Power of multifactor dimensionality reduction and penalized logistic regression for detecting gene-gene Interaction in a case-control study

BMC Medical Genetics

Volumn 10, Issue , 2009, Pages

  He, Hua ^a   Oetting, William S ^b   Brott, Marcia J ^b   Basu, Saonli ^a  

^a UNIVERSITY OF MINNESOTA   (United States)

^b UNIVERSITY OF MINNESOTA   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ABC TRANSPORTER; ANKYRIN; B LYMPHOCYTE GROWTH FACTOR; FRIZZLED PROTEIN; GLUCURONOSYLTRANSFERASE 1A9; MUCIN 1; MULTIDRUG RESISTANCE PROTEIN 1; PROTEIN TYROSINE KINASE; REPLICATION FACTOR C; SOMATOMEDIN BINDING PROTEIN 1; SUPEROXIDE DISMUTASE; VITAMIN D RECEPTOR;

ACUTE GRAFT REJECTION; ADULT; ARTICLE; CASE CONTROL STUDY; CONTROLLED STUDY; EFFECT SIZE; FEMALE; GENE FREQUENCY; GENE INTERACTION; GENOTYPE; HUMAN; HUMAN CELL; INTERMETHOD COMPARISON; KIDNEY GRAFT REJECTION; KIDNEY TRANSPLANTATION; LOGISTIC REGRESSION ANALYSIS; MAJOR CLINICAL STUDY; MALE; NONPARAMETRIC TEST; PENETRANCE; PROBABILITY; PROCESS MODEL; RECEIVER OPERATING CHARACTERISTIC; SINGLE NUCLEOTIDE POLYMORPHISM; ALGORITHM; COMPUTER SIMULATION; GENETIC EPISTASIS; STATISTICAL MODEL;

ALGORITHMS; CASE-CONTROL STUDIES; COMPUTER SIMULATION; EPISTASIS, GENETIC; LOGISTIC MODELS; MODELS, STATISTICAL; POLYMORPHISM, SINGLE NUCLEOTIDE;

EID: 74049126629     PISSN: None     EISSN: 14712350     Source Type: Journal    
DOI: 10.1186/1471-2350-10-127     Document Type: Article

References (31)

1. Glazier AM, Nadeau JH, Aitman TJ. Finding Genes That underlie Complex Traits. Science 2002, 298:2345-2349. 10.1126/science.1076641, 12493905.
2. Dreyer SD, Zhou G, Baldini A, Winterpacht A, Zabel B, Cole W, Johnson R, Lee B. Mutations in LMX1B cause abnormal skeletal patterning and renal dysplasia in nail patella syndrome. Nature Genetics 1998, 19:47-50. 10.1038/ng0598-47, 9590287.
3. Kerem B, Rommens J, Buchanan J, Markiewicz D, Cox T, Chakravarti A, Buchwald M, Tsui L. Identification of the Cystic-Fibrosis Gene - Genetic Analysis. Science 1989, 245:1073-1080. 10.1126/science.2570460, 2570460.
4. Hollander WF. Epistasis and hypostasis. J Hered 1955, 46:222-225.
5. Phillips PC. The language of gene interaction. Genetics 1998, 149:1167-1171. 1460246, 9649511.
6. Tyler AL, Asselbergs FW, Williams SM, Moore JH. Shadows of complexity: what biological networks reveal about epistasis and pleiotropy. Bioessays 2009, 31(2):220-227. 10.1002/bies.200800022, 19204994.
7. Bateson W. Mendels Principles of Heredity 1909, Cambridge University Press, Cambridge.
8. Fisher RA. The correlation between relatives on the supposition of Mendelian inheritance. Trans R Soc Edinb 1918, 52:399-433.
9. Moore JH, Williams SM. Traversing the conceptual divide between biological and statistical epistasis: systems biology and a more modern synthesis. BioEssays 2005, 27:637-646. 10.1002/bies.20236, 15892116.
10. Park M, Hastie T. Penalized logistic regression for detecting gene interactions. Biostatistics 2008, 9(1):30-50. 10.1093/biostatistics/kxm010, 17429103.
11. Tibshirani R. Regression shrinkage and selection via the Lasso. J R Stat Soc 1996, 58:267-288.
12. Kooperberg C, Ruczinski I, LeBlanc M, Hsu L. Sequence Analysis using Logic Regression. Genet Epidemiol 2001, 21(1):S626-S631.
13. Ritchie MD, Hahn LW, Roodi N, Bailey LR, Dupont WD, Parl FF, Moore JH. Multifactor-dimensionality Reduction Reveals HighOrder Interactions among Estrogen-Metabolism Genes in Sporadic Breast Cancer. Am J Hum Genet 2001, 69:138-147. 10.1086/321276, 1226028, 11404819.
14. Huang J, Lin A, Narasimhan B, Quertermous T, Hsiung C, Ho L, Grove J, Oliver M, Ranade K, Risch N. Tree-structured supervised learning and the genetics of hypertension. Proc Natl Acad Sci USA 2004, 101:10529-10534. 10.1073/pnas.0403794101, 489971, 15249660.
15. 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. 10.1101/gr.172901, 311041, 11230170.
16. Mandic D, Chambers J. Recurrent Neural Networks for Prediction: Architectures, Learning algorithms and Stability 2001, Wiley, London.
17. Ritchie MD, Hahn LW, Moore JH. Power of multifactor dimensionality reduction for detecting gene-gene interactions in the presence of genotyping error, missing data, phenocopy, and genetic heterogeneity. Genet Epidemiol 2003, 24:150-157. 10.1002/gepi.10218, 12548676.
18. Motsinger-Reif AA, Reif DM, Fanelli TJ, Ritchie MD. A Comparison of Analytical Methods for Genetic Association Studies. Genet Epidemiology 2008, 32:767-778. 10.1002/gepi.20345, 18561203.
19. Van Ness B, Ramos C, Haznadar M, Hoering A, Haessler J, Crowley J, Jacobus S, Oken M, Rajkumar V, Greipp P, Barlogie B, Durie B, Katz M, Atluri G, Fang G, Gupta R, Steinbach M, Kumar V, Mushlin R, Johnson D, Morgan G. Genomic variation in myeloma: design, content, and initial application of the Bank On A Cure SNP Panel to detect associations with progression-free survival. BMC Medicine 2008, 6:26. 10.1186/1741-7015-6-26, 2553089, 18778477.
20. Hardenbol P, Baner J, Jain M, Nilsson M, Namsaraev E, Karlin-Neumann G, Fakhrai-Rad H, Ronaghi M, Willis T, Landegren U, Davis R. Multiplexed genotyping with sequence-tagged molecular inversion probes. Nat Biotechnol 2003, 21(6):673-678. 10.1038/nbt821, 12730666.
21. Gradhand U, Kim R. Pharmacogenomics of MRP transporters (ABCC1-5) and BCRP (ABCG2). Drug Metab Rev 2008, 40(2):317-354. 10.1080/03602530801952617, 18464048.
22. Azarpira N, Bagheri M, Raisjalali G, Aghdaie M, Behzadi S, Salahi H, Rahsaz M, Darai M, Ashraf M, Geramizadeh B. Angiotensinogen, angiotensine converting enzyme and plasminogen activator inhibitor-1 gene polymorphism in chronic allograft dysfunction. Mol Biol Rep 2008, 44(1):86-91.
23. Madura K. Rad23 and Rpn10: perennial wallflowers join the melee. Trends Biochem Sci 2004, 29(12):637-640. 10.1016/j.tibs.2004.10.008, 15544949.
24. Zou L, Liu D, Elledge S. Replication protein A-mediated recruitment and activation of Rad17 complexes. Proc Natl Acad Sci USA 2003, 100(24):13827-13832. 10.1073/pnas.2336100100, 283506, 14605214.
25. Wang M, Windgassen D, Papoutsakis E. A global transcriptional view of apoptosis in human T-cell activation. BMC Med Genomics 2008, 23:1-53.
26. Moore JH, Gilbert JC, Tsai CT, Chiang FT, Holden T, Barney N, White BC. 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(2):252-61. 10.1016/j.jtbi.2005.11.036, 16457852.
27. Moore J. Analysis of Gene-Gene Interactions 2008, (Unit 1.14). Wiley-Liss, Inc., New York, Dracopoli NC, Haines JL, Korf BR, Moir DT, Morton CC, Seidman CE, Seidman JG, Smith DR, 2.
28. Hastie T, Tibshirani R, Friedman J. The Elements of Statistical Learning: Data Mining, Inference, and Prediction 2001, Springer, New York.
29. Good PI. Permutation Tests: A Practical Guide to Resampling Methods for Testing Hypothesis 2000, Springer, New York.
30. Coffey CS, Hebert PR, Ritchie MD, Krumholz HM, Morgan TM, Gaziano JM, Ridker PM, Moore JH. An application of conditional logistic regression and multifactor dimensionality reduction for detecting genegene interactions on risk of myocardial infarction: the importance of model validation. BMC Bioinform 2004, 4:49.
31. Hastie T, Tibshirani R. Generalized Additive Models 1999, CHAPMAN & HALL/CRC, Boca Raton.