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

Herr, Mathias H. and Dudbridge, Frank and Zavattari, Patrizia and Cucca, Francesco and Guja, Cristian and March, Ruth E. and Campbell, R. Duncan and Barnett, Anthony H. and Bain, Stephen Charles and Todd, John A. and Koeleman, Bobby P. C. (2000) Evaluation of fine mapping strategies for a multifactorial disease locus: systematic linkage and association analysis of IDDM1 in the HLA region on chromosome 6p21. Human Molecular Genetics, Vol. 9 (9), p. 1291-1301. eISSN 1460-2083. Article.

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Abstract

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 λs = 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 markers. The whole 14 Mb showed strong linkage. Then, each marker was analysed for evidence of allelic association, revealing evidence of disease association at one marker located within the 95% confidence interval of 1.7 cM obtained by linkage. Analysis of an additional 12 markers flanking this marker revealed 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 centromeric of the disease predisposing class II gene HLA-DQB1. We investigated the 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 disequilibrium with the class II susceptibility genes. Recombination within the major histocompatibility complex was rare and nearly absent in the class III region. We demonstrate that fine mapping of a multifactorial disease gene is possible with high accuracy even in a region with extraordinary linkage disequilibrium across distances of several Mb. The results will be applicable to association studies of disease loci with λs values < 2.7 except that much larger data sets will be required.

Item Type:Article
ID Code:4236
Status:Published
Refereed:Yes
Uncontrolled Keywords:Diabetes susceptibility genes, microsatellite markers, disequilibrium measures, autoimmune-disease, complex traits, recombination, power, MHC, predisposition, transmission
Subjects:Area 06 - Scienze mediche > MED/03 Genetica medica
Divisions:001 Università di Sassari > 01 Dipartimenti > Scienze biomediche
Publisher:Oxford University Press
eISSN:1460-2083
Deposited On:22 Jul 2010 11:38

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