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Tianmeng Lyu, Eric F Lock, Lynn E Eberly
High-dimensional linear classifiers, such as distance weighted discrimination (DWD) and versions of the support vector machine (SVM), are commonly used in biomedical research to distinguish groups of subjects based on a large number of features. However, their use is limited to applications where a single vector of features is measured for each subject. In practice, data are often multi-way, or measured over multiple dimensions. For example, metabolite abundance may be measured over multiple regions or tissues, or gene expression may be measured over multiple time points, for the same subjects...
January 23, 2017: Biostatistics
Abhishek Kaul, Ori Davidov, Shyamal D Peddada
SUMMARYThis paper is motivated by the recent interest in the analysis of high-dimensional microbiome data. A key feature of these data is the presence of "structural zeros" which are microbes missing from an observation vector due to an underlying biological process and not due to error in measurement. Typical notions of missingness are unable to model these structural zeros. We define a general framework which allows for structural zeros in the model and propose methods of estimating sparse high-dimensional covariance and precision matrices under this setup...
January 8, 2017: Biostatistics
Emily J Huang, Ethan X Fang, Daniel F Hanley, Michael Rosenblum
SUMMARYIn many randomized controlled trials, the primary analysis focuses on the average treatment effect and does not address whether treatment benefits are widespread or limited to a select few. This problem affects many disease areas, since it stems from how randomized trials, often the gold standard for evaluating treatments, are designed and analyzed. Our goal is to learn about the fraction who benefit from a new treatment using randomized trial data. We consider the case where the outcome is ordinal, with binary outcomes as a special case...
December 26, 2016: Biostatistics
Sebastian Meyer, Leonhard Held
SummaryRoutine public health surveillance of notifiable infectious diseases gives rise to weekly counts of reported cases-possibly stratified by region and/or age group. We investigate how an age-structured social contact matrix can be incorporated into a spatio-temporal endemic-epidemic model for infectious disease counts. To illustrate the approach, we analyze the spread of norovirus gastroenteritis over six age groups within the 12 districts of Berlin, 2011-2015, using contact data from the POLYMOD study...
December 26, 2016: Biostatistics
Duncan Lee, Sabyasachi Mukhopadhyay, Alastair Rushworth, Sujit K Sahu
SummaryIn the United Kingdom, air pollution is linked to around 40000 premature deaths each year, but estimating its health effects is challenging in a spatio-temporal study. The challenges include spatial misalignment between the pollution and disease data; uncertainty in the estimated pollution surface; and complex residual spatio-temporal autocorrelation in the disease data. This article develops a two-stage model that addresses these issues. The first stage is a spatio-temporal fusion model linking modeled and measured pollution data, while the second stage links these predictions to the disease data...
December 26, 2016: Biostatistics
Wei Fu, Jeffrey S Simonoff
SUMMARYTree methods (recursive partitioning) are a popular class of nonparametric methods for analyzing data. One extension of the basic tree methodology is the survival tree, which applies recursive partitioning to censored survival data. There are several existing survival tree methods in the literature, which are mainly designed for right-censored data. We propose two new survival trees for left-truncated and right-censored (LTRC) data, which can be seen as a generalization of the traditional survival tree for right-censored data...
December 26, 2016: Biostatistics
David Lenis, Cyrus F Ebnesajjad, Elizabeth A Stuart
SUMMARYOne of the main limitations of causal inference methods is that they rely on the assumption that all variables are measured without error. A popular approach for handling measurement error is simulation-extrapolation (SIMEX). However, its use for estimating causal effects have been examined only in the context of an additive, non-differential, and homoscedastic classical measurement error structure. In this article we extend the SIMEX methodology, in the context of a mean reverting measurement error structure, to a doubly robust estimator of the average treatment effect when a single covariate is measured with error but the outcome and treatment and treatment indicator are not...
December 19, 2016: Biostatistics
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January 2017: Biostatistics
Sunghwan Kim, Steffi Oesterreich, Seyoung Kim, Yongseok Park, George C Tseng
SummaryWith the rapid advances in technologies of microarray and massively parallel sequencing, data of multiple omics sources from a large patient cohort are now frequently seen in many consortium studies. Effective multi-level omics data integration has brought new statistical challenges. One important biological objective of such integrative analysis is to cluster patients in order to identify clinically relevant disease subtypes, which will form basis for tailored treatment and personalized medicine. Several methods have been proposed in the literature for this purpose, including the popular iCluster method used in many cancer applications...
January 2017: Biostatistics
Malka Gorfine, Yair Goldberg, Ya'acov Ritov
SummarySince survival data occur over time, often important covariates that we wish to consider also change over time. Such covariates are referred as time-dependent covariates. Quantile regression offers flexible modeling of survival data by allowing the covariates to vary with quantiles. This article provides a novel quantile regression model accommodating time-dependent covariates, for analyzing survival data subject to right censoring. Our simple estimation technique assumes the existence of instrumental variables...
January 2017: Biostatistics
Yu-Ru Su, Chong-Zhi Di, Li Hsu
SummaryThe development of next-generation sequencing technologies has allowed researchers to study comprehensively the contribution of genetic variation particularly rare variants to complex diseases. To date many sequencing analyses of rare variants have focused on marginal genetic effects and have not explored the potential role environmental factors play in modifying genetic risk. Analysis of gene-environment interaction (GxE) for rare variants poses considerable challenges because of variant rarity and paucity of subjects who carry the variants while being exposed...
January 2017: Biostatistics
Eva Petkova, Thaddeus Tarpey, Zhe Su, R Todd Ogden
In a randomized clinical trial (RCT), it is often of interest not only to estimate the effect of various treatments on the outcome, but also to determine whether any patient characteristic has a different relationship with the outcome, depending on treatment. In regression models for the outcome, if there is a non-zero interaction between treatment and a predictor, that predictor is called an "effect modifier". Identification of such effect modifiers is crucial as we move towards precision medicine, that is, optimizing individual treatment assignment based on patient measurements assessed when presenting for treatment...
January 2017: Biostatistics
Yoav Benjamini, Rami Cohen
SummaryHaving identified that the lack of replicability of results in earlier phases of clinical medical research stems largely from unattended selective inference, we offer a new hierarchical weighted false discovery rate controlling testing procedure alongside the single-level weighted procedure. These address the special structure of clinical research, where the comparisons of treatments involve both primary and secondary endpoints, by assigning weights that reflect the relative importance of the endpoints in the error being controlled...
January 2017: Biostatistics
Malka Gorfine, Nadia Bordo, Li Hsu
SummaryConsider a popular case-control family study where individuals with a disease under study (case probands) and individuals who do not have the disease (control probands) are randomly sampled from a well-defined population. Possibly right-censored age at onset and disease status are observed for both probands and their relatives. For example, case probands are men diagnosed with prostate cancer, control probands are men free of prostate cancer, and the prostate cancer history of the fathers of the probands is also collected...
January 2017: Biostatistics
Hong Zhu, Jing Ning, Yu Shen, Jing Qin
In this article, we consider methods for assessing covariate effects on survival outcome in the target population when data are collected under prevalent sampling. We investigate a flexible semiparametric density ratio model without the constraints of the constant disease incidence rate and discrete covariates as required in Shen and others 2012. For inference, we introduce two likelihood approaches with distinct computational algorithms. We first develop a full likelihood approach to obtain the most efficient estimators by an iterative algorithm...
January 2017: Biostatistics
Jason Roy, Kirsten J Lum, Michael J Daniels
Marginal structural models (MSMs) are a general class of causal models for specifying the average effect of treatment on an outcome. These models can accommodate discrete or continuous treatments, as well as treatment effect heterogeneity (causal effect modification). The literature on estimation of MSM parameters has been dominated by semiparametric estimation methods, such as inverse probability of treatment weighted (IPTW). Likelihood-based methods have received little development, probably in part due to the need to integrate out confounders from the likelihood and due to reluctance to make parametric modeling assumptions...
January 2017: Biostatistics
Ting-Huei Chen, Wei Sun
SummaryA large number of cancer drugs have been developed to target particular genes/pathways that are crucial for cancer growth. Drugs that share a molecular target may also have some common predictive omic features, e.g., somatic mutations or gene expression. Therefore, it is desirable to analyze these drugs as a group to identify the associated omic features, which may provide biological insights into the underlying drug response. Furthermore, these omic features may be robust predictors for any drug sharing the same target...
January 2017: Biostatistics
Marla Johnson, Elizabeth Purdom
Sequencing of messenger RNA (mRNA) can provide estimates of the levels of individual isoforms within the cell. It remains to adapt many standard statistical methods commonly used for analyzing gene expression levels to take advantage of this additional information. One novel question is whether we can find clusters of samples that are distinguished not by their gene expression but by their isoform usage. We propose a novel approach for clustering mRNA-Seq data that identifies such clusters. We show via simulation that our methods are more sensitive to finding clusters based on isoform usage than standard clustering techniques...
October 25, 2016: Biostatistics
F Towfic, R Kusko, B Zeskind
The article by Nygaard et al proposes that applying batch correction approaches to microarray data from studies with unbalanced designs may inadvertently exaggerate the differences observed. In seeking to illustrate their point, Nygaard et al. utilized a dataset (GSE61901) from a study we published (Towfic and others, 2014) and showed that one analysis pipeline utilizing the traditional approach to batch correction (ComBat) yielded over 1000 differentially expressed probesets, while an alternative approach proposed by Nygaard et al (utilizing batch as a fixed effect and averaging technical replicates) recovered 11 differentially expressed probesets...
October 25, 2016: Biostatistics
Matthew Stephens
SummaryWe introduce a new Empirical Bayes approach for large-scale hypothesis testing, including estimating false discovery rates (FDRs), and effect sizes. This approach has two key differences from existing approaches to FDR analysis. First, it assumes that the distribution of the actual (unobserved) effects is unimodal, with a mode at 0. This "unimodal assumption" (UA), although natural in many contexts, is not usually incorporated into standard FDR analysis, and we demonstrate how incorporating it brings many benefits...
October 17, 2016: Biostatistics
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