An-Najah Staff

For many years gene mapping studies have been performed through linkage analyzes based on pedigree data. Recently, linkage disequilibrium (LD) methods based on unrelated individuals have been advocated as powerful tools to refine estimates of gene location. Here we present a new mapping method, called HAPim, which scans a small chromosome region and returns the most probable position for a quantitative trait locus. For each postulated position, this method uses the expected frequency of the haplotypes comprising the trait locus and the two flanking markers. The derivation of these expected frequencies is based on a model describing the decay in LD from an initial mutation. Over several simulation scenarios HAPim was found to be as accurate as identity-by-descent methods, whilst being valuable in a wider range of populations.