Extended Data Fig. 3: Colocalization between GWAS-predicted and observed linkage signals for traits adjusted for polygenic scores (PGS).

a, The correlation between observed linkage signals for PGS-adjusted height and predicted linkage signals from 12,010 height-associated SNPs. b, The correlation between observed linkage signals for PGS-adjusted BMI and predicted linkage signals from 787 BMI-associated SNPs. Height was adjusted using a PGS based on the same 12,010 height-associated SNPs (explaining 38% of height variance), while BMI was adjusted using a PGS including 4,582 SNPs (explaining 9% of BMI variance). The x-axis in each panel displays the correlation (\(\hat{\phi }\)) between observed and predicted (from GWAS results; Methods) linkage signals. In each panel, the vertical dashed line represents the correlation between observed and predicted linkage signals from either height-associated SNPs (a) or 787 BMI-associated SNPs (b). Predicted linkage signals were also obtained under the null hypothesis (that is ‘the correlation between observed and predicted linkage signals is due to the curvature effect’) using 1,000 draws of random SNPs with similar minor allele frequency and linkage disequilibrium properties as trait-associated SNPs. The histogram in each panel represents the distribution of correlations (under the null) between observed linkage for the trait indicated in the corresponding column-panel and predicted linkage obtained from these 1,000 draws. The mean of correlations obtained under the null hypothesis is denoted \({\hat{\phi }}_{{\rm{CE}}}\). The P-values (P) reported in the top-left corner of each panel assess the statistical significance of the difference between \(\hat{\phi }\) and \({\hat{\phi }}_{{\rm{CE}}}\) using a two-sided Wald test. Numeric values are presented in Supplementary Table 10.