Joint analysis for genome-wide association studies in family-based designs.

In family-based data, association information can be partitioned into the between-family information and the within-family information. Based on this observation, Steen et al. (Nature Genetics. 2005, 683-691) proposed an interesting two-stage test for genome-wide association (GWA) studies under family-based designs which performs genomic screening and replication using the same data set. In the first stage, a screening test based on the between-family information is used to select markers. In the second stage, an association test based on the within-family information is used to test association at the selected markers. However, we learn from the results of case-control studies (Skol et al. Nature Genetics. 2006, 209-213) that this two-stage approach may be not optimal. In this article, we propose a novel two-stage joint analysis for GWA studies under family-based designs. For this joint analysis, we first propose a new screening test that is based on the between-family information and is robust to population stratification. This new screening test is used in the first stage to select markers. Then, a joint test that combines the between-family information and within-family information is used in the second stage to test association at the selected markers. By extensive simulation studies, we demonstrate that the joint analysis always results in increased power to detect genetic association and is robust to population stratification.