Linkage disequilibria of Korean single nucleotide polymorphisms

Abstract

The size of linkage disequilibrium (LD) blocks has been a subject of considerable debate as to whether it is now possible to use LD to map genes that cause diseases. There were little systematic data for LD block size in any ethnic populations. In this study, LD of Korean single nucleotide polymorphisms (SNP) have been determined in several chromosomal loci. Firstly, LD values (lD’l) were determined in a short range. The allele frequencies of 9 SNPs spanning approximately 6 kb in the APC gene were measured with 96 Korean samples, but one of the 9 SNPs included in NCBI dbSNP was not polymorphic in the tested Koreans. All 28 LD values were determined from the data of 8 SNPs. Although the linkage disequilibrium was not simply inverse-correlated with distance between SNPs, closely located SNPs were very tightly linked and LD value was still high. Although the total number of possible haplotypes of 8 SNPs is 256 ($2^8$), there are only 7 haplotypes because some SNPs are 100% linked. Secondly, LD’s were measured in longer ranges, and were compared with data of other ethnic groups, Americans of north-European descent, Swedish and Nigerians. Five SNPs around the ACVR2B gene were targeted. Two of the five sites were not polymorphic among Koreans, and only two LD values could be obtained. LD block of Koreans in the ACVR2B gene in Korean was about 120 kb, similar to those of the other ethnic groups. LD block of Koreans in the PCI gene was approximately 60 kb, slightly larger than those of the other ethnic groups. The results suggested that LD mapping would likely be practical in the Korean population.