Genome-wide analysis of genetic loci associated with Alzheimer disease

Abstract

Context: Genome-wide association studies (GWAS) have recently identified CLU, PICALM, and CR1 as novel genes for late-onset Alzheimer disease (AD).

Objectives: To identify and strengthen additional loci associated with AD and confirm these in an independent sample and to examine the contribution of recently identified genes to AD risk prediction in a 3-stage analysis of new and previously published GWAS on more than 35,000 persons (8371 AD cases).

Design, setting, and participants: In stage 1, we identified strong genetic associations (P < 10(-3)) in a sample of 3006 AD cases and 14,642 controls by combining new data from the population-based Cohorts for Heart and Aging Research in Genomic Epidemiology consortium (1367 AD cases [973 incident]) with previously reported results from the Translational Genomics Research Institute and the Mayo AD GWAS. We identified 2708 single-nucleotide polymorphisms (SNPs) with P < 10(-3). In stage 2, we pooled results for these SNPs with the European AD Initiative (2032 cases and 5328 controls) to identify 38 SNPs (10 loci) with P < 10(-5). In stage 3, we combined data for these 10 loci with data from the Genetic and Environmental Risk in AD consortium (3333 cases and 6995 controls) to identify 4 SNPs with P < 1.7x10(-8). These 4 SNPs were replicated in an independent Spanish sample (1140 AD cases and 1209 controls). Genome-wide association analyses were completed in 2007-2008 and the meta-analyses and replication in 2009.

Main outcome measure: Presence of Alzheimer disease.

Results: Two loci were identified to have genome-wide significance for the first time: rs744373 near BIN1 (odds ratio [OR],1.13; 95% confidence interval [CI],1.06-1.21 per copy of the minor allele; P = 1.59x10(-11)) and rs597668 near EXOC3L2/BLOC1S3/MARK4 (OR, 1.18; 95% CI, 1.07-1.29; P = 6.45x10(-9)). Associations of these 2 loci plus the previously identified loci CLU and PICALM with AD were confirmed in the Spanish sample (P < .05). However, although CLU and PICALM were confirmed to be associated with AD in this independent sample, they did not improve the ability of a model that included age, sex, and APOE to predict incident AD (improvement in area under the receiver operating characteristic curve from 0.847 to 0.849 in the Rotterdam Study and 0.702 to 0.705 in the Cardiovascular Health Study).

Conclusions: Two genetic loci for AD were found for the first time to reach genome-wide statistical significance. These findings were replicated in an independent population. Two recently reported associations were also confirmed. These loci did not improve AD risk prediction. While not clinically useful, they may implicate biological pathways useful for future research.

Figure 1

Figure showing the three-stage approach and the various studies included in the different stages.

Figure 2

Regional association plot for novel loci that were significantly associated (p<5×10⁻⁸) with AD in stage 3 analyses (rs744373 near BIN1, rs597668 near BLOC1S3 and MARK4). Each data marker represents the statistical significance (p-value) of each SNP plotted on the −log₁₀ scale against its chromosomal position (NCBI build 36).The blue diamonds show stage 1 p-values for the sentinel (top) SNP at each locus, whereas the grey and black diamonds show the p-values for this same SNP following stage 2 and stage 3 meta-analyses, respectively. P-values from stage 1 for additional SNPs at that locus are color- and size-coded according to the strength of their linkage disequilibrium with the top SNP as follows: r²<0.2 white; 0.2<r²<0.5 yellow; 0.5<r²<0.8 orange; r²>0.8 red. The fine scale recombination rate is shown by the blue line which shows the average frequency with which recombination occurs (exchange of genetic material between maternal and paternal chromosomes during meiosis) at that site. Genes located in the region shown (on either strand of the chromosome) are shown as green lines with Human Genome Organization (HUGO) gene nomenclature committee gene symbols, the length of the green line represents the size/extent of the gene and the arrow the direction in which transcription of mRNA occurs.

Figure 3

Regional association plot for novel loci that were significantly associated (p<5×10⁻⁸) with AD in stage 3 analyses (rs744373 near BIN1, rs597668 near BLOC1S3 and MARK4). Each data marker represents the statistical significance (p-value) of each SNP plotted on the −log₁₀ scale against its chromosomal position (NCBI build 36).The blue diamonds show stage 1 p-values for the sentinel (top) SNP at each locus, whereas the grey and black diamonds show the p-values for this same SNP following stage 2 and stage 3 meta-analyses, respectively. P-values from stage 1 for additional SNPs at that locus are color- and size-coded according to the strength of their linkage disequilibrium with the top SNP as follows: r²<0.2 white; 0.2<r²<0.5 yellow; 0.5<r²<0.8 orange; r²>0.8 red. The fine scale recombination rate is shown by the blue line which shows the average frequency with which recombination occurs (exchange of genetic material between maternal and paternal chromosomes during meiosis) at that site. Genes located in the region shown (on either strand of the chromosome) are shown as green lines with Human Genome Organization (HUGO) gene nomenclature committee gene symbols, the length of the green line represents the size/extent of the gene and the arrow the direction in which transcription of mRNA occurs.