Strategies for pathway-based analysis of genome-wide SNP data

Numerous genome-wide association studies (GWAS) have been performed in order to determine the susceptible loci of diseases. However, most diseases still cannot be explained by a single locus. Pathway-based methods address this problem by combining those small effects into groups of related genes or pathways. However, because pathway-based approaches consist of multiple steps, there is much room for improvement. This paper presents an improved method for translating list of SNPs from GWAS into list of genes. We incrementally adjusted and compared different modifications applied to Parkinson's disease (PD) genome-wide SNP data and then used GSEA-P to analyze the resulting list of genes. After careful adjustments, we are able to identify more relevant pathways that were not found previously.