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Score Statistics for Mapping Quantitative Trait Loci

Author

Listed:
  • Chang Myron N

    (University of Florida)

  • Wu Rongling

    (University of Florida)

  • Wu Samuel S

    (University of Florida)

  • Casella George

    (University of Florida)

Abstract

We propose a method to detect the existence of quantitative trait loci (QTL) in a backcross population using a score test. Since the score test only uses the MLEs of parameters under the null hypothesis, it is computationally simpler than the likelihood ratio test (LRT). Moreover, because the location parameter of the QTL is unidentifiable under the null hypothesis, the distribution of the maximum of the LRT statistics, typically the statistic of choice for testing H0: no QTL, does not have the standard chi-square distribution asymptotically under the null hypothesis. From the simple structure of the score test statistics, the asymptotic null distribution can be derived for the maximum of the square of score test statistics. Numerical methods are proposed to compute the asymptotic null distribution and the critical thresholds can be obtained accordingly. We show that the maximum of the LR test statistics and the maximum of the square of score statistics are asymptotically equivalent. Therefore, the critical threshold for the score test can be used for the LR test also. A simple backcross design is used to demonstrate the application of the score test to QTL mapping.

Suggested Citation

  • Chang Myron N & Wu Rongling & Wu Samuel S & Casella George, 2009. "Score Statistics for Mapping Quantitative Trait Loci," Statistical Applications in Genetics and Molecular Biology, De Gruyter, vol. 8(1), pages 1-37, February.
    • Handle: RePEc:bpj:sagmbi:v:8:y:2009:i:1:n:16
    DOI: 10.2202/1544-6115.1386
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    Citations

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    Cited by:

    1. Charles-Elie Rabier & Jean-Marc Azaïs & Jean-Michel Elsen & Céline Delmas, 2019. "Chi-square processes for gene mapping in a population with family structure," Statistical Papers, Springer, vol. 60(1), pages 239-271, February.
    2. Frommlet Florian & Ljubic Ivana & Arnardóttir Helga Björk & Bogdan Malgorzata, 2012. "QTL Mapping Using a Memetic Algorithm with Modifications of BIC as Fitness Function," Statistical Applications in Genetics and Molecular Biology, De Gruyter, vol. 11(4), pages 1-26, May.
    3. Charles-Elie Rabier, 2014. "On quantitative trait locus mapping with an interference phenomenon," TEST: An Official Journal of the Spanish Society of Statistics and Operations Research, Springer;Sociedad de Estadística e Investigación Operativa, vol. 23(2), pages 311-329, June.
    4. Guanfu Liu & Pengfei Li & Yukun Liu & Xiaolong Pu, 2020. "Hypothesis testing for quantitative trait locus effects in both location and scale in genetic backcross studies," Scandinavian Journal of Statistics, Danish Society for Theoretical Statistics;Finnish Statistical Society;Norwegian Statistical Association;Swedish Statistical Association, vol. 47(4), pages 1064-1089, December.

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