stages 1, 2 and 3, PM = 8.6 × 10 ), EPHA1 We applied uniform stringent quality control measures to all data- −10 (rs11767557; stages 1, 2 and 3, PM = 6.0 × 10 ) and CD33 sets to remove low-quality and redundant samples and problematic −9 (rs3865444; stages 1, 2 and 3, PM = 1.6 × 10 ). We also replicated SNPs (Supplementary Tables 3,4 and Online Methods). We per- −10 previous associations at CR1 (rs6701713; PM = 4.6 × 10 , formed an association analysis assuming an additive model on the −11 −8 PJ = 5.2 × 10 ), CLU (rs1532278; PM = 8.3 × 10 , PJ = 1.9 × log odds ratio scale with adjustment for population substructure −8 −14 −14 10 ), BIN1 (rs7561528; PM = 4.0 × 10 , PJ = 5.2 × 10 ) and using logistic regression for case-control data and generalized esti- −11 −10 PICALM (rs561655; PM = 7.0 × 10 , PJ = 1.0 × 10 ), but not at mating equations (GEE) with a logistic model for family data. We EXOC3L2, to late-onset Alzheimer’s disease susceptibility1–3. combined results from individual datasets in the meta-analysis using the inverse variance method, applying a genomic control to each Alzheimer’s disease is a neurodegenerative disorder affecting more dataset. We performed the joint analysis using GEE and incorpo- than 13% of individuals aged 65 years and older and 30–50% of indi- rated terms to adjust for population substructure and site-specific viduals aged 80 years and older4,5. Early work identified mutations in effects (Online Methods). For both approaches, we also examined Nature America, Inc. All rights reserved. All rights Inc. America, Nature APP, PSEN1 and PSEN2 that cause early-onset autosomal dominant an extended model of covariate adjustment that adjusted for age (age 1 6–9 1 Alzheimer’s disease and variants in APOE that affect late-onset at onset or death in cases and age at exam or death in controls), sex Alzheimer’s disease (LOAD) susceptibility10. Recent genome-wide and number of APOE ε4 alleles (0, 1 or 2). Genomic inflation factors © 20 association studies (GWAS) identified variants in CR1, CLU, PICALM (λ) for both the discovery meta-analysis and the joint analysis and and BIN1 as LOAD susceptibility loci1–3. However, because LOAD extended models were less than 1.05, indicating that there was not heritability estimates are high (h2 ≈ 60–80%)11, much of the genetic substantial inflation of the test statistics (Supplementary Table 3 and contribution to this condition remains unknown. Supplementary Fig. 1). Association findings from the meta-analysis To identify genetic variants associated with risk for Alzheimer’s and joint analysis were comparable. disease, the ADGC assembled a discovery dataset (stage 1, 8,309 indi- In stage 1, the strongest signal was from the APOE region −266 −253 viduals with LOAD (cases) and 7,366 cognitively normal elders (CNEs) (rs4420638; PM =1.1 × 10 , PJ =1.3 × 10 ; Supplementary as controls) using data from eight cohorts and a ninth newly assem- Table 5). Excluding the APOE region, SNPs at nine distinct loci −6 −4 bled cohort from the 29 National Institute on Aging (NIA)-funded yielded PM or PJ ≤ 10 (Table 1; all SNPs with P < 10 are shown Alzheimer Disease Centers (ADCs) (Supplementary Tables 1,2 in Supplementary Table 5). SNPs from these nine loci were carried and Supplementary Note), with data coordinated by the National forward to stage 2. Five of these loci had not previously been associ- Alzheimer Coordinating Center (NACC) and samples coordinated by ated with LOAD at a genome-wide significance level of P ≤ 5.0 × 10−8 the National Cell Repository for Alzheimer Disease (NCRAD). For (loci in MS4A, EPHA1, CD33, ARID5B and CD2AP). Because the the stage 2 replication, we used four additional datasets and addi- companion study12 identified SNPs at ABCA7 to be within a new tional samples from the ADCs (3,531 LOAD cases and 3,565 CNEs). LOAD locus, we included ABCA7-region SNPs in our stage 2 analysis The stage 3 replication used the results of association analyses provided and provided our results to researchers from that study. For all loci by three other consortia, including 6,992 LOAD cases and 24,666 listed in Table 1, we did not detect evidence for effect heterogeneity mixed-age controls, reported in a companion manuscript12. For stages 1 (Supplementary Fig. 2). One newly associated locus (in MS4A) was and 2, we used both a meta-analysis approach that integrated results significant in the stage 1+2 analysis. Four other loci approached but *A full list of authors and affiliations appears at the end of the paper. Received 27 September 2010; accepted 10 March 2011; published online 3 April 2011; doi:10.1038/ng.801 436 VOLUME 43 | NUMBER 5 | MAY 2011 NATURE GENETICS NATURE GE Table 1 Genome-wide association results for LOAD in the ADGC stage 1 and stage 2 datasets ADGC discovery (stage 1) ADGC replication (stage 2) Combined analysis (stage 1+2) Nearest SNP Chr.:Mb gene MA MAF # SNPs ORM (95% CI) PM ORJ (95% CI) PJ ORM (95% CI) PM ORJ (95% CI) PJ ORM (95% CI) PM ORJ (95% CI) PJ N ETICS rs6701713 1:207.8 CR1a A 0.20 7 1.18 1.4 × 10−8 1.19 3.5 × 10−9 1.13 0.004 1.13 0.004 1.16 4.6 × 10–10 1.17 5.2 × 10–11 1.11–1.25 1.12–1.26 1.04–1.23 1.04–1.24 1.11–1.22 1.12–1.23 rs7561528 2:127.9 BIN1a A 0.35 10 1.18 2.9 × 10−11 1.18 7.7 × 10−11 1.15 1.4 × 10–4 1.15 1.0 × 10–4 1.17 4.2 × 10–14 1.17 5.2 × 10–14 1.13–1.24 1.12–1.24 1.07–1.24 1.07–1.24 1.13–1.22 1.12–1.22 VOLUME 43 | NUMBER 5 | MAY 2011 rs9349407 6:47.5 CD2AP C 0.27 1 1.14 1.2 × 10−6 1.14 5.3 × 10−6 1.07 0.118 1.08 0.074 1.12 1.0 × 10–6 1.12 2.1 × 10–6 1.08–1.21 1.08–1.20 0.98–1.17 0.99–1.18 1.07–1.18 1.07–1.17 rs11767557 7:143.1 EPHA1b C 0.19 1 0.85 7.3 × 10−8 0.84 3.1 × 10−8 0.94 0.169 0.93 0.133 0.87 2.4 × 10–7 0.87 4.9 × 10–8 0.80–0.90 0.79–0.89 0.86–1.03 0.85–1.02 0.83–0.92 0.83–0.91 rs1532278 8:27.5 CLU a T 0.36 2 0.90 5.6 × 10−5 0.89 2.0 × 10−5 0.87 2.6 × 10–4 0.87 2.7 × 10–4 0.89 8.3 × 10–8 0.89 1.9 × 10–8 0.85–0.95 0.85–0.94 0.81–0.94 0.81–0.94 0.85–0.93 0.85–0.92 rs2588969 10:63.6 ARID5B A 0.37 0 0.88 1.1 × 10−6 0.88 6.9 × 10−7 1.05 0.234 1.05 0.189 0.93 0.001 0.93 7.7 × 10–4 0.84–0.93 0.84–0.93 0.97–1.13 0.98–1.13 0.89–0.97 0.89–0.97 rs4938933 11:60.0 MS4A4A C 0.39 22 0.88 5.2 × 10−8 0.87 4.5 × 10−8 0.90 0.005 0.90 0.004 0.88 1.7 × 10–9 0.88 1.7 × 10–9 0.84–0.92 0.83–0.92 0.84–0.97 0.84–0.97 0.85–0.92 0.85–0.92 rs561655 11:85.8 PICALM a G 0.34 36 0.88 1.2 × 10−7 0.88 4.6 × 10−7 0.86 8.4 × 10–5 0.86 3.7 × 10–5 0.87 7.0 × 10–11 0.87 1.0 × 10–10 0.84–0.92 0.84–0.93 0.80–0.93 0.80–0.92 0.84–0.91 0.84–0.91 rs3752246 19:1.1 ABCA7 d G 0.19 2 1.16 1.0 × 10−5 1.15 1.9 × 10−5 1.13 0.012 1.13 0.009 1.15 5.8 × 10–7 1.15 5.0 × 10–7 1.08–1.24 1.08–1.23 1.03–1.24 1.03–1.25 1.09–1.21 1.09–1.21 rs3865444 19:51.7 CD33c A 0.30 1 0.88 8.2 × 10–7 0.88 1.9 × 10−6 0.91 0.021 0.92 0.029 0.89 1.1 × 10–7 0.89 2.0 × 10–7 0.84–0.93 0.84–0.93 0.85–0.99 0.85–0.99 0.86–0.93 0.86–0.93 −6 Chr.:Mb, chromosome:position (build 19); MA, minor allele; MAF, minor allele frequency; # SNPs, the number of SNPs for which P ≤ 1 × 10 in meta-analysis from the combined analysis in stage 1+2; ORM, odds ratio in meta-analysis; PM, P value in meta-analysis; ORJ, odds Nature America, Inc.
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