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
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 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.Show more
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)
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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 AmericanNR
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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.

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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
PPM018569PSS011035|
European Ancestry|
13,781 individuals
PGP000488 |
Wang A W et al. Nature Genetics (2023)
Reported Trait: Prostate CancerOR: 2.09—Odds ratio (OR, top 10% vs 40-60%): 3.95Age, 10 PCs—
PPM018570PSS011030|
European Ancestry|
30,898 individuals
PGP000488 |
Wang A W et al. Nature Genetics (2023)
Reported Trait: Prostate CancerOR: 2.32—Odds ratio (OR, top 10% vs 40-60%): 3.51Age, 10 PCs—
PPM018572PSS011034|
African Ancestry|
639 individuals
PGP000488 |
Wang A W et al. Nature Genetics (2023)
Reported Trait: Prostate CancerOR: 1.76—Odds ratio (OR, top 10% vs 40-60%): 3.54Age, 10 PCs—
PPM018573PSS011031|
African Ancestry|
4,665 individuals
PGP000488 |
Wang A W et al. Nature Genetics (2023)
Reported Trait: Prostate CancerOR: 1.78—Odds ratio (OR, top 10% vs 40-60%): 3.54Age, sub-studies, 10 PCs—
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Evaluated Samples

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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
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—
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—
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