Polygenic Score (PGS) ID: PGS000817

Predicted Trait
Reported Trait Gamma-glutamyl transferase
Mapped Trait(s) serum gamma-glutamyl transferase measurement (EFO_0004532)
Released in PGS Catalog: July 29, 2021
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Score Details

Score Construction
PGS Name GRS200_GGT
Development Method
Name Variants associated with gamma-glutamyl transferase levels
Parameters p < 1e-9
Variants
Original Genome Build GRCh37
Number of Variants 200
Effect Weight Type beta
PGS Source
PGS Catalog Publication (PGP) ID PGP000201
Citation (link to publication) Pazoki R et al. Nat Commun (2021)
Ancestry Distribution
Source of Variant
Associations (GWAS)
European: 100%
437,194 individuals (100%)
Score Development/Training
European: 100%
753,010 individuals (100%)
PGS Evaluation
European: 100%
2 Sample Sets

Development Samples

Source of Variant Associations (GWAS)
Study Identifiers Sample Numbers Sample Ancestry Cohort(s)
GWAS Catalog: GCST90013407
Europe PMC: 33972514
 437,194 individuals European UKB
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
— 753,010 individuals European LifeLines, MVP, RS, UKB — — — — Meta-analysis of discovery and replication GWAS used to determine weights for SNPs within the GRS.

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
PPM002177 PSS001062|
European Ancestry|
3,620 individuals
 PGP000201 |
Pazoki R et al. Nat Commun (2021)
 Reported Trait: Serum gamma-glutamyl transferase level OR: 1.96 [1.72, 2.19] — — — —
PPM002174 PSS001061|
European Ancestry|
13,420 individuals
 PGP000201 |
Pazoki R et al. Nat Commun (2021)
 Reported Trait: Serum gamma-glutamyl transferase level β: 1.43 [1.35, 1.52] — — — Unit of measurement = U/L in gamma-glutamyl transferase

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
PSS001061 The serum concentration of gamma-glutamyl transferase (GGT) was measured from stored blood samples using the enzymatic rate analytical method on a Beckman Coulter AU5800. The manufacturer’s analytic range for ALT was 3–500 U/L, for ALP, 5–1500 U/L, and it was 5–1200 U/L for GGT. — 13,420 individuals — European — Airwave —
PSS001062 Serum concentrations of alanine transaminase (ALT), alkaline phosphatase (ALP), and gamma-glutamyl transferase (GGT) were measured from stored blood samples using the enzymatic rate analytical method on a Beckman Coulter AU5800. The manufacturer’s analytic range for ALT was 3–500 U/L, for ALP, 5–1500 U/L, and it was 5–1200 U/L for GGT. — 3,620 individuals — European — NFBC —