Comparative study of the linkage disequilibrium of an ENCODE region, chromosome 7p15, in Korean, Japanese, and Han Chinese samples

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...

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Bibliographic Details
Published in:Genomics (San Diego, Calif.) Calif.), 2006-03, Vol.87 (3), p.392-398
Main Authors: Lim, Jiyoung, Kim, Young Joo, Yoon, Yongsook, Kim, Soon Ok, Kang, HyoJin, Park, Jungsun, Han, A. Reum, Han, Bokghee, Oh, Burmseok, Kimm, Kyuchan, Yoon, Bangwon, Song, Kyuyoung
Format: Article
Language:English
Subjects:
7p15.2
Alleles
Asian Continental Ancestry Group - genetics
Biological and medical sciences
Chinese
Chromosomes, Human, Pair 7 - genetics
Classical genetics, quantitative genetics, hybrids
Comparison
ENCODE region
Fundamental and applied biological sciences. Psychology
Gene Frequency
Genes. Genome
Genetic Variation
Genetics of eukaryotes. Biological and molecular evolution
Genome, Human
Haplotype
Haplotypes
HapMap
Humans
Japanese
Korean
Linkage Disequilibrium
Methods, theories and miscellaneous
Molecular and cellular biology
Molecular genetics
Polymorphism, Single Nucleotide
tagSNP
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Summary: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 [The International HapMap Consortium, The International HapMap Project, Nature 426 (2003) 789–796. [1]].
ISSN:0888-7543
1089-8646
DOI:10.1016/j.ygeno.2005.11.002