investigation for an intra-genic short tandem repeat marker in the hla-drb1

the hla class ii genes of human major histocompatibility complex (mhc) exhibit an extensive degree of genetic polymorphism. this region subdivides into four sub-regions dp, do, dq, and dr. there are five different dr haplotypes that all contain a highly polymorphic allele called hla-drb1. in most recent studies, the association between hla-drb1 and a large number of diseases such as multiple sclerosis (ms) has been demonstrated. in the current study, m2_2_36 str marker located within exon 2 of hla-drb1 was subjected to bioinformatics analysis to investigate whether this str marker could play as a specific marker for genotyping of hla-drb1. this marker was searched in mhc (dbmhc) and the unists databases. then, the existence of this marker in all six different mhc haplotype sequences containing hla-drb1 as well as reference assembly sequence was investigated by clc main workbench software. the primers introduced for the marker were selected from the unists database and aligned against these six sequences by the same software. conserved regions next to the m2_2_36 with maximum alignment from all these sequences were selected and used to design specific primers. for e-pcr and blast bioinformatics tools were used to determine the physical mapping position(s) targeted by this primer pair. finally, the presence of m2_2_36 in other drb genes was analyzed using clc. our study showed that the introduced primer pairs for m2_2_36 in the db mhc and unists websites were not appropriate and adoptable for amplifying this marker. moreover, the existence of this marker in other functional hla-drb genes, such as drb3, drb4 and drb5, was indicated. in conclusion, m2_2_36 does not exist exclusively in hla-drb1 and cannot be used for special genotyping of this gene. however, this property can make it a useful genetic marker for drb haplotyping.