DINGO: increasing the power of locus discovery in maternal and fetal genome-wide association studies of perinatal traits

Liang-Dar Hwang (), Gabriel Cuellar-Partida, Loic Yengo, Jian Zeng, Jarkko Toivonen, Mikko Arvas, Robin N. Beaumont, Rachel M. Freathy, Gunn-Helen Moen, Nicole M. Warrington and David M. Evans ()
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Liang-Dar Hwang: The University of Queensland
Gabriel Cuellar-Partida: Inc
Loic Yengo: The University of Queensland
Jian Zeng: The University of Queensland
Jarkko Toivonen: Finnish Red Cross Blood Service
Mikko Arvas: Finnish Red Cross Blood Service
Robin N. Beaumont: University of Exeter
Rachel M. Freathy: University of Exeter
Gunn-Helen Moen: The University of Queensland
Nicole M. Warrington: The University of Queensland
David M. Evans: The University of Queensland

Nature Communications, 2024, vol. 15, issue 1, 1-14

Abstract: Abstract Perinatal traits are influenced by fetal and maternal genomes. We investigate the performance of three strategies to detect loci in maternal and fetal genome-wide association studies (GWASs) of the same quantitative trait: (i) the traditional strategy of analysing maternal and fetal GWASs separately; (ii) a two-degree-of-freedom test which combines information from maternal and fetal GWASs; and (iii) a one-degree-of-freedom test where signals from maternal and fetal GWASs are meta-analysed together conditional on estimated sample overlap. We demonstrate that the optimal strategy depends on the extent of sample overlap, correlation between phenotypes, whether loci exhibit fetal and/or maternal effects, and whether these effects are directionally concordant. We apply our methods to summary statistics from a recent GWAS meta-analysis of birth weight. Both the two-degree-of-freedom and meta-analytic approaches increase the number of genetic loci for birth weight relative to separately analysing the scans. Our best strategy identifies an additional 62 loci compared to the most recently published meta-analysis of birth weight. We conclude that whilst the two-degree-of-freedom test may be useful for the analysis of certain perinatal phenotypes, for most phenotypes, a simple meta-analytic strategy is likely to perform best, particularly in situations where maternal and fetal GWASs only partially overlap.

Date: 2024
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DOI: 10.1038/s41467-024-53495-9

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