Roadmap for Designing Phase I Clinical Trials of Radiation Therapy-Novel Agent Combinations | Clinical cancer research

Green 15 Chapple and Thall, 2018 (29) SUB-TITE SubTite on CRAN to http://cran.r-project.org Script Cheung and Chappell, 2000 (44) TITE-CRM titecrm function in R package dfcrm Script Bekele et al., 2008 (43) Predicted risk of toxicity https://biostatistics.mdanderson.org/SoftwareDownload/SingleSoftware/Index/69 graphic interface Polly, 2011 (24) Modified TITE-CRM R program for the simulation of operating characteristics available on request to the authors Script Yin et al., 2013 (46) Fractional CRM Shiny app available: https://demoyang.shinyapps.io/clinicaltrialdesignapp_fcrm/as well as the R software code on GitHub: https://github.com/ZhaoYangCICAMS/fCRM Both Andrillon et al., 2020 (23) Surv-CRM and iSurv-CRM The R code for the use of the Surv-CRM, the iSurv-CRM and the associated benchmark must be made freely available on GitHub Script Nord et al., 2019 (47) STARPAC bcrm R Package (61) Script Lin and Yin, 2016 (45) fNOC https://github.com/ruitaolin/NOC Script Yuan et al., 2018 (22) TITE BOIN https://www.trialdesign.org/ graphic interface Lin and Yuan, 2019 (41) TITE-Keyboard/TITE-mTPI R codes for implementation available on Github (https://github.com/ruitaolin/TITE-MAD). Software also available for free at http://www.trialdesign.org Both Yin and Yang, 2020 (42) Fractional CRM Shiny app available: https://demoyang.shinyapps.io/clinicaltrialdesignapp_fcrm/as well as the R software code on GitHub: https://github.com/ZhaoYangCICAMS/fCRM Both Lee et al., 2019 (56) TITE-CRM™ The software in R code form is available on GitHub and can be requested from the corresponding author (sml2114@cumc.columbia.edu) Script Huang and Kuan, 2014 (57) Modified TITE-CRM R code in supplementary material Script Du et al., 2019 (60) Extension of RMD Package R: phase1RMD at https://cran.r-project.org/web/packages/phase1RMD/index.html Script The appendix contains the R code for implementing the MCMC Wages et al., 2013 (25) PO-TITE titesim function in R package dfcrm Script amber 16 Salter et al., 2015 (27) Two-group TITE-CRM SAS Code, Additional data to Salter 2015 (62) Script Biard et al., 2021 (48) Modified TITE-CRM Implemented using the dfcrm R package Script Ivanova et al., 2016 (49) Quick Enrollment Design (RED) Web-based software available at http://cancer.unc.edu/biostatistics/program/ivanova/ graphic interface Mauguen et al., 2011 (50) TITE-EWOC Graphical R interface, GUIP1, which combines different model-guided adaptive designs (CRMB, CRML, EWOC, TITE-CRM, TITEEWOC) to simulate and conduct phase I cancer clinical trials graphic interface Tighiouart et al., 2014 (51) EWOC-PH https://biostatistics.csmc.edu/ewocWeb.php Both R ewoc_d1ph package of https://cran.r-project.org/web/packages/ewoc/index.html Zheng et al., 2016 (52) Three-parameter logistic method The CRM methods implemented using the dfcrm R package and the Bayesian logistic model implemented using the MCMCpack R package Script Liu et al., 2013 (53) DA CRM https://biostatistics.mdanderson.org/SoftwareDownload/SingleSoftware/Index/132 graphic interface Altzerinakou and Paoletti, 2020 (54) Joint model for longitudinal biomarkers and time-to-event toxicity None listed Jin et al., 2014 (21) Late onset – EffTox None listed Yuan and Yin, 2009 (55) Joint probability models for toxicity and efficacy as TITE outcomes None listed Thal, 2019 (28) Non-proportional odds and non-stratified proportional odds, model-based designs A computer program Nkcelldosefinding for implementing this methodology is available from https://users.soe.ucsc.edu/∼juheelee/ and also http://wileyonlinelibrary.com/journal/rss-datasets. Script Paoletti et al., 2015 (58) POMM-CRML and LMM-CRML Simulations were performed with an R program and ordinal packages to fit POMM and lme4 to fit the logistic model on repeated binary data Script Doussau et al., 2013 (59) POMM-CRML None listed Yin et al., 2017 (32) MDM Package R: phase1RMD at https://cran.r-project.org/web/packages/phase1RMD/index.html Script Yin et al., 2017 (31) MDM None listed Wheeler et al., 2019 (26) TITE-PIPE https://cran.r-project.org/web/packages/pipe.design/index.html Script Red 6 Chapple et al., 2019 (63) TITE-IR The titeIR package is available on the CRAN and provides the necessary infrastructure for the design of phase I trials Script Chen et al., 2014 (64) EWOC-NETS-TITE The manuscript indicates that the software is under development Koopmeiners and Modiano, 2014 (65) Joint probability model for efficacy and toxicity as TITE outcomes None listed Takeda et al., 2020 (66) TITE-BOIN-ET None listed Yan et al., 2019 (67) Generalization of TITE-CRM to bivariate results–TITE-B None listed Braun, 2006 (68) Generalization of TITE-CRM assuming toxicity times have a beta distribution None listed

Irene B. Bowles