A BAYESIAN METHOD FOR THE DETECTION OF EPISTASIS IN QUANTITATIVE TRAIT LOCI USING MARKOV CHAIN MONTE CARLO MODEL COMPOSITION WITH RESTRICTED MODEL SPACES

Edward L. Boone, Susan J. Simmons, Karl Ricanek

2011

Abstract

Epistasis or the interaction between loci on a genome is of great interest to geneticists. Herein, a powerful Bayesian method utilizing Markov chain Monte Carlo model composition approach using restricted spaces is developed for identifying epistatic effects in Recombinant Inbred Lines (RIL). The method is verified through a simulation study and applied to an Arabidopsis thaliana data set with cotyledon as the quantitative trait.

References

  1. Broman, K. W. (2005) The Genomes of Recombinant Inbred Lines Genetics, 169, 1133-1146.
  2. Broman, K. W. and Speed, T. P. (2002) A model selection approach for the identification of quantitative trait loci in experimental crosses. J.R. Statist. Soc. B, 64, 641- 656.
  3. Bolstad, W. M. (2010) Understanding Computational Bayesian Statistics. John Wiley, New York. ISBN 0- 470-04609-8
  4. Boone, E. L., Ye, K. and Smith, E. P. (2005) Assessment of two approximation methods for computing posterior model probabilities. Computational Statistics & Data Analysis, 48, 221-234.
  5. Boone, E. L., Simmons, S. J., Ye, K., Stapleton, A. E. (2006) Analyzing quantitative trait loci for the Arabidopsis thaliana using Markov chain monte carlo model composition with restricted and unrestricted model spaces. Statistical Methodology, 3, 69-78.
  6. Carlborg, O., Andersson, L. and Kinghorn, B. (2000) The Use of a Genetic Algorithm for Simultaneous Mapping of Multiple Interacting Quantitative Trait Loci Genetics, 155, 2003-2010.
  7. Chib, S. and Greenberg, E. (1995) MetropolisHastings Algorithm. cian, 49, 327335.
  8. Cockerham, C. (1954) An extension of the concept of partitioning hereditary variance for the analysis of covariances among relatives when epistasis is present. Genetics, 39, 859-882.
  9. Green, P. J. (1995) Reversible jump Markov chain Monte Carlo computation and Bayesian model determination. Biometrika, 82, 711-732.
  10. Hanlon, P. and Lorenz, A. (2005) A computational method to detect epistatic effects contributing to a quantitative trait. J. Thoer. Biol., 235, 350-364.
  11. Hansen,T. F. and Wagner, G. P. (2001) Modeling genetic architecture : a multilinear theory of gene interaction. Theor. Popul. Biol, 59, 61-86.
  12. Kao, C. H., Zeng, Z. B. and Teasdale, R. D. (1999) Multiple Interval Mapping for Quantitative Trait Loci. Genetics, 152, 1203-1216.
  13. Kao, C. H. and Zeng, Z-B. (2002) Modeling Epistasis of Quantitative Trait Loci Using Cockerham's Model. Genetics, 160, 1243-1261.
  14. Wang, T. and Zeng, Z.-B. (2006) Models and partition of varieance for quantitative trait loci with epistasis and linkage disequilibrium. BMC Genetics, 7, 9.
  15. Yandell, B. S., Mehta, T., Samprit, B., Shriner, D., Venkataraman, R., Moon, J. Y., Neeley, W. W., Wu, H., von Smith, R. and Yi, N. (2007) R/qtlbim: QTL with Bayesian Interval Mapping in experimental crosses. Bioinformatics, 23, 641-643.
  16. Yi, N., Xu, S. and Allison D. B. (2003) Bayesian Model Choice and Search Strategies for Mapping Interacting Quantitative Trait Loci Genetics, 165, 867-883.
  17. Yi, N., Yandell, B. S., Churchill, G. A., Allison, D. B., Eisen, E. J., and Pomp, D. (2005) Bayesian model selection for genome-wide epistatic quantitative trait loci analysis. Genetics, 170, 1333-1344.
  18. Yi, N., Samprit, B., Pomp, D. and Yandell, B. S. (2007) Bayesian Mapping of Genomewide Interacting Quantitative Trait Loci for Ordinal Traits Genetics, 176, 1855-1864.
  19. Yi, N., Shriner, D., Samprit, B., Mehta, T., Pomp, D. and Yandell, B. S. (2007) An efficient Bayesian model selection approach for interacting quantitative trait loci models with many effects. Genetics, 176, 1865-1877.
  20. Zeng, Z-B., Wang, T. and Zou, W. (2005) Modeling quantitative trait loci and interpretation of models. Genetics, 169, 1711-1725.
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Paper Citation


in Harvard Style

L. Boone E., J. Simmons S. and Ricanek K. (2011). A BAYESIAN METHOD FOR THE DETECTION OF EPISTASIS IN QUANTITATIVE TRAIT LOCI USING MARKOV CHAIN MONTE CARLO MODEL COMPOSITION WITH RESTRICTED MODEL SPACES . In Proceedings of the 3rd International Conference on Agents and Artificial Intelligence - Volume 1: ICAART, ISBN 978-989-8425-40-9, pages 71-78. DOI: 10.5220/0003139200710078


in Bibtex Style

@conference{icaart11,
author={Edward L. Boone and Susan J. Simmons and Karl Ricanek},
title={A BAYESIAN METHOD FOR THE DETECTION OF EPISTASIS IN QUANTITATIVE TRAIT LOCI USING MARKOV CHAIN MONTE CARLO MODEL COMPOSITION WITH RESTRICTED MODEL SPACES},
booktitle={Proceedings of the 3rd International Conference on Agents and Artificial Intelligence - Volume 1: ICAART,},
year={2011},
pages={71-78},
publisher={SciTePress},
organization={INSTICC},
doi={10.5220/0003139200710078},
isbn={978-989-8425-40-9},
}


in EndNote Style

TY - CONF
JO - Proceedings of the 3rd International Conference on Agents and Artificial Intelligence - Volume 1: ICAART,
TI - A BAYESIAN METHOD FOR THE DETECTION OF EPISTASIS IN QUANTITATIVE TRAIT LOCI USING MARKOV CHAIN MONTE CARLO MODEL COMPOSITION WITH RESTRICTED MODEL SPACES
SN - 978-989-8425-40-9
AU - L. Boone E.
AU - J. Simmons S.
AU - Ricanek K.
PY - 2011
SP - 71
EP - 78
DO - 10.5220/0003139200710078