Thalassemia is one of the most common monogenic disorders, with a high demand for carrier detection and prenatal diagnosis in the Iranian population. In view of the presence of a large number of mutations associated with the disease, the polymorphic markers present in the β-globin gene cluster region were commonly used in linkage analysis of the disease. Markers usually show a population-based dependent haplotype frequency. Among the polymorphic markers, five markers including AvaII, RsaI, HinfI, TaqI and Hind III were genotyped in 150 unrelated healthy individuals from the Iranian population. The haplotype frequency was estimated using PHASE program and linkage disequilibrium (LD) was analyzed by MIDAS program. Among the eight possible haplotypes, five haplotypes showed relatively high frequencies (≥ 5%), of which the haplotype AvaII-TaqI-HindIII with the highest frequency could be suggested as an informative haplotype for possible carrier detection and prenatal diagnosis of beta thalassemia in the Iranian population. Moreover, the LD results showed that RsaI and HinfI (located in the hotspot region) were not associated with the 5' sub-haplotypes or 3' sub-haplotypes, and therefore, these markers might be excluded as strong molecular diagnostic markers in beta globin gene region in the Iranian population.
