Robust inference of population structure for ancestry prediction and correction of stratification in the presence of relatedness

Genetic Epidemiology

Volumn 39, Issue 4, 2015, Pages 276-293

  Conomos, Matthew P ^a   Miller, Michael B ^b   Thornton, Timothy A ^a  

^a UNIVERSITY OF WASHINGTON   (United States)

^b UNIVERSITY OF MINNESOTA   (United States)

Author keywords

Admixture; Cryptic relatedness; GWAS; PCA; Pedigrees

Indexed keywords

ARTICLE; GENETIC ASSOCIATION; GENETIC SCREENING; GENETIC SIMILARITY; HAPLOTYPE MAP; HUMAN; HUMAN GENOME; PEDIGREE; POPULATION GENETICS; POPULATION STRUCTURE; PRINCIPAL COMPONENT ANALYSIS; STRATIFICATION; ALGORITHM; BIOLOGICAL MODEL; CHROMOSOME MAP; COMPUTER SIMULATION; GENETICS; POPULATION GROUP; SINGLE NUCLEOTIDE POLYMORPHISM;

ALGORITHMS; CHROMOSOME MAPPING; COMPUTER SIMULATION; GENETIC ASSOCIATION STUDIES; GENETICS, POPULATION; HAPMAP PROJECT; HUMANS; MODELS, GENETIC; POLYMORPHISM, SINGLE NUCLEOTIDE; POPULATION GROUPS; PRINCIPAL COMPONENT ANALYSIS;

EID: 84928029504     PISSN: 07410395     EISSN: 10982272     Source Type: Journal    
DOI: 10.1002/gepi.21896     Document Type: Article

References (33)

1. Abney M. 2009. A graphical algorithm for fast computation of identity coefficients and generalized kinship coefficients. Bioinformatics 25(12):1561-1563.
2. Alexander DH, Novembre J, Lange K. 2009. Fast model-based estimation of ancestry in unrelated individuals. Genome Res 19(9):1655-1664.
3. Balding DJ, Nichols RA. 1995. A method for quantifying differentiation between populations at multi-allelic loci and its implications for investigating identity and paternity. Genetica 96: 3-12.
4. Chen C-Y, Pollack S, Hunter DJ, Hirschhorn JN, Kraft P, Price AL. 2013. Improved ancestry inference using weights from external reference panels. Bioinformatics 29(11):1399-1406.
5. Devlin B, Roeder K. 1999. Genomic control for association studies. Biometrics 55(4):997-1004.
6. Gravel S, Zakharia F, Moreno-Estrada A, Byrnes JK, Muzzio M, Rodriguez-Flores JL, Kenny EE, Gignoux CR, Maples BK, Guiblet W and others. 2013. Reconstructing native american migrations from whole-genome and whole-exome data. PLoS Genet 9(12):e1004023.
7. Heath SC, Gut IG, Brennan P, McKay JD, Bencko V, Fabianova E, Foretova L, Georges M, Janout V, Kabesch M and others. 2008. Investigation of the fine structure of european populations with applications to disease association studies. Eur J Hum Genet 16(12):1413-1429.
8. International HapMap 3 Consortium. 2010. Integrating common and rare genetic variation in diverse human populations. Nature 467(7311):52-58.
9. Jackson JE. 1991. A User's Guide to Principal Components. New York: John Wiley.
10. Jolliffe IT. 1986. Principal Component Analysis. Berlin: Springer.
11. Kang HM, Sul JH, Zaitlen NA, Kong Sy, Freimer NB, Sabatti C, Eskin E and others. 2010. Variance component model to account for sample structure in genome-wide association studies. Nat Genet 42(4):348-354.
12. Laurie CC, Doheny KF, Mirel DB, Pugh EW, Bierut LJ, Bhangale T, Boehm F, Caporaso NE, Cornelis MC, Edenberg HJ and others. 2010. Quality control and quality assurance in genotypic data for genome-wide association studies. Genet Epidemiol 34(6):591-602.
13. Li JZ, Absher DM, Tang H, Southwick AM, Casto AM, Ramachandran S, Cann HM, Barsh GS, Feldman M, Cavalli-Sforza LL and others. 2008. Worldwide human relationships inferred from genome-wide patterns of variation. Science 319(5866):1100-1104.
14. Ma J, Amos CI. 2012. Principal components analysis of population admixture. PloS One 7(7):e40115.
15. Manichaikul A, Mychaleckyj JC, Rich SS, Daly K, Sale M, Chen WM. 2010. Robust relationship inference in genome-wide association studies. Bioinformatics 26(22):2867-2873.
16. Moltke I, Albrechtsen A. 2014. Relateadmix: a software tool for estimating relatedness between admixed individuals. Bioinformatics 30(7):1027-1028.
17. Novembre J, Johnson T, Bryc K, Kutalik Z, Boyko AR, Auton A, Indap A, King KS, Bergmann S, Nelson MR and others. 2008. Genes mirror geography within europe. Nature 456(7218):98-101.
18. Patterson N, Price AL, Reich D. 2006. Population structure and eigenanalysis. PLoS Genetics 2(12):e190.
19. Price AL, Patterson NJ, Plenge RM, Weinblatt ME, Shadick NA, Reich D. 2006. Principal components analysis corrects for stratification in genome-wide association studies. Nat Genet 38(8):904-909.
20. Price AL, Zaitlen NA, Reich D, Patterson N. 2010. New approaches to population stratification in genome-wide association studies. Nat Rev Genet 11(7):459-463.
21. Pritchard JK, Stephens M, Donnelly P. 2000. Inference of population structure using multilocus genotype data. Genetics 155(2):945-959.
22. Purcell S, Neale B, Todd-Brown K, Thomas L, Ferreira MA, Bender D, Maller J, Sklar P, De Bakker PI, Daly MJ and others. 2007. Plink: a tool set for whole-genome association and population-based linkage analyses. Am J Hum Genet 81(3):559-575.
23. Staples J, Nickerson DA, Below JE. 2013. Utilizing graph theory to select the largest set of unrelated individuals for genetic analysis. Genet Epidemiol 37(2):136-141.
24. Tang H, Peng J, Wang P, Risch NJ. 2005. Estimation of individual admixture: analytical and study design considerations. Genet Epidemiol 28(4):289-301.
25. Thornton T, Tang H, Hoffmann TJ, Ochs-Balcom HM, Caan BJ, Risch N. 2012. Estimating kinship in admixed populations. Am J Hum Genet 91(1):122-138.
26. Thornton TA, Bermejo JL. 2014. Local and global ancestry inference and applications to genetic association analysis for admixed populations. Genet Epidemiol 38(S1):S5-S12.
27. Wright S. 1949. The genetical structure of populations. Annal Eugenics 15(1):323-354.
28. Wu C, DeWan A, Hoh J, Wang Z. 2011. A comparison of association methods correcting for population stratification in case-control studies. Annal Hum Genet 75(3):418-427.
29. Yang J, Benyamin B, McEvoy BP, Gordon S, Henders AK, Nyholt DR, Madden PA, Heath AC, Martin NG, Montgomery GW and others. 2010. Common SNPs explain a large proportion of the heritability for human height. Nat Genet 42(7):565-569.
30. Yang J, Zaitlen NA, Goddard ME, Visscher PM, Price AL. 2014. Advantages and pitfalls in the application of mixed-model association methods. Nat Genet 46(2):100-106.
31. Zheng Q, Bourgain C. 2009. Kininbcoef: calculation of kinship and inbreeding coefficients. (http://galton.uchicago.edu/ mcpeek/software/index.html).
32. Zhou X, Stephens M. 2012. Genome-wide efficient mixed-model analysis for association studies. Nat Genet 44(7):821-824.
33. Zhu X, Li S, Cooper RS, Elston RC. 2008. A unified association analysis approach for family and unrelated samples correcting for stratification. Am J Hum Genet 82(2):352-365.