IDEAS home Printed from https://ideas.repec.org/a/spr/stabio/v9y2017i1d10.1007_s12561-016-9177-5.html
   My bibliography  Save this article

Estimation of Stratified Mark-Specific Proportional Hazards Models Under Two-Phase Sampling with Application to HIV Vaccine Efficacy Trials

Author

Listed:
  • Guangren Yang

    (Jinan University)

  • Yanqing Sun

    (University of North Carolina at Charlotte)

  • Li Qi

    (Biostatistics and Programming)

  • Peter B. Gilbert

    (University of Washington and Fred Hutchinson Cancer Center)

Abstract

An objective of preventive HIV vaccine efficacy trials is to understand how vaccine-induced immune responses to specific protein sequences of HIV-1 associate with subsequent infection with specific sequences of HIV, where the immune response biomarkers are measured in vaccine recipients via a two-phase sampling design. Motivated by this objective, we investigate the stratified mark-specific proportional hazards model under two-phase biomarker sampling, where the mark is the genetic distance of an infecting HIV-1 sequence to an HIV-1 sequence represented inside the vaccine. Estimation and inference procedures based on inverse probability weighting of complete-cases and on augmented inverse probability weighting of complete-cases are developed. Asymptotic properties of the estimators are derived and their finite-sample performances are examined in simulation studies. The methods are shown to have satisfactory performance and are applied to the RV144 vaccine trial to assess whether immune response correlates of HIV-1 infection are stronger for HIV-1 infecting sequences similar to the vaccine than for sequences distant from the vaccine.

Suggested Citation

  • Guangren Yang & Yanqing Sun & Li Qi & Peter B. Gilbert, 2017. "Estimation of Stratified Mark-Specific Proportional Hazards Models Under Two-Phase Sampling with Application to HIV Vaccine Efficacy Trials," Statistics in Biosciences, Springer;International Chinese Statistical Association, vol. 9(1), pages 259-283, June.
    • Handle: RePEc:spr:stabio:v:9:y:2017:i:1:d:10.1007_s12561-016-9177-5
    DOI: 10.1007/s12561-016-9177-5
    as

    Download full text from publisher

    File URL: http://link.springer.com/10.1007/s12561-016-9177-5
    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/s12561-016-9177-5?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. Yanqing Sun & Peter B. Gilbert, 2012. "Estimation of Stratified Mark‐Specific Proportional Hazards Models with Missing Marks," Scandinavian Journal of Statistics, Danish Society for Theoretical Statistics;Finnish Statistical Society;Norwegian Statistical Association;Swedish Statistical Association, vol. 39(1), pages 34-52, March.
    2. Halbo Zhou & C.‐Y. Wang, 2000. "Failure time regression with continuous covariates measured with error," Journal of the Royal Statistical Society Series B, Royal Statistical Society, vol. 62(4), pages 657-665.
    3. Sun, Yanqing & Li, Mei & Gilbert, Peter B., 2016. "Goodness-of-fit test of the stratified mark-specific proportional hazards model with continuous mark," Computational Statistics & Data Analysis, Elsevier, vol. 93(C), pages 348-358.
    4. M. Juraska & P. B. Gilbert, 2013. "Mark-Specific Hazard Ratio Model with Multivariate Continuous Marks: An Application to Vaccine Efficacy," Biometrics, The International Biometric Society, vol. 69(2), pages 328-337, June.
    5. Peter B. Gilbert & Yanqing Sun, 2015. "Inferences on relative failure rates in stratified mark-specific proportional hazards models with missing marks, with application to human immunodeficiency virus vaccine efficacy trials," Journal of the Royal Statistical Society Series C, Royal Statistical Society, vol. 64(1), pages 49-73, January.
    6. Kani Chen, 2001. "Generalized case–cohort sampling," Journal of the Royal Statistical Society Series B, Royal Statistical Society, vol. 63(4), pages 791-809.
    7. Michal Kulich & D.Y. Lin, 2004. "Improving the Efficiency of Relative-Risk Estimation in Case-Cohort Studies," Journal of the American Statistical Association, American Statistical Association, vol. 99, pages 832-844, January.
    8. Qi, Lihong & Wang, C.Y. & Prentice, Ross L., 2005. "Weighted Estimators for Proportional Hazards Regression With Missing Covariates," Journal of the American Statistical Association, American Statistical Association, vol. 100, pages 1250-1263, December.
    Full references (including those not matched with items on IDEAS)

    Citations

    Citations are extracted by the CitEc Project, subscribe to its RSS feed for this item.
    as


    Cited by:

    1. Yanqing Sun & Li Qi & Fei Heng & Peter B. Gilbert, 2020. "A hybrid approach for the stratified mark‐specific proportional hazards model with missing covariates and missing marks, with application to vaccine efficacy trials," Journal of the Royal Statistical Society Series C, Royal Statistical Society, vol. 69(4), pages 791-814, August.
    2. Yanqing Sun & Qiong Shou & Peter B. Gilbert & Fei Heng & Xiyuan Qian, 2023. "Semiparametric additive time‐varying coefficients model for longitudinal data with censored time origin," Biometrics, The International Biometric Society, vol. 79(2), pages 695-710, June.

    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. Yanqing Sun & Li Qi & Fei Heng & Peter B. Gilbert, 2020. "A hybrid approach for the stratified mark‐specific proportional hazards model with missing covariates and missing marks, with application to vaccine efficacy trials," Journal of the Royal Statistical Society Series C, Royal Statistical Society, vol. 69(4), pages 791-814, August.
    2. Dongxiao Han & Liuquan Sun & Yanqing Sun & Li Qi, 2017. "Mark-specific additive hazards regression with continuous marks," Lifetime Data Analysis: An International Journal Devoted to Statistical Methods and Applications for Time-to-Event Data, Springer, vol. 23(3), pages 467-494, July.
    3. Yanqing Sun & Xiyuan Qian & Qiong Shou & Peter B. Gilbert, 2017. "Analysis of two-phase sampling data with semiparametric additive hazards models," Lifetime Data Analysis: An International Journal Devoted to Statistical Methods and Applications for Time-to-Event Data, Springer, vol. 23(3), pages 377-399, July.
    4. Sun, Yanqing & Li, Mei & Gilbert, Peter B., 2016. "Goodness-of-fit test of the stratified mark-specific proportional hazards model with continuous mark," Computational Statistics & Data Analysis, Elsevier, vol. 93(C), pages 348-358.
    5. Jon Arni Steingrimsson & Robert L. Strawderman, 2017. "Estimation in the Semiparametric Accelerated Failure Time Model With Missing Covariates: Improving Efficiency Through Augmentation," Journal of the American Statistical Association, Taylor & Francis Journals, vol. 112(519), pages 1221-1235, July.
    6. Erik T. Parner & Per K. Andersen & Morten Overgaard, 2020. "Cumulative risk regression in case–cohort studies using pseudo-observations," Lifetime Data Analysis: An International Journal Devoted to Statistical Methods and Applications for Time-to-Event Data, Springer, vol. 26(4), pages 639-658, October.
    7. Zheng, Ming & Zhao, Ziqiang & Yu, Wen, 2013. "Quantile regression analysis of case-cohort data," Journal of Multivariate Analysis, Elsevier, vol. 122(C), pages 20-34.
    8. Craig A Magaret & David C Benkeser & Brian D Williamson & Bhavesh R Borate & Lindsay N Carpp & Ivelin S Georgiev & Ian Setliff & Adam S Dingens & Noah Simon & Marco Carone & Christopher Simpkins & Dav, 2019. "Prediction of VRC01 neutralization sensitivity by HIV-1 gp160 sequence features," PLOS Computational Biology, Public Library of Science, vol. 15(4), pages 1-35, April.
    9. Gongjun Xu & Tony Sit & Lan Wang & Chiung-Yu Huang, 2017. "Estimation and Inference of Quantile Regression for Survival Data Under Biased Sampling," Journal of the American Statistical Association, Taylor & Francis Journals, vol. 112(520), pages 1571-1586, October.
    10. Ying Yan & Haibo Zhou & Jianwen Cai, 2017. "Improving efficiency of parameter estimation in case-cohort studies with multivariate failure time data," Biometrics, The International Biometric Society, vol. 73(3), pages 1042-1052, September.
    11. Michal Juraska & Peter B. Gilbert, 2016. "Mark-specific hazard ratio model with missing multivariate marks," Lifetime Data Analysis: An International Journal Devoted to Statistical Methods and Applications for Time-to-Event Data, Springer, vol. 22(4), pages 606-625, October.
    12. Poulami Maitra & Leila D. A. F. Amorim & Jianwen Cai, 2020. "Multiplicative rates model for recurrent events in case-cohort studies," Lifetime Data Analysis: An International Journal Devoted to Statistical Methods and Applications for Time-to-Event Data, Springer, vol. 26(1), pages 134-157, January.
    13. Fei Heng & Yanqing Sun & Seunggeun Hyun & Peter B. Gilbert, 2020. "Analysis of the time-varying Cox model for the cause-specific hazard functions with missing causes," Lifetime Data Analysis: An International Journal Devoted to Statistical Methods and Applications for Time-to-Event Data, Springer, vol. 26(4), pages 731-760, October.
    14. Jing Zhang & Haibo Zhou & Yanyan Liu & Jianwen Cai, 2021. "Conditional screening for ultrahigh-dimensional survival data in case-cohort studies," Lifetime Data Analysis: An International Journal Devoted to Statistical Methods and Applications for Time-to-Event Data, Springer, vol. 27(4), pages 632-661, October.
    15. Jieli Ding & Tsui-Shan Lu & Jianwen Cai & Haibo Zhou, 2017. "Recent progresses in outcome-dependent sampling with failure time data," Lifetime Data Analysis: An International Journal Devoted to Statistical Methods and Applications for Time-to-Event Data, Springer, vol. 23(1), pages 57-82, January.
    16. Torben Martinussen & Klaus K. Holst & Thomas H. Scheike, 2016. "Cox regression with missing covariate data using a modified partial likelihood method," Lifetime Data Analysis: An International Journal Devoted to Statistical Methods and Applications for Time-to-Event Data, Springer, vol. 22(4), pages 570-588, October.
    17. Frank Eriksson & Torben Martinussen & Søren Feodor Nielsen, 2020. "Large sample results for frequentist multiple imputation for Cox regression with missing covariate data," Annals of the Institute of Statistical Mathematics, Springer;The Institute of Statistical Mathematics, vol. 72(4), pages 969-996, August.
    18. Erin E. Gabriel & Michael C. Sachs & Dean A. Follmann & Therese M‐L. Andersson, 2020. "A unified evaluation of differential vaccine efficacy," Biometrics, The International Biometric Society, vol. 76(4), pages 1053-1063, December.
    19. Carlos Forero & Josué Almansa & Núria Adroher & Jeroen Vermunt & Gemma Vilagut & Ron Graaf & Josep-Maria Haro & Jordi Alonso Caballero, 2014. "Partial Likelihood Estimation of IRT Models with Censored Lifetime Data: An Application to Mental Disorders in the ESEMeD Surveys," Psychometrika, Springer;The Psychometric Society, vol. 79(3), pages 470-488, July.
    20. Chiang, Chin-Tsang & Huang, Ming-Yueh & Bai, Ren-Hong, 2013. "Binary response models with M-phase case-control data," Journal of Multivariate Analysis, Elsevier, vol. 116(C), pages 332-348.

    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:9:y:2017:i:1:d:10.1007_s12561-016-9177-5. 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.