Polygenic Score (PGS) ID: PGS003766

Predicted Trait
Reported Trait Prostate cancer
Mapped Trait(s) prostate carcinoma (EFO_0001663)
Released in PGS Catalog: Dec. 19, 2023
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Terms and Licenses
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Score Details

Score Construction
PGS Name GRS.PCa.451.TOPMed
Development Method
Name Independent genome-wide significant variants included, identified from fine-mapping GWAS results. Variants were lifted-over from GRCh37 to GRCh38, proxy variants in TOPMED imputation panel were selected if no exact variant was available in TOPMed.
Parameters Variants/weights used were from multi-ancestry GWAS meta-analysis, with fine-mapping performed using mJAM (multi-ancestry Joint Analysis of Marginal summary statistics) to obtain conditional betas within each population.
Variants
Original Genome Build GRCh38
Number of Variants 451
Effect Weight Type beta
PGS Source
PGS Catalog Publication (PGP) ID PGP000488
Citation (link to publication) Wang A W et al. Nature Genetics (2023)
Ancestry Distribution
Source of Variant
Associations (GWAS)
Multi-ancestry (including European): 100%
  • European
  • African
  • East Asian
  • Hispanic or Latin American
944,762 individuals (100%)
PGS Evaluation
African: 50%
European: 50%
4 Sample Sets

Development Samples

Source of Variant Associations (GWAS)
Study Identifiers Sample Numbers Sample Ancestry Cohort(s)
GWAS Catalog: GCST90274713
[
  • 156,319 cases
  • , 788,443 controls
]
,
100.0 % Male samples
 European, African unspecified, East Asian, Hispanic or Latin American NR

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
PPM018569 PSS011035|
European Ancestry|
13,781 individuals
 PGP000488 |
Wang A W et al. Nature Genetics (2023)
 Reported Trait: Prostate Cancer OR: 2.09 — Odds ratio (OR, top 10% vs 40-60%): 3.95 Age, 10 PCs —
PPM018573 PSS011031|
African Ancestry|
4,665 individuals
 PGP000488 |
Wang A W et al. Nature Genetics (2023)
 Reported Trait: Prostate Cancer OR: 1.78 — Odds ratio (OR, top 10% vs 40-60%): 3.54 Age, sub-studies, 10 PCs —
PPM018570 PSS011030|
European Ancestry|
30,898 individuals
 PGP000488 |
Wang A W et al. Nature Genetics (2023)
 Reported Trait: Prostate Cancer OR: 2.32 — Odds ratio (OR, top 10% vs 40-60%): 3.51 Age, 10 PCs —
PPM018572 PSS011034|
African Ancestry|
639 individuals
 PGP000488 |
Wang A W et al. Nature Genetics (2023)
 Reported Trait: Prostate Cancer OR: 1.76 — Odds ratio (OR, top 10% vs 40-60%): 3.54 Age, 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
PSS011034 — —
[
  • 189 cases
  • , 450 controls
]
,
100.0 % Male samples
 — African American or Afro-Caribbean — MGI —
PSS011035 — —
[
  • 3,244 cases
  • , 10,537 controls
]
,
100.0 % Male samples
 — European — MGI —
PSS011030 — —
[
  • 2,352 cases
  • , 28,546 controls
]
,
100.0 % Male samples
 — European — EB —
PSS011031 — —
[
  • 2,505 cases
  • , 2,160 controls
]
,
100.0 % Male samples
 — African unspecified — MADCaP —