Technological Issues and Experimental Design of Gene Association Studies

Genome-wide association studies (GWAS), in which thousands of single-nucleotide polymorphisms (SNPs) spanning the genome are genotyped in individuals who are phenotypically well characterized, �currently represent the most popular strategy for identifying gene regions associated with common �diseases and related quantitative traits. Improvements in technology and throughput capability, development of powerful statistical tools, and more widespread acceptance of pooling-based genotyping approaches have led to greater utilization of GWAS in human genetics research. However, important considerations for optimal experimental design, including selection of the most appropriate genotyping platform, can enhance the utility of the approach even further. This chapter reviews experimental and technological issues that may affect the success of GWAS findings and proposes strategies for developing the most comprehensive, logical, and cost-effective approaches for genotyping given the population of interest.