DXS998-DXS548-FRAXAC1 represents a novel informative haplotype at the FMR1 locus in the Iranian population.

Fragile X syndrome, which is caused by mutation in the FMR1 gene region, is one of the most prevalent forms of mental retardation. Direct diagnosis of the disease is based on PCR and southern blot analysis, but because of technical problems, use of polymorphic DNA markers can be helpful for carrier detection and prenatal diagnosis in families with an affected individual. The polymorphic markers usually show a population-based haplotype frequency and heterozygosity. In the present study, genotyping and analysis of haplotype frequency of three microsatellite markers including DXS998, DXS548 and FRAXAC1 at the FMR1 gene region were carried out in 140 unrelated healthy women and 26 families from the Iranian population. The data indicated the presence of a novel allele for DXS998 in the Iranian population. Estimation of haplotype frequency using Arlequin program showed 50 different DXS998-DXS548-FRAXAC1 haplotypes for the input data of 5, 7 and 4 alleles, respectively. Among these haplotypes five of them showed relatively high frequencies (≥0.05). Analysis of linkage disequilibrium (LD) for the unrelated individuals using the PowerMarker computer program, showed that this haplotype combination can be an informative haplotype for linkage analysis in carrier detection and possible molecular diagnosis of fragile X in the Iranian population.