The R Journal: article published in 2020, volume 12:2

Analyzing Basket Trials under Multisource Exchangeability Assumptions
Michael J. Kane, Nan Chen, Alexander M. Kaizer, Xun Jiang, H. Amy Xia and Brian P. Hobbs , The R Journal (2020) 12:2, pages 342-358.

Abstract Basket designs are prospective clinical trials that are devised with the hypothesis that the presence of selected molecular features determine a patient’s subsequent response to a particular “targeted” treatment strategy. Basket trials are designed to enroll multiple clinical subpopulations to which it is assumed that the therapy in question offers beneficial efficacy in the presence of the targeted molecular profile. The treatment, however, may not offer acceptable efficacy to all subpopulations enrolled. Moreover, for rare disease settings, such as oncology wherein these trials have become popular, marginal measures of statistical evidence are difficult to interpret for sparsely enrolled subpopulations. Consequently, basket trials pose challenges to the traditional paradigm for trial design, which assumes inter-patient exchangeability. The package basket for the R programmming environment (R Core Team, 2019) facilitates the analysis of basket trials by implementing multi source exchangeability models. By evaluating all possible pairwise exchangeability relationships, this hierarchical modeling framework facilitates Bayesian posterior shrinkage among a collection of discrete and pre-specified subpopulations. Analysis functions are provided to implement posterior inference of the response rates and all possible exchangeability relationships between subpopulations. In addition, the package can identify “poolable” subsets of and report their response characteristics. The functionality of the package is demonstrated using data from an oncology study with subpopulations defined by tumor histology. Keywords: Bayesian analysis, basket design, hierarchical model, master protocol, oncology, patient heterogeneity

Received: 2020-05-01; online 2021-01-15, supplementary material, (452 B)
CRAN packages: basket, igraph
CRAN Task Views implied by cited CRAN packages: gR, Graphics, Optimization, Spatial

This article and supplementary materials are licensed under a Creative Commons Attribution 4.0 International license.

@article{RJ-2021-020,
  author = {Michael J. Kane and Nan Chen and Alexander M. Kaizer and Xun
          Jiang and H. Amy Xia and Brian P. Hobbs},
  title = {{Analyzing Basket Trials under Multisource Exchangeability
          Assumptions}},
  year = {2021},
  journal = {{The R Journal}},
  doi = {10.32614/RJ-2021-020},
  url = {https://doi.org/10.32614/RJ-2021-020},
  pages = {342--358},
  volume = {12},
  number = {2}
}