Browse > Article

Characterization of Single Nucleotide Polymorphisms in 55 Disease-Associated Genes in a Korean Population  

Lee, Seung-Ku (Medical Genomics Lab, CHA Research Institute, Pochon CHA University)
Kim, Hyoun-Geun (Medical Genomics Lab, CHA Research Institute, Pochon CHA University)
Kang, Jason-J. (Macrogen, Inc.)
Oh, Won-Il (Medipost, Co.)
Oh, Berm-Seok (Center for Genome Science, NIH, KCDC)
Kwack, Kyu-Bum (Medical Genomics Lab, CHA Research Institute, Pochon CHA University)
Publication Information
Genomics & Informatics / v.5, no.4, 2007 , pp. 152-160 More about this Journal
Abstract
Most common diseases are caused by multiple genetic and environmental factors. Among the genetic factors, single nucleotide polymorphisms (SNPs) are common DNA sequence variations in individuals and can serve as important genetic markers. Recently, investigations of gene-based and whole genome-based SNPs have been applied to association studies for marker discovery. However, SNPs are so population-specific that the association needs to be verified. Fifty-five genes and 384 SNPs were selected based on association with disease. Genotypes of 337 SNPs in candidate genes were determined using Illumina Sentrix Array Matrix (SAM) chips by an allele-specific extension method in 364 unrelated Korean individuals. Allelic frequencies of SNPs were compared with those of other populations obtained from the International HapMap database. Minor allele frequencies, linkage disequilibrium blocks, tagSNPs, and haplotypes of functional candidate SNPs in 55 genetic disease-associated genes were provided. Our data may provide useful information for the selection of genetic markers for gene-based genetic disease-association studies of the Korean population.
Keywords
disease-associated gene; single nucleotide polymorphism (SNP); haplotype; linkage disequilibrium; korean;
Citations & Related Records
Times Cited By KSCI : 1  (Citation Analysis)
연도 인용수 순위
1 Thorisson, G.A., Smith, A.V., Krishnan, L., and Stein, L.D. (2005). The International HapMap Project Web site. Genome Res. 15, 1592-1593   DOI   ScienceOn
2 Thorisson, G.A. and Stein, L.D. (2003). The SNP Consortium website: past, present and future. Nucleic Acids Res. 31, 124-127   DOI   ScienceOn
3 Tishkoff, S.A., and Verrelli, B.C. (2003). Patterns of human genetic diversity: implications for human evolutionary history and disease. Annu. Rev. Genomics. Hum. Genet. 4, 293-340   DOI   ScienceOn
4 Weiss, S.T., Silverman, E.K., and Palmer, L.J. (2001). Case-control association studies in pharmacogenetics. Pharmacogenomics J. 1, 157-158   DOI   ScienceOn
5 Barrett, J.C., Fry, B., Maller, J., and Daly, M.J. (2005). Haploview: analysis and visualization of LD and haplotype maps. Bioinformatics 21, 263-265   DOI   ScienceOn
6 Ghoussaini, M., Meyre, D., Lobbens, S., Charpentier, G., Clement, K., Charles, M.A., Tauber, M., Weill, J., and Froguel, P. (2005). Implication of the Pro12Ala polymorphism of the PPAR-gamma 2 gene in type 2 diabetes and obesity in the French population. BMC Med. Genet. 6, 11   DOI   ScienceOn
7 Hirschhorn, J.N., Lohmueller, K., Byrne, E., and Hirschhorn, K. (2002). A comprehensive review of genetic association studies. Genet. Med. 4, 45-61   DOI   ScienceOn
8 In, K.H., Asano, K., Beier, D., Grobholz, J., Finn, P.W., Silverman, E.K., Collins, T., Fischer, A.R., Keith, T.P., Serino, K., Kim, S.W., De Sanctis, G.T., Yandava, C., Pillari, A., Rubin, P., Kemp, J., Israel, E., Busse, W., Ledford, D., Murray, J.J., Segal, A., Tinkleman, D., and Drazen, J.M. (1997). Naturally occurring mutations in the human 5-lipoxygenase gene promoter that modify transcription factor binding and reporter gene transcription. J. Clin. Invest. 99, 1130-1137   DOI   ScienceOn
9 Knight, J.C. (2003). Functional implications of genetic variation in non-coding DNA for disease susceptibility and gene regulation. Clin. Sci. (Lond) 104, 493-501   DOI   ScienceOn
10 Knight, J.C. (2005). Regulatory polymorphisms underlying complex disease traits. J. Mol. Med. 83, 97-109   DOI   ScienceOn
11 Sherry, S.T., Ward, M.H., Kholodov, M., Baker, J., Phan, L., Smigielski, E.M., and Sirotkin, K. (2001). dbSNP: the NCBI database of genetic variation. Nucleic Acids Res. 29, 308-311   DOI   ScienceOn
12 Hinds, D.A., Stuve, L.L., Nilsen, G.B., Halperin, E., Eskin, E., Ballinger, D.G., Frazer, K.A., and Cox, D.R. (2005). Whole-genome patterns of common DNA variation in three human populations. Science 307, 1072-1079   DOI   ScienceOn
13 Pritchard, J.K. and Cox, N.J. (2002). The allelic architecture of human disease genes: common disease-common variant...or not? Hum. Mol. Genet. 11, 2417-2423   DOI   ScienceOn
14 Kammerer, S., Roth, R.B., Reneland, R., Marnellos, G., Hoyal, C.R., Markward, N.J., Ebner, F., Kiechle, M., Schwarz-Boeger, U., Griffiths, L.R., Ulbrich, C., Chrobok, K., Forster, G., Praetorius, G.M., Meyer, P., Rehbock, J., Cantor, C. R., Nelson, M. R., and Braun, A. (2004). Large-scale association study identifies ICAM gene region as breast and prostate cancer susceptibility locus. Cancer Res. 64, 8906-8910   DOI   ScienceOn
15 Becker, K.G., Barnes, K.C., Bright, T.J., and Wang, S.A. (2004). The genetic association database. Nat. Genet. 36, 431-432   DOI   ScienceOn
16 Patil, N., Berno, A.J., Hinds, D.A., Barrett, W.A., Doshi, J.M., Hacker, C.R., Kautzer, C.R., Lee, D.H., Marjoribanks, C., McDonough, D.P., Nguyen, B.T., Norris, M.C., Sheehan, J.B., Shen, N., Stern, D., Stokowski, R.P., Thomas, D.J., Trulson, M.O., Vyas, K.R., Frazer, K.A., Fodor, S.P., and Cox, D.R. (2001). Blocks of limited haplotype diversity revealed by high-resolution scanning of human chromosome 21. Science 294, 1719-1723   DOI   ScienceOn
17 Lorentzon, M., Lorentzon, R., and Nordstrom, P. (2000). Vitamin D receptor gene polymorphism is associated with birth height, growth to adolescence, and adult stature in healthy caucasian men: a cross-sectional and longitudinal study. J. Clin. Endocrinol. Metab. 85, 1666-1670   DOI
18 Tanaka, T., Ikari, K., Furushima, K., Okada, A., Tanaka, H., Furukawa, K., Yoshida, K., Ikeda, T., Ikegawa, S., Hunt, S.C., Takeda, J., Toh, S., Harata, S., Nakajima, T., and Inoue, I. (2003). Genomewide linkage and linkage disequilibrium analyses identify COL6A1, on chromosome 21, as the locus for ossification of the posterior longitudinal ligament of the spine. Am. J. Hum. Genet. 73, 812-822   DOI   ScienceOn
19 Sachidanandam, R., Weissman, D., Schmidt, S.C., Kakol, J.M., Stein, L.D., Marth, G., Marth, G., Sherry, S., Mullikin, J.C., Mortimore, B.J., Willey, D.L., Hunt, S.E., Cole, C.G., Coggill, P.C., Rice, C.M., Ning, Z., Rogers, J., Bentley, D.R., Kwok, P.Y., Mardis, E.R., Yeh, R.T., Schultz, B., Cook, L., Davenport, R., Dante, M., Fulton, L., Hillier, L., Waterston, R.H., McPherson, J.D., Gilman, B., Schaffner, S., Van Etten, W.J., Reich, D., Higgins, J., Daly, M.J., Blumenstiel, B., Baldwin, J., Stange-Thomann, N., Zody, M.C., Linton, L., Lander, E.S., Altshuler, D., and International SNP Map Working Group. (2001). A map of human genome sequence variation containing 1.42 million single nucleotide polymorphisms. Nature 409, 928-933   DOI   ScienceOn
20 Uitterlinden, A.G., Fang, Y., Bergink, A.P., van Meurs, J.B., van Leeuwen, H. P., and Pols, H. A. (2002). The role of vitamin D receptor gene polymorphisms in bone biology. Mol. Cell. Endocrinol. 197, 15-21   DOI   ScienceOn
21 Gabriel, S.B., Schaffner, S.F., Nguyen, H., Moore, J.M., Roy, J., Blumenstiel, B., Higgins, J., DeFelice, M., Lochner, A., Faggart, M., Liu-Cordero, S.N., Rotimi, C., Adeyemo, A., Cooper, R., Ward, R., Lander, E.S., Daly, M.J., and Altshuler, D. (2002). The structure of haplotype blocks in the human genome. Science 296, 2225-2229   DOI   ScienceOn
22 Crawford, D.C., Carlson, C.S., Rieder, M.J., Carrington, D.P., Yi, Q., Smith, J.D., Eberle, M.A., Kruglyak, L., and Nickerson, D.A. (2004). Haplotype diversity across 100 candidate genes for inflammation, lipid metabolism, and blood pressure regulation in two populations. Am. J. Hum. Genet. 74, 610-622   DOI   ScienceOn
23 Ozaki, K., Inoue, K., Sato, H., Iida, A., Ohnishi, Y., Sekine, A., Sato, H., Odashiro, K., Nobuyoshi, M., Hori, M., Nakamura, Y., and Tanaka, T. (2004). Functional variation in LGALS2 confers risk of myocardial infarction and regulates lymphotoxin-alpha secretion in vitro. Nature 429, 72-75   DOI   ScienceOn
24 Cardon, L.R., and Abecasis, G.R. (2003). Using haplotype blocks to map human complex trait loci. Trends Genet. 19, 135-140   DOI   ScienceOn
25 Knight, J.C., Keating, B.J., and Kwiatkowski, D.P. (2004). Allele-specific repression of lymphotoxin-alpha by activated B cell factor-1. Nat. Genet. 36, 394-399   DOI   ScienceOn
26 Fan, J.B., Oliphant, A., Shen, R., Kermani, B.G., Garcia, F., Gunderson, K.L., Hansen, M., Steemers, F., Butler, S.L., Deloukas, P., Galver, L., Hunt, S., McBride, C., Bibikova, M., Rubano, T., Chen, J., Wickham, E., Doucet, D., Chang, W., Campbell, D., Zhang, B., Kruglyak, S., Bentley, D., Haas, J., Rigault, P., Zhou, L., Stuelpnagel, J., and Chee, M.S. (2003). Highly parallel SNP genotyping. Cold Spring Harb. Symp. Quant. Biol. 68, 69-78
27 Cargill, M., Altshuler, D., Ireland, J., Sklar, P., Ardlie, K., Patil, N., Shaw, N., Lane, C.R., Lim, E.P., Kalyanaraman, N., Nemesh, J., Ziaugra, L., Friedland, L., Rolfe, A., Warrington, J., Lipshutz, R., Daley, G.Q., and Lander, E.S. (1999). Characterization of single-nucleotide polymorphisms in coding regions of human genes. Nat. Genet. 22, 231-238   DOI   ScienceOn
28 Wilson, A.G., Symons, J.A., McDowell, T.L., McDevitt, H.O., and Duff, G.W. (1997). Effects of a polymorphism in the human tumor necrosis factor alpha promoter on transcriptional activation. Proc. Natl. Acad. Sci. U S A 94, 3195-3199
29 Kiel, D.P., Myers, R.H., Cupples, L.A., Kong, X.F., Zhu, X.H., Ordovas, J., Schaefer, E.J., Felson, D.T., Rush, D., Wilson, P.W., Eisman, J.A., and Holick, M.F. (1997). The BsmI vitamin D receptor restriction fragment length polymorphism (bb) influences the effect of calcium intake on bone mineral density. J. Bone Miner Res. 12, 1049-57   DOI   ScienceOn
30 Jung, H.Y., Park, J.S., Park, Y.J., Kim, Y.J., Kimm, K.C., and Koh, I.S. (2004). HapAnalyzer: Minimum Haplotype Analysis System for Association Studies. Genomics & Informatics 2, 107-109
31 Skoog, T., van't Hooft, F. M., Kallin, B., Jovinge, S., Boquist, S., Nilsson, J., Eriksson, P., and Hamsten, A. (1999). A common functional polymorphism (C→A substitution at position -863) in the promoter region of the tumour necrosis factor-alpha (TNF-alpha) gene associated with reduced circulating levels of TNF-alpha. Hum. Mol. Genet. 8, 1443-1449   DOI   ScienceOn