Genetic ancestry inference using support vector machines, and the active emergence of a unique American population This article has been corrected since online publication and a corrigendum is also printed in this issue

European Journal of Human Genetics

Volumn 21, Issue 5, 2013, Pages 554-562

  Haasl, Ryan J ^a   McCarty, Catherine A ^b   Payseur, Bret A ^a  

^a UNIVERSITY OF WISCONSIN MADISON   (United States)

^b ESSENTIA INSTITUTE OF RURAL HEALTH   (United States)

Author keywords

Admixture; Genetic ancestry; Population structure; Principal component analysis; Support vector machine

Indexed keywords

ANALYTICAL ERROR; ARTICLE; COMPUTER SIMULATION; CORRELATIONAL STUDY; EUROPE; EUROPEAN AMERICAN; GENETIC VARIABILITY; GENOMICS; GENOTYPE; GEOGRAPHY; HUMAN; POPULATION GENETICS; PRINCIPAL COMPONENT ANALYSIS; PRIORITY JOURNAL; SUPPORT VECTOR MACHINE; WESTERN HEMISPHERE;

ANALYSIS OF VARIANCE; COMPUTER SIMULATION; DATABASES, GENETIC; EUROPEAN CONTINENTAL ANCESTRY GROUP; GENETIC VARIATION; GENETICS, POPULATION; GENOTYPE; HUMANS; PRINCIPAL COMPONENT ANALYSIS; SUPPORT VECTOR MACHINES; WISCONSIN;

EID: 84876664978     PISSN: 10184813     EISSN: 14765438     Source Type: Journal    
DOI: 10.1038/ejhg.2012.258     Document Type: Article

References (46)

1. Smith MW, Patterson N, Lautenberger JA et al: A high-density admixture map for disease gene discovery in African Americans. Am J Hum Genet 2004; 74: 1001-1013. (Pubitemid 38568970)
2. Lind JM, Hutcheson-Dilks HB, Williams SM et al: Elevated male European and female African contributions to the genomes of African American individuals. Hum Genet 2007; 120: 713-722. (Pubitemid 44942855)
3. Basu A, Tang H, Zhu X et al: Genome-wide distribution of ancestry in Mexican Americans. Hum Genet 2008; 124: 207-214.
4. Via M, Gignoux CR, Roth LA et al: History shaped the geographic distribution of genomic admixture on the island of Puerto Rico. PLoS One 2001; 6: e16513.
5. Sloan CD, Andrew AD, Duell EJ et al: Genetic population structure analysis in New Hampshire reveals Eastern European ancestry. PLoS One 2009; 4: e6928.
6. Hoggart CJ, Shriver MD, Kittles RA et al: Design and analysis of admixture mapping studies. Am J Hum Genet 2004; 74: 965-978. (Pubitemid 38568969)
7. Patterson N, Hattangadi N, Lane B et al: Methods for high-density admixture mapping of disease genes. Am J Hum Genet 2004; 74: 979-1000. (Pubitemid 38578397)
8. Sankararaman S, Sridhar S, Kimmel G et al: Estimating local ancestry in admixed populations. Am J Hum Genet 2008; 82: 290-303. (Pubitemid 351726099)
9. Price AL, Tandon A, Patterson N et al: Sensitive detection of chromosomal segments of distinct ancestry in admixed populations. PLoS Genet 2009; 5: e1000519.
10. Gravel S: Population genetics models of local ancestry. Genetics 2012; 191: 607-619.
11. McCarty CA, Wilke RA, Giampietro PF et al: Marshfield Clinic Personalized Medicine Research Project (PMRP): design, methods, and recruitment for a large populationbased biobank. Pers Med 2005; 2: 49-79.
12. Everest KA: How Wisconsin Came by Its Large German Element Wisconsin Historical Collections; Madison, WI 1892; vol 12: 299-334.
13. Voss PR, Vernoff DL, Long DD: Wisconsin's People: A Portrait of Wisconsin's Population on the Threshold of the 21st Century. Wisconsin Blue Book: Madison, WI, 2003-2004; pp 99-173.
14. Shriver MD, Kittles RA: Genetic ancestry and the search for personalized genetic histories. Nat Rev Genet 2004; 5: 611-618. (Pubitemid 39005755)
15. Via M, Ziv E, Burchard EG: Recent advances of genetic ancestry testing in biomedical research and direct to consumer testing. Clin Genet 2009; 76: 225-235.
16. Weiss KM, Long JC: Non-Darwinian estimation: my ancestors, my genes' ancestors. Genome Res 2009; 19: 703-710.
17. Royal CD, Novembre J, Fullerton SM et al: Inferring genetic ancestry: opportunities, challenges, and implications. Am J Hum Genet 2010; 86: 661-673.
18. Lee SSJ, Bolnick DA, Duster T et al: The illusive gold standard in genetic ancestry testing. Science 2009; 325: 38-39.
19. Callaway E: Ancestry testing goes for pinpoint accuracy. Nature 2012; 486: 7.
20. McVean G: A genealogical interpretation of principal components analysis. PLoS Genet 2009; 5: e1000686.
21. Nelson MR, Bryc K, King KS et al: The Population Reference Sample, POPRES: a resource for population, disease, and pharmacological genetics research. Am J Hum Genet 2008; 83: 347-358.
22. Purcell S, Neall 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)
23. Patterson N, Price AL, Reich D: Population structure and eigenanalysis. PLoS Genet 2006; 2: e190.
24. Lee S, Zou F, Wright FA: Convergence and prediction of principal component scores in high-dimensional settings. Ann Statist 2010; 38: 3605-3629.
25. Cortes C, Vapnik V: Support vector networks. Mach Learn 1995; 20: 273-297.
26. R Development Core Team: R: A language and environment for statistical computing: Vienna, Austria. URL. http://www.Rproject. org/.
27. Dimitriadou E, Hornik K, Leisch F et al: e1071: Misc Functions of the Department of Statistics (e1071), TU Wien. R Package Version 2011; 1: 5-26; http://cran.r-project. org/web/packages/e1071/index.html.
28. Weir BS, Cockeram CC: Estimating F-statistics for the analysis of population structure. Evolution 1984; 38: 1358-1370. (Pubitemid 16277759)
29. Rousset FR: Genetic differentiation and estimation of gene flow from F-statistics under isolation by distance. Genetics 1997; 145: 1219-1228.
30. Haasl RJ, Payseur BA: Multi-locus inference of population structure: a comparison between single nucleotide polymorphisms and microsatellites. Heredity 2011; 106: 158-171.
31. Novembre J, Johnson T, Bryc K et al: Genes mirror geography within Europe. Nature 2008; 456: 98-101.
32. Verdu P, Rosenberg NA: A general mechanistic model for admixture histories of hybrid populations. Genetics 2011; 189: 1413-1426.
33. 23andMe website. http://www.23andme.com/ancestry (Accessed 20 July 2012).
34. Lao O, Lu TT, Nothnagel M et al: Correlation between genetic and geographic structure in Europe. Curr Biol 2008; 18: 1241-1248.
35. Price AL, Helgason A, Palsson S et al: The impact of divergence time on the nature of population structure: an example from Iceland. PLoS Genet 2009; 5: e1000505.
36. Jombart T, Devillard S, Balloux F: Discriminant analysis of principal components: a new method for the analysis of genetically structured populations. BMC Genet 2010; 11: 94.
37. Drineas P, Lewis J, Paschou P: Inferring geographic coordinates of origin for Europeans using small panels of ancestry informative markers. PLoS One 2010; 5: e11892.
38. 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.
39. Eriksson N, Macpherson JM, Tung JY et al: Web-based, participant-driven studies yield novel genetic associations for common traits. PLoS Genet 2010; 6: e1000993.
40. Winney B, Boumertit A, Day T et al: People of the British Isles: preliminary analysis of genotypes an surnames in a UK-control population. Eur J Hum Genet 2012; 20: 203-210.
41. Pritchard JK, Wen X, Falush D: 2010Documentation for structure software: version 2.3; Accessed at. http: //pritch.bsd.uchicago.edu/structure.html.
42. Engelhardt BE, Stephens M: Analysis of population structure: a unifying framework and novel methods based on sparse factor analysis. PLoS Genet 2010; 6: e1001117.
43. Burnett MS, Strain KJ, Lesnick TG et al: Reliability of self-reported ancestry among siblings: implications for genetic association studies. Am J Epidemiol 2006; 163: 486-492.
44. Price AL, Butler J, Patterson N et al: Discerning the ancestry of European Americans in genetic association studies. PLoS Genet 2008; 4: e236.
45. Tian C, Kosoy R, Nassir R et al: European population genetic substructure: further definition of ancestry informative markers for distinguishing among diverse European ethnic groups. Mol Med 2009; 15: 371-383.
46. Novembre J, Stephens M: Interpreting principal component analyses of spatial population genetic variation. Nat Genet 2008; 40: 646-649. (Pubitemid 351601222)