Bayesian Design and Analysis of Mouse Clinical Trials with MiniPDX and PDX Models for Translational Oncology
Pub. online: 9 September 2026
Type: Methodology Article
Open Access
Area: Biomedical Research
1
These authors contributed equally to this work.
Accepted
17 July 2026
17 July 2026
Published
9 September 2026
9 September 2026
Abstract
The MiniPDX model is a cost-effective preclinical platform that replicates human tumor microenvironments in mice, enabling rapid drug response evaluation in precision oncology. In contrast, the patient-derived xenograft (PDX) model offers a more comprehensive but slower and costlier approach by engrafting human tumors into immunodeficient mice to evaluate efficacy in a physiologically relevant context. In this study, we present an integrated Bayesian framework that supports both separate and joint analyses of MiniPDX and PDX data. Our models borrow information across biomarker-defined subgroups and between assays, improving the efficiency and precision of drug effect estimation. Furthermore, we implement an adaptive sample size re-estimation procedure for MiniPDX experiments, allowing for more flexible designs and optimized resource utilization. Together, these methods provide a Bayesian framework that improves estimation efficiency for small-sample MiniPDX and PDX experiments and offers a principled adaptive sample-size rule, helping to identify biomarker-defined subpopulations with distinct predictive profiles for treatment response.
References
Berry, D. A. (2006). Bayesian clinical trials. Nature Reviews Drug Discovery 5(1) 27–36. Publisher: Nature Publishing Group TLDR: The rationale underlying Bayesian clinical trials is explained, the potential of such trials to improve the effectiveness of drug development is discussed, and the potential for smaller more informative trials and for patients to receive better treatment is discussed. https://doi.org/10.1038/nrd1927. Accessed 2025-05-08.
Bertotti, A., Migliardi, G., Galimi, F., Sassi, F., Torti, D., Isella, C., Corà, D., Di Nicolantonio, F., Buscarino, M., Petti, C. et al. (2011). A molecularly annotated platform of patient-derived xenografts (“xenopatients”) identifies HER2 as an effective therapeutic target in cetuximab-resistant colorectal cancer. Cancer Discovery 1(6) 508–523.
Gelman, A. (2006). Prior distributions for variance parameters in hierarchical models. Bayesian Analysis 1(3) 515–534. https://doi.org/10.1214/06-BA117A. MR2221284
Giovagnoli, A. (2021). The Bayesian Design of Adaptive Clinical Trials. International Journal of Environmental Research and Public Health 18(2) 530. TLDR: A brief overview of the recent literature on adaptive design of clinical trials from a Bayesian perspective for statistically not so sophisticated readers, pointing at further interesting reading material. https://doi.org/10.3390/ijerph18020530. Accessed 2025-05-19.
Golchi, S., Willard, J. J., Pullenayegum, E., Bassani, D. G., Pell, L. G., Thorlund, K. Roth, D. E. (2022). A Bayesian adaptive design for clinical trials of rare efficacy outcomes with multiple definitions. Clinical Trials (London, England) 19(6) 613–622. TLDR: A Bayesian adaptive design is proposed that enables monitoring and utilizing multiple composite outcomes based on rare events to optimize the trial design operating characteristics and maintain a realistic probability of stopping in trials with low event rates. https://doi.org/10.1177/17407745221118366. https://doi.org/10.1002/cjs.11699. MR4429845
Kelter, R. (2023). Reducing the false discovery rate of preclinical animal research with Bayesian statistical decision criteria. Statistical Methods in Medical Research 32(10) 1880–1901. Publisher: SAGE Publications Ltd STM TLDR: Simulation shows that a shift towards statistical approaches which explicitly incorporate the minimum clinically important difference reduces the false discovery rate of frequentist approaches and that Bayesian statistical decision criteria can improve the reliability of preclinical animal research by reducing the number of false-positive findings. https://doi.org/10.1177/09622802231184636. Accessed 2025-05-19. https://doi.org/10.1177/09622802231184636. MR4651763
Neuenschwander, B., Branson, M. Gsponer, T. (2008). Critical aspects of the Bayesian approach to phase I cancer trials. Statistics in Medicine 27(13) 2420–2439. TLDR: The Bayesian approach to finding the maximum-tolerated dose in phase I cancer trials is discussed and a comparison with the continual reassessment method (CRM) is performed with data from an actual trial and a simulation study. https://doi.org/10.1002/sim.3230. https://doi.org/10.1002/sim.3230. MR2432497
Pallmann, P., Bedding, A. W., Choodari-Oskooei, B., Dimairo, M., Flight, L., Hampson, L. V., Holmes, J., Mander, A. P., Odondi, L., Sydes, M. R., Villar, S. S., Wason, J. M. S., Weir, C. J., Wheeler, G. M., Yap, C. Jaki, T. (2018). Adaptive designs in clinical trials: why use them, and how to run and report them. BMC Medicine 16(1) 29. TLDR: This tutorial paper provides guidance on key aspects of adaptive designs that are relevant to clinical triallists, and emphasises the general principles of transparency and reproducibility and suggest how best to put them into practice. https://doi.org/10.1186/s12916-018-1017-7. Accessed 2025-05-19. https://doi.org/10.1002/sim.2252. MR2225183
Research, C. f. D. E. a. (2020). Adaptive Design Clinical Trials for Drugs and Biologics Guidance for Industry. Publisher: FDA. https://www.fda.gov/regulatory-information/search-fda-guidance-documents/adaptive-design-clinical-trials-drugs-and-biologics-guidance-industry Accessed 2025-05-19.
Rokita, J. L., Rathi, K. S., Cardenas, M. F., Upton, K. A., Jayaseelan, J., Cross, K. L., Pfeil, J., Egolf, L. E., Way, G. P., Farrel, A., Kendsersky, N. M., Patel, K., Gaonkar, K. S., Modi, A., Berko, E. R., Lopez, G., Vaksman, Z., Mayoh, C., Nance, J., McCoy, K., Haber, M., Evans, K., McCalmont, H., Bendak, K., Böhm, J. W., Marshall, G. M., Tyrrell, V., Kalletla, K., Braun, F. K., Qi, L., Du, Y., Zhang, H., Lindsay, H. B., Zhao, S., Shu, J., Baxter, P., Morton, C., Kurmashev, D., Zheng, S., Chen, Y., Bowen, J., Bryan, A. C., Leraas, K. M., Coppens, S. E., Doddapaneni, H., Momin, Z., Zhang, W., Sacks, G. I., Hart, L. S., Krytska, K., Mosse, Y. P., Gatto, G. J., Sanchez, Y., Greene, C. S., Diskin, S. J., Vaske, O. M., Haussler, D., Gastier-Foster, J. M., Kolb, E. A., Gorlick, R., Li, X. -N., Reynolds, C. P., Kurmasheva, R. T., Houghton, P. J., Smith, M. A., Lock, R. B., Raman, P., Wheeler, D. A. Maris, J. M. (2019). Genomic Profiling of Childhood Tumor Patient-Derived Xenograft Models to Enable Rational Clinical Trial Design. Cell Reports 29(6) 1675–16899. Publisher: Elsevier TLDR: Genomically characterize 261 PDX models from 37 unique pediatric cancers; demonstrate faithful recapitulation of histologies and subtypes; refine the understanding of relapsed disease; and use expression signatures to classify tumors for TP53 and NF1 pathway inactivation. https://doi.org/10.1016/j.celrep.2019.09.071. Accessed 2025-05-19.
Walley, R., Sherington, J., Rastrick, J., Detrait, E., Hanon, E. Watt, G. (2016). Using Bayesian analysis in repeated preclinical in vivo studies for a more effective use of animals. Pharmaceutical Statistics 15(3) 277–285. TLDR: It is concluded that using Bayesian methods in stable repeated in vivo studies can result in a more effective use of animals, either by reducing the total number of animals used or by increasing the precision of key treatment differences. https://doi.org/10.1002/pst.1748.
Welch, C., Forster, M., Ronaldson, S., Keding, A., Corbacho-Martín, B. Tharmanathan, P. (2024). The performance of a Bayesian value-based sequential clinical trial design in the presence of an equivocal cost-effectiveness signal: evidence from the HERO trial. BMC Medical Research Methodology 24(1) 155. TLDR: Evidence from the two retrospective applications of this Bayesian value-adaptive design suggests that, when the cost-effectiveness signal in a clinical trial is unambiguous, the Bayesian value-adaptive design can stop the trial before it reaches its maximum sample size, potentially saving research costs when compared with the alternative fixed sample size design. https://doi.org/10.1186/s12874-024-02248-9. Accessed 2025-05-19.
Zhang, B., Magiera, L., Candido, J., Muraeva, O., Coates Ulrichsen, J., Eyles, J., Galvani, E. Karp, N. A. (2024). Bayesian modeling for analyzing heterogeneous response in preclinical mouse tumor models. Science Translational Medicine 16(771) 9004. TLDR: A statistical method called INSPECT (IN vivo reSPonsE Classification of Tumors) for analyzing heterogeneous responses through Bayesian modeling is developed and shown that INSPECT methodology is more accurate and sensitive than existing methods with respect to balancing false-negative and false-positive rates. https://doi.org/10.1126/scitranslmed.adi9004. Accessed 2025-05-09.
Zhang, F., Wang, W., Long, Y., Liu, H., Cheng, J., Guo, L., Li, R., Meng, C., Yu, S., Zhao, Q., Lu, S., Wang, L., Wang, H. Wen, D. (2018). Characterization of drug responses of mini patient-derived xenografts in mice for predicting cancer patient clinical therapeutic response. Cancer Communications (London) 38(1) 60. https://doi.org/10.1186/s40880-018-0329-5.