IDEAS home Printed from https://ideas.repec.org/a/plo/pone00/0051198.html
   My bibliography  Save this article

Analysis of Genome-Wide Association Studies with Multiple Outcomes Using Penalization

Author

Listed:
  • Jin Liu
  • Jian Huang
  • Shuangge Ma

Abstract

Genome-wide association studies have been extensively conducted, searching for markers for biologically meaningful outcomes and phenotypes. Penalization methods have been adopted in the analysis of the joint effects of a large number of SNPs (single nucleotide polymorphisms) and marker identification. This study is partly motivated by the analysis of heterogeneous stock mice dataset, in which multiple correlated phenotypes and a large number of SNPs are available. Existing penalization methods designed to analyze a single response variable cannot accommodate the correlation among multiple response variables. With multiple response variables sharing the same set of markers, joint modeling is first employed to accommodate the correlation. The group Lasso approach is adopted to select markers associated with all the outcome variables. An efficient computational algorithm is developed. Simulation study and analysis of the heterogeneous stock mice dataset show that the proposed method can outperform existing penalization methods.

Suggested Citation

  • Jin Liu & Jian Huang & Shuangge Ma, 2012. "Analysis of Genome-Wide Association Studies with Multiple Outcomes Using Penalization," PLOS ONE, Public Library of Science, vol. 7(12), pages 1-12, December.
    • Handle: RePEc:plo:pone00:0051198
    DOI: 10.1371/journal.pone.0051198
    as

    Download full text from publisher

    File URL: https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0051198
    Download Restriction: no
    File URL: https://journals.plos.org/plosone/article/file?id=10.1371/journal.pone.0051198&type=printable
    Download Restriction: no
    File URL: https://libkey.io/10.1371/journal.pone.0051198?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. Kun Chen & Kung‐Sik Chan & Nils Chr. Stenseth, 2012. "Reduced rank stochastic regression with a sparse singular value decomposition," Journal of the Royal Statistical Society Series B, Royal Statistical Society, vol. 74(2), pages 203-221, March.
    2. Ming Yuan & Ali Ekici & Zhaosong Lu & Renato Monteiro, 2007. "Dimension reduction and coefficient estimation in multivariate linear regression," Journal of the Royal Statistical Society Series B, Royal Statistical Society, vol. 69(3), pages 329-346, 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. Luo, Chongliang & Liang, Jian & Li, Gen & Wang, Fei & Zhang, Changshui & Dey, Dipak K. & Chen, Kun, 2018. "Leveraging mixed and incomplete outcomes via reduced-rank modeling," Journal of Multivariate Analysis, Elsevier, vol. 167(C), pages 378-394.
    2. Mishra, Aditya & Dey, Dipak K. & Chen, Yong & Chen, Kun, 2021. "Generalized co-sparse factor regression," Computational Statistics & Data Analysis, Elsevier, vol. 157(C).
    3. Goh, Gyuhyeong & Dey, Dipak K. & Chen, Kun, 2017. "Bayesian sparse reduced rank multivariate regression," Journal of Multivariate Analysis, Elsevier, vol. 157(C), pages 14-28.
    4. Kohei Yoshikawa & Shuichi Kawano, 2023. "Sparse reduced-rank regression for simultaneous rank and variable selection via manifold optimization," Computational Statistics, Springer, vol. 38(1), pages 53-75, March.
    5. Kun Chen & Yanyuan Ma, 2017. "Analysis of Double Single Index Models," Scandinavian Journal of Statistics, Danish Society for Theoretical Statistics;Finnish Statistical Society;Norwegian Statistical Association;Swedish Statistical Association, vol. 44(1), pages 1-20, March.
    6. Chen, Canyi & Xu, Wangli & Zhu, Liping, 2022. "Distributed estimation in heterogeneous reduced rank regression: With application to order determination in sufficient dimension reduction," Journal of Multivariate Analysis, Elsevier, vol. 190(C).
    7. Feng, Sanying & Lian, Heng & Zhu, Fukang, 2016. "Reduced rank regression with possibly non-smooth criterion functions: An empirical likelihood approach," Computational Statistics & Data Analysis, Elsevier, vol. 103(C), pages 139-150.
    8. Fujikoshi, Yasunori & Sakurai, Tetsuro, 2016. "High-dimensional consistency of rank estimation criteria in multivariate linear model," Journal of Multivariate Analysis, Elsevier, vol. 149(C), pages 199-212.
    9. Dong, Ruipeng & Li, Daoji & Zheng, Zemin, 2021. "Parallel integrative learning for large-scale multi-response regression with incomplete outcomes," Computational Statistics & Data Analysis, Elsevier, vol. 160(C).
    10. Dmitry Kobak & Yves Bernaerts & Marissa A. Weis & Federico Scala & Andreas S. Tolias & Philipp Berens, 2021. "Sparse reduced‐rank regression for exploratory visualisation of paired multivariate data," Journal of the Royal Statistical Society Series C, Royal Statistical Society, vol. 70(4), pages 980-1000, August.
    11. Pan Shang & Lingchen Kong, 2021. "Regularization Parameter Selection for the Low Rank Matrix Recovery," Journal of Optimization Theory and Applications, Springer, vol. 189(3), pages 772-792, June.
    12. Qiu, Yue & Zheng, Yuchen, 2023. "Improving box office projections through sentiment analysis: Insights from regularization-based forecast combinations," Economic Modelling, Elsevier, vol. 125(C).
    13. Hu, Jianhua & Liu, Xiaoqian & Liu, Xu & Xia, Ningning, 2022. "Some aspects of response variable selection and estimation in multivariate linear regression," Journal of Multivariate Analysis, Elsevier, vol. 188(C).
    14. Härdle, Wolfgang Karl & Huang, Chen & Chao, Shih-Kang, 2016. "Factorisable sparse tail event curves with expectiles," SFB 649 Discussion Papers 2016-018, Humboldt University Berlin, Collaborative Research Center 649: Economic Risk.
    15. Arash Karimzadeh & Omidreza Shoghli & Sepehr Sabeti & Hamed Tabkhi, 2022. "Multi-Asset Defect Hotspot Prediction for Highway Maintenance Management: A Risk-Based Machine Learning Approach," Sustainability, MDPI, vol. 14(9), pages 1-27, April.
    16. Fanhua Shang & Yuanyuan Liu & Fanjie Shang & Hongying Liu & Lin Kong & Licheng Jiao, 2020. "A Unified Scalable Equivalent Formulation for Schatten Quasi-Norms," Mathematics, MDPI, vol. 8(8), pages 1-19, August.
    17. Kharratzadeh, Milad & Coates, Mark, 2017. "Semi-parametric order-based generalized multivariate regression," Journal of Multivariate Analysis, Elsevier, vol. 156(C), pages 89-102.
    18. Luwan Zhang & Grace Wahba & Ming Yuan, 2016. "Distance shrinkage and Euclidean embedding via regularized kernel estimation," Journal of the Royal Statistical Society Series B, Royal Statistical Society, vol. 78(4), pages 849-867, September.
    19. Limin Li & Zhongsheng Wang & Hongkai Jiang, 2015. "Storage battery remaining useful life prognosis using improved unscented particle filter," Journal of Risk and Reliability, , vol. 229(1), pages 52-61, February.
    20. Luo, Ruiyan & Qi, Xin, 2017. "Signal extraction approach for sparse multivariate response regression," Journal of Multivariate Analysis, Elsevier, vol. 153(C), pages 83-97.

    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:pone00:0051198. 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.