SEARCH

SEARCH BY CITATION

References

  • Albert, J. H. & Chib, S. (1993) Bayesian analysis of binary and polychotomous response data. J. Am. Stat. Assoc. 88, 669679.
  • Amin, N., Van Duijn, C. M. & Aulchenko, Y. S. (2007) A genomic background based method for association analysis in related individuals. PLoS One 12, e1274.
  • Astle, W. & Balding, D. J. (2009) Population structure and cryptic relatedness in genetic association studies. Stat. Sci. 24, 451471.
  • Aulchenko, Y. S., de Koning, D.-J. & Haley, C. (2007a) Genomewide rapid association using mixed model and regression: A fast and simple method for genomewide pedigree-based quantitative trait loci association analysis. Genetics 177, 577585.
  • Aulchenko, Y. S., Ripke, S., Isaacs, A., & Van Duijn, C. M. (2007b) GenABEL: An R library for genome-wide association analysis. Bioinformatics 23, 12941296.
  • Ayers, K. L. & Cordell, H. J. (2010) SNP selection in genome-wide and candidate gene studies via penalized logistic regression. Genet. Epidemiol. 34, 879891.
  • Bradbury, P. J., Zhang, Z., Kroon, D. E., Casstevens, T. M., Ramdoss, Y. & Buckler, E. S. (2007) TASSEL: Software for association mapping of complex traits in diverse samples. Bioinformatics 23, 26332635.
  • Calus, M. P. L. & Veerkamp, R. F. (2007) Accuracy of breeding values when using and ignoring the polygenic effect in genomic breeding value estimation with a marker density of one SNP per cM. J. Anim. Breed. Genet. 124, 362368.
  • Cho, S., Kim, K., Kim, Y. J., Lee, J. K., Cho, Y. S., Lee, J. Y., Han, B. G., H. K. ans Ott, J. & Park, T. (2010) Joint identification of multiple genetic variants via elastic-net variable selection in a genome wide association analysis. Ann. Hum. Genet. 74, 416428.
  • Churchill, G. A. & Doerge, R. W. (1994) Empirical threshold values for quantitative trait mapping. Genetics 138, 963971.
  • Crooks, L., Sahana, G., de Koning, D.-J., Lund, M. S. & Carlborg, O. (2009) Comparison of analyses of the QTLMAS XII common dataset. II: Genome-wide association and fine mapping. BMC Proc. 3, S2
  • Dellaportas, P., Forster, J. J. & Ntzoufras, I. (2002) On Bayesian model and variable selection using MCMC. Stat. Comput. 12, 2736.
  • Du, F.-X. & Hoeschele, I. (2000) Estimation of additive, dominance and epistatic variance components using finite locus models implemented with a single-site Gibbs and a descent graph sampler. Genet. Res. 76, 187198.
  • Du, F.-X., Hoeschele, I. & Gage-Lahti, K. M. (1999) Estimation of additive and dominance variance components in finite polygenic models and complex pedigrees. Genet. Res. 74, 179187.
  • Ewans, W. J. & Spielman, R. S. (1995) The transmission/disequilibrium test: History, subdivision, and admixture. Am. J. Hum. Genet. 57, 455464.
  • Fan, J. & Lv, J. (2008) Sure independence screening for ultrahigh dimensional feature space. J. R. Stat. Soc. B 70, 849911.
  • Fisher, R. A. (1918) The correlation between relatives on the supposition of Mendelian inheritance. Trans. R. Soc. Edinburg 52, 399433.
  • Habier, D., Fernando, R. L. & Dekkers, J. C. M., (2007) The impact of genetic relationship information on genome-assisted breeding values. Genetics 177, 23892397.
  • Hoggart, C. J., Whittaker, J. C., De Iorio, M. & Balding, D. J. (2008) Simultaneous analysis of all SNPs in genome-wide and re-sequencing association studies. PLoS Genet. 4, e1000130.
  • Hoti, F. & Sillanpää, M. J. (2006) Bayesian mapping of genotype × expression interactions on quantitative and qualitative traits. Heredity 97, 418.
  • Iwata, H., Ebana, K., Fukuoka, S., Jannink, J.-L. & Hayashi, T. (2009) Bayesian multilocus association mapping on ordinal and censored traits and its application to the analysis of genetic variation among Oryza sativa L. germplasms. Theor. Appl. Genet. 118, 865880.
  • Iwata, H., Uga, Y., Yoshioka, Y., Ebana, K. & Hayashi, T. (2007) Bayesian association mapping of multiple quantitative trait loci and its application to the analysis of genetic variation among Oryza sativa L. germplasms. Theor. Appl. Genet. 114, 14371449.
  • Kang, H. M., Sul, J. H., Service, S. K., Zaitlen, N. A., Kong, S. E. & Freimer, N. B. (2010) Variance component model to account for sample structure in genome-wide association studies. Nat. Genet. 42, 348354.
  • 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.
  • Kass, R. E. & Raftery, A. E. (1995) Bayes factors. J. Am. Stat. Assoc. 90, 773795.
  • Kärkkäinen, H. P. & Sillanpää, M. J. (2012) Back to basics for Bayesian model building in genomic selection. Genetics 191, 969987.
  • Kuo, L. & Mallick, B. (1998) Variable selection for regression models. Sankhya Ser. B 60, 6581.
  • Lange, K. (1997) Mathematical and statistical methods for genetic analysis (1st ed.). In: Statistics for Biology and Health . New York : Springer.
  • Li, J., Das, K., Fu, G., Li, R. & Wu, R. (2011) The Bayesian LASSO for genome-wide association studies. Bioinformatics 27, 516523.
  • Li, Z. & Sillanpää, M. J. (2012) Estimation of quantitative trait locus effects with epistasis by variational Bayes algorithms. Genetics 190, 231249.
  • Lippert, C., Listgarten, J., Liu, Y., Kadie, C. M., Davidson, R. I. & Heckerman, D. (2011) FaST linear mixed models for genome-wide association studies. Nat. Methods 8, 833835.
  • Lund, M. S., Sahana, G., de Koning, D.-J., Su, G. & Carlborg, O. (2009) Comparison of analyses of the QTLMAS XII common dataset. I: Genomic selection. BMC Proc. 3, S1.
  • Meuwissen, T. H. E., Hayesm, B. & Goddard, M. E., (2001) Prediction of total genetic value using genome-wide dense marker maps. Genetics 157, 18191829.
  • Mutshinda, C. M. & Sillanpää, M. J. (2010) Extended Bayesian LASSO for multiple quantitative trait loci mapping and unobserved phenotype prediction. Genetics 186, 10671075.
  • O’Hara, R. B. & Sillanpää, M. J. (2009) A review of Bayesian variable selection methods: what, how and which. Bayesian Anal. 4, 85118.
  • Park, T. & Casella, G. (2008) The Bayesian Lasso. J. Am. Stat. Assoc. 103, 681686.
  • Peloso, G. M., Dupuis, J. & Lunetta, K. L. (2011) Evaluation of methods accounting for population structure with pedigree data and continuous outcomes. Genet. Epidemiol. 35, 427436.
  • Pikkuhookana, P. & Sillanpää, M. J. (2009) Correcting for relatedness in Bayesian models for genomic data association analysis. Heredity 103, 223237.
  • 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, 904909.
  • Price, A. L., Zaitlen, N. A., Reich, D. & Patterson, N. (2010) New approaches to population stratification in genome-wide association studies. Nat. Rev. Genet. 11, 459463.
  • Purcell, S. (2009) PLINK 1.07. http://pngu.mgh.harvard.edu/purcell/plink/. Accessed August 27, 2012.
  • Purcell, S., Neale, B., Todd-Brown, K., Thomas, L., Ferreira, M. A. R., Bender, D., Maller, J., Sklar, P., de Bakker, P. I. W., 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.
  • Setakis, E., Stirnadel, H. & Balding, D. J. (2006) Logistic regression protects against population structure in genetic association studies. Genome Res. 16, 290296.
  • Sillanpää, M. J. (2011) Overview of techniques to account for confounding due to population stratification and cryptic relatedness in genomic data association analyses. Heredity 106, 511519.
  • Sillanpää, M. J. & Bhattacharjee, M. (2005) Bayesian association-based fine mapping in small chromosomal segments. Genetics 169, 427439.
  • Solberg, T. R., Sonesson, A. K., Woolliams, J. A., Ødegard, J. & Meuwissen, T. H. E. (2009) Persistence of accuracy of genome-wide breeding values over generations when including a polygenic effect. Genet. Sel. Evol. 41, 53.
  • The International HapMap Consortium (2003) The International HapMap Project. Nature 426, 789796.
  • Thompson, E. A. & Skolnick, M. H. (1977) Likelihoods on complex pedigrees for quantitative traits. In: Proceedings of the International Conference on Quantitative Genetics (eds. E. Pollack, O. Kempthorne, and T. B. Bailey Jr), pp. 815818. Ames : Iowa State University Press.
  • VanRaden, P. M. (2008) Efficient methods to compute genomic predictions. J. Dairy Sci. 91, 44144423.
  • Wang, Y., Localio, R. & Rebbeck, T. R. (2005) Bias correction with a single null marker for population stratification in candidate gene association studies. Hum. Hered. 59, 165175.
  • Weeks, D. & Lathrop, G. (1995) Polygenic disease: Methods for mapping complex disease traits. Trends Genet. 11, 513519.
  • Wu, T. T., Chen, Y. F., Hastie, T., Sobel, E. & Lange, K. (2009) Genome-wide association analysis by lasso penalized logistic regression. Bioinformatics 25, 714721.
  • Xu, S. (2003) Estimating polygenic effects using markers of the entire genome. Genetics 163, 789801.
  • Xu, S. (2010) An expectation-maximization algorithm for the Lasso estimation of quantitative trait locus effects. Heredity 105, 483494.
  • Yi, N., Shriner, D., Banerjee, S., Mehta, T., Pomp, D. & Yandell, B. S. (2007) An efficient Bayes model selection approach for interacting quantitative trait loci models with many effects. Genetics 176, 18651877.
  • Yi, N. & Xu, S. (2008) Bayesian LASSO for quantitative trait loci mapping. Genetics 179, 10451055.
  • Yu, J., Pressoir, G., Briggs, W. H., Bi, I. V., Yamasaki, M., Doebley, J. F., McMullen, M. D., Gaut, B. S., Nielsen, D. M., Holland, J. B., Kresovich, S. & Buckler, E. S. (2006) A unified mixed-model method for association mapping that accounts for multiple levels of relatedness. Nat. Genet. 38, 202208.
  • Zhang, Z., Buckler, E. S., Casstevens, T. M. & Bradbury, P. J. (2009) Software engineering the mixed model for genome-wide association studies. Brief Bioinf. 10, 664675.