Sample size calculation for phylogenetic case linkage.
Ontology highlight
ABSTRACT:
SUBMITTER: Wohl S
PROVIDER: S-EPMC8284614 | biostudies-literature |
REPOSITORIES: biostudies-literature
Similar Datasets
Project description:The case-cohort (CC) study design usually has been used for risk factor assessment in epidemiologic studies or disease prevention trials for rare diseases. The sample size/power calculation for a stratified CC (SCC) design has not been addressed before. This article derives such result based on a stratified test statistic. Simulation studies show that the proposed test for the SCC design utilizing small sub-cohort sampling fractions is valid and efficient for situations where the disease rate is low. Furthermore, optimization of sampling in the SCC design is discussed and compared with proportional and balanced sampling techniques. An epidemiological study is provided to illustrate the sample size calculation under the SCC design.
| S-EPMC4159408 | biostudies-other
Project description:BackgroundMulti-centre randomized controlled clinical trials play an important role in modern evidence-based medicine. Advantages of collecting data from more than one site are numerous, including accelerated recruitment and increased generalisability of results. Mixed models can be applied to account for potential clustering in the data, in particular when many small centres contribute patients to the study. Previously proposed methods on sample size calculation for mixed models only considered balanced treatment allocations which is an unlikely outcome in practice if block randomisation with reasonable choices of block length is used.MethodsWe propose a sample size determination procedure for multi-centre trials comparing two treatment groups for a continuous outcome, modelling centre differences using random effects and allowing for arbitrary sample sizes. It is assumed that block randomisation with fixed block length is used at each study site for subject allocation. Simulations are used to assess operation characteristics such as power of the sample size approach. The proposed method is illustrated by an example in disease management systems.ResultsA sample size formula as well as a lower and upper boundary for the required overall sample size are given. We demonstrate the superiority of the new sample size formula over the conventional approach of ignoring the multi-centre structure and show the influence of parameters such as block length or centre heterogeneity. The application of the procedure on the example data shows that large blocks require larger sample sizes, if centre heterogeneity is present.ConclusionUnbalanced treatment allocation can result in substantial power loss when centre heterogeneity is present but not considered at the planning stage. When only few patients by centre will be recruited, one has to weigh the risk of imbalance between treatment groups due to large blocks and the risk of unblinding due to small blocks. The proposed approach should be considered when planning multi-centre trials.
| S-EPMC6267841 | biostudies-literature
Project description:Since the era of evidence-based medicine, it has become a matter of course to use statistics to create objective evidence in clinical research. As an extension of this, it has become essential in clinical research to calculate the correct sample size to demonstrate a clinically significant difference before starting the study. Also, because sample size calculation methods vary from study design to study design, there is no formula for sample size calculation that applies to all designs. It is very important for us to understand this. In this review, each sample size calculation method suitable for various study designs was introduced using the R program (R Foundation for Statistical Computing). In order for clinical researchers to directly utilize it according to future research, we presented practice codes, output results, and interpretation of results for each situation.
| S-EPMC10020745 | biostudies-literature
Project description:Case-parent trio studies considering genotype data from children affected by a disease and their parents are frequently used to detect single nucleotide polymorphisms (SNPs) associated with disease. The most popular statistical tests for this study design are transmission/disequilibrium tests (TDTs). Several types of these tests have been developed, for example, procedures based on alleles or genotypes. Therefore, it is of great interest to examine which of these tests have the highest statistical power to detect SNPs associated with disease. Comparisons of the allelic and the genotypic TDT for individual SNPs have so far been conducted based on simulation studies, since the test statistic of the genotypic TDT was determined numerically. Recently, however, it has been shown that this test statistic can be presented in closed form. In this article, we employ this analytic solution to derive equations for calculating the statistical power and the required sample size for different types of the genotypic TDT. The power of this test is then compared with the one of the corresponding score test assuming the same mode of inheritance as well as the allelic TDT based on a multiplicative mode of inheritance, which is equivalent to the score test assuming an additive mode of inheritance. This is, thus, the first time the power of these tests are compared based on equations, yielding instant results and omitting the need for time-consuming simulation studies. This comparison reveals that these tests have almost the same power, with the score test being slightly more powerful.
| S-EPMC4206700 | biostudies-literature
Project description:Genetic association studies, testing the relationship between genetic variants and disease status, are useful tools for identifying genes that grant susceptibility to complex disorders. In such studies, an inadequate sample size may provide unreliable results: a small sample is unable to accurately describe the population, whereas a large sample makes the study expensive and complex to run. However, in genetic association studies, the sample size calculation is often overlooked or inadequately assessed for the small number of parameters included. In light of this, herein we list and discuss the role of the statistical and genetic parameters to be considered in the sample size calculation, show examples reporting incorrect estimation and, by using a genetic software program, we provide a practical approach for the assessment of the adequate sample size in a hypothetical study aimed at analyzing a gene-disease association.
| S-EPMC9863799 | biostudies-literature
Project description:We propose a systematic method for testing and identifying a subgroup with an enhanced treatment effect. We adopts a change-plane technique to first test the existence of a subgroup, and then identify the subgroup if the null hypothesis on non-existence of such a subgroup is rejected. A semiparametric model is considered for the response with an unspecified baseline function and an interaction between a subgroup indicator and treatment. A doubly-robust test statistic is constructed based on this model, and asymptotic distributions of the test statistic under both null and local alternative hypotheses are derived. Moreover, a sample size calculation method for subgroup detection is developed based on the proposed statistic. The finite sample performance of the proposed test is evaluated via simulations. Finally, the proposed methods for subgroup identification and sample size calculation are applied to a data from an AIDS study.
| S-EPMC5553128 | biostudies-other
Project description:One of the main objectives of microarray analysis is to identify differentially expressed genes for different types of cells or treatments. Many statistical methods have been proposed to assess the treatment effects in microarray experiments.In this paper, we consider discovery of the genes that are differentially expressed among K (> 2) treatments when each set of K arrays consists of a block. In this case, the array data among K treatments tend to be correlated because of block effect. We propose to use the blocked one-way ANOVA F-statistic to test if each gene is differentially expressed among K treatments. The marginal p-values are calculated using a permutation method accounting for the block effect, adjusting for the multiplicity of the testing procedure by controlling the false discovery rate (FDR). We propose a sample size calculation method for microarray experiments with a blocked one-way design. With FDR level and effect sizes of genes specified, our formula provides a sample size for a given number of true discoveries.The calculated sample size is shown via simulations to provide an accurate number of true discoveries while controlling the FDR at the desired level.
| S-EPMC2702333 | biostudies-literature
Project description:BackgroundObservational burden of illness studies are used in pharmacoepidemiology to address a variety of objectives, including contextualizing the current treatment setting, identifying important treatment gaps, and providing estimates to parameterize economic models. Methodologies such as retrospective chart review may be utilized in settings for which existing datasets are not available or do not include sufficient clinical detail. While specifying the number of charts to be extracted and/or determining whether the number that can feasibly extracted will be clinically meaningful is an important study design consideration, there is a lack of rigorous methods available for sample size calculation in this setting. The objective of this study was to develop recommended sample size calculations for use in such studies.MethodsCalculations for identifying the optimal feasible sample size calculations were derived, for studies characterizing treatment patterns and medical costs, based on the ability to comprehensively observe treatments and maximize precision of resulting 95% confidence intervals. For cost outcomes, if the standard deviation is not known, the coefficient of variation cv can be used as an alternative. A case study of a chart review of advanced melanoma (MELODY) was used to characterize plausible values for cv in a real-world example.ResultsAcross sample sizes, any treatment given with greater than 1% frequency has a high likelihood of being observed. For a sample of size 200, and a treatment given to 5% of the population, the precision of a 95% confidence interval (CI) is expected to be ±0.03. For cost outcomes, for the median cv value observed in the MELODY study (0.72), a sample size of approximately 200 would be required to generate a 95% CI precise to within ±10% of the mean.ConclusionThis study presents a formal guidance on sample size calculations for retrospective burden of illness studies. The approach presented here is methodologically rigorous and designed for practical application in real-world retrospective chart review studies.
| S-EPMC6325730 | biostudies-literature
Project description:Sample sizes for randomized controlled trials are typically based on power calculations. They require us to specify values for parameters such as the treatment effect, which is often difficult because we lack sufficient prior information. The objective of this paper is to provide an alternative design which circumvents the need for sample size calculation. In a simulation study, we compared a meta-experiment approach to the classical approach to assess treatment efficacy. The meta-experiment approach involves use of meta-analyzed results from 3 randomized trials of fixed sample size, 100 subjects. The classical approach involves a single randomized trial with the sample size calculated on the basis of an a priori-formulated hypothesis. For the sample size calculation in the classical approach, we used observed articles to characterize errors made on the formulated hypothesis. A prospective meta-analysis of data from trials of fixed sample size provided the same precision, power and type I error rate, on average, as the classical approach. The meta-experiment approach may provide an alternative design which does not require a sample size calculation and addresses the essential need for study replication; results may have greater external validity.
| S-EPMC4928786 | biostudies-literature
Project description:In this paper, we propose a testing procedure for detecting and estimating the subgroup with an enhanced treatment effect in survival data analysis. Here, we consider a new proportional hazard model that includes a nonparametric component for the covariate effect in the control group and a subgroup-treatment-interaction effect defined by a change plane. We develop a score-type test for detecting the existence of the subgroup, which is doubly robust against misspecification of the baseline effect model or the propensity score but not both under mild assumptions for censoring. When the null hypothesis of no subgroup is rejected, the change-plane parameters that define the subgroup can be estimated on the basis of supremum of the normalized score statistic. The asymptotic distributions of the proposed test statistic under the null and local alternative hypotheses are established. On the basis of established asymptotic distributions, we further propose a sample size calculation formula for detecting a given subgroup effect and derive a numerical algorithm for implementing the sample size calculation in clinical trial designs. The performance of the proposed approach is evaluated by simulation studies. An application to an AIDS clinical trial data is also given for illustration.
| S-EPMC5698151 | biostudies-literature