Polygenic Score (PGS) ID: PGS000662

Predicted Trait
Reported Trait Prostate Cancer
Mapped Trait(s) prostate carcinoma (EFO_0001663)
Released in PGS Catalog: Jan. 7, 2021
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Score Details

Score Construction
PGS Name GRS.PCa.269
Variants
Original Genome Build GRCh37
Number of Variants 269
Development Method
Name Independent genome-wide significant variants identified by fine-mapping using JAM (Joint Analysis of Marginal summary statistics)
Parameters Population-specific betas were combined using an inverse Z-score-weighted fixed-effects meta-analysis to obtain multi-ancestry conditional betas.
PGS Source
PGS Catalog Publication (PGP) ID PGP000122
Citation (link to publication) Conti DV et al. Nat Genet (2021)

Contributing Samples

Source of Variant Associations (GWAS)
Study Identifiers Sample Numbers Sample Ancestry
GWAS Catalog: GCST011049
EuropePMC: 33398198
177,526 individuals,
100.0 % Male samples
European
GWAS Catalog: GCST011049
EuropePMC: 33398198
21,354 individuals,
100.0 % Male samples
African American or Afro-Caribbean, African unspecified
GWAS Catalog: GCST011049
EuropePMC: 33398198
27,420 individuals,
100.0 % Male samples
East Asian
GWAS Catalog: GCST011049
EuropePMC: 33398198
7,953 individuals,
100.0 % Male samples
Hispanic or Latin American

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
PPM001365 PSS000596 PGP000122 Conti DV et al. (2021) Reported Trait: Prostate Cancer AUROC: 0.833 Odds ratio (OR, top 10% versus 40-60% GRS): 4.17
Overall Net Reclassification Index (NRI [%]): 59.4
Age, 10 PCs
PPM001366 PSS000595 PGP000122 Conti DV et al. (2021) Reported Trait: Prostate Cancer AUROC: 0.679 Odds ratio (OR, top 10% versus 40-60% GRS): 3.53 Age, 10 PCs, study

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
PSS000595
[
  • 1,586 cases
  • , 1,047 controls
]
,
100.0 % Male samples
African unspecified CAUG
PSS000596
[
  • 6,852 cases
  • , 193,117 controls
]
,
100.0 % Male samples
European UKB