Abstract：
:An attractive application of expression technologies is to predict drug efficacy or safety using expression data of biomarkers. To evaluate the performance of various classification methods for building predictive models, we applied these methods on six expression datasets. These datasets were from studies using microarray technologies and had either two or more classes. From each of the original datasets, two subsets were generated to simulate two scenarios in biomarker applications. First, a 50-gene subset was used to simulate a candidate gene approach when it might not be practical to measure a large number of genes/biomarkers. Next, a 2000-gene subset was used to simulate a whole genome approach. We evaluated the relative performance of several classification methods by using leave-one-out cross-validation and bootstrap cross-validation. Although all methods perform well in both subsets for a relative easy dataset with two classes, differences in performance do exist among methods for other datasets. Overall, partial least squares discriminant analysis (PLS-DA) and support vector machines (SVM) outperform all other methods. We suggest a practical approach to take advantage of multiple methods in biomarker applications.
journal_name
J Biopharm Statjournal_title
Journal of biopharmaceutical statisticsauthors
Man MZ,Dyson G,Johnson K,Liao Bdoi
10.1081/BIP-200035491keywords:
subject
Has Abstractpub_date
2004-11-01 00:00:00pages
1065-84issue
4eissn
1054-3406issn
1520-5711journal_volume
14pub_type
杂志文章abstract：:Due to the importance of precision medicine, it is essential to identify the right patients for the right treatment. Biomarkers, which have been commonly used in clinical research as well as in clinical practice, can facilitate selection of patients with a good response to the treatment. In this paper, we describe a b...
journal_title：Journal of biopharmaceutical statistics
pub_type： 杂志文章
doi：10.1080/10543406.2018.1434191
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abstract：:We develop a Bayesian approach for estimating vaccine efficacy for susceptibility (VEs) and infectiousness (VEI) using outbreak size household data. Our method allows for heterogeneity in transmission probabilities due to factors that are related to individuals' characteristics, such as age, in addition to vaccination...
journal_title：Journal of biopharmaceutical statistics
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doi：10.1080/10543400600719467
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abstract：:Laboratory data with a lower quantification limit (censored data) are sometimes analyzed by replacing non-quantifiable values with a single value equal to or less than the quantification limit, yielding possibly biased point estimates and variance estimates that are too small. Motivated by a three-period, three-treatm...
journal_title：Journal of biopharmaceutical statistics
pub_type： 杂志文章
doi：10.1080/10543406.2014.920858
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abstract：:Sample size estimation (SSE) is an important issue in the planning of clinical studies. While larger studies are likely to have sufficient power, it may be unethical to expose more patients than necessary to answer a scientific question. Budget considerations may also cause one to limit the study to an adequate size t...
journal_title：Journal of biopharmaceutical statistics
pub_type： 杂志文章,评审
doi：10.1080/10543406.2015.1092031
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abstract：:Classification measures play essential roles in the assessment and construction of classifiers. Hence, determining how to prevent these measures from being affected by individual observations has become an important problem. In this paper, we propose several indexes based on the influence function and the concept of l...
journal_title：Journal of biopharmaceutical statistics
pub_type： 杂志文章
doi：10.1080/10543406.2017.1377728
更新日期：2018-01-01 00:00:00
abstract：:Pharmacokinetic studies of drug and metabolite concentrations in the blood are usually conducted as crossover trials, especially in phases I and II. A longitudinal series of measurements is collected on each subject within each period. However, much of the dependence among such observations, within and between periods...
journal_title：Journal of biopharmaceutical statistics
pub_type： 杂志文章
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abstract：:Clinical trials with data-driven decision rules often pursue multiple clinical objectives such as the evaluation of several endpoints or several doses of an experimental treatment. These complex analysis strategies give rise to "multivariate" multiplicity problems with several components or sources of multiplicity. A ...
journal_title：Journal of biopharmaceutical statistics
pub_type： 杂志文章
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abstract：:For administrative convenience or cost efficiency, we may often employ a cluster randomized trial (CRT), in which randomized units are clusters of patients rather than individual patients. Furthermore, because of ethical reasons or patient's decision, it is not uncommon to encounter data in which there are patients no...
journal_title：Journal of biopharmaceutical statistics
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doi：10.1080/10543400903350465
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abstract：:The Wilcoxon-Mann-Whitney (WMW) test is the most commonly used nonparametric method to compare two treatments when the underlying distribution of the outcome variable is not normally distributed. In the presence of stratum effects, the van Elteren (vE) test, a stratified WMW test, can be used to adjust for the stratum...
journal_title：Journal of biopharmaceutical statistics
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abstract：:In clinical trials of drug development, patients are often followed for a certain period of time, and the outcome variables are measured at scheduled time intervals. The main interest of the trial is the treatment efficacy at a prespecified time point, which is often the last visit. In such trials, patient dropout is ...
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abstract：:The small n, Sequential, Multiple Assignment, Randomized Trial (snSMART) is a two-stage clinical trial design for rare diseases motivated by the comparison of three active treatments for isolated skin vasculitis in the ongoing clinical trial ARAMIS (a randomized multicenter study for isolated skin vasculitis, NCT09239...
journal_title：Journal of biopharmaceutical statistics
pub_type： 杂志文章
doi：10.1080/10543406.2020.1815032
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abstract：:We extend the development of the expression of the Fisher information matrix in nonlinear mixed effects models for designs evaluation. We consider the dependence of the marginal variance of the observations with the mean parameters and assume an heteroscedastic variance error model. Complex models with interoccasions ...
journal_title：Journal of biopharmaceutical statistics
pub_type： 杂志文章
doi：10.1081/BIP-120019267
更新日期：2003-05-01 00:00:00
abstract：:We assess the QT effect using an exposure-response model in a "thorough QT/QTc study" with a four-period crossover design in which the treatments are placebo, positive control, higher dose of investigational drug, and therapeutic dose of investigational drug. In the study, QTc interval values and the drug concentratio...
journal_title：Journal of biopharmaceutical statistics
pub_type： 杂志文章
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abstract：:This article deals with seven special issues related to the assumptions, applicability, and practical use of formulas for calculating power or sample size, respectively, for comparative clinical trials with time-to-event endpoints, with particular focus on the well-known Freedman and Schoenfeld methods. All problems a...
journal_title：Journal of biopharmaceutical statistics
pub_type： 杂志文章
doi：10.1080/10543406.2014.1000546
更新日期：2015-01-01 00:00:00
abstract：:Large sample size imbalance is not uncommon in the biosimilar development. At the beginning of a product development, sample sizes of a biosimilar and a reference product may be limited. Thus, a sample size calculation may not be feasible. During the development stage, more batches of reference products may be added a...
journal_title：Journal of biopharmaceutical statistics
pub_type： 杂志文章
doi：10.1080/10543406.2016.1265544
更新日期：2017-01-01 00:00:00
abstract：:As more biologic products are going off patent protection, the development of follow-on biologic products (also known as biosimilars) has gained much attention from both the biotechnology industry and regulatory agencies. Unlike small molecules, the development of biologic products is not only more complicated but als...
journal_title：Journal of biopharmaceutical statistics
pub_type： 杂志文章
doi：10.1080/10543406.2014.941991
更新日期：2014-01-01 00:00:00
abstract：:In analytical similarity assessment of a biosimilar product, key quality attributes of the test and reference products need to be shown statistically similar. When there were multiple references, similarity among the reference products is also required. We proposed a simultaneous confidence approach based on the fiduc...
journal_title：Journal of biopharmaceutical statistics
pub_type： 杂志文章
doi：10.1080/10543406.2019.1657142
更新日期：2019-01-01 00:00:00
abstract：:Gene expression profiling has played an important role in cancer risk classification and has shown promising results. Since gene expression profiling often involves determination of a set of top rank genes for analysis, it is important to evaluate how modeling performance varies with the number of selected top ranked ...
journal_title：Journal of biopharmaceutical statistics
pub_type： 杂志文章
doi：10.1080/10543400802277967
更新日期：2008-01-01 00:00:00
abstract：:We present a new computational method for identifying regulated pathway components in transcript profiling (TP) experiments by evaluating transcriptional activity in the context of known biological pathways. We construct a graph representing thousands of protein functional relationships by integrating knowledge from p...
journal_title：Journal of biopharmaceutical statistics
pub_type： 杂志文章
doi：10.1081/BIP-200025678
更新日期：2004-08-01 00:00:00
abstract：:After a group sequential test, the naive confidence interval (CI) is usually biased in the sense that it does not cover the true parameter at the correct nominal level. Furthermore, when the stopping time is taken into account, the actual conditional confidence coverage probability can be much less accurate. In this a...
journal_title：Journal of biopharmaceutical statistics
pub_type： 杂志文章
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abstract：:In a clinical dose finding study with active control a new drug with several dose levels is compared with an active comparator drug. The main focus of such studies often lies on the estimation of a target dose that leads to the same efficacy as the control. This article investigates the finite sample properties of the...
journal_title：Journal of biopharmaceutical statistics
pub_type： 杂志文章
doi：10.1080/10543406.2014.920343
更新日期：2015-01-01 00:00:00
abstract：:Sample size calculation based on normal approximations is often associated with the loss of statistical power for a single-arm trial with a time-to-event endpoint. Recently, Wu (2015) derived the exact variance for the one-sample log-rank test under the alternative and showed that a single-arm one-stage study based on...
journal_title：Journal of biopharmaceutical statistics
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abstract：:In the early stages of traditional drug development, the frequency of dosing (e.g., QD, BID, etc.) is typically determined by the pharmacokinetic properties of a compound. After an appropriate dose frequency is chosen, the magnitude of dose is then evaluated via parallel-group dose-response trials. For some drugs, how...
journal_title：Journal of biopharmaceutical statistics
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abstract：:We propose an adaptive two-stage dose-response design where a prespecified adaptation rule is used to add and/or drop treatment arms between the stages. We extend the multiple comparison procedures-modeling (MCP-Mod) approach into a two-stage design. In each stage, we use the same set of candidate dose-response models...
journal_title：Journal of biopharmaceutical statistics
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doi：10.1080/10543406.2013.813519
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abstract：:We introduce the idea of a design to detect signals of efficacy in early phase clinical trials. Such a design features three possible decisions: to kill the compound; to continue with staged development; or to continue with accelerated development of the compound. We describe how such studies improve the trade-off bet...
journal_title：Journal of biopharmaceutical statistics
pub_type： 杂志文章,评审
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abstract：:Using multistage adaptive group sequential test designs, the investigator may perform data-driven changes in the design during the course of the trial without inflation of the Type I error rate. This is possible, for example, through the use of the inverse normal method of combining the p-values from the separate stag...
journal_title：Journal of biopharmaceutical statistics
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doi：10.1081/BIP-120024196
更新日期：2003-11-01 00:00:00
abstract：:In method comparison and reliability studies, it is often important to assess agreement between multiple measurements made by different methods, devices, laboratories, observers, or instruments. For continuous data, the concordance correlation coefficient (CCC) is a popular index for assessing agreement between multip...
journal_title：Journal of biopharmaceutical statistics
pub_type： 杂志文章
doi：10.1080/10543400701329497
更新日期：2007-01-01 00:00:00
abstract：:For noninferiority testing with the maximum allowable noninferiority margin being prespecified, one can perform valid statistical testing at the same alpha level for multiple noninferiority hypotheses with margins being smaller than this maximum margin. This is easily comprehensible because only one confidence level i...
journal_title：Journal of biopharmaceutical statistics
pub_type： 杂志文章
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更新日期：2004-05-01 00:00:00
abstract：:Highly clustered count data are commonly seen in medical device clinical studies such as cardiac rhythm management. For instance, anti-arrhythmia shocks delivered from an implantable cardioverter-defibrillator (ICD) often occur as "storms", i.e., multiple shocks within a short period of time. There are unique challeng...
journal_title：Journal of biopharmaceutical statistics
pub_type： 杂志文章
doi：10.1080/10543400701668241
更新日期：2008-01-01 00:00:00
abstract：:Bayesian decision procedures have already been proposed for and implemented in Phase I dose-escalation studies in healthy volunteers. The procedures have been based on pharmacokinetic responses reflecting the concentration of the drug in blood plasma and are conducted to learn about the dose-response relationship whil...
journal_title：Journal of biopharmaceutical statistics
pub_type： 杂志文章
doi：10.1080/10543400701645165
更新日期：2007-01-01 00:00:00
