IDEAS home Printed from https://ideas.repec.org/a/spr/stabio/v8y2016i1d10.1007_s12561-014-9124-2.html
   My bibliography  Save this article

Bayesian Two-Stage Biomarker-Based Adaptive Design for Targeted Therapy Development

Author

Listed:
  • Xuemin Gu

    (The University of Texas MD Anderson Cancer Center)

  • Nan Chen

    (The University of Texas MD Anderson Cancer Center)

  • Caimiao Wei

    (The University of Texas MD Anderson Cancer Center)

  • Suyu Liu

    (The University of Texas MD Anderson Cancer Center)

  • Vassiliki A. Papadimitrakopoulou

    (The University of Texas MD Anderson Cancer Center)

  • Roy S. Herbst

    (Yale School of Medicine)

  • J. Jack Lee

    (The University of Texas MD Anderson Cancer Center)

Abstract

We propose a Bayesian two-stage biomarker-based adaptive randomization (AR) design for the development of targeted agents. The design has three main goals: (1) to test the treatment efficacy, (2) to identify prognostic and predictive markers for the targeted agents, and (3) to provide better treatment for patients enrolled in the trial. To treat patients better, both stages are guided by the Bayesian AR based on the individual patient’s biomarker profiles. The AR in the first stage is based on a known marker. A Go/No-Go decision can be made in the first stage by testing the overall treatment effects. If a Go decision is made at the end of the first stage, a two-step Bayesian lasso strategy will be implemented to select additional prognostic or predictive biomarkers to refine the AR in the second stage. We use simulations to demonstrate the good operating characteristics of the design, including the control of per-comparison type I and type II errors, high probability in selecting important markers, and treating more patients with more effective treatments. Bayesian adaptive designs allow for continuous learning. The designs are particularly suitable for the development of multiple targeted agents in the quest of personalized medicine. By estimating treatment effects and identifying relevant biomarkers, the information acquired from the interim data can be used to guide the choice of treatment for each individual patient enrolled in the trial in real time to achieve a better outcome. The design is being implemented in the BATTLE-2 trial in lung cancer at the MD Anderson Cancer Center.

Suggested Citation

  • Xuemin Gu & Nan Chen & Caimiao Wei & Suyu Liu & Vassiliki A. Papadimitrakopoulou & Roy S. Herbst & J. Jack Lee, 2016. "Bayesian Two-Stage Biomarker-Based Adaptive Design for Targeted Therapy Development," Statistics in Biosciences, Springer;International Chinese Statistical Association, vol. 8(1), pages 99-128, June.
    • Handle: RePEc:spr:stabio:v:8:y:2016:i:1:d:10.1007_s12561-014-9124-2
    DOI: 10.1007/s12561-014-9124-2
    as

    Download full text from publisher

    File URL: http://link.springer.com/10.1007/s12561-014-9124-2
    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/s12561-014-9124-2?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. Lukas Meier & Sara Van De Geer & Peter Bühlmann, 2008. "The group lasso for logistic regression," Journal of the Royal Statistical Society Series B, Royal Statistical Society, vol. 70(1), pages 53-71, February.
    3. Hu, Feifang & Rosenberger, William F., 2003. "Optimality, Variability, Power: Evaluating Response-Adaptive Randomization Procedures for Treatment Comparisons," Journal of the American Statistical Association, American Statistical Association, vol. 98, pages 671-678, January.
    4. Park, Trevor & Casella, George, 2008. "The Bayesian Lasso," Journal of the American Statistical Association, American Statistical Association, vol. 103, pages 681-686, June.
    5. DiMasi, Joseph A. & Hansen, Ronald W. & Grabowski, Henry G., 2003. "The price of innovation: new estimates of drug development costs," Journal of Health Economics, Elsevier, vol. 22(2), pages 151-185, March.
    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. 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.
    2. Matthew Hindman, 2015. "Building Better Models," The ANNALS of the American Academy of Political and Social Science, , vol. 659(1), pages 48-62, May.
    3. Fabian Scheipl & Thomas Kneib & Ludwig Fahrmeir, 2013. "Penalized likelihood and Bayesian function selection in regression models," AStA Advances in Statistical Analysis, Springer;German Statistical Society, vol. 97(4), pages 349-385, October.
    4. 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.
    5. Nicolas Städler & Peter Bühlmann & Sara Geer, 2010. "ℓ 1 -penalization for mixture regression models," TEST: An Official Journal of the Spanish Society of Statistics and Operations Research, Springer;Sociedad de Estadística e Investigación Operativa, vol. 19(2), pages 209-256, August.
    6. Nicolai Meinshausen & Peter Bühlmann, 2010. "Stability selection," Journal of the Royal Statistical Society Series B, Royal Statistical Society, vol. 72(4), pages 417-473, September.
    7. G. Yi & J. Q. Shi & T. Choi, 2011. "Penalized Gaussian Process Regression and Classification for High-Dimensional Nonlinear Data," Biometrics, The International Biometric Society, vol. 67(4), pages 1285-1294, December.
    8. 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.
    9. 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).
    10. 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.
    11. repec:jss:jstsof:33:i01 is not listed on IDEAS
    12. Osamu Komori & Shinto Eguchi & John B. Copas, 2015. "Generalized t-statistic for two-group classification," Biometrics, The International Biometric Society, vol. 71(2), pages 404-416, June.
    13. Jean-Pierre Dubé & Sanjog Misra, 2017. "Personalized Pricing and Consumer Welfare," NBER Working Papers 23775, National Bureau of Economic Research, Inc.
    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. Gilles Celeux & Mohammed El Anbari & Jean-Michel Marin & Christian P. Robert, 2010. "Regularization in Regression : Comparing Bayesian and Frequentist Methods in a Poorly Informative Situation," Working Papers 2010-43, Center for Research in Economics and Statistics.
    16. Yang, Yanlin & Hu, Xuemei & Jiang, Huifeng, 2022. "Group penalized logistic regressions predict up and down trends for stock prices," The North American Journal of Economics and Finance, Elsevier, vol. 59(C).
    17. Korobilis, Dimitris, 2013. "Hierarchical shrinkage priors for dynamic regressions with many predictors," International Journal of Forecasting, Elsevier, vol. 29(1), pages 43-59.
    18. Friedman, Jerome H. & Hastie, Trevor & Tibshirani, Rob, 2010. "Regularization Paths for Generalized Linear Models via Coordinate Descent," Journal of Statistical Software, Foundation for Open Access Statistics, vol. 33(i01).
    19. Yuan Jiang & Yunxiao He & Heping Zhang, 2016. "Variable Selection With Prior Information for Generalized Linear Models via the Prior LASSO Method," Journal of the American Statistical Association, Taylor & Francis Journals, vol. 111(513), pages 355-376, March.
    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.
    21. Yu-Zhu Tian & Man-Lai Tang & Wai-Sum Chan & Mao-Zai Tian, 2021. "Bayesian bridge-randomized penalized quantile regression for ordinal longitudinal data, with application to firm’s bond ratings," Computational Statistics, Springer, vol. 36(2), pages 1289-1319, June.

    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:stabio:v:8:y:2016:i:1:d:10.1007_s12561-014-9124-2. 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.