A batch-effect adjusted Simon's two-stage design for cancer vaccine clinical studies

Chenguang Wang, Zhixin Wang, Gary L. Rosner, Warner K. Huh, Richard B.S. Roden, Sejong Bae

Research output: Contribution to journalArticlepeer-review


In the development of cancer treatment vaccines, phase II clinical studies are conducted to examine the efficacy of a vaccine in order to screen out vaccines with minimal activity. Immune responses are commonly used as the primary endpoint for assessing vaccine efficacy. With respect to study design, Simon's two-stage design is a popular format for phase II cancer clinical studies because of its simplicity and ethical considerations. Nonetheless, it is not straightforward to apply Simon's two-stage design to cancer vaccine studies when performing immune assays in batches, as outcomes from multiple patients may be correlated with each other in the presence of batch effects. This violates the independence assumption of Simon's two-stage design. In this paper, we numerically explore the impact of batch effects on Simon's two-stage design, propose a batch-effect adjusted Simon's two-stage design, demonstrate the proposed design by both a simulation study and a therapeutic human papillomavirus vaccine trial, and briefly introduce a software that implements the proposed design.

Original languageEnglish (US)
Pages (from-to)1075-1088
Number of pages14
Issue number3
StatePublished - Sep 2021


  • Simon's two-stage design
  • batch effect
  • cancer vaccine
  • clinical trial design
  • phase II study

ASJC Scopus subject areas

  • Statistics and Probability
  • Biochemistry, Genetics and Molecular Biology(all)
  • Immunology and Microbiology(all)
  • Agricultural and Biological Sciences(all)
  • Applied Mathematics


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