Multilevel Intervention Stepped Wedge Designs (MLI-SWDs)

Multilevel interventions (MLIs) hold promise for reducing health inequities by intervening at multiple types of social determinants of health consistent with the socioecological model of health. In spite of their potential, methodological challenges related to study design compounded by a lack of tools for sample size calculation inhibit their development. We help address this gap by proposing the Multilevel Intervention Stepped Wedge Design (MLI-SWD), a hybrid experimental design which combines cluster-level (CL) randomization using a Stepped Wedge design (SWD) with independent individual-level (IL) randomization. The MLI-SWD is suitable for MLIs where the IL intervention has a low risk of interference between individuals in the same cluster, and it enables estimation of the component IL and CL treatment effects, their interaction, and the combined intervention effect. The MLI-SWD accommodates cross-sectional and cohort designs as well as both incomplete (clusters are not observed in every study period) and complete observation patterns. We adapt recent work using generalized estimating equations for SWD sample size calculation to the multilevel setting and provide an R package for power and sample size calculation. Furthermore, motivated by our experiences with the ongoing NC Works 4 Health study, we consider how to apply the MLI-SWD when individuals join clusters over the course of the study. This situation arises when unemployment MLIs include IL interventions that are delivered while the individual is unemployed. This extension requires carefully considering whether the study interventions will satisfy additional causal assumptions but could permit randomization in new settings

The application of exponential random graph models to collaboration networks in biomedical and health sciences: a review

Collaboration has become crucial in solving scientific problems in biomedical and health sciences. There is a growing interest in applying social network analysis to professional associations aiming to leverage expertise and resources for optimal synergy. As a set of computational and statistical methods for analyzing social networks, exponential random graph models (ERGMs) examine complex collaborative networks due to their uniqueness of allowing for non-independent variables in network modeling. This study took a review approach to collect and analyze ERGM applications in health sciences by following the protocol of a systematic review. We included a total of 30 studies. The bibliometric characteristics revealed significant authors, institutions, countries, funding agencies, and citation impact associated with the publications. In addition, we observed five types of ERGMs for network modeling (standard ERGM and its extensions—Bayesian ERGM, temporal ERGM, separable temporal ERGM, and multilevel ERGM). Most studies (80%) used the standard ERGM, which possesses only endogenous and exogenous variables examining either micro- (individual-based) or macro-level (organization-based) collaborations without exploring how the links between individuals and organizations contribute to the overall network structure. Our findings help researchers (a) understand the extant research landscape of ERGM applications in health sciences, (b) learn to control and predict connection occurrence in a collaborative network, and (c) better design ERGM-applied studies to examine complex relations and social system structure, which is native to professional collaborations

Biclustering with heterogeneous variance

In cancer research, as in all of medicine, it is important to classify patients into etiologically and therapeutically relevant subtypes to improve diagnosis and treatment. One way to do this is to use clustering methods to find subgroups of homogeneous individuals based on genetic profiles together with heuristic clinical analysis. A notable drawback of existing clustering methods is that they ignore the possibility that the variance of gene expression profile measurements can be heterogeneous across subgroups, and methods that do not consider heterogeneity of variance can lead to inaccurate subgroup prediction. Research has shown that hypervariability is a common feature among cancer subtypes. In this paper, we present a statistical approach that can capture both mean and variance structure in genetic data. We demonstrate the strength of our method in both synthetic data and in two cancer data sets. In particular, our method confirms the hypervariability of methylation level in cancer patients, and it detects clearer subgroup patterns in lung cancer data

Efficient and Robust Approaches for Analysis of SMARTs: Illustration using the ADAPT-R Trial

Personalized intervention strategies, in particular those that modify treatment based on a participant's own response, are a core component of precision medicine approaches. Sequential Multiple Assignment Randomized Trials (SMARTs) are growing in popularity and are specifically designed to facilitate the evaluation of sequential adaptive strategies, in particular those embedded within the SMART. Advances in efficient estimation approaches that are able to incorporate machine learning while retaining valid inference can allow for more precise estimates of the effectiveness of these embedded regimes. However, to the best of our knowledge, such approaches have not yet been applied as the primary analysis in SMART trials. In this paper, we present a robust and efficient approach using Targeted Maximum Likelihood Estimation (TMLE) for estimating and contrasting expected outcomes under the dynamic regimes embedded in a SMART, together with generating simultaneous confidence intervals for the resulting estimates. We contrast this method with two alternatives (G-computation and Inverse Probability Weighting estimators). The precision gains and robust inference achievable through the use of TMLE to evaluate the effects of embedded regimes are illustrated using both outcome-blind simulations and a real data analysis from the Adaptive Strategies for Preventing and Treating Lapses of Retention in HIV Care (ADAPT-R) trial (NCT02338739), a SMART with a primary aim of identifying strategies to improve retention in HIV care among people living with HIV in sub-Saharan Africa

Doubly robust learning for estimating individualized treatment with censored data

Individualized treatment rules recommend treatments based on individual patient characteristics in order to maximize clinical benefit. When the clinical outcome of interest is survival time, estimation is often complicated by censoring. We develop nonparametric methods for estimating an optimal individualized treatment rule in the presence of censored data. To adjust for censoring, we propose a doubly robust estimator which requires correct specification of either the censoring model or survival model, but not both; the method is shown to be Fisher consistent when either model is correct. Furthermore, we establish the convergence rate of the expected survival under the estimated optimal individualized treatment rule to the expected survival under the optimal individualized treatment rule. We illustrate the proposed methods using simulation study and data from a Phase III clinical trial on non-small cell lung cancer

Impact of gonadectomy on maturational changes in brain volume in adolescent macaques

Adolescence is a transitional period between childhood and adulthood characterized by significant changes in global and regional brain tissue volumes. It is also a period of increasing vulnerability to psychiatric illness. The relationship between these patterns and increased levels of circulating sex steroids during adolescence remains unclear. The objective of the current study was to determine whether gonadectomy, prior to puberty, alters adolescent brain development in male rhesus macaques. Ninety-six structural MRI scans were acquired from 12 male rhesus macaques (8 time points per animal over a two-year period). Six animals underwent gonadectomy and 6 animals underwent a sham operation at 29 months of age. Mixed-effects models were used to determine whether gonadectomy altered developmental trajectories of global and regional brain tissue volumes. We observed a significant effect of gonadectomy on the developmental trajectory of prefrontal gray matter (GM), with intact males showing peak volumes around 3.5 years of age with a subsequent decline. In contrast, prefrontal GM volumes continued to increase in gonadectomized males until the end of the study. We did not observe a significant effect of gonadectomy on prefrontal white matter or on any other global or regional brain tissue volumes, though we cannot rule out that effects might be detected in a larger sample. Results suggest that the prefrontal cortex is more vulnerable to gonadectomy than other brain regions

Medical Records-Based Postmarketing Safety Evaluation of Rare Events with Uncertain Status

We develop a simple statistic for comparing rates of rare adverse events between treatment groups in post-marketing safety studies where the events have uncertain status. In this setting, the statistic is asymptotically equivalent to the logrank statistic, but the limiting distribution has Poisson and binomial components instead of being Guassian. We develop two new procedures for computing critical values, a Gaussian approximation and a parametric bootstrap. Both numerical and asymptotic properties of the procedures are studied. The test procedures are demonstrated on a post-marketing safety study of the RotaTeq vaccine. This vaccine was developed to reduce the incidence of severe diarrhea in infants

Cell cycle plasticity underlies fractional resistance to palbociclib in ER+/HER2− breast tumor cells

The CDK4/6 inhibitor palbociclib blocks cell cycle progression in Estrogen receptor-positive, human epidermal growth factor 2 receptor-negative (ER+/HER2-) breast tumor cells. Despite the drug's success in improving patient outcomes, a small percentage of tumor cells continues to divide in the presence of palbociclib-a phenomenon we refer to as fractional resistance. It is critical to understand the cellular mechanisms underlying fractional resistance because the precise percentage of resistant cells in patient tissue is a strong predictor of clinical outcomes. Here, we hypothesize that fractional resistance arises from cell-to-cell differences in core cell cycle regulators that allow a subset of cells to escape CDK4/6 inhibitor therapy. We used multiplex, single-cell imaging to identify fractionally resistant cells in both cultured and primary breast tumor samples resected from patients. Resistant cells showed premature accumulation of multiple G1 regulators including E2F1, retinoblastoma protein, and CDK2, as well as enhanced sensitivity to pharmacological inhibition of CDK2 activity. Using trajectory inference approaches, we show how plasticity among cell cycle regulators gives rise to alternate cell cycle "paths" that allow individual tumor cells to escape palbociclib treatment. Understanding drivers of cell cycle plasticity, and how to eliminate resistant cell cycle paths, could lead to improved cancer therapies targeting fractionally resistant cells to improve patient outcomes

Detection of gene pathways with predictive power for breast cancer prognosis

<p>Abstract</p> <p>Background</p> <p>Prognosis is of critical interest in breast cancer research. Biomedical studies suggest that genomic measurements may have independent predictive power for prognosis. Gene profiling studies have been conducted to search for predictive genomic measurements. Genes have the inherent pathway structure, where pathways are composed of multiple genes with coordinated functions. The goal of this study is to identify gene pathways with predictive power for breast cancer prognosis. Since our goal is fundamentally different from that of existing studies, a new pathway analysis method is proposed.</p> <p>Results</p> <p>The new method advances beyond existing alternatives along the following aspects. First, it can assess the predictive power of gene pathways, whereas existing methods tend to focus on model fitting accuracy only. Second, it can account for the joint effects of multiple genes in a pathway, whereas existing methods tend to focus on the marginal effects of genes. Third, it can accommodate multiple heterogeneous datasets, whereas existing methods analyze a single dataset only. We analyze four breast cancer prognosis studies and identify 97 pathways with significant predictive power for prognosis. Important pathways missed by alternative methods are identified.</p> <p>Conclusions</p> <p>The proposed method provides a useful alternative to existing pathway analysis methods. Identified pathways can provide further insights into breast cancer prognosis.</p