Nonparametric Bounds and Sensitivity Analysis of Treatment Effects

Preventable Fraction in the Context of Disease Progression

The relevance of the epidemiologic concept of preventable fraction to the study of the population-level impact of preventive exposures is unequivocal. Here, we discuss how the preventable fraction can be usefully understood for the class of outcomes that relate to disease progression (e.g., clinical severity given diagnosis), and, under the principal stratification framework, derive an expression for this quantity for this type of outcome. In particular, we show that, in the context of disease progression, the preventable fraction is a function of the effect on the postdiagnosis outcome in the principal stratum in the unexposed group who would have disease regardless of exposure status. This work will facilitate an understanding of the contribution of principal effects to the impact of preventive exposures at the population level.

Overcoming Data Gaps in Life Course Epidemiology by Matching Across Cohorts

Life course epidemiology is hampered by the absence of large studies with exposures and outcomes measured at different life stages in the same individuals. We describe when the effect of an exposure ( A ) on an outcome ( Y ) in a target population is identifiable in a combined ("synthetic") cohort created by pooling an early-life cohort including measures of A with a late-life cohort including measures of Y . We enumerate causal assumptions needed for unbiased effect estimation in the synthetic cohort and illustrate by simulating target populations under four causal models. From each target population, we randomly sampled early- and late-life cohorts and created a synthetic cohort by matching individuals from the two cohorts based on mediators and confounders. We estimated the effect of A on Y in the synthetic cohort, varying matching variables, the match ratio, and the strength of association between matching variables and A . Finally, we compared bias in the synthetic cohort estimates when matching variables did not d-separate A and Y to the bias expected in the original cohort. When the set of matching variables includes all variables d-connecting exposure and outcome (i.e., variables blocking all backdoor and front-door pathways), the synthetic cohort yields unbiased effect estimates. Even when matching variables did not fully account for confounders, the synthetic cohort estimate was sometimes less biased than comparable estimates in the original cohort. Methods based on merging cohorts may hasten the evaluation of early- and mid-life determinants of late-life health but rely on available measures of both confounders and mediators.

Partial Identification of the Effects of Sustained Treatment Strategies

Although many epidemiologic studies focus on point identification, it is also possible to partially identify causal effects under consistency and the data alone. However, the literature on the so-called "assumption-free" bounds has focused on settings with time-fixed exposures. We describe assumption-free bounds for the effects of both static and dynamic sustained interventions. To provide intuition for the width of the bounds, we also discuss a mathematical connection between assumption-free bounds and clone-censor-weight approaches to causal effect estimation. The bounds, which are often wide in practice, can provide important information about the degree to which causal analyses depend on unverifiable assumptions made by investigators.

Sensitivity analysis for causality in observational studies for regulatory science

Objective

The United States Congress passed the 21st Century Cures Act mandating the development of Food and Drug Administration guidance on regulatory use of real-world evidence. The Forum on the Integration of Observational and Randomized Data conducted a meeting with various stakeholder groups to build consensus around best practices for the use of real-world data (RWD) to support regulatory science. Our companion paper describes in detail the context and discussion of the meeting, which includes a recommendation to use a causal roadmap for study designs using RWD. This article discusses one step of the roadmap: the specification of a sensitivity analysis for testing robustness to violations of causal model assumptions.

Methods

We present an example of a sensitivity analysis from a RWD study on the effectiveness of Nifurtimox in treating Chagas disease, and an overview of various methods, emphasizing practical considerations on their use for regulatory purposes.

Results

Sensitivity analyses must be accompanied by careful design of other aspects of the causal roadmap. Their prespecification is crucial to avoid wrong conclusions due to researcher degrees of freedom. Sensitivity analysis methods require auxiliary information to produce meaningful conclusions; it is important that they have at least two properties: the validity of the conclusions does not rely on unverifiable assumptions, and the auxiliary information required by the method is learnable from the corpus of current scientific knowledge.

Conclusions

Prespecified and assumption-lean sensitivity analyses are a crucial tool that can strengthen the validity and trustworthiness of effectiveness conclusions for regulatory science.

A second evidence factor for a second control group

In an observational study of the effects caused by a treatment, a second control group is used in an effort to detect bias from unmeasured covariates, and the investigator is content if no evidence of bias is found. This strategy is not entirely satisfactory: two control groups may differ significantly, yet the difference may be too small to invalidate inferences about the treatment, or the control groups may not differ yet nonetheless fail to provide a tangible strengthening of the evidence of a treatment effect. Is a firmer conclusion possible? Is there a way to analyze a second control group such that the data might report measurably strengthened evidence of cause and effect, that is, insensitivity to larger unmeasured biases? Evidence factor analyses are not commonly used with a second control group: most analyses compare the treated group to each control group, but analyses of that kind are partially redundant; so, they do not constitute evidence factors. An alternative analysis is proposed here, one that does yield two evidence factors, and with a carefully designed test statistic, is capable of extracting strong evidence from the second factor. The new technical work here concerns the development of a test statistic with high design sensitivity and high Bahadur efficiency in a sensitivity analysis for the second factor. A study of binge drinking as a cause of high blood pressure is used as an illustration.

Application of estimand framework in ICH E9 (R1) to vaccine trials

Over the past decades, the primary interest in vaccine efficacy or immunogenicity evaluation mostly focuses on the biological effect of immunization in complying with the vaccination schedule in a targeted population. The safety questions, which are essential for vaccines as they are generally given to large healthy populations, need to be clearly defined to reflect the risk assessment of interest. ICH E9 (R1) provides a structured framework to clarify the clinical questions and formulate the treatment effect as an estimand. This paper applies the estimand framework to vaccine clinical trials on common clinical questions regarding efficacy, immunogenicity, and safety.

BOUNDS ON THE CONDITIONAL AND AVERAGE TREATMENT EFFECT WITH UNOBSERVED CONFOUNDING FACTORS

For observational studies, we study the sensitivity of causal inference when treatment assignments may depend on unobserved confounders. We develop a loss minimization approach for estimating bounds on the conditional average treatment effect (CATE) when unobserved confounders have a bounded effect on the odds ratio of treatment selection. Our approach is scalable and allows flexible use of model classes in estimation, including nonparametric and black-box machine learning methods. Based on these bounds for the CATE, we propose a sensitivity analysis for the average treatment effect (ATE). Our semiparametric estimator extends/bounds the augmented inverse propensity weighted (AIPW) estimator for the ATE under bounded unobserved confounding. By constructing a Neyman orthogonal score, our estimator of the bound for the ATE is a regular root-n estimator so long as the nuisance parameters are estimated at the o p n - 1 / 4 rate. We complement our methodology with optimality results showing that our proposed bounds are tight in certain cases. We demonstrate our method on simulated and real data examples, and show accurate coverage of our confidence intervals in practical finite sample regimes with rich covariate information.

Using principal stratification in analysis of clinical trials

The ICH E9(R1) addendum (2019) proposed principal stratification (PS) as one of five strategies for dealing with intercurrent events. Therefore, understanding the strengths, limitations, and assumptions of PS is important for the broad community of clinical trialists. Many approaches have been developed under the general framework of PS in different areas of research, including experimental and observational studies. These diverse applications have utilized a diverse set of tools and assumptions. Thus, need exists to present these approaches in a unifying manner. The goal of this tutorial is threefold. First, we provide a coherent and unifying description of PS. Second, we emphasize that estimation of effects within PS relies on strong assumptions and we thoroughly examine the consequences of these assumptions to understand in which situations certain assumptions are reasonable. Finally, we provide an overview of a variety of key methods for PS analysis and use a real clinical trial example to illustrate them. Examples of code for implementation of some of these approaches are given in Supplemental Materials.

Clarifying the causes of consistent and inconsistent findings in genetics

As research in genetics has advanced, some findings have been unexpected or shown to be inconsistent between studies or datasets. The reasons these inconsistencies arise are complex. Results from genetic studies can be affected by various factors including statistical power, linkage disequilibrium, quality control, confounding and selection bias, as well as real differences from interactions and effect modifiers, which may be informative about the mechanisms of traits and disease. Statistical artefacts can manifest as differences between results but they can also conceal underlying differences, which implies that their critical examination is important for understanding the underpinnings of traits. In this review, we examine these factors and outline how they can be identified and conceptualised with structural causal models. We explain the consequences they have on genetic estimates, such as genetic associations, polygenic scores, family‐ and genome‐wide heritability, and describe methods to address them to aid in the estimation of true effects of genetic variation. Clarifying these factors can help researchers anticipate when results are likely to diverge and aid researchers' understanding of causal relationships between genes and complex traits.

Decision-Making Authority During Tele-ICU Care Reduces Mortality and Length of Stay-A Systematic Review and Meta-Analysis

OBJECTIVES

Although the current coronavirus disease 2019 pandemic demonstrates the urgent need for the integration of tele-ICUs, there is still a lack of uniform regulations regarding the level of authority. We conducted a systematic review and meta-analysis to evaluate the impact of the level of authority in tele-ICU care on patient outcomes.

DATA SOURCES

We searched MEDLINE, EMBASE, CENTRAL, and Web of Science from inception until August 30, 2020.

STUDY SELECTION

We searched for randomized controlled trials and observational studies comparing standard care plus tele-ICU care with standard care alone in critically ill patients.

DATA EXTRACTION

Two authors performed data extraction and risk of bias assessment. Mean differences and risk ratios were calculated using a random-effects model.

DATA SYNTHESIS

A total of 20 studies with 477,637 patients (ntele-ICU care = 292,319, ncontrol = 185,318) were included. Although "decision-making authority" as the level of authority was associated with a significant reduction in ICU mortality (pooled risk ratio, 0.82; 95% CI, 0.71-0.94; p = 0.006), we found no advantage of tele-ICU care in studies with "expert tele-consultation" as the level of authority. With regard to length of stay, "decision-making authority" resulted in an advantage of tele-ICU care (ICU length of stay: pooled mean difference, -0.78; 95% CI, -1.46 to -0.10; p = 0.14; hospital length of stay: pooled mean difference, -1.54; 95% CI, -3.13 to 0.05; p = 0.06), whereas "expert tele-consultation" resulted in an advantage of standard care (ICU length of stay: pooled mean difference, 0.31; 95% CI, 0.10-0.53; p = 0.005; hospital length of stay: pooled mean difference, 0.58; 95% CI, -0.04 to 1.21; p = 0.07).

CONCLUSIONS

In contrast to expert tele-consultations, decision-making authority during tele-ICU care reduces mortality and length of stay in the ICU. This work confirms the urgent need for evidence-based ICU telemedicine guidelines and reveals potential benefits of uniform regulations regarding the level of authority when providing tele-ICU care.

Post-randomization Biomarker Effect Modification Analysis in an HIV Vaccine Clinical Trial

While the HVTN 505 trial showed no overall efficacy of the tested vaccine to prevent HIV infection over placebo, markers measuring immune response to vaccination were strongly correlated with infection. This finding generated the hypothesis that some marker-defined vaccinated subgroups were partially protected whereas others had their risk increased. This hypothesis can be assessed using the principal stratification framework (Frangakis and Rubin, 2002) for studying treatment effect modification by an intermediate response variable, using methods in the sub-field of principal surrogate (PS) analysis that studies multiple principal strata. Unfortunately, available methods for PS analysis require an augmented study design not available in HVTN 505, and make untestable structural risk assumptions, motivating a need for more robust PS methods. Fortunately, another sub-field of principal stratification, survivor average causal effect (SACE) analysis (Rubin, 2006) - which studies effects in a single principal stratum - provides many methods not requiring an augmented design and making fewer assumptions. We show how, for a binary intermediate response variable, methods developed for SACE analysis can be adapted to PS analysis, providing new and more robust PS methods. Application to HVTN 505 supports that the vaccine partially protected individuals with vaccine-induced T-cells expressing certain combinations of functions.

Sensitivity analysis of treatment effect to unmeasured confounding in observational studies with survival and competing risks outcomes

No unmeasured confounding is often assumed in estimating treatment effects in observational data, whether using classical regression models or approaches such as propensity scores and inverse probability weighting. However, in many such studies collection of confounders cannot possibly be exhaustive in practice, and it is crucial to examine the extent to which the resulting estimate is sensitive to the unmeasured confounders. We consider this problem for survival and competing risks data. Due to the complexity of models for such data, we adapt the simulated potential confounder approach of Carnegie et al (2016), which provides a general tool for sensitivity analysis due to unmeasured confounding. More specifically, we specify one sensitivity parameter to quantify the association between an unmeasured confounder and the exposure or treatment received, and another set of parameters to quantify the association between the confounder and the time-to-event outcomes. By varying the magnitudes of the sensitivity parameters, we estimate the treatment effect of interest using the stochastic expectation-maximization (EM) and the EM algorithms. We demonstrate the performance of our methods on simulated data, and apply them to a comparative effectiveness study in inflammatory bowel disease. An R package "survSens" is available on CRAN that implements the proposed methodology.

Combining planned and discovered comparisons in observational studies

In observational studies of treatment effects, it is common to have several outcomes, perhaps of uncertain quality and relevance, each purporting to measure the effect of the treatment. A single planned combination of several outcomes may increase both power and insensitivity to unmeasured bias when the plan is wisely chosen, but it may miss opportunities in other cases. A method is proposed that uses one planned combination with only a mild correction for multiple testing and exhaustive consideration of all possible combinations fully correcting for multiple testing. The method works with the joint distribution of $\kappa^{T}\left( \mathbf{T}-\boldsymbol{\mu}\right) /\sqrt {\boldsymbol{\kappa}^{T}\boldsymbol{\Sigma\boldsymbol{\kappa}}}$ and $max_{\boldsymbol{\lambda}\neq\mathbf{0}}$$\,\lambda^{T}\left( \mathbf{T} -\boldsymbol{\mu}\right) /$$\sqrt{\boldsymbol{\lambda}^{T}\boldsymbol{\Sigma \lambda}}$ where $\kappa$ is chosen a priori and the test statistic $\mathbf{T}$ is asymptotically $N_{L}\left( \boldsymbol{\mu},\boldsymbol{\Sigma}\right) $. The correction for multiple testing has a smaller effect on the power of $\kappa^{T}\left( \mathbf{T}-\boldsymbol{\mu }\right) /\sqrt{\boldsymbol{\kappa}^{T}\boldsymbol{\Sigma\boldsymbol{\kappa} }}$ than does switching to a two-tailed test, even though the opposite tail does receive consideration when $\lambda=-\kappa$. In the application, there are three measures of cognitive decline, and the a priori comparison $\kappa$ is their first principal component, computed without reference to treatment assignments. The method is implemented in an R package sensitivitymult.

Sharp bounds on the relative treatment effect for ordinal outcomes

For ordinal outcomes, the average treatment effect is often ill-defined and hard to interpret. Echoing Agresti and Kateri, we argue that the relative treatment effect can be a useful measure, especially for ordinal outcomes, which is defined as γ = pr { Y i ( 1 ) > Y i ( 0 ) } - pr { Y i ( 1 ) < Y i ( 0 ) } , with Y i ( 1 ) and Y i ( 0 ) being the potential outcomes of unit i under treatment and control, respectively. Given the marginal distributions of the potential outcomes, we derive the sharp bounds on γ , which are identifiable parameters based on the observed data. Agresti and Kateri focused on modeling strategies under the assumption of independent potential outcomes, but we allow for arbitrary dependence.

Epidemiology, genetic epidemiology and Mendelian randomisation: more need than ever to attend to detail

In the current era, with increasing availability of results from genetic association studies, finding genetic instruments for inferring causality in observational epidemiology has become apparently simple. Mendelian randomisation (MR) analyses are hence growing in popularity and, in particular, methods that can incorporate multiple instruments are being rapidly developed for these applications. Such analyses have enormous potential, but they all rely on strong, different, and inherently untestable assumptions. These have to be clearly stated and carefully justified for every application in order to avoid conclusions that cannot be replicated. In this article, we review the instrumental variable assumptions and discuss the popular linear additive structural model. We advocate the use of tests for the null hypothesis of ‘no causal effect’ and calculation of the bounds for a causal effect, whenever possible, as these do not rely on parametric modelling assumptions. We clarify the difference between a randomised trial and an MR study and we comment on the importance of validating instruments, especially when considering them for joint use in an analysis. We urge researchers to stand by their convictions, if satisfied that the relevant assumptions hold, and to interpret their results causally since that is the only reason for performing an MR analysis in the first place.

Likelihood-based inference for bounds of causal parameters

It is a common causal inference problem that, even with theoretically infinite samples, we might be able to only provide bounds for the parameters of interest. This problem occurs naturally, for example, in estimating causal interaction between two risk factors and in estimating the average causal effect using the instrumental variable or Mendelian randomization method. Current procedures include linear programming to get the estimated bounds, plus bootstrapping to get confidence intervals. We describe a likelihood-based procedure that automatically yields the interval estimate from the flat likelihood region and show some theory that allows us to construct confidence intervals from this non-regular likelihood. Finally, we illustrate the procedure with examples from the estimation of causal interaction between two risk factors and the treatment effect under partial compliance.