Abstract:
:Development of HIV resistance mutations is a major cause for failure of antiretroviral treatment. This article proposes a method for jointly modeling the processes of viral genetic changes and treatment failure. Because the viral genome is measured with uncertainty, a hidden Markov model is used to fit the viral genetic process. The uncertain viral genotype is included as a time-dependent covariate in a Cox model for failure time, and an expectation-maximization algorithm is used to estimate the model parameters. This model allows simultaneous evaluation of the sequencing uncertainty and the effect of resistance mutation on the risk of virological and immunological failures. Various model checking tests are provided to assess the appropriateness of the model. Simulation studies are performed to investigate the finite-sample properties of the proposed methods, which are then applied to data collected in three phase II clinical trials testing antiretroviral treatments containing the drug efavirenz.
journal_name
Biometricsjournal_title
Biometricsauthors
Hu C,De Gruttola Vdoi
10.1111/j.1541-0420.2006.00635.xsubject
Has Abstractpub_date
2007-03-01 00:00:00pages
60-8issue
1eissn
0006-341Xissn
1541-0420pii
BIOM635journal_volume
63pub_type
杂志文章相关文献
BIOMETRICS文献大全abstract::Serial dilution assays are widely employed for estimating substance concentrations and minimum inhibitory concentrations. The Poisson-Bernoulli model for such assays is appropriate for count data but not for continuous measurements that are encountered in applications involving substance concentrations. This paper pre...
journal_title:Biometrics
pub_type: 杂志文章
doi:10.1111/j.0006-341x.1999.01215.x
更新日期:1999-12-01 00:00:00
abstract::In sampling certain types of materials, such as bags of fertilizer, or subsampling large quantities of water, as might be done in investigating the density of plankton in certain environmental situations, it is customary to composite the samples. That is, several samples are drawn, mixed into a composite sample, and a...
journal_title:Biometrics
pub_type: 杂志文章
doi:
更新日期:1976-06-01 00:00:00
abstract::Precision medicine seeks to provide treatment only if, when, to whom, and at the dose it is needed. Thus, precision medicine is a vehicle by which healthcare can be made both more effective and efficient. Individualized treatment rules operationalize precision medicine as a map from current patient information to a re...
journal_title:Biometrics
pub_type: 杂志文章
doi:10.1111/biom.12743
更新日期:2018-03-01 00:00:00
abstract::The Colton model for the choice between two medical treatments is studied, with the additional assumption that there is a time lag between the administration of the treatments and the availability of the responses. Two simple procedures are suggested for dealing with patients who arrive during the waiting period, caus...
journal_title:Biometrics
pub_type: 杂志文章
doi:
更新日期:1981-03-01 00:00:00
abstract::Multinomial data arise in many areas of the life sciences, such as mark-recapture studies and phylogenetics, and will often by overdispersed, with the variance being higher than predicted by a multinomial model. The quasi-likelihood approach to modeling this overdispersion involves the assumption that the variance is ...
journal_title:Biometrics
pub_type: 杂志文章
doi:10.1111/biom.13194
更新日期:2020-09-01 00:00:00
abstract::This paper proposes a generalized estimating equations approach for the analysis of spatially correlated binary data when there are large numbers of spatially correlated observations on a moderate number of subjects. This approach is useful when the scientific focus is on modeling the marginal mean structure. Proper m...
journal_title:Biometrics
pub_type: 杂志文章
doi:
更新日期:1995-06-01 00:00:00
abstract::The clinical trial design in which the endpoint is measured both at baseline and at the end of the study is used in a variety of situations. For two-group designs, test such as the t test or analysis of covariance are commonly used to evaluate treatment efficacy. Often such pretest-posttest trials restrict participati...
journal_title:Biometrics
pub_type: 杂志文章
doi:
更新日期:1991-06-01 00:00:00
abstract::Procedures for estimating the genetic parameters of plant populations frequently employ progeny testing to ascertain the genotype of maternal plants. However, when experimental resources are limited (e.g., electrophoretic markers), the large progeny sizes required for accurate typing severely restricts the numbers of ...
journal_title:Biometrics
pub_type: 杂志文章
doi:
更新日期:1975-03-01 00:00:00
abstract::Jolliffe and Jolliffe (1997, Biometrics 53, 1136-1142) proposed various models for data from an experiment on memory in coal tits. This article describes an alternative model, which fits equally well and which may be simpler to interpret. ...
journal_title:Biometrics
pub_type: 杂志文章
doi:10.1111/j.0006-341x.1999.00660.x
更新日期:1999-06-01 00:00:00
abstract::When the observed data are contaminated with errors, the standard two-sample testing approaches that ignore measurement errors may produce misleading results, including a higher type-I error rate than the nominal level. To tackle this inconsistency, a nonparametric test is proposed for testing equality of two distribu...
journal_title:Biometrics
pub_type: 杂志文章
doi:10.1111/biom.13207
更新日期:2020-09-01 00:00:00
abstract::The data set presented relates a binomial response to ordered levels of an explanatory variable, representing doses of a drug, with data collected at several centers. A study goal is to test independence of the response and the ordinal factor, assuming under the alternative only that the binomial parameter is a monoto...
journal_title:Biometrics
pub_type: 杂志文章
doi:
更新日期:1996-09-01 00:00:00
abstract::Bayesian experimental design is investigated for Bayesian analysis of nonlinear mixed-effects models. Existence of the posterior risk for parameter estimation is shown. When the same prior distribution is used for both design and inference, existence of the preposterior risk for design is also proven. If the prior dis...
journal_title:Biometrics
pub_type: 杂志文章
doi:10.1111/j.0006-341X.2004.00148.x
更新日期:2004-03-01 00:00:00
abstract::The objective of this article is to develop a hypothesis-testing procedure to determine whether a common source outbreak has ended. We consider the case when neither the calendar date of exposure to the pathogen nor the exact incubation period distribution is known. The hypothesis-testing procedure is based on the spa...
journal_title:Biometrics
pub_type: 杂志文章
doi:10.1111/j.1541-0420.2005.00421.x
更新日期:2006-03-01 00:00:00
abstract::In a presentation of various methods for assessing the sensitivity of regression results to unmeasured confounding, Lin, Psaty, and Kronmal (1998, Biometrics54, 948-963) use a conditional independence assumption to derive algebraic relationships between the true exposure effect and the apparent exposure effect in a re...
journal_title:Biometrics
pub_type: 杂志文章
doi:10.1111/j.1541-0420.2008.01024.x
更新日期:2008-06-01 00:00:00
abstract::We propose optimal choice of the design parameters for random discontinuation designs (RDD) using a Bayesian decision-theoretic approach. We consider applications of RDDs to oncology phase II studies evaluating activity of cytostatic agents. The design consists of two stages. The preliminary open-label stage treats al...
journal_title:Biometrics
pub_type: 杂志文章
doi:10.1111/j.1541-0420.2011.01623.x
更新日期:2012-03-01 00:00:00
abstract::Experimental designs that include repeated measures of binary response variables over time and under different conditions are common in biology. In such settings, it is often desirable to characterize the response pattern over time. When response variables are continuous, this characterization can be made in terms of ...
journal_title:Biometrics
pub_type: 杂志文章
doi:
更新日期:1988-12-01 00:00:00
abstract::This paper studies randomization model methods for analyzing data from a multicenter study comparing the effectiveness of two treatments. The Mantel-Haenszel mean score statistic, which can be used for continuous or ordered categorical response variables, is shown to be a useful nonparametric alternative to standard l...
journal_title:Biometrics
pub_type: 杂志文章
doi:
更新日期:1995-09-01 00:00:00
abstract::We consider inference for the reaction rates in discretely observed networks such as those found in models for systems biology, population ecology, and epidemics. Most such networks are neither slow enough nor small enough for inference via the true state-dependent Markov jump process to be feasible. Typically, infere...
journal_title:Biometrics
pub_type: 杂志文章
doi:10.1111/biom.12152
更新日期:2014-06-01 00:00:00
abstract::Life-table methodology for interval-censored survival times is used to estimate marginal survival probabilities from data consisting of independent cohorts of correlated responses. We restrict our attention to situations where response times within cohorts are exchangeable and the marginal survival distributions are t...
journal_title:Biometrics
pub_type: 杂志文章
doi:
更新日期:1997-09-01 00:00:00
abstract::We discuss the assessment of age- and time-specific disease incidence using prevalence data. A method is described for conveniently fitting a discrete-time multiplicative model, subject to positivity constraints, using the EM-algorithm. Together with smoothing, it allows essentially nonparametric assessment of inciden...
journal_title:Biometrics
pub_type: 杂志文章
doi:
更新日期:1996-06-01 00:00:00
abstract::A class of adaptive weighted log-rank statistics is described where the vector of weights is chosen in a data-dependent way from a family of "smooth" weight vectors. A parametric family of weight vectors is identified which includes most shapes of weighting vectors that will be near optimal in many cancer prevention a...
journal_title:Biometrics
pub_type: 临床试验,杂志文章,随机对照试验
doi:
更新日期:1991-09-01 00:00:00
abstract::Whenever inference for variance components is required, the choice between one-sided and two-sided tests is crucial. This choice is usually driven by whether or not negative variance components are permitted. For two-sided tests, classical inferential procedures can be followed, based on likelihood ratios, score stati...
journal_title:Biometrics
pub_type: 杂志文章
doi:10.1111/1541-0420.00032
更新日期:2003-06-01 00:00:00
abstract::In diagnostic medicine, estimating the diagnostic accuracy of a group of raters or medical tests relative to the gold standard is often the primary goal. When a gold standard is absent, latent class models where the unknown gold standard test is treated as a latent variable are often used. However, these models have b...
journal_title:Biometrics
pub_type: 杂志文章
doi:10.1111/j.1541-0420.2012.01789.x
更新日期:2012-12-01 00:00:00
abstract::Moment methods for analyzing repeated binary responses have been proposed by Liang and Zeger (1986, Biometrika 73, 13-22), and extended by Prentice (1988, Biometrics 44, 1033-1048). In their generalized estimating equations (GEE), both Liang and Zeger (1986) and Prentice (1988) estimate the parameters associated with ...
journal_title:Biometrics
pub_type: 杂志文章
doi:
更新日期:1994-03-01 00:00:00
abstract::This paper considers the impact of bias in the estimation of the association parameters for longitudinal binary responses when there are drop-outs. A number of different estimating equation approaches are considered for the case where drop-out cannot be assumed to be a completely random process. In particular, standar...
journal_title:Biometrics
pub_type: 杂志文章
doi:10.1111/j.0006-341x.2001.00015.x
更新日期:2001-03-01 00:00:00
abstract::The "biometric school" founded by K. Pearson, F. Galton, and W. F. R. Weldon was concerned especially with heredity and variation, and between the wars "biometry" was not widely used as a general term for quantitative biology. The foundation of the Biometric Society encouraged this wider usage, and medical and biologi...
journal_title:Biometrics
pub_type: 杂志文章
doi:
更新日期:1985-12-01 00:00:00
abstract::Directed acyclic graphical (DAG) models are increasingly employed in the study of physical and biological systems to model direct influences between variables. Identifying the graph from data is a challenging endeavor, which can be more reasonably tackled if the variables are assumed to satisfy a given ordering; in th...
journal_title:Biometrics
pub_type: 杂志文章
doi:10.1111/biom.12018
更新日期:2013-06-01 00:00:00
abstract::Adaptive line transect sampling offers the potential of improved population density estimation efficiency over conventional line transect sampling when populations are spatially clustered. In adaptive sampling, survey effort is increased when areas of high animal density are located, thereby increasing the number of o...
journal_title:Biometrics
pub_type: 杂志文章
doi:10.1111/j.0006-341x.2002.00862.x
更新日期:2002-12-01 00:00:00
abstract::In this article, we study nonparametric estimation of the mean function of a counting process with panel observations. We introduce the gamma frailty variable to account for the intracorrelation between the panel counts of the counting process and construct a maximum pseudo-likelihood estimate with the frailty variabl...
journal_title:Biometrics
pub_type: 杂志文章
doi:10.1111/j.0006-341x.2003.00126.x
更新日期:2003-12-01 00:00:00
abstract::Increasingly, genetic studies of tumors of the same histologic diagnosis are elucidating subtypes that are distinct with respect to clinical endpoints such as response to treatment and survival. This raises concerns about the efficiency of using the simple log-rank test for analysis of treatment effect on survival in ...
journal_title:Biometrics
pub_type: 杂志文章
doi:10.1111/j.0006-341x.2002.00232.x
更新日期:2002-03-01 00:00:00