Polygenic Score (PGS) ID: PGS004872

Predicted Trait
Reported Trait Prostate cancer
Mapped Trait(s) prostate carcinoma (EFO_0001663)
Released in PGS Catalog: June 27, 2024
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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 INTERVENE_MegaPRS_Prostate_cancer
Development Method
Name megaprs.auto
Parameters BayesR, p1=0.5, p2=0.2, p3=0.2, p4=0.1
Variants
Original Genome Build GRCh37
Number of Variants 765,876
Effect Weight Type beta
PGS Source
PGS Catalog Publication (PGP) ID PGP000618
Citation (link to publication) Jermy B et al. Nat Commun (2024)
Ancestry Distribution
Source of Variant
Associations (GWAS)
European: 100%
140,254 individuals (100%)
Score Development/Training
European: 100%
404 individuals (100%)
PGS Evaluation
European: 100%
8 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
— 404 individuals European 1000G — — — non-Finnish Europeans —

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
PPM021157 PSS011627|
European Ancestry|
204,761 individuals
 PGP000618 |
Jermy B et al. Nat Commun (2024)
 Reported Trait: Incident Prostate Cancer HR: 1.96 [1.92, 1.99] — — PCs 1-10 —
PPM021158 PSS011626|
European Ancestry|
17,270 individuals
 PGP000618 |
Jermy B et al. Nat Commun (2024)
 Reported Trait: Incident Prostate Cancer HR: 1.66 [1.59, 1.73] C-index: 0.65 [0.64, 0.66] — PCs 1-10 —
PPM021159 PSS011625|
European Ancestry|
32,747 individuals
 PGP000618 |
Jermy B et al. Nat Commun (2024)
 Reported Trait: Incident Prostate Cancer HR: 1.85 [1.77, 1.93] C-index: 0.67 [0.65, 0.68] — PCs 1-10 —
PPM021160 PSS011624|
European Ancestry|
12,058 individuals
 PGP000618 |
Jermy B et al. Nat Commun (2024)
 Reported Trait: Incident Prostate Cancer HR: 1.86 [1.74, 2.0] C-index: 0.68 [0.66, 0.7] — PCs 1-10 —
PPM021161 PSS011622|
European Ancestry|
19,798 individuals
 PGP000618 |
Jermy B et al. Nat Commun (2024)
 Reported Trait: Incident Prostate Cancer HR: 2.12 [1.69, 2.66] — — PCs 1-10 —
PPM021163 PSS011621|
European Ancestry|
181,814 individuals
 PGP000618 |
Jermy B et al. Nat Commun (2024)
 Reported Trait: Incident Prostate Cancer HR: 1.98 [1.94, 2.01] C-index: 0.69 [0.69, 0.7] — PCs 1-10 —
PPM021164 PSS011620|
European Ancestry|
68,883 individuals
 PGP000618 |
Jermy B et al. Nat Commun (2024)
 Reported Trait: Incident Prostate Cancer HR: 1.79 [1.72, 1.87] C-index: 0.67 [0.65, 0.68] — PCs 1-10 —
PPM021162 PSS011623|
European Ancestry|
7,018 individuals
 PGP000618 |
Jermy B et al. Nat Commun (2024)
 Reported Trait: Incident Prostate Cancer HR: 1.61 [1.42, 1.83] C-index: 0.66 [0.62, 0.7] — PCs 1-10 —

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
PSS011620 — —
[
  • 2,142 cases
  • , 66,741 controls
]
 — European — EB —
PSS011621 — —
[
  • 13,697 cases
  • , 168,117 controls
]
 — European — FinnGen —
PSS011622 — —
[
  • 86 cases
  • , 19,712 controls
]
 — European — G&H —
PSS011623 — —
[
  • 226 cases
  • , 6,792 controls
]
 — European — GS:SFHS —
PSS011624 — —
[
  • 854 cases
  • , 11,204 controls
]
 — European — GEL —
PSS011625 — —
[
  • 1,987 cases
  • , 30,760 controls
]
 — European — HUNT —
PSS011626 — —
[
  • 2,332 cases
  • , 14,938 controls
]
 — European — MGBB —
PSS011627 — —
[
  • 11,638 cases
  • , 193,123 controls
]
 — European — UKB —