Polygenic Score (PGS) ID: PGS003415

Predicted Trait
Reported Trait Prostate cancer
Mapped Trait(s) prostate carcinoma (EFO_0001663)
Released in PGS Catalog: Feb. 8, 2023
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Score Details

Score Construction
PGS Name PGS268_PCa
Development Method
Name Genome-wide rare pathogenic variants
Parameters NR
Variants
Original Genome Build NR
Number of Variants 268
Effect Weight Type beta
PGS Source
PGS Catalog Publication (PGP) ID PGP000428
Citation (link to publication) Nyberg T et al. J Clin Oncol (2022)
Ancestry Distribution
Source of Variant
Associations (GWAS)
European: 84.9%
East Asian: 7.3%
African: 5.7%
Hispanic or Latin American: 2.1%
374,507 individuals (100%)
Score Development/Training
European: 100%
20,952 individuals (100%)
PGS Evaluation
European: 100%
1 Sample Sets

Development Samples

Source of Variant Associations (GWAS)
Study Identifiers Sample Numbers Sample Ancestry Cohort(s)
GWAS Catalog: GCST011049
Europe PMC: 33398198
 177,526 individuals European NR
GWAS Catalog: GCST011049
Europe PMC: 33398198
 21,354 individuals African American or Afro-Caribbean,African unspecified NR
GWAS Catalog: GCST011049
Europe PMC: 33398198
 27,420 individuals East Asian NR
GWAS Catalog: GCST011049
Europe PMC: 33398198
 7,953 individuals Hispanic or Latin American NR
GWAS Catalog: GCST006085
Europe PMC: 29892016
 140,254 individuals European NR
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
—
[
  • 16,633 cases
  • , 4,319 controls
]
,
100.0 % Male samples
 European UKGPCS — — — — —

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
PPM017067 PSS010112|
European Ancestry|
170,850 individuals
 PGP000428 |
Nyberg T et al. J Clin Oncol (2022)
 Reported Trait: 5 years incident prostate cancer risk — C-index: 0.79 [0.783, 0.797] — — —
PPM017068 PSS010112|
European Ancestry|
170,850 individuals
 PGP000428 |
Nyberg T et al. J Clin Oncol (2022)
 Reported Trait: 10 years incident prostate cancer risk — C-index: 0.772 [0.768, 0.777] — — —

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
PSS010112 — — 170,850 individuals,
100.0 % Male samples
 — European — UKB —