SNP@Evolution: A hierarchical database of positive selection on the human genome

BMC Evolutionary Biology

Volumn 9, Issue 1, 2009, Pages

  Cheng, Feng ^a,b   Chen, Wei ^a,b   Richards, Elliott ^c,d   Deng, Libin ^a,e   Zeng, Changqing ^a,e  

^a Chinese Academy of Sciences and China National Center for Bioinformation   (China)

^b UNIVERSITY OF CHINESE ACADEMY OF SCIENCES   (China)

^c BRIGHAM YOUNG UNIVERSITY   (United States)

^d BAYLOR COLLEGE OF MEDICINE   (United States)

^e NANCHANG UNIVERSITY   (China)

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; CHROMOSOME; COMPUTER INTERFACE; DATA BASE; EVOLUTION; GENETIC VARIABILITY; HAPLOTYPE MAP; HETEROZYGOSITY; HUMAN GENETICS; HUMAN GENOME; SINGLE NUCLEOTIDE POLYMORPHISM; DNA SEQUENCE; GENETIC DATABASE; GENETIC SELECTION; HUMAN; METHODOLOGY; MOLECULAR EVOLUTION;

DATABASES, GENETIC; EVOLUTION, MOLECULAR; GENOME, HUMAN; HUMANS; POLYMORPHISM, SINGLE NUCLEOTIDE; SELECTION (GENETICS); SEQUENCE ANALYSIS, DNA; USER-COMPUTER INTERFACE;

EID: 70350333874     PISSN: None     EISSN: 14712148     Source Type: Journal    
DOI: 10.1186/1471-2148-9-221     Document Type: Article

References (33)

1. Evidence for balancing selection from nucleotide sequence analyses of human G6PD. BC Verrelli JH McDonald G Argyropoulos G Destro-Bisol A Froment A Drousiotou G Lefranc AN Helal J Loiselet SA Tishkoff, American journal of human genetics 2002 71 5 1112 1128 10.1086/344345 12378426
2. Genetic signatures of strong recent positive selection at the lactase gene. T Bersaglieri PC Sabeti N Patterson T Vanderploeg SF Schaffner JA Drake M Rhodes DE Reich JN Hirschhorn, American journal of human genetics 2004 74 6 1111 1120 10.1086/421051 15114531
3. Ongoing adaptive evolution of ASPM, a brain size determinant in Homo sapiens. N Mekel-Bobrov SL Gilbert PD Evans EJ Vallender JR Anderson RR Hudson SA Tishkoff BT Lahn, Science. 2005 309 5741 1720 1722 10.1126/science.1116815 16151010
4. Genomic insights into positive selection. S Biswas JM Akey, Trends Genet 2006 22 8 437 446 10.1016/j.tig.2006.06.005 16808986
5. Genome-wide scans for loci under selection in humans. J Ronald JM Akey, Human genomics 2005 2 2 113 125 16004726
6. Global landscape of recent inferred Darwinian selection for Homo sapiens. ET Wang G Kodama P Baldi RK Moyzis, Proceedings of the National Academy of Sciences of the United States of America 2006 103 1 135 140 10.1073/pnas. 0509691102 16371466
7. A haplotype map of the human genome. The International HapMap Consortium, Nature 2005 437 7063 1299 1320 10.1038/nature04226 16255080
8. A second generation human haplotype map of over 3.1 million SNPs. KA Frazer DG Ballinger DR Cox DA Hinds LL Stuve RA Gibbs JW Belmont A Boudreau P Hardenbol SM Leal, et al. Nature 2007 449 7164 851 861 10.1038/nature06258 17943122
9. A high-resolution survey of deletion polymorphism in the human genome. DF Conrad TD Andrews NP Carter ME Hurles JK Pritchard, Nature genetics 2006 38 1 75 81 10.1038/ng1697 16327808
10. Detection of large-scale variation in the human genome. AJ Iafrate L Feuk MN Rivera ML Listewnik PK Donahoe Y Qi SW Scherer C Lee, Nature genetics 2004 36 9 949 951 10.1038/ng1416 15286789
11. Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project. E Birney JA Stamatoyannopoulos A Dutta R Guigo TR Gingeras EH Margulies Z Weng M Snyder ET Dermitzakis RE Thurman, et al. Nature 2007 447 7146 799 816 10.1038/nature05874 17571346
12. DNA methylation profiling of the human major histocompatibility complex: a pilot study for the human epigenome project. VK Rakyan T Hildmann KL Novik J Lewin J Tost AV Cox TD Andrews KL Howe T Otto A Olek, et al. PLoS Biol 2004 2 12 405 10.1371/journal.pbio.0020405 15550986
13. Global variation in copy number in the human genome. R Redon S Ishikawa KR Fitch L Feuk GH Perry TD Andrews H Fiegler MH Shapero AR Carson W Chen, et al. Nature 2006 444 7118 444 454 10.1038/nature05329 17122850 (Pubitemid 44809057)
14. Relative impact of nucleotide and copy number variation on gene expression phenotypes. BE Stranger MS Forrest M Dunning CE Ingle C Beazley N Thorne R Redon CP Bird A de Grassi C Lee, et al. Science. 2007 315 5813 848 853 17289997 10.1126/science.1136678 (Pubitemid 46255837)
15. Genome-wide associations of gene expression variation in humans. BE Stranger MS Forrest AG Clark MJ Minichiello S Deutsch R Lyle S Hunt B Kahl SE Antonarakis S Tavare, et al. PLoS genetics 2005 1 6 78 10.1371/journal.pgen. 0010078 16362079
16. A genome-wide association study of global gene expression. AL Dixon L Liang MF Moffatt W Chen S Heath KC Wong J Taylor E Burnett I Gut M Farrall, et al. Nature genetics 2007 39 10 1202 1207 10.1038/ng2109 17873877
17. Common deletion polymorphisms in the human genome. SA McCarroll TN Hadnott GH Perry PC Sabeti MC Zody JC Barrett S Dallaire SB Gabriel C Lee MJ Daly, et al. Nature genetics 2006 38 1 86 92 10.1038/ng1696 16468122
18. Interrogating a high-density SNP map for signatures of natural selection. JM Akey G Zhang K Zhang L Jin MD Shriver, Genome research 2002 12 12 1805 1814 10.1101/gr.631202 12466284
19. Genome-wide detection and characterization of positive selection in human populations. PC Sabeti P Varilly B Fry J Lohmueller E Hostetter C Cotsapas X Xie EH Byrne SA McCarroll R Gaudet, et al. Nature 2007 449 7164 913 918 10.1038/nature06250 17943131
20. The genomic distribution of population substructure in four populations using 8,525 autosomal SNPs. MD Shriver GC Kennedy EJ Parra HA Lawson V Sonpar J Huang JM Akey KW Jones, Human genomics 2004 1 4 274 286 15588487
21. Large-scale SNP analysis reveals clustered and continuous patterns of human genetic variation. MD Shriver R Mei EJ Parra V Sonpar I Halder SA Tishkoff TG Schurr SI Zhadanov LP Osipova TD Brutsaert, et al. Human genomics 2005 2 2 81 89 16004724
22. Genomic regions exhibiting positive selection identified from dense genotype data. CS Carlson DJ Thomas MA Eberle JE Swanson RJ Livingston MJ Rieder DA Nickerson, Genome research 2005 15 11 1553 1565 10.1101/gr.4326505 16251465
23. Measures of human population structure show heterogeneity among genomic regions. BS Weir LR Cardon AD Anderson DM Nielsen WG Hill, Genome research 2005 15 11 1468 1476 10.1101/gr.4398405 16251456
24. Detecting recent positive selection in the human genome from haplotype structure. PC Sabeti DE Reich JM Higgins HZ Levine DJ Richter SF Schaffner SB Gabriel JV Platko NJ Patterson GJ McDonald, et al. Nature 2002 419 6909 832 837 10.1038/nature01140 12397357
25. A map of recent positive selection in the human genome. BF Voight S Kudaravalli X Wen JK Pritchard, PLoS Biol 2006 4 3 72 10.1371/journal.pbio. 0040072 16494531
26. SNP@Ethnos: a database of ethnically variant single-nucleotide polymorphisms. J Park S Hwang YS Lee SC Kim D Lee, Nucleic acids research 2007 35 Database 711 715 10.1093/nar/gkl962 17135185
27. SelSim: a program to simulate population genetic data with natural selection and recombination. CC Spencer G Coop, Bioinformatics 2004 20 18 3673 3675 10.1093/bioinformatics/bth417 15271777
28. Genomic signatures of positive selection in humans and the limits of outlier approaches. JL Kelley J Madeoy JC Calhoun W Swanson JM Akey, Genome Res 2006 16 8 980 989 10.1101/gr.5157306 16825663
29. Constructing genomic maps of positive selection in humans: where do we go from here? JM Akey, Genome Res 2009 19 5 711 722 10.1101/gr.086652.108 19411596
30. Signals of recent positive selection in a worldwide sample of human populations. JK Pickrell G Coop J Novembre S Kudaravalli JZ Li D Absher BS Srinivasan GS Barsh RM Myers MW Feldman, et al. Genome Res 2009 19 5 826 837 10.1101/gr.087577.108 19307593
31. A scan for genetic determinants of human hair morphology: EDAR is associated with Asian hair thickness. A Fujimoto R Kimura J Ohashi K Omi R Yuliwulandari L Batubara MS Mustofa U Samakkarn W Settheetham-Ishida T Ishida, et al. Hum Mol Genet 2008 17 6 835 843 10.1093/hmg/ddm355 18065779
32. The generic genome browser: a building block for a model organism system database. LD Stein C Mungall S Shu M Caudy M Mangone A Day E Nickerson JE Stajich TW Harris A Arva, et al. Genome research 2002 12 10 1599 1610 10.1101/gr.403602 12368253
33. SIFT: Predicting amino acid changes that affect protein function. PC Ng S Henikoff, Nucleic acids research 2003 31 13 3812 3814 10.1093/nar/gkg509 12824425