Targeted resequencing of two genes, RAGE and POLL, confirms findings from a genome-wide scan for adaptive evolution and provides evidence for positive selection in additional populations

Human Molecular Genetics

Volumn 18, Issue 4, 2009, Pages 779-784

  Kelley, Joanna L ^a   Turkheimer, Kayley ^a   Haney, Margo ^a   Swanson, Willie J ^a  

^a UNIVERSITY OF WASHINGTON   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

DNA POLYMERASE; DNA POLYMERASE LAMBDA; RENAL TUMOR ANTIGEN; TUMOR ANTIGEN; UNCLASSIFIED DRUG;

ARTICLE; CHINESE; ETHNIC GROUP; GENE LOCUS; GENE RESEQUENCING; GENE SEQUENCE; GENETIC SELECTION; HAN CHINESE; HUMAN; POPULATION DIFFERENTIATION; POPULATION GENETICS; POSITIVE SELECTION; PRIORITY JOURNAL; SINGLE NUCLEOTIDE POLYMORPHISM; SUB-SAHARAN AFRICAN;

ANTIGENS, NEOPLASM; CONTINENTAL POPULATION GROUPS; DNA POLYMERASE BETA; EVOLUTION, MOLECULAR; GENETICS, POPULATION; GENOME-WIDE ASSOCIATION STUDY; HUMANS; MITOGEN-ACTIVATED PROTEIN KINASES; POLYMORPHISM, SINGLE NUCLEOTIDE; SELECTION (GENETICS);

EID: 59049088682     PISSN: 09646906     EISSN: 14602083     Source Type: Journal    
DOI: 10.1093/hmg/ddn399     Document Type: Article

References (35)

1. Sabeti, P.C., Varilly, P., Fry, B., Lohmueller, J., Hostetter, E., Cotsapas, C., Xie, X., Byrne, E.H., McCarroll, S.A., Gaudet, R. et al. (2007) Genome-wide detection and characterization of positive selection in human populations. Nature, 449, 913-918.
2. Williamson, S.H., Hubisz, M.J., Clark, A.G., Payseur, B.A., Bustamante, C.D. and Nielsen, R. (2007) Localizing recent adaptive evolution in the human genome. PLoS Genet., 3, e90.
3. Kimura, R., Fujimoto, A., Tokunaga, K. and Ohashi, J. (2007) A practical genome scan for population-specific strong selective sweeps that have reached fixation. PLoS ONE, 2, e286.
4. Tang, K., Thornton, K.R. and Stoneking, M. (2007) A new approach for using genome scans to detect recent positive selection in the human genome. PLoS Biol., 5, e171.
5. International_HapMap_Consortium (2007) A second generation human haplotype map of over 3.1 million SNPs. Nature, 449, 851-861.
6. Akey, J.M., Eberle, M.A., Rieder, M.J., Carlson, C.S., Shriver, M.D., Nickerson, D.A. and Kruglyak, L. (2004) Population history and natural selection shape patterns of genetic variation in 132 genes. PLoS Biol., 2, e286.
7. 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. et al. (2005) Natural selection on protein-coding genes in the human genome. Nature, 437, 1153-1157.
8. Carlson, C.S., Thomas, D.J., Eberle, M.A., Swanson, J.E., Livingston, R.J., Rieder, M.J. and Nickerson, D.A. (2005) Genomic regions exhibiting positive selection identified from dense genotype data. Genome Res. 15, 1553-1565.
9. Clark, A.G., Glanowski, S., Nielsen, R., Thomas, P., Kejariwal, A., Todd, M.J., Tanenbaum, D.M., Civello, D., Lu, F., Murphy, B. et al. (2003) Positive selection in the human genome inferred from human-chimp-mouse orthologous gene alignments. Cold Spring Harb. Symp. Quant. Biol., 68, 471-477.
10. International_HapMap_Consortium (2005) A haplotype map of the human genome. Nature, 437, 1299-1320.
11. Kelley, J.L., Madeoy, J., Calhoun, J.C., Swanson, W. and Akey, J.M. (2006) Genomic signatures of positive selection in humans and the limits of outlier approaches. Genome Res., 16, 980-989.
12. Nielsen, R., Bustamante, C., Clark, A.G., Glanowski, S., Sackton, T.B., Hubisz, M.J., Fledel-Alon, A., Tanenbaum, D.M., Civello, D., White, T.J. et al. (2005) A scan for positively selected genes in the genomes of humans and chimpanzees. PLoS Biol., 3, e170.
13. Sabeti, P.C., Reich, D.E., Higgins, J.M., Levine, H.Z., Richter, D.J., Schaffner, S.F., Gabriel, S.B., Platko, J.V., Patterson, N.J., McDonald, G.J. et al. (2002) Detecting recent positive selection in the human genome from haplotype structure. Nature, 419, 832-837.
14. Voight, B.F., Kudaravalli, S., Wen, X. and Pritchard, J.K. (2006) A map of recent positive selection in the human genome. PLoS Biol., 4 e72.
15. Wang, E.T., Kodama, G., Baldi, P. and Moyzis, R.K. (2006) Global landscape of recent inferred Darwinian selection for Homo sapiens. Proc. Natl Acad. Sci. USA, 103, 135-140.
16. 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.
17. Biswas, S. and Akey, J.M. (2006) Genomic insights into positive selection. Trends Genet., 22, 437-446.
18. 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.
19. Fay, J.C. and Wu, C.I. (2000) Hitchhiking under positive Darwinian selection. Genetics, 155, 1405-1413.
20. Fay, J.C., Wyckoff, G.J. and Wu, I. (2001) Positive and negative selection on the human genome. Genetics, 158, 1227-1234.
21. Rosenberg, N.A., Pritchard, J.K., Weber, J.L., Cann, H.M., Kidd, K.K., Zhivotovsky, L.A. and Feldman, M.W. (2002) Genetic structure of human populations. Science, 298, 2381-2385.
22. Tajima, F. (1989) Statistical method for testing the neutral mutation hypothesis by DNA polymorphism. Genetics, 123, 585-595.
23. Drummond, D.A. and Wilke, C.O. (2008) Mistranslation-induced protein misfolding as a dominant constraint on coding-sequence evolution. Cell, 134, 341-352.
24. Powers, E.T. and Balch, W.E. (2008) Costly mistakes: Translational infidelity and protein homeostasis. Cell, 134, 204-206.
25. 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.
26. Gilad, Y., Oshlack, A. and Rifkin, S.A. (2006) Natural selection on gene expression. Trends Genet., 22, 456-461.
27. Rozen, S. and Skaletsky, H. (2000) Primer3 on the WWW for general users and for biologist programmers. Methods Mol. Biol., 132, 365-386.
28. Ewing, B. and Green, P. (1998) Base-calling of automated sequencer traces using phred. II. Error probabilities. Genome Res., 8, 186-194.
29. Ewing, B., Hillier, L., Wendl, M.C. and Green, P. (1998) Base-calling of automated sequencer traces using phred. I. Accuracy assessment. Genome Res., 8, 175-185.
30. Nickerson, D.A., Tobe, V.O. and Taylor, S.L. (1997) PolyPhred: automating the detection and genotyping of single nucleotide substitutions using fluorescence-based resequencing. Nucleic Acids Res., 25, 2745-2751.
31. Gordon, D., Abajian, C. and Green, P. (1998) Consed: A graphical tool for sequence finishing. Genome Res., 8, 195-202.
32. Stephens, M., Smith, N.J. and Donnelly, P. (2001) A new statistical method for haplotype reconstruction from population data. Am. J. Hum. Genet., 68, 978-989.
33. Excoffier, L., Laval, G. and Scheider, S. (2005) Arlequin ver. 3.0: An integrated software package for population genetics data analysis. Evol Bioinform Online, 1, 47-50.
34. Rozas, J., Sanchez-DelBarrio, J.C., Messeguer, X. and Rozas, R. (2003) DnaSP, DNA polymorphism analyses by the coalescent and other methods. Bioinformatics, 19, 2496-2497.
35. Kimura, M. (1968) Evolutionary rate at the molecular level. Nature 217, 624-626.