armDNA: A functional beta model for detecting age-related genomewide DNA methylation marks.

Abstract:

:DNA methylation has been shown to play an important role in many complex diseases. The rapid development of high-throughput DNA methylation scan technologies provides great opportunities for genomewide DNA methylation-disease association studies. As methylation is a dynamic process involving time, it is quite plausible that age contributes to its variation to a large extent. Therefore, in analyzing genomewide DNA methylation data, it is important to identify age-related DNA methylation marks and delineate their functional relationship. This helps us to better understand the underlying biological mechanism and facilitate early diagnosis and prognosis analysis of complex diseases. We develop a functional beta model for analyzing DNA methylation data and detecting age-related DNA methylation marks on the whole genome by naturally taking sampling scheme into account and accommodating flexible age-methylation dynamics. We focus on DNA methylation data obtained through the widely used bisulfite conversion technique and propose to use a beta model to relate the DNA methylation level to the age. Adjusting for certain confounders, the functional age effect is left completely unspecified, offering great flexibility and allowing extra data dynamics. An efficient algorithm is developed for estimating unknown parameters, and the Wald test is used to detect age-related DNA methylation marks. Simulation studies and several real data applications were provided to demonstrate the performance of the proposed method.

journal_name

Stat Methods Med Res

authors

Wang C,Shen Q,Du L,Xu J,Zhang H

doi

10.1177/0962280216683571

subject

Has Abstract

pub_date

2018-09-01 00:00:00

pages

2627-2640

issue

9

eissn

0962-2802

issn

1477-0334

journal_volume

27

pub_type

杂志文章
  • Penalized count data regression with application to hospital stay after pediatric cardiac surgery.

    abstract::Pediatric cardiac surgery may lead to poor outcomes such as acute kidney injury (AKI) and prolonged hospital length of stay (LOS). Plasma and urine biomarkers may help with early identification and prediction of these adverse clinical outcomes. In a recent multi-center study, 311 children undergoing cardiac surgery we...

    journal_title:Statistical methods in medical research

    pub_type: 杂志文章

    doi:10.1177/0962280214530608

    authors: Wang Z,Ma S,Zappitelli M,Parikh C,Wang CY,Devarajan P

    更新日期:2016-12-01 00:00:00

  • Cluster analysis and related techniques in medical research.

    abstract::In this paper we review methods of cluster analysis in the context of classifying patients on the basis of clinical and/or laboratory type observations. Both hierarchical and non-hierarchical methods of clustering are considered, although the emphasis is on the latter type, with particular attention devoted to the mix...

    journal_title:Statistical methods in medical research

    pub_type: 杂志文章,评审

    doi:10.1177/096228029200100103

    authors: McLachlan GJ

    更新日期:1992-01-01 00:00:00

  • Re-weighted inference about hepatitis C virus-infected communities when analysing diagnosed patients referred to liver clinics.

    abstract::To project national hepatitis C virus (HCV) burden, unbiased estimation of HCV progression to liver cirrhosis is required for the whole community of HCV-infected individuals. However, widely varying estimates of progression rates to cirrhosis have been produced. This disparity is partly associated with the statistical...

    journal_title:Statistical methods in medical research

    pub_type: 杂志文章

    doi:10.1177/0962280208094688

    authors: Fu B,Tom BD,Bird SM

    更新日期:2009-06-01 00:00:00

  • Bayesian nonparametric inference for the three-class Youden index and its associated optimal cutoff points.

    abstract::The three-class Youden index serves both as a measure of medical test accuracy and a criterion to choose the optimal pair of cutoff values for classifying subjects into three ordinal disease categories (e.g. no disease, mild disease, advanced disease). We present a Bayesian nonparametric approach for estimating the th...

    journal_title:Statistical methods in medical research

    pub_type: 杂志文章

    doi:10.1177/0962280217742538

    authors: Carvalho VI,Branscum AJ

    更新日期:2018-03-01 00:00:00

  • Efficient Monte Carlo evaluation of resampling-based hypothesis tests with applications to genetic epidemiology.

    abstract::Monte Carlo evaluation of resampling-based tests is often conducted in statistical analysis. However, this procedure is generally computationally intensive. The pooling resampling-based method has been developed to reduce the computational burden but the validity of the method has not been studied before. In this arti...

    journal_title:Statistical methods in medical research

    pub_type: 杂志文章

    doi:10.1177/0962280216661876

    authors: Fung WK,Yu K,Yang Y,Zhou JY

    更新日期:2018-05-01 00:00:00

  • Components of variance in a group-randomized trial analysed via a random-coefficients model: the Rapid Early Action for Coronary Treatment (REACT) trial.

    abstract::Rapid Early Action for Coronary Treatment (REACT) was a multisite trial testing a community intervention to reduce the delay between onset of symptoms of acute myocardial infarction (MI) and patients' arrival at a hospital emergency department. The study employed a group-randomized trial design, with ten communities r...

    journal_title:Statistical methods in medical research

    pub_type: 临床试验,杂志文章,随机对照试验

    doi:10.1177/096228020000900204

    authors: Murray DM,Feldman HA,McGovern PG

    更新日期:2000-04-01 00:00:00

  • Accurate quantification of uncertainty in epidemic parameter estimates and predictions using stochastic compartmental models.

    abstract::Stochastic transmission dynamic models are needed to quantify the uncertainty in estimates and predictions during outbreaks of infectious diseases. We previously developed a calibration method for stochastic epidemic compartmental models, called Multiple Shooting for Stochastic Systems (MSS), and demonstrated its comp...

    journal_title:Statistical methods in medical research

    pub_type: 杂志文章

    doi:10.1177/0962280218805780

    authors: Zimmer C,Leuba SI,Cohen T,Yaesoubi R

    更新日期:2019-12-01 00:00:00

  • A comparison of imputation strategies in cluster randomized trials with missing binary outcomes.

    abstract::In cluster randomized trials, clusters of subjects are randomized rather than subjects themselves, and missing outcomes are a concern as in individual randomized trials. We assessed strategies for handling missing data when analysing cluster randomized trials with a binary outcome; strategies included complete case, a...

    journal_title:Statistical methods in medical research

    pub_type: 杂志文章

    doi:10.1177/0962280214530030

    authors: Caille A,Leyrat C,Giraudeau B

    更新日期:2016-12-01 00:00:00

  • Sample size calculation for treatment effects in randomized trials with fixed cluster sizes and heterogeneous intraclass correlations and variances.

    abstract::When comparing two different kinds of group therapy or two individual treatments where patients within each arm are nested within care providers, clustering of observations may occur in both arms. The arms may differ in terms of (a) the intraclass correlation, (b) the outcome variance, (c) the cluster size, and (d) th...

    journal_title:Statistical methods in medical research

    pub_type: 杂志文章

    doi:10.1177/0962280214563100

    authors: Candel MJ,van Breukelen GJ

    更新日期:2015-10-01 00:00:00

  • Shared parameter models for joint analysis of longitudinal and survival data with left truncation due to delayed entry - Applications to cystic fibrosis.

    abstract::Many longitudinal studies observe time to occurrence of a clinical event such as death, while also collecting serial measurements of one or more biomarkers that are predictive of the event, or are surrogate outcomes of interest. Joint modeling can be used to examine the relationship between the biomarker and the event...

    journal_title:Statistical methods in medical research

    pub_type: 杂志文章

    doi:10.1177/0962280218764193

    authors: Schluchter MD,Piccorelli AV

    更新日期:2019-05-01 00:00:00

  • Estimating the dependence of mixed sensitive response types in randomized response technique.

    abstract::Sensitive questions are often involved in healthcare or medical survey research. Much empirical evidence has shown that the randomized response technique is useful for the collection of truthful responses. However, few studies have discussed methods to estimate the dependence of sensitive responses of multiple types. ...

    journal_title:Statistical methods in medical research

    pub_type: 杂志文章

    doi:10.1177/0962280219847492

    authors: Chu AM,So MK,Chan TW,Tiwari A

    更新日期:2020-03-01 00:00:00

  • Adaptive non-inferiority margins under observable non-constancy.

    abstract::A central assumption in the design and conduct of non-inferiority trials is that the active-control therapy will have the same degree of effectiveness in the planned non-inferiority trial as in the prior placebo-controlled trials used to define the non-inferiority margin. This is referred to as the 'constancy' assumpt...

    journal_title:Statistical methods in medical research

    pub_type: 杂志文章

    doi:10.1177/0962280218801134

    authors: Hanscom B,Hughes JP,Williamson BD,Donnell D

    更新日期:2019-10-01 00:00:00

  • Extending backcalculation to analyse BSE data.

    abstract::We review the origins of backcalculation (or back projection) methods developed for the analysis of AIDS (acquired immunodeficiency syndrome) incidence data. These techniques have been used extensively for >15 years to deconvolute clinical case incidence, given knowledge of the incubation period distribution, to obtai...

    journal_title:Statistical methods in medical research

    pub_type: 杂志文章,评审

    doi:10.1191/0962280203sm337ra

    authors: Donnelly CA,Ferguson NM,Ghani AC,Anderson RM

    更新日期:2003-06-01 00:00:00

  • Statistical methods for longitudinal and clustered designs with binary responses.

    abstract::Dependent binary response data arise frequently in practice due to repeated measurements in longitudinal studies or to subsampling primary sampling units as in fields such as teratology and ophthalmology. Several classes of approaches have recently been proposed to analyse such repeated binary outcome data. The differ...

    journal_title:Statistical methods in medical research

    pub_type: 杂志文章,评审

    doi:10.1177/096228029200100303

    authors: Neuhaus JM

    更新日期:1992-01-01 00:00:00

  • Joint nested frailty models for clustered recurrent and terminal events: An application to colonoscopy screening visits and colorectal cancer risks in Lynch Syndrome families.

    abstract::Joint models for recurrent and terminal events have not been yet developed for clustered data. The goals of our study are to develop a statistical framework for modelling clustered recurrent and terminal events and to perform dynamic predictions of the terminal event in family studies. We propose a joint nested frailt...

    journal_title:Statistical methods in medical research

    pub_type: 杂志文章

    doi:10.1177/0962280219863076

    authors: Choi YH,Jacqmin-Gadda H,Król A,Parfrey P,Briollais L,Rondeau V

    更新日期:2020-05-01 00:00:00

  • Assessing the reliability of ordered categorical scales using kappa-type statistics.

    abstract::Methods for the analysis of reliability of ordered categorical scales are discussed, focussing on the limitation of the single summary-weighted kappa coefficients. A symmetric matrix of kappa-type coefficients is suggested as an alternative. The method is proposed as being suitable for ordinal scale where there is no ...

    journal_title:Statistical methods in medical research

    pub_type: 杂志文章

    doi:10.1191/0962280205sm413oa

    authors: Roberts C,McNamee R

    更新日期:2005-10-01 00:00:00

  • Practical issues arising in an exploratory analysis evaluating progression-free survival as a surrogate endpoint for overall survival in advanced colorectal cancer.

    abstract::This paper is based on a conference presentation in which several authors presented results from analyses of the same dataset concerning the evaluation of progression-free survival (PFS) as a surrogate endpoint for overall survival in advanced colorectal cancer clinical trials. In evaluating a potential surrogate endp...

    journal_title:Statistical methods in medical research

    pub_type: 杂志文章

    doi:10.1177/0962280207081860

    authors: Hughes MD

    更新日期:2008-10-01 00:00:00

  • The application of multidimensional scaling methods to epidemiological data.

    abstract::This paper illustrates the use of multidimensional scaling methods (MDS) to examine space-time patterns in epidemic data. The paper begins by outlining the principles of MDS. The model is then formally specified and illustrated by application to two data sets. The first is partly a tutorial example. It uses monthly re...

    journal_title:Statistical methods in medical research

    pub_type: 杂志文章

    doi:10.1177/096228029500400202

    authors: Cliff AD,Haggett P,Smallman-Raynor MR,Stroup DF,Williamson GD

    更新日期:1995-06-01 00:00:00

  • Modelling breast cancer tumour growth for a stable disease population.

    abstract::Statistical models of breast cancer tumour progression have been used to further our knowledge of the natural history of breast cancer, to evaluate mammography screening in terms of mortality, to estimate overdiagnosis, and to estimate the impact of lead-time bias when comparing survival times between screen detected ...

    journal_title:Statistical methods in medical research

    pub_type: 杂志文章

    doi:10.1177/0962280217734583

    authors: Isheden G,Humphreys K

    更新日期:2019-03-01 00:00:00

  • Maximum likelihood estimation based on Newton-Raphson iteration for the bivariate random effects model in test accuracy meta-analysis.

    abstract::A bivariate generalised linear mixed model is often used for meta-analysis of test accuracy studies. The model is complex and requires five parameters to be estimated. As there is no closed form for the likelihood function for the model, maximum likelihood estimates for the parameters have to be obtained numerically. ...

    journal_title:Statistical methods in medical research

    pub_type: 杂志文章

    doi:10.1177/0962280219853602

    authors: Willis BH,Baragilly M,Coomar D

    更新日期:2020-04-01 00:00:00

  • Longitudinal prostate-specific antigen reference ranges: Choosing the underlying model of age-related changes.

    abstract::Serial measurements of prostate-specific antigen (PSA) are used as a biomarker for men diagnosed with prostate cancer following an active monitoring programme. Distinguishing pathological changes from natural age-related changes is not straightforward. Here, we compare four approaches to modelling age-related change i...

    journal_title:Statistical methods in medical research

    pub_type: 杂志文章

    doi:10.1177/0962280213503928

    authors: Simpkin AJ,Metcalfe C,Martin RM,Lane JA,Donovan JL,Hamdy FC,Neal DE,Tilling K

    更新日期:2016-10-01 00:00:00

  • Analysis of clustered data in receiver operating characteristic studies.

    abstract::Clustered data is not simply correlated data, but has its own unique aspects. In this paper, various methods for correlated receiver operating characteristic (ROC) curve data that have been extended specifically to clustered data are reviewed. For those methods that have not yet been extended, suggestions for their ap...

    journal_title:Statistical methods in medical research

    pub_type: 杂志文章,评审

    doi:10.1177/096228029800700402

    authors: Beam CA

    更新日期:1998-12-01 00:00:00

  • Unconditional tests for comparing two ordered multinomials.

    abstract::We consider two exact unconditional procedures to test the difference between two multinomials with ordered categorical data. Exact unconditional procedures are compared to other approaches based on the Wilcoxon mid-rank test and the proportional odds model. We use a real example from an arthritis pain study to illust...

    journal_title:Statistical methods in medical research

    pub_type: 杂志文章

    doi:10.1177/0962280212450957

    authors: Shan G,Ma C

    更新日期:2016-02-01 00:00:00

  • Allele-sharing among affected relatives: non-parametric methods for identifying genes.

    abstract::Non-parametric linkage analysis examines similarities among affected relatives in alleles of one or more genetic markers (pieces of DNA at known locations on a chromosome). The objective is to evaluate departures from the null hypothesis that the markers are not near a disease gene. Under the null hypothesis, Mendel's...

    journal_title:Statistical methods in medical research

    pub_type: 杂志文章,评审

    doi:10.1177/096228020101000103

    authors: Shih MC,Whittemore AS

    更新日期:2001-02-01 00:00:00

  • Inferential tools in penalized logistic regression for small and sparse data: A comparative study.

    abstract::This paper focuses on inferential tools in the logistic regression model fitted by the Firth penalized likelihood. In this context, the Likelihood Ratio statistic is often reported to be the preferred choice as compared to the 'traditional' Wald statistic. In this work, we consider and discuss a wider range of test st...

    journal_title:Statistical methods in medical research

    pub_type: 杂志文章

    doi:10.1177/0962280216661213

    authors: Siino M,Fasola S,Muggeo VM

    更新日期:2018-05-01 00:00:00

  • Semiparametric models for multilevel overdispersed count data with extra zeros.

    abstract::This study proposes semiparametric models for analysis of hierarchical count data containing excess zeros and overdispersion simultaneously. The methods discussed in this paper handle nonlinear covariate effects through flexible semiparametric multilevel regression techniques. This is performed by providing a comprehe...

    journal_title:Statistical methods in medical research

    pub_type: 杂志文章

    doi:10.1177/0962280216657376

    authors: Mahmoodi M,Moghimbeigi A,Mohammad K,Faradmal J

    更新日期:2018-04-01 00:00:00

  • Bayesian nonparametric mixed-effects joint model for longitudinal-competing risks data analysis in presence of multiple data features.

    abstract::Recently, the joint analysis of longitudinal and survival data has been an active research area. Most joint models focus on survival data with only one type of failure. The research on joint modeling of longitudinal and competing risks survival data is sparse. Even so, many joint models for this type of data assume pa...

    journal_title:Statistical methods in medical research

    pub_type: 杂志文章

    doi:10.1177/0962280215597939

    authors: Lu T

    更新日期:2017-10-01 00:00:00

  • Modeling fecundity in the presence of a sterile fraction using a semi-parametric transformation model for grouped survival data.

    abstract::The analysis of fecundity data is challenging and requires consideration of both highly timed and interrelated biologic processes in the context of essential behaviors such as sexual intercourse during the fertile window. Understanding human fecundity is further complicated by presence of a sterile population, i.e. co...

    journal_title:Statistical methods in medical research

    pub_type: 杂志文章

    doi:10.1177/0962280212438646

    authors: McLain AC,Sundaram R,Buck Louis GM

    更新日期:2016-02-01 00:00:00

  • Performance of informative priors skeptical of large treatment effects in clinical trials: A simulation study.

    abstract::One of the main advantages of Bayesian analyses of clinical trials is their ability to formally incorporate skepticism about large treatment effects through the use of informative priors. We conducted a simulation study to assess the performance of informative normal, Student- t, and beta distributions in estimating r...

    journal_title:Statistical methods in medical research

    pub_type: 杂志文章

    doi:10.1177/0962280215620828

    authors: Pedroza C,Han W,Truong VTT,Green C,Tyson JE

    更新日期:2018-01-01 00:00:00

  • On the power of the Cochran-Armitage test for trend in the presence of misclassification.

    abstract::The Cochran-Armitage (CA) test is commonly used in both epidemiology and genetics to test for linear trend in two-way tables with a binary outcome. There has been increasing interest in the power and size of the test and in determination of sample size, especially when there is potential misclassification in the 'expo...

    journal_title:Statistical methods in medical research

    pub_type: 杂志文章

    doi:10.1177/0962280211406424

    authors: Buonaccorsi JP,Laake P,Veierød MB

    更新日期:2014-06-01 00:00:00