Characterization and specification of microsatellite markers in the HLA-DRB1 gene region: A revision to major histocompatibility complex database

Abstract

Association between HLA-DRB1 and a large number of diseases such as multiple sclerosis, type I diabetes and rheumatoid arthritis has been demonstrated. In the present study, we attempted to identify and characterize potential microsatellites in the HLA-DRB1 gene region to find specific markers for genotyping and linkage analysis of this gene. The microsatellites including M2_3_22, M2_2_36, D6S2878, D6S2805, D6S2879 and D6S2880 were selected from microsatellite resource in the Major Histocompatibility Complex database (dbMHC). In silico analysis showed that only M2_3_22 was specific for HLA-DRB1. Moreover, our findings revealed some more accurate characteristics of the other investigated microsatellites. M2_3_22 existed as a single copy in all the MHC haplotype sequences and was located next to HLA-DRB1. Therefore, a new set of primers compatible with all the last published MHC haplotype sequences were designed and used to amplify M2_3_22 in 164 DNA samples obtained from unrelated Iranian individuals. M2_3_22 was successfully amplified in all DNA samples and three different alleles were identified. This locus was found in the Hardy-Weinberg equilibrium (P> 0.05) in the studied population. Together, the findings suggested that M2_3_22 could be introduced as a specific locus in the HLA-DRB1 gene region for linkage analysis and disease association studies. © 2013 American Society for Histocompatibility and Immunogenetics.