Fig. 2: A decreased effective number of chromosome segments can improve the polygenic prediction accuracy. | Nature Communications

Fig. 2: A decreased effective number of chromosome segments can improve the polygenic prediction accuracy.

From: Efficient polygenic risk scores for biobank scale data by exploiting phenotypes from inferred relatives

Fig. 2: A decreased effective number of chromosome segments can improve the polygenic prediction accuracy.

The effective number of chromosome segments (Me) (a), the actual prediction accuracy (b) and the fold change of the prediction accuracy from each degree relatives with respect to that from unrelated samples in the large- and small-scale design (c). Accuracy of polygenic scores was calculated as the correlation between the polygenic score and the phenotype adjusted for batch, assessment center, sex, age and ten principal components of ancestry. Me is computed by the inverse of variance of genomic relationships between discovery and target sample. The dot points and error bars in (b) and (c) represent the mean values and 95% confidence intervals from the analyses of 50 complex traits. The boxplots (b) show the first to the third quartile of prediction accuracies for 50 complex traits and the whiskers reflect the maximum and minimum values within 1.5 × interquantile range for each group.

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