across the genome (unweighted in the case of LDLc), an allelic score consisting of variants from known regions only (i.e. SNPs that met p<5×10−8 in the meta-analysis of the relevant phenotype), and a weighted genome-wide allelic score with known variants (+/−500 KB) removed from the score's construction. This was to contrast the performance of a completely agnostic strategy (i.e. utilizing all the SNPs) versus the strategy of only using known regions in construction of the scores. Finally, we examined the performance of LD pruning (as defined above) on the ability of weighted allelic scores to predict case-control status in the WTCCC dataset.
