1
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Young JG. Story-led Causal Inference. Epidemiology 2024; 35:289-294. [PMID: 38630506 DOI: 10.1097/ede.0000000000001704] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/19/2024]
Affiliation(s)
- Jessica G Young
- From the Department of Population Medicine, Harvard Medical School and Harvard Pilgrim Health Care Institute, Boston, MA
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2
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Stensrud MJ, Nevo D, Obolski U. Distinguishing Immunologic and Behavioral Effects of Vaccination. Epidemiology 2024; 35:154-163. [PMID: 38180882 DOI: 10.1097/ede.0000000000001699] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2024]
Abstract
The interpretation of vaccine efficacy estimands is subtle, even in randomized trials designed to quantify the immunologic effects of vaccination. In this article, we introduce terminology to distinguish between different vaccine efficacy estimands and clarify their interpretations. This allows us to explicitly consider the immunologic and behavioral effects of vaccination, and establish that policy-relevant estimands can differ substantially from those commonly reported in vaccine trials. We further show that a conventional vaccine trial allows the identification and estimation of different vaccine estimands under plausible conditions if one additional post-treatment variable is measured. Specifically, we utilize a "belief variable" that indicates the treatment an individual believed they had received. The belief variable is similar to "blinding assessment" variables that are occasionally collected in placebo-controlled trials in other fields. We illustrate the relations between the different estimands, and their practical relevance, in numerical examples based on an influenza vaccine trial.
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Affiliation(s)
- Mats J Stensrud
- From the Department of Mathematics, École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
| | - Daniel Nevo
- Department of Statistics and Operations Research, Tel Aviv University, Tel Aviv, Israel
| | - Uri Obolski
- School of Public Health, Tel Aviv University, Tel Aviv, Israel
- Porter School of the Environment and Earth Sciences, Tel Aviv University, Tel Aviv, Israel
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3
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Janvin M, Young JG, Ryalen PC, Stensrud MJ. Causal inference with recurrent and competing events. LIFETIME DATA ANALYSIS 2024; 30:59-118. [PMID: 37173588 PMCID: PMC10764453 DOI: 10.1007/s10985-023-09594-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/27/2021] [Accepted: 02/14/2023] [Indexed: 05/15/2023]
Abstract
Many research questions concern treatment effects on outcomes that can recur several times in the same individual. For example, medical researchers are interested in treatment effects on hospitalizations in heart failure patients and sports injuries in athletes. Competing events, such as death, complicate causal inference in studies of recurrent events because once a competing event occurs, an individual cannot have more recurrent events. Several statistical estimands have been studied in recurrent event settings, with and without competing events. However, the causal interpretations of these estimands, and the conditions that are required to identify these estimands from observed data, have yet to be formalized. Here we use a formal framework for causal inference to formulate several causal estimands in recurrent event settings, with and without competing events. When competing events exist, we clarify when commonly used classical statistical estimands can be interpreted as causal quantities from the causal mediation literature, such as (controlled) direct effects and total effects. Furthermore, we show that recent results on interventionist mediation estimands allow us to define new causal estimands with recurrent and competing events that may be of particular clinical relevance in many subject matter settings. We use causal directed acyclic graphs and single world intervention graphs to illustrate how to reason about identification conditions for the various causal estimands based on subject matter knowledge. Furthermore, using results on counting processes, we show that our causal estimands and their identification conditions, which are articulated in discrete time, converge to classical continuous time counterparts in the limit of fine discretizations of time. We propose estimators and establish their consistency for the various identifying functionals. Finally, we use the proposed estimators to compute the effect of blood pressure lowering treatment on the recurrence of acute kidney injury using data from the Systolic Blood Pressure Intervention Trial.
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Affiliation(s)
- Matias Janvin
- Department of Mathematics, École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland.
| | - Jessica G Young
- Department of Population Medicine, Harvard Medical School and Harvard Pilgrim Health Care Institute, Boston, USA
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, USA
- CAUSALab, Harvard T.H. Chan School of Public Health, Boston, USA
| | - Pål C Ryalen
- Department of Biostatistics, University of Oslo, Oslo, Norway
| | - Mats J Stensrud
- Department of Mathematics, École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
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4
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Breum MS, Munch A, Gerds TA, Martinussen T. Estimation of separable direct and indirect effects in a continuous-time illness-death model. LIFETIME DATA ANALYSIS 2024; 30:143-180. [PMID: 37270750 PMCID: PMC10764601 DOI: 10.1007/s10985-023-09601-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/14/2022] [Accepted: 04/19/2023] [Indexed: 06/05/2023]
Abstract
In this article we study the effect of a baseline exposure on a terminal time-to-event outcome either directly or mediated by the illness state of a continuous-time illness-death process with baseline covariates. We propose a definition of the corresponding direct and indirect effects using the concept of separable (interventionist) effects (Robins and Richardson in Causality and psychopathology: finding the determinants of disorders and their cures, Oxford University Press, 2011; Robins et al. in arXiv:2008.06019 , 2021; Stensrud et al. in J Am Stat Assoc 117:175-183, 2022). Our proposal generalizes Martinussen and Stensrud (Biometrics 79:127-139, 2023) who consider similar causal estimands for disentangling the causal treatment effects on the event of interest and competing events in the standard continuous-time competing risk model. Unlike natural direct and indirect effects (Robins and Greenland in Epidemiology 3:143-155, 1992; Pearl in Proceedings of the seventeenth conference on uncertainty in artificial intelligence, Morgan Kaufmann, 2001) which are usually defined through manipulations of the mediator independently of the exposure (so-called cross-world interventions), separable direct and indirect effects are defined through interventions on different components of the exposure that exert their effects through distinct causal mechanisms. This approach allows us to define meaningful mediation targets even though the mediating event is truncated by the terminal event. We present the conditions for identifiability, which include some arguably restrictive structural assumptions on the treatment mechanism, and discuss when such assumptions are valid. The identifying functionals are used to construct plug-in estimators for the separable direct and indirect effects. We also present multiply robust and asymptotically efficient estimators based on the efficient influence functions. We verify the theoretical properties of the estimators in a simulation study, and we demonstrate the use of the estimators using data from a Danish registry study.
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Affiliation(s)
- Marie Skov Breum
- Section of Biostatistics, Department of Public Health, University of Copenhagen, Copenhagen, Denmark.
| | - Anders Munch
- Section of Biostatistics, Department of Public Health, University of Copenhagen, Copenhagen, Denmark
| | - Thomas A Gerds
- Section of Biostatistics, Department of Public Health, University of Copenhagen, Copenhagen, Denmark
| | - Torben Martinussen
- Section of Biostatistics, Department of Public Health, University of Copenhagen, Copenhagen, Denmark
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5
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Le Coënt Q, Legrand C, Rondeau V. Time-to-event surrogate endpoint validation using mediation analysis and meta-analytic data. Biostatistics 2023; 25:98-116. [PMID: 36398615 DOI: 10.1093/biostatistics/kxac044] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2021] [Revised: 10/24/2022] [Accepted: 10/25/2022] [Indexed: 12/17/2023] Open
Abstract
With the ongoing development of treatments and the resulting increase in survival in oncology, clinical trials based on endpoints such as overall survival may require long follow-up periods to observe sufficient events and ensure adequate statistical power. This increase in follow-up time may compromise the feasibility of the study. The use of surrogate endpoints instead of final endpoints may be attractive for these studies. However, before a surrogate can be used in a clinical trial, it must be statistically validated. In this article, we propose an approach to validate surrogates when both the surrogate and final endpoints are censored event times. This approach is developed for meta-analytic data and uses a mediation analysis to decompose the total effect of the treatment on the final endpoint as a direct effect and an indirect effect through the surrogate. The meta-analytic nature of the data is accounted for in a joint model with random effects at the trial level. The proportion of the indirect effect over the total effect of the treatment on the final endpoint can be computed from the parameters of the model and used as a measure of surrogacy. We applied this method to investigate time-to-relapse as a surrogate endpoint for overall survival in resectable gastric cancer.
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Affiliation(s)
- Quentin Le Coënt
- Department of Biostatistics, Bordeaux Population Health Research Center, INSERM U1219, 146 rue Léo Saignat, 33076 Bordeaux, France
| | - Catherine Legrand
- ISBA/LIDAM, UCLouvain, 20 Voie du Roman Pays, B-1348 Louvain-la-Neuve, Belgium
| | - Virginie Rondeau
- Department of Biostatistics, Bordeaux Population Health Research Center, INSERM U1219, 146 rue Léo Saignat, 33076 Bordeaux, France
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6
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Niu F, Zheng C, Liu L. Exploring causal mechanisms and quantifying direct and indirect effects using a joint modeling approach for recurrent and terminal events. Stat Med 2023; 42:4028-4042. [PMID: 37461207 PMCID: PMC11075700 DOI: 10.1002/sim.9846] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2022] [Revised: 06/21/2023] [Accepted: 07/01/2023] [Indexed: 09/05/2023]
Abstract
Recurrent events are commonly encountered in biomedical studies. In many situations, there exist terminal events, such as death, which are potentially related to the recurrent events. Joint models of recurrent and terminal events have been proposed to address the correlation between recurrent events and terminal events. However, there is a dearth of suitable methods to rigorously investigate the causal mechanisms between specific exposures, recurrent events, and terminal events. For example, it is of interest to know how much of the total effect of the primary exposure of interest on the terminal event is through the recurrent events, and whether preventing recurrent event occurrences could lead to better overall survival. In this work, we propose a formal causal mediation analysis method to compute the natural direct and indirect effects. A novel joint modeling approach is used to take the recurrent event process as the mediator and the survival endpoint as the outcome. This new joint modeling approach allows us to relax the commonly used "sequential ignorability" assumption. Simulation studies show that our new model has good finite sample performance in estimating both model parameters and mediation effects. We apply our method to an AIDS study to evaluate how much of the comparative effectiveness of the two treatments and the effect of CD4 counts on the overall survival are mediated by recurrent opportunistic infections.
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Affiliation(s)
- Fang Niu
- Department of Biostatistics, University of Nebraska Medical Center, Nebraska, U.S.A
| | - Cheng Zheng
- Department of Biostatistics, University of Nebraska Medical Center, Nebraska, U.S.A
| | - Lei Liu
- Division of Biostatistics, Washington University in St. Louis, Missouri, U.S.A
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7
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Li Y, Mathur MB, Solomon DH, Ridker PM, Glynn RJ, Yoshida K. Effect Measure Modification by Covariates in Mediation: Extending Regression-based Causal Mediation Analysis. Epidemiology 2023; 34:661-672. [PMID: 37527449 PMCID: PMC10468257 DOI: 10.1097/ede.0000000000001643] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/03/2023]
Abstract
Existing methods for regression-based mediation analysis assume that the exposure-mediator effect, exposure-outcome effect, and mediator-outcome effect are constant across levels of the baseline characteristics of patients. However, investigators often have insight into how these underlying effects may be modified by baseline characteristics and are interested in how the resulting mediation effects, such as the natural direct effect (NDE), the natural indirect effect. (NIE), and the proportion mediated, are modified by these baseline characteristics. Motivated by an empirical example of anti-interleukin-1 therapy's benefit on incident anemia reduction and its mediation by an early change in an inflammatory biomarker, we extended the closed-form regression-based causal mediation analysis with effect measure modification (EMM). Using a simulated numerical example, we demonstrated that naive analysis without considering EMM can give biased estimates of NDE and NIE and visually illustrated how baseline characteristics affect the presence and magnitude of EMM of NDE and NIE. We then applied the extended method to the empirical example informed by pathophysiologic insights into potential EMM by age, diabetes, and baseline inflammation. We found that the proportion modified through the early post-treatment inflammatory biomarker was greater for younger, nondiabetic patients with lower baseline level of inflammation, suggesting differential usefulness of the early post-treatment inflammatory biomarker in monitoring patients depending on baseline characteristics. To facilitate the adoption of EMM considerations in causal mediation analysis by the wider clinical and epidemiologic research communities, we developed a free- and open-source R package, regmedint.
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Affiliation(s)
- Yi Li
- Department of Epidemiology, Biostatistics and Occupational Health, School of Population and Global Health, Faculty of Medicine, McGill University, Montreal, QC, Canada
- Division of Rheumatology, Inflammation, and Immunity, Department of Medicine, Brigham and Women’s Hospital, Boston, MA, USA
| | - Maya B. Mathur
- Quantitative Science Unit, Department of Medicine, Stanford University, Palo Alto, CA, USA
| | - Daniel H. Solomon
- Division of Rheumatology, Inflammation, and Immunity, Department of Medicine, Brigham and Women’s Hospital, Boston, MA, USA
- Department of Medicine, Harvard Medical School, Boston, MA, USA
- Division of Pharmacoepidemiology and Pharmacoeconomics, Department of Medicine, Brigham and Women’s Hospital, Boston, MA, USA
| | - Paul M. Ridker
- Department of Medicine, Harvard Medical School, Boston, MA, USA
- Division of Preventive Medicine, Department of Medicine, Brigham and Women’s Hospital, Boston, MA, USA
- Division of Cardiovascular Medicine, Department of Medicine, Brigham and Women’s Hospital, Boston, MA, USA
| | - Robert J. Glynn
- Department of Medicine, Harvard Medical School, Boston, MA, USA
- Division of Pharmacoepidemiology and Pharmacoeconomics, Department of Medicine, Brigham and Women’s Hospital, Boston, MA, USA
- Division of Preventive Medicine, Department of Medicine, Brigham and Women’s Hospital, Boston, MA, USA
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Kazuki Yoshida
- Division of Rheumatology, Inflammation, and Immunity, Department of Medicine, Brigham and Women’s Hospital, Boston, MA, USA
- Department of Medicine, Harvard Medical School, Boston, MA, USA
- OM1, Inc. MA, USA
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8
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Zeng S, Lange EC, Archie EA, Campos FA, Alberts SC, Li F. A Causal Mediation Model for Longitudinal Mediators and Survival Outcomes with an Application to Animal Behavior. JOURNAL OF AGRICULTURAL, BIOLOGICAL, AND ENVIRONMENTAL STATISTICS 2023; 28:197-218. [PMID: 37415781 PMCID: PMC10321498 DOI: 10.1007/s13253-022-00490-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/15/2021] [Revised: 01/26/2022] [Accepted: 01/28/2022] [Indexed: 07/08/2023]
Abstract
In animal behavior studies, a common goal is to investigate the causal pathways between an exposure and outcome, and a mediator that lies in between. Causal mediation analysis provides a principled approach for such studies. Although many applications involve longitudinal data, the existing causal mediation models are not directly applicable to settings where the mediators are measured on irregular time grids. In this paper, we propose a causal mediation model that accommodates longitudinal mediators on arbitrary time grids and survival outcomes simultaneously. We take a functional data analysis perspective and view longitudinal mediators as realizations of underlying smooth stochastic processes. We define causal estimands of direct and indirect effects accordingly and provide corresponding identification assumptions. We employ a functional principal component analysis approach to estimate the mediator process and propose a Cox hazard model for the survival outcome that flexibly adjusts the mediator process. We then derive a g-computation formula to express the causal estimands using the model coefficients. The proposed method is applied to a longitudinal data set from the Amboseli Baboon Research Project to investigate the causal relationships between early adversity, adult physiological stress responses, and survival among wild female baboons. We find that adversity experienced in early life has a significant direct effect on females' life expectancy and survival probability, but find little evidence that these effects were mediated by markers of the stress response in adulthood. We further developed a sensitivity analysis method to assess the impact of potential violation to the key assumption of sequential ignorability. Supplementary materials accompanying this paper appear on-line.
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Affiliation(s)
| | | | - Elizabeth A Archie
- Department of Biological Sciences, University of Notre Dame, Notre Dame, IN, USA
| | - Fernando A Campos
- Department of Antropology, University of Texas at San Antonio, San Antonio, TX, USA
| | - Susan C Alberts
- Department of Biology, Duke University, Durham, NC, USA.; Department of Evolutionary Anthropology, Duke University, Durham, NC, USA
| | - Fan Li
- Department of Statistical Science, Duke University, 214 Old Chemistry Building, Durham, NC 27708, USA
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9
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Martinussen T, Stensrud MJ. Estimation of separable direct and indirect effects in continuous time. Biometrics 2023; 79:127-139. [PMID: 34506039 DOI: 10.1111/biom.13559] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2020] [Revised: 08/04/2021] [Accepted: 08/26/2021] [Indexed: 11/29/2022]
Abstract
Many research questions involve time-to-event outcomes that can be prevented from occurring due to competing events. In these settings, we must be careful about the causal interpretation of classical statistical estimands. In particular, estimands on the hazard scale, such as ratios of cause-specific or subdistribution hazards, are fundamentally hard to interpret causally. Estimands on the risk scale, such as contrasts of cumulative incidence functions, do have a clear causal interpretation, but they only capture the total effect of the treatment on the event of interest; that is, effects both through and outside of the competing event. To disentangle causal treatment effects on the event of interest and competing events, the separable direct and indirect effects were recently introduced. Here we provide new results on the estimation of direct and indirect separable effects in continuous time. In particular, we derive the nonparametric influence function in continuous time and use it to construct an estimator that has certain robustness properties. We also propose a simple estimator based on semiparametric models for the two cause-specific hazard functions. We describe the asymptotic properties of these estimators and present results from simulation studies, suggesting that the estimators behave satisfactorily in finite samples. Finally, we reanalyze the prostate cancer trial from Stensrud et al. (2020).
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Affiliation(s)
| | - Mats Julius Stensrud
- Department of Mathematics, École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
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10
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Yan Y, Ren M, de Leon A. Measurement error correction in mediation analysis under the additive hazards model. COMMUN STAT-SIMUL C 2023. [DOI: 10.1080/03610918.2023.2170412] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Affiliation(s)
- Ying Yan
- School of Mathematics, Sun Yat-sen University, Guangzhou, China
| | - Mingchen Ren
- Department of Mathematics and Statistics, University of Calgary, Calgary, Canada
| | - Alexander de Leon
- Department of Mathematics and Statistics, University of Calgary, Calgary, Canada
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11
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Tanner KT, Sharples LD, Daniel RM, Keogh RH. Methods of analysis for survival outcomes with time-updated mediators, with application to longitudinal disease registry data. Stat Methods Med Res 2022; 31:1959-1975. [PMID: 35711168 PMCID: PMC9523823 DOI: 10.1177/09622802221107104] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Mediation analysis is a useful tool to illuminate the mechanisms through which an exposure affects an outcome but statistical challenges exist with time-to-event outcomes and longitudinal observational data. Natural direct and indirect effects cannot be identified when there are exposure-induced confounders of the mediator-outcome relationship. Previous measurements of a repeatedly-measured mediator may themselves confound the relationship between the mediator and the outcome. To overcome these obstacles, two recent methods have been proposed, one based on path-specific effects and one based on an additive hazards model and the concept of exposure splitting. We investigate these techniques, focusing on their application to observational datasets. We apply both methods to an analysis of the UK Cystic Fibrosis Registry dataset to identify how much of the relationship between onset of cystic fibrosis-related diabetes and subsequent survival acts through pulmonary function. Statistical properties of the methods are investigated using simulation. Both methods produce unbiased estimates of indirect and direct effects in scenarios consistent with their stated assumptions but, if the data are measured infrequently, estimates may be biased. Findings are used to highlight considerations in the interpretation of the observational data analysis.
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Affiliation(s)
- Kamaryn T Tanner
- Department of Medical Statistics, London School of Hygiene and Tropical Medicine, UK
- Kamaryn T Tanner, London School of Hygiene and Tropical Medicine, Dept of Medical Statistics, London WC1E 7HT, UK.
| | - Linda D Sharples
- Department of Medical Statistics, London School of Hygiene and Tropical Medicine, UK
| | | | - Ruth H Keogh
- Department of Medical Statistics, London School of Hygiene and Tropical Medicine, UK
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12
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Zheng C, Liu L. Quantifying direct and indirect effect for longitudinal mediator and survival outcome using joint modeling approach. Biometrics 2022; 78:1233-1243. [PMID: 33871871 PMCID: PMC8523594 DOI: 10.1111/biom.13475] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2020] [Revised: 03/03/2021] [Accepted: 04/08/2021] [Indexed: 12/01/2022]
Abstract
Longitudinal biomarkers are widely used in biomedical and translational researches to monitor the progressions of diseases. Methods have been proposed to jointly model longitudinal data and survival data, but its causal mechanism is yet to be investigated rigorously. Understanding how much of the total treatment effect is through the biomarker is important in understanding the treatment mechanism and evaluating the biomarker. In this work, we propose a causal mediation analysis method to compute the direct and indirect effects, when a joint modeling approach is used to take the longitudinal biomarker as the mediator and the survival endpoint as the outcome. Such a joint modeling approach allows us to relax the commonly used "sequential ignorability" assumption. We demonstrate how to evaluate longitudinally measured biomarkers using our method with two case studies, an AIDS study and a liver cirrhosis study.
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Affiliation(s)
- Cheng Zheng
- Department of Biostatistics, University of Nebraska Medical Center, Omaha, Nebraska, USA
| | - Lei Liu
- Division of Biostatistics, Washington University in St. Louis, St. Louis, Missouri, USA
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13
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Tai AS, Lin PH, Huang YT, Lin SH. Path-specific effects in the presence of a survival outcome and causally ordered multiple mediators with application to genomic data. Stat Methods Med Res 2022; 31:1916-1933. [PMID: 35635267 DOI: 10.1177/09622802221104239] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
Causal multimediation analysis (i.e. the causal mediation analysis with multiple mediators) is critical for understanding the effectiveness of interventions, especially in medical research. Deriving the path-specific effects of exposure on the outcome through a set of mediators can provide detail about the causal mechanism of interest However, existing models are usually restricted to partial decomposition, which can only be used to evaluate the cumulative effect of several paths. In genetics studies, partial decomposition fails to reflect the real causal effects mediated by genes, especially in complex gene regulatory networks. Moreover, because of the lack of a generalized identification procedure, the current multimediation analysis cannot be applied to the estimation of path-specific effects for any number of mediators. In this study, we derive the interventional analogs of path-specific effect for complete decomposition to address the difficulty of nonidentifiability. On the basis of two survival models of the outcome, we derive the generalized analytic forms for interventional analogs of path-specific effects by assuming the normal distributions of mediators. We apply the new methodology to investigate the causal mechanism of signature genes in lung cancer based on the cell cycle pathway, and the results clarify the gene pathway in cancer.
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Affiliation(s)
- An-Shun Tai
- Department of Statistics, 34912National Cheng Kung University, Tainan.,Institute of Statistics, 34914National Yang Ming Chiao Tung University, Hsin-Chu
| | - Pei-Hsuan Lin
- Institute of Statistics, 34914National Yang Ming Chiao Tung University, Hsin-Chu
| | - Yen-Tsung Huang
- Institute of Statistical Science, 38017Academia Sinica, Taipei
| | - Sheng-Hsuan Lin
- Institute of Statistics, 34914National Yang Ming Chiao Tung University, Hsin-Chu
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14
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Stensrud MJ, Dukes O. Translating questions to estimands in randomized clinical trials with intercurrent events. Stat Med 2022; 41:3211-3228. [PMID: 35578779 PMCID: PMC9321763 DOI: 10.1002/sim.9398] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2021] [Revised: 03/02/2022] [Accepted: 03/14/2022] [Indexed: 11/08/2022]
Abstract
Intercurrent (post‐treatment) events occur frequently in randomized trials, and investigators often express interest in treatment effects that suitably take account of these events. Contrasts that naively condition on intercurrent events do not have a straight‐forward causal interpretation, and the practical relevance of other commonly used approaches is debated. In this work, we discuss how to formulate and choose an estimand, beyond the marginal intention‐to‐treat effect, from the point of view of a decision maker and drug developer. In particular, we argue that careful articulation of a practically useful research question should either reflect decision making at this point in time or future drug development. Indeed, a substantially interesting estimand is simply a formalization of the (plain English) description of a research question. A common feature of estimands that are practically useful is that they correspond to possibly hypothetical but well‐defined interventions in identifiable (sub)populations. To illustrate our points, we consider five examples that were recently used to motivate consideration of principal stratum estimands in clinical trials. In all of these examples, we propose alternative causal estimands, such as conditional effects, sequential regime effects, and separable effects, that correspond to explicit research questions of substantial interest.
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Affiliation(s)
- Mats J Stensrud
- Department of Mathematics, École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
| | - Oliver Dukes
- Department of Statistics and Data Science, The Wharton School, University of Pennsylvania, Philadelphia, Pennsylvania, USA.,Department of Applied Mathematics, Statistics and Computer Science, Ghent University, Ghent, Belgium
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15
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Shrier I, Suzuki E. The primary importance of the research question: implications for understanding natural versus controlled direct effects. Int J Epidemiol 2022; 51:1041-1046. [PMID: 35512027 DOI: 10.1093/ije/dyac090] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2021] [Accepted: 04/13/2022] [Indexed: 11/14/2022] Open
Affiliation(s)
- Ian Shrier
- Centre for Clinical Epidemiology, Lady Davis Institute, Jewish General Hospital, McGill University, Montreal, QC, Canada
| | - Etsuji Suzuki
- Department of Epidemiology, Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama University, Okayama, Japan
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16
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Stensrud MJ, Robins JM, Sarvet A, Tchetgen Tchetgen EJ, Young JG. Conditional separable effects. J Am Stat Assoc 2022. [DOI: 10.1080/01621459.2022.2071276] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Affiliation(s)
- Mats J. Stensrud
- Department of Mathematics, Ecole Polytechnique Fédérale de Lausanne, Switzerland
| | - James M. Robins
- Department of Epidemiology, Harvard T. H. Chan School of Public Health, USA
| | - Aaron Sarvet
- Department of Mathematics, Ecole Polytechnique Fédérale de Lausanne, Switzerland
| | | | - Jessica G. Young
- Department of Epidemiology, Harvard T. H. Chan School of Public Health, USA
- Department of Population Medicine, Harvard Medical School, USA
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17
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Ryan O, Hamaker EL. Time to Intervene: A Continuous-Time Approach to Network Analysis and Centrality. PSYCHOMETRIKA 2022; 87:214-252. [PMID: 34165691 PMCID: PMC9021117 DOI: 10.1007/s11336-021-09767-0] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/29/2020] [Revised: 04/16/2021] [Accepted: 04/22/2021] [Indexed: 05/08/2023]
Abstract
Network analysis of ESM data has become popular in clinical psychology. In this approach, discrete-time (DT) vector auto-regressive (VAR) models define the network structure with centrality measures used to identify intervention targets. However, VAR models suffer from time-interval dependency. Continuous-time (CT) models have been suggested as an alternative but require a conceptual shift, implying that DT-VAR parameters reflect total rather than direct effects. In this paper, we propose and illustrate a CT network approach using CT-VAR models. We define a new network representation and develop centrality measures which inform intervention targeting. This methodology is illustrated with an ESM dataset.
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Affiliation(s)
- Oisín Ryan
- Utrecht University, Padualaan 14, 3584 CH,, Utrecht, The Netherlands.
| | - Ellen L Hamaker
- Utrecht University, Padualaan 14, 3584 CH,, Utrecht, The Netherlands
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18
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Chan KCG, Gao F, Xia F. Discussion on "Causal mediation of semicompeting risks" by Yen-Tsung Huang. Biometrics 2021; 77:1155-1159. [PMID: 34510414 DOI: 10.1111/biom.13520] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2020] [Revised: 12/09/2020] [Accepted: 12/24/2020] [Indexed: 12/01/2022]
Affiliation(s)
- Kwun Chuen Gary Chan
- Department of Biostatistics and Department of Health Systems and Population, University of Washington, Seattle, Washington, USA
| | - Fei Gao
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
| | - Fan Xia
- Department of Epidemiology, University of Washington, Seattle, Washington, USA
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19
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Stensrud MJ, Hernán MA, Tchetgen Tchetgen EJ, Robins JM, Didelez V, Young JG. A generalized theory of separable effects in competing event settings. LIFETIME DATA ANALYSIS 2021; 27:588-631. [PMID: 34468923 PMCID: PMC8536652 DOI: 10.1007/s10985-021-09530-8] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/28/2020] [Accepted: 07/16/2021] [Indexed: 05/04/2023]
Abstract
In competing event settings, a counterfactual contrast of cause-specific cumulative incidences quantifies the total causal effect of a treatment on the event of interest. However, effects of treatment on the competing event may indirectly contribute to this total effect, complicating its interpretation. We previously proposed the separable effects to define direct and indirect effects of the treatment on the event of interest. This definition was given in a simple setting, where the treatment was decomposed into two components acting along two separate causal pathways. Here we generalize the notion of separable effects, allowing for interpretation, identification and estimation in a wide variety of settings. We propose and discuss a definition of separable effects that is applicable to general time-varying structures, where the separable effects can still be meaningfully interpreted as effects of modified treatments, even when they cannot be regarded as direct and indirect effects. For these settings we derive weaker conditions for identification of separable effects in studies where decomposed, or otherwise modified, treatments are not yet available; in particular, these conditions allow for time-varying common causes of the event of interest, the competing events and loss to follow-up. We also propose semi-parametric weighted estimators that are straightforward to implement. We stress that unlike previous definitions of direct and indirect effects, the separable effects can be subject to empirical scrutiny in future studies.
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Affiliation(s)
- Mats J Stensrud
- Department of Mathematics, Ecole Polytechnique Fédérale de Lausanne, Lausanne, Switzerland.
| | - Miguel A Hernán
- Department of Epidemiology, Harvard T. H. Chan School of Public Health, Boston, USA
- Department of Biostatistics, Harvard T. H. Chan School of Public Health, Boston, USA
- CAUSALab, Harvard T.H. Chan School of Public Health, Boston, USA
| | | | - James M Robins
- Department of Epidemiology, Harvard T. H. Chan School of Public Health, Boston, USA
- Department of Biostatistics, Harvard T. H. Chan School of Public Health, Boston, USA
- CAUSALab, Harvard T.H. Chan School of Public Health, Boston, USA
| | - Vanessa Didelez
- Leibniz Institute for Prevention Research and Epidemiology - BIPS, Bremen, Germany
- Faculty of Mathematics/Computer Science, University of Bremen, Bremen, Germany
| | - Jessica G Young
- Department of Epidemiology, Harvard T. H. Chan School of Public Health, Boston, USA
- CAUSALab, Harvard T.H. Chan School of Public Health, Boston, USA
- Department of Population Medicine, Harvard Medical School and Harvard Pilgrim Health Care Institute, Boston, USA
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20
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Fulcher IR, Shpitser I, Didelez V, Zhou K, Scharfstein DO. Discussion on "Causal mediation of semicompeting risks" by Yen-Tsung Huang. Biometrics 2021; 77:1165-1169. [PMID: 34510405 DOI: 10.1111/biom.13519] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2020] [Revised: 01/11/2021] [Accepted: 03/04/2021] [Indexed: 01/15/2023]
Abstract
Huang proposes a method for assessing the impact of a point treatment on mortality either directly or mediated by occurrence of a nonterminal health event, based on data from a prospective cohort study in which the occurrence of the nonterminal health event may be preemptied by death but not vice versa. The author uses a causal mediation framework to formally define causal quantities known as natural (in)direct effects. The novelty consists of adapting these concepts to a continuous-time modeling framework based on counting processes. In an effort to posit "scientifically interpretable estimands," statistical and causal assumptions are introduced for identification. In this commentary, we argue that these assumptions are not only difficult to interpret and justify, but are also likely violated in the hepatitis B motivating example and other survival/time to event settings as well.
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Affiliation(s)
- Isabel R Fulcher
- Department of Global Health and Social Medicine, Harvard Medical School, Boston, Massachusetts, USA
| | - Ilya Shpitser
- Department of Computer Science, Johns Hopkins University, Baltimore, Maryland, USA
| | - Vanessa Didelez
- Leibniz Institute for Prevention Research and Epidemiology - BIPS, Bremen, Germany and Departments of Mathematics and Computer Science, University of Bremen, Bremen, Germany
| | - Kali Zhou
- Division of Gastrointestinal and Liver Diseases, Keck School of Medicine, University of Southern California, Los Angeles, California, USA
| | - Daniel O Scharfstein
- Department of Population Health Sciences, University of Utah School of Medicine, Salt Lake City, Utah, USA
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21
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Stensrud MJ, Young JG, Martinussen T. Discussion on "Causal mediation of semicompeting risks" by Yen-Tsung Huang. Biometrics 2021; 77:1160-1164. [PMID: 34478563 DOI: 10.1111/biom.13523] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2020] [Revised: 02/13/2021] [Accepted: 02/16/2021] [Indexed: 11/30/2022]
Affiliation(s)
- Mats J Stensrud
- Department of Mathematics, Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
| | - Jessica G Young
- Department of Population Medicine, Harvard Medical School and Harvard Pilgrim Health Care Institute, Boston, Massachusetts, USA
| | - Torben Martinussen
- Department of Biostatistics, University of Copenhagen, Copenhagen, Denmark
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22
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Zhang H, Zheng Y, Hou L, Zheng C, Liu L. Mediation analysis for survival data with High-Dimensional mediators. Bioinformatics 2021; 37:3815-3821. [PMID: 34343267 PMCID: PMC8570823 DOI: 10.1093/bioinformatics/btab564] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2021] [Revised: 07/18/2021] [Accepted: 07/29/2021] [Indexed: 11/12/2022] Open
Abstract
MOTIVATION Mediation analysis has become a prevalent method to identify causal pathway(s) between an independent variable and a dependent variable through intermediate variable(s). However, little work has been done when the intermediate variables (mediators) are high-dimensional and the outcome is a survival endpoint. In this paper, we introduce a novel method to identify potential mediators in a causal framework of high-dimensional Cox regression. RESULTS We first reduce the data dimension through a mediation-based sure independence screening (SIS) method. A de-biased Lasso inference procedure is used for Cox's regression parameters. We adopt a multiple-testing procedure to accurately control the false discovery rate (FDR) when testing high-dimensional mediation hypotheses. Simulation studies are conducted to demonstrate the performance of our method. We apply this approach to explore the mediation mechanisms of 379,330 DNA methylation markers between smoking and overall survival among lung cancer patients in the TCGA lung cancer cohort. Two methylation sites (cg08108679 and cg26478297) are identified as potential mediating epigenetic markers. AVAILABILITY Our proposed method is available with the R package HIMA at https://cran.r-project.org/web/packages/HIMA/. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Haixiang Zhang
- Center for Applied Mathematics, Tianjin University, Tianjin, 300072, China
| | - Yinan Zheng
- Department of Preventive Medicine, Northwestern University, Chicago, IL, 60611, USA
| | - Lifang Hou
- Department of Preventive Medicine, Northwestern University, Chicago, IL, 60611, USA
| | - Cheng Zheng
- Department of Biostatistics, University of Nebraska Medical Center, Omaha, NE, 68198, USA
| | - Lei Liu
- Division of Biostatistics, Washington University in St. Louis, St. Louis, MO, 63110, USA
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23
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Identified Versus Interesting Causal Effects in Fertility Trials and Other Settings With Competing or Truncation Events. Epidemiology 2021; 32:569-572. [PMID: 34042075 DOI: 10.1097/ede.0000000000001357] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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24
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Zeng S, Rosenbaum S, Alberts SC, Archie EA, Li F. Causal mediation analysis for sparse and irregular longitudinal data. Ann Appl Stat 2021. [DOI: 10.1214/20-aoas1427] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Affiliation(s)
- Shuxi Zeng
- Department of Statistical Science, Duke University
| | | | - Susan C. Alberts
- Departments of Biology and Evolutionary Anthropology, Duke University
| | | | - Fan Li
- Department of Statistical Science, Duke University
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25
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Abstract
Causal mediation analysis is a useful tool for epidemiologic research, but it has been criticized for relying on a "cross-world" independence assumption that counterfactual outcome and mediator values are independent even in causal worlds where the exposure assignments for the outcome and mediator differ. This assumption is empirically difficult to verify and problematic to justify based on background knowledge. In the present article, we aim to assist the applied researcher in understanding this assumption. Synthesizing what is known about the cross-world independence assumption, we discuss the relationship between assumptions for causal mediation analyses, causal models, and nonparametric identification of natural direct and indirect effects. In particular, we give a practical example of an applied setting where the cross-world independence assumption is violated even without any post-treatment confounding. Further, we review possible alternatives to the cross-world independence assumption, including the use of bounds that avoid the assumption altogether. Finally, we carry out a numeric study in which the cross-world independence assumption is violated to assess the ensuing bias in estimating natural direct and indirect effects. We conclude with recommendations for carrying out causal mediation analyses.
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26
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Lok JJ, Bosch RJ. Causal Organic Indirect and Direct Effects: Closer to the Original Approach to Mediation Analysis, with a Product Method for Binary Mediators. Epidemiology 2021; 32:412-420. [PMID: 33783395 PMCID: PMC8362675 DOI: 10.1097/ede.0000000000001339] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
Mediation analysis, which started in the mid-1980s, is used extensively by applied researchers. Indirect and direct effects are the part of a treatment effect that is mediated by a covariate and the part that is not. Subsequent work on natural indirect and direct effects provides a formal causal interpretation, based on cross-worlds counterfactuals: outcomes under treatment with the mediator set to its value without treatment. Organic indirect and direct effects avoid cross-worlds counterfactuals, using so-called organic interventions on the mediator while keeping the initial treatment fixed at treatment. Organic indirect and direct effects apply also to settings where the mediator cannot be set. In linear models where the outcome model does not have treatment-mediator interaction, both organic and natural indirect and direct effects lead to the same estimators as in the original formulation of mediation analysis. Here, we generalize organic interventions on the mediator to include interventions combined with the initial treatment fixed at no treatment. We show that the product method holds in linear models for organic indirect and direct effects relative to no treatment even if there is treatment-mediator interaction. Moreover, we find a product method for binary mediators. Furthermore, we argue that the organic indirect effect relative to no treatment is very relevant for drug development. We illustrate the benefits of our approach by estimating the organic indirect effect of curative HIV treatments mediated by two HIV persistence measures, using data on interruption of antiretroviral therapy without curative HIV treatments combined with an estimated or hypothesized effect of the curative HIV treatments on these mediators. See video abstract at http://links.lww.com/EDE/B796.
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Affiliation(s)
- Judith J Lok
- From the Department of Mathematics and Statistics, Boston University, Boston, MA
| | - Ronald J Bosch
- Center for Biostatistics in AIDS Research, Harvard T.H. Chan School of Public Health, Boston, MA
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27
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Moreno-Betancur M, Moran P, Becker D, Patton GC, Carlin JB. Mediation effects that emulate a target randomised trial: Simulation-based evaluation of ill-defined interventions on multiple mediators. Stat Methods Med Res 2021; 30:1395-1412. [PMID: 33749386 PMCID: PMC8371283 DOI: 10.1177/0962280221998409] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Many epidemiological questions concern potential interventions to alter the pathways presumed to mediate an association. For example, we consider a study that investigates the benefit of interventions in young adulthood for ameliorating the poorer mid-life psychosocial outcomes of adolescent self-harmers relative to their healthy peers. Two methodological challenges arise. First, mediation methods have hitherto mostly focused on the elusive task of discovering pathways, rather than on the evaluation of mediator interventions. Second, the complexity of such questions is invariably such that there are no well-defined mediator interventions (i.e. actual treatments, programs, etc.) for which data exist on the relevant populations, outcomes and time-spans of interest. Instead, researchers must rely on exposure (non-intervention) data, that is, on mediator measures such as depression symptoms for which the actual interventions that one might implement to alter them are not well defined. We propose a novel framework that addresses these challenges by defining mediation effects that map to a target trial of hypothetical interventions targeting multiple mediators for which we simulate the effects. Specifically, we specify a target trial addressing three policy-relevant questions, regarding the impacts of hypothetical interventions that would shift the mediators' distributions (separately under various interdependence assumptions, jointly or sequentially) to user-specified distributions that can be emulated with the observed data. We then define novel interventional effects that map to this trial, simulating shifts by setting mediators to random draws from those distributions. We show that estimation using a g-computation method is possible under an expanded set of causal assumptions relative to inference with well-defined interventions, which reflects the lower level of evidence that is expected with ill-defined interventions. Application to the self-harm example in the Victorian Adolescent Health Cohort Study illustrates the value of our proposal for informing the design and evaluation of actual interventions in the future.
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Affiliation(s)
- Margarita Moreno-Betancur
- Department of Paediatrics, University of Melbourne, Melbourne, Australia.,Murdoch Children's Research Institute, Melbourne, Australia
| | - Paul Moran
- Centre for Academic Mental Health, School of Social & Community Medicine, University of Bristol, Bristol, UK
| | - Denise Becker
- Murdoch Children's Research Institute, Melbourne, Australia
| | - George C Patton
- Department of Paediatrics, University of Melbourne, Melbourne, Australia.,Murdoch Children's Research Institute, Melbourne, Australia
| | - John B Carlin
- Department of Paediatrics, University of Melbourne, Melbourne, Australia.,Murdoch Children's Research Institute, Melbourne, Australia
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28
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Mitchell A, Fall T, Melhus H, Wolk A, Michaëlsson K, Byberg L. Is the effect of Mediterranean diet on hip fracture mediated through type 2 diabetes mellitus and body mass index? Int J Epidemiol 2021; 50:234-244. [PMID: 33367703 PMCID: PMC7938512 DOI: 10.1093/ije/dyaa239] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/06/2020] [Indexed: 12/05/2022] Open
Abstract
BACKGROUND We examined whether the inverse association between adherence to a Mediterranean diet and hip fracture risk is mediated by incident type 2 diabetes mellitus (T2DM) and body mass index (BMI). METHODS We included 50 755 men and women from the Cohort of Swedish Men and the Swedish Mammography Cohort who answered lifestyle and medical questionnaires in 1997 and 2008 (used for calculation of the Mediterranean diet score 9mMED; low, medium, high) and BMI in 1997, and incident T2DM in 1997-2008). The cumulative incidence of hip fracture from the National Patient Register (2009-14) was considered as outcome. RESULTS We present conditional odds ratios (OR) 9[95% confidence interval, CI) of hip fracture for medium and high adherence to mMED, compared with low adherence. The total effect ORs were 0.82 (0.71, 0.95) and 0.75 (0.62, 0.91), respectively. The controlled direct effect of mMED on hip fracture (not mediated by T2DM, considering BMI as an exposure-induced confounder), calculated using inverse probability weighting of marginal structural models, rendered ORs of 0.82 (0.72, 0.95) and 0.73 (0.60, 0.88), respectively. The natural direct effect ORs (not mediated by BMI or T2DM, calculated using flexible mediation analysis) were 0.82 (0.71, 0.95) and 0.74(0.61, 0.89), respectively. The path-specific indirect and partial indirect natural effects ORs (through BMI or T2DM) were close to 1. CONCLUSIONS Mediterranean diet has a direct effect on hip fracture risk via pathways other than through T2DM and BMI. We cannot exclude mediating effects of T2DM or BMI, or that their effects cancel each other out.
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Affiliation(s)
- Adam Mitchell
- Department of Surgical Sciences, Orthopaedics, Uppsala University, Uppsala, Sweden
| | - Tove Fall
- Department of Medical Sciences, Molecular Epidemiology, Uppsala University, Uppsala, Sweden
| | - Håkan Melhus
- Department of Medical Sciences, Clinical Pharmacogenomics and Osteoporosis, Uppsala University, Uppsala, Sweden
| | - Alicja Wolk
- Department of Surgical Sciences, Orthopaedics, Uppsala University, Uppsala, Sweden
- Institute of Environmental Medicine, Cardiovascular and Nutritional Epidemiology, Karolinska Institutet, Stockholm, Sweden
| | - Karl Michaëlsson
- Department of Surgical Sciences, Orthopaedics, Uppsala University, Uppsala, Sweden
| | - Liisa Byberg
- Department of Surgical Sciences, Orthopaedics, Uppsala University, Uppsala, Sweden
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29
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Cai X, Loh WW, Crawford FW. Identification of causal intervention effects under contagion. JOURNAL OF CAUSAL INFERENCE 2021; 9:9-38. [PMID: 34676152 PMCID: PMC8528235 DOI: 10.1515/jci-2019-0033] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Defining and identifying causal intervention effects for transmissible infectious disease outcomes is challenging because a treatment - such as a vaccine - given to one individual may affect the infection outcomes of others. Epidemiologists have proposed causal estimands to quantify effects of interventions under contagion using a two-person partnership model. These simple conceptual models have helped researchers develop causal estimands relevant to clinical evaluation of vaccine effects. However, many of these partnership models are formulated under structural assumptions that preclude realistic infectious disease transmission dynamics, limiting their conceptual usefulness in defining and identifying causal treatment effects in empirical intervention trials. In this paper, we propose causal intervention effects in two-person partnerships under arbitrary infectious disease transmission dynamics, and give nonparametric identification results showing how effects can be estimated in empirical trials using time-to-infection or binary outcome data. The key insight is that contagion is a causal phenomenon that induces conditional independencies on infection outcomes that can be exploited for the identification of clinically meaningful causal estimands. These new estimands are compared to existing quantities, and results are illustrated using a realistic simulation of an HIV vaccine trial.
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Affiliation(s)
- Xiaoxuan Cai
- Department of Biostatistics, Yale School of Public Health
| | - Wen Wei Loh
- Department of Data Analysis, University of Ghent
| | - Forrest W Crawford
- Department of Biostatistics, Yale School of Public Health
- Department of Statistics & Data Science, Yale University
- Department of Ecology and Evolutionary Biology, Yale University
- Yale School of Management
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30
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Nguyen TQ, Schmid I, Stuart EA. Clarifying causal mediation analysis for the applied researcher: Defining effects based on what we want to learn. Psychol Methods 2020; 26:2020-52228-001. [PMID: 32673039 PMCID: PMC8496983 DOI: 10.1037/met0000299] [Citation(s) in RCA: 54] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/20/2023]
Abstract
The incorporation of causal inference in mediation analysis has led to theoretical and methodological advancements-effect definitions with causal interpretation, clarification of assumptions required for effect identification, and an expanding array of options for effect estimation. However, the literature on these results is fast-growing and complex, which may be confusing to researchers unfamiliar with causal inference or unfamiliar with mediation. The goal of this article is to help ease the understanding and adoption of causal mediation analysis. It starts by highlighting a key difference between the causal inference and traditional approaches to mediation analysis and making a case for the need for explicit causal thinking and the causal inference approach in mediation analysis. It then explains in as-plain-as-possible language existing effect types, paying special attention to motivating these effects with different types of research questions, and using concrete examples for illustration. This presentation differentiates 2 perspectives (or purposes of analysis): the explanatory perspective (aiming to explain the total effect) and the interventional perspective (asking questions about hypothetical interventions on the exposure and mediator, or hypothetically modified exposures). For the latter perspective, the article proposes tapping into a general class of interventional effects that contains as special cases most of the usual effect types-interventional direct and indirect effects, controlled direct effects and also a generalized interventional direct effect type, as well as the total effect and overall effect. This general class allows flexible effect definitions which better match many research questions than the standard interventional direct and indirect effects. (PsycInfo Database Record (c) 2020 APA, all rights reserved).
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Affiliation(s)
- Trang Quynh Nguyen
- Department of Mental Health, Johns Hopkins Bloomberg School of Public Health
| | - Ian Schmid
- Department of Mental Health, Johns Hopkins Bloomberg School of Public Health
| | - Elizabeth A Stuart
- Department of Mental Health, Johns Hopkins Bloomberg School of Public Health
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31
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Stensrud MJ, Young JG, Didelez V, Robins JM, Hernán MA. Separable Effects for Causal Inference in the Presence of Competing Events. J Am Stat Assoc 2020. [DOI: 10.1080/01621459.2020.1765783] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
Affiliation(s)
- Mats J. Stensrud
- Department of Epidemiology, Harvard T. H. Chan School of Public Health, Boston, MA
- Department of Biostatistics, University of Oslo, Oslo, Norway
| | - Jessica G. Young
- Department of Population Medicine, Harvard Medical School and Harvard Pilgrim Health Care Institute, Boston, MA
| | - Vanessa Didelez
- Leibniz Institute for Prevention Research and Epidemiology – BIPS, Bremen, Germany
- Faculty of Mathematics/Computer Science, University of Bremen, Bremen, Germany
| | - James M. Robins
- Department of Epidemiology, Harvard T. H. Chan School of Public Health, Boston, MA
- Department of Biostatistics, Harvard T. H. Chan School of Public Health, Boston, MA
| | - Miguel A. Hernán
- Department of Epidemiology, Harvard T. H. Chan School of Public Health, Boston, MA
- Department of Biostatistics, Harvard T. H. Chan School of Public Health, Boston, MA
- Harvard-MIT Division of Health Sciences and Technology, Cambridge, MA
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32
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Borgan Ø, Gjessing HK. Special issue dedicated to Odd O. Aalen. LIFETIME DATA ANALYSIS 2019; 25:587-592. [PMID: 31463654 DOI: 10.1007/s10985-019-09483-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/17/2019] [Accepted: 08/21/2019] [Indexed: 06/10/2023]
Affiliation(s)
- Ørnulf Borgan
- Department of Mathematics, University of Oslo, Oslo, Norway.
| | - Håkon K Gjessing
- Norwegian Institute of Public Health, Oslo, Norway
- Department for Global Health and Primary Care, University of Bergen, Bergen, Norway
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33
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Aalen OO, Stensrud MJ, Didelez V, Daniel R, Røysland K, Strohmaier S. Time‐dependent mediators in survival analysis: Modeling direct and indirect effects with the additive hazards model. Biom J 2019; 62:532-549. [DOI: 10.1002/bimj.201800263] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2018] [Revised: 01/14/2019] [Accepted: 01/15/2019] [Indexed: 11/06/2022]
Affiliation(s)
- Odd O. Aalen
- Oslo Center for Biostatistics and Epidemiology Department for Biostatistics, IMB University of Oslo Oslo Norway
| | - Mats J. Stensrud
- Oslo Center for Biostatistics and Epidemiology Department for Biostatistics, IMB University of Oslo Oslo Norway
- Department of Medicine Diakonhjemmet Hospital Oslo Norway
| | - Vanessa Didelez
- Leibniz Institute for Prevention Research and Epidemiology—BIPS Bremen Germany
- Faculty of Mathematics/Computer Science University of Bremen Bremen Germany
| | - Rhian Daniel
- Division of Population Medicine Cardiff University UK
| | - Kjetil Røysland
- Oslo Center for Biostatistics and Epidemiology Department for Biostatistics, IMB University of Oslo Oslo Norway
| | - Susanne Strohmaier
- Institute of Clinical Biometrics Center for Medical Statistics, Informatics, and Intelligent Systems Medical University of Vienna Vienna Austria
- Department of Epidemiology Center for Public Health Medical University of Vienna Vienna Austria
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