Polygenic Score (PGS) ID: PGS004883

Predicted Trait
Reported Trait Knee osteoarthritis
Mapped Trait(s) osteoarthritis, knee (EFO_0004616)
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_Knee_osteoarthritis
Development Method
Name megaprs.auto
Parameters BayesR, p1=0.69, p2=0.2, p3=0.1, p4=0.01
Variants
Original Genome Build GRCh37
Number of Variants 952,133
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%
403,124 individuals (100%)
Score Development/Training
European: 100%
404 individuals (100%)
PGS Evaluation
European: 100%
7 Sample Sets

Development Samples

Source of Variant Associations (GWAS)
Study Identifiers Sample Numbers Sample Ancestry Cohort(s)
GWAS Catalog: GCST007090
Europe PMC: 30664745
 403,124 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
PPM021238 PSS011600|
European Ancestry|
37,245 individuals
 PGP000618 |
Jermy B et al. Nat Commun (2024)
 Reported Trait: Incident knee osteoarthritis HR: 1.19 [1.17, 1.22] C-index: 0.56 [0.55, 0.57] — PCs 1-10 —
PPM021239 PSS011599|
European Ancestry|
69,715 individuals
 PGP000618 |
Jermy B et al. Nat Commun (2024)
 Reported Trait: Incident knee osteoarthritis HR: 1.32 [1.28, 1.35] C-index: 0.58 [0.57, 0.59] — PCs 1-10 —
PPM021240 PSS011598|
European Ancestry|
29,427 individuals
 PGP000618 |
Jermy B et al. Nat Commun (2024)
 Reported Trait: Incident knee osteoarthritis HR: 1.37 [1.3, 1.44] C-index: 0.6 [0.58, 0.61] — PCs 1-10 —
PPM021241 PSS011596|
European Ancestry|
44,188 individuals
 PGP000618 |
Jermy B et al. Nat Commun (2024)
 Reported Trait: Incident knee osteoarthritis HR: 1.17 [1.1, 1.24] — — PCs 1-10 —
PPM021242 PSS011597|
European Ancestry|
7,018 individuals
 PGP000618 |
Jermy B et al. Nat Commun (2024)
 Reported Trait: Incident knee osteoarthritis HR: 1.28 [1.17, 1.39] C-index: 0.6 [0.57, 0.62] — PCs 1-10 —
PPM021243 PSS011595|
European Ancestry|
412,090 individuals
 PGP000618 |
Jermy B et al. Nat Commun (2024)
 Reported Trait: Incident knee osteoarthritis HR: 1.32 [1.31, 1.34] C-index: 0.59 [0.58, 0.59] — PCs 1-10 —
PPM021244 PSS011594|
European Ancestry|
199,868 individuals
 PGP000618 |
Jermy B et al. Nat Commun (2024)
 Reported Trait: Incident knee osteoarthritis HR: 1.17 [1.16, 1.18] C-index: 0.56 [0.56, 0.56] — 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
PSS011594 — —
[
  • 38,047 cases
  • , 161,821 controls
]
 — European — EB —
PSS011595 — —
[
  • 46,914 cases
  • , 365,176 controls
]
 — European — FinnGen —
PSS011596 — —
[
  • 1,053 cases
  • , 43,135 controls
]
 — European — G&H —
PSS011597 — —
[
  • 538 cases
  • , 6,480 controls
]
 — European — GS:SFHS —
PSS011598 — —
[
  • 1,600 cases
  • , 27,827 controls
]
 — European — GEL —
PSS011599 — —
[
  • 5,041 cases
  • , 64,674 controls
]
 — European — HUNT —
PSS011600 — —
[
  • 8,184 cases
  • , 29,061 controls
]
 — European — MGBB —