Conditional linkage disequilibrium analysis of a complex disease superlocus, IDDM1 in the HLA region, reveals the presence of independent modifying gene effects influencing the type 1 diabetes risk encoded by the major HLA-DQB1,-DRB1 disease loci

Type 1 diabetes mellitus is a common disease with a complex mode of inherit ance. Its aetiology is underpinned by a major locus, insulin-dependent diab etes mellitus 1 (IDDM1) in the human leukocyte antigen (HLA) region of chro mosome 6p21, and an unknown number of loci of lesser individual effect. In linkage analyses IDDM1 is a single peak, but it is evident that the linkage is caused by allelic variation of three adjacent genes in a 75 kb region, namely the class II genes, HLA-DRB1, -DQA1 and -DQB1, However, even these t hree genes may not explain all of the HLA association. We investigated, in the founder population of Sardinia, whether non-DQ/DR polymorphic markers w ithin a 9.452 Mb region encompassing the whole HLA complex further influenc e the disease risk, after taking into account linkage disequilibrium with t he disease loci HLA-DQB1, -DQA1 and -DRS1, We generalized the conditional a ssociation test, the haplotype method, to detect marker associations that a re independent of the main DR/DQ disease associations. Three regions were i dentified as risk modifiers. These associations were not only independent o f the polymorphic exon 2 sequences of HLA-DQB1, -DQA1 and -DRB1, but also i ndependent of each other. The individual contributions of these risk modifi ers were relatively modest but their combined impact was highly significant . Together, alleles of single nucleotide polymorphisms at the DMB and DOE g enes, and the microsatellite locus TNFc, identified similar to 40% of Sardi nian DR3 haplotypes as non-predisposing, This conditional analysis approach can be applied to any chromosome region involved in the predisposition to complex traits.