Table 1

Performance of different PRS methods on the BCAC-IL cohort

MethodOR per 1SDTop 10% ORSNPs (n)
P+T EUR-LD1.43±0.081.43±0.271483±502
P+T target set LD1.39±0.071.65±0.258591±5136
LDpred21.31±0.071.96±0.43740 919±18
Lassosum1.56±0.092.1±0.2465 632±16 126

  • Performance of different PRS methods on the BCAC-IL cohort. ORs per 1 SD and top 10% OR were obtained using the nested CV outlined in figure 1. The last column is the average number of SNPs. Shown are means and SEMs over the six holdout sets.

  • BCAC-IL, BCAC cohort from Israel; CV, cross validation; PRS, polygenic risk score; P+T EUR-LD, pruning and thresholding using European linkage disequilibrium; P+T target set LD, pruning and thresholding using linkage disequilibrium of the target population.