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Linear regressions with period and group fixed effects are widely used to estimate treatment effects. We show that they estimate weighted sums of the average treatment effects (ATE) in each group and period, with weights that may be negative. Due to the negative weights, the linear regression coefficient may for instance be negative while all the ATEs are positive. We propose another estimator that solves this issue. In the two applications we revisit, it is significantly different from the linear regression estimator.

Background Mediation analysis tests whether the relationship between two variables is explained by a third intermediate variable. We sought to describe the usage and reporting of mediation analysis with time-to-event outcomes in published healthcare research. Methods A systematic search of Medline, Embase, and Web of Science was executed in December 2016 to identify applications of mediation analysis to healthcare research involving a clinically relevant time-to-event outcome. We summarized usage over time and reporting of important methodological characteristics. Results We included 149 primary studies, published from 1997 to 2016. Most studies were published after 2011 ( n  = 110, 74%), and the annual number of studies nearly doubled in the last year (from n  = 21 to n  = 40). A traditional approach (causal steps or change in coefficient) was most commonly taken ( n  = 87, 58%), and the majority of studies ( n  = 114, 77%) used a Cox Proportional Hazards regression for the outcome. Few studies ( n  = 52, 35%) mentioned any of the assumptions or limitations fundamental to a causal interpretation of mediation analysis. Conclusion There is increasing use of mediation analysis with time-to-event outcomes. Current usage is limited by reliance on traditional methods and the Cox Proportional Hazards model, as well as low rates of reporting of underlying assumptions. There is a need for formal criteria to aid authors, reviewers, and readers reporting or appraising such studies.

Mediation analysis with high-dimensional DNA methylation markers is important in identifying epigenetic pathways between environmental exposures and health outcomes. There have been some methodology developments of mediation analysis with high-dimensional mediators. However, high-dimensional mediation analysis methods for time-to-event outcome data are still yet to be developed. To address these challenges, we propose a new high-dimensional mediation analysis procedure for survival models by incorporating sure independent screening and minimax concave penalty techniques for variable selection, with the Sobel and the joint method for significance test of indirect effect. The simulation studies show good performance in identifying correct biomarkers, false discovery rate control, and minimum estimation bias of the proposed procedure. We also apply this approach to study the causal pathway from smoking to overall survival among lung cancer patients potentially mediated by 365,307 DNA methylations in the TCGA lung cancer cohort. Mediation analysis using a Cox proportional hazards model estimates that patients who have serious smoking history increase the risk of lung cancer through methylation markers including cg21926276, cg27042065, and cg26387355 with significant hazard ratios of 1.2497(95%CI: 1.1121, 1.4045), 1.0920(95%CI: 1.0170, 1.1726), and 1.1489(95%CI: 1.0518, 1.2550), respectively. The three methylation sites locate in the three genes which have been showed to be associated with lung cancer event or overall survival. However, the three CpG sites (cg21926276, cg27042065 and cg26387355) have not been reported, which are newly identified as the potential novel epigenetic markers linking smoking and survival of lung cancer patients. Collectively, the proposed high-dimensional mediation analysis procedure has good performance in mediator selection and indirect effect estimation.

Background The natural indirect effect (NIE) and mediation proportion (MP) are two measures of primary interest in mediation analysis. The standard approach for mediation analysis is through the product method, which involves a model for the outcome conditional on the mediator and exposure and another model describing the exposure–mediator relationship. The purpose of this article is to comprehensively develop and investigate the finite-sample performance of NIE and MP estimators via the product method. Methods With four common data types with a continuous/binary outcome and a continuous/binary mediator, we propose closed-form interval estimators for NIE and MP via the theory of multivariate delta method, and evaluate its empirical performance relative to the bootstrap approach. In addition, we have observed that the rare outcome assumption is frequently invoked to approximate the NIE and MP with a binary outcome, although this approximation may lead to non-negligible bias when the outcome is common. We therefore introduce the exact expressions for NIE and MP with a binary outcome without the rare outcome assumption and compare its performance with the approximate estimators. Results Simulation studies suggest that the proposed interval estimator provides satisfactory coverage when the sample size ≥500 for the scenarios with a continuous outcome and sample size ≥20,000 and number of cases ≥500 for the scenarios with a binary outcome. In the binary outcome scenarios, the approximate estimators based on the rare outcome assumption worked well when outcome prevalence less than 5% but could lead to substantial bias when the outcome is common; in contrast, the exact estimators always perform well under all outcome prevalences considered. Conclusions Under samples sizes commonly encountered in epidemiology and public health research, the proposed interval estimator is valid for constructing confidence interval. For a binary outcome, the exact estimator without the rare outcome assumption is more robust and stable to estimate NIE and MP. An R package mediateP is developed to implement the methods for point and variance estimation discussed in this paper.