RFLP characterization of the upstream regulatory region of the HLA‐DQA1 gene

We have performed population and family studies of the distribution of DNA restriction length polymorphisms (RFLPs) in the 5' region of the HLA-DQA1 gene using a probe which corresponds to a sequence of the 5' flanking region of HLA-DQA1. Southern analysis detected four polymorphic fragments (X1, X2, X3 and X4) with XbaI and three fragments (E1, E2 and E3) with EcoRI. Family segregation studies showed that these RFLPs segregated in cis with the parental HLA haplotypes. Analysis of haplotypic associations of the X and E polymorphisms with each other and with HLA-DQA1 alleles demonstrates that DQA1 alleles can be further subtyped according to the particular XE combination which they carry. Hence, definition of these alleles provides new markers for HLA haplotyping and allows further splitting of otherwise identical DQA1 alleles. This information may be helpful for studies of association of disease susceptibility and autoimmunity with HLA haplotypes.