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(Variants and weights)

Polygenic Score (PGS) ID: PGS000067

Predicted Trait

Reported Trait: Prostate cancer
Mapped Trait(s) (Experimental Factor Ontology (EFO) IDs): prostate carcinoma

Score Details

Name: PCa_PHS

Original Genome Build: NR
Number of Variants: 54

PGS Development Method: Polygenic Hazard Score
PGS Development Details/Relevant Parameters: Trend test p-value < 1e-6; selection of SNPs by logistic regresssion; SNP weights determined by Cox proportional hazards regression

Citation: Seibert TM et al. BMJ (2018) | PGS Catalog Publication ID: PGP000047

Contributing Samples

Score Development/Training
Detailed Phenotype Description (e.g. ICD/SNOMED codes used to identify cases) Sample Numbers Sample Ancestry Additional Ancestry Description Cohort(s) Additional Sample/Cohort Information
Case numbers refer to "any prostate cancer (PCa)"; of those cases 10 635 have aggressive PCa, and 5406 have very aggressive PCa (Gleason score ≥7, stage T3-T4, PSA concentration ≥10 ng/mL, nodal metastasis, or distant metastasis) 31,747 individuals
[ 18,868 cases, 12,879 controls]
100.00 % Male samples
European PRACTICAL consortium

Performance Metrics

Disclaimer: The performance metrics are displayed as reported by the source studies. It is important to note that metrics are not necessarily comparable with each other. For example, metrics depend on the sample characteristics (described by the PGS Catalog Sample Set [PSS] ID), phenotyping, and statistical modelling. Please refer to the source publication for additional guidance on performance.
PGS Performance Metric (PPM) ID PGS Catalog Sample Set (PSS) ID Performance Source Trait PGS Effect Sizes
(per SD change)
PGS Classification Metrics Other Metrics Covariates Included in PGS Model PGS Performance: Other Relevant Information
PPM000182 PSS000105 Seibert TM et al. (2018) Reported Trait: aggressive prostate cancer HR (Hazard ratio; top 2% vs. average risk): 2.9 [2.4 - 3.4]
PPM000183 PSS000105 Seibert TM et al. (2018) Reported Trait: aggressive prostate cancer (age at onset) z-test (p-value) < 1e-16
PPM000184 PSS000106 Seibert TM et al. (2018) Reported Trait: any prostate cancer HR (Hazard ratio; top 2% vs. average risk): 2.5 [2.2 - 2.8]
PPM000185 PSS000106 Seibert TM et al. (2018) Reported Trait: any prostate cancer (age at onset) z-test (p-value) < 1e-16
PPM000186 PSS000107 Seibert TM et al. (2018) Reported Trait: very aggressive prostate cancer HR (Hazard ratio; top 2% vs. average risk): 3.0 [2.2 - 4.0]
PPM000187 PSS000107 Seibert TM et al. (2018) Reported Trait: very aggressive prostate cancer (age at onset) z-test (p-value) < 1e-11

Evaluated Samples

PGS Catalog Sample Set (PSS) ID Detailed Phenotype Description (e.g. ICD/SNOMED codes used to identify cases) Sample Numbers Sample Ancestry Additional Ancestry Description Cohort(s) Additional Sample/Cohort Information
PSS000105 Men screened with PSA testing, who did not receive a diagnosis of prostate cancer. 4,828 individuals
100.00 % Male samples
European ProtecT
PSS000105 Men screened with PSA testing (3.0 ng/L or higher), who received a diagnosis of aggressive prostate cancer (defined as any of Gleason score ≥7, stage T3-T4, PSA concentration ≥10 ng/mL, nodal metastasis, or distant metastasis) 628 individuals
[ 628 cases]
100.00 % Male samples
European ProtecT
PSS000106 Men screened with PSA testing, who did not receive a diagnosis of prostate cancer. 4,828 individuals
100.00 % Male samples
European ProtecT
PSS000106 Men screened with PSA testing (3.0 ng/L or higher), who received a diagnosis of prostate cancer. 1,583 individuals
[ 1,583 cases]
100.00 % Male samples
European ProtecT
PSS000107 Men screened with PSA testing, who did not receive a diagnosis of prostate cancer. 4,828 individuals
100.00 % Male samples
European ProtecT
PSS000107 Men screened with PSA testing (3.0 ng/L or higher), who received a diagnosis of very aggressive prostate cancer (defined as any of Gleason score ≥8, stage T3-4, positive nodes, or distant metastases) 220 individuals
[ 220 cases]
100.00 % Male samples
European ProtecT