A genome-wide analysis of population structure in the Finnish Saami with implications for genetic association studies

European Journal of Human Genetics

Volumn 19, Issue 3, 2011, Pages 347-352

  Huyghe, Jeroen R ^a   Fransen, Erik ^a   Hannula, Samuli ^b   Van Laer, Lut ^a   Van Eyken, Els ^a   Mäki Torkko, Elina ^b,c   Aikio, Pekka ^b   Sorri, Martti ^b   Huentelman, Matthew J ^d   Camp, Guy Van ^a  

^a UNIVERSITY OF ANTWERP   (Belgium)

^b UNIVERSITY OF OULU   (Finland)

^c LINKÖPING UNIVERSITY   (Sweden)

^d TRANSLATIONAL GENOMICS RESEARCH INSTITUTE   (United States)

Author keywords

genetic association studies; population isolates; population structure; Saami

Indexed keywords

ARTICLE; GENE FREQUENCY; GENETIC ANALYSIS; GENETIC ASSOCIATION; GENETIC VARIABILITY; GENOTYPE; GEOGRAPHIC DISTRIBUTION; HOMOZYGOSITY; HUMAN; MAJOR CLINICAL STUDY; POPULATION GENETIC STRUCTURE; PRIORITY JOURNAL; SINGLE NUCLEOTIDE POLYMORPHISM;

ASIAN CONTINENTAL ANCESTRY GROUP; CHROMOSOME MAPPING; ETHNIC GROUPS; EUROPEAN CONTINENTAL ANCESTRY GROUP; GENETIC ASSOCIATION STUDIES; GENETICS, POPULATION; GENOME, HUMAN; HUMANS; MODELS, GENETIC; POLYMORPHISM, SINGLE NUCLEOTIDE; SCANDINAVIA;

EID: 79951810840     PISSN: 10184813     EISSN: 14765438     Source Type: Journal    
DOI: 10.1038/ejhg.2010.179     Document Type: Article

References (41)

1. Service S, DeYoung J, Karayiorgou M et al: Magnitude and distribution of linkage disequilibrium in population isolates and implications for genome-wide association studies. Nat Genet 2006; 38: 556-560.
2. Peltonen L, Jalanko A, Varilo T: Molecular genetics of the Finnish disease heritage. Hum Mol Genet 1999; 8: 1913-1923. (Pubitemid 29458670)
3. Lowe JK, Maller JB, Pe'er I et al: Genome-wide association studies in an isolated founder population from the Pacific Island of Kosrae. PLoS Genet 2009; 5: e1000365.
4. Helgason A, Yngvadottir B, Hrafnkelsson B, Gulcher J, Stefansson K: An Icelandic example of the impact of population structure on association studies. Nat Genet 2005; 37: 90-95. (Pubitemid 40070945)
5. Jakkula E, Rehnstrom K, Varilo T et al: The genome-wide patterns of variation expose significant substructure in a founder population. Am J Hum Genet 2008; 83: 787-794.
6. The International HapMap Consortium: A second generation human haplotype map of over 3.1 million SNPs. Nature 2007; 449: 851-861.
7. Li JZ, Absher DM, Tang H et al: Worldwide human relationships inferred from genome-wide patterns of variation. Science 2008; 319: 1100-1104. (Pubitemid 351300793)
8. Terwilliger JD, Zöllner S, Laan M, Pääbo S: Mapping genes through the use of linkage disequilibrium generated by genetic drift: 'drift mapping' in small populations with no demographic expansion. Hum Hered 1998; 48: 138-154. (Pubitemid 28220760)
9. Laan M, Pääbo S: Demographic history and linkage disequilibrium in human populations. Nat Genet 1997; 17: 435-438. (Pubitemid 27518392)
10. Laan M, Pääbo S: Mapping genes by drift-generated linkage disequilibrium. Am J Hum Genet 1998; 63: 654-656. (Pubitemid 30418648)
11. Cavalli-Sforza LL, Menozzi P, Piazza A: The history and geography of human genes. Princeton, N.J: Princeton University Press, 1994.
12. Peltonen L, Palotie A, Lange K: Use of population isolates for mapping complex traits. Nat Rev Genet 2000; 1: 182-190.
13. Tambets K, Rootsi S, Kivisild T et al: The western and eastern roots of the Saami-the story of genetic 'outliers' told by mitochondrial DNA and Y chromosomes. Am J Hum Genet 2004; 74: 661-682. (Pubitemid 38420096)
14. Ingman M, Gyllensten U: A recent genetic link between Sami and the Volga-Ural region of Russia. Eur J Hum Genet 2007; 15: 115-120. (Pubitemid 44921675)
15. Johansson A, Ingman M, Mack SJ, Erlich H, Gyllensten U: Genetic origin of the Swedish Sami inferred from HLA class I and class II allele frequencies. Eur J Hum Genet 2008; 16: 1341-1349.
16. Huyghe JR, Fransen E, Hannula S et al: Genome-wide SNP analysis reveals no gain in power for association studies of common variants in the Finnish Saami. Eur J Hum Genet 2010; 18: 569-574.
17. Van Laer L, Huyghe JR, Hannula S et al: A genome-wide association study for age-related hearing impairment in the Saami. Eur J Hum Genet 2010; 18: 685-693.
18. Purcell S, Neale B, Todd-Brown K et al: PLINK: a tool set for whole-genome association and population-based linkage analyses. Am J Hum Genet 2007; 81: 559-575. (Pubitemid 47330214)
19. The International HapMap Consortium: The International HapMap Project. Nature 2003; 426: 789-796.
20. Rosenberg NA: Standardized subsets of the HGDP-CEPH Human Genome Diversity Cell Line Panel, accounting for atypical and duplicated samples and pairs of close relatives. Ann Hum Genet 2006; 70: 841-847. (Pubitemid 44530648)
21. Douglas JA, Sandefur CI: Ped Mine- a simulated annealing algorithm to identify maximally unrelated individuals in population isolates. Bioinformatics 2008; 24: 1106-1108. (Pubitemid 351514064)
22. Alexander DH, Novembre J, Lange K: Fast model-based estimation of ancestry in unrelated individuals. Genome Res 2009; 19: 1655-1664.
23. Rosenberg NA: DISTRUCT: a program for the graphical display of population structure. Mol Ecol Notes 2004; 4: 137-138. (Pubitemid 38261335)
24. Price AL, Patterson NJ, Plenge RM, Weinblatt ME, Shadick NA, Reich D: Principal components analysis corrects for stratification in genome-wide association studies. Nat Genet 2006; 38: 904-909. (Pubitemid 44141658)
25. Bingham J, Sudarsanam S: Visualizing large hierarchical clusters in hyperbolic space. Bioinformatics 2000; 16: 660-661.
26. Reynolds J, Weir BS, Cockerham CC: Estimation of the coancestry coefficient: basis for a short-term genetic distance. Genetics 1983; 105: 767-779. (Pubitemid 14246280)
27. Excoffier L, Laval G, Schneider S: Arlequin ver. 3.0: an integrated package for population genetics data analysis. Evol Bioinform Online 2005; 1: 47-50.
28. Devlin B, Roeder K: Genomic control for association studies. Biometrics 1999; 55: 997-1004.
29. Tang H, Peng J, Wang P, Risch NJ: Estimation of individual admixture: analytical and study design considerations. Genet Epidemiol 2005; 28: 289-301. (Pubitemid 40559542)
30. McVean G: A genealogical interpretation of principal components analysis. PLoS Genet 2009; 5: e1000686.
31. 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; 16: 1413-1429.
32. Novembre J, Stephens M: Interpreting principal component analyses of spatial population genetic variation. Nat Genet 2008; 40: 646-649. (Pubitemid 351601222)
33. Huyghe JR, Fransen E, Hannula S et al: Genome-wide SNP analysis reveals no gain in power for association studies of common variants in the Finnish Saami. Eur J Hum Genet 2009.
34. Price AL, Tandon A, Patterson N et al: Sensitive detection of chromosomal segments of distinct ancestry in admixed populations. PLoS Genet 2009; 5: e1000519.
35. Novembre J, Johnson T, Bryc K et al: Genes mirror geography within Europe. Nature 2008; 456: 98-101.
36. Salmela E, Lappalainen T, Fransson I et al: Genome-wide analysis of single nucleotide polymorphisms uncovers population structure in Northern Europe. PLoS ONE 2008; 3: e3519.
37. Lao O, Lu TT, Nothnagel M et al: Correlation between genetic and geographic structure in Europe. Curr Biol 2008; 18: 1241-1248.
38. Nelis M, Esko T, Magi R et al: Genetic structure of Europeans: a view from the North-East. PLoS One 2009; 4: e5472.
39. Kang HM, Sul JH, Service SK et al: Variance component model to account for sample structure in genome-wide association studies. Nat Genet.
40. Zhang Z, Ersoz E, Lai CQ et al: Mixed linear model approach adapted for genome-wide association studies. Nat Genet.
41. Kristiansson K, Naukkarinen J, Peltonen L: Isolated populations and complex disease gene identification. Genome Biol 2008; 9: 109.