IDEAS home Printed from https://ideas.repec.org/a/bpj/sagmbi/v14y2015i3p265-277n4.html
   My bibliography  Save this article

Modeling gene-covariate interactions in sparse regression with group structure for genome-wide association studies

Author

Listed:
  • Li Yun
  • O’Connor George T.

    (Pulmonary Center, Department of Medicine, Boston University School of Medicine, MA 02118, USA)

  • Dupuis Josée

    (Department of Biostatistics, Boston University School of Public Health, MA 02118, USA)

  • Kolaczyk Eric

    (Department of Mathematics and Statistics, Boston University, MA 02215, USA)

Abstract

In genome-wide association studies (GWAS), it is of interest to identify genetic variants associated with phenotypes. For a given phenotype, the associated genetic variants are usually a sparse subset of all possible variants. Traditional Lasso-type estimation methods can therefore be used to detect important genes. But the relationship between genotypes at one variant and a phenotype may be influenced by other variables, such as sex and life style. Hence it is important to be able to incorporate gene-covariate interactions into the sparse regression model. In addition, because there is biological knowledge on the manner in which genes work together in structured groups, it is desirable to incorporate this information as well. In this paper, we present a novel sparse regression methodology for gene-covariate models in association studies that not only allows such interactions but also considers biological group structure. Simulation results show that our method substantially outperforms another method, in which interaction is considered, but group structure is ignored. Application to data on total plasma immunoglobulin E (IgE) concentrations in the Framingham Heart Study (FHS), using sex and smoking status as covariates, yields several potentially interesting gene-covariate interactions.

Suggested Citation

  • Li Yun & O’Connor George T. & Dupuis Josée & Kolaczyk Eric, 2015. "Modeling gene-covariate interactions in sparse regression with group structure for genome-wide association studies," Statistical Applications in Genetics and Molecular Biology, De Gruyter, vol. 14(3), pages 265-277, June.
    • Handle: RePEc:bpj:sagmbi:v:14:y:2015:i:3:p:265-277:n:4
    DOI: 10.1515/sagmb-2014-0073
    as

    Download full text from publisher

    File URL: https://doi.org/10.1515/sagmb-2014-0073
    Download Restriction: For access to full text, subscription to the journal or payment for the individual article is required.
    File URL: https://libkey.io/10.1515/sagmb-2014-0073?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
    ---><---

    As the access to this document is restricted, you may want to search for a different version of it.

    References listed on IDEAS

    as
    1. Zou, Hui, 2006. "The Adaptive Lasso and Its Oracle Properties," Journal of the American Statistical Association, American Statistical Association, vol. 101, pages 1418-1429, December.
    2. Radchenko, Peter & James, Gareth M., 2010. "Variable Selection Using Adaptive Nonlinear Interaction Structures in High Dimensions," Journal of the American Statistical Association, American Statistical Association, vol. 105(492), pages 1541-1553.
    3. Hui Zou & Trevor Hastie, 2005. "Addendum: Regularization and variable selection via the elastic net," Journal of the Royal Statistical Society Series B, Royal Statistical Society, vol. 67(5), pages 768-768, November.
    4. Choi, Nam Hee & Li, William & Zhu, Ji, 2010. "Variable Selection With the Strong Heredity Constraint and Its Oracle Property," Journal of the American Statistical Association, American Statistical Association, vol. 105(489), pages 354-364.
    5. Jian Huang & Shuange Ma & Huiliang Xie & Cun-Hui Zhang, 2009. "A group bridge approach for variable selection," Biometrika, Biometrika Trust, vol. 96(2), pages 339-355.
    6. Hui Zou & Trevor Hastie, 2005. "Regularization and variable selection via the elastic net," Journal of the Royal Statistical Society Series B, Royal Statistical Society, vol. 67(2), pages 301-320, April.
    7. Fan J. & Li R., 2001. "Variable Selection via Nonconcave Penalized Likelihood and its Oracle Properties," Journal of the American Statistical Association, American Statistical Association, vol. 96, pages 1348-1360, December.
    8. Ming Yuan & Yi Lin, 2006. "Model selection and estimation in regression with grouped variables," Journal of the Royal Statistical Society Series B, Royal Statistical Society, vol. 68(1), pages 49-67, February.
    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. Loann David Denis Desboulets, 2018. "A Review on Variable Selection in Regression Analysis," Econometrics, MDPI, vol. 6(4), pages 1-27, November.
    2. Jonathan Boss & Alexander Rix & Yin‐Hsiu Chen & Naveen N. Narisetty & Zhenke Wu & Kelly K. Ferguson & Thomas F. McElrath & John D. Meeker & Bhramar Mukherjee, 2021. "A hierarchical integrative group least absolute shrinkage and selection operator for analyzing environmental mixtures," Environmetrics, John Wiley & Sons, Ltd., vol. 32(8), December.
    3. Diego Vidaurre & Concha Bielza & Pedro Larrañaga, 2013. "A Survey of L1 Regression," International Statistical Review, International Statistical Institute, vol. 81(3), pages 361-387, December.
    4. Takumi Saegusa & Tianzhou Ma & Gang Li & Ying Qing Chen & Mei-Ling Ting Lee, 2020. "Variable Selection in Threshold Regression Model with Applications to HIV Drug Adherence Data," Statistics in Biosciences, Springer;International Chinese Statistical Association, vol. 12(3), pages 376-398, December.
    5. Pei Wang & Shunjie Chen & Sijia Yang, 2022. "Recent Advances on Penalized Regression Models for Biological Data," Mathematics, MDPI, vol. 10(19), pages 1-24, October.
    6. Justin B. Post & Howard D. Bondell, 2013. "Factor Selection and Structural Identification in the Interaction ANOVA Model," Biometrics, The International Biometric Society, vol. 69(1), pages 70-79, March.
    7. Yanfang Zhang & Chuanhua Wei & Xiaolin Liu, 2022. "Group Logistic Regression Models with l p,q Regularization," Mathematics, MDPI, vol. 10(13), pages 1-15, June.
    8. Young Joo Yoon & Cheolwoo Park & Erik Hofmeister & Sangwook Kang, 2012. "Group variable selection in cardiopulmonary cerebral resuscitation data for veterinary patients," Journal of Applied Statistics, Taylor & Francis Journals, vol. 39(7), pages 1605-1621, January.
    9. Yanming Li & Bin Nan & Ji Zhu, 2015. "Multivariate sparse group lasso for the multivariate multiple linear regression with an arbitrary group structure," Biometrics, The International Biometric Society, vol. 71(2), pages 354-363, June.
    10. Wenyan Zhong & Xuewen Lu & Jingjing Wu, 2021. "Bi-level variable selection in semiparametric transformation models with right-censored data," Computational Statistics, Springer, vol. 36(3), pages 1661-1692, September.
    11. Mingqiu Wang & Guo-Liang Tian, 2016. "Robust group non-convex estimations for high-dimensional partially linear models," Journal of Nonparametric Statistics, Taylor & Francis Journals, vol. 28(1), pages 49-67, March.
    12. Shanshan Qin & Hao Ding & Yuehua Wu & Feng Liu, 2021. "High-dimensional sign-constrained feature selection and grouping," Annals of the Institute of Statistical Mathematics, Springer;The Institute of Statistical Mathematics, vol. 73(4), pages 787-819, August.
    13. Kaida Cai & Hua Shen & Xuewen Lu, 2022. "Adaptive bi-level variable selection for multivariate failure time model with a diverging number of covariates," TEST: An Official Journal of the Spanish Society of Statistics and Operations Research, Springer;Sociedad de Estadística e Investigación Operativa, vol. 31(4), pages 968-993, December.
    14. Tutz, Gerhard & Pößnecker, Wolfgang & Uhlmann, Lorenz, 2015. "Variable selection in general multinomial logit models," Computational Statistics & Data Analysis, Elsevier, vol. 82(C), pages 207-222.
    15. Shuichi Kawano, 2014. "Selection of tuning parameters in bridge regression models via Bayesian information criterion," Statistical Papers, Springer, vol. 55(4), pages 1207-1223, November.
    16. Yize Zhao & Matthias Chung & Brent A. Johnson & Carlos S. Moreno & Qi Long, 2016. "Hierarchical Feature Selection Incorporating Known and Novel Biological Information: Identifying Genomic Features Related to Prostate Cancer Recurrence," Journal of the American Statistical Association, Taylor & Francis Journals, vol. 111(516), pages 1427-1439, October.
    17. Capanu, Marinela & Giurcanu, Mihai & Begg, Colin B. & Gönen, Mithat, 2023. "Subsampling based variable selection for generalized linear models," Computational Statistics & Data Analysis, Elsevier, vol. 184(C).
    18. Zeyu Bian & Erica E. M. Moodie & Susan M. Shortreed & Sahir Bhatnagar, 2023. "Variable selection in regression‐based estimation of dynamic treatment regimes," Biometrics, The International Biometric Society, vol. 79(2), pages 988-999, June.
    19. Wentao Wang & Jiaxuan Liang & Rong Liu & Yunquan Song & Min Zhang, 2022. "A Robust Variable Selection Method for Sparse Online Regression via the Elastic Net Penalty," Mathematics, MDPI, vol. 10(16), pages 1-18, August.
    20. Zanhua Yin, 2020. "Variable selection for sparse logistic regression," Metrika: International Journal for Theoretical and Applied Statistics, Springer, vol. 83(7), pages 821-836, October.

    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:bpj:sagmbi:v:14:y:2015:i:3:p:265-277:n:4. 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: Peter Golla (email available below). General contact details of provider: https://www.degruyter.com .

    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.