IDEAS home Printed from https://ideas.repec.org/a/plo/pone00/0217283.html
   My bibliography  Save this article

Tournaments between markers as a strategy to enhance genomic predictions

Author

Listed:
  • Diógenes Ferreira Filho
  • Júlio Sílvio de Sousa Bueno Filho
  • Luciana Correia de Almeida Regitano
  • Maurício Mello de Alencar
  • Rosiana Rodrigues Alves
  • Sarah Laguna Conceição Meirelles

Abstract

Analysis of a large number of markers is crucial in both genome-wide association studies (GWAS) and genome-wide selection (GWS). However there are two methodological issues that restrict statistical analysis: high dimensionality (p≫n) and multicollinearity. Although there are methodologies that can be used to fit models for data with high dimensionality (eg, the Bayesian Lasso), a big problem that can occurs in this cases is that the predictive ability of the model should perform well for the individuals used to fit the model, but should not perform well for other individuals, restricting the applicability of the model. This problem can be circumvent by applying some selection methodology to reduce the number of markers (but keeping the markers associated with the phenotypic trait) before adjusting a model to predict GBVs. We revisit a tournament-based strategy between marker samples, where each sample has good statistical properties for estimation: n>p and low collinearity. Such tournaments are elaborated using multiple linear regression to eliminate markers. This method is adapted from previous works found in the literature. We used simulated data as well as real data derived from a study with SNPs in beef cattle. Tournament strategies not only circumvent the p≫n issue, but also minimize spurious associations. For real data, when we selected a few more than 20 markers, we obtained correlations greater than 0.70 between predicted Genomic Breeding Values (GBVs) and phenotypes in validation groups of a cross-validation scheme; and when we selected a larger number of markers (more than 100), the correlations exceeded 0.90, showing the efficiency in identifying relevant SNPs (or segregations) for both GWAS and GWS. In the simulation study, we obtained similar results.

Suggested Citation

  • Diógenes Ferreira Filho & Júlio Sílvio de Sousa Bueno Filho & Luciana Correia de Almeida Regitano & Maurício Mello de Alencar & Rosiana Rodrigues Alves & Sarah Laguna Conceição Meirelles, 2019. "Tournaments between markers as a strategy to enhance genomic predictions," PLOS ONE, Public Library of Science, vol. 14(6), pages 1-17, June.
    • Handle: RePEc:plo:pone00:0217283
    DOI: 10.1371/journal.pone.0217283
    as

    Download full text from publisher

    File URL: https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0217283
    Download Restriction: no
    File URL: https://journals.plos.org/plosone/article/file?id=10.1371/journal.pone.0217283&type=printable
    Download Restriction: no
    File URL: https://libkey.io/10.1371/journal.pone.0217283?utm_source=ideas
    LibKey link: if access is restricted and if your library uses this service, LibKey will redirect you to where you can use your library subscription to access this item
    ---><---

    References listed on IDEAS

    as
    1. Park, Trevor & Casella, George, 2008. "The Bayesian Lasso," Journal of the American Statistical Association, American Statistical Association, vol. 103, pages 681-686, June.
    Full references (including those not matched with items on IDEAS)

    Most related items

    These are the items that most often cite the same works as this one and are cited by the same works as this one.
    1. Li, Chunyu & Lou, Chenxin & Luo, Dan & Xing, Kai, 2021. "Chinese corporate distress prediction using LASSO: The role of earnings management," International Review of Financial Analysis, Elsevier, vol. 76(C).
    2. Armagan, Artin & Dunson, David, 2011. "Sparse variational analysis of linear mixed models for large data sets," Statistics & Probability Letters, Elsevier, vol. 81(8), pages 1056-1062, August.
    3. Martin Feldkircher & Florian Huber & Gary Koop & Michael Pfarrhofer, 2022. "APPROXIMATE BAYESIAN INFERENCE AND FORECASTING IN HUGE‐DIMENSIONAL MULTICOUNTRY VARs," International Economic Review, Department of Economics, University of Pennsylvania and Osaka University Institute of Social and Economic Research Association, vol. 63(4), pages 1625-1658, November.
    4. Eliaz, Kfir & Spiegler, Ran, 2022. "On incentive-compatible estimators," Games and Economic Behavior, Elsevier, vol. 132(C), pages 204-220.
    5. Oguzhan Cepni & I. Ethem Guney & Norman R. Swanson, 2020. "Forecasting and nowcasting emerging market GDP growth rates: The role of latent global economic policy uncertainty and macroeconomic data surprise factors," Journal of Forecasting, John Wiley & Sons, Ltd., vol. 39(1), pages 18-36, January.
    6. Hauzenberger, Niko, 2021. "Flexible Mixture Priors for Large Time-varying Parameter Models," Econometrics and Statistics, Elsevier, vol. 20(C), pages 87-108.
    7. Korobilis, Dimitris, 2015. "Quantile forecasts of inflation under model uncertainty," MPRA Paper 64341, University Library of Munich, Germany.
    8. Bernardi, Mauro & Costola, Michele, 2019. "High-dimensional sparse financial networks through a regularised regression model," SAFE Working Paper Series 244, Leibniz Institute for Financial Research SAFE.
    9. Damien Rousselière, 2019. "A Flexible Approach to Age Dependence in Organizational Mortality: Comparing the Life Duration for Cooperative and Non-Cooperative Enterprises Using a Bayesian Generalized Additive Discrete Time Survi," Journal of Quantitative Economics, Springer;The Indian Econometric Society (TIES), vol. 17(4), pages 829-855, December.
    10. Chakraborty, Sounak, 2012. "Bayesian multiple response kernel regression model for high dimensional data and its practical applications in near infrared spectroscopy," Computational Statistics & Data Analysis, Elsevier, vol. 56(9), pages 2742-2755.
    11. Virginia X. He & Matt P. Wand, 2024. "Bayesian generalized additive model selection including a fast variational option," AStA Advances in Statistical Analysis, Springer;German Statistical Society, vol. 108(3), pages 639-668, September.
    12. Ji, Yonggang & Lin, Nan & Zhang, Baoxue, 2012. "Model selection in binary and tobit quantile regression using the Gibbs sampler," Computational Statistics & Data Analysis, Elsevier, vol. 56(4), pages 827-839.
    13. Hu, Guanyu, 2021. "Spatially varying sparsity in dynamic regression models," Econometrics and Statistics, Elsevier, vol. 17(C), pages 23-34.
    14. Lee Anthony & Caron Francois & Doucet Arnaud & Holmes Chris, 2012. "Bayesian Sparsity-Path-Analysis of Genetic Association Signal using Generalized t Priors," Statistical Applications in Genetics and Molecular Biology, De Gruyter, vol. 11(2), pages 1-31, January.
    15. Jan Prüser, 2021. "Forecasting US inflation using Markov dimension switching," Journal of Forecasting, John Wiley & Sons, Ltd., vol. 40(3), pages 481-499, April.
    16. Michael Pfarrhofer & Anna Stelzer, 2019. "High-frequency and heteroskedasticity identification in multicountry models: Revisiting spillovers of monetary shocks," Papers 1912.03158, arXiv.org, revised Dec 2024.
    17. Luis Castro-Martín & Maria del Mar Rueda & Ramón Ferri-García, 2020. "Inference from Non-Probability Surveys with Statistical Matching and Propensity Score Adjustment Using Modern Prediction Techniques," Mathematics, MDPI, vol. 8(6), pages 1-19, June.
    18. Celso Brunetti & Marc Joëts & Valérie Mignon, 2023. "Reasons Behind Words: OPEC Narratives and the Oil Market," Working Papers hal-04196053, HAL.
    19. Niko Hauzenberger & Michael Pfarrhofer, 2021. "Bayesian State‐Space Modeling for Analyzing Heterogeneous Network Effects of US Monetary Policy," Scandinavian Journal of Economics, Wiley Blackwell, vol. 123(4), pages 1261-1291, October.
    20. Juan Armando Torres Munguía, 2018. "What is behind homicide gender gaps in Mexico? A spatial semiparametric approach," Ibero America Institute for Econ. Research (IAI) Discussion Papers 236, Ibero-America Institute for Economic Research.

    More about this item

    Statistics

    Access and download statistics

    Corrections

    All material on this site has been provided by the respective publishers and authors. You can help correct errors and omissions. When requesting a correction, please mention this item's handle: RePEc:plo:pone00:0217283. See general information about how to correct material in RePEc.

    If you have authored this item and are not yet registered with RePEc, we encourage you to do it here. This allows to link your profile to this item. It also allows you to accept potential citations to this item that we are uncertain about.

    If CitEc recognized a bibliographic reference but did not link an item in RePEc to it, you can help with this form .

    If you know of missing items citing this one, you can help us creating those links by adding the relevant references in the same way as above, for each refering item. If you are a registered author of this item, you may also want to check the "citations" tab in your RePEc Author Service profile, as there may be some citations waiting for confirmation.

    For technical questions regarding this item, or to correct its authors, title, abstract, bibliographic or download information, contact: plosone (email available below). General contact details of provider: https://journals.plos.org/plosone/ .

    Please note that corrections may take a couple of weeks to filter through the various RePEc services.

    IDEAS is a RePEc service. RePEc uses bibliographic data supplied by the respective publishers.