MACOED: A multi-objective ant colony optimization algorithm for SNP epistasis detection in genome-wide association studies

Bioinformatics

Volumn 31, Issue 5, 2015, Pages 634-641

  Jing, Peng Jie ^a,b   Shen, Hong Bin ^a,b  

^a SHANGHAI JIAO TONG UNIVERSITY   (China)

^b BEIJING UNIVERSITY OF POSTS AND TELECOMMUNICATIONS   (China)

Author keywords

[No Author keywords available]

Indexed keywords

ALGORITHM; ANIMAL; ANT; BAYES THEOREM; BIOLOGICAL MODEL; EPISTASIS; GENETIC ASSOCIATION; GENETICS; GENOME; SINGLE NUCLEOTIDE POLYMORPHISM; STATISTICAL MODEL;

ALGORITHMS; ANIMALS; ANTS; BAYES THEOREM; EPISTASIS, GENETIC; GENOME; GENOME-WIDE ASSOCIATION STUDY; LOGISTIC MODELS; MODELS, BIOLOGICAL; POLYMORPHISM, SINGLE NUCLEOTIDE;

EID: 84928987535     PISSN: 13674803     EISSN: 14602059     Source Type: Journal    
DOI: 10.1093/bioinformatics/btu702     Document Type: Article

References (24)

1. Avramopoulos, D. (2009) Genetics of Alzheimer's disease: recent advances. Genome Med., 1, 34.
2. Balding, D.J. (2006) A tutorial on statistical methods for population association studies. Nat. Rev. Genet., 7, 781-791.
3. Burton, P.R. et al. (2007) Genome-wide association study of 14, 000 cases of seven common diseases and 3, 000 shared controls. Nature, 447, 661-678.
4. Chaharsooghi, S.K. et al. (2008) An effective ant colony optimization algorithm (ACO) for multi-objective resource allocation problem (MORAP). Appl. Math. Comput., 200, 167-177.
5. Churchill, G.A. et al. (2004) The Collaborative Cross, a community resource for the genetic analysis of complex traits. Nat. Genet., 36, 1133-1137.
6. Deb, K. (1999) Multi-objective genetic algorithms: problem difficulties and construction of test problems. Evol. Comput., 7, 205-230.
7. Deb, K. et al. (2002) A fast and elitist multiobjective genetic algorithm: NSGA-II. IEEE Trans. Evol. Comput., 6, 182-197.
8. Fontanesi, L. et al. (2012) A genome wide association study for backfat thickness in Italian Large White pigs highlights new regions affecting fat deposition including neuronal genes. BMC Genomics, 13, 583.
9. Greene, C.S. et al. (2008) Ant colony optimization for genome-wide genetic analysis. In D., Marco et al (eds). Ant Colony Optimization and Swarm Intelligence. Springer, Heidelberg, pp. 37-47.
10. Han, B. et al. (2012) Genetic studies of complex human diseases: characterizing SNP-disease associations using Bayesian networks. BMC Syst. Biol., 6, S14.
11. Jiang, X. et al. (2011) Learning genetic epistasis using Bayesian network scoring criteria. BMC Bioinformatics, 12, 89.
12. Moore, J.H. et al. (2010) Bioinformatics challenges for genome-wide association studies. Bioinformatics, 26, 445-455.
13. North, B.V. et al. (2005) Application of logistic regression to case-control association studies involving two causative loci. Hum. Hered., 59, 79-87.
14. Reiman, E.M. et al. (2007) GAB2 alleles modify Alzheimer's risk in APOE epsilon4 carriers. Neuron, 54, 713-720.
15. 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.
16. Shang, J. et al. (2011) Performance analysis of novel methods for detecting epistasis. BMC Bioinformatics, 12, 475.
17. Urbanowicz, R.J. et al. (2012) GAMETES: a fast, direct algorithm for generating pure, strict, epistatic models with random architectures. BioData Mining, 5, 1-14.
18. Van Steen, K. (2012) Travelling the world of gene-gene interactions. Brief. Bioinform., 13, 1-19.
19. Wan, X. et al. (2010) BOOST: a fast approach to detecting gene-gene interactions in genome-wide case-control studies. Am. J. Hum. Genet., 87, 325-340.
20. Wang, Y. et al. (2010) AntEpiSeeker: detecting epistatic interactions for case-control studies using a two-stage ant colony optimization algorithm. BMC Res. Notes, 3, 117.
21. Wu, T.T. et al. (2009) Genome-wide association analysis by lasso penalized logistic regression. Bioinformatics, 25, 714-721.
22. Xie, M. et al. (2012) Detecting genome-wide epistases based on the clustering of relatively frequent items. Bioinformatics, 28, 5-12.
23. Zhang, X. et al. (2012) Mining genome-wide genetic markers. PLoS Comput. Biol., 8, e1002828.
24. Zhang, Y. and Liu, J.S. (2007) Bayesian inference of epistatic interactions in case-control studies. Nat. Genet., 39, 1167-1173.