Application to UK Biobank

We applied LDAK-KVIK to 40 quantiative traits from the UK Biobank, and compared its performance to Regenie, Bolt-LMM, and classical regression.

For every trait, we first evaluated the number of independent significantly associated loci for each method. Next, we computed the percentage difference in number of significant loci with linear regression. These are plotted against the estimated SNP heritability of the trait.

We found that LDAK-KVIK, Regenie and Bolt-LMM all had increased power over classical linear regression, with increasing power for SNPs with higher heritabiliy. For most traits, LDAK-KVIK identified more statistically significant loci compared to Regenie, but less than Bolt-LMM.