Allelic frequencies and heterozygosities of microsatellite markers covering the whole genome in the Korean

Abstract

Microsatellite markers are an essential tool for genetic linkage analysis because of their high polymorphism content. Four hundred commercially available markers covering the entire genome were genotyped from 578 sib individuals from 249 Korean families. Allelic frequencies and heterozygosities were determined for each marker loci and compared between Korean, Taiwanese, Japanese and Caucasian populations. In the three Asian populations, 10-13% of the markers had less than 0.6 heterozygosity, whereas in the Caucasian population, only 0.5% of the markers had less than 0.6 heterozygosity. Mean identical by descent (IBD) values were calculated for 578 sib individuals.Analysis of IBD values greater than 0.5 suggested that markers with low heterozygosity can also provide positive linkages, at least for the IBD sharing method of model-free linkage analysis. The data presented in this study will be a useful reference for genome-wide screens of Koreans and comparative studies with other ethnic populations.

No influence of parental origin of intact X chromosome and/or Y chromosome sequences on three-year height response to growth hormone therapy in Turner syndrome

“…Confirmation of the parental origin of the intact X chromosome was analyzed by comparing the patient and parental DNA using nine highly polymorphic X chromosome microsatellites ( DXS 1060 , DXS 8051 , DXS 1228 , DXS 1214 , DXS 986 , DXS 990 , DXS 1001 , DXS 104 , and DXS 8043 ), which were derived from the ABI PRISM Linkage Mapping Set MD-10 (Applied Biosystems Inc., Foster City, CA, USA). Highly polymorphic microsatellite markers were selected for their high percentage of heterozygosity (70.5%-86%), their allele number, and their location on both Xp and Xq based on a Korean reference 11) . PCR amplification was performed under the following conditions: 95℃ for 2 minutes, then 35 cycles at 95℃ for 20 seconds, 58℃ for 40 seconds, 72℃ for 30 seconds, and 72℃ for 45 minutes 11) .…”

“…Highly polymorphic microsatellite markers were selected for their high percentage of heterozygosity (70.5%-86%), their allele number, and their location on both Xp and Xq based on a Korean reference 11) . PCR amplification was performed under the following conditions: 95℃ for 2 minutes, then 35 cycles at 95℃ for 20 seconds, 58℃ for 40 seconds, 72℃ for 30 seconds, and 72℃ for 45 minutes 11) . None of the 45,X patients had hidden X fragments detected using X chromosome microsatellites.…”