The design of genetic studies of complex diseases is dependent on the extent and distribution of linkage disequilibrium (LD) across the genome in different populations. Here, we characterize the extent of LD in the Azores (Western, Central, and Eastern island groups) and mainland Portugal populations. LD was evaluated in the Xq13.3 region by genotyping eight STR markers spanning 20.9 Mb. Standardized multiallelic disequilibrium coefficient (D') analysis indicates that the Western group presents higher values when compared with the Central and Eastern groups. However, all island groups show values of D' lower than 0.5 and 0.33, suggesting no extensive LD in these populations. Taken together, the data show that the Azorean population presents a lower D' (0.142) than mainland Portugal (0.226). Although, both populations do not show extensive LD, the easy reconstruction of large pedigrees in the Azorean population is a valuable resource for the fine mapping of disease genes.

Overall, the Azorean population can be analysed as a homogeneous genetic group, which consequently, would present, possibly, the same drug-reaction profile. In terms of genomic medicine, these results will have a significant impact on the design of future genetic and pharmacogenomic studies in the Azorean population.

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