Establishment of an optimized set of 406 microsatellite markers covering the whole genome for the Japanese population

Microsatellites. an essential tool for genetic linkage analyses, are select ed in genetic studies on the basis of both informativeness and their positi ons with respect to one another on the genetic map. In order to establish a microsatellite marker set useful for linkage studies in the Japanese popul ation, we first genotyped 64 unrelated Japanese subjects, using 400 microsa tellite markers from a commercially available set (ABI PRISM Linkage Mappin g Set-MD10) and then determined the allelic frequencies and heterozygositie s for these marker loci in the population. In order to optimize the set, we replaced 41 markers having a heterozygosity lower than 0.6 with as many in formative markers in the corresponding loci, and newly added six markers in the set to minimize the several gaps found at intervals of over 20cM. We f inally established a set comprising 406 microsatellites with average interv als of 9cM (maximum, 17cM) and minimum heterozygosities of over 0.6 (mean, 0.76). All data generated in this study, including the specific polymerase chain reaction (PCR) primer sequences of the newly added markers, are freel y available to all researchers at our web site. The genetic tool establishe d here should facilitate genetic linkage studies of various hereditary dise ases, especially in the Japanese.