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Identification and Characterization of Human Genes Targeted by Natural Selection

  • Ryu, Ha-Jung (Asan Institute for Life Sciences, University of Ulsan College of Medicine) ;
  • Kim, Young-Joo (KRIBB) ;
  • Park, Young-Kyu (KRIBB) ;
  • Kim, Jae-Jung (Asan Institute for Life Sciences, University of Ulsan College of Medicine) ;
  • Park, Mi-Young (Asan Institute for Life Sciences, University of Ulsan College of Medicine) ;
  • Seo, Eul-Ju (Genome Research Center for Birth Defects and Genetic Disorders, Asan Medical Center, University of Ulsan College of Medicine) ;
  • Yoo, Han-Wook (Genome Research Center for Birth Defects and Genetic Disorders, Asan Medical Center, University of Ulsan College of Medicine) ;
  • Park, In-Sook (Genome Research Center for Birth Defects and Genetic Disorders, Asan Medical Center, University of Ulsan College of Medicine) ;
  • Oh, Berm-Seok (Department of Biomedical Engineering, Kyung Hee University School of Medicine) ;
  • Lee, Jong-Keuk (Asan Institute for Life Sciences, University of Ulsan College of Medicine)
  • Published : 2008.12.31

Abstract

The human genome has evolved as a consequence of evolutionary forces, such as natural selection. In this study, we investigated natural selection on the human genes by comparing the numbers of nonsynonymous (NS) and synonymous (S) mutations in individual genes. We initially collected all coding SNP data of all human genes from the public dbSNP. Among the human genes, we selected 3 different selection groups of genes: positively selected genes (NS/S${\geq}$3), negatively selected genes (NS/S${\leq}$1/3) and neutral selection genes (0.9

Keywords

single nucleotide polymorphism (SNP);natural selection;disease genes;ethnicity

References

  1. Vitkup, D., Sander, C., and Church, G.M. (2003). The amino- acid mutational spectrum of human genetic disease. Genome Biology 4, R72 https://doi.org/10.1186/gb-2003-4-11-r72
  2. The International HapMap Consortium. (2005). A haplotype map of the human genome. Nature 437, 1299-1320 https://doi.org/10.1038/nature04226
  3. Salamon, H., Klitz, W., Easteal, S., Gao, X., Erlich, H.A., Fernandez-Vina, M., Trachtenberg, E.A., McWeeney, S.K., Nelson, M.P., and Thomson, G. (1999). Evolution of HLA class II molecules: allelic and amino acid site variability across populations. Genetics 152, 393-400
  4. The International HapMap Consortium. (2003). The International HapMap Project. Nature 426, 789-796 https://doi.org/10.1038/nature02168
  5. Halliburton, R. (2004). Introduction to Population (NJ, USA: Pearson Education Inc.)
  6. Arbiza, L., Duchi, S., Montaner, D., Burguest, J., Pantoja- Uceda, D., Pineda-Lucena, A., Dopazo, J., and Dopazo, H. (2006). Selective pressures at a codon-level predict deleterious mutations in human disease genes. J. Mol. Biol. 358, 1390-1404 https://doi.org/10.1016/j.jmb.2006.02.067
  7. Bamshad, M., and Wooding, S.P. (2003). Signatures of natural selection in the human genome. Nat. Rev. Genet. 4, 99-111 https://doi.org/10.1038/nrg999
  8. Collin, G.B., Marshall, J.D., Ikeda, A., So, W.V., Russell- Eggitt, I., Maffei, P., Beck, S., Boerkoel, C.F., Sicolo, N., Martin, M., Nishina, P.M., and Naggert, J.K. (2002). Mutations in ALMS1 cause obesity, type 2 diabetes and neurosensory degeneration in Alstrom syndrome. Nat. Genet. 31, 74-78 https://doi.org/10.1038/ng867
  9. Bustamante, C.D., Fledel-Alon, A., Williamson, S., Nielsen, R., Hubisz, M.T., Glanowski, S., Tanenbaum, D.M., White, T.J., Sninsky, J.J., Hernandez, R.D., Civello, D., Adams, M.D., Cargill, M., and Clark, A.G. (2005). Natural selection on protein-coding genes in the human genome. Nature 437, 1153-1157 https://doi.org/10.1038/nature04240
  10. Biswas, S., and Akey, J.M. (2006). Genomic insights into positive selection. Trends Genet. 22, 437-446 https://doi.org/10.1016/j.tig.2006.06.005
  11. Bersaglieri, T., Sabeti, P.C., Patterson, N., Vanderploeg, T., Schaffner, S.F., Drake, J.A., Rhodes, M., Reich, D.E., and Hirschhorn, J.N. (2004). Genetic signatures of strong recent positive selection at the lactase gene. Am. J. Hum. Genet. 74, 1111-1120 https://doi.org/10.1086/421051
  12. Johnson, B.E., and Janne, P.A. (2005). Epidermal growth factor receptor mutations in patients with non-small cell lung cancer. Cancer Res. 65, 7525-7529 https://doi.org/10.1158/0008-5472.CAN-05-1257
  13. Nielsen, R., Hellmann, I., Hubisz, M., Bustamante, C., and Clark, A.G. (2007). Recent and ongoing selection in the human genome. Nat. Rev. Genet. 8, 857-868
  14. Nielsen, R. (2005). Molecular signatures of natural selection. Annu. Rev. Genet. 39, 197-218 https://doi.org/10.1146/annurev.genet.39.073003.112420
  15. Ramensky, V., Bork, P., and Sunyaev, S. (2002). Human non-synonymous SNPs: server and survey. Nucleic Acids Res. 30, 3894-3900 https://doi.org/10.1093/nar/gkf493
  16. Deeble, V.J., Roberts, E., Jackson, A., Lench, N., Karbani, G., and Woods, C.G. (2000). The continuing failure to recognise Alstrom syndrome and further evidence of genetic homogeneity. J. Med. Genet. 37, 219 https://doi.org/10.1136/jmg.37.3.219
  17. Gilad, Y., Segre, D., Skorecki, K., Nachman, M.W., Lancet, D., and Sharon, D. (2000). Dichotomy of single-nucleotide polymorphism haplotypes in olfactory receptor genes and pseudogenes. Nat. Genet. 26, 221-224 https://doi.org/10.1038/79957
  18. Hamblin, M.T., and Di Rienzo, A. (2000). Detection of the signature of natural selection in humans: evidence from the Duffy blood group locus. Am. J. Hum. Genet. 66, 1669-1679 https://doi.org/10.1086/302879
  19. Marshall, J.D., Ludman, M.D., Shea, S.E., Salisbury, S.R., Willi, S.M., LaRoche, R.G., and Nishina, P.M. (1997). Genealogy, natural history, and phenotype of Alstrom syndrome in a large Acadian kindred and three additional families. Am. J. Med. Genet. 73, 150-161 https://doi.org/10.1002/(SICI)1096-8628(19971212)73:2<150::AID-AJMG9>3.0.CO;2-Y
  20. Ng, P.C., and Henikoff, S. (2003). SIFT: predicting amino acid changes that affect protein function. Nucleic Acids Res. 31, 3812-3814 https://doi.org/10.1093/nar/gkg509
  21. Richeldi, L., Sorrentino, R., and Saltini, C. (1993). HLA-DPB1 glutamate 69: a genetic marker of beryllium disease. Science 262, 242-244 https://doi.org/10.1126/science.8105536
  22. Sabeti, P.C., Schaffner, S.F., Fry, B., Lohmueller, J., Varilly, P., Shamovsky, O., Palma, A., Mikkelsen, T.S., Altshuler, D., and Lander, E.S. (2006). Positive natural selection in the human lineage. Science 312, 1614-1620 https://doi.org/10.1126/science.1124309
  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