A gene-based method for detecting gene-gene co-association in a case-control association study

European Journal of Human Genetics

Volumn 18, Issue 5, 2010, Pages 582-587

  Peng, Qianqian ^a   Zhao, Jinghua ^b   Xue, Fuzhong ^a  

^a SHANDONG UNIVERSITY   (China)

^b ADDENBROOKE S HOSPITAL   (United Kingdom)

Author keywords

Canonical correlation; Gene based; Gene gene co association

Indexed keywords

DELTA OPIATE RECEPTOR; KAPPA OPIATE RECEPTOR; MU OPIATE RECEPTOR;

ANALYTICAL ERROR; ARTICLE; CASE CONTROL STUDY; COMPUTER PROGRAM; CONTROLLED STUDY; CORRELATION ANALYSIS; GENE INTERACTION; GENE LINKAGE DISEQUILIBRIUM; GENETIC ASSOCIATION; GENETIC CORRELATION; HUMAN; NULL HYPOTHESIS; PRIORITY JOURNAL; SAMPLE SIZE; SINGLE NUCLEOTIDE POLYMORPHISM; STATISTICAL ANALYSIS;

CASE-CONTROL STUDIES; GENES; GENOME-WIDE ASSOCIATION STUDY; HUMANS; LINKAGE DISEQUILIBRIUM; MODELS, GENETIC; MODELS, STATISTICAL; POLYMORPHISM, SINGLE NUCLEOTIDE;

EID: 77951622841     PISSN: 10184813     EISSN: 14765438     Source Type: Journal    
DOI: 10.1038/ejhg.2009.223     Document Type: Article

References (40)

1. Wu XS, Jin L, Xiong MM: Composite measure of linkage disequilibrium for testing interaction between unlinked loci. Eur J Hum Genet 2008; 16: 1160.
2. Moore JH: A global view of epistasis. Nat Genet 2005; 37: 13-14.
3. Fisher RA: The correlation between relatives on the supposition of Mendelian inheritance. Philos Trans R Soc 1918; 52: 399-433.
4. Cockerham CC: An extension of the concept of partitioning hereditary variance for analysis of covariances among relatives when epistasis is present. Genetics 1954; 39: 859-882.
5. Kempthorne O: The correlation between relatives in a random mating population. Proc R Soc Lond B Biol Sci 1954; 143: 103-113.
6. Cordell HJ: Epistasis: what it means, what it doesn't mean, and statistical methods to detect it in humans. Hum Mol Genet 2002; 11: 2463-2468.
7. Zhao J, Jin L, Xiong M: Test for interaction between two unlinked loci. Am J Hum Genet 2006; 79: 831-845.
8. Brassat D, Motsinger AA, Caillier SJ et al: Multifactor dimensionality reduction reveals gene-gene interactions associated with multiple sclerosis susceptibility in African Americans. Genes Immun 2006; 7: 310-315.
9. Moore JH, Gilbert JC, Tsai CT et al: A flexible computational framework for detecting, characterizing, and interpreting statistical patterns of epistasis in genetic studies of human disease susceptibility. J Theor Biol 2006; 241: 252-261.
10. Nelson MR, Kardia SLR, Ferrell RE, Sing CF: A combinatorial partitioning method to identify multilocus genotypic partitions that predict quantitative trait variation. Genome Res 2001; 11: 458-470.
11. Moore JH, Hahn LW: A cellular automata approach to detecting interactions among single-nucleotide polymorphisms in complex multifactorial diseases. Pac Symp Biocomput 2002; 7: 53-64.
12. Chen CH, Chang CJ, Yang WS, Chen CL, Fann CS: A genome-wide scan using tree-based association analysis for candidate loci related to fasting plasma glucose levels. BMC Genet 2003; 4 (Suppl 1): S65.
13. Ccok NR, Zee RYL, Ridker PM: Tree and spline based association analysis of gene-gene interaction models for ischemic stroke. Stat Med 2004; 23: 1439-1453.
14. Bureau A, Dupuis J, Falls K et al: Identifying SNPs predictive of phenotype using random forests. Genet Epidemiol 2005; 28: 171-182.
15. Dong CZ, Chu X, Wang Y et al: Exploration of gene-gene interaction effects using entropy-based methods. Eur J Hum Genet 2008; 16: 229-235.
16. Kang G, Yue W, Zhang J, Cui Y, Zuo Y, Zhang D: An entropy-based approach for testing genetic epistasis underlying complex diseases. J Theor Biol 2008; 250: 362-374.
17. Zhang FY, Wagener D: An approach to incorporate linkage disequilibrium structure into genomic association analysis. J Genet Genomics 2008; 35: 381-385.
18. Gauderman WJ, Murcray C, Gilliland F, Conti DV: Testing association between disease and multiple SNPs in a candidate gene. Genet Epidemiol 2007; 31: 383-395.
19. Oh S, Park T: Association tests based on the principal-component analysis. BMC Proc 2007; 1 (Suppl 1): S130.
20. Hotelling H: Relations between two sets of variants. Biometrika 1936; 28: 321-377.
21. Hudson RR: Generating samples under a Wright-Fisher neutral model of genetic variation. Bioinformatics 2002; 18: 337-338.
22. Marchini J, Donnelly P, Cardon LR: Genome-wide strategies for detecting multiple loci that influence complex diseases. Nat Genet 2005; 37: 413-417.
23. Li WT, Reich J: A complete enumeration and classification of two-locus disease models. Hum Hered 2000; 50: 334-349.
24. Lawley DN: Tests of significance in canonical analysis. Biometrika 1959; 46: 59-66.
25. Konishi S: Normalizing transformations of some statistics in multivariate analysis. Biometrika 1981; 68: 647-651.
26. Fisher RA: On the 'probable error' of a coefficient of correlation deduced from a small sample. Metron 1921; 1: 3-32.
27. Konishi S: An approximation to the distribution of the sample correlation coefficient. Biometrika 1978; 65: 654-656.
28. Konishi S: Normalizing and variance stabilizing transformations for intraclass correlations. Ann Inst Stat Math 1985; 37: 87-94.
29. Zhang D, Shao C, Shao M et al: Effect of M-opioid receptor gene polymorphisms on heroin-induced subjective responses in a Chinese population. Biol Psychiatry 2007; 61: 1244-1251.
30. Plenge RM, Seielstad M, Padyukov L et al: TRAF1-C5 as a risk locus for rheumatoid arthritis\a genomewide study. N Engl J Med 2007; 357: 1199-1209.
31. Neale B, Sham P: The future of association studies: gene-based analysis and replication. Am J Hum Genet 2004; 75: 353-362.
32. Miettinen O: Confounding and effect-modification. Am J Epidemiol 1974; 100: 350-353.
33. Ahlbom A, Alfredsson L: Interaction: A word with two meanings creates confusion. Eur J Epidemiol 2005; 20: 563-564.
34. Sora I, Funada M, Uhl GR: The mu-opioid receptor is necessary for [D-Pen2,D-Pen5]enkephalin-induced analgesia. Eur J Pharmacol 1997; 324: R1-R2.
35. Becker A, Grecksch G, Brodemann R et al: Morphine self-administration in mu-opioid receptor-deficient mice. Naunyn-Schmiedebergs Arch Pharmacol 2000; 361: 584-589.
36. Gomes I, Jordan BA, Gupta A, Trapaidze N, Nagy V, Devi LA: Heterodimerization of mu and delta opioid receptors: A role in opiate synergy. J Neurosci 2000; 20: RC110.
37. Kieffer BL, Gaveriaux-Ruff C: Exploring the opioid system by gene knockout. Prog Neurobiol 2002; 66: 285-306.
38. Gomes I, Gupta A, Filipovska J, Szeto H, Pintar J, Devi L: A role for heterodimerization of mu and delta opiate receptors in enhancing morphine analgesia. Proc Natl Acad Sci USA 2004; 101: 5135-5139.
39. Snook L, Milligan G, Kieffer B, Massotte D: mu-delta opioid receptor functional interaction: Insight using receptor-G protein fusions. J Pharmacol Exp Ther 2006; 318: 683-690.
40. Jordan BA, Devi LA: G-protein-coupled receptor heterodimerization modulates receptor function. Nature 1999; 399: 697-700.