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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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)
Study Identifiers Sample Numbers Sample Ancestry Cohort(s)
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
— 9,671 individuals,
100.0 % Male samples
 European UKB — — — — —

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
PPM019509 PSS011221|
European Ancestry|
68,516 individuals
 PGP000517 |
Monti R et al. Am J Hum Genet (2024)
 Reported Trait: Prostate cancer OR: 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] 0 beta = log(or)/sd_pgs
PPM019510 PSS011232|
European Ancestry|
171,474 individuals
 PGP000517 |
Monti R et al. Am J Hum Genet (2024)
 Reported Trait: Prostate cancer OR: 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] 0 beta = log(or)/sd_pgs
PPM019511 PSS011245|
South Asian Ancestry|
19,738 individuals
 PGP000517 |
Monti R et al. Am J Hum Genet (2024)
 Reported Trait: Prostate cancer OR: 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] 0 beta = log(or)/sd_pgs
PPM019512 PSS011261|
European Ancestry|
31,410 individuals
 PGP000517 |
Monti R et al. Am J Hum Genet (2024)
 Reported Trait: Prostate cancer OR: 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] 0 beta = log(or)/sd_pgs
PPM019513 PSS011289|
South Asian Ancestry|
4,976 individuals
 PGP000517 |
Monti R et al. Am J Hum Genet (2024)
 Reported Trait: Prostate cancer OR: 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] 0 beta = log(or)/sd_pgs
PPM019514 PSS011274|
European Ancestry|
41,305 individuals
 PGP000517 |
Monti R et al. Am J Hum Genet (2024)
 Reported Trait: Prostate cancer OR: 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] 0 beta = log(or)/sd_pgs

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
PSS011274 — —
[
  • 2,417 cases
  • , 38,888 controls
]
,
100.0 % Male samples
 — European — UKB —
PSS011245 — —
[
  • 95 cases
  • , 19,643 controls
]
,
100.0 % Male samples
 — South Asian — G&H —
PSS011221 — —
[
  • 2,227 cases
  • , 66,289 controls
]
,
100.0 % Male samples
 — European — EB —
PSS011289 — —
[
  • 110 cases
  • , 4,866 controls
]
,
100.0 % Male samples
 — South Asian — UKB —
PSS011261 — —
[
  • 2,242 cases
  • , 29,168 controls
]
,
100.0 % Male samples
 — European — HUNT —
PSS011232 C3_PROSTATE, ICD10: C61, ICD9: 185 —
[
  • 13,606 cases
  • , 157,868 controls
]
,
100.0 % Male samples
 — European — FinnGen —