Identification of gene-gene interactions in the presence of missing data using the multifactor dimensionality reduction method

Genetic Epidemiology

Volumn 33, Issue 7, 2009, Pages 646-656

  Namkung, Junghyun ^a,b   Elston, Robert C ^c   Yang, Jun Mo ^b   Park, Taesung ^a  

^a Seoul National University   (South Korea)

^b Sungkyunkwan University School of Medicine   (South Korea)

^c CASE WESTERN RESERVE UNIVERSITY   (United States)

Author keywords

Association study; Gene gene interaction; Missing genotypes; Multifactor dimensionality reduction

Indexed keywords

ARTICLE; ATOPIC DERMATITIS; CONTROLLED STUDY; DATA ANALYSIS; DATA MINING; DISEASE PREDISPOSITION; GENE INTERACTION; GENE LOCUS; GENETIC TRAIT; GENOTYPE; SIMULATION;

ALGORITHMS; CASE-CONTROL STUDIES; CHROMOSOME MAPPING; COMPUTER SIMULATION; EXONS; GENETIC PREDISPOSITION TO DISEASE; GENOTYPE; HUMANS; INTRONS; MODELS, GENETIC; MODELS, STATISTICAL; MOLECULAR EPIDEMIOLOGY; ODDS RATIO; PATTERN RECOGNITION, AUTOMATED; PROMOTER REGIONS, GENETIC;

EID: 69449084184     PISSN: 07410395     EISSN: 10982272     Source Type: Journal    
DOI: 10.1002/gepi.20416     Document Type: Article

References (23)

1. Andrew AS, Nelson HH, Kelsey KT, Moore JH, Meng AC, Casella DP, Tosteson TD, Schned AR, Karagas MR. 2006. Concordance of multiple analytical approaches demonstrates a complex relationship between DNA repair gene SNPs, smoking and bladder cancer susceptibility. Carcinogenesis 27:1030-1037.
2. Bush WS, Dudek SM, Ritchie MD. 2006. Parallel multifactor dimensionality reduction: a tool for the large-scale analysis of gene-gene interactions. Bioinformatics 22:2173-2174.
3. Chung Y, Lee SY, Elston RC, Park T. 2007. Odds ratio based multifactor-dimensionality reduction method for detecting genegene interactions. Bioinformatics 23:71-76. (Pubitemid 46017858)
4. Dempster AP, Laird NM, Rubin DB. 1977. Maximum likelihood from incomplete data via the EM algorithm. J Roy Stat Soc B 39:1-38.
5. Hahn LW, Ritchie MD, Moore JH. 2003. Multifactor dimensionality reduction software for detecting gene-gene and gene-environment interactions. Bioinformatics 19:376-382.
6. Kim HT, Lee JY, Han BG, Kimm K, Oh B, Shin HD, Namkung JH, Kim E, Park T, Yang JM. 2007. Association analysis of sphingomyelinase 2 polymorphisms for the extrinsic type of atopic dermatitis in Koreans. J Dermatol Sci 46:143-146. (Pubitemid 46467281)
7. Little RJA, Rubin DB. 2002. Statistical Analysis with Missing Data, 2nd edition. New York: Wiley-Interscience.
8. Moore JH. 2003. The ubiquitous nature of epistasis in determining susceptibility to common human diseases. Hum Hered 56: 73-82.
9. Moore JH, Williams SM. 2002. New strategies for identifying genegene interactions in hypertension. Ann Med 34:88-95.
10. Moore JH, Gilbert JC, Tsai CT, Chiang FT, Holden T, Barney N, White BC. 2006. A flexible computational framework for detecting, characterizing, and interpreting statistical patterns of epistasis in genetic studies of human disease susceptibility. J Theor Biol 241:252-261. (Pubitemid 43993963)
11. Motsinger AA, Ritchie MD. 2006. Multifactor dimensionality reduction: an analysis strategy for modelling and detecting gene-gene interactions in human genetics and pharmacogenomics studies. Hum Genomics 2:318-328.
12. Qin ZS, Niu T, Liu JS. 2002. Partition-ligation-expectation maximization algorithm for haplotype inference with single nucleotide polymorphisms. Am J Hum Genet 71:1242-1247. (Pubitemid 35305248)
13. Risch N. 1990. Linkage strategies for genetically complex traits. I. Multilocus models. Am J Hum Genet 46:222-228. (Pubitemid 20077590)
14. Ritchie MD, Hahn LW, Roodi N, Bailey LR, Dupont WD, Parl FF, Moore JH. 2001. Multifactor-dimensionality reduction reveals high-order interactions among estrogen-metabolism genes in sporadic breast cancer. Am J Hum Genet 69:138-147. (Pubitemid 32614026)
15. Ritchie MD, Hahn LW, Moore JH. 2003. Power of multifactor dimensionality reduction for detecting gene-gene interactions in the presence of genotyping error, missing data, phenocopy, and genetic heterogeneity. Genet Epidemiol 24:150-157.
16. Scheet P, Stephens M. 2006. A fast and flexible statistical model for largescale population genotype data: applications to inferring missing genotypes and haplotypic phase. Am J Hum Genet 78:629-644.
17. Schultz Larsen F. 1993. Atopic dermatitis: a genetic-epidemiologic study in a population-based twin sample. J Am Acad Dermatol 28:719-723.
18. Sherriff A, Ott J. 2001. Applications of neural networks for gene finding. Adv Genet 42:287-297. (Pubitemid 33804420)
19. Tahri-Daizadeh N, Tregouet DA, Nicaud V, Manuel N, Cambien F, Tiret L. 2003. Automated detection of informative combined effects in genetic association studies of complex traits. Genome Res 13:1952-1960. (Pubitemid 36987203)
20. Velez DR, White BC, Motsinger AA, Bush WS, Ritchie MD, Williams SM, Moore JH. 2007. A balanced accuracy function for epistasis modeling in imbalanced datasets using multifactor dimensionality reduction. Genet Epidemiol 31:306-315.
21. Wolf JB, Brodie ED, Wade MJ. 2000. Epistatsis and the Evolutionary Process. Oxford: Oxford University Press.
22. Wu CFJ. 1983. On the convergence properties of the EM algorithm. Ann Stat 11:95-103.
23. Zhang H, Bonney G. 2000. Use of classification trees for association studies. Genet Epidemiol 19:323-332. (Pubitemid 30951896)