from the second stage of a two-stage GWA study is either analyzed separately as a replication-based sample or the data is combined with data from the first stage and the combined data is analyzed jointly. A recent alternative approach for reducing the cost of a large-scale case-control genetic association study and to increase the statistical power to detect an association when present is to use freely available genotype data on a large number of subjects from previous genome-wide association scans as control data in the current study. The effective use of a large public control dataset for comparison with multiple case datasets for different phenotypes was illustrated by the Wellcome Trust’s Case Control Collaboration (WTCCC) GWA study on 14,000 cases of seven common diseases and 3,000 shared controls (Wellcome Trust Case Control Consortium, 2007). In this study, based on British subjects of European descent, the WTCCC identified 24 independent associations (p < 5 × 10−7) for bipolar disorder, coronary artery disease, Crohn’s disease, rheumatoid arthritis, type 1 diabetes and type 2 diabetes using 2,000 independent cases for each disorder.
