Polygenic Score (PGS) ID: PGS002792

Predicted Trait
Reported Trait Prostate cancer
Mapped Trait(s) prostate carcinoma (EFO_0001663)
Released in PGS Catalog: Sept. 29, 2022
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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 PRS67_Pca
Development Method
Name Genome-wide significant SNPs
Parameters NR
Variants
Original Genome Build NR
Number of Variants 67
Effect Weight Type log(OR)
PGS Source
PGS Catalog Publication (PGP) ID PGP000371
Citation (link to publication) Ruan X et al. Prostate (2022)
Ancestry Distribution
Source of Variant
Associations (GWAS)
European: 91.2%
Multi-ancestry (including European): 3.2%
  • European
  • Hispanic or Latin American
  • African
  • East Asian
  • Additional Diverse Ancestries
  • Not Reported
Not Reported: 2.1%
African: 1.9%
East Asian: 1.3%
Hispanic or Latin American: 0.4%
549,905 individuals (100%)
Score Development/Training
European: 96.2%
African: 2.8%
East Asian: 1.1%
109,323 individuals (100%)
PGS Evaluation
African: 100%
1 Sample Sets

Development Samples

Source of Variant Associations (GWAS)
Study Identifiers Sample Numbers Sample Ancestry Cohort(s)
GWAS Catalog: GCST001942
Europe PMC: 23535732
22,548 individuals European NR
Europe PMC: 20197460
[
  • 8,309 cases
  • , 9,286 controls
]
,
100.0 % Male samples
European, Hispanic or Latin American, African unspecified, East Asian, Oceanian, Not reported
(White, Hispanic, Black, Japanese, Native Hawaiian, Unknown)
NR
GWAS Catalog: GCST001148
Europe PMC: 21743467
13,560 individuals European NR
GWAS Catalog: GCST000488
Europe PMC: 19767753
3,748 individuals European NR
GWAS Catalog: GCST000153
Europe PMC: 18264098
23,226 individuals European NR
GWAS Catalog: GCST000489
Europe PMC: 19767754
37,350 individuals European NR
GWAS Catalog: GCST011048
Europe PMC: 33398198
177,526 individuals European NR
GWAS Catalog: GCST002606
Europe PMC: 25217961
67,543 individuals European NR
GWAS Catalog: GCST002606
Europe PMC: 25217961
10,463 individuals Sub-Saharan African, African American or Afro-Caribbean NR
GWAS Catalog: GCST002606
Europe PMC: 25217961
6,954 individuals East Asian NR
GWAS Catalog: GCST002606
Europe PMC: 25217961
2,080 individuals Hispanic or Latin American NR
GWAS Catalog: GCST006083
Europe PMC: 29892016
73,475 individuals European NR
GWAS Catalog: GCST000154
Europe PMC: 18264096
2,329 individuals European NR
Europe PMC: 19767752
[
  • 5,504 cases
  • , 5,834 controls
]
,
100.0 % Male samples
Not reported NR
GWAS Catalog: GCST000017
Europe PMC: 17401363
2,329 individuals European NR
GWAS Catalog: GCST000019
Europe PMC: 17401366
4,517 individuals European NR
GWAS Catalog: GCST000128
Europe PMC: 18073375
2,834 individuals European NR
Europe PMC: 18758462
[
  • 2,899 cases
  • , 1,722 controls
]
,
100.0 % Male samples
European NR
GWAS Catalog: GCST000152
Europe PMC: 18264097
3,748 individuals European NR
GWAS Catalog: GCST001147
Europe PMC: 21743057
7,240 individuals European NR
Europe PMC: 26025378
[
  • 25,723 cases
  • , 26,274 controls
]
,
100.0 % Male samples
European NR
GWAS Catalog: GCST000307
Europe PMC: 19117981
2,834 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
105,126 individuals European UKB
3,008 individuals African American or Afro-Caribbean
(African American)
AAPC
1,189 individuals East Asian
(Chinese)
NR ChinaPCa

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
PPM015449 PSS009955|
African Ancestry|
3,008 individuals
PGP000371 |
Ruan X et al. Prostate (2022)
Reported Trait: Prostate cancer risk Odds Ratio (OR, top vs average percentile): 1.77 [1.22, 2.58] disease diagnostic age or age at recruitment, subgroups and 10 principal components

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
PSS009955 3,008 individuals African American or Afro-Caribbean
(African American)
AAPC