Genome-wide association study (GWAS), which is a powerful tool for investigating the genetic architecture of polygenic disease in humans, is generally applied for identification of genetic factors of disease susceptibility, clinical phenotypes and treatment response. The differences in allele frequencies of genome-wide distributedsingle nucleotide polymorphisms (SNPs) are analyzed with microarray technique or other technologies, that allow simultaneous genotyping from tens'of thousands to several millions SNPs per sample. The power toexplore highly-reliable differences between compared groups of patients aind controls allowed GWAS to become a common approach for identification of genetic susceptibility for complex diseases with polygenic nature. The main achievements and challenges of GWAS in multiple sclerosis (MS), which is a prototype example of complex disease, are reviewed here for identification of MS causative genes, which expand the knowledge on molecular mechanisms of MS pathogenesis and genetic risk factors.
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