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An Empirical Bayes risk prediction model using multiple traits for sequencing data

Author

Listed:
  • Li Gengxin

    (Department of Mathematics and Statistics, Wright State University, 3640 Colonel Glenn Hwy, Dayton, OH 45435, USA)

  • Cui Yuehua

    (Department of Statistics and Probability, Michigan State University, 619 Red Cedar Rd, East Lansing, MI 48824,USA)

  • Zhao Hongyu

    (Department of Biostatistics, Yale School of Public Health, 60 College Street, New Haven, CT 06520, USA)

Abstract

The rapidly developing sequencing technologies have led to improved disease risk prediction through identifying many novel genes. Many prediction methods have been proposed to use rich genomic information to predict binary disease outcomes. It is intuitive that these methods can be further improved by making efficient use of the rich information in measured quantitative traits that are correlated with binary outcomes. In this article, we propose a novel Empirical Bayes prediction model that uses information from both quantitative traits and binary disease status to improve risk prediction. Our method is built on a new statistic that better infers the gene effect on multiple traits, and it also enjoys the good theoretical properties. We then consider using sequencing data by combining information from multiple rare variants in individual genes to strengthen the signals of causal genetic effects. In simulation study, we find that our proposed Empirical Bayes approach is superior to other existing methods in terms of feature selection and risk prediction. We further evaluate the effectiveness of our proposed method through its application to the sequencing data provided by the Genetic Analysis Workshop 18.

Suggested Citation

  • Li Gengxin & Cui Yuehua & Zhao Hongyu, 2015. "An Empirical Bayes risk prediction model using multiple traits for sequencing data," Statistical Applications in Genetics and Molecular Biology, De Gruyter, vol. 14(6), pages 551-573, December.
    • Handle: RePEc:bpj:sagmbi:v:14:y:2015:i:6:p:551-573:n:4
    DOI: 10.1515/sagmb-2015-0060
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    References listed on IDEAS

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    1. Senn, Stephen, 2008. "A Note Concerning a Selection Paradox of Dawid's," The American Statistician, American Statistical Association, vol. 62, pages 206-210, August.
    2. Efron, Bradley, 2009. "Empirical Bayes Estimates for Large-Scale Prediction Problems," Journal of the American Statistical Association, American Statistical Association, vol. 104(487), pages 1015-1028.
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