Polygenic Score (PGS) ID: PGS004042

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 ldpred2.CV.GCST006085.Prostate_cancer
Development Method
Name LDpred2.CV
Parameters p:0.01,h2:0.1292,nosparse
Variants
Original Genome Build GRCh38
Number of Variants 1,045,276
Effect Weight Type beta
PGS Source
PGS Catalog Publication (PGP) ID PGP000517
Citation (link to publication) Monti R et al. Am J Hum Genet (2024)
Ancestry Distribution
Source of Variant
Associations (GWAS)
European: 100%
140,254 individuals (100%)
Score Development/Training
European: 100%
9,671 individuals (100%)
PGS Evaluation
European: 66.7%
South Asian: 33.3%
6 Sample Sets

Development Samples

Source of Variant Associations (GWAS)
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Study Identifiers
Sample Numbers
Sample Ancestry
Cohort(s)
GWAS Catalog: GCST006085
Europe PMC: 29892016
140,254 individualsEuropeanNR
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Score Development/Training
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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
—9,671 individuals,
100.0 % Male samples
EuropeanUKB—————
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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
PPM019509PSS011221|
European Ancestry|
68,516 individuals
PGP000517 |
Monti R et al. Am J Hum Genet (2024)
Reported Trait: Prostate cancerOR: 1.84253 [1.76511474, 1.9233483]
β: 0.61114 [0.5682157, 0.65406757]		AUROC: 0.66712 [0.65580582, 0.67842704]R²: 0.08368 [0.07334262, 0.09443435]0beta = log(or)/sd_pgs
PPM019510PSS011232|
European Ancestry|
171,474 individuals
PGP000517 |
Monti R et al. Am J Hum Genet (2024)
Reported Trait: Prostate cancerOR: 2.11238 [2.07329005, 2.15220653]
β: 0.74782 [0.72913674, 0.76649361]		AUROC: 0.69944 [0.69492796, 0.7039464]R²: 0.12024 [0.1150319, 0.12575818]0beta = log(or)/sd_pgs
PPM019511PSS011245|
South Asian Ancestry|
19,738 individuals
PGP000517 |
Monti R et al. Am J Hum Genet (2024)
Reported Trait: Prostate cancerOR: 2.18207 [1.79180061, 2.65733751]
β: 0.78027 [0.58322104, 0.97732469]		AUROC: 0.71782 [0.66712303, 0.76852111]R²: 0.09364 [0.05088803, 0.14629713]0beta = log(or)/sd_pgs
PPM019512PSS011261|
European Ancestry|
31,410 individuals
PGP000517 |
Monti R et al. Am J Hum Genet (2024)
Reported Trait: Prostate cancerOR: 1.93239 [1.8472515, 2.02145706]
β: 0.65876 [0.61369886, 0.70381857]		AUROC: 0.67779 [0.66648658, 0.68909316]R²: 0.0943 [0.0823039, 0.10674354]0beta = log(or)/sd_pgs
PPM019513PSS011289|
South Asian Ancestry|
4,976 individuals
PGP000517 |
Monti R et al. Am J Hum Genet (2024)
Reported Trait: Prostate cancerOR: 2.29829 [1.90607316, 2.77121128]
β: 0.83216 [0.64504519, 1.01928451]		AUROC: 0.727 [0.68076039, 0.77324327]R²: 0.10782 [0.06568955, 0.16319521]0beta = log(or)/sd_pgs
PPM019514PSS011274|
European Ancestry|
41,305 individuals
PGP000517 |
Monti R et al. Am J Hum Genet (2024)
Reported Trait: Prostate cancerOR: 2.05028 [1.96459765, 2.13969686]
β: 0.71798 [0.67528746, 0.76066416]		AUROC: 0.69166 [0.68106518, 0.70224548]R²: 0.11435 [0.10241705, 0.12708645]0beta = log(or)/sd_pgs
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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
PSS011221——
[
  • 2,227 cases
  • , 66,289 controls
]
,
100.0 % Male samples
—European—EB—
PSS011232C3_PROSTATE, ICD10: C61, ICD9: 185—
[
  • 13,606 cases
  • , 157,868 controls
]
,
100.0 % Male samples
—European—FinnGen—
PSS011245——
[
  • 95 cases
  • , 19,643 controls
]
,
100.0 % Male samples
—South Asian—G&H—
PSS011261——
[
  • 2,242 cases
  • , 29,168 controls
]
,
100.0 % Male samples
—European—HUNT—
PSS011274——
[
  • 2,417 cases
  • , 38,888 controls
]
,
100.0 % Male samples
—European—UKB—
PSS011289——
[
  • 110 cases
  • , 4,866 controls
]
,
100.0 % Male samples
—South Asian—UKB—
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