Extended Data Fig. 5: Mean Z2 statistic for direct genetic effects when imputing parental genotypes from cousins using the conditional Gaussian formula (Supplementary Note 3).
From: Family-based genome-wide association study designs for increased power and robustness
Mean Z2 statistics, which are expected to be above 1 (dashed line) when there is bias due to population stratification, and the corresponding 95% jackknife confidence intervals over 3,000 SNPs are presented. For each Fst, we simulated 2 subpopulations, each with 2,500 unrelated cousin pairs and 3,000 SNPs, where the subpopulation allele frequencies were drawn from the Balding-Nichols model: \(Beta(\frac{1-{F}_{st}}{2{F}_{st}},\frac{1-{F}_{st}}{2{F}_{st}})\); imputation of parental genotypes was carried out using the conditional Gaussian method.
