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Journal of Zhejiang University SCIENCE B

, Volume 8, Issue 11, pp 792–801 | Cite as

Mapping of quantitative trait loci using the skew-normal distribution

  • Fernandes Elisabete 
  • Pacheco António 
  • Penha-Gonçalves Carlos 
Article

Abstract

In standard interval mapping (IM) of quantitative trait loci (QTL), the QTL effect is described by a normal mixture model. When this assumption of normality is violated, the most commonly adopted strategy is to use the previous model after data transformation. However, an appropriate transformation may not exist or may be difficult to find. Also this approach can raise interpretation issues. An interesting alternative is to consider a skew-normal mixture model in standard IM, and the resulting method is here denoted as skew-normal IM. This flexible model that includes the usual symmetric normal distribution as a special case is important, allowing continuous variation from normality to non-normality. In this paper we briefly introduce the main peculiarities of the skew-normal distribution. The maximum likelihood estimates of parameters of the skew-normal distribution are obtained by the expectation-maximization (EM) algorithm. The proposed model is illustrated with real data from an intercross experiment that shows a significant departure from the normality assumption. The performance of the skew-normal IM is assessed via stochastic simulation. The results indicate that the skew-normal IM has higher power for QTL detection and better precision of QTL location as compared to standard IM and nonparametric IM.

Key words

Interval mapping (IM) Quantitative trait loci (QTL) Skew-normal distribution Expectation-maximization (EM) algorithm 

CLC number

Q78 TP31 

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Copyright information

© Springer-Verlag 2007

Authors and Affiliations

  • Fernandes Elisabete 
    • 1
    • 2
    • 4
  • Pacheco António 
    • 3
  • Penha-Gonçalves Carlos 
    • 4
  1. 1.Centre for Mathematics and Its ApplicationsIST-Technical University of LisbonLisboaPortugal
  2. 2.Department of Statistics and Operational Research, Faculty of SciencesUniversity of LisbonLisboaPortugal
  3. 3.Department of Mathematics and Centre for Mathematics and Its ApplicationsIST-Technical University of LisbonLisboaPortugal
  4. 4.Gulbenkian Institute of ScienceOeirasPortugal

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