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      Recent Developments in Mendelian Randomization Studies

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          Abstract

          Purpose of Review

          Mendelian randomization (MR) is a strategy for evaluating causality in observational epidemiological studies. MR exploits the fact that genotypes are not generally susceptible to reverse causation and confounding, due to their fixed nature and Mendel’s First and Second Laws of Inheritance. MR has the potential to provide information on causality in many situations where randomized controlled trials are not possible, but the results of MR studies must be interpreted carefully to avoid drawing erroneous conclusions.

          Recent Findings

          In this review, we outline the principles behind MR, as well as assumptions and limitations of the method. Extensions to the basic approach are discussed, including two-sample MR, bidirectional MR, two-step MR, multivariable MR, and factorial MR. We also consider some new applications and recent developments in the methodology, including its ability to inform drug development, automation of the method using tools such as MR-Base, and phenome-wide and hypothesis-free MR.

          Summary

          In conjunction with the growing availability of large-scale genomic databases, higher level of automation and increased robustness of the methods, MR promises to be a valuable strategy to examine causality in complex biological/omics networks, inform drug development and prioritize intervention targets for disease prevention in the future.

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          Most cited references26

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          'Mendelian randomization': can genetic epidemiology contribute to understanding environmental determinants of disease?

          Associations between modifiable exposures and disease seen in observational epidemiology are sometimes confounded and thus misleading, despite our best efforts to improve the design and analysis of studies. Mendelian randomization-the random assortment of genes from parents to offspring that occurs during gamete formation and conception-provides one method for assessing the causal nature of some environmental exposures. The association between a disease and a polymorphism that mimics the biological link between a proposed exposure and disease is not generally susceptible to the reverse causation or confounding that may distort interpretations of conventional observational studies. Several examples where the phenotypic effects of polymorphisms are well documented provide encouraging evidence of the explanatory power of Mendelian randomization and are described. The limitations of the approach include confounding by polymorphisms in linkage disequilibrium with the polymorphism under study, that polymorphisms may have several phenotypic effects associated with disease, the lack of suitable polymorphisms for studying modifiable exposures of interest, and canalization-the buffering of the effects of genetic variation during development. Nevertheless, Mendelian randomization provides new opportunities to test causality and demonstrates how investment in the human genome project may contribute to understanding and preventing the adverse effects on human health of modifiable exposures.
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            Assessing the suitability of summary data for two-sample Mendelian randomization analyses using MR-Egger regression: the role of the I2 statistic

            Background MR-Egger regression has recently been proposed as a method for Mendelian randomization (MR) analyses incorporating summary data estimates of causal effect from multiple individual variants, which is robust to invalid instruments. It can be used to test for directional pleiotropy and provides an estimate of the causal effect adjusted for its presence. MR-Egger regression provides a useful additional sensitivity analysis to the standard inverse variance weighted (IVW) approach that assumes all variants are valid instruments. Both methods use weights that consider the single nucleotide polymorphism (SNP)-exposure associations to be known, rather than estimated. We call this the `NO Measurement Error’ (NOME) assumption. Causal effect estimates from the IVW approach exhibit weak instrument bias whenever the genetic variants utilized violate the NOME assumption, which can be reliably measured using the F-statistic. The effect of NOME violation on MR-Egger regression has yet to be studied. Methods An adaptation of the I 2 statistic from the field of meta-analysis is proposed to quantify the strength of NOME violation for MR-Egger. It lies between 0 and 1, and indicates the expected relative bias (or dilution) of the MR-Egger causal estimate in the two-sample MR context. We call it I G X 2 . The method of simulation extrapolation is also explored to counteract the dilution. Their joint utility is evaluated using simulated data and applied to a real MR example. Results In simulated two-sample MR analyses we show that, when a causal effect exists, the MR-Egger estimate of causal effect is biased towards the null when NOME is violated, and the stronger the violation (as indicated by lower values of I G X 2 ), the stronger the dilution. When additionally all genetic variants are valid instruments, the type I error rate of the MR-Egger test for pleiotropy is inflated and the causal effect underestimated. Simulation extrapolation is shown to substantially mitigate these adverse effects. We demonstrate our proposed approach for a two-sample summary data MR analysis to estimate the causal effect of low-density lipoprotein on heart disease risk. A high value of I G X 2 close to 1 indicates that dilution does not materially affect the standard MR-Egger analyses for these data. Conclusions Care must be taken to assess the NOME assumption via the I G X 2 statistic before implementing standard MR-Egger regression in the two-sample summary data context. If I G X 2 is sufficiently low (less than 90%), inferences from the method should be interpreted with caution and adjustment methods considered.
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              Using published data in Mendelian randomization: a blueprint for efficient identification of causal risk factors

              Finding individual-level data for adequately-powered Mendelian randomization analyses may be problematic. As publicly-available summarized data on genetic associations with disease outcomes from large consortia are becoming more abundant, use of published data is an attractive analysis strategy for obtaining precise estimates of the causal effects of risk factors on outcomes. We detail the necessary steps for conducting Mendelian randomization investigations using published data, and present novel statistical methods for combining data on the associations of multiple (correlated or uncorrelated) genetic variants with the risk factor and outcome into a single causal effect estimate. A two-sample analysis strategy may be employed, in which evidence on the gene-risk factor and gene-outcome associations are taken from different data sources. These approaches allow the efficient identification of risk factors that are suitable targets for clinical intervention from published data, although the ability to assess the assumptions necessary for causal inference is diminished. Methods and guidance are illustrated using the example of the causal effect of serum calcium levels on fasting glucose concentrations. The estimated causal effect of a 1 standard deviation (0.13 mmol/L) increase in calcium levels on fasting glucose (mM) using a single lead variant from the CASR gene region is 0.044 (95 % credible interval −0.002, 0.100). In contrast, using our method to account for the correlation between variants, the corresponding estimate using 17 genetic variants is 0.022 (95 % credible interval 0.009, 0.035), a more clearly positive causal effect. Electronic supplementary material The online version of this article (doi:10.1007/s10654-015-0011-z) contains supplementary material, which is available to authorized users.
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                Author and article information

                Contributors
                Jie.Zheng@bristol.ac.uk
                Journal
                Curr Epidemiol Rep
                Curr Epidemiol Rep
                Current Epidemiology Reports
                Springer International Publishing (Cham )
                2196-2995
                22 November 2017
                22 November 2017
                2017
                : 4
                : 4
                : 330-345
                Affiliations
                [1 ]ISNI 0000 0004 1936 7603, GRID grid.5337.2, MRC Integrative Epidemiology Unit, , University of Bristol, ; Oakfield House, Bristol, UK
                [2 ]ISNI 0000 0000 9320 7537, GRID grid.1003.2, University of Queensland Diamantina Institute, Translational Research Institute, , University of Queensland, ; Brisbane, QLD Australia
                Article
                128
                10.1007/s40471-017-0128-6
                5711966
                29226067
                0e835bfc-068a-4709-9690-7e08b54c660e
                © The Author(s) 2017

                Open Access This article is distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made.

                History
                Funding
                Funded by: University of Bristol
                Categories
                Genetic Epidemiology (C Amos, Section Editor)
                Custom metadata
                © Springer International Publishing AG, part of Springer Nature 2017

                mendelian randomization,databases and automation tools for causal inference,hypothesis-free causality,drug development,disease progression

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