Genomics & Informatics

Korea Genome Organization (한국유전체학회)
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Development of KHapmap Browser using DAS for Korean HapMap Research

  • Published : 2008.06.30
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Abstract

The Korean HapMap Project has been carried out for the last 5 years since it started in June, 2003. The project generated data for a sum of 1,764,000 Korean SNPs and formally registered the data to the dbSNP of NCBI (The dbSNP website. 2008). We have developed a series of software programs for association studies as well as for the comparison and analysis of Korean HapMap data with four other populations (CEPH, Yoruba, Han Chinese, and Japanese populations). The KHapmap Browser was developed and integrated to provide haplotype retrieval and comparative study tools of human ethnicities for comprehensive disease association studies (http://www.khapmap.org). On that basis, GBrowse was adopted in the KHapmap Browser for inherent Korean genetic data, and a provision of extended services was pledged with the distributed sequence annotation system (DAS). The dynamic linking service of the KHapmap Browser to other tools in our intranetwork environment provides many enhanced functions over GBrowse without DAS. KHapmap Browser is expected to be an invaluable tool for the study of Korean and international Hapmap data.

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References

  1. Abecasis, G.R., Noguchi, E., Heinzmann, A., Traherne, J.A., Bhattacharyya, S., et al. (2001). Extent and distribution of linkage disequilibrium in three genome regions. Am. J. Hum. Genet. 68, 191-197. https://doi.org/10.1086/316944
  2. 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. https://doi.org/10.1093/bioinformatics/bth457
  3. Berners-Lee, T., Hendler, J., and Lassila, O. (2001). The Semantic Web. Scientific American Magazine.
  4. Mungall, C.J., Misra, S., Berman, B.P., Carlson, J., Frise, E., Harris, N., Marshall, B., Shu, S., Kaminker, J.S., Prochnik, S.E., Smith, C.D., Smith, E., Tupy, J.L., Wiel, C., Rubin, G.M., and Lewis, S.E. (2002). An integrated computational pipeline and database to support whole-genome sequence annotation. Genome Biology 3, research0081.1-0081.11 https://doi.org/10.1186/gb-2002-3-12-research0081
  5. Daly, M.J., Rioux, J.D., Schaffner, S.F., Hudson, T.J., and Lander, E.S. (2001). High resolution haplotype structure in the human genome. Nat. Genet. 29, 229-232. https://doi.org/10.1038/ng1001-229
  6. Dowell, R.D., Jokerst, R.M., Day, A., Eddy, S.R., and Stein, L. (2001). The distributed annotation system. BMC Bioinformatics 2, 7. https://doi.org/10.1186/1471-2105-2-7
  7. Gabriel, S.B., Schaffner, S.F., Nguyen, H., Moore, J.M., Roy, J., Blumenstiel, B., Higgins, J., De-Felice, 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. https://doi.org/10.1126/science.1069424
  8. Kang, H., Choi, K.O., Kim, B.D., Kim, S., and Kim, Y.J. (2005). FESD: a functional element SNPs database in human. Nucleic Acids Res. 33, D518-D522. https://doi.org/10.1093/nar/gki082
  9. Kim, H.J., Kim, I.H., Shin, K.H., Park, Y.K., Kang, H., and Kim, Y.J. (2007). FESD II: a revised functional element SNP database of human ethnicities. Genomics & Informatics 5, 188-193.
  10. Kuhn, R.M., Karolchik, D., Zweig, A.S., Trumbower, H., Thomas, D.J., Thakkapallayil, A., Sugnet, C.W., Stanke, M., Smith, K.E., Siepel, A., Rosenbloom, K.R., Rhead, B., Raney, B.J., Pohl, A., Pedersen, J.S., Hsu, F., Hinrichs, A.S., Harte, R.A., Diekhans, M., Clawson, H., Bejerano, G., Barber, G.P., Baertsch, R., Haussler, D., and Kent, W.J. (2007). The UCSC genome browser database: update 2007. Nucleic Acids Res. 35, D668-673. https://doi.org/10.1093/nar/gkl928
  11. Lee, J.E., Jang, H.Y., Kim, S., Yoo, Y.K., Hwang, J.J., Jun, H.J., Lee, K., Son, O., Yang, J.M., Ahn, K.S., Kim, E., Lee, H.W., Song, K., Kim, H.L., Lee, S.G., Yoon, Y., Kimm, K., Han, B.G., Oh, B., Kim, C.B., Jin, H., Choi, K.O., Kang, H., and Kim, Y.J. (2008). Chromosome 22 LD map comparison between Korean and other populations. Genomics & Informatics 6, 18-28. https://doi.org/10.5808/GI.2008.6.1.018
  12. Olason, P.I. (2005). Integrating protein annotation resources through the Distributed Annotation System. Nucleic Acids Res. 33, W468-470. https://doi.org/10.1093/nar/gki463
  13. Prlic, A., Down, T.A., Kulesha, E., Finn, R.D., Kahari, A., and Hubbard, T.J. (2007). Integrating sequence and structural biology with DAS. BMC Bioinformatics 8, 333. https://doi.org/10.1186/1471-2105-8-333
  14. Redon, R., Ishikawa, S., Fitch, K.R., Feuk, L., Perry, G.H., Andrews, T.D., Fiegler, H., et al. (2006). Global variation in copy number in the human genome. Nature 444, 444-454. https://doi.org/10.1038/nature05329
  15. Reich, D.E., Cargill, M., Bolk, S., Ireland, J., Sabeti, P.C., Richter, D.J., Lavery, T., Kouyoumjian, R., Farhadian, S.F., Ward, R., and Lander, E.S. (2001). Linkage disequilibrium in the human genome. Nature 411, 199-204. https://doi.org/10.1038/35075590
  16. 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
  17. Stein, L., Sternberg, P., Durbin, R., Thierry-Mieg, J., and Spieth, J. (2000). WormBase: network access to the genome and biology of Caenorhabditis elegans. Nucleic Acids Res. 28, 82-86. https://doi.org/10.1093/nar/28.18.e82
  18. Stein, L.D., and the GMOD development team. (2008). GBrowse Configuration HOWTO.
  19. Subramaniam, S. (1998). The Biology Workbench--a seamless database and analysis environment for the biologist. Proteins 32, 1-2. https://doi.org/10.1002/(SICI)1097-0134(19980701)32:1<1::AID-PROT1>3.0.CO;2-Q
  20. Thorisson, G.A., Smith, A.V., Krishnan, L., and Stein, L.D. (2005). The International HapMap Project Web site. Genome Research 15, 1591-1593.
  21. The dbSNP web site. (2008). http://www.ncbi.nlm.nih.gov/projects/SNP
  22. The International HapMap web site. (2008). http://www.hapmap.org
  23. The International HapMap Consortium. (2007). A second generation human haplotype map of over 3.1 million SNPs. Nature 449, 851-861. https://doi.org/10.1038/nature06258
  24. The ApiDB/EuPathDB Project Team. (2008). The PlasmoDB web site. http://www.plasmodb.org/plasmo
  25. The Department of Genetics and Genomic Biology. (2008). http://projects.tcag.ca/variation/cgi-bin/gbrowse/hg18.
  26. The ENCODE Project Consortium. (2007). Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project. Nature 447, 799-816. https://doi.org/10.1038/nature05874
  27. The FlyBase web site. (2008). http://flybase.net
  28. The Perlegen Sciences. (2008). http://genome.perlegen.com/browser/index_v2.html
  29. The WormBase web site. (2008). http://www.wormbase.org.

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