Exploiting linkage disequilibrium in population isolates

A comparison of haplotype frequencies between unrelated cases and controls from population isolates identifies a strong signal for the presence/absenc e of the discrete phenotype in an interval on chromosome 6 bounded by marke rs 34 and 35. We define a dissimilarity index, D, which is sensitive to dif ferences in allele distributions and differences in the patterns of linkage disequilibrium between cases and controls. We describe two statistical met hods to utilize D: a method appropriate for a single moderately sized sampl e and a sequential approach appropriate for multiple small independent samp les. (C) 2001 Wiley-Liss, Inc.