A Comparison of Alternative Network Meta-Analysis Methods in the Presence of Nonproportional Hazards: A Case Study in First-Line Advanced or Metastatic Renal Cell Carcinoma.

OBJECTIVES: Network meta-analysis (NMA) of time-to-event outcomes based on constant hazard ratios can result in biased findings when the proportional hazards (PHs) assumption does not hold in a subset of trials. We aimed to summarize the published non-PH NMA methods for time-to-event outcomes, demonstrate their application, and compare their results. METHODS: The following non-PH NMA methods were compared through an illustrative case study in oncology of 4 randomized controlled trials in terms of progression-free survival and overall survival: (1) 1-step or (2) 2-step multivariate NMAs based on traditional survival distributions or fractional polynomials, (3) NMAs with restricted cubic splines for baseline hazard, and (4) restricted mean survival NMA. RESULTS: For progression-free survival, the PH assumption did not hold across trials and non-PH NMA methods better reflected the relative treatment effects over time. The most flexible models (fractional polynomials and restricted cubic splines) fit better to the data than the other approaches. Estimated hazard ratios obtained with different non-PH NMA methods were similar at 5 years of follow-up but differed thereafter in the extrapolations. Although there was no strong evidence of PH violation for overall survival, non-PH NMA methods captured this uncertainty in the relative treatment effects over time. CONCLUSIONS: When the PH assumption is questionable in a subset of the randomized controlled trials, we recommend assessing alternative non-PH NMA methods to estimate relative treatment effects for time-to-event outcomes. We propose a transparent and explicit stepwise model selection process considering model fit, external constraints, and clinical validity. Given inherent uncertainty, sensitivity analyses are suggested.

Indirect treatment comparison of nivolumab versus placebo as adjuvant treatment for resected melanoma.

BACKGROUND: Nivolumab (an anti-programmed death-1 antibody) is an adjuvant standard of care for patients with high-risk resected melanoma, although a watch-and-wait strategy remains an option. In the absence of head-to-head evidence, an indirect treatment comparison (ITC) of adjuvant nivolumab versus placebo, the proxy for a watch-and-wait strategy, was conducted in patients with high-risk resected melanoma. METHODS: An ITC using the Bucher method compared nivolumab with placebo using intention-to-treat population data from the phase III CheckMate 238 (nivolumab vs ipilimumab; minimum follow-up, 4 years; NCT02388906) and European Organisation for Research and Treatment of Cancer (EORTC) 18071 (ipilimumab vs placebo; minimum follow-up, ≈4.5 years; NCT00636168) trials. The end-points were recurrence-free survival (RFS), distant metastasis-free survival (DMFS) and overall survival (OS). To account for cross-trial differences in staging and subsequent therapy, additional analyses examined patients with stage IIIB/IIIC disease and adjusted post-recurrence survival in EORTC 18071, respectively. RESULTS: Nivolumab versus placebo was associated with clinically meaningful improvements in RFS (hazard ratio [HR], 0.53; 95% confidence interval [CI], 0.42-0.68) and OS (HR, 0.63; 95% CI, 0.45-0.89). Nivolumab versus placebo was also associated with clinically meaningful improvements in RFS (HR, 0.53; 95% CI, 0.40-0.69), DMFS (HR, 0.62; 95% CI, 0.46-0.83) and OS (HR, 0.67; 95% CI, 0.47-0.97) in patients with stage IIIB/IIIC disease and in OS (HR, 0.65; 95% CI, 0.46-0.92) in the overall population after adjusting post-recurrence survival in EORTC 18071. CONCLUSION: This ITC shows that adjuvant nivolumab provides clinically meaningful improvements in RFS, DMFS and OS versus a watch-and-wait strategy in high-risk resected melanoma.

Survival analysis for AdVerse events with VarYing follow-up times (SAVVY)-estimation of adverse event risks.

BACKGROUND: The SAVVY project aims to improve the analyses of adverse events (AEs), whether prespecified or emerging, in clinical trials through the use of survival techniques appropriately dealing with varying follow-up times and competing events (CEs). Although statistical methodologies have advanced, in AE analyses, often the incidence proportion, the incidence density, or a non-parametric Kaplan-Meier estimator are used, which ignore either censoring or CEs. In an empirical study including randomized clinical trials from several sponsor organizations, these potential sources of bias are investigated. The main purpose is to compare the estimators that are typically used to quantify AE risk within trial arms to the non-parametric Aalen-Johansen estimator as the gold-standard for estimating cumulative AE probabilities. A follow-up paper will consider consequences when comparing safety between treatment groups. METHODS: Estimators are compared with descriptive statistics, graphical displays, and a more formal assessment using a random effects meta-analysis. The influence of different factors on the size of deviations from the gold-standard is investigated in a meta-regression. Comparisons are conducted at the maximum follow-up time and at earlier evaluation times. CEs definition does not only include death before AE but also end of follow-up for AEs due to events related to the disease course or safety of the treatment. RESULTS: Ten sponsor organizations provided 17 clinical trials including 186 types of investigated AEs. The one minus Kaplan-Meier estimator was on average about 1.2-fold larger than the Aalen-Johansen estimator and the probability transform of the incidence density ignoring CEs was even 2-fold larger. The average bias using the incidence proportion was less than 5%. Assuming constant hazards using incidence densities was hardly an issue provided that CEs were accounted for. The meta-regression showed that the bias depended mainly on the amount of censoring and on the amount of CEs. CONCLUSIONS: The choice of the estimator of the cumulative AE probability and the definition of CEs are crucial. We recommend using the Aalen-Johansen estimator with an appropriate definition of CEs whenever the risk for AEs is to be quantified and to change the guidelines accordingly.

Indirect treatment comparison of nivolumab versus placebo for the adjuvant treatment of melanoma.

INTRODUCTION: Until recently, adjuvant treatment options for stage III and IV resectable melanoma have been limited. Patients were often managed through routine surveillance. The phase III randomised controlled trial (RCT) CheckMate 238 (238) demonstrated the safety and efficacy of nivolumab as an adjuvant treatment for melanoma in patients with stage IIIB/C or IV disease (American Joint Committee on Cancer [AJCC], 7th edition) versus ipilimumab. The study objective was to estimate the relative efficacy, safety and health-related quality of life (HRQoL) between nivolumab and routine surveillance. METHODS: Indirect treatment comparisons (ITCs) of nivolumab versus placebo were constructed using data from 238 and EORTC 18071. EORTC 18071 is a phase III RCT comparing ipilimumab with placebo in patients with resected stage IIIA-IIIC melanoma (AJCC, 6th edition). ITCs were performed using the Bucher comparison method and patient-level data for efficacy, safety and HRQoL. RESULTS: For the efficacy outcomes, nivolumab performed significantly better than placebo for recurrence-free survival (hazard ratio [HR]: 0.53 [95% confidence interval {CI}: 0.41, 0.68]) and distant metastases-free survival (HR: 0.59 [95% CI: 0.44, 0.78]). Safety ITCs indicated that patients receiving nivolumab had a greater hazard of experiencing an adverse event (AE) and AEs leading to treatment discontinuation, whereas there was a non-significant increased hazard of experiencing a serious AE. HRQoL ITCs showed comparable time to deterioration in 14 of the 15 QLQ-C30 domains; only the dyspnoea domain significantly favoured placebo. CONCLUSION: Nivolumab was associated with significantly improved efficacy outcomes versus placebo, whereas maintaining patient's overall HRQoL. Across the different analysis and populations, there was a high level of consistency in the effect size.

On estimands and the analysis of adverse events in the presence of varying follow-up times within the benefit assessment of therapies.

The analysis of adverse events (AEs) is a key component in the assessment of a drug's safety profile. Inappropriate analysis methods may result in misleading conclusions about a therapy's safety and consequently its benefit-risk ratio. The statistical analysis of AEs is complicated by the fact that the follow-up times can vary between the patients included in a clinical trial. This paper takes as its focus the analysis of AE data in the presence of varying follow-up times within the benefit assessment of therapeutic interventions. Instead of approaching this issue directly and solely from an analysis point of view, we first discuss what should be estimated in the context of safety data, leading to the concept of estimands. Although the current discussion on estimands is mainly related to efficacy evaluation, the concept is applicable to safety endpoints as well. Within the framework of estimands, we present statistical methods for analysing AEs with the focus being on the time to the occurrence of the first AE of a specific type. We give recommendations which estimators should be used for the estimands described. Furthermore, we state practical implications of the analysis of AEs in clinical trials and give an overview of examples across different indications. We also provide a review of current practices of health technology assessment (HTA) agencies with respect to the evaluation of safety data. Finally, we describe problems with meta-analyses of AE data and sketch possible solutions.

Tiotropium and Salmeterol in COPD Patients at Risk of Exacerbations: A Post Hoc Analysis from POET-COPD(®).

INTRODUCTION: Among patients with chronic obstructive pulmonary disease (COPD), the frequency and severity of past exacerbations potentiates future events. The impact of current therapies on exacerbation frequency and severity in patients with different exacerbation risks is not well known. METHODS: A post hoc analysis of patients at low (≤1 exacerbation [oral steroids/antibiotics requirement] and no COPD-related hospitalization in the year preceding trial entry) or high (≥2 exacerbations [oral steroids/antibiotics requirement] or ≥1 COPD-related hospitalization[s] in the year preceding trial entry) exacerbation risk, from the Prevention of Exacerbations with Tiotropium in Chronic Obstructive Pulmonary Disease (POET-COPD(®)) database. RESULTS: Compared with salmeterol, tiotropium significantly increased time to first COPD exacerbation (hazard ratio 0.84; 95% confidence interval [CI] 0.76-0.92; p = 0.0002) and reduced the number of COPD exacerbations (rate ratio 0.90; 95% CI 0.81-0.99; p = 0.0383) in patients at high exacerbation risk. With treatment, the risk of remaining in the high-risk exacerbator subgroup was statistically lower with tiotropium versus salmeterol (risk ratio [RR] 0.89; 95% CI 0.80-1.00; p = 0.0478). For low-risk patients, time to first COPD exacerbation and number of COPD exacerbations were numerically lower with tiotropium versus salmeterol. With treatment, the risk of transitioning from a low to a high exacerbation risk was lower with tiotropium versus salmeterol (RR 0.87; 95% CI 0.71-1.07; p = 0.1968). DISCUSSION: This analysis confirms the higher efficacy of tiotropium versus salmeterol in prolonging time to first COPD exacerbation and reducing number of exacerbations in patients both at low and high exacerbation risk. FUNDING: Boehringer Ingelheim and Pfizer. CLINICAL TRIAL REGISTRATION NUMBER: ClinicalTrials.gov NCT00563381.

Effects of Tiotropium on Exacerbations in Patients with COPD with Low or High Risk of Exacerbations: A Post-Hoc Analysis from the 4-Year UPLIFT® Trial.

Background: A history of past exacerbations is a predictor of future events for patients with chronic obstructive pulmonary disease (COPD). Very little is known about the effect of pharmacologic therapies on patients with frequent or infrequent exacerbations. Methods: We conducted a post-hoc analysis of the Understanding Potential Long-term Impacts on Function with Tiotropium (UPLIFT®)trial database. Patients were classified as having a low risk of exacerbations if they experienced ≤1 exacerbation and no COPD-related hospitalization(s) in the year preceding trial entry or as high risk of exacerbations if they had ≥2 exacerbations (courses of oral steroids/antibiotics) or ≥1 COPD-related hospitalization(s) in the year preceding the trial. Results: In patients at low risk or high risk for exacerbations, compared to placebo, tiotropium significantly reduced: 1) the time to first COPD exacerbation (hazard ratio [HR]: 0.81; 95% confidence interval [CI]: 0.74, 0.88; p <0.0001; HR: 0.89; 95% CI: 0.81, 0.97; p=0.0066, respectively); 2) the number of COPD exacerbations (rate ratio [RR]: 0.79; 95% CI: 0.72, 0.86; p<0.0001; RR: 0.88; 95% CI: 0.81; 0.95; p=0.0009). Furthermore, upon treatment with tiotropium, the proportion of patients transitioning from the low- to the high-risk exacerbations group was statistically lower compared to placebo (RR: 0.78; 95% CI: 0.67, 0.92; p=0.0030) Conclusions: This analysis shows that tiotropium reduces the risk of subsequent exacerbation and also prolongs time to first exacerbation, in both the high- and low-risk exacerbator subgroups. It also decreases the proportion of patients who shift from the low- to the high-risk exacerbations group compared to placebo.

Absolute Bioavailability and Effect of Food on the Disposition of Safinamide Immediate Release Tablets in Healthy Adult Subjects.

The objectives of this study were to establish the basic intravenous (IV) single-dose PK of safinamide and its major human metabolites, the absolute bioavailability (BA) and food effect on safinamide tablets. Fourteen healthy adult male and female subjects received 50 mg safinamide single-dose treatments according to a randomized, 3-period, 2-sequence crossover design: immediate release (IR) tablets, administered after an overnight fast and after a standardized high-fat, high-calorie breakfast, and IV solution, administered over 30 minutes. Treatments were separated by wash-out intervals of at least 17 days. Serial blood samples were collected for 240 hours postdosing to evaluate safinamide parent drug and metabolite concentrations for the determination of PK parameters. The absolute BA of safinamide 50 mg IR tablets was high, with geoMean AUC0-∞ ratios of about 95% (90% CI: 90-99%) indicating that safinamide is virtually completely absorbed after oral administration. Safinamide IR tablets did not display a food effect on exposure parameters; both 90% CIs for the ratios fed/fasted of AUC0-∞ and Cmax were entirely within the bioequivalence acceptance margins of 80-125%. Only tmax was delayed by about 30% in the fed state. Oral and IV safinamide 50 mg single-dose administrations were generally well tolerated.

Large scale analysis of protein-binding cavities using self-organizing maps and wavelet-based surface patches to describe functional properties, selectivity discrimination, and putative cross-reactivity.

A new method to discover similar substructures in protein binding pockets, independently of sequence and folding patterns or secondary structure elements, is introduced. The solvent-accessible surface of a binding pocket, automatically detected as a depression on the protein surface, is divided into a set of surface patches. Each surface patch is characterized by its shape as well as by its physicochemical characteristics. Wavelets defined on surfaces are used for the description of the shape, as they have the great advantage of allowing a comparison at different resolutions. The number of coefficients to describe the wavelets can be chosen with respect to the size of the considered data set. The physicochemical characteristics of the patches are described by the assignment of the exposed amino acid residues to one or more of five different properties determinant for molecular recognition. A self-organizing neural network is used to project the high-dimensional feature vectors onto a two-dimensional layer of neurons, called a map. To find similarities between the binding pockets, in both geometrical and physicochemical features, a clustering of the projected feature vector is performed using an automatic distance- and density-based clustering algorithm. The method was validated with a small training data set of 109 binding cavities originating from a set of enzymes covering 12 different EC numbers. A second test data set of 1378 binding cavities, extracted from enzymes of 13 different EC numbers, was then used to prove the discriminating power of the algorithm and to demonstrate its applicability to large scale analyses. In all cases, members of the data set with the same EC number were placed into coherent regions on the map, with small distances between them. Different EC numbers are separated by large distances between the feature vectors. A third data set comprising three subfamilies of endopeptidases is used to demonstrate the ability of the algorithm to detect similar substructures between functionally related active sites. The algorithm can also be used to predict the function of novel proteins not considered in training data set.

Comparison of substructural epitopes in enzyme active sites using self-organizing maps.

This paper presents a new algorithm to compare substructural epitopes in protein binding cavities. Through the comparison of binding cavities accommodating well characterized ligands with cavities whose actual guests are yet unknown, it is possible to draw some conclusions on the required shape of a putative ligand likely to bind to the latter cavities. To detect functional relationships among proteins, their binding-site exposed physicochemical characteristics are described by assigning generic pseudocenters to the functional groups of the amino acids flanking the particular active site. The cavities are divided into small local regions of four pseudocenters having the shape of a pyramid with triangular basis. To find similar local regions, an emergent self-organizing map is used for clustering. Two local regions within the same cluster are similar and form the basis for the superpositioning of the corresponding cavities to score this match. First results show that the similarities between enzymes with the same EC number can be found correctly. Enzymes with different EC numbers are detected to have no common substructures. These results indicate the benefit of this method and motivate further studies.