Recent technological advances allow the rapid generation of vast quantities of molecular biological data [1,2]. At the same time, the sequencing of the human genome and subsequent efforts to catalogue the variation within it[3] have created opportunities for testing thousands of sequence variations for association with disease, behavioural traits and physiological markers. Such applications are appealing because of the relative lack of success, to date, of positional cloning strategies that start with family-based linkage mapping [4], most likely due to insufficient sample sizes to detect genes of modest effect [5]. The whole-genome association scan is an increasingly feasible study design in which the genotyped markers are sufficiently closely spaced to detect linkage disequilibrium (LD) with all aetiological variants, and well-powered sample sizes are more attainable [6]. Some initial studies have been performed in special populations[7,8] and in small samples of outbred populations;[9,10] genome-wide admixture scans are imminent[11,12] and, ultimately, routine scans will be performed for common diseases in large cohorts of outbred populations [13].
