TEAM: Efficient two-locus epistasis tests in human genome-wide association study

Bioinformatics

Volumn 26, Issue 12, 2010, Pages

  Zhang, Xiang ^a   Huang, Shunping ^a   Zou, Fei ^b   Wang, Wei ^a  

^a UNIVERSITY OF NORTH CAROLINA   (United States)

^b IL   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ALGORITHM; ARTICLE; COMPUTER PROGRAM; ETHNIC AND RACIAL GROUPS; GENETIC ASSOCIATION; GENETIC EPISTASIS; GENETICS; GENOMICS; HUMAN; HUMAN GENOME; METHODOLOGY;

ALGORITHMS; EPISTASIS, GENETIC; GENOME, HUMAN; GENOME-WIDE ASSOCIATION STUDY; GENOMICS; HUMANS; POPULATION GROUPS; SOFTWARE;

EID: 77954182718     PISSN: 13674803     EISSN: 14602059     Source Type: Journal    
DOI: 10.1093/bioinformatics/btq186     Document Type: Article

References (28)

1. Balding, D.J. (2006) A tutorial on statistical methods for population association studies. Nat. Rev. Genet., 7, 781-791.
2. Carlborg, O. et al. (2000) The use of a genetic algorithm for simultaneous mapping of multiple interacting quantitative trait loci. Genetics, 155, 2003-2010.
3. Churchill, G.A. and Doerge, R.W. (1994) Empirical threshold values for quantitative trait mapping. Genetics, 138, 963-971.
4. Cormen, T.H. et al. (2001) Introduction to Algorithms. MIT Press and McGraw-Hill.
5. Dudoit, S. and Laan, M.J. (2008) Multiple Testing Procedures with Applications to Genomics. Springer.
6. Eisner, J. (1997) State-of-the-art algorithms for minimum spanning trees: a tutorial discussion. Manuscript, University of Pennsylvania.
7. Evans, D.M. et al. (2006) Two-stage two-locus models in genome-wide association. PLoS Genet., 2, e157.
8. Graham, R.L. and Hell, P. (1985) On the history of the minimum spanning tree problem. Ann. History Comput., 7, 43-57.
9. Hirschhorn, J.N. and Daly, M.J. (2005) Genome-wide association studies for common diseases and complex traits. Nat. Rev. Genet., 6, 95-108.
10. Hoh, J. and Ott, J. (2003) Mathematical multi-locus approaches to localizing complex human trait genes. Nat. Rev. Genet., 4, 701-709.
11. Hoh, J. et al. (2000) Selecting snps in two-stage analysis of disease association data: a model-free approach. Ann. Hum. Genet., 64, 413-417.
12. Lewontin, R.C. and Kojima, K. (1960) The evolutionary dynamics of complex polymorphisms. Evolution, 14, 458-472.
13. Miller, R.G. (1981) Simultaneous Statistical Inference. Springer, New York.
14. Musani, S.K. et al. (2007) Detection of gene x gene interactions in genome-wide association studies of human population data. Hum. Hered., 63, 67-84.
15. Nelson, M.R. et al. (2001) A combinatorial partitioning method to identify multilocus genotypic partitions that predict quantitative trait variation. Genome Res., 11, 458-470.
16. Ritchie, M.D. et al. (2001) Multifactor-dimensionality reduction reveals high-order interactions among estrogen-metabolism genes in sporadic breast cancer. Am. J. Hum. Genet., 69, 138-147.
17. Roberts, A. et al. (2007) Inferring missing genotypes in large snp panels using fast nearest-neighbor searches over sliding windows. In Proceeding of ISMB.
18. Saxena, R. et al. (2007) Genome-wide association analysis identifies loci for type 2 diabetes and triglyceride levels. Science, 316, 1331-1336.
19. Scuteri, A. et al. (2007) Genome-wide association scan shows genetic variants in the fto gene are associated with obesity-related traits. PLoS Genet., 3, 1200-1210.
20. The Wellcome Trust Case Control Consortium (2007) Genome-wide association study of 14,000 cases of seven common diseases and 3,000 shared controls. Nature, 447, 661-678.
21. Wade, C.M. and Daly, M.J. (2005) Genetic variation in laboratory mice. Nat. Genet., 37, 1175-1180.
22. Weedon, M. et al. (2007) A common variant of hmga2 is associated with adult and childhood height in the general population. Nat. Genet., 39, 1245-1250.
23. Westfall, P.H. and Young, S.S. (1993) Resampling-based Multiple Testing. Wiley, New York.
24. Wright, F.A. et al. (2007) Simulating association studies: a data-based resampling method for candidate regions or whole genome scans. Bioinformatics, 23, 2581-2588.
25. Yang, C. et al. (2009) SNPHarvester: a filtering-based approach for detecting epistatic interactions in genomewide association studies. Bioinformatics, 25, 504-511.
26. Zhang, X. et al. (2008) FastANOVA: an efficient algorithm for genome-wide association study. In Proceeding of KDD.
27. Zhang, X. et al. (2009a) COE: a general approach for efficient genome-wide two-locus epistatic test in disease association study. In Proceeding of RECOMB.
28. Zhang, X. et al. (2009b) FastChi: an efficient algorithm for analyzing gene-gene interactions. In Proceeding of PSB.