Design and analysis of biomarker-integrated clinical trials with adaptive threshold detection and flexible patient enrichment

Biomarker-guided adaptive enrichment design with threshold detection for clinical trials with time-to-event outcome

Biomarker-guided designs are increasingly used to evaluate personalized treatments based on patients' biomarker status in Phase II and III clinical trials. With adaptive enrichment, these designs can improve the efficiency of evaluating the treatment effect in biomarker-positive patients by increasing their proportion in the randomized trial. While time-to-event outcomes are often used as the primary endpoint to measure treatment effects for a new therapy in severe diseases like cancer and cardiovascular diseases, there is limited research on biomarker-guided adaptive enrichment trials in this context. Such trials almost always adopt hazard ratio methods for statistical measurement of treatment effects. In contrast, restricted mean survival time (RMST) has gained popularity for analyzing time-to-event outcomes because it offers more straightforward interpretations of treatment effects and does not require the proportional hazard assumption. This paper proposes a two-stage biomarker-guided adaptive RMST design with threshold detection and patient enrichment. We develop sophisticated methods for identifying the optimal biomarker threshold and biomarker-positive subgroup, treatment effect estimators, and approaches for type I error rate, power analysis, and sample size calculation. We present a numerical example of re-designing an oncology trial. An extensive simulation study is conducted to evaluate the performance of the proposed design.

Improving power in adaptive expansion of biomarker populations in phase 3 clinical trials

With the availability of unprecedented human genomic biomarker data, incorporating such biomarker data has received a lot of attention in phase 3 clinical trials. One particular enrichment design proposed recently in the literature is to recruit more biomarker positive patients in an all-comer study if the treatment effect in the biomarker negative group is less promising than expected. The intuition is to improve the chance of success of the trial since the success rate in the all-comer population may be low. We propose an enrichment design that unifies the existing biomarker adaptive designs for phase 3 clinical trials. In addition, we propose a new test accounting for the correlations among the test statistics based on different groups of patients, including all-comers, biomarker positive patients only, and biomarker negative patients only. We investigate the theoretical properties of the design and demonstrate the new test accurately controls the type I error rate and gains power over existing methods through extensive simulations. A computer program is developed for power calculations given a set of design parameters, including the proportion of biomarker positive patients, the distribution of the failure time in each treatment and biomarker group, and the number of patients in the first stage and the second stage (i.e. the enrichment stage), among others.

Testing for a treatment effect in a selected subgroup

There is a growing interest in clinical trials that investigate how patients may respond differently to an experimental treatment depending on the basis of some biomarker measured on a continuous scale, and in particular to identify some threshold value for the biomarker above which a positive treatment effect can be considered to have been demonstrated. This can be statistically challenging when the same data are used both to select the threshold and to test the treatment effect in the subpopulation that it defines. This paper describes a hierarchical testing framework to give familywise type I error rate control in this setting and proposes two specific tests that can be used within this framework. One, a simple test based on the estimated value from a linear regression model with treatment by biomarker interaction, is powerful but can lead to type I error rate inflation if the assumptions of the linear model are not met. The other is more robust to these assumptions, but can be slightly less powerful when the assumptions hold.

Cross-validated risk scores adaptive enrichment (CADEN) design

We propose a Cross-validated ADaptive ENrichment design (CADEN) in which a trial population is enriched with a subpopulation of patients who are predicted to benefit from the treatment more than an average patient (the sensitive group). This subpopulation is found using a risk score constructed from the baseline (potentially high-dimensional) information about patients. The design incorporates an early stopping rule for futility. Simulation studies are used to assess the properties of CADEN against the original (non-enrichment) cross-validated risk scores (CVRS) design which constructs a risk score at the end of the trial. We show that when there exists a sensitive group of patients, CADEN achieves a higher power and a reduction in the expected sample size compared to the CVRS design. We illustrate the application of the design in two real clinical trials. We conclude that the new design offers improved statistical efficiency over the existing non-enrichment method, as well as increased benefit to patients. The method has been implemented in an R package caden.

Finding the best subgroup with differential treatment effect with multiple outcomes

Precision medicine aims to identify specific patient subgroups that may benefit the most from a particular treatment than the whole population. Existing definitions for the best subgroup in subgroup analysis are based on a single outcome and do not consider multiple outcomes; specifically, outcomes of different types. In this article, we introduce a definition for the best subgroup under a multiple-outcome setting with continuous, binary, and censored time-to-event outcomes. Our definition provides a trade-off between the subgroup size and the conditional average treatment effects (CATE) in the subgroup with respect to each of the outcomes while taking the relative contribution of the outcomes into account. We conduct simulations to illustrate the proposed definition. By examining the outcomes of urinary tract infection and renal scarring in the RIVUR clinical trial, we identify a subgroup of children that would benefit the most from long-term antimicrobial prophylaxis.