Genomic landscape of positive natural selection in Northern European populations

European Journal of Human Genetics

Volumn 18, Issue 4, 2010, Pages 471-478

  Lappalainen, Tuuli ^a   Salmela, Elina ^a   Andersen, Peter M ^b   Dahlman Wright, Karin ^c   Sistonen, Pertti ^d   Savontaus, Marja Liisa ^e   Schreiber, Stefan ^f   Lahermo, Päivi ^a   Kere, Juha ^a,c,g  

^a UNIVERSITY OF HELSINKI   (Finland)

^b UMEÅ UNIVERSITY HOSPITAL   (Sweden)

^c KAROLINSKA INSTITUTE   (Sweden)

^d Finnish Red Cross   (Finland)

^e UNIVERSITY OF TURKU   (Finland)

^f UNIVERSITY OF KIEL   (Germany)

^g KAROLINSKA UNIVERSITY HOSPITAL   (Sweden)

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; EUROPE; GENE FREQUENCY; GENE SEQUENCE; GENETIC ASSOCIATION; GENETIC DATABASE; GENETIC VARIABILITY; HAPLOTYPE; MOLECULAR EVOLUTION; NATURAL SELECTION; POPULATION GENETICS; PRIORITY JOURNAL; SINGLE NUCLEOTIDE POLYMORPHISM; STATISTICAL MODEL;

EUROPE; EVOLUTION; GENE FREQUENCY; GENETIC VARIATION; GENETICS, POPULATION; GENOME, HUMAN; GENOME-WIDE ASSOCIATION STUDY; HUMANS; POLYMORPHISM, SINGLE NUCLEOTIDE; SELECTION, GENETIC;

EID: 77949656388     PISSN: 10184813     EISSN: 14765438     Source Type: Journal    
DOI: 10.1038/ejhg.2009.184     Document Type: Article

References (54)

1. Blekhman R, Man O, Herrmann L et al: Natural selection on genes that underlie human disease susceptibility. Curr Biol 2008; 12: 883-889.
2. Bustamante CD, Fledel-Alon A, Williamson S et al: Natural selection on protein-coding genes in the human genome. Nature 2005; 7062: 1153-1157.
3. Carlson CS, Thomas DJ, Eberle MA et al: Genomic regions exhibiting positive selection identified from dense genotype data. Genome Res 2005; 11: 1553-1565.
4. Akey JM, Zhang G, Zhang K, Jin L, Shriver MD: Interrogating a high-density SNP map for signatures of natural selection. Genome Res 2002; 12: 1805-1814.
5. Oleksyk TK, Zhao K, De La Vega FM, Gilbert DA, O'Brien SJ, Smith MW: Identifying selected regions from heterozygosity and divergence using a light-coverage genomic dataset from two human populations. PLoS ONE 2008; 3: e1712.
6. O'Reilly PF, Birney E, Balding DJ: Confounding between recombination and selection, and the Ped/Pop method for detecting selection. Genome Res 2008; 8: 1304-1313.
7. Sabeti PC, Varilly P, Fry B et al: Genome-wide detection and characterization of positive selection in human populations. Nature 2007; 7164: 913-918.
8. Wang ET, Kodama G, Baldi P, Moyzis RK: Global landscape of recent inferred Darwinian selection for Homo sapiens. Proc Natl Acad Sci USA 2006; 1: 135-140.
9. Voight BF, Kudaravalli S, Wen X, Pritchard JK: A map of recent positive selection in the human genome. PLoS Biol 2006; 3: e72.
10. Tang K, Thornton KR, Stoneking M: A new approach for using genome scans to detect recent positive selection in the human genome. PLoS Biol 2007; 7: e171.
11. Williamson SH, Hubisz MJ, Clark AG, Payseur BA, Bustamante CD, Nielsen R: Localizing recent adaptive evolution in the human genome. PLoS Genet 2007; 6: e90.
12. International HapMap ConsortiumFrazer KA, Ballinger DG et al: A second generation human haplotype map of over 3.1 million SNPs. Nature 2007; 7164: 851-861.
13. Hinds DA, Stuve LL, Nilsen GB et al: Whole-genome patterns of common DNA variation in three human populations. Science 2005; 5712: 1072-1079.
14. Heath SC, Gut IG, Brennan P et al: Investigation of the fine structure of European populations with applications to disease association studies. Eur J Hum Genet 2008; 12: 1413-1429.
15. Jakobsson M, Scholz SW, Scheet P et al: Genotype, haplotype and copy-number variation in worldwide human populations. Nature 2008; 7181: 998-1003.
16. Li JZ, Absher DM, Tang H et al: Worldwide human relationships inferred from genome-wide patterns of variation. Science 2008; 5866: 1100-1104.
17. Novembre J, Johnson T, Bryc K et al: Genes mirror geography within Europe. Nature 2008; 7219: 274.
18. Salmela E, Lappalainen T, Fransson I et al: Genome-wide analysis of single nucleotide polymorphisms uncovers population structure in Northern Europe. PLoS ONE 2008; 10: e3519.
19. Kimura R, Ohashi J, Matsumura Y et al: Gene flow and natural selection in oceanic human populations inferred from genome-wide SNP typing. Mol Biol Evol 2008; 8: 1750-1761.
20. Pickrell JK, Coop G, Novembre J et al: Signals of recent positive selection in a worldwide sample of human populations. Genome Res 2009; 5: 826-837.
21. Krawczak M, Nikolaus S, von Eberstein H, Croucher PJ, El Mokhtari NE, Schreiber S: PopGen: population-based recruitment of patients and controls for the analysis of complex genotype-phenotype relationships. Community Genet 2006; 1: 55-61.
22. Wellcome Trust Case Control Consortium: Genome-wide association study of 14 000 cases of seven common diseases and 3000 shared controls. Nature 2007; 7145: 661-678.
23. International HapMap Consortium: A haplotype map of the human genome. Nature 2005; 7063: 1299-1320.
24. Sabeti PC, Reich DE, Higgins JM et al: Detecting recent positive selection in the human genome from haplotype structure. Nature 2002; 6909: 832-837.
25. Weir BS, Cockerham CC: Estimating F-statistics for the analysis of population structure. Evolution 1984; 38: 1358-1370.
26. Bandelt HJ, Forster P, Rohl A: Median-joining networks for inferring intraspecific phylogenies. Mol Biol Evol 1999; 1: 37-48.
27. Polzin T, Daneschmand SV: On Steiner trees and minimum spanning trees in hypergraphs. Operations Res Lett 2003; 31: 12-20.
28. Spencer CC, Coop G: SelSim: a program to simulate population genetic data with natural selection and recombination. Bioinformatics 2004; 18: 3673-3675.
29. Loftus SK, Larson DM, Baxter LL et al: Mutation of melanosome protein RAB38 in chocolate mice. Proc Natl Acad Sci USA 2002; 7: 4471-4476.
30. Oiso N, Riddle SR, Serikawa T, Kuramoto T, Spritz RA: The rat Ruby (R) locus is Rab38: identical mutations in Fawn-hooded and Tester-Moriyama rats derived from an ancestral Long Evans rat sub-strain. Mamm Genome 2004; 4: 307-314.
31. Osanai K, Oikawa R, Higuchi J et al: A mutation in Rab38 small GTPase causes abnormal lung surfactant homeostasis and aberrant alveolar structure in mice. Am J Pathol 2008; 5: 1265-1274.
32. Ben-Israel H, Sharf R, Rechavi G, Kleinberger T: Adenovirus E4orf4 protein down-regulates MYC expression through interaction with the PP2A-B55 subunit. J Virol 2008; 19: 9381-9388.
33. Dagda RK, Merrill RA, Cribbs JT et al: The spinocerebellar ataxia 12 gene product and protein phosphatase 2A regulatory subunit Bbeta2 antagonizes neuronal survival by promoting mitochondrial fission. J Biol Chem 2008; 52: 36241-36248.
34. Stockman A, Smithson HE, Webster AR et al: The loss of the PDE6 deactivating enzyme, RGS9, results in precocious light adaptation at low light levels. J Vis 2008; 8: 10.1-10.10.
35. Hartong DT, Pott JW, Kooijman AC: Six patients with bradyopsia (slow vision): clinical features and course of the disease. Ophthalmology 2007; 12: 2323-2331.
36. Bersaglieri T, Sabeti PC, Patterson N etal: Genetic signatures of strong recent positive selection at the lactase gene. Am J Hum Genet 2004; 6: 1111-1120.
37. Thompson EE, Kuttab-Boulos H, Witonsky D, Yang L, Roe BA, Di Rienzo A: CYP3A variation and the evolution of salt-sensitivity variants. Am J Hum Genet 2004; 6:1059-1069.
38. Lamason RL, Mohideen MA, Mest JR et al: SLC24A5, a putative cation exchanger, affects pigmentation in zebrafish and humans. Science 2005; 5755: 1782-1786.
39. Arking DE, Pfeufer A, Post W et al: A common genetic variant in the NOS1 regulator NOS1AP modulates cardiac repolarization. Nat Genet 2006; 6: 644-651.
40. Levy D, Larson MG, Benjamin EJ et al: Framingham Heart Study 100K Project: genome-wide associations for blood pressure and arterial stiffness. BMC Med Genet 2007; 8 (Suppl 1): S3.
41. Pacheco AG, Cardoso CC, Moraes MO: IFNG +874T/A, IL10 \1082G/A and TNF \308G/A polymorphisms in association with tuberculosis susceptibility: a metaanalysis study. Hum Genet 2008; 5: 477-484.
42. Silverberg MS, Cho JH, Rioux JD et al: Ulcerative colitis-risk loci on chromosomes 1p36 and 12q15 found by genome-wide association study. Nat Genet 2009; 2: 216-220.
43. Wratten NS, Memoli H, Huang Y et al: Identification of a schizophrenia-associated functional noncoding variant in NOS1AP Am J Psychiatry 2009; 166: 434-441.
44. Coon KD, Myers AJ, Craig DW et al: A high-density whole-genome association study reveals that APOE is the major susceptibility gene for sporadic late-onset Alzheimer's disease. J Clin Psychiatry 2007; 4: 613-618.
45. Willer CJ, Sanna S, Jackson AU et al: Newly identified loci that influence lipid concentrations and risk of coronary artery disease. Nat Genet 2008; 2: 161-169.
46. Nielsen R, Hellmann I, Hubisz M, Bustamante C, Clark AG: Recent and ongoing selection in the human genome. Nat Rev Genet 2007; 11: 857-868.
47. Marchini J, Cardon LR, Phillips MS, Donnelly P: The effects of human population structure on large genetic association studies. Nat Genet 2004; 5: 512-517.
48. Lange EM, Sun J, Lange LA et al: Family-based samples can play an important role in genetic association studies. Cancer Epidemiol Biomarkers Prev 2008; 9: 2208-2214.
49. Freedman ML, Reich D, Penney KL et al: Assessing the impact of population stratification on genetic association studies. Nat Genet 2004; 4: 388-393.
50. Wong ML, Whelan F, Deloukas P et al: Phosphodiesterase genes are associated with susceptibility to major depression and antidepressant treatment response. Proc Natl Acad Sci USA 2006; 41: 15124-15129.
51. Teshima KM, Coop G, Przeworski M: How reliable are empirical genomic scans for selective sweeps? Genome Res 2006; 6: 702-712.
52. Hofer T, Ray N, Wegmann D, Excoffier L: Large allele frequency differences between human continental groups are more likely to have occurred by drift during range expansions than by selection. Ann Hum Genet 2009; 1: 95-108.
53. Huttley GA, Smith MW, Carrington M, O'Brien SJ: A scan for linkage disequilibrium across the human genome. Genetics 1999; 4: 1711-1722.
54. Nielsen R, Williamson S, Kim Y, Hubisz MJ, Clark AG, Bustamante C: Genomic scans for selective sweeps using SNP data. Genome Res 2005; 11: 1566-1575.