Polygenic Score (PGS) ID: PGS005099

Predicted Trait
Reported Trait Prostate specific antigen
Mapped Trait(s) prostate specific antigen amount (OBA_2050200)
Additional Trait Information log(PSA) in men without prostate cancer
Released in PGS Catalog: Feb. 26, 2025
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Terms and Licenses
PGS obtained from the Catalog should be cited appropriately, and used in accordance with any licensing restrictions set by the authors. See EBI Terms of Use (https://www.ebi.ac.uk/about/terms-of-use/) for additional details.

Score Details

Score Construction
PGS Name psa2024_prs_447
Development Method
Name mJam
Parameters P<5e-8, r2<0.01, Independent from mJam
Variants
Original Genome Build GRCh37
Number of Variants 447
Effect Weight Type beta
PGS Source
PGS Catalog Publication (PGP) ID PGP000692
Citation (link to publication) Hoffmann TJ et al. Nat Genet (2025)
Ancestry Distribution
Score Development/Training
European: 75.7%
African: 15.7%
Hispanic or Latin American: 6.8%
Additional Asian Ancestries: 1.8%
392,522 individuals (100%)
PGS Evaluation
African: 28.6%
European: 28.6%
Hispanic or Latin American: 14.3%
Additional Asian Ancestries: 14.3%
Additional Diverse Ancestries: 14.3%
7 Sample Sets

Development Samples

Score Development/Training
Study Identifiers Sample Numbers Sample Ancestry Cohort(s) Phenotype Definitions & Methods Age of Study Participants Participant Follow-up Time Additional Ancestry Description Additional Sample/Cohort Information
GWAS Catalog: GCST90461907
Europe PMC: 39930085
 61,745 individuals African unspecified 12 cohorts
  • AAPC
  • ,BioMe
  • ,BioVU
  • ,COMPASS
  • ,GERA
  • ,MADCaP
  • ,MDC
  • ,MEC
  • ,MVP
  • ,PLCO
  • ,SCCS
  • ,UKB
 — — — — —
GWAS Catalog: GCST90461907
Europe PMC: 39930085
 6,967 individuals Asian unspecified 12 cohorts
  • AAPC
  • ,BioMe
  • ,BioVU
  • ,COMPASS
  • ,GERA
  • ,MADCaP
  • ,MDC
  • ,MEC
  • ,MVP
  • ,PLCO
  • ,SCCS
  • ,UKB
 — — — — —
GWAS Catalog: GCST90461907
Europe PMC: 39930085
 297,166 individuals European 12 cohorts
  • AAPC
  • ,BioMe
  • ,BioVU
  • ,COMPASS
  • ,GERA
  • ,MADCaP
  • ,MDC
  • ,MEC
  • ,MVP
  • ,PLCO
  • ,SCCS
  • ,UKB
 — — — — —
GWAS Catalog: GCST90461907
Europe PMC: 39930085
 26,644 individuals Hispanic or Latin American 12 cohorts
  • AAPC
  • ,BioMe
  • ,BioVU
  • ,COMPASS
  • ,GERA
  • ,MADCaP
  • ,MDC
  • ,MEC
  • ,MVP
  • ,PLCO
  • ,SCCS
  • ,UKB
 — — — — —

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) 		PGS Sample Set ID
(PSS) 		Performance Source Trait PGS Effect Sizes
(per SD change) 		Classification Metrics Other Metrics Covariates Included in the Model PGS Performance:
Other Relevant Information
PPM022209 PSS011850|
European Ancestry|
22,173 individuals
 PGP000692 |
Hoffmann TJ et al. Nat Genet (2025)
 Reported Trait: log(PSA) — — Partial R2: 0.109 age, ancestry pcs Partial r2: variation explained by the PGS only, but derived from a fully adjusted model that includes listed covariates
PPM022213 PSS011848|
African Ancestry|
1,173 individuals
 PGP000692 |
Hoffmann TJ et al. Nat Genet (2025)
 Reported Trait: log(PSA) — — Partial R2: 0.07 age, ancestry pcs Partial r2: variation explained by the PGS only, but derived from a fully adjusted model that includes listed covariates
PPM022217 PSS011849|
Additional Asian Ancestries|
257 individuals
 PGP000692 |
Hoffmann TJ et al. Nat Genet (2025)
 Reported Trait: log(PSA) — — Partial R2: 0.035 age, ancestry pcs Partial r2: variation explained by the PGS only, but derived from a fully adjusted model that includes listed covariates
PPM022221 PSS011846|
European Ancestry|
11,922 individuals
 PGP000692 |
Hoffmann TJ et al. Nat Genet (2025)
 Reported Trait: log(PSA) — — Partial R2: 0.113 age, ancestry pcs Partial r2: variation explained by the PGS only, but derived from a fully adjusted model that includes listed covariates
PPM022225 PSS011844|
African Ancestry|
2,469 individuals
 PGP000692 |
Hoffmann TJ et al. Nat Genet (2025)
 Reported Trait: log(PSA) — — Partial R2: 0.053 age, ancestry pcs Partial r2: variation explained by the PGS only, but derived from a fully adjusted model that includes listed covariates
PPM022229 PSS011847|
Additional Diverse Ancestries|
1,783 individuals
 PGP000692 |
Hoffmann TJ et al. Nat Genet (2025)
 Reported Trait: log(PSA) — — Partial R2: 0.086 age, ancestry pcs Partial r2: variation explained by the PGS only, but derived from a fully adjusted model that includes listed covariates
PPM022233 PSS011845|
Hispanic or Latin American Ancestry|
1,336 individuals
 PGP000692 |
Hoffmann TJ et al. Nat Genet (2025)
 Reported Trait: log(PSA) — — Partial R2: 0.096 age, ancestry pcs Partial r2: variation explained by the PGS only, but derived from a fully adjusted model that includes listed covariates

Evaluated Samples

PGS Sample Set ID
(PSS) 		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
PSS011844 Prostate specific antigen — 2,469 individuals,
100.0 % Male samples
 — African unspecified — AllofUs —
PSS011845 Prostate specific antigen — 1,336 individuals,
100.0 % Male samples
 — Hispanic or Latin American — AllofUs —
PSS011846 Prostate specific antigen — 11,922 individuals,
100.0 % Male samples
 — European — AllofUs —
PSS011847 Prostate specific antigen — 1,783 individuals,
100.0 % Male samples
 — Other — AllofUs —
PSS011848 Prostate specific antigen — 1,173 individuals,
100.0 % Male samples
 — African unspecified — SELECT —
PSS011849 Prostate specific antigen — 257 individuals,
100.0 % Male samples
 — Asian unspecified — SELECT —
PSS011850 Prostate specific antigen — 22,173 individuals,
100.0 % Male samples
 — European — SELECT —