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http://dx.doi.org/10.5808/GI.2014.12.1.42

Identification of Ethnically Specific Genetic Variations in Pan-Asian Ethnos  

Yang, Jin Ok (Korean BioInformation Center (KOBIC), Korea Research Institute of Bioscience and Biotechnology (KRIBB))
Hwang, Sohyun (Korean BioInformation Center (KOBIC), Korea Research Institute of Bioscience and Biotechnology (KRIBB))
Kim, Woo-Yeon (Bioinformatics Team, CSP R&D Center, Samsung SDS)
Park, Seong-Jin (Korean BioInformation Center (KOBIC), Korea Research Institute of Bioscience and Biotechnology (KRIBB))
Kim, Sang Cheol (Samsung Genome Institute, Samsung Medical Center)
Park, Kiejung (Korean BioInformation Center (KOBIC), Korea Research Institute of Bioscience and Biotechnology (KRIBB))
Lee, Byungwook (Korean BioInformation Center (KOBIC), Korea Research Institute of Bioscience and Biotechnology (KRIBB))
The HUGO Pan-Asian SNP Consortium (The HUGO Pan-Asian SNP Consortium)
Publication Information
Genomics & Informatics / v.12, no.1, 2014 , pp. 42-47 More about this Journal
Abstract
Asian populations contain a variety of ethnic groups that have ethnically specific genetic differences. Ethnic variants may be highly relevant in disease and human differentiation studies. Here, we identified ethnically specific variants and then investigated their distribution across Asian ethnic groups. We obtained 58,960 Pan-Asian single nucleotide polymorphisms of 1,953 individuals from 72 ethnic groups of 11 Asian countries. We selected 9,306 ethnic variant single nucleotide polymorphisms (ESNPs) and 5,167 ethnic variant copy number polymorphisms (ECNPs) using the nearest shrunken centroid method. We analyzed ESNPs and ECNPs in 3 hierarchical levels: superpopulation, subpopulation, and ethnic population. We also identified ESNP- and ECNP-related genes and their features. This study represents the first attempt to identify Asian ESNP and ECNP markers, which can be used to identify genetic differences and predict disease susceptibility and drug effectiveness in Asian ethnic populations.
Keywords
classification; DNA copy number variations; ethnic groups; genotype; single nucleotide polymorphism;
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1 Rusk N. Expanding HapMap. Nat Methods 2010;7:780-781.   DOI
2 Sebat J, Lakshmi B, Troge J, Alexander J, Young J, Lundin P, et al. Large-scale copy number polymorphism in the human genome. Science 2004;305:525-528.   DOI   ScienceOn
3 Park J, Hwang S, Lee YS, Kim SC, Lee D. SNP@Ethnos: a database of ethnically variant single-nucleotide polymorphisms. Nucleic Acids Res 2007;35:D711-D715.   DOI
4 Tibshirani R, Hastie T, Narasimhan B, Chu G. Diagnosis of multiple cancer types by shrunken centroids of gene expression. Proc Natl Acad Sci U S A 2002;99:6567-6572.   DOI   ScienceOn
5 Maglott D, Ostell J, Pruitt KD, Tatusova T. Entrez Gene: gene-centered information at NCBI. Nucleic Acids Res 2011; 39:D52-D57.   DOI
6 Kantola AK, Ryynänen MJ, Lhota F, Keski-Oja J, Koli K. Independent regulation of short and long forms of latent TGF-beta binding protein (LTBP)-4 in cultured fibroblasts and human tissues. J Cell Physiol 2010;223:727-736.
7 Glessner JT, Wang K, Cai G, Korvatska O, Kim CE, Wood S, et al. Autism genome-wide copy number variation reveals ubiquitin and neuronal genes. Nature 2009;459:569-573.   DOI   ScienceOn
8 Hong H, Xu L, Liu J, Jones WD, Su Z, Ning B, et al. Technical reproducibility of genotyping SNP arrays used in genome- wide association studies. PLoS One 2012;7:e44483.   DOI
9 Cordell HJ, Darlay R, Charoen P, Stewart A, Gullett AM, Lambert HJ, et al. Whole-genome linkage and association scan in primary, nonsyndromic vesicoureteric reflux. J Am Soc Nephrol 2010;21:113-123.   DOI   ScienceOn
10 Moen T, Hayes B, Nilsen F, Delghandi M, Fjalestad KT, Fevolden SE, et al. Identification and characterisation of novel SNP markers in Atlantic cod: evidence for directional selection. BMC Genet 2008;9:18.
11 Latter BD. Selection in finite populations with multiple alleles. 3. Genetic divergence with centripetal selection and mutation. Genetics 1972;70:475-490.
12 McCarroll SA, Altshuler DM. Copy-number variation and association studies of human disease. Nat Genet 2007;39(7 Suppl):S37-S42.   DOI   ScienceOn
13 Kehrer-Sawatzki H, Cooper DN. Copy number variation and disease: preface. Cytogenet Genome Res 2008;123:5-6.   DOI
14 Schrider DR, Hahn MW. Gene copy-number polymorphism in nature. Proc Biol Sci 2010;277:3213-3221.   DOI
15 HUGO Pan-Asian SNP Consortium, Abdulla MA, Ahmed I, Assawamakin A, Bhak J, Brahmachari SK, et al. Mapping human genetic diversity in Asia. Science 2009;326:1541-1545.   DOI   ScienceOn
16 Ngamphiw C, Assawamakin A, Xu S, Shaw PJ, Yang JO, Ghang H, et al. PanSNPdb: the Pan-Asian SNP genotyping database. PLoS One 2011;6:e21451.   DOI
17 Scheet P, Stephens M. A fast and flexible statistical model for large-scale population genotype data: applications to inferring missing genotypes and haplotypic phase. Am J Hum Genet 2006;78:629-644.   DOI   ScienceOn
18 Cooper GM, Mefford HC. Detection of copy number variation using SNP genotyping. Methods Mol Biol 2011;767:243-252.   DOI
19 Wong KK, deLeeuw RJ, Dosanjh NS, Kimm LR, Cheng Z, Horsman DE, et al. A comprehensive analysis of common copy-number variations in the human genome. Am J Hum Genet 2007;80:91-104.   DOI   ScienceOn
20 Claw KG, Tito RY, Stone AC, Verrelli BC. Haplotype structure and divergence at human and chimpanzee serotonin transporter and receptor genes: implications for behavioral disorder association analyses. Mol Biol Evol 2010;27:1518-1529.   DOI