A novel variational Bayes multiple locus Z-statistic for genome-wide association studies with Bayesian model averaging

Bioinformatics

Volumn 28, Issue 13, 2012, Pages 1738-1744

  Logsdon, Benjamin A ^a   Carty, Cara L ^a   Reiner, Alexander P ^a   Dai, James Y ^a,b   Kooperberg, Charles ^a  

^a UNIVERSITY OF WASHINGTON   (United States)

^b USA   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

AFRICAN AMERICAN; ALGORITHM; ARTICLE; BAYES THEOREM; BODY HEIGHT; EVALUATION; GENE LOCUS; GENETIC ASSOCIATION; GENETICS; HUMAN; REGRESSION ANALYSIS; SINGLE NUCLEOTIDE POLYMORPHISM; STATISTICAL MODEL;

AFRICAN AMERICANS; ALGORITHMS; BAYES THEOREM; BODY HEIGHT; GENETIC LOCI; GENOME-WIDE ASSOCIATION STUDY; HUMANS; MODELS, STATISTICAL; POLYMORPHISM, SINGLE NUCLEOTIDE; REGRESSION ANALYSIS;

EID: 84863994823     PISSN: 13674803     EISSN: 14602059     Source Type: Journal    
DOI: 10.1093/bioinformatics/bts261     Document Type: Article

References (33)

1. Allen, H. et al. (2010) Hundreds of variants clustered in genomic loci and biological pathways affect human height. Nature, 467, 832-838.
2. Beal, M. (2003)Variational algorithms for approximate Bayesian inference. PhD Thesis, University of London.
3. Benjamini, Y. and Hochberg, Y. (1995) Controlling the false discovery rate: a practical and powerful approach to multiple testing. J. Roy. Stat. Soc. B. Met., 57, 289-300.
4. Bishop, C. (2006) Pattern Recognition and Machine Learning. Springer, New York.
5. Carbonetto, P. and Stephens, M. (2011) Scalable variational inference for bayesian variable selection in regression, and its accuracy in genetic association studies. Bayesian Analysis, 6, 1-42.
6. Carty, C.L. et al. (2011) Genome-wide association study of body height in africanamericans. Hum. Mol. Genet., 21, 711-720.
7. Chen, J. and Chen, Z. (2008) Extended bayesian information criteria for model selection with large model spaces. Biometrika, 95, 759-771.
8. Eichler, E. et al. (2010) Missing heritability and strategies for finding the underlying causes of complex disease. Nat. Rev. Genet., 11, 446-450.
9. Fan, J. and Li, R. (2001) Variable selection via nonconcave penalized likelihood and its oracle properties. J. Am. Stat. Assoc., 96, 1348-1360.
10. Friedman, R. et al. (2010) glmnet: Lasso and elastic-net regularized generalized linear models. J. Stat. Softw., 33, 1-22.
11. Gibson, G. (2010) Hints of hidden heritability in gwas. Nat. Genet., 42, 558-560.
12. He, Q. and Lin, D. (2011) A variable selection method for genome-wide association studies. Bioinformatics, 27, 1-8.
13. Hirschhorn, J. et al. (2001) Genomewide linkage analysis of stature in multiple populations reveals several regions with evidence of linkage to adult height. Am. J. Hum. Genet., 69, 106-116.
14. Hoggart, C. et al. (2008) Simultaneous analysis of all snps in genome-wide and resequencing association studies. PLoS Genet., 4, e1000130.
15. Kullback, S. and Leibler, R. (1951) On information and sufficiency. Ann. Math. Stat., 22, 79-86.
16. Li, J. et al. (2011) The bayesian lasso for genome-wide association studies. Bioinformatics, 27, 516-523.
17. Logsdon, B. et al. (2010) A variational bayes algorithm for fast and accurate multiple locus genome-wide association analysis. BMC Bioinformatics, 11, 58.
18. Maher, B. (2008) Personal genomes: the case of the missing heritability. Nature, 456, 18-21.
19. Makowsky, R. et al. (2011) Beyond missing heritability: prediction of complex traits. PLoS Genet., 7, e1002051.
20. Manolio, T. et al. (2009) Finding the missing heritability of complex diseases. Nature, 461, 747-753.
21. McCarthy, M. and Hirschhorn, J. (2008) Genome-wide association studies: potential next steps on a genetic journey. Hum. Mol. Genet., 17, R156-R165.
22. Parisi, G. (1988) Statistical Field Theory. Addison Wesley Publishing Company.
23. Price, A. et al. (2010) New approaches to population stratification in genome-wide association studies. Nat. Rev. Genet., 11, 459-463.
24. Sale, M. et al. (2005) Loci contributing to adult height and body mass index in african american families ascertained for type 2 diabetes. Ann. Hum. Genet., 69, 517-527.
25. Tibshirani, R. (1996) Regression shrinkage and selection via the lasso. J. Roy. Stat. Soc. B Met., 267-288.
26. Weedon, M. et al. (2008) Genome-wide association analysis identifies 20 loci that influence adult height. Nat. Genet., 40, 575-583.
27. The Women's Health Initiative Study Group (1998) Design of the women's health initiative clinial trial and observational study. Control Clin. Trials, 19, 61-109.
28. Wu, T. et al. (2009) Genome-wide association analysis by lasso penalized logistic regression. Bioinformatics, 25, 714-721.
29. Yang, J. et al. (2010) Common snps explain a large proportion of the heritability for human height. Nat. Genet., 42, 565-569.
30. Yen, T.J. (2011)Amajorization-minimization approach to variable selection using spike and slab priors. Ann. Stat., 39, 1748-1775.
31. Zhang, C. (2010) Nearly unbiased variable selection under minimax concave penalty. Ann. Stat., 38, 894-942.
32. Zhao, P. andYu, B. (2006) On model selection consistency of lasso. J. Mach. Learn Res., 7, 2541-2563.
33. Zou, H. et al. (2007) On the degrees of freedom of the lasso. Ann. Stat., 35, 2173-2192.