Genome Wide SNP Analysis for Inferring the Population Structure and Genetic Homogeneity of Koreans

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Study of genome-wide SNPs, mitochondrial DNA and Y-chromosomal DNA variation can provide a valuable information about the population structure and peopling of human populations. To explain a genetic …

Study of genome-wide SNPs, mitochondrial DNA and Y-chromosomal DNA variation can provide a valuable information about the population structure and peopling of human populations. To explain a genetic homogeneity of Koreans and population structure of Koreans and the East Asian populations, we analyzed 153 individuals from the Korea and 77 individuals from the East Asia at 46,559 common single-nucleotide polymorphic loci. The 137 CHB and 113 JPT individuals at 25,769 common SNPs from the International HapMap project were further analyzed to reveal the population structure of the East Asians. Principal Component analyses (PCA) and population differentiation () are examined. In the PCA test, the Jeju individuals were slightly different from other Koreans but their values were not significant. This reflect the genetic homogeneity of Korea population. In general, all the individual samples studied here were clustered into subset of ethnic origin according to their geographical location except Mongolians. Whole genome sequencing of Koreans and other population genome by next generation sequencing technology will provide great opportunity to understand the population expansion and peopling of Korea better.

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  • 1. ‫ొ׆‬ր෈‫ࢂڍ‬ு ୪ு   กఢ࣐  Â஼෉ஜ    Թࢳୢ߃ ൚ ,5 (FOPNF$MPVE 4NBMM $*$  ছ૷ਏ ছొ֜ ছొ۩ߦ   ۚ֝۩෈֗ ୀ઴ր෈۩෈ ঍ࡣր෈ऀ ‫ࢭڋي‬ଲૈଭր෈ୢվ ࢫ ‫ొ׆‬ր෈઴֜ী  ౦ْ వੲਏ ‫ْ֜ܛ‬ ۚ۩ߦ  ૬ઊ Basic Science Journal of Dankook University Vol.19 December 2013, ⛚#Ḟ
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  • 4. ‫ొ׆‬ր෈‫ࢂڍ‬ு ୪ு   0ᶣFSTᶣ0.05: not significantly differentiated; FSTᶤ0.25: significantly differentiated; FST=1:completelyisolated(WrightS,1978) 1 Chromosome; 2 SNPs fo rwhich p values less than 10 -3 are listed; 3 p values for the Cochran-Armitage trend test of genotype frequencies; 4 notavailable
  • 5. ‫ొ׆‬ր෈‫ࢂڍ‬ு ୪ு  
  • 6. ‫ొ׆‬ր෈‫ࢂڍ‬ு ୪ு   ૦ኞ⃶ᑺ [1] Cavalli-Sforza LL, Menozzi P and Piazza A (1994) The history and genography of human genes. Princeton University Press, Princeton. [2] Chen J, Zheng H, Bei JX, Sun L, Jia WH, Li T, Zhang F, Seielstad M, Zeng YX, Zhang X and Liu J (2009) Genetic structure of the Han Chinese population revealed by genome-wideSNP variation. Am. J. Hum. Genet. 85: 775-785. [3] Excoffier L. and Lischer HE (2010) Arlequin suite ver 3.5: A new series of programs to perform population genetics analyses under Linux and Windows. Mol. Ecol. Resour. 10: 564-567. [4] Friedlaender JS, Friedlaender FR, Reed FA, Kidd KK, Kidd JR, Chambers GK, Lea RA, Loo JH, Koki G, Hodgson JA, et al. (2008) The genetic structure of Pacific Islanders. PLoS Genet. 4: e19. [5] Han MS, Hong SB, Choi SK, Cho YH, Jin HJ, Kwak KD and Kim W (2002) Population Genetic Data on the Thirteen CODIS Short Tandem Repeat Loci in Koreans Korean J. Genet. 24: 83-87. [6] Hong SS, Suh JA, Chae JJ, Goh SH, Kim YS, Kim UK, Namkoong Y and Lee CC (1993) Frequency distribution of alleles at D1S80 and apo-B 3' VNTR loci in Korean populations. Mol. Cell. 3: 457-453. [7] Jakkula E, Rehnström K, Varilo T, Pietiläinen OP, Paunio T, Pedersen NL, deFaire U, Järvelin MR, Saharinen J, Freimer N, et al. (2008) The genome- wide patterns of variation expose significant substructure in a founder population. Am. J. Hum. Genet. 83: 787-794. [8] Jin HJ, Kwak KD, Hammer MF, Nakahori Y, Shinka T, Lee JW, Jin F, Jia X, Tyler-Smith C and Kim W (2003) Y-chromosomal DNA haplogroups and their implications for the dual origins of the Koreans. Hum. Genet. 114: 27-35. [9] Jin HJ, Kwak KD, Hong SB, Shin DJ, Han MS, Tyler-Smith C and Kim W (2006) Forensic genetic analysis of mitochondrial DNA hypervariable region I/IIsequences: an expanded Korean population database. Forensic Sci. Int. 158: 125-130. [10] Jin HJ, Tyler-Smith C and Kim W (2009) The peopling of Korea revealed by analyses of mitochondrial DNA and Y-chromosomal markers. PLoS One. 4: e4210. [11] Jin HJ, Kim KC and Kim W (2010) Genetic diversity of two haploid markers in the Udegey population from southeastern Siberia. Am. J. Phys. Anthropol. 142: 303-313. [12] Jung J, Kang H, Cho YS, Oh JH, Ryu MH, Chung HW, Seo JS, Lee JE, Oh B, Bhak J et al (2010) Gene flow between the Korean peninsula and its neighboring countries. PLoS ONE 5: e11855. [13] Karafet T, Xu L, Du R, Wang W, Feng S, Wells RS, Redd AJ, Zegura SL and Hammer MF (2001) Paternal population history of East Asia: sources, patterns, and microevolutionary processes. Am. J. Hum. Genet. 69: 615-628. [14] Kim YJ and Jin HJ (2012) Dissecting the genetic structure of Korean population using genome-wide SNP arrays. Genes Genom. 35: 355-363. [15] Kim W, Shin DJ, Harihara S and Kim YJ (2000) Y chromosomal DNA variation in east Asian populations and its potential for inferring the peopling of Korea. J. Hum. Genet. 45: 76-83. [16] Liu XG, Tan LJ, Lei SF, Liu YJ, Shen H, Wang L, Yan H, Guo YF, Xiong DH, Chen XD, et al. (2009) Genome-wide association and replication studies identified TRHR as an important gene for lean body mass. Am. J. Hum. Genet. 84: 418-23. [17] Nei M and Roychoudhury AK (1993) Evolutionary relationships of human populations on a global scale. Mol. Biol. Evol. 10: 927-943. [18] Price AL, Patterson NJ, Plenge RM, Weinblatt ME, Shadick NA and Reich D (2006) Principal components analysis corrects for stratification in genome-wide association studies. Nat. Genet. 38: 904-909. [19] Saha N and Tay JS (1992) Origin of the Koreans: a population genetic study. Am. J. Phys. Anthropol. 88: 27-36. [20] The International HapMap Consortium (2005) The International HapMap Project. Nature 426: 789-796. [21] The International HapMap Consortium (2007) A haplotype map of the human genome. Nature 437: 1299-1320.
  • 7. ‫ొ׆‬ր෈‫ࢂڍ‬ு ୪ு   Study of genome-wide SNPs, mitochondrial DNA and Y-chromosomal DNA variation can provide a valuable information about the population structure and peopling of human populations. To explain a genetic homogeneity of Koreans and population structure of Koreans and the East Asian populations, we analyzed 153 individuals from the Korea and 77 individuals from the East Asia at 46,559 common single-nucleotide polymorphic loci. The 137 CHB and 113 JPT individuals at 25,769 common SNPs from the International HapMap project were further analyzed to reveal the population structure of the East Asians. Principal Component analyses (PCA) and population differentiation ( ) are examined. In the PCA test, the Jeju individuals were slightly different from other Koreans but their values were not significant. This reflect the genetic homogeneity of Korea population. In general, all the individual samples studied here were clustered into subset of ethnic origin according to their geographical location except Mongolians. Whole genome sequencing of Koreans and other population genome by next generation sequencing technology will provide great opportunity to understand the population expansion and peopling of Korea better. [22] Wellcome Trust Case Control Consortium (2007) Genome-wide association study of 14,000 cases of seven common diseases and 3,000 shared controls. Nature 447: 661-678. [23] Wright S (1978) Evolution and the genetics of Population. Vol. 4. Variability Within and Among Natural Population. Univ. of Chicago Press, Chicago [24] Tian C, Kosoy R, Lee A, Ransom M, Belmont JW, Gregersen PK and Seldin MF (2008) Analysis of East Asia genetic substructure using genome- wide SNP arrays. PLoS One. 3: e3862 [25] Turner CG (1990) Major features of Sundadonty and Sinodonty, including suggestions about East Asian microevolution, population history, and late Pleistocene relationships with Australian aboriginals. Am. J. Phys. Anthropol. 82: 295-317. [26] Zhang XJ, Huang W, Yang S, Sun LD, Zhang FY, Zhu QX, Zhang FR, Zhang C, Du WH, Pu XM, et al. (2009) Psoriasis genome-wide association study identifies susceptibility variants within LCE gene cluster at 1q21. Nat. Genet. 42: 205-210.