A novel statistical method for decontaminating T-cell receptor sequencing data.

The T-cell receptor (TCR) repertoire is highly diverse among the population and plays an essential role in initiating multiple immune processes. TCR sequencing (TCR-seq) has been developed to profile the T cell repertoire. Similar to other high-throughput experiments, contamination can happen during several steps of TCR-seq, including sample collection, preparation and sequencing. Such contamination creates artifacts in the data, leading to inaccurate or even biased results. Most existing methods assume 'clean' TCR-seq data as the starting point with no ability to handle data contamination. Here, we develop a novel statistical model to systematically detect and remove contamination in TCR-seq data. We summarize the observed contamination into two sources, pairwise and cross-cohort. For both sources, we provide visualizations and summary statistics to help users assess the severity of the contamination. Incorporating prior information from 14 existing TCR-seq datasets with minimum contamination, we develop a straightforward Bayesian model to statistically identify contaminated samples. We further provide strategies for removing the impacted sequences to allow for downstream analysis, thus avoiding any need to repeat experiments. Our proposed model shows robustness in contamination detection compared with a few off-the-shelf detection methods in simulation studies. We illustrate the use of our proposed method on two TCR-seq datasets generated locally.

Bayesian adaptive model selection design for optimal biological dose finding in phase I/II clinical trials.

Identification of the optimal dose presents a major challenge in drug development with molecularly targeted agents, immunotherapy, as well as chimeric antigen receptor T-cell treatments. By casting dose finding as a Bayesian model selection problem, we propose an adaptive design by simultaneously incorporating the toxicity and efficacy outcomes to select the optimal biological dose (OBD) in phase I/II clinical trials. Without imposing any parametric assumption or shape constraint on the underlying dose-response curves, we specify curve-free models for both the toxicity and efficacy endpoints to determine the OBD. By integrating the observed data across all dose levels, the proposed design is coherent in dose assignment and thus greatly enhances efficiency and accuracy in pinning down the right dose. Not only does our design possess a completely new yet flexible dose-finding framework, but it also has satisfactory and robust performance as demonstrated by extensive simulation studies. In addition, we show that our design enjoys desirable coherence properties, while most of existing phase I/II designs do not. We further extend the design to accommodate late-onset outcomes which are common in immunotherapy. The proposed design is exemplified with a phase I/II clinical trial in chronic lymphocytic leukemia.

REDOMA: Bayesian random-effects dose-optimization meta-analysis using spike-and-slab priors.

The rise of cutting-edge precision cancer treatments has led to a growing significance of the optimal biological dose (OBD) in modern oncology trials. These trials now prioritize the consideration of both toxicity and efficacy simultaneously when determining the most desirable dosage for treatment. Traditional approaches in early-phase oncology trials have conventionally relied on the assumption of a monotone relationship between treatment efficacy and dosage. However, this assumption may not hold valid for novel oncology therapies. In reality, the dose-efficacy curve of such treatments may reach a plateau at a specific dose, posing challenges for conventional methods in accurately identifying the OBD. Furthermore, achieving reliable identification of the OBD is typically not possible based on a single small-sample trial. With data from multiple phase I and phase I/II trials, we propose a novel Bayesian random-effects dose-optimization meta-analysis (REDOMA) approach to identify the OBD by synthesizing toxicity and efficacy data from each trial. The REDOMA method can address trials with heterogeneous characteristics. We adopt a curve-free approach based on a Gamma process prior to model the average dose-toxicity relationship. In addition, we utilize a Bayesian model selection framework that uses the spike-and-slab prior as an automatic variable selection technique to eliminate monotonic constraints on the dose-efficacy curve. The good performance of the REDOMA method is confirmed by extensive simulation studies.

Design and sample size determination for multiple-dose randomized phase II trials for dose optimization.

The U.S. Food and Drug Administration (FDA) has launched Project Optimus to shift dose selection from the maximum tolerated dose (MTD) to the dose that produces the optimal risk-benefit tradeoff. One approach highlighted in the FDA's guidance involves conducting a randomized phase II trial following the completion of a phase I trial, where multiple doses (typically including the MTD and one or two doses lower than the MTD) are compared to identify the optimal dose that maximizes the benefit-risk tradeoff. This article focuses on the design of such a multiple-dose randomized trial, specifically the determination of the sample size. We generalized the standard definitions of type I error and power to accommodate the unique characteristics of dose optimization and derived a decision rule along with an algorithm to determine the optimal sample size. The resulting design is referred to as MERIT (Multiple-dosE RandomIzed Trial design for dose optimization based on toxicity and efficacy). Simulation studies demonstrate that MERIT has desirable operating characteristics, and a sample size between 20 and 40 per dosage arm often offers reasonable power and type I errors to ensure patient safety and benefit. To facilitate the implementation of the MERIT design, we provide software, available at https://www.trialdesign.org.

Signet ring cells and conditional survival after trimodality therapy for esophageal adenocarcinoma.

BACKGROUND AND METHODS: Although signet ring cell (SRC) histology is associated with resistance to neoadjuvant chemoradiotherapy and worse overall survival (OS) in esophageal adenocarcinoma (EAC), its prognostic relationship among patients who survive the early period following resection is unknown. EAC patients who underwent trimodality therapy at a single institution (2006-2018) were identified. Bayesian multivariable regression (BMR) analyses of OS and additional OS from a 3-year landmark were performed. RESULTS: Of 631 patients, SRCs were present in 16.0% (N = 101). SRC was associated with shorter median OS (45.8 [95% confidence interval: 31.0-96.7] vs. 79.8 [63.0-107.2] months; p = 0.014). In BMR analysis, the absence of an SRC component was moderately associated with improved OS (probability of beneficial effect, PBE = 0.879). Three-year conditional BMR analysis of additional OS (N = 357) showed that SRC status no longer had a prognostic effect (PBE = 0.546); higher pathological stage was strongly associated with worse additional OS (PBE < 0.001). CONCLUSIONS: The presence of SRC portends worse OS following trimodality therapy for EAC. However, this prognostic impact is dynamic and abates by 3 years postoperatively. In contrast, a higher pathological stage is strongly associated with poor overall and 3-year conditional survival. DISCUSSION: These findings may inform postoperative patient counseling and surveillance protocols.

Bayesian sequential monitoring strategies for trials of digestive cancer therapeutics.

BACKGROUND: New therapeutics in oncology have presented challenges to existing paradigms and trial designs in all phases of drug development. As a motivating example, we considered an ongoing phase II trial planned to evaluate the combination of a MET inhibitor and an anti-PD-L1 immunotherapy to treat advanced oesogastric carcinoma. The objective of the paper was to exemplify the planning of an adaptive phase II trial with novel anti-cancer agents, including prolonged observation windows and joint sequential evaluation of efficacy and toxicity. METHODS: We considered various candidate designs and computed decision rules assuming correlations between efficacy and toxicity. Simulations were conducted to evaluate the operating characteristics of all designs. RESULTS: Design approaches allowing continuous accrual, such as the time-to-event Bayesian Optimal Phase II design (TOP), showed good operating characteristics while ensuring a reduced trial duration. All designs were sensitive to the specification of the correlation between efficacy and toxicity during planning, but TOP can take that correlation into account more easily. CONCLUSIONS: While specifying design working hypotheses requires caution, Bayesian approaches such as the TOP design had desirable operating characteristics and allowed incorporating concomittant information, such as toxicity data from concomitant observations in another relevant patient population (e.g., defined by mutational status).

Adaptive Bayesian information borrowing methods for finding and optimizing subgroup-specific doses.

In precision oncology, integrating multiple cancer patient subgroups into a single master protocol allows for the simultaneous assessment of treatment effects in these subgroups and promotes the sharing of information between them, ultimately reducing sample sizes and costs and enhancing scientific validity. However, the safety and efficacy of these therapies may vary across different subgroups, resulting in heterogeneous outcomes. Therefore, identifying subgroup-specific optimal doses in early-phase clinical trials is crucial for the development of future trials. In this article, we review various innovative Bayesian information-borrowing strategies that aim to determine and optimize subgroup-specific doses. Specifically, we discuss Bayesian hierarchical modeling, Bayesian clustering, Bayesian model averaging or selection, pairwise borrowing, and other relevant approaches. By employing these Bayesian information-borrowing methods, investigators can gain a better understanding of the intricate relationships between dose, toxicity, and efficacy in each subgroup. This increased understanding significantly improves the chances of identifying an optimal dose tailored to each specific subgroup. Furthermore, we present several practical recommendations to guide the design of future early-phase oncology trials involving multiple subgroups when using the Bayesian information-borrowing methods.

On the relative conservativeness of Bayesian logistic regression method in oncology dose-finding studies.

The Bayesian logistic regression method (BLRM) is a widely adopted and flexible design for finding the maximum tolerated dose in oncology phase I studies. However, the BLRM design has been criticized in the literature for being overly conservative due to the use of the overdose control rule. Recently, a discussion paper titled "Improving the performance of Bayesian logistic regression model with overall control in oncology dose-finding studies" in Statistics in Medicine has proposed an overall control rule to address the "excessive conservativeness" of the standard BLRM design. In this short communication, we discuss the relative conservativeness of the standard BLRM design and also suggest a dose-switching rule to further enhance its performance.

Comparative review of novel model-assisted designs for phase I/II clinical trials.

In recent years, both model-based and model-assisted designs have emerged to efficiently determine the optimal biological dose (OBD) in phase I/II trials for immunotherapy and targeted cellular agents. Model-based designs necessitate repeated model fitting and computationally intensive posterior sampling for each dose-assignment decision, limiting their practical application in real trials. On the other hand, model-assisted designs employ simple statistical models and facilitate the precalculation of a decision table for use throughout the trial, eliminating the need for repeated model fitting. Due to their simplicity and transparency, model-assisted designs are often preferred in phase I/II trials. In this paper, we systematically evaluate and compare the operating characteristics of several recent model-assisted phase I/II designs, including TEPI, PRINTE, Joint i3+3, BOIN-ET, STEIN, uTPI, and BOIN12, in addition to the well-known model-based EffTox design, using comprehensive numerical simulations. To ensure an unbiased comparison, we generated 10,000 dosing scenarios using a random scenario generation algorithm for each predetermined OBD location. We thoroughly assess various performance metrics, such as the selection percentages, average patient allocation to OBD, and overdose percentages across the eight designs. Based on these assessments, we offer design recommendations tailored to different objectives, sample sizes, and starting dose locations.

A generalized calibrated Bayesian hierarchical modeling approach to basket trials with multiple endpoints.

A basket trial simultaneously evaluates a treatment in multiple cancer subtypes, offering an effective way to accelerate drug development in multiple indications. Many basket trials are designed and monitored based on a single efficacy endpoint, primarily the tumor response. For molecular targeted or immunotherapy agents, however, a single efficacy endpoint cannot adequately characterize the treatment effect. It is increasingly important to use more complex endpoints to comprehensively assess the risk-benefit profile of such targeted therapies. We extend the calibrated Bayesian hierarchical modeling approach to monitor phase II basket trials with multiple endpoints. We propose two generalizations, one based on the latent variable approach and the other based on the multinomial-normal hierarchical model, to accommodate different types of endpoints and dependence assumptions regarding information sharing. We introduce shrinkage parameters as functions of statistics measuring homogeneity among subgroups and propose a general calibration approach to determine the functional forms. Theoretical properties of the generalized hierarchical models are investigated. Simulation studies demonstrate that the monitoring procedure based on the generalized approach yields desirable operating characteristics.

Early drug development in solid tumours: analysis of National Cancer Institute-sponsored phase 1 trials.

BACKGROUND: The low expectation of clinical benefit from phase 1 cancer therapeutics trials might negatively affect patient and physician participation, study reimbursement, and slow the progress of oncology research. Advances in cancer drug development, meanwhile, might have favourably improved treatment responses; however, little comprehensive data exist describing the response and toxicity associated with phase 1 trials across solid tumours. The aim of the study is to evaluate the trend of toxicity and response in phase 1 trials for solid tumours over time. METHODS: We analysed patient-level data from the Cancer Therapy Evaluation Program of the National Cancer Institute-sponsored investigator-initiated phase 1 trials for solid tumours, from Jan 1, 2000, to May 31, 2019. We assessed risks of treatment-related death (grade 5 toxicity ratings possibly, probably, or definitely attributable to treatment), all on-treatment deaths (deaths during protocol treatment regardless of attribution), grade 3-4 toxicity, and proportion of overall response (complete response and partial response) and complete response rate in the study periods of 2000-05, 2006-12, and 2013-2019, and evaluated their trends over time. We also analysed cancer type-specific and investigational agent-specific response, and analysed the trend of response in each cancer type over time. Univariate associations of overall response rates with patients' baseline characteristics (age, sex, performance status, BMI, albumin concentration, and haemoglobin concentration), enrolment period, investigational agents, and trial design were assessed using risk ratio based on the modified Poisson regression model. FINDINGS: We analysed 465 protocols that enrolled 13 847 patients using 261 agents. 144 (31%) trials used a monotherapy and 321 (69%) used combination therapies. The overall treatment-related death rate was 0·7% (95% CI 0·5-0·8) across all periods. Risks of treatment-related deaths did not change over time (p=0·52). All on-treatment death risk during the study period was 8·0% (95% CI 7·6-8·5). The most common grade 3-4 adverse events were haematological; grade 3-4 neutropenia occurred in 2336 (16·9%) of 13 847 patients, lymphopenia in 1230 (8·9%), anaemia in 894 (6·5%), and thrombocytopenia in 979 (7·1%). The overall response rate for all trials during the study period was 12·2% (95% CI 11·5-12·8; 1133 of 9325 patients) and complete response rate was 2·7% (2·4-3·0; 249 of 9325). Overall response increased from 9·6% (95% CI 8·7-10·6) in 2000-05 to 18·0% (15·7-20·5) in 2013-19, and complete response rates from 2·5% (2·0-3·0) to 4·3% (3·2-5·7). Overall response rates for combination therapy were substantially higher than for monotherapy (15·8% [15·0-16·8] vs 3·5% [2·8-4·2]). The overall response by class of agents differed across diseases. Anti-angiogenesis agents were associated with higher overall response rate for bladder, colon, kidney and ovarian cancer. DNA repair inhibitors were associated with higher overall response rate in ovarian and pancreatic cancer. The rates of overall response over time differed markedly by disease; there were notable improvements in bladder, breast, and kidney cancer and melanoma, but no change in the low response of pancreatic and colon cancer. INTERPRETATION: During the past 20 years, the response rate in phase 1 trials nearly doubled without an increase in the treatment-related death rate. However, there is significant heterogeneity in overall response by various factors such as cancer type, investigational agent, and trial design. Therefore, informed decision making is crucial for patients before participating in phase 1 trials. This study provides updated encouraging outcomes of modern phase 1 trials in solid tumours. FUNDING: National Cancer Institute.

Bayesian single-to-double arm transition design using both short-term and long-term endpoints.

The choice between single-arm designs versus randomized double-arm designs has been contentiously debated in the literature of phase II oncology trials. Recently, as a compromise, the single-to-double arm transition design was proposed, combining the two designs into one trial over two stages. Successful implementation of the two-stage transition design requires a suspension period at the end of the first stage to collect the response data of the already enrolled patients. When the evaluation of the primary efficacy endpoint is overly long, the between-stage suspension period may unfavorably prolong the trial duration and cause a delay in treating future eligible patients. To accelerate the trial, we propose a Bayesian single-to-double arm design with short-term endpoints (BSDS), where an intermediate short-term endpoint is used for making early termination decisions at the end of the single-arm stage, followed by an evaluation of the long-term endpoint at the end of the subsequent double-arm stage. Bayesian posterior probabilities are used as the primary decision-making tool at the end of the trial. Design calibration steps are proposed for this Bayesian monitoring process to control the frequentist operating characteristics and minimize the expected sample size. Extensive simulation studies have demonstrated that our design has comparable power and average sample size but a much shorter trial duration than conventional single-to-double arm design. Applications of the design are illustrated using two phase II oncology trials with binary endpoints.

BOB: Bayesian optimal design for biosimilar trials with co-primary endpoints.

For regulatory approval of a biosimilar product, extensive evaluations should be performed by rigorous clinical trials to establish the similarity between the reference product and the proposed biosimilar in terms of both efficacy and safety. Existing designs for biosimilar trials often use a single primary efficacy endpoint in trial monitoring, and then separately evaluate the safety of the biosimilar product in a secondary analysis at the trial completion. However, ignoring the safety endpoint and the correlation between safety and efficacy in trial monitoring may lead to a high false positive rate, or it may delay the termination of the trial when dissimilarity in safety is early detected. We propose a Bayesian optimal design for biosimilar trials by incorporating both safety and efficacy endpoints in a unified framework. Based on a Bayesian joint safety and efficacy model, we sequentially use a so-called Bayesian biosimilar probability to make go/no-go decisions. We calibrate the Bayesian design to maximize the statistical power while maintaining the frequentist type I error rate at the nominal level. We carry out extensive simulation studies to show that the design has desirable performance in terms of the false positive rate and the average sample size. We also apply the proposed design to a biosimilar trial evaluating a ranibizumab product.

TITE-BOIN12: A Bayesian phase I/II trial design to find the optimal biological dose with late-onset toxicity and efficacy.

In the era of immunotherapies and targeted therapies, the focus of early phase clinical trials has shifted from finding the maximum tolerated dose to identifying the optimal biological dose (OBD), which maximizes the toxicity-efficacy trade-off. One major impediment to using adaptive designs to find OBD is that efficacy or/and toxicity are often late-onset, hampering the designs' real-time decision rules for treating new patients. To address this issue, we propose the model-assisted TITE-BOIN12 design to find OBD with late-onset toxicity and efficacy. As an extension of the BOIN12 design, the TITE-BOIN12 design also uses utility to quantify the toxicity-efficacy trade-off. We consider two approaches, Bayesian data augmentation and an approximated likelihood method, to enable real-time decision making when some patients' toxicity and efficacy outcomes are pending. Extensive simulations show that, compared to some existing designs, TITE-BOIN12 significantly shortens the trial duration while having comparable or higher accuracy to identify OBD and a lower risk of overdosing patients. To facilitate the use of the TITE-BOIN12 design, we develop a user-friendly software freely available at http://www.trialdesign.org.

Time-to-event model-assisted designs for dose-finding trials with delayed toxicity.

Two useful strategies to speed up drug development are to increase the patient accrual rate and use novel adaptive designs. Unfortunately, these two strategies often conflict when the evaluation of the outcome cannot keep pace with the patient accrual rate and thus the interim data cannot be observed in time to make adaptive decisions. A similar logistic difficulty arises when the outcome is late-onset. Based on a novel formulation and approximation of the likelihood of the observed data, we propose a general methodology for model-assisted designs to handle toxicity data that are pending due to fast accrual or late-onset toxicity and facilitate seamless decision making in phase I dose-finding trials. The proposed time-to-event model-assisted designs consider each dose separately and the dose-escalation/de-escalation rules can be tabulated before the trial begins, which greatly simplifies trial conduct in practice compared to that under existing methods. We show that the proposed designs have desirable finite and large-sample properties and yield performance that is comparable to that of more complicated model-based designs. We provide user-friendly software for implementing the designs.

uTPI: A utility-based toxicity probability interval design for phase I/II dose-finding trials.

Unlike chemotherapy, the maximum tolerated dose (MTD) of molecularly targeted agents and immunotherapy may not pose significant clinical benefit over the lower doses. By simultaneously considering both toxicity and efficacy endpoints, phase I/II trials can identify a more clinically meaningful dose for subsequent phase II trials than traditional toxicity-based phase I trials in terms of risk-benefit tradeoff. To strengthen and simplify the current practice of phase I/II trials, we propose a utility-based toxicity probability interval (uTPI) design for finding the optimal biological dose, based on a numerical utility that provides a clinically meaningful, one-dimensional summary representation of the patient's bivariate toxicity and efficacy outcome. The uTPI design does not rely on any parametric specification of the dose-response relationship, and it directly models the dose desirability through a quasi binomial likelihood. Toxicity probability intervals are used to screen out overly toxic dose levels, and then the dose escalation/de-escalation decisions are made adaptively by comparing the posterior desirability distributions of the adjacent levels of the current dose. The uTPI design is flexible in accommodating various dose desirability formulations, while only requiring minimum design parameters. It has a clear decision structure such that a dose-assignment decision table can be calculated before the trial starts and can be used throughout the trial, which simplifies the practical implementation of the design. Extensive simulation studies demonstrate that the proposed uTPI design yields desirable as well as robust performance under various scenarios.

The use of local and nonlocal priors in Bayesian test-based monitoring for single-arm phase II clinical trials.

Bayesian sequential monitoring is widely used in adaptive phase II studies where the objective is to examine whether an experimental drug is efficacious. Common approaches for Bayesian sequential monitoring are based on posterior or predictive probabilities and Bayesian hypothesis testing procedures using Bayes factors. In the first part of the paper, we briefly show the connections between test-based (TB) and posterior probability-based (PB) sequential monitoring approaches. Next, we extensively investigate the choice of local and nonlocal priors for the TB monitoring procedure. We describe the pros and cons of different priors in terms of operating characteristics. We also develop a user-friendly Shiny application to implement the TB design.

An adaptive trial design to optimize dose-schedule regimes with delayed outcomes.

This paper proposes a two-stage phase I-II clinical trial design to optimize dose-schedule regimes of an experimental agent within ordered disease subgroups in terms of the toxicity-efficacy trade-off. The design is motivated by settings where prior biological information indicates it is certain that efficacy will improve with ordinal subgroup level. We formulate a flexible Bayesian hierarchical model to account for associations among subgroups and regimes, and to characterize ordered subgroup effects. Sequentially adaptive decision-making is complicated by the problem, arising from the motivating application, that efficacy is scored on day 90 and toxicity is evaluated within 30 days from the start of therapy, while the patient accrual rate is fast relative to these outcome evaluation intervals. To deal with this in a practical manner, we take a likelihood-based approach that treats unobserved toxicity and efficacy outcomes as missing values, and use elicited utilities that quantify the efficacy-toxicity trade-off as a decision criterion. Adaptive randomization is used to assign patients to regimes while accounting for subgroups, with randomization probabilities depending on the posterior predictive distributions of utilities. A simulation study is presented to evaluate the design's performance under a variety of scenarios, and to assess its sensitivity to the amount of missing data, the prior, and model misspecification.

On the relative efficiency of model-assisted designs: a conditional approach.

In phase I dose-finding trials, model-assisted designs are a novel class of designs that combine the simplicity of algorithm-based methods with the superior performance of model-based methods. Examples of model-assisted designs include the modified toxicity probability (mTPI), Bayesian optimal interval (BOIN) and keyboard designs. To achieve simplicity, these model-assisted methods model only "local" data observed at the current dose, typically using a binomial model, to guide dose assignments. This potentially causes efficiency loss, however, by ignoring the data observed in other doses. To investigate this issue, we propose a conditional approach that utilizes the data from both current and adjacent (i.e., next higher or lower) doses to make the dose-assignment decisions. Specifically, we propose the conditional optimal interval (COIN) design, as the conditional approach extension of the BOIN design. We investigate the theoretical properties of the COIN design and conduct extensive numerical studies to examine its performance in comparison with existing model-assisted designs. We also present the conditional approach to the keyboard design. We observe that the conditional approach improves patient allocation, but yields similar maximum-tolerated dose (MTD) identification accuracy as the model-assisted designs, suggesting only minor efficiency loss using local data under the model-assisted designs.

Nonparametric overdose control with late-onset toxicity in phase I clinical trials.

Under the framework of Bayesian model selection, we propose a nonparametric overdose control (NOC) design for dose finding in phase I clinical trials. Each dose assignment is guided via a feasibility bound, which thereby can control the number of patients allocated to excessively toxic dose levels. Several aspects of the NOC design are explored, including the coherence property in dose assignment, calibration of design parameters, and selection of the maximum tolerated dose (MTD). We further propose a fractional NOC (fNOC) design in conjunction with a so-called fractional imputation approach, to account for late-onset toxicity outcomes. Extensive simulation studies have been conducted to show that both the NOC and fNOC designs have robust and satisfactory finite-sample performance compared with the existing dose-finding designs. The proposed methods also possess several desirable properties: treating patients more safely and also neutralizing the aggressive escalation to overly toxic doses when the toxicity outcomes are late-onset. The fNOC design is exemplified with a real cancer phase I trial.