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Strategies for power calculations in predictive biomarker studies in survival data.

ABSTRACT: Biomarkers and genomic signatures represent potentially predictive tools for precision medicine. Validation of predictive biomarkers in prospective or retrospective studies requires statistical justification of power and sample size. However, the design of these studies is complex and the statistical methods and associated software are limited, especially in survival data. Herein, we address common statistical design issues relevant to these two types of studies and provide guidance and a general template for analysis.A statistical interaction effect in the Cox proportional hazards model is used to describe predictive biomarkers. The analytic form by Peterson et al. and Lachin is utilized to calculate the statistical power for both prospective and retrospective studies.We demonstrate that the common mistake of using only Hazard Ratio's Ratio (HRR) or two hazard ratios (HRs) can mislead power calculations. We establish that the appropriate parameter settings for prospective studies require median survival time (MST) in 4 subgroups (treatment and control in positive biomarker, treatment and control in negative biomarker). For the retrospective study which has fixed survival time and censored status, we develop a strategy to harmonize the hypothesized parameters and the study cohort. Moreover, we provide an easily-adapted R software application to generate a template of statistical plan for predictive biomarker validation so investigators can easily incorporate into their study proposals.Our study provides guidance and software to help biostatisticians and clinicians design sound clinical studies for testing predictive biomarkers.

SUBMITTER: Chen DT

PROVIDER: S-EPMC5348326 | biostudies-literature | 2016 Dec

REPOSITORIES: biostudies-literature

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Strategies for power calculations in predictive biomarker studies in survival data.

Chen Dung-Tsa DT Huang Po-Yu PY Lin Hui-Yi HY Haura Eric B EB Antonia Scott J SJ Cress W Douglas WD Gray Jhanelle E JE

Oncotarget 20161201 49

<h4>Purpose</h4>Biomarkers and genomic signatures represent potentially predictive tools for precision medicine. Validation of predictive biomarkers in prospective or retrospective studies requires statistical justification of power and sample size. However, the design of these studies is complex and the statistical methods and associated software are limited, especially in survival data. Herein, we address common statistical design issues relevant to these two types of studies and provide guida ...[more]

PMID: 27661007

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Project description:BACKGROUND:Researchers and funders should consider the statistical power of planned Individual Participant Data (IPD) meta-analysis projects, as they are often time-consuming and costly. We propose simulation-based power calculations utilising a two-stage framework, and illustrate the approach for a planned IPD meta-analysis of randomised trials with continuous outcomes where the aim is to identify treatment-covariate interactions. METHODS:The simulation approach has four steps: (i) specify an underlying (data generating) statistical model for trials in the IPD meta-analysis; (ii) use readily available information (e.g. from publications) and prior knowledge (e.g. number of studies promising IPD) to specify model parameter values (e.g. control group mean, intervention effect, treatment-covariate interaction); (iii) simulate an IPD meta-analysis dataset of a particular size from the model, and apply a two-stage IPD meta-analysis to obtain the summary estimate of interest (e.g. interaction effect) and its associated p-value; (iv) repeat the previous step (e.g. thousands of times), then estimate the power to detect a genuine effect by the proportion of summary estimates with a significant p-value. RESULTS:In a planned IPD meta-analysis of lifestyle interventions to reduce weight gain in pregnancy, 14 trials (1183 patients) promised their IPD to examine a treatment-BMI interaction (i.e. whether baseline BMI modifies intervention effect on weight gain). Using our simulation-based approach, a two-stage IPD meta-analysis has <?60% power to detect a reduction of 1 kg weight gain for a 10-unit increase in BMI. Additional IPD from ten other published trials (containing 1761 patients) would improve power to over 80%, but only if a fixed-effect meta-analysis was appropriate. Pre-specified adjustment for prognostic factors would increase power further. Incorrect dichotomisation of BMI would reduce power by over 20%, similar to immediately throwing away IPD from ten trials. CONCLUSIONS:Simulation-based power calculations could inform the planning and funding of IPD projects, and should be used routinely.

Project description:Genome-wide association studies (GWAS) aim to identify genetic variants related to diseases by examining the associations between phenotypes and hundreds of thousands of genotyped markers. Because many genes are potentially involved in common diseases and a large number of markers are analyzed, it is crucial to devise an effective strategy to identify truly associated variants that have individual and/or interactive effects, while controlling false positives at the desired level. Although a number of model selection methods have been proposed in the literature, including marginal search, exhaustive search, and forward search, their relative performance has only been evaluated through limited simulations due to the lack of an analytical approach to calculating the power of these methods. This article develops a novel statistical approach for power calculation, derives accurate formulas for the power of different model selection strategies, and then uses the formulas to evaluate and compare these strategies in genetic model spaces. In contrast to previous studies, our theoretical framework allows for random genotypes, correlations among test statistics, and a false-positive control based on GWAS practice. After the accuracy of our analytical results is validated through simulations, they are utilized to systematically evaluate and compare the performance of these strategies in a wide class of genetic models. For a specific genetic model, our results clearly reveal how different factors, such as effect size, allele frequency, and interaction, jointly affect the statistical power of each strategy. An example is provided for the application of our approach to empirical research. The statistical approach used in our derivations is general and can be employed to address the model selection problems in other random predictor settings. We have developed an R package markerSearchPower to implement our formulas, which can be downloaded from the Comprehensive R Archive Network (CRAN) or http://bioinformatics.med.yale.edu/group/.

Project description:Manual wheelchair propulsion is known to be inefficient and causes upper extremity pain, fatigue, and injury. Power-assisted wheelchairs can mitigate these effects through motors that reduce users' effort and load during propulsion. Among the different control strategies proposed to govern the user-wheelchair interaction, impedance control-based ones appear to be the most natural and effective. It can change the apparent dynamical properties of the wheelchair, particularly mass and friction, and automatically compensate for external disturbances such as terrain conditions. This study investigates the advantages and disadvantages of this control strategy employing predictive simulations of locomotion with power-assisted wheelchairs in different scenarios. The simulations are generated using a biomechanically realistic model of the upper extremities and their interaction with the power-assisted wheelchair by solving an optimal control problem. Investigated scenarios include steady-state locomotion vs. a transient maneuver starting from rest, movement on a ramp vs. a level surface, and different choices of reference model parameters. The results reveal that the investigated impedance control-based strategy can effectively reproduce the reference model and reduce the user's effort, with a more significant effect of inertia in the transient maneuver and of friction in steady-state locomotion. However, the simulations also show that imposing a first-order, linear reference model with constant parameters can produce disadvantageous locomotion patterns, particularly in the recovery phase, leading to unnecessary energy dissipation and consequent increase in energy consumption from the batteries. These observations indicate there is room for improvement, for instance, by exploring energy regeneration in the recovery phase or by switching reference model nature or parameters along the cycle. To the best of our knowledge, this is the first investigation of impedance control-based strategies for power-assisted wheelchairs using predictive simulations and a realistic, nonlinear model of the user-wheelchair system.

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Strategies for power calculations in predictive biomarker studies in survival data.

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Strategies for power calculations in predictive biomarker studies in survival data.

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