Table 3.
GREML (genome-based restricted maximum likelihood) analyses results for proportion of phenotypic variance explained by genetic variance
| GRM | Phenotype | SNPs (N) | Samples (N) | No prevalence specified | At PCa prevalence of 0.001 | At HR PCa prevalence of 0.0004 | P value |
|---|---|---|---|---|---|---|---|
| V(G)/Vp ± SE (%) | V(G)/Vp_L ± SE (%) | V(G)/Vp_L ± SE (%) | |||||
| Common SNPs | PCa | 49534 | 780a | 48.19 ± 22.2 | 17.78 ± 8.19 | 4.77E-03 | |
| Common SNPs | HRPCa | 49534 | 679a | 38.45 ± 26.59 | 16.15 ± 11.17 | 0.065 | |
| Common SNPs | ISUP grade group | 49534 | 372 | 1E-06 ± 44.93 | 0.5 | ||
| Common + Rare SNPs | PCa | 80421 | 780a | 50.7 ± 25.13 | 18.7 ± 9.27 | 0.014 | |
| Common + Rare SNPs | HRPCa | 80421 | 679a | 23.93 ± 25.74 | 8.8 ± 9.47 | 0.148 | |
| Common + Rare SNPs | ISUP grade group | 80421 | 372 | 1E-06 ± 33.84 | 0.5 | ||
| Cases vs controls top SNPs | PCa | 16 | 780a | 13.73 ± 4.82 | 5.07 ± 1.78 | 1.59E-25 | |
| HRPCa top SNPs | HRPCa | 24 | 679a | 25.13 ± 6.29 | 9.24 ± 2.31 | 2.30E-44 | |
| HRPCa top SNPs | HRPCa among cases | 24 | 372 | 25.01 ± 6.81 | 7.78 ± 2.12 | 1.34E-22 | |
| HRPCa top SNPs | ISUP grade group | 24 | 372 | 17.75 ± 5.9 | 3.89E-16 |
Phenotypes included prostate cancer (PCa) diagnosis; high risk prostate cancer (HRPCa), defined as high risk (ISUP 3-5) versus low risk (ISUP 1-2) or no PCa (controls); or ISUP grade group (1 to 5). Genetic relationship matrices (GRM) were constructed using all autosomal SNPs that passed EWAS QC (common SNPs), common plus rare autosomal SNPs, or top autosomal SNPs from EWAS analyses (P < 1E−04). V(G)/Vp refers to the ratio of genetic variance (V(G)) over phenotypic variance (Vp), while V(G)/Vp_L indicates V(G)/Vp transformed to the underlying liability scale based on the prevalence supplied.
SE standard error.
aIncludes samples that are lacking age, which were excluded from EWAS analyses.