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Please use this identifier to cite or link to this item: http://repository.li.mahidol.ac.th/dspace/handle/123456789/22974
Title: Similarity of the allele frequency and linkage disequilibrium pattern of single nucleotide polymorphisms in drug-related gene loci between Thai and northern East Asian populations: Implications for tagging SNP selection in Thais
Authors: Surakameth Mahasirimongkol
Wasun Chantratita
Somying Promso
Ekawat Pasomsab
Natini Jinawath
Wallaya Jongjaroenprasert
Viraphong Lulitanond
Phanida Krittayapoositpot
Sissades Tongsima
Pathom Sawanpanyalert
Naoyuki Kamatani
Yusuke Nakamura
Thanyachai Sura
Thailand Ministry of Public Health
Mahidol University
Khon Kaen University
Suratthani Hospital
Thailand National Center for Genetic Engineering and Biotechnology
Tokyo Women's Medical University
Riken
Institute of Medical Science The University of Tokyo
Keywords: Biochemistry, Genetics and Molecular Biology;Medicine
Issue Date: 1-Oct-2006
Citation: Journal of Human Genetics. Vol.51, No.10 (2006), 896-904
Abstract: The similarity of the marker allele frequency and linkage disequilibrium structure between two populations are major factors for the determination of the transferability and efficiency of haplotype tagging SNP derived from one population to use for an indirect association study in another population. To prove the similarity between northern East Asian populations in Hapmap and Thais, 861 SNP in 166 drug-related genes shared between Thais, Han Chinese and Japanese were analyzed for their correlation statistics. Allele frequency, Fst statistics and linkage disequilibrium statistics (r 2) showed a high correlation between these populations. TagSNP sets derived by an aggressive tagging algorithm from these 861 SNP in Japanese and Chinese were used to test the coverage of East Asia-derived tagSNP in Thais. TagSNP derived from Japanese and Chinese are comparable in the percentage of coverage of the alleles captured with tagSNP at r 2≥0.8 (93% vs. 93%) in these drug-related gene loci. Additional tagSNP sets derived from the combination of Japanese- and Chinese-derived tagging SNP sets were used to test the coverage in Thais. The later set improved the percentage of coverage of alleles captured with tagSNP at r 2≥0.8-98% for these sites. High similarity between Thais and northern East Asian allele frequency and linkage disequilibrium statistics supported that tagSNPs derived from the northern East Asian population should be useful for an indirect association study in Thais. The combination of non-overlapping Japanese derived tagSNP and Chinese-derived tagSNP improved the percentage of genomic coverage in Thais, at least in these drug-related gene loci. © 2006 The Japan Society of Human Genetics and Springer.
URI: https://www.scopus.com/inward/record.uri?partnerID=HzOxMe3b&scp=33749080794&origin=inward
http://repository.li.mahidol.ac.th/dspace/handle/123456789/22974
ISSN: 14345161
Appears in Collections:Scopus 2006-2010

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