Integrate GWAS, eQTL, and mQTL Data to Identify Alzheimer’s Disease-Related Genes

It is estimated that the impact of related genes on the risk of Alzheimer’s disease (AD) is nearly 70%. Identifying candidate causal genes can help treatment and diagnosis. The maturity of sequencing technology and the reduction of cost make genome-wide association study (GWAS) become an important means to find disease-related mutation sites. Because of linkage disequilibrium (LD), neither the gene regulated by SNP nor the specific SNP can be determined. Because GWAS is affected by sample size and interaction, we introduced empirical Bayes (EB) to make a meta-analysis of GWAS to greatly eliminate the bias caused by sample and the interaction of SNP. In addition, most SNPs are in the noncoding region, so it is not clear how they relate to phenotype. In this paper, expression quantitative trait locus (eQTL) studies and methylation quantitative trait locus (mQTL) studies are combined with GWAS to find the genes associated with Alzheimer disease in expression levels by pleiotropy. Summary data-based Mendelian randomization (SMR) is introduced to integrate GWAS and eQTL/mQTL data. Finally, we prioritized 274 significant SNPs, which belong to 20 genes by eQTL analysis and 379 significant SNPs, which belong to seven known genes by mQTL. Among them, 93 SNPs and 2 genes are overlapped. Finally, we did 10 case studies to prove the effectiveness of our method.