A Novel Method to Detect Gene-Gene Interactions in Structured Populations: MDR-SP

Annals of Human Genetics

Volumn 75, Issue 6, 2011, Pages 742-754

  Niu, Adan ^a   Zhang, Shuanglin ^a   Sha, Qiuying ^a  

^a MICHIGAN TECHNOLOGICAL UNIVERSITY   (United States)

Author keywords

Association study; Interaction; MDR in structured populations (MDR SP); Multifactor dimensionality reduction (MDR); Population stratification

Indexed keywords

ARTICLE; GENE INTERACTION; GENETIC ANALYSIS; GENETIC ASSOCIATION; MODEL; MULTIFACTOR DIMENSIONALITY REDUCTION; MULTIFACTOR DIMENSIONALITY REDUCTION IN STRUCTURED POPULATION; PRIORITY JOURNAL;

GENETIC ASSOCIATION STUDIES; GENETICS, POPULATION; HUMANS; MULTIFACTOR DIMENSIONALITY REDUCTION; STATISTICS AS TOPIC;

EID: 80053517681     PISSN: 00034800     EISSN: 14691809     Source Type: Journal    
DOI: 10.1111/j.1469-1809.2011.00681.x     Document Type: Article

References (48)

1. Bastone, L., Reilly, M., Rader, D. J. & Foulkes, A. S. (2004) MDR and PRP: A comparison of methods for high-order genotype-phenotype associations. Hum Hered 58, 82-92.
2. Bauchet, M., McEvoy, B., Pearson, L. N., Quillen, E. E., Sarkisian, T., Hovhannesyan, K., Deka, R., Bradley, D. G. & Shriver, M. D. (2007) Measuring European population stratification with microarray genotype data. Am J Hum Genet 80, 948-956.
3. Bhattacharjee, B., Wang, Z., Ciampa, J., Kraft, P., Chanock, S., Yu, K. & Chatterjee, N. (2010) Using principal components of genetic variation for robust and powerful detection of gene-gene interactions in case-control and case-only studies. Am J Hum Genet 86, 331-342.
4. Calle, M. L., Urrea, V., Malats, N. & Van Steen, K. (2007) MB-MDR: Model-based multifactor dimensionality reduction for detecting interactions in high-dimensional genomic data. Technical Report No. 24, Department of Systems Biology, Universitat de Vic
5. Campbell, C. D., Ogburn, E. L., Lunetta, K. L., Lyon, H. N., Freedman, M. L., Groop, L. C., Altshuler, D., Ardlie, K. G. & Hirschhorn, J. N. (2005) Demonstrating stratification in a European American 496 population. Nat Genet 37, 868-872.
6. Cattaert, T., Calle, M. L., Dudek, S. M., John, J. M. M., Lishout, F. O. V., Urrea, V., Ritchie, M. D. & Steen, K. V. (2011) Model-based multifactor dimensionality reduction for detecting epistasis in case-control data in the presence of noise. Ann Hum Genet 75, 78-89.
7. Cattaert, T., Urrea, V., Naj, A. C., De Lobel, L., De Wit, V., Fu, M., John, J. M. M., Shen, H., Calle, M. L., Ritchie, M. D., Edwards, T. L. & Van Steen, K. (2010) FAM-MDR: A flexible family-based multifactor dimensionality reduction technique to detect epistasis using related individuals. PLoS ONE 5, e10304, doi:.
8. Chen, H. S., Zhu, X., Zhao, H. & Zhang, S. (2003) Qualitative semi-parametric test for genetic associations in case-control designs under structured populations. Ann Hum Genet 67, 250-264.
9. Cho, Y. M., Ritchie, M. D., Moore, J. H., Park, J. Y., Lee, K. U., Shin, H. D., Lee, H. K. & Park, K. S. (2004) Multifactor-dimensionality reduction shows a two-locus interaction associated with Type 2 diabetes mellitus. Diabetologia 47, 549-554.
10. Coffey, C. S., Hebert, P. R., Ritchie, M. D., Krumholz, H. M., Gaziano, J. M., Ridker, P. M., Brown, N. J., Vaughan, D. E. & Moore, J. H. (2004) An application of conditional logistic regression and multifactor dimensionality reduction for detecting gene-gene interactions on risk of myocardial infarction: The importance of model validation. BMC Bioinform 5, 49.
11. Cordell, H. J. (2002) Epistasis: What it means, what it doesn't mean, and statistical methods to detect it in humans. Hum Mol Genet 11, 2463-2468.
12. Cordell, H. J., Todd, J. A., Hill, N. J., Lord, C. J., Lyons, P. A., Peterson, L. B., Wicker, L. S. & Clayton, D. G. (2001) Statistical modeling of interlocus interactions in a complex disease: Rejection of the multiplicative model of epistasis in type 1 diabetes. Genetics 158, 357-367.
13. Culverhouse, R., Klein, T. & Shannon, W. (2004) Detecting epistatic interactions contributing to quantitative traits. Genet Epidemiol 27, 141-152.
14. Devlin, B. & Roeder, K. (1999) Genomic control for association studies. Biometrics 55, 997-1004.
15. Devlin, B., Roeder, K. & Wasserman, L. (2001) Genomic control, a new approach to genetic-based association studies. Theor Popul Biol 60, 155-166.
16. Gui, J. A., Andrew, A. S., Andrews, P., Nelson, H. M., Kelsey, K. T., Karagas, M. R. & Moore, J. H. (2010) A simple and computationally efficient sampling approach to covariate adjustment for multifactor dimensionality reduction analysis of epistasis. Hum Hered 70, 219-225.
17. He, H., Oetting, W. S., Brott, M. J. & Basu, S. (2009) Pair-wise multifactor dimensionality reduction method to detect gene-gene interactions in a case-control study. Hum Hered 69, 60-70.
18. International HapMap Consortium (2005) A haplotype map of the human genome. Nature 437, 1299-1320.
19. Kang, H. M., Sul, J. H., Service, S. K., Zaitlen, N. A., Kong, S., Freimer, N. B., Sabatti, C. & Eskin, E. (2010) Variance component model to account for sample structure in genome-wide association studies. Nat Genet 42, 348-354.
20. Knowler, W. C., Williams, R. C., Pettitt, D. J. & Steinberg, A. G. (1988) Gm 3; 5, 13, 14 and type 2 diabetes mellitus: An association in American Indians with genetic admixture. Am J Hum Genet 43, 520-526.
21. Lander, E. S. & Schork, N. J. (1994) Genetic dissection of complex traits. Science 265, 2037-2048.
22. Li, M., Reilly, C. & Hanson, T. (2008) A semi-parametric test to detect associations between quantitative traits and candidate genes in structured populations. Bioinformatics 24, 2356-2362.
23. Li, M., Reilly, M. P., Rader, D. J. & Wang, L. S. (2010) Correcting population stratification in genetic association studies using a phylogenetic approach. Bioinformatics 26, 798-806.
24. Li, Q. & Yu, K. (2008) Improved correction for population stratification in genome-wide association studies by identifying hidden population structures. Genet Epidemiol 32, 215-226.
25. Lou, X., Chen, G., Yan, L., Ma, J., Zhu, J., Elston, R. & Li, M. (2007) A generalized combinatorial approach for detecting gene-by-gene and gene-by-environment interactions with application to nicotine dependence. Am J Hum Genet 80, 1125-1137.
26. Marchini, J., Cardon, L. R., Phillips, M. S. & Donnelly, P. (2004) The effects of human population 498 structure on large genetic association studies. Nat Genet 36, 512-517.
27. Martin, E. R., Ritchie, M. D., Hahn, L., Kang, S. & Moore, J. H. (2006) A novel method to identify gene-gene effects in nuclear families: The MDR-PDT. Genet Epidemiol 30, 111-123.
28. Moore, J. H. (2004) Computational analysis of gene-gene interactions using multifactor dimensionality reduction. Expert Rev Mol Diagn 4, 795-803.
29. Moore, J. H. & Williams, S. M. (2002) New strategies for identifying gene-gene interactions in hypertension. Ann Med 34, 88-95.
30. Namkung, J., Elston, R. C., Yang, J. M. & Park, T. (2009) Identification of gene-gene interactions in the presence of missing data using the multifactor dimensionality reduction method. Genet Epidemiol 33, 646-656.
31. Nelson, M. R., Kardia, S. L., Ferrell, R. E. & Sing, C. F. (2001) A combinatorial partitioning method to identify multi-locus genotypic partitions that predict quantitative trait variation. Genome Res 11, 458-470.
32. Pattin, K. A., Pattin, K. A., White, B. C., Barney, N., Gui, J., Nelson, H. H., Kelsey, K. T., Andrew, A. S., Karagas, M. R. & Moore, J. H. (2009) A computationally efficient hypothesis testing method for epistasis analysis using multifactor dimensionality reduction. Genet Epidemiol 33, 87-94.
33. Price, A. L., Patterson, N. J., Plenge, R. M., Weinblatt, M. E., Shadick, N. A. & Reich, D. (2006) Principal components analysis corrects for stratification in genome-wide association studies. Nat Genet 38, 904-909.
34. Pritchard, J. K. & Rosenberg, N. A. (1999) Use of unlinked genetic markers to detect population stratification in association studies. Am J Hum Genet 65, 220-228.
35. Pritchard, J. K., Stephens, M., Rosenberg, N. A. & Donnelly, P. (2000) Association mapping in structured populations. Am J Hum Genet 67, 170-181.
36. Qin, S., Zhao, X., Pan, Y., Liu, J., Feng, G., Fu, J., Bao, J., Zhang, Z. & He, L. (2005) An association study of the N-methyl-D-aspartate receptor NR1 subunit gene (GRIN 1) and NR2B subunit gene (GR1N2B) in schizophrenia with universal DNA microarray. Eur J Hum Genet 13, 807-814.
37. Reich, D. E. & Goldstein, D. B. (2001) Detecting association in a case-control study while correcting for population stratification. Genet Epidemiol 20, 4-16.
38. Ritchie, M. D., Hahn, L. W. & Moore, J. H. (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.
39. Ritchie, M. D., Hahn, L. W., Roodi, N., Bailey, L. R., Dupont, W. D., Parl, F. F. & Moore, J. H. (2001) Multifactor-dimensionality reduction reveals high-order interactions among estrogen-metabolism genes in sporadic breast cancer. Am J Hum Genet 69, 138-147.
40. Satten, G. A., Flanders, W. D. & Yang, Q. (2001) Accounting for unmeasured population substructure in case-control studies of genetic association using a novel latent-class model. Am J Hum Genet 68, 466-477.
41. Sha, Q., Zhu, X., Cooper, R. & Zhang, S. (2006) A combinatorial searching method for detecting a set of interacting loci associated with complex traits. Ann Hum Genet 70, 677-692.
42. Stevenson, A. G. (2002) EVD: Extreme value distributions. R News 2, 31-32.
43. Velez, D. R., White, B. C., Motsinger, A. A., Bush, W. S., Ritchie, M. D., Williams, S. M. & Moore, J. H. (2007) A balanced accuracy function for epistasis modeling in imbalanced datasets using multifactor dimensionality reduction. Genet Epidemiol 31, 306-315.
44. Williams, S. M., Ritchie, M. D., Phillips, J. A., III, Dawson, E., Prince, M., Dzhura, E., Willis, A., Semenya, A., Summar, M., White, B. C., Addy, J. H., Kpodonu, J., Wong, U., Felder, R. A., Jose, P. A. & Moore J. H. (2004) Multilocus analysis of hypertension: A hierarchical approach. Hum Hered 57, 28-38.
45. Winham, S. J., Slater, A. J. & Motsinger-Reif, A. A. (2010) A comparison of internal validation techniques for multifactor dimensionality reduction. BMC Bioinformatics 11, 394.
46. Zhang, S. L., Zhu, X. & Zhao, H. (2003) On a semi-parameter test to detect associations between quantitative trait and candidate genes using unrelated individuals. Genet Epidemiol 24, 45-56.
47. Zhang, Z., Ersoz, E., Lai, C. Q., Todhunter, R. J., Tiwari, H. K., Gore, M. A., Bradbury, P., Yu, J., Arnett, D. K., Ordovas, J. M. & Buckler, E. S. (2010) Mixed linear model approach adapted for genome-wide association studies. Nat Genet 42, 355-360.
48. Zhu, X., Zhang, S., Zhao, H. & Cooper, R. S. (2002) Association mapping, using a mixture model for complex traits. Genet Epidemiol 23, 181-196.