A semiparametric test to detect associations between quantitative traits and candidate genes in structured populations

Bioinformatics

Volumn 24, Issue 20, 2008, Pages 2356-2362

  Li, Meijuan ^a   Reilly, Cavan ^a   Hanson, Timothy ^a  

^a UNIVERSITY OF MINNESOTA   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ACCURACY; ANALYTICAL ERROR; ARABIDOPSIS; ARTICLE; CONTROLLED STUDY; GENE MAPPING; GENETIC MARKER; GENOTYPE; NONHUMAN; NORMAL DISTRIBUTION; PARAMETRIC TEST; POPULATION GENETIC STRUCTURE; POPULATION STRUCTURE; PRIORITY JOURNAL; QUANTITATIVE TRAIT; SIMULATION; STATISTICAL MODEL;

EID: 53749087160     PISSN: 13674803     EISSN: 13674811     Source Type: Journal    
DOI: 10.1093/bioinformatics/btn455     Document Type: Article

References (40)

1. Aranzana,M.J. et al. (2005) Genome-wide association mapping in Arabidopsis identifies previously known flowering time and pathogen resistance genes. PLoS Genet., 1, e60.
2. Azzalini,A. and Capitanio,A. (1999) Statistical applications of the multivariate skew-normal distribution. J. R. Stat. Soc. Ser. B, 61, 579-602.
3. Bacanu,S. et al. (2002) Association studies for quantitative traits in structured populations. Genet. Epidemiol., 22, 78-93.
4. Devlin,B. and Roeder,K. (1999) Genomic control for association studies. Biometrics, 55, 997-1004.
5. Devlin,B. et al. (2001) Genomic control, a new approach to genetic-based association studies. Theor. Popul. Biol., 60, 155-166.
6. Ferguson,T.S. (1974) Prior distributions on spaces of probability measures. Ann. Stat., 2, 615-629.
7. Geisser,S. and Eddy,W.F. (1979) A predictive approach to model selection. J. Am. Stat. Assoc., 74, 153-160.
8. Han,C. and Carlin,B.P (2001) Markov chain Monte Carlo methods for computing Bayes factors: A comparative review. J. Am. Stat. Assoc. 96, 1122-1132.
9. Hanson,T. (2006) Inference for mixtures of finite Polya tree models. J. Am. Stat. Assoc., 101, 1548-1565.
10. Hardy,O.J. and Vekemans,X. (2002) SPAGeDi: A versatile computer program to analyse spatial genetic structure at the individual or population levels. Mol. Ecol. Notes, 2, 618-620.
11. Hastbacka,J. et al. (1992) Linkage disequilibrium mapping in isolated founder populations: Diastrophic dysplasia in Finland. Nat. Genet., 2, 204-211.
12. Hoggart,C.J. et al. (2003) Control of confounding of genetic associations in stratified populations. Am. J. Hum. Genet., 72 1492-1504.
13. Jakobsson,M. et al. (2008) Genotype, haplotype and copy-number variation in worldwide human populations. Nature, 451, 998-1003.
14. Kang,H.K. et al. (2008) Efficient control of population structure in model organism association mapping. Genetics, 178, 1709-1723.
15. Kass,R.E. and Raftery,A.E. (1995) Bayes factors. J. Am. Stat. Assoc. 90, 773-795.
16. Kelker,D. and Kelker,H. (1986) The effect of skewness on selection in a plant breeding program. Euphytica, 99, 33-54.
17. Lacher,D. (1987) Interpretation of laboratory results using multidimensional scaling and principal component analysis. Ann. Clin. Lab. Sci., 17, 412-417.
18. Lander,E.S. and Schork,N.J. (1994) Genetic dissection of complex traits. Science, 99, 33-54.
19. Lavine,M. (1992) Some aspects of Polya tree distributions for statistical modeling. Ann. Stat., 20, 1222-1235.
20. Lee,I. and Amasino,R.M. (1995) Effect of vernalization, photoperiod, and light quality on the flowering phenotype of arabidopsis plants containing the FRIGIDA gene. Plant Physiol., 108, 157-162.
21. Leisch,F. et al. (1998) On the generation of correlated artificial binary data. In Working Article Series, SFB 'Adaptive Information Systems and Modelling in Economics and Management Science', Vienna University of Economics.
22. Lettre,G. et al. (2007) Genetic model testing and statistical power in population-based association studies of quantitative traits. Genet. Epidemiol., 31, 358-362.
23. Long,A.D. and Langley,C.H. (1999) The power of association studies to detect the contribution of candidate genetic loci to variation in complex traits. Genome Res., 9, 720-731.
24. Morton,N.E. (1984) Trials of segregation analysis by deterministic and macro simulation. In Chakravarti,A. (ed.) Human Population Genetics: The Pittsburgh Symposium. Van Nostrand Reinhold, New York. pp. 83-107.
25. Nordborg,M. et al. (2005) The pattern of polymorphism in Arabidopsis thaliana. PLoS Biol., 3, e196.
26. Price,A.L. et al. (2006) Principal components analysis corrects for stratification in genome-wide association studies. Nat. Genet. 38, 904-909.
27. Pritchard,J.K. and Donnelly,P. (2001) Case-control studies of association in structured or admixtured populations. Theor. Popul. Biol., 60, 227-237.
28. Pritchard,J.K. et al. (2000) Inference of population structure using multilocus genotype data. Genetics, 155, 945-959.
29. Rajeevan,H. (2003) ALFRED the ALlele FREquency Database update. Nucleic Acids Res., 31, 270-271.
30. Redden,D.T. et al. (2006) Regional admixture mapping and structured association testing: Conceptual unificcation and an extensible general linear model. PLoS Genet., 2, e137.
31. Reich,D.E. and Goldstein,D.B. (2001) Detecting association in a case-control study while correcting for population stratification. Genet. Epidemiol., 20, 4-16.
32. Ritland,K. (1996) Estimators for pairwise relatedness and individual inbreeding coefficients. Genet. Res., 67, 175-185.
33. Rogers,J.S. (1972) Measures of genetic similarity and genetic distance. Studies in genetics, VII. Univ. Tex. Publ.,, 2713, 145-153.
34. Tommasini,L. et al. (2007) Association mapping of Stagonospora nodorum blotch resistance in modern European winter wheat varieties. TAG Theor. Appl. Genet., 115, 697-708.
35. Wickelmaier,F. (2003) An Introduction to MDS.Available at http://perception.inrialpes.fr/~Arnaud/indexation/mds03.pdf
36. Wessel,J. and Schork,N.J. (2006) Generalized genomic distance based regression methodology for multilocus association analysis. Am. J. Hum. Gen., 79, 792-807.
37. Yu,J. et al. (2006) A unified mixed-model method for association mapping that accounts for multiple levels of relatedness. Nat. Genet. 38, 203-208.
38. Zhang,S. et al. (2003) On a semiparametric test to detect associations between quantitative traits and candidate genes using unrelated individuals. Genet. Epidemiol., 24, 44-56.
39. Zhang,L. et al. (2006) Bayesian modeling for genetic association in case-control studies: Accounting for unknown population substructure. Stat. Modelling, 6, 352-372.
40. Zhao,K. et al. (2007) An arabidopsis example of association mapping in structured samples, PLoS Genet., 3, e4.