Polygenic Score (PGS) ID: PGS000333

Predicted Trait
Reported Trait Prostate cancer
Mapped Trait(s) prostate carcinoma (EFO_0001663)
Released in PGS Catalog: Sept. 18, 2020
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Score Details

Score Construction
PGS Name PRS_PC
Variants
Original Genome Build hg19
Number of Variants 6,606,785
Development Method
Name LDpred
Parameters ρ = 0.01; LD radius = 4000; LD reference panel = 2,690 Finnish individuals [autosomal variants only]
PGS Source
PGS Catalog Publication (PGP) ID PGP000100
Citation (link to publication) Mars N et al. Nat Med (2020)

Contributing Samples

Source of Variant Associations (GWAS)
Study Identifiers Sample Numbers Sample Ancestry
GWAS Catalog: GCST006085
EuropePMC: 29892016		 140,254 individuals European
Score Development/Training
Phenotype Definitions and Methods Participant Follow-up Time Sample Numbers Age of Study Participants Sample Ancestry Additional Ancestry Description Cohort(s) Additional Sample/Cohort Information
National registries were used to assess disease incidence. Follow-up ended at first-ever diagnosis of the disease of interest, death or at the end of follow-up on December 31, 2018, whichever came first. Disease endpoints are defined in Table S9. — 21,813 individuals,
47.3 % Male samples
 Mean (Age At Baseline) = 48.0 years European
(Finnish)		 — FINRISK Used to select optimal threshold of ρ for all subsequent analyses. FINRISK surveys from 1992, 1997, 2002 and 2007

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 ID
(PPM ID) 		PGS Sample Set ID
(PSS ID) 		Performance Source Trait PGS Effect Sizes
(per SD change) 		PGS Classification Metrics Other Metrics Covariates Included in the Model PGS Performance: Other Relevant Information
PPM000890 PSS000446 PGP000100
Mars N et al. (2020) 		Reported Trait: Prostate cancer (incident and prevalent cases) HR: 1.83 [1.78, 1.9] — — genotyping array/batch, 10 ancestry PCs —
PPM000895 PSS000447 PGP000100
Mars N et al. (2020) 		Reported Trait: Incident prostate cancer — C-index: 0.857 — age, genotyping array/batch, 10 ancestry PCs 10-year risk
PPM000900 PSS000447 PGP000100
Mars N et al. (2020) 		Reported Trait: Incident prostate cancer — C-index: 0.866 — age, family history, history of benign prostate hyperplasia, genotyping array/batch, 10 ancestry PCs 10-year risk

Evaluated Samples

PGS Sample Set ID
(PSS ID) 		Phenotype Definitions and Methods Participant Follow-up Time Sample Numbers Age of Study Participants Sample Ancestry Additional Ancestry Description Cohort(s) Additional Sample/Cohort Information
PSS000446 National registries were used to assess disease incidence. Follow-up ended at first-ever diagnosis of the disease of interest, death or at the end of follow-up on December 31, 2018, whichever came first. Disease endpoints are defined in Table S9. —
[
  • 3,617 cases
  • , 55,509 controls
]
,
100.0 % Male samples
 — European
(Finnish)		 — FinnGen —
PSS000447 National registries were used to assess disease incidence. Follow-up ended at first-ever diagnosis of the disease of interest, death or at the end of follow-up on December 31, 2018, whichever came first. Disease endpoints are defined in Table S9. —
[
  • 1,172 cases
  • , 47,679 controls
]
 — European
(Finnish)		 — FinnGen —