A two‐step procedure for constructing confidence intervals of trait loci with application to a rheumatoid arthritis dataset

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Abstract
Preliminary genome screens are usually succeeded by fine mapping analyses focusing on the regions that signal linkage. It is advantageous to reduce the size of the regions where follow‐up studies are performed, since this will help better tackle, among other things, the multiplicity adjustment issue associated with them. We describe a two‐step approach that uses a confidence set inference procedure as a tool for intermediate mapping (between preliminary genome screening and fine mapping) to further localize disease loci. Apart from the usual Hardy‐Weiberg and linkage equilibrium assumptions, the only other assumption of the proposed approach is that each region of interest houses at most one of the disease‐contributing loci. Through a simulation study with several two‐locus disease models, we demonstrate that our method can isolate the position of trait loci with high accuracy. Application of this two‐step procedure to the data from the Arthritis Research Campaign National Repository also led to highly encouraging results. The method not only successfully localized a well‐characterized trait contributing locus on chromosome 6, but also placed its position to narrower regions when compared to their LOD support interval counterparts based on the same data. Genet. Epidemiol. 30:18–29, 2006.