The number of genome-wide association studies (GWAS) of complex human diseases has increased markedly in recent years with the availability of low-cost, high-density genotyping and large, well-characterized sample sets. Like other genomic applications, the production of GWAS data involves industrial-scale processes for which systems of quality control and quality assurance (QC/QA) are essential. This article describes a system of QC/QA for GWAS with a focus on the genotypic data. We define QC as steps taken to monitor and control the quality of a product as it is being produced, while QA is defined as a post-production review of product quality. In this case, the ‘product’ is a set of GWAS data produced for the purpose of detecting genotype-phenotype associations and gene-environment interactions. The QC/QA system is illustrated with examples from four projects in the ‘Gene Environment Association Studies’ (GENEVA) program [Cornelis, et al. 2010]. GENEVA projects consist of case-control, cohort, and family-based study designs. We focus here on QC/QA for case-control study designs, but many of the principles also apply to other designs.
