An efficient weighted tag SNP-set analytical method in genome-wide association studies

BACKGROUND: Single-nucleotide polymorphism (SNP)-set analysis in Genome-wide association studies (GWAS) has emerged as a research hotspot for identifying genetic variants associated with disease susceptibility. But most existing methods of SNP-set analysis are affected by the quality of SNP-set, and poor quality of SNP-set can lead to low power in GWAS. RESULTS: In this research, we propose an efficient weighted tag-SNP-set analytical method to detect the disease associations. In our method, we first design a fast algorithm to select a subset of SNPs (called tag SNP-set) from a given original SNP-set based on the linkage disequilibrium (LD) between SNPs, then assign a proper weight to each of the selected tag SNP respectively and test the joint effect of these weighted tag SNPs. The intensive simulation results show that the power of weighted tag SNP-set-based test is much higher than that of weighted original SNP-set-based test and that of un-weighted tag SNP-set-based test. We also compare the powers of the weighted tag SNP-set-based test based on four types of tag SNP-sets. The simulation results indicate the method of selecting tag SNP-set impacts the power greatly and the power of our proposed method is the highest. CONCLUSIONS: From the analysis of simulated replicated data sets, we came to a conclusion that weighted tag SNP-set-based test is a powerful SNP-set test in GWAS. We also designed a faster algorithm of selecting tag SNPs which include most of information of original SNP-set, and a better weighted function which can describe the status of each tag SNP in GWAS.