Odds ratio-based genetic algorithms for generating SNP barcodes of genotypes to predict disease susceptibility

OMICS A Journal of Integrative Biology

Volumn 12, Issue 1, 2008, Pages 71-81

  Chang, Hsueh Wei ^a   Chuang, Li Yeh ^b   Ho, Chang Hsuan ^d   Chang, Phei Lang ^c   Yang, Cheng Hong ^d  

^a KAOHSIUNG MEDICAL UNIVERSITY   (Taiwan)

^b I SHOU UNIVERSITY   (Taiwan)

^c CHANG GUNG UNIVERSITY   (Taiwan)

^d NATIONAL KAOHSIUNG UNIVERSITY OF APPLIED SCIENCES   (Taiwan)

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; BONE DENSITY; DISEASE PREDISPOSITION; GENETIC ALGORITHM; GENETIC RISK; GENOTYPE; OSTEOPOROSIS; PRIORITY JOURNAL; SINGLE NUCLEOTIDE POLYMORPHISM;

ALGORITHMS; AUTOMATIC DATA PROCESSING; BODY MASS INDEX; GENETIC PREDISPOSITION TO DISEASE; GENOTYPE; HUMANS; ODDS RATIO; POLYMORPHISM, SINGLE NUCLEOTIDE;

EID: 40349093248     PISSN: 15362310     EISSN: None     Source Type: Journal    
DOI: 10.1089/omi.2007.0036     Document Type: Article

References (35)

1. ABERLE, J., HOPFER, I., BEIL, F.U., et al. (2006). Association of peroxisome proliferator-activated receptor delta +294T/C with body mass index and interaction with peroxisome proliferator-activated receptor alpha L162V. Int J Obes (Lond) 30, 1709-1713.
2. BAIER, R.J., LOGGINS, J., and YANAMANDRA, K. (2006). IL-10, IL-6 and CD14 polymorphisms and sepsis outcome in ventilated very low birth weight infants. BMC Med 4, 10.
3. BROOKES, A.J. (1999). The essence of SNPs. Gene 234, 177-186.
4. CANTOR, C.R. (2005). The use of genetic SNPs as new diagnostic markers in preventive medicine. Ann N Y Acad Sci 1055, 48-57.
5. CARNEIRO, A., LEITE, P., SILVA FILHO, D., et al. (1998). Genetic algorithms applied to hydrothermal system scheduling. Proceedings of the POWERCON apos;98. 1998 International Conference on Power System Technology vol. 1, 547-551.
6. CHUNG, Y., LEE, S.Y., ELSTON, R.C., et al. (2007). Odds ratio based multifactor-dimensionality reduction method for detecting gene-gene interactions. Bioinformatics 23, 71-76.
7. DAVIS, L. (1989). Adapting operator probabilities in genetic algorithms. Proceeding of the 3rd International Conference on Genetic algorithms.
8. DEB, K., AGRAWAL, S., PRATAP, A., et al. (2002). A fast elitist non-dominated sorting genetic algorithm for multiobjective optimization: NSGA-II. IEEE Trans. Evol. Comput. 6, 182-197.
9. DIAS ALEXANDRE, H.F., and DE VASCONCELOS, J.A. (2002). Multiobjective genetic algorithms applied to solve optimization problems. IEEE Trans Magnet 38, 1133-1136.
10. DUDBRIDGE, F., and KOELEMAN, B.P. (2004). Efficient computation of significance levels for multiple associations in large studies of correlated data, including genomewide association studies. Am J Hum Genet 75, 424-435.
11. GIGUERE, Y., and ROUSSEAU, F. (2000). The genetics of osteoporosis: 'complexities and difficulties'. Clin Genet 57, 161-169.
12. GOLDGERG, D.E. (1989). Genetic Algorithms in Search, Optimization, and Machine Learning. (Addison-Wesley, New York).
13. GRAY, I.C., CAMPBELL, D.A., and SPURR, N.K. (2000). Single nucleotide polymorphisms as tools in human genetics. Hum Mol Genet 9, 2403-2408.
14. HAMON, S.C., KARDIA, S.L., BOERWINKLE, E., et al. (2006). Evidence for consistent intragenic and intergenic interactions between SNP effects in the APOA1/C3/A4/A5 gene cluster. Hum Hered 61, 87-96.
15. HIRSCHHORN, J.N., and DALY, M.J. (2005). Genome-wide association studies for common diseases and complex traits. Nat Rev Genet 6, 95-108.
16. HOLLAND, J. (1992). Adaptation in Nature and Artificial Systems. (MIT Press, Cambridge, MA).
17. HOU, E.S., ANSARI, N., and REN, H. (1994). A genetic algorithm for multiprocessor scheduling. IEEE Trans Parallel Distrib Sys 5, 113-120.
18. KIM, S., and ZHANG, B.T. (2001). Evolutionary learning of web-document structure for information retrieval. 2001 Congr Evolut Comput 2, 1253-1260.
19. LI, J., and JI, L. (2005). Adjusting multiple testing in multilocus analyses using the eigenvalues of a correlation matrix. Heredity 95, 221-227.
20. LIN, G.T., TSENG, H.F., CHANG, C.K., et al. (2008). SNP combinations in chromosome-wide genes are associated with bone mineral density in Taiwanese women. Chin J Physiol 91, 1-10.
21. MCKINNEY, B.A., REIF, D.M., RITCHIE, M.D., et al. (2006). Machine learning for detecting gene-gene interactions: a review. Appl Bioinformatics 5, 77-88.
22. MUSANI, S.K., SHRINER, D., LIU, N., et al. (2007). Detection of gene x gene interactions in genome-wide association studies of human population data. Hum Hered 63, 67-84.
23. NELSON, M.R., KARDIA, S.L., FERRELL, R.E., et al. (2001). A combinatorial partitioning method to identify multilocus genotypic partitions that predict quantitative trait variation. Genome Res 11, 458-470.
24. OH, I.S., LEE, J.S., MOON, B.R. (2004). Hybrid genetic algorithms for feature selection. IEEE Trans Pattern Anal Machine Intell 26, 1424-1437.
25. PULLAN, W. (2003). Adapting the genetic algorithm to the traveling salesman problem. CEC '03. 2003 Congr Evolut Comput 2, 1029-1035.
26. RITCHIE, M.D., HAHN, L.W., ROODI, N., 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.
27. RITCHIE, M.D., WHITE, B.C., PARKER, J.S., et al. (2003). Optimization of neural network architecture using genetic programming improves detection and modeling of gene-gene interactions in studies of human diseases. BMC Bioinformatics 4, 28.
28. RIZZOLI, R., BONJOUR, J.P., FERRARI, S.L. (2001). Osteoporosis, genetics and hormones. J Mol Endocrinol 26, 79-94.
29. ROSES, A.D., SAUNDERS, A.M., HUANG, Y., et al. (2007). Complex disease-associated pharmacogenetics: drug efficacy, drug safety, and confirmation of a pathogenetic hypothesis (Alzheimer's disease). Pharmacogenomics J 7, 10-28.
30. SACHIDANANDAM, R., WEISSMAN, D., SCHMIDT, S.C., et al. (2001). A map of human genome sequence variation containing 1.42 million single nucleotide polymorphisms. Nature 409, 928-933.
31. SUMMERS, K.M., and BROCK, T.P. (2005). Impact of pharmacist-led community bone mineral density screenings. Ann Pharmacother 39, 243-248.
32. THORNTON-WELLS, T.A., MOORE, J.H., HAINES, J.L. (2004). Genetics, statistics and human disease: analytical retooling for complexity. Trends Genet 20, 640-647.
33. TSAI, C.F., TSAI, C.W., CHEN, C.P., et al. (2002). A multiple-searching approach to genetic algorithms for solving traveling salesman problem. Joint Conference on Information Sciences, pp. 362-366.
34. VAFAIE, H., and DE JONG, K. (1992). Genetic algorithms as a tool for feature selection in machine learning. Proceeding of the 4th International Conference on Tools with Artificial Intelligence, pp. 200-203.
35. WESTFALL, P.H., ZAYKIN, D.V., YOUNG, S.S. (2002). Multiple tests for genetic effects in association studies. Methods Mol Biol 184, 143-168.