Polygenic Score (PGS) ID: PGS005107

Predicted Trait
Reported Trait Prostate-specific antigen (PSA) levels
Mapped Trait(s) prostate specific antigen amount (OBA_2050200)
Released in PGS Catalog: Dec. 16, 2024
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Score Details

Score Construction
PGS Name PGS-PSA111
Development Method
Name Genome-wide significant SNPs
Parameters Excluded SNPs nominally associated with prostate cancer in unadjusted analyses (p < 0.001) and had same direction of association with prostate cancer and PSA levels with a nominal association (p < 0.05) after index event bias adjustment
Variants
Original Genome Build GRCh37
Number of Variants 111
Effect Weight Type beta
PGS Source
PGS Catalog Publication (PGP) ID PGP000696
Citation (link to publication) Shi M et al. EBioMedicine (2023)
Ancestry Distribution
Source of Variant
Associations (GWAS)
European: 89.6%
African: 3.7%
East Asian: 3.5%
Hispanic or Latin American: 3.2%
95,768 individuals (100%)
PGS Evaluation
Multi-ancestry (including European): 100%
  • European
  • African
1 Sample Sets

Development Samples

Source of Variant Associations (GWAS)
Study Identifiers Sample Numbers Sample Ancestry Cohort(s)
GWAS Catalog: GCST90301330
Europe PMC: 37264206
 85,824 individuals European BioVU, GERA, MDC, PLCO, UKB
GWAS Catalog: GCST90301330
Europe PMC: 37264206
 3,509 individuals African American or Afro-Caribbean BioVU, GERA, MDC, PLCO, UKB
GWAS Catalog: GCST90301330
Europe PMC: 37264206
 3,337 individuals East Asian BioVU, GERA, MDC, PLCO, UKB
GWAS Catalog: GCST90301330
Europe PMC: 37264206
 3,098 individuals Hispanic or Latin American BioVU, GERA, MDC, PLCO, 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
PPM022292 PSS011904|
Multi-ancestry (including European)|
3,110 individuals
 PGP000696 |
Shi M et al. EBioMedicine (2023)
 Reported Trait: Prostate specific antigen level > 4 ng/mL HR: 1.22 [1.11, 1.35] — — Age at first PSA measurement, 10 PCs —

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
PSS011904 — Median = 6.2 years
IQR = [3.7, 10.9] years		 3,110 individuals,
100.0 % Male samples
 Median = 56.6 years
IQR = [51.4, 61.5] years		 European, African unspecified — BioVU No prostate cancer and prostate specific antigen level < 4 mg/mL at baseline