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Using Structural Equation Modeling to Jointly Estimate Maternal and Foetal Effects on Birthweight in the UK Biobank

By Nicole M. Warrington, Rachel Freathy, Michael C. Neale, David M. Evans

Posted 06 Jul 2017
bioRxiv DOI: 10.1101/160044 (published DOI: 10.1093/ije/dyy015)

Background: To date, 60 genetic variants have been robustly associated with birthweight. It is unclear whether these associations represent the effect of an individual's own genotype on their birthweight, their mother's genotype, or both. Methods: We demonstrate how structural equation modelling (SEM) can be used to estimate both maternal and foetal effects when phenotype information is present for individuals in two generations and genotype information is available on the older individual. We conduct an extensive simulation study to assess the bias, power and type 1 error rates of the SEM and also apply the SEM to birthweight data in the UK Biobank study. Results: Unlike simple regression models, our approach is unbiased when there is both a maternal and foetal effect. The method can be used when either the individual's own phenotype or the phenotype of their offspring is not available, and allows the inclusion of summary statistics from additional cohorts where raw data cannot be shared. We show that the type 1 error rate of the method is appropriate, there is substantial statistical power to detect a genetic variant that has a moderate effect on the phenotype, and reasonable power to detect whether it is a foetal and/or maternal effect. We also identify a subset of birth weight associated SNPs that have opposing maternal and foetal effects in the UK Biobank. Conclusions: Our results show that SEM can be used to estimate parameters that would be difficult to quantify using simple statistical methods alone.

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