A novel approach for multi-SNP GWAS and its application in Alzheimer’s disease

BACKGROUND: Genome-wide association studies (GWAS) have effectively identified genetic factors for many diseases. Many diseases, including Alzheimer’s disease (AD), have epistatic causes, requiring more sophisticated analyses to identify groups of variants which together affect phenotype. RESULTS: Based on the GWAS statistical model, we developed a multi-SNP GWAS analysis to identify pairs of variants whose common occurrence signaled the Alzheimer’s disease phenotype. CONCLUSIONS: Despite not having sufficient data to demonstrate significance, our preliminary experimentation identified a high correlation between GRIA3 and HLA-DRB5 (an AD gene). GRIA3 has not been previously reported in association with AD, but is known to play a role in learning and memory. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1186/s12859-016-1093-7) contains supplementary material, which is available to authorized users.