At each p-value threshold, for every pair of SNPs with LD r2 > 0.5 in which both SNPs in the pair were below the current p-value threshold, the effect of the SNP with the higher p-value was set to zero, so that the SNP did not contribute to the polygenic score. As a result, all SNPs that remained in the polygenic score after pruning were in low mutual LD (r2 < 0.5).
