Identification of Interacting Genes in Genome-Wide Association Studies Using a Model-Based Two-Stage Approach

Annals of Human Genetics

Volumn 74, Issue 5, 2010, Pages 406-415

  Zhang, Zhaogong ^a,b   Niu, Adan ^a   Sha, Qiuying ^a  

^a MICHIGAN TECHNOLOGICAL UNIVERSITY   (United States)

^b HEILONGJIANG UNIVERSITY   (China)

Author keywords

[No Author keywords available]

Indexed keywords

AMYOTROPHIC LATERAL SCLEROSIS; ARTICLE; GENE FREQUENCY; GENE IDENTIFICATION; GENE INTERACTION; GENETIC HETEROGENEITY; GENOTYPE; HEREDITY; PATHOGENESIS; PRIORITY JOURNAL; SINGLE NUCLEOTIDE POLYMORPHISM; BIOLOGICAL MODEL; GENETIC ASSOCIATION; GENETIC PREDISPOSITION; GENETICS; HUMAN;

AMYOTROPHIC LATERAL SCLEROSIS; GENETIC PREDISPOSITION TO DISEASE; GENOME-WIDE ASSOCIATION STUDY; HUMANS; MODELS, GENETIC; POLYMORPHISM, SINGLE NUCLEOTIDE;

EID: 77955610154     PISSN: 00034800     EISSN: 14691809     Source Type: Journal    
DOI: 10.1111/j.1469-1809.2010.00594.x     Document Type: Article

References (27)

1. Arking D E, Pfeufer A, Post W, Kao W H, Newton-Cheh C, Ikeda M, West K, Kashuk C, Akyol M, Perz S, Jalilzadeh S, Illig T, Gieger C, Guo C Y, Larson M G, Wichmann H E, Marbán E, O'Donnell C J, Hirschhorn J N, Kääb S, Spooner P M, Meitinger T, Chakravarti A. A common genetic variant in the NOS1 regulator NOS1AP modulates cardiacrepolarization. Nat Genet 2006, 38:644-651.
2. Aston C E, Ralph D A, Lalo D P, Manjeshwar S, Gramling B A, Defreese D C, West A D, Branam D E, Thompson L F, Craft M A, Mitchell D S, Shimasaki C D, Mulvihill J J, Jupe E R. Oligogenic combinations associated with breast cancer risk in women under 53 years of age. Hum Genet 2005, 116:208-221.
3. Culverhouse R, Klein T, Shannon W. Detecting epistatic interactions contributing to quantitative traits. Genet Epidemiol 2004, 27:141-152.
4. Dong C, Li W D, Li D, Price R A. Interaction between obesity-susceptibility loci in chromosome regions 2p25-p24 and 13q13-q21. Eur J Hum Genet 2005, 13:102-108.
5. Evans D M, Marchini J, Morris A P, Cardon L R. Two-stage two-locus models in genome-wide association. PLoS. Genetics 2006, 2:1424-1432.
6. Herbert A, Gerry N P, McQueen M B, Heid I M, Pfeufer A, Illig T, Wichmann H E, Meitinger T, Hunter D, Hu F B, Colditz G, Hinney A, Hebebrand J, Koberwitz K, Zhu X, Cooper R, Ardlie K, Lyon H, Hirschhorn J N, Laird N M, Lenburg M E, Lange C, Christman M F. A common genetic variant is associated with adult and childhood obesity. Science 2006, 312:279-283.
7. Hildebrand J D, Soriano P. Shroom, a PDZ domain-containing actin-binding protein, is required for neural tube morphogenesis in mice. Cell 1999, 99:485-497.
8. Hodge S E. Some epistatic two-locus models of disease.I. Relative risks and identity-by-descent distributions in affected sib pairs. Am J Hum Genet 1981, 33:381-395.
9. A second generation human haplotype map of over 3.1 million SNPs. Nature 2007, 449:851-861. International HapMap Consortium
10. Katoh H, Negishi M. RhoG activates Rac1 by direct interaction with the Dock180-binding protein Elmo. Nature 2003, 424:461-464.
11. Marchini J, Donnelly P, Cardon L R. Genome-wide strategies for detecting multiple loci that influence complex diseases. Nat Genet 2005, 37:413-417.
12. Millstein J, Conti D V, Gilliland F D, Gauderman W J. A testing framework for identifying susceptibility genes in the presence of epistasis. Am J Hum Genet 2006, 78:15-27.
13. Moore J H. Computational analysis of gene-gene interactions using multifactor dimensionality reduction. Expert Review of Molecular Diagnostics 2004, 4:795-803.
14. Nelson M R, Kardia S L, Ferrell R E, Sing C F. A combinatorial partitioning method to identify multilocus genotypic partitions that predict quantitative trait variation. Genome Res 2001, 11:458-470.
15. Pickrell J, Clerget-Darpoux F, Bourgain C. Power of genome-wide association studies in the presence of interacting loci. Genet Epidemiol 2007, 31:748-762.
16. Risch N. Linkage strategies for genetically complex traits.I. Multilocus models. Am J Hum Genet 1990, 46:222-228.
17. Risch N J. Search for genetic determinations in the new millenium. Nature 2000, 405:847-856.
18. Ritchie M D, Hahn L W, Roodi N, Bailey L R, Dupont W D, Parl F F, Moore J H. Multifactor-dimensionality reduction reveals high-order interactions among Estrogen- Metabolism genes in sporadic breast cancer. Am J Hum Genet 2001, 69:138-147.
19. Ritchie M D, Hahn L W, Moore J H. 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.
20. Roldan V, Gonzalez-Conejero R, Marin F, Pineda J, Vicente V, Corral J. Five pro-thrombotic polymorphisms and the prevalence of premature myocardial infarction. Haematologica 2005, 90:421-423.
21. Schymick J C, Scholz S W, Fung H C, Britton A, Arepalli S, Gibbs J R, Lombardo F, Matarin M, Kasperaviciute D, Hernandez D G, Crews C, Bruijn L, Rothstein J, Mora G, Restagno G, Chiò A, Singleton A, Hardy J, Traynor B J. Genome-wide genotyping in amyotrophic lateral sclerosis and neurologically normal controls: first stage analysis and public release of data. Lancet Neurol 2007, 6:322-328.
22. Sha Q, Zhu X, Zuo Y, Cooper R, Zhang S. A combinatorial searching method for detecting a set of interacting loci associated with complex traits. Ann Hum Genet 2006, 70:677-692.
23. Sladek R, Rocheleau G, Rung J, Dina C, Shen L, Serre D, Boutin P, Vincent D, Belisle A, Hadjadj S, Balkau B, Heude B, Charpentier G, Hudson T J, Montpetit A, Pshezhetsky A,V, Prentki M, Posner B I, Balding D J, Meyre D, Polychronakos C, Froguel P. A genome-wide association study identifies novel risk loci for type 2 diabetes. Nature 2007, 445:881-885.
24. Templeton A R. Epistasis and complex trait. Epistasis and the Evolutionary Process 2000, Wade MBrodie BWolf J. In, eds, Oxford, Oxford University Press
25. Xiong M, Zhao J, Boerwinkle E. Generalized T2 test for genome association studies. Am J Hum Genet 2003, 70:1257-1286.
26. Zhang Z, Zhang S, Wong M Y, Wareham N J, Sha Q. An ensemble learning approach jointly modeling main and interaction effects in genetic association studies. Genet Epidemiol 2008, 32:285-300.
27. Zhao J, Jin L, Xiong M. Test for interaction between two unlinked loci. Am J Hum Genet 2006, 79:831-845.