Polygenic Score (PGS) ID: PGS004928

Predicted Trait
Reported Trait Metabolic syndrome
Mapped Trait(s) metabolic syndrome (EFO_0000195)
Released in PGS Catalog: Oct. 29, 2024
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Score Details

Score Construction
PGS Name MetS_gSEM
Development Method
Name PRS-CS
Parameters Reference panel = 1000 Genomes phase 3 European, phi = 0.01, a = 1, b = 0.5, Monte Carlo iteration = 1000, burn-in interations = 500, Markov chain thinning factor = 5
Variants
Original Genome Build GRCh37
Number of Variants 916,017
Effect Weight Type beta
PGS Source
PGS Catalog Publication (PGP) ID PGP000664
Citation (link to publication) Park S et al. Nat Genet (2024)
Ancestry Distribution
Source of Variant
Associations (GWAS)
European: 100%
1,252,787 individuals (100%)
PGS Evaluation
East Asian: 50%
European: 50%
2 Sample Sets

Development Samples

Source of Variant Associations (GWAS)
Study Identifiers Sample Numbers Sample Ancestry Cohort(s)
GWAS Catalog: GCST90444488
 1,252,787 individuals European FinnGen, GIANT, GLGC, MAGIC, MVP

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
PPM021715 PSS011760|
East Asian Ancestry|
62,314 individuals
 PGP000664 |
Park S et al. Nat Genet (2024)
 Reported Trait: Metabolic syndrome OR: 1.18 [1.155, 1.205] — R²: 0.018 sex, age, genetic PCs (1-10) Logistic regression, Computed McFadden's pseudo-R^2
PPM021714 PSS011761|
European Ancestry|
11,139 individuals
 PGP000664 |
Park S et al. Nat Genet (2024)
 Reported Trait: Metabolic syndrome OR: 1.239 [1.191, 1.289] — R²: 0.046 sex, age, genetic PCs (1-10) Logistic regression, Computed McFadden's pseudo-R^2

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
PSS011760 We used criteria defined by AHA/NHLBI was used to define MetS for individuals in KoGES. The criteria are as follows: elevated waist circumference (Asian with WCmen ≥90 cm and WCwomen ≥80 cm, elevated TG (TG ≥150 mg/dL), sex-specific reduced HDL-C (HDL-Cmen <40 mg/dL and HDL-Cwomen <50 mg/dL), elevated blood pressure (systolic ≥130 mmHg and diastolic ≥85 mmHg), and elevated FG (FG ≥100 mg/dL). The individuals were categorized as MetS positive if they satisfied three out of five criteria. —
[
  • 10,684 cases
  • , 51,630 controls
]
 — East Asian
(Korean)		 — KoGES —
PSS011761 We assigned the dichotomous MetS status based on AHA/NHLBI that consists of five criteria as follows: population- and sex-specific elevated waist circumference (WC, European with WCmen ≥102 cm and WCwomen ≥88 cm), elevated triglycerides (TG, TG ≥150 mg/dL), sex-specific reduced high-density lipoprotein cholesterol (HDL-C, HDL-Cmen <40 mg/dL and HDL-Cwomen < 50mg/dL), elevated blood pressure (BP, systolic ≥130 mmHg and diastolic ≥85 mmHg), and elevated fasting glucose (FG, FG ≥100 mg/dL). The individuals who satisfied three out of five criteria based on AHA/NHLBI were categorized as MetS case. —
[
  • 4,641 cases
  • , 6,498 controls
]
 — European — UKB —