Extended Data Fig. 6: Reduced quality control for UKBb GWAS.
From: Evaluating and improving heritability models using summary statistics
For our main analysis of the UKBb GWAS, we first identified individuals with values for all 14 phenotypes, then filtered so that no pair remained with allelic correlation >0.02 (Supplementary Note 6). As a secondary analysis, we instead identified individuals with values for any of the 14 phenotypes, then filtered so that no pair remained with allelic correlation >0.03125. This increased the number of individuals from 130,080 to 246,655, with on average 236k phenotypic values per GWAS (range 201k to 247k). The first plot shows that increasing the sample size does not change the ranking of models based on the Akaike Information Criterion. The remaining three plots shows that it does not significantly change estimates of SNP heritability or average functional enrichments from the BLD-LDAK Model, nor estimates of the selection-related parameter α from the BLD-LDAK + Alpha Model (horizontal and vertical segments indicate 95% confidence intervals; numbers indicate how many of the pairs of estimates are inconsistent either nominally or after Bonferroni correction).
