Genome-wide analysis of single nucleotide polymorphisms uncovers population structure in Northern Europe

PLoS ONE

Volumn 3, Issue 10, 2008, Pages

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

^a UNIVERSITY OF HELSINKI   (Finland)

^b KAROLINSKA INSTITUTE   (Sweden)

^c UMEÅ UNIVERSITY HOSPITAL   (Sweden)

^d UNIVERSITY OF KIEL   (Germany)

^e Finnish Red Cross   (Finland)

^f UNIVERSITY OF TURKU   (Finland)

^g FOLKHÄLSAN INSTITUTE OF GENETICS   (Finland)

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; CONTROLLED STUDY; EUROPE; FINLAND; GENE LINKAGE DISEQUILIBRIUM; GENETIC DRIFT; GENETIC VARIABILITY; GENOME ANALYSIS; GERMANY; HAPLOTYPE MAP; HUMAN; POPULATION DIFFERENTIATION; POPULATION GENETIC STRUCTURE; POPULATION RESEARCH; POPULATION SIZE; SINGLE NUCLEOTIDE POLYMORPHISM; STRUCTURE ANALYSIS; SWEDEN; UNITED KINGDOM; COHORT ANALYSIS; COMPARATIVE STUDY; GENE FREQUENCY; GENETIC ASSOCIATION; GENETIC MARKER; GENETICS; LANGUAGE; MALE; POPULATION;

COHORT STUDIES; EUROPE; FINLAND; GENE FREQUENCY; GENETIC MARKERS; GENOME-WIDE ASSOCIATION STUDY; HUMANS; LANGUAGE; MALE; POLYMORPHISM, SINGLE NUCLEOTIDE; POPULATION;

EID: 55849116691     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0003519     Document Type: Article

References (52)

1. Freedman ML, Reich D, Penney KL, McDonald GJ, Mignault AA, et al. (2004) Assessing the impact of population stratification on genetic association studies. Nat Genet 36: 388-393.
2. Marchini J, Cardon LR, Phillips MS, Donnelly P (2004) The effects of human population structure on large genetic association studies. Nat Genet 36: 512-517.
3. Seldin MF, Shigeta R, Villoslada P, Selmi C, Tuomilehto J, et al. (2006) European population substructure: clustering of northern and southern populations. PLoS Genet 15: e143.
4. Wellcome Trust Case Control Consortium (2007) Genome-wide association study of 14000 cases of seven common diseases and 3000 shared controls. Nature 447: 661-678.
5. Bauchet M, McEvoy B, Pearson LN, Quillen EE, Sarkisian T, et al. (2007) Measuring European population stratification with microarray genotype data. Am J Hum Genet 80: 948-956.
6. Jakobsson M, Scholz SW, Scheet P, Gibbs JR, VanLiere JM, et al. (2008) Genotype, haplotype and copy-number variation in worldwide human populations. Nature 451: 998-1003.
7. Lao O, Lu TT, Nothnagel M, Junge O, Freitag-Wolf S, et al. (2008) Correlation between genetic and geographic structure in Europe. Curr Biol 18: 1241-1248.
8. Li JZ, Absher DM, Tang H, Southwick AM, Casto AM, et al. (2008) Worldwide human relationships inferred from genome-wide patterns of variation. Science 319: 1100-1104.
9. Novembre J, Johnson T, Bryc K, Kutalik Z, Boyko AR, et al. (2008) Genes mirror geography within Europe. Nature, In press. DOI 10.1038/ nature07331.
10. Price AL, Butler J, Patterson N, Capelli C, Pascali VL, et al. (2008) Discerning the ancestry of European Americans in genetic association studies. PLoS Genet 4: e236.
11. Tian C, Plenge RM, Ransom M, Lee A, Villoslada P, et al. (2008) Analysis and application of European genetic substructure using 300 K SNP information. PLoS Genet 4: e4.
12. International HapMap Consortium (2007) A second generation human haplotype map of over 3.1 million SNPs. Nature 449: 851-861.
13. Nevanlinna HR (1972) The Finnish population structure. Hereditas 71: 195-236.
14. Pitkänen K (1994) Suomen väestön historialliset kehityslinjat (Historical trends in the development of the Finnish population). In: Koskinen S, Martelin T, Notkola IL, Notkola V, Pitkänen K, eds. Suomen väestö (The population of Finland). Hämeenlinna Finland: Gaudeamus. pp 19-63.
15. De la Chapelle A, Wright FA (1998) Linkage disequilibrium mapping in isolated populations: The example of Finland revisited. Proc Natl Acad Sci 95: 12416-12423.
16. Kere J (2001) Human population genetics: Lessons from Finland. Annu Rev Genomics Hum Genet 2: 103-128.
17. Norio R (2003) Finnish Disease Heritage I: characteristics, causes, background. Hum Genet 112: 441-456.
18. Norio R (2003) Finnish Disease Heritage II: population prehistory and genetic roots of Finns. Hum Genet 112: 457-469.
19. Siiriäinen A (2003) The Stone and Bronze Ages. In: Helle K, Jansson T, eds. The Cambridge History of Scandinavia. Cambridge: Cambridge University Press. pp 43-59.
20. Lappalainen T, Laitinen V, Salmela E, Andersen P, Huoponen K, et al. (2008) Migration Waves to the Baltic Sea Region. Ann Hum Genet. 72: 337-348.
21. Cavalli-Sforza LL, Menozzi P, Piazza A (1994) History and geography of human genes. Princeton: Princeton University Press. 428 p.
22. Lahermo P, Savontaus ML, Sistonen P, Béres J, de Knijff P, et al. (1999) Y chromosomal polymorphisms reveal founding lineages in the Finns and the Saami. Eur J Hum Genet 7: 447-458.
23. Lappalainen T, Koivumäki S, Salmela E, Huoponen K, Sistonen P, et al. (2006) Regional differences among the Finns: a Y-chromosomal perspective. Gene 19: 207-215.
24. Kittles RA, Perola M, Peltonen L, Bergen AW, Aragon RA, et al. (1998) Dual origins of Finns revealed by Y chromosome haplotype variation. Am J Hum Genet 62: 1171-1179.
25. Hedman M, Pimenoff V, Lukka M, Sistonen P, Sajantila A (2004) Analysis of 16 Y STR loci in the Finnish population reveals a local reduction in the diversity of male lineages. Forensic Sci Int 28: 37-43.
26. Workman PL, Mielke JH, Nevanlinna HR (1976) The genetic structure of Finland. Am J Phys Anthrop 44: 341-368.
27. Hannelius U, Salmela E, Lappalainen T, Guillot G, Lindgren CM, et al. (2008) Population substructure in Finland and Sweden revealed by the use of spatial coordinates and a small number of unlinked autosomal SNPs. BMC Genet 19: 54.
28. Varilo T, Paunio T, Parker A, Perola M, Meyer J, et al. (2003) The interval of linkage disequilibrium (LD) detected with microsatellite and SNP markers in chromosomes of Finnish populations with different histories. Hum Mol Genet 1: 51-59.
29. Uimari P, Kontkanen O, Visscher PM, Pirskanen M, Fuentes R, et al. (2005) Genome-wide linkage disequilibrium from 100000 SNPs in the East Finland founder population. Twin Res Hum Genet 8: 185-197.
30. Service S, DeYoung J, Karayiorgou M, Roos JL, Pretorious H, et al. (2006) Magnitude and distribution of linkage disequilibrium in population isolates and implications for genome-wide association studies. Nat Genet 38: 556-560.
31. Karlsson AO, Wallerström T, Götherström A, Holmlund G (2006) Y-chromosome diversity in Sweden-a long-time perspective. Eur J Hum Genet 14: 963-970.
32. Lappalainen T, Hannelius U, Salmela E, von Döbeln U, Lindgren CM, et al. (2008) Population structure in contemporary Sweden-A Y-chromosomal and mitochondrial DNA analysis. Ann Hum Genet. In press. DOI 10.1111/ j.1469-1809.2008.00487.x.
33. Einarsdottir E, Egerbladh I, Beckman L, Holmberg D, Escher SA (2007) The genetic population structure of northern Sweden and its implications for mapping genetic diseases. Hereditas 144: 171-180.
34. Kaessmann H, Zöllner S, Gustafsson AC, Wiebe V, Laan M, et al. (2002) Extensive linkage disequilibrium in small human populations in Eurasia. Am J Hum Genet 70: 673-685.
35. Steffens M, Lamina C, Illig T, Bettecken T, Vogler R, et al. (2006) SNP-based analysis of genetic substructure in the German population. Hum Hered 62: 20-29.
36. Kayser M, Lao O, Anslinger K, Augustin C, Bargel G, et al. (2005) Significant genetic differentiation between Poland and Germany follows present-day political borders as revealed by Y-chromosome analysis. Hum Genet 117: 428-443.
37. Buse DK (2005) The regions of Germany. Westport: Greenwood Press. 312 p.
38. Helgason A, Yngvadóttir B, Hrafnkelsson B, Gulcher J, Stefánsson K (2004) An Icelandic example of the impact of population structure on association studies. Nat Genet 37: 90-95.
39. Cavalli-Sforza LL, Feldman MW (2003) The application of molecular genetic approaches to the study of human evolution. Nat Genet 33 Suppl: 266-275.
40. Virtaranta-Knowles K, Sistonen P, Nevanlinna HR (1991) A population genetic study in Finland: comparison of the Finnish- and Swedish-speaking populations. Hum Hered 41: 248-264.
41. Lahermo P, Sajantila A, Sistonen P, Lukka M, Aula P, et al. (1996) The genetic relationship between the Finns and the Finnish Saami (Lapps): analysis of nuclear DNA and mtDNA. Am J Hum Genet 58: 1309-13022.
42. Clark AG, Hubisz MJ, Bustamante CD, Williamson SH, Nielsen R (2005) Ascertainment bias in studies of human genome-wide polymorphism. Genome Res 15: 1496-1502.
43. Kristiansson K, Naukkarinen J, Peltonen L (2008) Isolated populations and complex disease gene identification. Genome Biol 26: 109.
44. Krawczak M, Nikolaus S, von Eberstein H, Croucher PJ, El Mokhtari NE, et al. (2006) PopGen: population-based recruitment of patients and controls for the analysis of complex genotype-phenotype relationships. Community Genet 9: 55-61.
45. Purcell S, Neale B, Todd-Brown K, Thomas L, Ferreira MAR, et al. (2007) PLINK: a tool set for whole-genome association and population-based linkage analyses. Am J Hum Genet 81: 559-575.
46. R Development Core Team (2008) R: A language and environment for statistical computing. Vienna, Austria: R Foundation for Statistical Computing.
47. Aulchenko Y with contributions from, Struchalin M, Ripke S, Johnson T (2008) GenABEL: genome-wide SNP association analysis. R package version 1.3-5.
48. Nychka D (2007) fields: Tools for spatial data. R package version 4.1.
49. Dray S, Dufour AB (2007) The ade4 package: implementing the duality diagram for ecologists. Journal of Statistical Software 22: 1-20.
50. Falush D, Stephens M, Pritchard JK (2003) Inference of population structure using multilocus genotype data: linked loci and correlated allele frequencies. Genetics 164: 1567-1587.
51. Excoffier L, Laval G, Schneider S (2005) Arlequin ver. 3.0: An integrated software package for population genetics data analysis. Evolutionary Bioinformatics Online 1: 47-50.
52. Clayton DG, Walker NM, Smyth DJ, Pask R, Cooper JD, et al. (2005) Population structure, differential bias and genomic control in a large-scale case-control association study. Nat Genet 37: 1243-1246.