SEARCH

SEARCH BY CITATION

References

  • 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. (2005) Oligogenic combinations associated with breast cancer risk in women under 53 years of age. Hum Genet 116, 208221.
  • Barrett, J. C., Clayton, D. G., Concannon, P., Akolkar, B., Cooper, J. D., Erlich, H. A., Julier, C., Morahan, G., Nerup, J., Nierras, C., Plagnol, V., Pociot, F., Schuilenburg, H., Smyth, D. J., Stevens, H., Todd, J. A., Walker, N. M., Rich, S. S. & The Type 1 Diabetes Genetics Consortium (2009) Genome-wide association study and meta-analysis find that over 40 loci affect risk of type 1 diabetes. Nat Genet 41, 703707.
  • Becker, T., Schumacher, J., Cichon, S., Baur, M. P. & Knapp, M. (2005) Haplotype interaction analysis of unlinked regions. Genet Epidemiol 29, 313322.
  • Chapman, J. & Clayton, D. (2007) Detecting association using epistatic information. Genet Epidemiol 31, 894909.
  • 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, 549554.
  • Chung, Y., Lee, S. Y., Elston, R. C. & Park, T. (2006) Odds ratio based multifactor-dimensionality reduction method for detecting gene–gene interactions. Bioinformatics 23, 7176.
  • Clayton, D. G. (2009) Prediction and interaction in complex disease genetics: experience in type 1 diabetes. PLoS Genet 5, e1000540.
  • Cooper, J. D., Smyth, D. J., Smiles, A. M., Plagnol, V., Walker, N. M., Allen, J. E., Downes, K., Barrett, J. C., Healy, B. C., Mychaleckyj, J. C., Warram, J. H. & Todd, J. A. (2008) Meta-analysis of genome-wide association study data identifies additional type 1 diabetes risk loci. Nat Genet 40, 13991401.
  • Cordell, H. J. (2009) Detecting gene–gene interactions that underlie human diseases. Nat Rev Genet 10, 392404.
  • Culverhouse, R., Suarez, B. K., Lin, J. & Reich, T. (2002) A perspective on epistasis: limits of models displaying no main effect. Am J Hum Genet 70, 461471.
  • Easton, D. F., Pooley, K. A., Dunning, A. M., Pharoah, P. D. P., Thompson, D., Ballinger, D. G., Struewing, J. P., Morrison, J., Field, H., Luben, R., Wareham, N., Ahmed, S., Healey, C. S., Bowman, R., Meyer, K. B., Haiman, C. A., Kolonel, L. K., Henderson, B. E., Le Marchand, L., Brennan, P., Sangrajrang, S., Gaborieau, V., Odefrey, F., Shen, C. Y., Wu, P. E., Wang, H. C., Eccles, D., Evans, D. G., Peto, J., Fletcher, O., Johnson, N., Seal, S., Stratton, M. R., Rahman, N., Chenevix-Trench, G., Bojesen, S. E., Nordestgaard, B. G., Axelsson, C. K., Garcia-Closas, M., Brinton, L., Chanock, S., Lissowska, J., Peplonska, B., Nevanlinna, H., Fagerholm, R., Eerola, H., Kang, D., Yoo, K. Y., Noh, D. Y., Ahn, S. H., Hunter, D. J., Hankinson, S. E., Cox, D. G., Hall, P., Wedren, S., Liu, J. J., Low, Y. L., Bogdanova, N., Schurmann, P., Dork, T., Tollenaar, R. A. E. M., Jacobi, C. E., Devilee, P., Klijn, J. G. M., Sigurdson, A. J., Doody, M. M., Alexander, B. H., Zhang, J. H., Cox, A., Brock, I. W., MacPherson, G., Reed, M. W. R., Couch, F. J., Goode, E. L., Olson, J. E., Meijers-Heijboer, H., Van Den Ouweland, A., Uitterlinden, A., Rivadeneira, F., Milne, R. L., Ribas, G., Gonzalez-Neira, A., Benitez, J., Hopper, J. L., McCredie, M., Southey, M., Giles, G. G., Schroen, C., Justenhoven, C., Brauch, H., Hamann, U., Ko, Y. D., Spurdle, A. B., Beesley, J., Chen, X. Q., Mannermaa, A., Kosma, V. M., Kataja, V., Hartikainen, J., Day, N. E., Cox, D. R. & Ponder, B. A. J. (2007) Genome-wide association study identifies novel breast cancer susceptibility loci. Nature 447, 10871093.
  • Emily, M., Mailund, T., Hein, J., Schauser, L. & Schierup, M. H. (2009) Using biological networks to search for interacting loci in genome-wide association studies. Eur J Hum Genet 17, 12311240.
  • Erdmann, J., Großhennig, A., Braund, P. S., König, I. R., Hengstenberg, C., Hall, A. S., Linsel-Nitschke, P., Kathiresan, S., Wright, B., Tregouet, D. A., Cambien, F., Bruse, P., Aherrahrou, Z., Wagner, A. K., Stark, K., Schwartz, S. M., Salomaa, V., Elosua, R., Melander, O., Voight, B. F., O’Donnell, C. J., Peltonen, L., Siscovick, D. S., Altshuler, D., Merlini, P. A., Peyvandi, F., Bernardinelli, L., Ardissino, D., Schillert, A., Blankenberg, S., Zeller, T., Wild, P., Schwarz, D. F., Tiret, L., Perret, C., Schreiber, S., El Mokhtari, N. E., Schafer, A., Marz, W., Renner, W., Bugert, P., Kluter, H., Schrezenmeir, J., Rubin, D., Ball, S. G., Balmforth, A. J., Wichmann, H. E., Meitinger, T., Fischer, M., Meisinger, C., Baumert, J., Peters, A., Ouwehand, W. H., Deloukas, P., Thompson, J. R., Ziegler, A., Samani, N. J. & Schunkert, H. (2009) New susceptibility locus for coronary artery disease on chromosome 3q22. 3. Nat Genet 41, 280282.
  • Fellay, J., Shianna, K. V., Ge, D., Colombo, S., Ledergerber, B., Weale, M., Zhang, K. L., Gumbs, C., Castagna, A., Cossarizza, A., Cozzi-Lepri, A., De Luca, A., Easterbrook, P., Francioli, P., Mallal, S., Martinez-Picado, J., Miro, J. M., Obel, N., Smith, J. P., Wyniger, J., Descombes, P., Antonarakis, S. E., Letvin, N. L., McMichael, A. J., Haynes, B. F., Telenti, A. & Goldstein, D. B. (2007) A whole-genome association study of major determinants for host control of HIV-1. Science 317, 944947.
  • Ferreira, T., Donnelly, P. & Marchini, J. (2007) Powerful Bayesian gene–gene interaction analysis. Am J Hum Genet 81(Suppl.), 32.
  • Gayán, J., González-Pérez, A., Bermudo, F., Sáez, M. E., Royo, J. L., Quintas, A., Galan, J. J., Morón, F. J., Ramirez-Lorca, R., Real, L. M. & Ruiz, A. (2008) A method for detecting epistasis in genome-wide studies using case-control multi-locus association analysis. BMC Genomics 9, 360.
  • Hahn, L. W., Ritchie, M. D. & Moore, J. H. (2003) Multifactor dimensionality reduction software for detecting gene–gene and gene-environment interactions. Bioinformatics 19, 376382.
  • Hirschhorn, J. N., Lohmueller, K., Byrne, E. & Hirschhorn, K. (2002) A comprehensive review of genetic association studies. Genet Med 4, 4561.
  • Kang, H. M., Zaitlen, N. A., Wade, C. M., Kirby, A., Heckerman, D., Daly, M. J. & Eskin, E. (2008) Efficient control of population structure in model organism association mapping. Genetics 178, 17091723.
  • Kim, J. H., Sen, S., Avery, C. S., Simpson, E., Chandler, P., Nishina, P. M., Churchill, G. A. & Naggert, J. K. (2001) Genetic analysis of a new mouse model for non-insulin-dependent diabetes. Genomics 74, 273286.
  • Lai, H. C., Lin, W. Y., Lin, Y. W., Chang, C. C., Yu, M. H., Chen, C. C. & Chu, T. Y. (2005) Genetic polymorphisms of FAS and FASL (CD95/CD95L) genes in cervical carcinogenesis: An analysis of haplotype and gene–gene interaction. Gynecol Oncol 99, 113118.
  • Lindley, D. V. & Smith, A. F. M. (1972) Bayes estimates for the linear model. J R Stat Soc Series B Stat Methodol 34, 141.
  • Ma, D. Q., Whitehead, P. L., Menold, M. M., Martin, E. R., Ashley-Koch, A. E., Mei, H., Ritchie, M. D., DeLong, G. R., Abramson, R. K., Wright, H. H., Cuccaro, M. L., Hussman, J. P., Gilbert, J. R. & Pericak-Vance, M. A. (2005) Identification of significant association and gene–gene interaction of GABA receptor subunit genes in autism. Am J Hum Genet 77, 377388.
  • Mackay, T. F. C. (2001) The genetic architecture of quantitative traits. Annu Rev Genet 35, 303339.
  • Maher, B. (2008) Personal genomes: The case of the missing heritability. Nature 456, 1821.
  • Maller, J. B., Fagerness, J. A., Reynolds, R. C., Neale, B. M., Daly, M. J. & Seddon, J. M. (2007) Variation in complement factor 3 is associated with risk of age-related macular degeneration. Nat Genet 39, 12001201.
  • Marchini, J., Donnelly, P. & Cardon, L. (2005) Genome-wide strategies for detecting multiple loci that influence complex diseases. Nat Genet 37, 413417.
  • Marchini, J. & Howie, B. (2010) Genotype imputation for genome-wide association studies. Nat Rev Genet 11, 499511.
  • McPherson, R., Pertsemlidis, A., Kavaslar, N., Stewart, A., Roberts, R., Cox, D. R., Hinds, D., Pennacchio, L. A., Tybjaerg-Hansen, A., Folsom, A. R., Boerwinkle, E., Hobbs, H. H. & Cohen, J. C. (2007) A common allele on chromosome 9 associated with coronary heart disease. Science 316, 14881491.
  • Moore, J. H. (2003) The ubiquitous nature of epistasis in determining susceptibility to common human diseases. Hum Hered 56, 7382.
  • Moore, J. H. (2004) Computational analysis of gene–gene interactions using multifactor dimensionality reduction. Expert Rev Mol Diagn 4, 795803.
  • Moore, J. H. & Williams, S. M. (2002) New strategies for identifying gene–gene interactions in hypertension. Ann Med 34, 8895.
  • Mukherjee, B. & Chatterjee, N. (2008) Exploiting gene-environment independence for analysis of case–control studies: an empirical Bayes-type shrinkage estimator to trade-off between bias and efficiency. Biometrics 64, 685694.
  • Musani, S. K., Shriner, D., Liu, N., Feng, R., Coffey, C. S., Yi, N., Tiwari, H. & Allison, D. B. (2007) Detection of gene x gene interactions in genome-wide association studies of human population data. Hum Hered 63, 6784.
  • Nelson, M. R., Kardia, S. L. R., Ferrell, R. E. & Sing, C. F. (2001) A combinatorial partitioning method to identify multilocus genotypic partitions that predict quantitative trait variation. Genome Res 11, 458470.
  • O’Hagan, A. & Forster, J. (2004) Kendall's advanced theory of statistics, volume 2B: Bayesian inference. Arnold, London .
  • Plenge, R. M., Seielstad, M., Padyukov, L., Lee, A. T., Remmers, E. F., Ding, B., Liew, A., Khalili, H., Chandrasekaran, A., Davies, L. R. L., Li, W., Tan, A. K. S., Bonnard, C., Ong, R. T., Thalamuthu, A., Pettersson, S., Liu, C., Tian, C., Chen, W. V., Carulli, J. P., Beckman, E. M., Altshuler, D., Alfredsson, L., Criswell, L. A., Amos, C. I., Seldin, M. F., Kastner, D. L., Klareskog, L. & Gregersen, P. K. (2007) TRAF1-C5 as a risk locus for rheumatoid arthritis–a genomewide study. N Engl J Med 357, 11991209.
  • Purcell, S., Neale, B., Todd-Brown, K., Thomas, L., Ferreira, M. A., Bender, D., Maller, J., Sklar, P., de Bakker, P. I., Daly, M. J. & Sham, P. C. (2007) PLINK: a tool set for whole-genome association and population-based linkage analyses. Am J Hum Genet 81, 559575.
  • 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 (GRIN1) and NR2B subunit gene (GRIN2B) in schizophrenia with universal DNA microarray. Eur J Hum Genet 13, 807814.
  • Routman, E. J. & Cheverud, J. M. (1997) Gene effects on a quantitative trait: two-locus epistatic effects measured at microsatellite markers and at estimated QTL. Evolution 51, 16541662.
  • Segre, D., DeLuna, A., Church, G. M. & Kishony, R. (2004) Modular epistasis in yeast metabolism. Nat Genet 37, 7783.
  • Servin, B. & Stephens, M. (2007) Imputation-based analysis of association studies: candidate regions and quantitative traits. PLoS Genet 3, e114.
  • Shimomura, K., Low-Zeddies, S. S., King, D. P., Steeves, T. D. L., Whiteley, A., Kushla, J., Zemenides, P. D., Lin, A., Vitaterna, M. H., Churchill, G. A. & Takahashi, J. S. (2001) Genome-wide epistatic interaction analysis reveals complex genetic determinants of circadian behavior in mice. Genome Res 11, 959980.
  • Sing, C. F., Haviland, M. B. & Reilly, S. L. (1996) Genetic architecture of common multifactorial diseases. Ciba Found Symp 197, 211229.
  • 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. (2007) A genome-wide association study identifies novel risk loci for type 2 diabetes. Nature 445, 881885.
  • Stephens, M. & Balding, D. J. (2009) Bayesian statistical methods for genetic association studies. Nat Rev Genet 10, 681690.
  • The Wellcome Trust Case Control Consortium (2007) Genome-wide association study of 14,000 cases of seven common diseases and 3,000 shared controls. Nature 447, 661678.
  • Topol, E. J., Smith, J., Plow, E. F. & Wang, Q. K. (2006) Genetic susceptibility to myocardial infarction and coronary artery disease. Hum Mol Genet 15, R117R123.
  • Tsai, C. T., Hwang, J. J., Ritchie, M. D., Moore, J. H., Chiang, F. T., Lai, L. P., Hsu, K. L., Tseng, C. D., Lin, J. L. & Tseng, Y. Z. (2007) Renin-angiotensin system gene polymorphisms and coronary artery disease in a large angiographic cohort: detection of high order gene–gene interaction. Atherosclerosis 195, 172180.
  • Voight, B. F., Scott, L. J., Steinthorsdottir, V., Morris, A. P., Dina, C., Welch, R. P., Zeggini, E., Huth, C., Aulchenko, Y. S., Thorleifsson, G., McCulloch, L. J., Ferreira, T., Grallert, H., Amin, N., Wu, G. M., Willer, C. J., Raychaudhuri, S., McCarroll, S. A., Langenberg, C., Hofmann, O. M., Dupuis, J., Qi, L., Segre, A. V., van Hoek, M., Navarro, P., Ardlie, K., Balkau, B., Benediktsson, R., Bennett, A. J., Blagieva, R., Boerwinkle, E., Bonnycastle, L. L., Bostrom, K. B., Bravenboer, B., Bumpstead, S., Burtt, N. P., Charpentier, G., Chines, P. S., Cornelis, M., Couper, D. J., Crawford, G., Doney, A. S. F., Elliott, K. S., Elliott, A. L., Erdos, M. R., Fox, C. S., Franklin, C. S., Ganser, M., Gieger, C., Grarup, N., Green, T., Griffin, S., Groves, C. J., Guiducci, C., Hadjadj, S., Hassanali, N., Herder, C., Isomaa, B., Jackson, A. U., Johnson, P. R. V., Jorgensen, T., Kao, W. H. L., Klopp, N., Kong, A., Kraft, P., Kuusisto, J., Lauritzen, T., Li, M., Lieverse, A., Lindgren, C. M., Lyssenko, V., Marre, M., Meitinger, T., Midthjell, K., Morken, M. A., Narisu, N., Nilsson, P., Owen, K. R., Payne, F., Perry, J. R. B., Petersen, A. K., Platou, C., Proenca, C., Prokopenko, I., Rathmann, W., Rayner, N. W., Robertson, N. R., Rocheleau, G., Roden, M., Sampson, M. J., Saxena, R., Shields, B. M., Shrader, P., Sigurdsson, G., Sparso, T., Strassburger, K., Stringham, H. M., Sun, Q., Swift, A. J., Thorand, B., Tichet, J., Tuomi, T., van Dam, R. M., van Haeften, T. W., van Herpt, T., van Vliet-Ostaptchouk, J. V., Walters, G. B., Weedon, M. N., Wijmenga, C., Witteman, J., The MAGIC Investigators, The GIANT Consortium, Bergman, R. N., Cauchi, S., Collins, F. S., Gloyn, A. L., Gyllensten, U., Hansen, T., Hide, W. A., Hitman, G. A., Hofman, A., Hunter, D. J., Hveem, K., Laakso, M., Mohlke, K. L., Morris, A. D., Palmer, C. N. A., Pramstaller, P. P., Rudan, I., Sijbrands, E., Stein, L. D., Jaakko, T., Uitterlinden, A., Walker, M., Wareham, N. J., Watanabe, R. M., Abecasis, G. R., Boehm, B. O., Campbell, H., Daly, M. J., Hattersley, A. T., Hu, F. B., Meigs, J. B., Pankow, J. S., Pedersen, O., Wichmann, H. E., Barroso, I., Florez, J. C., Frayling, T. M., Groop, L., Sladek, R., Thorsteinsdottir, U., Wilson, J. F., Illig, T., Froguel, P., van Duijn, C. M., Stefansson, K., Altshuler, D., Boehnke, M. & McCarthy, M. I. (2010) Twelve type 2 diabetes susceptibility loci identified through large-scale association analysis. Nat Genet 42, 579589.
  • Wakefield, J. (2008) Bayes factors for genome-wide association studies: comparison with P-values. Genet Epidemiol 33, 7986.
  • Warden, C. H., Stone, S., Chiu, S., Diament, A. L., Corva, P., Shattuck, D., Riley, R., Hunt, S. C., Easlick, J., Fisler, J. S. & Medrano, J. F. (2004) Identification of a congenic mouse line with obesity and body length phenotypes. Mamm Genome 15, 460471.
  • Ways, J. A., Cicila, G. T., Garrett, M. R. & Koch, L. G. (2002) A genome scan for loci associated with aerobic running capacity in rats. Genomics 80, 1320.
  • Williams, S. M., Haines, J. L. & Moore, J. H. (2004) The use of animal models in the study of complex disease: all else is never equal or why do so many human studies fail to replicate animal findings? Bioessays 26, 170179.
  • Zeggini, E., Scott, L. J., Saxena, R., Voight, B. F., Marchini, J. L., Hu, T., de Bakker, P. I. W., Abecasis, G. R., Almgren, P., Andersen, G., Ardlie, K., Bostroem, K. B., Bergman, R. N., Bonnycastle, L. L., Borch-Johnsen, K., Burtt, N. P., Chen, H., Chines, P. S., Daly, M. J., Deodhar, P., Ding, C. J., Doney, A. S. F., Duren, W. L., Elliott, K. S., Erdos, M. R., Frayling, T. M., Freathy, R. M., Gianniny, L., Grallert, H., Grarup, N., Groves, C. J., Guiducci, C., Hansen, T., Herder, C., Hitman, G. A., Hughes, T. E., Isomaa, B., Jackson, A. U., Jorgensen, T., Kong, A., Kubalanza, K., Kuruvilla, F. G., Kuusisto, J., Langenberg, C., Lango, H., Lauritzen, T., Li, Y., Lindgren, C. M., Lyssenko, V., Marvelle, A. F., Meisinger, C., Midthjell, K., Mohlke, K. L., Morken, M. A., Morris, A. D., Narisu, N., Nilsson, P., Owen, K. R., Palmer, C. N. A., Payne, F., Perry, J. R. B., Pettersen, E., Platou, C., Prokopenko, I., Qi, L., Qin, L., Rayner, N. W., Rees, M., Roix, J. J., Sandbaek, A., Shields, B., Sjogren, M., Steinthorsdottir, V., Stringham, H. M., Swift, A. J., Thorleifsson, G., Thorsteinsdottir, U., Timpson, N. J., Tuomi, T., Tuomilehto, J., Walker, M., Watanabe, R. M., Weedon, M. N., Willer, C. J., The Wellcome Trust Case Control Consortium, Illig, T., Hveem, K., Hu, F. B., Laakso, M., Stefansson, K., Pedersen, O., Wareham, N. J., Barroso, I., Hattersley, A. T., Collins, F. S., Groop, L., McCarthy, M. I., Boehnke, M. & Altshuler, D. (2008) Meta-analysis of genome-wide association data and large-scale replication identifies additional susceptibility loci for type 2 diabetes. Nat Genet 40, 638645.
  • Zerba, K. E., Ferrell, R. E. & Sing, C. F. (2000) Complex adaptive systems and human health: the influence of common genotypes of the apolipoprotein E (ApoE) gene polymorphism and age on the relational order within a field of lipid metabolism traits. Hum Genet 107, 466475.
  • Zhang, Y. & Liu, J. S. (2007) Bayesian inference of epistatic interactions in case-control studies. Nat Genet 39, 11671173.
  • Zhao, J., Jin, L. & Xiong, M. (2006) Test for interaction between two unlinked loci. Am J Hum Genet 79, 831845.
  • Zubenko, G. S., Hughes III, H. B. & Stiffler, J. S. (2001) D10S1423 identifies a susceptibility locus for Alzheimer's disease in a prospective, longitudinal, double-blind study of asymptomatic individuals. Mol Psychiatry 6, 413419.