AntEpiSeeker: Detecting epistatic interactions for case-control studies using a two-stage ant colony optimization algorithm

BMC Research Notes

Volumn 3, Issue , 2010, Pages

  Wang, Yupeng ^a,b   Liu, Xinyu ^a,b   Robbins, Kelly ^a   Rekaya, Romdhane ^a,b  

^a UNIVERSITY OF GEORGIA   (United States)

^b UNIVERSITY OF GEORGIA   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

EID: 77953271464     PISSN: None     EISSN: 17560500     Source Type: Journal    
DOI: 10.1186/1756-0500-3-117     Document Type: Article

References (28)

1. Genetic association studies. HJ Cordell DG Clayton, Lancet 2005 366 1121 1131 10.1016/S0140-6736(05)67424-7 16182901
2. Epistasis: what it means, what it doesn't mean, and statistical methods to detect it in humans. HJ Cordell, Hum Mol Genet 2002 11 2463 2468 10.1093/hmg/11.20.2463 12351582
3. Multifactor-dimensionality reduction reveals high-order interactions among estrogen-metabolism genes in sporadic breast cancer. MD Ritchie LW Hahn N Roodi LR Bailey WD Dupont FF Parl JH Moore, Am J Hum Genet 2001 69 138 147 10.1086/321276 11404819
4. Multifactor-dimensionality reduction shows a two-locus interaction associated with type 2 diabetes mellitus. YM Cho MD Ritchie JH Moore JY Park KU Lee HD Shin HK Lee KS Park, Diabetologia 2004 47 549 554 10.1007/s00125-003- 1321-3 14730379
5. Renin-angiotensin system gene polymorphisms and atrial fibrillation. CT Tsai LP Lai JL Lin FT Chiang JJ Hwang MD Ritchie JH Moore KL Hsu CD Tseng CS Liau YZ Tseng, Circulation 2004 109 1640 1646 10.1161/01.CIR.0000124487.36586.26 15023884
6. A combinatorial partitioning method to identify multilocus genotypic partitions that predict quantitative trait variation. MR Nelson SL Kardia RE Ferrell CF Sing, Genome Res 2001 11 458 470 10.1101/gr.172901 11230170
7. Detecting epistatic interactions contributing to quantitative traits. R Culverhouse T Klein W Shannon, Genet Epidemiol 2004 27 141 152 10.1002/gepi.20006 15305330
8. A testing framework for identifying susceptibility genes in the presence of epistasis. J Millstein DV Conti FD Gilliland WJ Gauderman, Am J Hum Genet 2006 78 15 27 10.1086/498850 16385446
9. Backward genotype-trait association (BGTA) - based dissection of complex traits in case-control design. T Zeng H Wang SH Lo, Hum Hered 2006 62 196 212 10.1159/000096995 17114886
10. Complement factor H polymorphism in age-related macular degeneration. RJ Klein C Zeiss EY Chew JY Tsai RS Sackler C Haynes AK Henning JP SanGiovanni SM Mane ST Mayne,, et al. Science 2005 308 385 389 10.1126/science.1109557 15761122
11. Bayesian inference of epistatic interactions in case-control studies. Y Zhang JS Liu, Nat Genet 2007 39 1167 1173 10.1038/ng2110 17721534
12. SNPHarvester: a filtering-based approach for detecting epistatic interactions in genome-wide association studies. C Yang Z He X Wan Q Yang H Xue W Yu, Bioinformatics 2009 25 504 511 10.1093/bioinformatics/btn652 19098029
13. Ant colonies for the travelling salesman problem. M Dorigio LM Gambardella, Biosystems 1997 43 73 81 10.1016/S0303-2647(97)01708-5 9231906
14. Ant colony optimization for genome-wide genetic analysis. CS Greene BC White JH Moore, Lect Notes Comput Sci 2008 5217/2008 37 47 full-text 19526069
15. Optimal use of expert knowledge in ant colony optimization for the analysis of epistasis in human disease. CS Greene JM Gilmore J Kiralis PC Andrews JH Moore, Lect Notes Comput Sci 2009 5483/2009 92 103 full-text 20046968
16. Genome-wide strategies for detecting multiple loci that influence complex diseases. J Marchini P Donnelly LR Cardon, Nat Genet 2005 37 413 417 10.1038/ng1537 15793588
17. Parallel Ant Colonies for the quadratic assignment problem. EG Talbi O Roux C Fonlupt D Robillard, Future Generation Computer System 2001 17 441 449 10.1016/S0167-739X(99)00124-7 (Pubitemid 32092215)
18. An ANTS heuristic for the frequency assignment problem. V Maniezzo A Carbonaro, Future Generation Computer Systems 2000 16 927 935 10.1016/S0167-739X(00)00046-7
19. New Ideas in Optimization. M Dorigo G Di Caro, New Ideas in Optimization McGraw-Hill, Corne D, Dorigo M, Glover F, 1999
20. Ant Algorithms for Discrete Optimization. M Dorigo G Di Caro LM Gambardella, Artificial Life 1999 5 137 172 10.1162/106454699568728 10633574
21. The ant colony algorithm for feature selection in high-dimension gene expression data for disease classification. KR Robbins W Zhang JK Bertrand R Rekaya, Math Med Bio 2007 24 413 26 10.1093/imammb/dqn001
22. M Dorigo T Stützle, Ant Colony Optimization The MIT Press 2004
23. A random forest approach to the detection of epistatic interactions in case-control studies. R Jiang W Tang X Wu W Fu, BMC Bioinformatics 2009 10 Suppl 1 65 10.1186/1471-2105-10-S1-S65 19208169
24. MegaSNPHunter: a learning approach to detect disease predisposition SNPs and high level interactions in genome wide association study. X Wan C Yang Q Yang H Xue NL Tang W Yu, BMC Bioinformatics 2009 10 13 10.1186/1471-2105-10-13 19134182
25. The International HapMap Project. The International HapMap Consortium, Nature 2003 426 789 796 10.1038/nature02168 14685227
26. Genome-wide association study of 14,000 cases of seven common diseases and 3,000 shared controls. Wellcome Trust Case Control Consortium, Nature 2007 447 661 678 10.1038/nature05911 17554300
27. Two independent alleles at 6q23 associated with risk of rheumatoid arthritis. RM Plenge C Cotsapas L Davies AL Price PI de Bakker J Maller I Pe'er NP Burtt B Blumenstiel M DeFelice M Parkin R Barry W Winslow C Healy RR Graham BM Neale E Izmailova R Roubenoff AN Parker R Glass EW Karlson N Maher DA Hafler DM Lee MF Seldin EF Remmers AT Lee L Padyukov L Alfredsson J Coblyn ME Weinblatt SB Gabriel S Purcell L Klareskog PK Gregersen NA Shadick MJ Daly D Altshuler, Nat Genet 2007 39 1477 1482 10.1038/ng.2007.27 17982456
28. Common variants at CD40 and other loci confer risk of rheumatoid arthritis. S Raychaudhuri EF Remmers AT Lee R Hackett C Guiducci NP Burtt L Gianniny BD Korman L Padyukov FA Kurreeman M Chang JJ Catanese B Ding S Wong AH van der Helm-van Mil BM Neale J Coblyn J Cui PP Tak GJ Wolbink JB Crusius IE van der Horst-Bruinsma LA Criswell CI Amos MF Seldin DL Kastner KG Ardlie L Alfredsson KH Costenbader D Altshuler TW Huizinga NA Shadick ME Weinblatt N de Vries J Worthington M Seielstad RE Toes EW Karlson AB Begovich L Klareskog PK Gregersen MJ Daly RM Plenge, Nat Genet 2008 40 1216 1223 10.1038/ng.233 18794853