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

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Title
Comparative study of the linkage disequilibrium of an ENCODE region, chromosome 7p15, in Korean, Japanese, and Han Chinese samples
Author(s)
J Lim; Young Joo Kim; Y Yoon; S O Kim; Hyojin Kang; Jungsun Park; A Reum Han; B Han; B Oh; K Kimm; B Yoon; K Song
Bibliographic Citation
Genomics, vol. 87, no. 3, pp. 392-398
Publication Year
2006
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 [The International HapMap Consortium, The International HapMap Project, Nature 426 (2003) 789-796. [1]].
Keyword
7p15.2ChinesecomparisonENCODE regionhaplotypeHapMapJapaneseKoreanLDtagSNP
ISSN
0888-7543
Publisher
Elsevier
DOI
http://dx.doi.org/10.1016/j.ygeno.2005.11.002
Type
Article
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1. Journal Articles > Journal Articles
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