title: Comparative study of the linkage disequilibrium of an ENCODE region, chromosome 7p15, in Korean, Japanese, and Han Chinese samples.
abstract: The extent and pattern of linkage disequilibrium (LD) in the human genome provide important information for disease gene mapping. Previous studies have shown that LDs vary depending on chromosomal regions and populations. As the Asian samples of the International HapMap Project consisted of Japanese and Chinese populations, it was of interest whether we could use the HapMap data as a reference to carry out association studies of common complex diseases in a closely related population, such as Koreans. We have compared the LD and recombination patterns defined by single-nucleotide polymorphisms (SNPs) in ENCODE region ENm010, chromosome 7p15.2, in Korean, Japanese, and Chinese samples and further tested the robustness of tagSNPs among the Asian samples. We genotyped 792 SNPs in 500 kb (chromosome 7: 26699793-27199792, NCBI build 34) from 90 unrelated Koreans by fluorescence polarization detection and compared the data with Asian data from the HapMap project. Despite some differences in the position of high LD region boundaries, the overall patterns of LD were remarkably similar across the three samples, reflecting strong genetic affinities among them. Furthermore, the haplotype tag SNP transferability across the three samples was greater than 90%. Our results support the initial suggestion that the populations genotyped in the HapMap project might serve as reference populations for the selection of tagSNPs in association studies.
authors.affiliation: Department of Biochemistry and Molecular Biology, University of Ulsan College of Medicine, 388-1 Poongnap-Dong, Songpa-Gu, Seoul 138-736, Korea.
authors.forename: Jiyoung
authors.initials: J
authors.lastname: Lim
authors.forename: Young Joo
authors.initials: YJ
authors.lastname: Kim
authors.forename: Yongsook
authors.initials: Y
authors.lastname: Yoon
authors.forename: Soon Ok
authors.initials: SO
authors.lastname: Kim
authors.forename: Hyojin
authors.initials: H
authors.lastname: Kang
authors.forename: Jungsun
authors.initials: J
authors.lastname: Park
authors.forename: A Reum
authors.initials: AR
authors.lastname: Han
authors.forename: Bokghee
authors.initials: B
authors.lastname: Han
authors.forename: Burmseok
authors.initials: B
authors.lastname: Oh
authors.forename: Kyuchan
authors.initials: K
authors.lastname: Kimm
authors.forename: Bangwon
authors.initials: B
authors.lastname: Yoon
authors.forename: Kyuyoung
authors.initials: K
authors.lastname: Song
mesh_terms: D000483:Alleles; D044466:Asian People / Q000235:genetics*; D002897:Chromosomes, Human, Pair 7 / Q000235:genetics*; D005787:Gene Frequency; D014644:Genetic Variation; D015894:Genome, Human; D006239:Haplotypes; D006801:Humans; D015810:Linkage Disequilibrium; D020641:Polymorphism, Single Nucleotide