Detection and modeling of disease susceptibility locus effects: How much can be learned from contrast of populations?

We report the results of our analyses of the GAW11 Problem 2 data set, usin g information from three different populations. In the first part of the pa per, we used classical population genetic tests to compare affected individ uals from the different populations, stratifying on the environmental facto rs. Thanks to existing linkage disequilibrium in one population, we found o ne of the disease susceptibility loci. In the second part of the paper, we used the marker association segregation chi(2) method to model the role of this disease susceptibility locus in the different populations and draw som e inferences regarding the model used at that locus to generate the data. ( (C)) 1999 Wiley-Liss, Inc.