Genome-wide association tests by two-stage approaches with unified analysis of families and unrelated individuals

Multiple testing is a problem in genome-wide or region-wide association studies. In this report, we consider a study design given by the Genetic Analysis Workshop 15 (GAW15) Problem 3 - nuclear families (parents with their affected children) and unrelated controls. Based on this design, we propose three two-stage approaches to deal with the problem of multiple testing. The tests in the first stage, statistically independent of the association test used in the second stage, are used to screen or select single-nucleotide polymorphisms (SNPs). Then, in the second stage, a family-based association test is performed on a much smaller set of selected SNPs. Thus, the problem of multiple testing is much less severe. Our simulation studies and application to the dense SNP data of chromosome 6 in the GAW15 Problem 3 show that the two-stage methods are more powerful than the one-stage method (using the family-based association test only).