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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 |
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| 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 |
| Affiliation: | (1) Department of Medical Sciences, Ministry of Public Health, Center for International Cooperation, Foreign Affairs Section, 3rd Floor, Building 1, Nonthaburi, 11000, Thailand;(2) Department of Pathology, Faculty of Medicine, Ramathibodhi Hospital, Mahidol University, Bangkok, Thailand;(3) Endocrine unit, Department of Medicine, Faculty of Medicine, Ramathibodhi Hospital, Mahidol University, Bangkok, Thailand;(4) Department of Microbiology, Khon Kaen University, Khon Kaen, Thailand;(5) Department of Internal Medicine, Suratthani hospital, Suratthani, Thailand;(6) National Center for Genetic Engineering and Biotechnology, Pathumthani, Thailand;(7) Institute of Rheumatology, Tokyo Women’s Medical University, Tokyo, Japan;(8) Research Group for Personalized Medicine, SRC, RIKEN, Yokohama, Japan;(9) Laboratory of Molecular Medicine, Human Genome Center, Institute of Medical Science, University of Tokyo, Tokyo, Japan;(10) Medical Genetics and Molecular Medicine Unit, Department of Medicine, Faculty of Medicine, Ramathibodhi Hospital, Mahidol University, Bangkok, Thailand |
| 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. |
| Keywords: | Thai Thailand Allele frequency Linkage disequilibrium Hapmap TagSNP Transferability |
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