Extended Data Fig. 6: Performance evaluation of HDL-L and LAVA in simulated genetic analysis with fully overlapping samples.

The figure presents the comparative analysis of HDL-L and LAVA in estimating heritability and genetic covariance from 50 simulation repeats. The predetermined genome-wide true genetic correlation was varying from −0.5, 0, 0.5, with the heritability of trait 1 (\({h}_{1}^{2}\)) on the whole genome set at 0.2, the heritability of trait 2 (\({h}_{2}^{2}\)) on the whole genome set at 0.4, and 10% of SNPs were randomly selected as causal variants. The analysis was conducted on 2,468 genomic loci and 50 simulation replicates. For the boxplots, the central line in each box marks the median value, the lower and upper edges represent the first and third quartiles (Q1 and Q3), and the whiskers extend 1.5 \(\times\) IQR (interquartile range) beyond Q1 or Q3. a, Boxplots of false positive rate. b, P-value distribution under null hypothesis. The P-value was derived by comparing the two-sided likelihood ratio test (LRT) statistic to a chi-squared distribution with 1 degree of freedom. c, Boxplots of true positive rate. d, Boxplots of mean squared error for heritabilities and genetic covariance.