There have been no unanimous criteria for declaring such replication in circumstances in which no SNP provides “genome wide significance” with the same phase of association in “template” GWA analyses of data from multiple independent samples. Replication of nominally significant associations for the same SNP (approach (1), here) is among the criteria most used to date [43], [44]. This “nontemplate” GWA analytic approach is likely to perform best when large association signals are found in each independent sample, when the same SNP sets are studied in each, when the disease exhibits little locus heterogeneity and when there are good matches between the fine patterns of linkage disequilibrium of the samples being studied and the reference samples (commonly, Hap Map) used to infer the underlying patterns of linkage disequilibrium. Few “replication” samples manifest all of these features. Although the current European- and African-American samples were recruited in parallel and evaluated with the same SNPs, the racial/ethnic differences between the participants suggest that the samples are likely to manifest differences in fine patterns of linkage disequilibrium and in phase of association at
