Characterization of 458 single nucleotide polymorphisms of disease candidate genes in the Korean population

Abstract

Single nucleotide polymorphisms (SNPs) are considered as very promising genetic markers for complex disease gene hunting. However, it has been demonstrated that there are significant ethnic differences in genetic variations. In order to investigate the genetic variations in the Korean population and their ethnic differences, a large number of SNPs of 161 disease candidate genes were collected from a publicly available SNP database and then tested for the distribution of allele frequency in the Korean population. Of all 458 SNPs tested, approximately 43.9% were polymorphic in the Korean population, whereas 44.5% were monomorphic. The remaining 11.6% were failed in the test. Significant differences have been observed when SNP allele frequency pattern of Koreans was compared with those of Caucasians and Africans, whereas this pattern was highly similar between Korean and Japanese populations. Our data indicate that although many of the SNPs available in publicly available database, especially coding-region SNPs (cSNPs), can be used as informative genetic markers for disease association studies, an extensive verification of public SNPs in a particular population studied should be undertaken prior to their association studies.

Gene-Based Single Nucleotide Polymorphisms and Linkage Disequilibrium Patterns of 29 Asthma Candidate Genes in the Chromosome 5q31–33 Region in Koreans

“…The data suggest that the genetic origins of the Korean population are distinct from other ethnic populations, but very similar to the Japanese. The results reconfirm that extensive verification of public SNPs in a particular population is required prior to association studies, as reported previously [20]. …”

Association between Bone Mineral Density and LDL Receptor-Related Protein 5 Gene Polymorphisms in Young Korean Men

“…Because previously reported restriction enzyme analyses of polymerase chain reaction (PCR) were not available, genotyping for A400V, V667M, R1036Q and A1525V polymorphisms was performed by SNP-IT™ assays using the SNP stream 25K™ System (Orchid Biosciences, New Jersey, U.S.A.) (22). Briefly, the genomic DNA region spanning the polymorphic site was PCR-amplified using one phosphothiolated primer and one regular PCR primer.…”

Identification of single nucleotide polymorphisms in the tumor necrosis factor (TNF) and TNF receptor superfamily in the Korean population

“…SNP Genotyping for Allele Frequency SNP genotyping was performed by SNP-IT assays with the SNPstream 25K System (Orchid Biosciences, Princeton, New Jersey) as previously described [10]. Briefly, the genomic DNA region spanning the polymorphic site was PCR-amplified with one phosphothiolated primer and one regular PCR primer.…”