Evaluation of fine mapping strategies for a multifactorial disease locus: systematic linkage and association analysis of IDDM1 in the HLA region on chromosome 6p21

The positional cloning of multifactorial disease genes is a major challenge in human genetics. We have therefore empirically tested the utility of the available polymorphic microsatellite map to locate the already identified type 1 diabetes locus IDDM1 (sibling risk/population prevalence ratio lambd a(s) = 2.7) within a 14 Mb region of chromosome 6p21 linked to disease. In a two-stage approach to fine mapping, linkage was evaluated in 385 affected sib-pair families using 13 evenly spaced polymorphic microsatellite marker s. The whole 14 Mb showed strong linkage. Then, each marker was analysed fo r evidence of allelic association, revealing evidence of disease associatio n at one marker located within the 95% confidence interval of 1.7 cM obtain ed by linkage. Analysis of an additional 12 markers flanking this marker re vealed a highly specific region of 570 kb associated with disease (P = 7.5 x 10(-35)), which included the HLA class II genes, known to be the primary determinants of IDDM1. The peak of association was as close as 85 kb centro meric of the disease-predisposing class II gene HLA-DQB1. We investigated t he importance of the underlying inter-marker linkage disequilibrium, marker informativity and recombination for fine mapping and demonstrate that the majority of disease association in the region can be explained by linkage d isequilibrium with the class II susceptibility genes. Recombination within the major histocompatibility complex was rare and nearly absent in the clas s III region. We demonstrate that fine mapping of a multifactorial disease gene is possible with high accuracy even in a region with extraordinary lin kage disequilibrium across distances of several Mb. The results will be app licable to association studies of disease loci with lambda(s) values <2.7 e xcept that much larger data sets will be required.