Genome-Wide Association Studies

Genome-wide genotyping and analysis approaches offer the opportunity to examine patterns of variation across a large number of genomic positions for association with occurrence of disease or the distribution of traits of interest. Genome-wide association studies (GWAS) efforts require rigorous planning and careful study design at their outset. The primary design elements for consideration include genotyping technology or platform, data set sample design (family-based, case-control, cohort), and statistical analysis strategy. This chapter discusses each of these design elements in more detail. The statistical analyses used for GWAS in case-control or cohort samples have become mostly standardized in recent years. However, alternative statistical analysis approaches have begun to emerge as well. These are described in more detail. In addition to the standard GWAS approaches described in this chapter, the single nucleotide polymorphism (SNP) data generated by a genome-wide SNP array can be used for many other different types of analyses.