An allelic cluster of DQ alpha restriction fragments is associated with multiple sclerosis: evidence that a second haplotype may influence disease susceptibility.

Extensive analysis of restriction fragment length polymorphism using HLA class II and T-cell receptor gene probes has been carried out in an attempt to identify genetic markers more strongly associated with multiple sclerosis than the classically defined antigens DR2, Dw2, and DQw1. The use of DNA pooled from groups of patients and controls from northeast Scotland enabled the screening of 14 restriction endonucleases with five HLA-D region probes (DP alpha, DP beta, DQ alpha, DQ beta, DR beta) and two T-cell antigen receptor probes. Restriction fragment length polymorphisms which discriminated between multiple sclerosis and control pools were identified with four restriction enzymes: Msp1 (DQ alpha), BamH1, Bgl11, and Taq1 (DQ beta). No discriminatory polymorphism was seen with any of the other enzyme/probe combinations. Subsequent Southern blot analysis of individual DNA samples was carried out using these enzymes and probes in two independently conducted studies, in Northern Ireland and northeast Scotland. Following Msp1-digestion and hybridization to DQ alpha, a 3.25-kb fragment was observed in 31% of Scottish patients but in only 4% of controls from the same population. Furthermore, when only DR2-positive individuals were analyzed, there was a significant excess of this fragment in patients from both Scotland (28, or 2.9%) and Northern Ireland (20, or 3.4%). Although the DQ alpha gene characterized by this fragment remains to be determined, this fragment exhibits apparent allelism to DQw1. Therefore, these data raise the possibility that two different DQ alleles, one on each haplotype, may jointly contribute to disease susceptibility.