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 selected in genetic studies on the basis of both informativeness and their positions with respect to one another on the genetic map. In order to establish a microsatellite marker set useful for linkage studies in the Japanese population, we first genotyped 64 unrelated Japanese subjects, using 400 microsatellite markers from a commercially available set (ABI PRISM Linkage Mapping Set-MD10) and then determined the allelic frequencies and heterozygosities 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 informative markers in the corresponding loci, and newly added six markers in the set to minimize the several gaps found at intervals of over 20 cM. We finally established a set comprising 406 microsatellites with average intervals of 9cM (maximum, 17 cM) 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 freely available to all researchers at our web site. The genetic tool established here should facilitate genetic linkage studies of various hereditary diseases, especially in the Japanese.