Table 1.
The optimal PRSs associated with risks of stroke and its subtypes in the training sets
| Outcomes | Method | PRS source* | No of variants | ORSD (95% CI) | P value | Note |
| Any stroke (N=7412 pairs) | ||||||
| Previous study | PGS002259 | 448 | 1.13 (1.09 to 1.16) | 1.44×10–11 | ||
| C+T | GCST005838 (p=1×10-6, r2=0) | 38 | 1.11 (1.07 to 1.14) | 1.90×10–9 | ||
| LDpred | GCST005838 (ρ=0.01, Ref=1KGP-EAS) | 1 017 531 | 1.14 (1.10 to 1.18) | 3.38×10–14 | Optimal | |
| Ischaemic stroke (N=3844 pairs) | ||||||
| Previous study | PGS000039 | 1 563 569 | 1.07 (1.01 to 1.12) | 0.012 | ||
| C+T | GCST90018864 (p=0.02, r2=0.8) | 32 158 | 1.18 (1.13 to 1.24) | 3.55×10–11 | Optimal | |
| LDpred | GCST90018864 (ρ=0.01, Ref=1KGP-EUR) | 1 017 672 | 1.17 (1.11 to 1.23) | 1.46×10–9 | ||
| Intracerebral haemorrhage (N=4296 pairs) | ||||||
| C+T | GCST90018870 (p=0.001, r2=0.2) | 1326 | 1.09 (1.04 to 1.14) | 1.37×10–4 | ||
| LDpred | GCST90018870 (ρ=0.1, Ref=1KGP-EUR) | 1 017 664 | 1.10 (1.05 to 1.15) | 3.09×10–5 | Optimal | |
| Subarachnoid haemorrhage (N=359 pairs) | ||||||
| C+T | GCST90018703 (p=0.4, r2=0) | 7899 | 1.25 (1.06 to 1.47) | 9.21×10–3 | Optimal | |
| LDpred | GCST90018923 (ρ=0.01, Ref=1KGP-EUR) | 1 017 665 | 1.15 (0.98 to 1.35) | 0.096 | ||
The current table only displays the optimal PRS obtained from different strategies (previous study, C+T and LDpred) for each disease outcome. The detailed results of all PRSs can be found in online supplemental table 7.
*'PGS’ indicates the index in the PGS Catalogue. ‘GCST’ indicates the index in the GWAS Catalogue. The information in brackets is the parameter used for developing the PRS.
C+T, clumping and thresholding; EAS, East Asian; EUR, European; 1KGP, 1000 Genomes Project (Phase 3); PRS, polygenic risk score; Ref, reference population.