A test of Hardy-Weinberg equilibrium in structured populations

Genetic Epidemiology

Volumn 35, Issue 7, 2011, Pages 671-678

  Sha, Qiuying ^a   Zhang, Shuanglin ^a  

^a MICHIGAN TECHNOLOGICAL UNIVERSITY   (United States)

Author keywords

Genotyping errors; Hardy Weinberg equilibrium; Population stratification; Population structure

Indexed keywords

ARTICLE; CHI SQUARE TEST; DISEASE ASSOCIATION; GENE FREQUENCY; GENETIC MODEL; GENOTYPE; HARDY WEINBERG DISTRIBUTION LAW; HUMAN; STRATIFICATION;

AMYOTROPHIC LATERAL SCLEROSIS; GENE FREQUENCY; GENETIC PREDISPOSITION TO DISEASE; GENETICS, POPULATION; HUMANS; MODELS, GENETIC; MODELS, STATISTICAL;

EID: 80054739236     PISSN: 07410395     EISSN: 10982272     Source Type: Journal    
DOI: 10.1002/gepi.20617     Document Type: Article

References (38)

1. 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.
2. Bauchet M, McEvoy B, Pearson LN, Quillen EE, Sarkisian T, Hovhannesyan K, Deka R, Bradley DG, Shriver MD. 2007. Measuring European population stratification with microarray genotype data. Am J Hum Genet 80:948-956.
3. Chen HS, Zhu X, Zhao H, Zhang S. 2003. Qualitative semi-parametric test for genetic associations in case-control designs under structured populations. Ann Hum Genet 67:250-264.
4. Cockerham CC. 1967. Group inbreeding and coancestry. Genetics 56:789-792.
5. Cockerham CC. 1969. Variance of gene frequencies. Evolution 23:72-78.
6. Cox D, Kraft P. 2006. Quantification of the power of Hardy-Weinberg equilibrium testing to detect genotyping error. Hum Heredity 61:10-14.
7. Crow J, Kimura M. 1970. An Introduction to Population Genetics Theory. New York: Harper and Row.
8. Cupples LA, Beyene J, Bickeböller H, Daw EW, Fallin MD, Gauderman WJ, Ghosh S, Goode EL, Hauser ER, Hinrichs A, Kent, Jr JW, Martin LJ, Martinez M, Neuman RJ, Province M, Szymczak S, Wilcox MA, Ziegler A, MacCluer JW, Almasy L. 2009. Genetic analysis workshop 16: Strategies for genome-wide association study analyses. BMC Proc 3:S1.
9. Deng HW, Chen WM, Recker RR. 2001. Population admixture: detection by Hardy-Weinberg test and its quantitative effects on linkage-disequilibrium methods for localizing genes underlying complex traits. Genetics 157:885-897.
10. Devlin B, Roeder K. 1999. Genomic control for association studies. Biometrics 55:997-1004.
11. Devlin B, Roeder K, Wasserman L. 2001. Genomic control, a new approach to genetic-based association studies. Theor Popul Biol 60:155-166.
12. Gomes I, Collins A, Lonjou C, Thomas NS, Wilkinson J, Watson M, Morton N. 1999. Hardy-Weinberg quality control. Ann Hum Genet 63:535-538.
13. Hartl DL, Clark AG. 1989. Principles of Population Genetics, 2nd edition. Sunderland, MA: Sinauer Associates, Inc.
14. Hosking L, Lumsden S, Lewis K, Yeo A, McCarthy L, Bansal A, Riley J, Purvis I, Xu CF. 2004. Detection of genotyping errors by Hardy-Weinberg equilibrium testing. Eur J Hum Genet 12:395-399.
15. Ionita-Laza I, McQueen MB, Laird NM, Lange C. 2007. Genome-wide weighted hypothesis testing in family-based association studies, with an application to a 100k scan. Am J Hum Genet 81:607-614.
16. Kang HM, Sul JH, Service SK, Zaitlen NA, Kong S, Freimer NB, Sabatti C, Eskin E. 2010. Variance component model to account for sample structure in genome-wide association studies. Nat Genet 42:348-354.
17. Knowler WC, Williams RC, Pettitt DJ, Steinberg AG. 1988. Gm3;5, 13, 14 and type 2 diabetes mellitus: an association in American Indians with genetic admixture. Am J Hum Genet 43:520-526.
18. Lander ES, Schork NJ. 1994. Genetic dissection of complex traits. Science 265:2037-2048.
19. Leal S. 2005. Detection of genotyping errors and pseudo-snps via deviations from hardy-weinberg equilibrium. Genet Epidemiol 29:204-214.
20. Li M, Li C. 2008. Assessing departure from Hardy-Weinberg Equilibrium in the presence of disease association. Genet Epidemiol 32:589-599.
21. Li M, Reilly C, Hanson T. 2008. A semi-parametric test to detect associations between quantitative traits and candidate genes in structured populations. Bioinformatics 24:2356-2362.
22. Price AL, Patterson NJ, Plenge RM, Weinblatt ME, Shadick NA, Reich D. 2006. PCs analysis corrects for stratification in genome-wide association studies. Nat Genet 38:904-909.
23. Pritchard JK, Rosenberg NA. 1999. Use of unlinked genetic markers to detect population stratification in association studies. Am J Hum Genet 65:220-228.
24. Pritchard JK, Stephens M, Rosenberg NA, Donnelly P. 2000. Association mapping in structured populations. Am J Hum Genet 67:170-181.
25. Qin H, Feng T, Zhang S, Sha Q. 2010. A data-driven weighting scheme for family-based genome-wide association studies. Eur J Hum Genet 18:596-603.
26. Reich DE, Goldstein DB. 2001. Detecting association in a case-control study while correcting for population stratification. Genet Epidemiol 20:4-16.
27. Satten GA, Flanders WD, Yang Q. 2001. Accounting for unmeasured population substructure in case-control studies of genetic association using a novel latent-class model. Am J Hum Genet 68:466-477.
28. Schaid DJ, Batzler AJ, Jenkins GD, Hilderbrandt MAT. 2006. Exact tests of Hardy-Weinberg equilibrium and homogeneity of disequilibrium across strata. Am J Hum Genet 79:1071-1080.
29. Schymick JC, Scholz SW, Fung HC, Britton A, Arepalli S, Gibbs JR, Lombardo F, Matarin M, Kasperaviciute D, Hernandez DG, Crews C, Bruijn L, Rothstein J, Mora G, Restagno G, Chió A, Singleton A, Hardy J, Traynor BJ. 2007. Genome-wide genotyping in amyotrophic lateral sclerosis and neurologically normal controls: first stage analysis and public release of data. Lancet Neurol 6:322-328.
30. The International HapMap Consortium. 2007. A second generation human haplotype map of over 3.1 million SNPs. Nature 449:851-861.
31. Wang J, Shete S. 2010. Using both cases and controls for testing Hardy-Weinberg proportions in a genetic association study. Hum Hered 69:212-218.
32. Weir BS. 1996. Disequilibrium. Genetic Data Analysis II. Sunderland, MA: Sinaur Associates. p 91-139.
33. Weir BS, Hill WG, Cardon LR. 2004. Allelic association patterns for a dense SNP map. Genet Epidemiol 27:442-450.
34. Wigginton JE, Cutler DJ, Abecasis GR. 2005. A note on exact tests of Hardy-Weinberg equilibrium. Am J Hum Genet 76:887-893.
35. Yu C, Zhang S, Zhou C, Sile S. 2009. A likelihood ratio test of population Hardy-Weinberg equilibrium for case-control studies. Genet Epidemiol 33:275-280.
36. Zhang S, Zhu X, Zhao H. 2003. On a semi-parametric test to detect associations between quantitative traits and candidate genes using unrelated individuals. Genet Epidemiol 24:44-56.
37. Zhang Z, Ersoz E, Lai CQ, Todhunter RJ, Tiwari HK, Gore MA, Bradbury P, Yu J, Arnett DK, Ordovas JM, Buckler ES. 2010. Mixed linear model approach adapted for genome-wide association studies. Nat Genet 42:355-360.
38. Zhu X, Zhang S, Zhao H, Cooper RS. 2002. Association mapping, using a mixture model for complex traits. Genet Epidemiol 23:181-196.