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. 2022 Jun 9;54(6):897–905. doi: 10.1038/s41588-022-01085-0

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© The Author(s) 2022

Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as 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. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons license and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/.

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Extended Data Fig. 3 — Here we compare theoretical predictions to results from simulated data for the effective sample size for estimation of direct genetic effects using parental genotypes imputed from both phased and unphased sibling genotype data relative to estimating direct genetic effects using genetic differences between siblings. For 3,000 independent families, we simulated three different traits affected by direct, paternal, and maternal effects of 1,000 SNPs with minor allele frequency 0.5 (Supplementary Note Section 12.1). The overall variance explained by the combined direct, paternal, and maternal effects varied between the simulations, leading to different correlations between siblings’ phenotypes. We computed theoretical expectations based on formulae derived in Supplementary Note Section 4.3, which are drawn as the red curve (theoretical expectation for imputation from unphased data) and the black curve (theoretical expectation for imputation from phased data). The simulation results for unphased data are given by the black circles, and the simulation results for the phased data are given by black triangles. The relative effective sample size is given by the ratio between the sampling variance for estimation of direct effects when using differences between siblings to the sampling variance when using parental genotypes imputed from phased or unphased data.