Analysis of the linkage disequilibrium extension in the Azores Islands (Portugal)

Abstract

The design of genetic studies of complex diseases is dependent on the extension and distribution of linkage disequilibrium (LD) across the genome and populations. Here, we characterize the LD extension in the Azores (Western, Central and Eastern islands groups) and mainland Portugal populations. LD was evaluated in three chromosomic regions: the Xq13.3, the Y-chromosome and the HLA (6p21) for the Azorean population. The results obtained in the Western group for the Xq13.3 markers provide significant evidence of LD in 10 comparisons, after correction. In the São Miguel island population, the assessment of LD for HLA demonstrated a total of 13 out of 36 pairs with significant LD, with the largest genetic distance (2.5 Mb) between HLA-DRB1 and D6S265. The pairwise association between Y-markers in the Azorean population revealed 46% pairs with significant LD. In addition, D′ analysis indicates that the Western group presents higher values when compared with the Central and Eastern groups. Taken together, the data show that the Azorean population presents a lower D′ (0.142) compared with 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.