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Korean Society for Biochemistry and Molecular Biology (생화학분자생물학회)
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KAREBrowser: SNP database of Korea Association REsource Project

  • Hong, Chang-Bum (Division of Structural and Functional Genomics, Center for Genome Science, National Institute of Health) ;
  • Kim, Young-Jin (Division of Structural and Functional Genomics, Center for Genome Science, National Institute of Health) ;
  • Moon, Sang-Hoon (Division of Structural and Functional Genomics, Center for Genome Science, National Institute of Health) ;
  • Shin, Young-Ah (Division of Structural and Functional Genomics, Center for Genome Science, National Institute of Health) ;
  • Cho, Yoon-Shin (Division of Structural and Functional Genomics, Center for Genome Science, National Institute of Health) ;
  • Lee, Jong-Young (Division of Structural and Functional Genomics, Center for Genome Science, National Institute of Health)
  • Received : 2011.08.05
  • Accepted : 2011.10.05
  • Published : 2012.01.31
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Abstract

The International HapMap Project and the Human Genome Diversity Project (HGDP) provide plentiful resources on human genome information to the public. However, this kind of information is limited because of the small sample size in both databases. A Genome-Wide Association Study has been conducted with 8,842 Korean subjects as a part of the Korea Association Resource (KARE) project. In an effort to build a publicly available browsing system for genome data resulted from large scale KARE GWAS, we developed the KARE browser. This browser provides users with a large amount of single nucleotide polymorphisms (SNPs) information comprising 1.5 million SNPs from population-based cohorts of 8,842 samples. KAREBrowser was based on the generic genome browser (GBrowse), a web-based application tool developed for users to navigate and visualize the genomic features and annotations in an interactive manner. All SNP information and related functions are available at the web site http://ksnp.cdc. go.kr/karebrowser/.

Keywords

References

  1. Thorisson, G. A. and Stein, L. D. (2003) The SNP Consortium website: past, present and future. Nucleic Acids Res. 31, 124-127. https://doi.org/10.1093/nar/gkg052
  2. International HapMap Consortium. (2003) The International HapMap Project. Nature 426, 789-796. https://doi.org/10.1038/nature02168
  3. Kato, N., Takeuchi, F., Tabara, Y., Kelly, T. N., Go, M. J., Sim, X., Tay, W. T., Chen, C. H., Zhang, Y., Yamamoto, K., Katsuya, T., Yokota, M., Kim, Y. J., Ong, R. T., Nabika, T., Gu, D., Chang, L. C., Kokubo, Y., Huang, W., Ohnaka, K., Yamori, Y., Nakashima, E., Jaquish, C. E., Lee, J. Y., Seielstad, M., Isono, M., Hixson, J. E., Chen, Y. T., Miki, T., Zhou, X., Sugiyama, T., Jeon, J. P., Liu, J. J., Takayanagi, R., Kim, S. S., Aung, T., Sung, Y. J., Zhang, X., Wong, T. Y., Han, B. G., Kobayashi, S., Ogihara, T., Zhu, D., Iwai, N., Wu, J. Y., Teo, Y. Y., Tai, E. S., Cho, Y. S. and He, J. (2011) Meta-analysis of genome-wide association studies identifies common variants associated with blood pressure variation in east Asians. Nat. Genet. 43, 531-538. https://doi.org/10.1038/ng.834
  4. Soranzo, N., Spector, T. D., Mangino, M., Kuhnel, B., Rendon, A., Teumer, A., Willenborg, C., Wright, B., Chen, L., Li, M., Salo, P., Voight, B. F., Burns, P., Laskowski, R. A., Xue, Y., Menzel, S., Altshuler, D., Bradley, J. R., Bumpstead, S., Burnett, M. S., Devaney, J., Doring, A., Elosua, R., Epstein, S. E., Erber, W., Falchi, M., Garner, S. F., Ghori, M. J., Goodall, A. H., Gwilliam, R., Hakonarson, H. H., Hall, A. S., Hammond, N., Hengstenberg, C., Illig, T., Konig, I. R., Knouff, C. W., McPherson, R., Melander, O., Mooser, V., Nauck, M., Nieminen, M. S., O'Donnell, C. J., Peltonen, L., Potter, S. C., Prokisch, H., Rader, D. J., Rice, C. M., Roberts, R., Salomaa, V., Sambrook, J., Schreiber, S., Schunkert, H., Schwartz, S. M., Serbanovic-Canic, J., Sinisalo, J., Siscovick, D. S., Stark, K., Surakka, I., Stephens, J., Thompson, J. R., Volker, U., Volzke, H., Watkins, N. A., Wells, G. A., Wichmann, H. E., Van Heel, D. A., Tyler-Smith, C., Thein, S. L., Kathiresan, S., Perola, M., Reilly, M. P., Stewart, A. F., Erdmann, J., Samani, N. J., Meisinger, C., Greinacher, A., Deloukas, P., Ouwehand, W. H. and Gieger, C. (2009) A genome-wide meta-analysis identifies 22 loci associated with eight hematological parameters in the HaemGen consortium. Nat. Genet. 41, 1182-1190. https://doi.org/10.1038/ng.467
  5. Kim, Y. J., Go, M. J., Hu, C., Hong, C. B., Kim, Y. K., Lee, J. Y., Hwang, J. Y., Oh, J. H., Kim, D. J., Kim, N. H., Kim, S., Hong, E. J., Kim, J. H., Min, H., Kim, Y., Zhang, R., Jia, W., Okada, Y., Takahashi, A., Kubo, M., Tanaka, T., Kamatani, N., Matsuda, K., Park, T., Oh, B., Kimm, K., Kang, D., Shin, C., Cho, N. H., Kim, H. L., Han, B. G. and Cho, Y. S. (2011) Large-scale genome-wide association studies in east Asians identify new genetic loci influencing metabolic traits. Nat. Genet. 43, 990-995. https://doi.org/10.1038/ng.939
  6. Marchini, J., Howie, B., Myers, S., McVean, G. and Donnelly, P. (2007) A new multipoint method for genome-wide association studies by imputation of genotypes. Nat. Genet. 39, 906-913. https://doi.org/10.1038/ng2088
  7. [Li, Y., Willer, C., Sanna, S. and Abecasis, G. (2009) Genotype imputation. Annu Rev Genomics Hum. Genet. 10, 387-406. https://doi.org/10.1146/annurev.genom.9.081307.164242
  8. Koike, A., Nishida, N., Inoue, I., Tsuji, S. and Tokunaga, K. (2009) Genome-wide association database developed in the Japanese Integrated Database Project. J. Hum. Genet. 54, 543-546. https://doi.org/10.1038/jhg.2009.68
  9. Stein, L. D., Mungall, C., Shu, S., Caudy, M., Mangone, M., Day, A., Nickerson, E., Stajich, J. E., Harris, T. W., Arva, A. and Lewis, S. (2002) The generic genome browser: a building block for a model organism system database. Genome Res. 12, 1599-1610. https://doi.org/10.1101/gr.403602
  10. Cho, Y. S., Go, M. J., Kim, Y. J., Heo, J. Y., Oh, J. H., Ban, H. J., Yoon, D., Lee, M. H., Kim, D. J., Park, M., Cha, S. H., Kim, J. W., Han, B. G., Min, H., Ahn, Y., Park, M. S., Han, H. R., Jang, H. Y., Cho, E. Y., Lee, J. E., Cho, N. H., Shin, C., Park, T., Park, J. W., Lee, J. K., Cardon, L., Clarke, G., McCarthy, M. I., Lee, J. Y., Oh, B. and Kim, H. L. (2009) A large-scale genome- wide association study of Asian populations uncovers genetic factors influencing eight quantitative traits. Nat. Genet. 41, 527-534. https://doi.org/10.1038/ng.357
  11. Purcell, S., Neale, B., Todd-Brown, K., Thomas, L., Ferreira, M. A., Bender, D., Maller, J., Sklar, P., de Bakker, P. I., Daly, M. J. and Sham, P. C. (2007) PLINK: a tool set for whole-genome association and population-based linkage analyses. Am. J. Hum. Genet. 81, 559-575. https://doi.org/10.1086/519795

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