We now report application of this nontemplate strategy to identify overall replication of groups of results from GWA studies of samples of individuals with dependence on alcohol and illegal substances vs matched controls [21], (http://www.ncbi.nlm. nih.gov/gap). We separately compare data from independent samples of individuals with European-American genetic backgrounds and samples of individuals with African-American genetic backgrounds. These data come from individual genotyping and multiple-pool genotyping approaches that use 1 M SNP Illumina and Affymetrix platforms, respectively. The results focus attention on chromosomal regions that are identified by clusters of SNPs for which case vs control differences achieve nominal statistical significance in multiple samples from the same racial/ethnic group. We describe the high confidence with which this approach rejects the null hypothesis that clusters of nominally-significant SNPs from different samples of individuals from the same racial/ethnic group identify the same chromosomal regions with frequencies expected by chance. We note the more modest levels of confidence that this approach provides for identification of individual SNPs, individual chromosomal regions, individual genes and for the overlap between data from samples of the two
