Bayesian Phase I/II Biomarker-Based Dose Finding for Precision Medicine With Molecularly Targeted Agents

References

• Agresti, A. (2002), Categorical Data Analysis , New York: Wiley.
   Google Scholar
• Albert, J. , and Chib, S. (1993), “Bayesian Analysis of Binary and Polychotomous Response Data,” Journal of the American Statistical Association , 88, 669–679.
   Web of Science ®Google Scholar
• Babb, J. S. , and Rogatko, A. (2001), “Patient Specific Dosing in a Phase I Cancer Trial,” Statistics in Medicine , 20, 2079–2090.
   PubMed Web of Science ®Google Scholar
• Bekele, B. N. , and Thall, P. F. (2004), “Dose-Finding Based on Multiple Toxicities in a Soft Tissue Sarcoma Trial,” Journal of the American Statistical Association , 99, 26–35.
   Web of Science ®Google Scholar
• Burnham, A. J. , Viveros, R. , and Macgregor, J. F. (1996), “Frameworks for Latent Variable Multivariate Regression,” Journal of Chemometrics , 10, 31–45.
   Web of Science ®Google Scholar
• Cox, C. (1995), “Location-Scale Cumulative Odds Models for Ordinal Data: A Generalized Non-Linear Model Approach,” Statistics in Medicine , 14, 1191–1203.
   PubMed Web of Science ®Google Scholar
• de Jong, S. (1993), “SIMPLS: An Alternative Approach to Partial Least Squares Regression,” Chemometrics and Intelligent Laboratory Systems , 18, 251–263.
   Web of Science ®Google Scholar
• Frank, I. , and Friedman, J. (1993), “A Statistical View of Some Chemometrics Regression Tools,” Technometrics , 35, 109–135.
   Web of Science ®Google Scholar
• Garthwaite, P. (1994), “An Interpretation of Partial Least Squares,” Journal of the American Statistical Association , 89, 122–127.
   Web of Science ®Google Scholar
• Gelman, A. , Jakulin, A. , Pittau, M. G. , and Su, Y. S. (2008), “A Weakly Informative Default Prior Distribution for Logistic and Other Regression Models,” The Annals of Applied Statistics , 2, 1360–1383.
   Web of Science ®Google Scholar
• Houede, N. , Thall, P. , Nguyen, H. , Paoletti, X. , and Kramar, A. (2010), “Utility-Based Optimization of Combination Therapy Using Ordinal Toxicity and Efficacy in Phase I/II Trials,” Biometrics , 66, 532–540.
   PubMed Web of Science ®Google Scholar
• Indahl, U. , Liland, K. , and Nas, T. (2009), “Canonical Partial Least Squares—A Unified PLS Approach to Classification and Regression Problems,” Journal of Chemometrics , 23, 495–504.
   Web of Science ®Google Scholar
• Ivanova, A. , and Wang, K. (2006), “Bivariate Isotonic Design for Dose-Finding With Ordered Groups,” Biometrics , 25, 2018–2026.
   Google Scholar
• Jin, I. H. , Liu, S. , Thall, P. , and Yuan, Y. (2014), “Using Data Augmentation to Facilitate Conduct of Phase I/II Clinical Trials With Delayed Outcomes,” Journal of American Statistical Association , 109, 525–536.
   PubMed Web of Science ®Google Scholar
• Liu, S. , and Yuan, Y. (2015), “Bayesian Optimal Interval Designs for Phase I Clinical Trials,” Journal of the Royal Statistical Society , Series C, 64, 507–523.
   Google Scholar
• Mevik, B. H. , Wehrens, R. , and Liland, K. H. (2013), pls: Partial Least Squares and Principle Component Regression, R Package Version 2.4-3 . Available at http://CRAN.R-project.org/package=pls .
   Google Scholar
• McCullagh, P. (1980), “Regression Models for Ordinal Data,” Journal of the Royal Statistical Society , Series B, 42, 109–142.
   Google Scholar
• Nguyen, D. , and Rocke, D. (2002), “Multi-Class Cancer Classification via Partial Least Squares With gene Expression Profiles,” Bioinformatics , 18, 1216–1226.
   PubMed Web of Science ®Google Scholar
• O’Quigley, J. , and Paoletti, X. (2003), “Continual Reassessment Method for Ordered Groups,” Biometrics , 59, 430–440.
   PubMed Web of Science ®Google Scholar
• O’Quigley, J. , Pepe, M. , and Fisher, L. (1990), “Continual Reassessment Method: A Practical Design for Phase I Clinical Trials in Cancer,” Biometrics , 46, 33–48.
   PubMed Web of Science ®Google Scholar
• Piantadosi, S. , and Liu, G. (1996), “Improved Designs for Dose-Escalation Studies Using Pharmacokinetic Measurements,” Statistics in Medicine , 15, 1605–1618.
   PubMed Web of Science ®Google Scholar
• Postel-Vinay, S. , Arkenau, H. T. , Olmos, D. , Ang, J., Barriuso, J., Ashley, S., Banerji, U., De-Bono, J., Judson, I., and Kaye, S. (2009), “Clinical Benefit in Phase I Trials of Novel Molecularly Targeted Agents: Does Dose Matter?” BritishJournal of Cancer , 100, 1373–1378.
   PubMed Web of Science ®Google Scholar
• Riviere, M. K. , Yuan, Y. , Dubois, F. , and Zohar, S. (2015), “A Bayesian Dose-Finding Design for Clinical Trials Combining a Cytotoxic Agent With a Molecularly Targeted Agent,” Journal of the Royal Statistical Society , Series C, 64, 215–229.
   Google Scholar
• Stone, M. , and Brooks, R. J. (1990), “Continuum Regression: Cross-Validated Sequentially Constructed Prediction Embracing Ordinary Least Squares, Partial Least Squares and Principal Component Regression,” Journal of the Royal Statistical Society , Series B, 52, 237–269.
   Google Scholar
• Thall, P. , Nguyen, H. , and Estey, E. (2008), “Patient-Specific Dose Finding Based on Bivariate Outcomes and Covariates,” Biometrics , 64, 1126–1136.
   PubMed Web of Science ®Google Scholar
• Yuan, Y. , Hess, K. R. , Hilsenbeck, S. G. , and Gilbert, M. R. (2016), “Bayesian Optimal Interval Design: A Simple and Well-Performing Design forPhase I Oncology Trials,” Clinical Cancer Research , 22, 4291–4301.
   PubMed Web of Science ®Google Scholar
• Yuan, Y. , and Yin, G. (2009), “Bayesian Dose Finding by Jointly Modeling Toxicity and Efficacy as Time-to-Event Outcomes,” Journal of the Royal Statistical Society , Series C, 58, 719–736.
   Google Scholar
• ——— (2011), “Robust EM Continual Reassessment Method in Oncology Dose Finding,” Journal of the American Statistical Association , 106, 818–831.
   PubMed Web of Science ®Google Scholar
• Yuan, Z. , and Chappell, R. (2004), “Isotonic Designs for Phase I Cancer Clinical Trials With Multiple Risk Groups,” Clinical Trials , 1, 499–508.
   PubMedGoogle Scholar
• Zang, Y. , Lee, J. , and Yuan, Y. (2014), “Phase I Dose-Finding Trial Designs for Identifying Optimal Biological Dose for Molecularly Targeted Agents,” Clinical Trials , 11, 319–327.
   PubMed Web of Science ®Google Scholar