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
GRM	Phenotype	SNPs (N)	Samples (N)	V(G)/Vp ± SE (%)	V(G)/Vp_L ± SE (%)	V(G)/Vp_L ± SE (%)	P value
Common SNPs	PCa	49534	780^a	48.19 ± 22.2	17.78 ± 8.19		4.77E-03
Common SNPs	HRPCa	49534	679^a	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	780^a	50.7 ± 25.13	18.7 ± 9.27		0.014
Common + Rare SNPs	HRPCa	80421	679^a	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	780^a	13.73 ± 4.82	5.07 ± 1.78		1.59E-25
HRPCa top SNPs	HRPCa	24	679^a	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.

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