IDEAS home Printed from https://ideas.repec.org/a/spr/compst/v36y2021i2d10.1007_s00180-020-01060-5.html
   My bibliography  Save this article

Integrative analysis of multiple types of genomic data using an accelerated failure time frailty model

Author

Listed:
  • Shirong Deng

    (Wuhan University)

  • Jie Chen

    (Augusta University)

  • Huidong Shi

    (Augusta University)

Abstract

As the high throughput technologies rapidly develop, multiple types of genomic data become available within and across different studies. It has become a challenging task in modern statistical research to use all types of genomic data to infer some disease-prone genetic information. In this work, we propose an integrative analysis of multiple and different types of genomic data, clinical covariates and survival data under a framework of an accelerated failure time with frailty model. The proposed integrative approach aims to answer some aspects of the complex problem in genomic data analysis by finding relevant genomic features and inferring patients’ survival time using identified features. The proposed integrative approach is developed using a weighted least-squares with a sparse group LASSO penalty as the objective function to simultaneously estimate and select the relevant features. Extensive simulation studies are conducted to assess the performance of the proposed method with two types of genomic data, DNA methylation data and copy number variation data, on 600 genes and three clinical covariates. The simulation results show promises of the proposed method. The proposed method is applied to the analysis of the Cancer Genome Atlas data on Glioblastoma, a lethal brain cancer, and biologically interpretable results are obtained.

Suggested Citation

  • Shirong Deng & Jie Chen & Huidong Shi, 2021. "Integrative analysis of multiple types of genomic data using an accelerated failure time frailty model," Computational Statistics, Springer, vol. 36(2), pages 1499-1532, June.
    • Handle: RePEc:spr:compst:v:36:y:2021:i:2:d:10.1007_s00180-020-01060-5
    DOI: 10.1007/s00180-020-01060-5
    as

    Download full text from publisher

    File URL: http://link.springer.com/10.1007/s00180-020-01060-5
    File Function: Abstract
    Download Restriction: Access to the full text of the articles in this series is restricted.
    File URL: https://libkey.io/10.1007/s00180-020-01060-5?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. Jin Liu & Shuangge Ma & Jian Huang, 2014. "Integrative Analysis of Cancer Diagnosis Studies with Composite Penalization," Scandinavian Journal of Statistics, Danish Society for Theoretical Statistics;Finnish Statistical Society;Norwegian Statistical Association;Swedish Statistical Association, vol. 41(1), pages 87-103, March.
    2. Thierry Chekouo & Francesco C. Stingo & James D. Doecke & Kim-Anh Do, 2017. "A Bayesian integrative approach for multi-platform genomic data: A kidney cancer case study," Biometrics, The International Biometric Society, vol. 73(2), pages 615-624, June.
    3. Hsin-Chieh Wu & Yu-Ching Lin & Cheng-Hsin Liu & Hsiang-Ching Chung & Ya-Ting Wang & Ya-Wen Lin & Hsin-I. Ma & Pang-Hsien Tu & Sean E. Lawler & Ruey-Hwa Chen, 2014. "USP11 regulates PML stability to control Notch-induced malignancy in brain tumours," Nature Communications, Nature, vol. 5(1), pages 1-16, May.
    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. Gregory Vaughan & Robert Aseltine & Kun Chen & Jun Yan, 2017. "Stagewise generalized estimating equations with grouped variables," Biometrics, The International Biometric Society, vol. 73(4), pages 1332-1342, December.
    2. Zhang, Qingzhao & Ma, Shuangge & Huang, Yuan, 2021. "Promote sign consistency in the joint estimation of precision matrices," Computational Statistics & Data Analysis, Elsevier, vol. 159(C).
    3. Weibing Li & Thierry Chekouo, 2022. "Bayesian group selection with non-local priors," Computational Statistics, Springer, vol. 37(1), pages 287-302, March.
    4. Jin Liu & Jian Huang & Yawei Zhang & Qing Lan & Nathaniel Rothman & Tongzhang Zheng & Shuangge Ma, 2014. "Integrative analysis of prognosis data on multiple cancer subtypes," Biometrics, The International Biometric Society, vol. 70(3), pages 480-488, September.
    5. Wu, Cen & Zhang, Qingzhao & Jiang, Yu & Ma, Shuangge, 2018. "Robust network-based analysis of the associations between (epi)genetic measurements," Journal of Multivariate Analysis, Elsevier, vol. 168(C), pages 119-130.
    6. Fang, Kuangnan & Fan, Xinyan & Zhang, Qingzhao & Ma, Shuangge, 2018. "Integrative sparse principal component analysis," Journal of Multivariate Analysis, Elsevier, vol. 166(C), pages 1-16.

    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:spr:compst:v:36:y:2021:i:2:d:10.1007_s00180-020-01060-5. 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: Sonal Shukla or Springer Nature Abstracting and Indexing (email available below). General contact details of provider: http://www.springer.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.