Bayesian network analysis incorporating genetic anchors complements conventional Mendelian randomization approaches for exploratory analysis of causal relationships in complex data

Autoři: Richard Howey aff001;  So-Youn Shin aff001;  Caroline Relton aff002;  George Davey Smith aff002;  Heather J. Cordell aff001
Působiště autorů: Institute of Genetic Medicine, Newcastle University, Newcastle, United Kingdom aff001;  MRC Integrative Epidemiology Unit, University of Bristol, Bristol, United Kingdom aff002;  Population Health Sciences, University of Bristol, Bristol, United Kingdom aff003
Vyšlo v časopise: Bayesian network analysis incorporating genetic anchors complements conventional Mendelian randomization approaches for exploratory analysis of causal relationships in complex data. PLoS Genet 16(3): e1008198. doi:10.1371/journal.pgen.1008198
Kategorie: Research Article
doi: 10.1371/journal.pgen.1008198


Mendelian randomization (MR) implemented through instrumental variables analysis is an increasingly popular causal inference tool used in genetic epidemiology. But it can have limitations for evaluating simultaneous causal relationships in complex data sets that include, for example, multiple genetic predictors and multiple potential risk factors associated with the same genetic variant. Here we use real and simulated data to investigate Bayesian network analysis (BN) with the incorporation of directed arcs, representing genetic anchors, as an alternative approach. A Bayesian network describes the conditional dependencies/independencies of variables using a graphical model (a directed acyclic graph) with an accompanying joint probability. In real data, we found BN could be used to infer simultaneous causal relationships that confirmed the individual causal relationships suggested by bi-directional MR, while allowing for the existence of potential horizontal pleiotropy (that would violate MR assumptions). In simulated data, BN with two directional anchors (mimicking genetic instruments) had greater power for a fixed type 1 error than bi-directional MR, while BN with a single directional anchor performed better than or as well as bi-directional MR. Both BN and MR could be adversely affected by violations of their underlying assumptions (such as genetic confounding due to unmeasured horizontal pleiotropy). BN with no directional anchor generated inference that was no better than by chance, emphasizing the importance of directional anchors in BN (as in MR). Under highly pleiotropic simulated scenarios, BN outperformed both MR (and its recent extensions) and two recently-proposed alternative approaches: a multi-SNP mediation intersection-union test (SMUT) and a latent causal variable (LCV) test. We conclude that BN incorporating genetic anchors is a useful complementary method to conventional MR for exploring causal relationships in complex data sets such as those generated from modern “omics” technologies.

Klíčová slova:

Algorithms – Genetic predisposition – Instrumental variable analysis – Metabolic networks – Metabolites – Network analysis – Research errors – Simulation and modeling


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