Mendelian Randomization (MR) is a popular method in epidemiology and genetics that uses genetic variation as instrumental variables for causal inference. Existing MR methods usually assume most genetic variants are valid instrumental variables that identify a common causal effect. There is a general lack of awareness that this effect homogeneity assumption can be violated when there are multiple causal pathways involved, even if all the instrumental variables are valid. In this article, we introduce a latent mixture model MR-PATH that groups instruments that yield similar causal effect estimates together. We develop a Monte-Carlo EM algorithm to fit this mixture model, derive approximate confidence intervals for uncertainty quantification, and adopt a modified Bayesian Information Criterion (BIC) for model selection. We verify the efficacy of the Monte-Carlo EM algorithm, confidence intervals, and model selection criterion using numerical simulations. We identify potential mechanistic heterogeneity when applying our method to estimate the effect of high-density lipoprotein cholesterol on coronary heart disease and the effect of adiposity on type II diabetes.
Multivariable Mendelian randomization with weak instruments: a comparison of Bayesian and frequentist methods
Sydney School of Public Health, University of Sydney（悉尼大学公共卫生学院）；MRC Biostatistics Unit, University of Cambridge（剑桥大学医学研究委员会生物统计单元）；Cardiovascular Epidemiology Unit, University of Cambridge（剑桥大学心血管流行病学单元）
Our approach to Mendelian Randomization (MR) analysis is designed to increase reproducibility of causal effect "discoveries" by: (i) using a Bayesian approach to inference; (ii) replacing the point null hypothesis with a region of practical equivalence consisting of values of negligible magnitude for the effect of interest, while exploiting the ability of Bayesian analysis to quantify the evidence of the effect falling inside/outside the region; (iii) rejecting the usual binary decision logic in favour of a ternary logic where the hypothesis test may result in either an acceptance or a rejecti…
Background: Mendelian randomization (MR) is a useful approach to causal inference from observational studies when randomised controlled trials are not feasible. However, study heterogeneity of two association studies required in MR is often overlooked. When dealing with large studies, recently developed Bayesian MR is limited by its computational expensiveness. Methods: We addressed study heterogeneity by proposing a random effect Bayesian MR model with multiple exposures and outcomes. For large studies, we adopted a subset posterior aggregation method to tackle the problem of computation. In …
We expand Mendelian Randomization (MR) methodology to deal with randomly missing data on either the exposure or the outcome variable, and furthermore with data from nonindependent individuals (eg components of a family). Our method rests on the Bayesian MR framework proposed by Berzuini et al (2018), which we apply in a study of multiplex Multiple Sclerosis (MS) Sardinian families to characterise the role of certain plasma proteins in MS causation. The method is robust to presence of pleiotropic effects in an unknown number of instruments, and is able to incorporate inter-individual kinship in…
The use of genetic variants as instrumental variables - an approach known as Mendelian randomization - is a popular epidemiological method for estimating the causal effect of an exposure (phenotype, biomarker, risk factor) on a disease or health-related outcome from observational data. Instrumental variables must satisfy strong, often untestable assumptions, which means that finding good genetic instruments among a large list of potential candidates is challenging. This difficulty is compounded by the fact that many genetic variants influence more than one phenotype through different causal pa…
Background In a study performed on multiplex Multiple Sclerosis (MS) Sardinian families to identify disease causing plasma proteins, application of Mendelian Randomization (MR) methods encounters difficulties due to relatedness of individuals, correlation between finely mapped genotype instrumental variables (IVs) and presence of missing exposures. Method We specialize the method of Berzuini et al (2018) to deal with these difficulties. The proposed method allows pedigree structure to enter the specification of the outcome distribution via kinship matrix, and treating missing exposures as addi…
Our Bayesian approach to Mendelian Randomisation uses multiple instruments to assess the putative causal effect of an exposure on an outcome. The approach is robust to violations of the (untestable) Exclusion Restriction condition, and hence it does not require instruments to be independent of the outcome conditional on the exposure and on the confounders of the exposure-outcome relationship. The Bayesian approach offers a rigorous handling of the uncertainty (e.g. about the estimated instrument-exposure associations), freedom from asymptotic approximations of the null distribution and the pos…
Mendelian randomization (MR) is a popular method in genetic epidemiology to estimate the effect of an exposure on an outcome by using genetic instruments. These instruments are often selected from a combination of prior knowledge from genome wide association studies (GWAS) and data-driven instrument selection procedures or tests. Unfortunately, when testing for the exposure effect, the instrument selection process done a priori is not accounted for. This paper studies and highlights the bias resulting from not accounting for the instrument selection process by focusing on a recent data-driven …
Selection bias affects Mendelian randomization investigations when selection into the study sample depends on a collider between the genetic variant and confounders of the risk factor-outcome association. However, the relative importance of selection bias for Mendelian randomization compared to other potential biases is unclear. We performed an extensive simulation study to assess the impact of selection bias on a typical Mendelian randomization investigation. Selection bias had a severe impact on bias and Type 1 error rates in our simulation study, but only when selection effects were large. …
Mendelian randomization is the use of genetic variants to assess the existence of a causal relationship between a risk factor and an outcome of interest. Here, we focus on two-sample summary-data Mendelian randomization analyses with many correlated variants from a single gene region, and particularly on cis-Mendelian randomization studies which use protein expression as a risk factor. Such studies must rely on a small, curated set of variants from the studied region; using all variants in the region requires inverting an ill-conditioned genetic correlation matrix and results in numerically un…
Mendelian randomization implemented through instrumental variable analysis is frequently discussed in causality and recently the number of applications on real data is increasing. However, there are very few discussions to address modern biomedical questions such as the integration of large scale omics in causality. While in the age of large omics, we face several hundred or thousands of components with little knowledge about the underlying structures, the focus of the field is on small scales and mostly with known structures. The availability of large omic data accentuates the need for techni…
Mendelian randomization is the use of genetic variants as instrumental variables to assess whether a risk factor is a cause of a disease outcome. Increasingly, Mendelian randomization investigations are conducted on the basis of summarized data, rather than individual-level data. These summarized data comprise the coefficients and standard errors from univariate regression models of the risk factor on each genetic variant, and of the outcome on each genetic variant. A causal estimate can be derived from these associations for each individual genetic variant, and a combined estimate can be obta…
The funnel plot is a graphical visualisation of summary data estimates from a meta-analysis, and is a useful tool for detecting departures from the standard modelling assumptions. Although perhaps not widely appreciated, a simple extension of the funnel plot can help to facilitate an intuitive interpretation of the mathematics underlying a meta-analysis at a more fundamental level, by equating it to determining the centre of mass of a physical system. We used this analogy, with some success, to explain the concepts of weighing evidence and of biased evidence to a young audience at the Cambridg…
Mendelian randomization (MR) is a method of exploiting genetic variation to unbiasedly estimate a causal effect in presence of unmeasured confounding. MR is being widely used in epidemiology and other related areas of population science. In this paper, we study statistical inference in the increasingly popular two-sample summary-data MR design. We show a linear model for the observed associations approximately holds in a wide variety of settings when all the genetic variants satisfy the exclusion restriction assumption, or in genetic terms, when there is no pleiotropy. In this scenario, we der…
Two-sample summary-data Mendelian randomization (MR) has become a popular research design to estimate the causal effect of risk exposures. With the sample size of GWAS continuing to increase, it is now possible to utilize genetic instruments that are only weakly associated with the exposure. To maximize the statistical power of MR, we propose a genome-wide design where more than a thousand genetic instruments are used. For the statistical analysis, we use an empirical partially Bayes approach where instruments are weighted according to their strength, thus weak instruments bring less variation…
The treatment effect in a specific subgroup is often of interest in randomized clinical trials. When the subgroup is characterized by the absence of certain post-randomization events, a naive analysis on the subset of patients without these events may be misleading. The principal stratification framework allows one to define an appropriate causal estimand in such settings. Statistical inference for the principal stratum estimand hinges on scientifically justified assumptions, which can be included with Bayesian methods through prior distributions. Our motivating example is a large randomized p…
Many causal questions involve interactions between units, also known as interference, for example between individuals in households, students in schools, or firms in markets. In this paper, we formalize the concept of a conditioning mechanism, which provides a framework for constructing valid and powerful randomization tests under general forms of interference. We describe our framework in the context of two-stage randomized designs and apply our approach to a randomized evaluation of an intervention targeting student absenteeism in the School District of Philadelphia. We show improvements ove…
Interference exists when a unit's outcome depends on another unit's treatment assignment. For example, intensive policing on one street could have a spillover effect on neighboring streets. Classical randomization tests typically break down in this setting because many null hypotheses of interest are no longer sharp under interference. A promising alternative is to instead construct a conditional randomization test on a subset of units and assignments for which a given null hypothesis is sharp. Finding these subsets is challenging, however, and existing methods are limited to special cases or …
We define causal estimands for experiments on single time series, extending the potential outcome framework to dealing with temporal data. Our approach allows the estimation of some of these estimands and exact randomization based p-values for testing causal effects, without imposing stringent assumptions. We test our methodology on simulated "potential autoregressions,"which have a causal interpretation. Our methodology is partially inspired by data from a large number of experiments carried out by a financial company who compared the impact of two different ways of trading equity futures con…
Mendelian randomization (MR) is a powerful method that uses genetic variants as instrumental variables (IVs) to infer the causal effect of a modifiable exposure on an outcome. Although recent years have seen many extensions of basic MR methods to be robust to certain violations of assumptions, few methods were proposed to infer bi-directional causal relationships, especially for phenotypes with limited biological understandings. The presence of horizontal pleiotropy adds another layer of complexity. In this article, we show that assumptions for common MR methods are often impossible or too str…
Instrumental variables have been widely used to estimate the causal effect of a treatment on an outcome. Existing confidence intervals for causal effects based on instrumental variables assume that all of the putative instrumental variables are valid; a valid instrumental variable is a variable that affects the outcome only by affecting the treatment and is not related to unmeasured confounders. However, in practice, some of the putative instrumental variables are likely to be invalid. This paper presents two tools to conduct valid inference and tests in the presence of invalid instruments. Fi…
Based on the physical randomization of completely randomized experiments, Rigdon and Hudgens (2015) propose two approaches to obtaining exact confidence intervals for the average causal effect on a binary outcome. They construct the first confidence interval by combining, with the Bonferroni adjustment, the prediction sets for treatment effects among treatment and control groups, and the second one by inverting a series of randomization tests. With sample size $n$, their second approach requires performing $O(n^4)$ randomization tests. We demonstrate that the physical randomization also justif…
The method of instrumental variables (IV) provides a framework to study causal effects in both randomized experiments with noncompliance and in observational studies where natural circumstances produce as-if random nudges to accept treatment. Traditionally, inference for IV relied on asymptotic approximations of the distribution of the Wald estimator or two-stage least squares, often with structural modeling assumptions and/or moment conditions. In this paper, we utilize the randomization inference approach to IV inference. First, we outline the exact method, which uses the randomized assignme…
Randomization inference for stepped-wedge designs with noncompliance with application to a palliative care pragmatic trial
University of Chicago（芝加哥大学）；Data Science Institute, University of Chicago（芝加哥大学数据科学研究所）；University of Pennsylvania（宾夕法尼亚大学）；Department of Medicine, University of Pennsylvania（宾夕法尼亚大学医学系）；Department of Mathematics and Statistics, Mississippi State University（密西西比州立大学数学与统计系）；Department of Statistics and Data Science, University of Pennsylvania（宾夕法尼亚大学统计与数据科学系）；Yale School of Public Health（耶鲁公共卫生学院）
Many previous causal inference studies require no interference, that is, the potential outcomes of a unit do not depend on the treatments of other units. However, this no-interference assumption becomes unreasonable when a unit interacts with other units in the same group or cluster. In a motivating application, a university in China admits students through two channels: the college entrance exam (also known as Gaokao) and recommendation (often based on Olympiads in various subjects). The university randomly assigns students to dorms, each of which hosts four students. Students within the same…
Although complete randomization ensures covariate balance on average, the chance for observing significant differences between treatment and control covariate distributions increases with many covariates. Rerandomization discards randomizations that do not satisfy a predetermined covariate balance criterion, generally resulting in better covariate balance and more precise estimates of causal effects. Previous theory has derived finite sample theory for rerandomization under the assumptions of equal treatment group sizes, Gaussian covariate and outcome distributions, or additive causal effects,…
Background: Many genome-wide association studies have detected genomic regions associated with traits, yet understanding the functional causes of association often remains elusive. Utilizing systems approaches and focusing on intermediate molecular phenotypes might facilitate biologic understanding. Results: The availability of exome sequencing of two populations of African-Americans and European-Americans from the Atherosclerosis Risk in Communities study allowed us to investigate the effects of annotated loss-of-function (LoF) mutations on 122 serum metabolites. To assess the findings, we bu…
Mobile health studies can leverage longitudinal sensor data from smartphones to guide the application of personalized medical interventions. In this paper, we propose that adoption of an instrumental variable approach for randomized trials with imperfect compliance provides a natural framework for personalized causal inference of medication response in mobile health studies. Randomized treatment suggestions can be easily delivered to the study participants via electronic messages popping up on the smart-phone screen. Under quite general assumptions we can identify the causal effect of the actu…
A framework for causal inference from two-level factorial designs is proposed. The framework utilizes the concept of potential outcomes that lies at the center stage of causal inference and extends Neyman's repeated sampling approach for estimation of causal effects and randomization tests based on Fisher's sharp null hypothesis to the case of 2-level factorial experiments. The framework allows for statistical inference from a finite population, permits definition and estimation of estimands other than "average factorial effects" and leads to more flexible inference procedures than those based…
Technological advancements in the field of mobile devices and wearable sensors have helped overcome obstacles in the delivery of care, making it possible to deliver behavioral treatments anytime and anywhere. Increasingly the delivery of these treatments is triggered by predictions of risk or engagement which may have been impacted by prior treatments. Furthermore the treatments are often designed to have an impact on individuals over a span of time during which subsequent treatments may be provided. Here we discuss our work on the design of a mobile health smoking cessation experimental study…
Randomized trials of infectious disease interventions, such as vaccines, often focus on groups of connected or potentially interacting individuals. When the pathogen of interest is transmissible between study subjects, interference may occur: individual infection outcomes may depend on treatments received by others. Epidemiologists have defined the primary causal effect of interest -- called the "susceptibility effect" -- as a contrast in infection risk under treatment versus no treatment, while holding exposure to infectiousness constant. A related quantity -- the "direct effect" -- is define…
