Polygenic Score (PGS) ID: PGS000683

Predicted Trait
Reported Trait Gamma-glutamyl transferase [U/L]
Mapped Trait(s) serum gamma-glutamyl transferase measurement (EFO_0004532)
Released in PGS Catalog: Feb. 3, 2021
Download Score FTP directory
Terms and Licenses
Creative Commons Attribution 4.0 International (CC BY 4.0)

Score Details

Score Construction
PGS Name snpnet.Gamma_glutamyltransferase
Development Method
Name snpnet
Parameters 1,080,968 variants as input (directly genotyped variants, imputed HLA allelotypes, and CNVs)
Variants
Original Genome Build hg19
Number of Variants 17,323
Effect Weight Type beta
PGS Source
PGS Catalog Publication (PGP) ID PGP000128
Citation (link to publication) Sinnott-Armstrong N et al. Nat Genet (2021)
Ancestry Distribution
Score Development/Training
European: 100%
255,256 individuals (100%)
PGS Evaluation
European: 40%
African: 20%
East Asian: 20%
South Asian: 20%
10 Sample Sets

Development Samples

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
223,327 individuals European
(British)		 UKB — — — — Training
31,929 individuals European
(British)		 UKB — — — — Validation

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
PPM001411 PSS000689|
African Ancestry|
6,015 individuals
 PGP000128 |
Sinnott-Armstrong N et al. Nat Genet (2021)
 Reported Trait: Gamma glutamyltransferase [U/L] — — R²: 0.12099
Spearman's ρ: 0.187		 Age, sex, PCs(1-40) —
PPM001446 PSS000690|
East Asian Ancestry|
1,081 individuals
 PGP000128 |
Sinnott-Armstrong N et al. Nat Genet (2021)
 Reported Trait: Gamma glutamyltransferase [U/L] — — R²: 0.16131
Spearman's ρ: 0.33		 Age, sex, PCs(1-40) —
PPM001481 PSS000691|
European Ancestry|
23,560 individuals
 PGP000128 |
Sinnott-Armstrong N et al. Nat Genet (2021)
 Reported Trait: Gamma glutamyltransferase [U/L] — — R²: 0.26555
Spearman's ρ: 0.36		 Age, sex, PCs(1-40) —
PPM001516 PSS000692|
South Asian Ancestry|
7,336 individuals
 PGP000128 |
Sinnott-Armstrong N et al. Nat Genet (2021)
 Reported Trait: Gamma glutamyltransferase [U/L] — — R²: 0.20072
Spearman's ρ: 0.338		 Age, sex, PCs(1-40) —
PPM001551 PSS000693|
European Ancestry|
63,756 individuals
 PGP000128 |
Sinnott-Armstrong N et al. Nat Genet (2021)
 Reported Trait: Gamma glutamyltransferase [U/L] — — R²: 0.24765
Spearman's ρ: 0.375		 Age, sex, PCs(1-40) —
PPM007340 PSS007146|
African Ancestry|
6,097 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
|Ext.		 Reported Trait: Gamma glutamyltransferase — — R²: 0.03855 [0.02938, 0.04773]
Incremental R2 (full-covars): 0.00086
PGS R2 (no covariates): 0.01203 [0.00677, 0.0173]		 age, sex, UKB array type, Genotype PCs —
PPM007341 PSS007147|
East Asian Ancestry|
1,614 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
|Ext.		 Reported Trait: Gamma glutamyltransferase — — R²: 0.03443 [0.01745, 0.05141]
Incremental R2 (full-covars): 0.0016
PGS R2 (no covariates): 0.02608 [0.01117, 0.04098]		 age, sex, UKB array type, Genotype PCs —
PPM007342 PSS007148|
European Ancestry|
23,750 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
|Ext.		 Reported Trait: Gamma glutamyltransferase — — R²: 0.04954 [0.04429, 0.05479]
Incremental R2 (full-covars): 0.00169
PGS R2 (no covariates): 0.03621 [0.03165, 0.04076]		 age, sex, UKB array type, Genotype PCs —
PPM007343 PSS007149|
South Asian Ancestry|
7,426 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
|Ext.		 Reported Trait: Gamma glutamyltransferase — — R²: 0.04001 [0.0315, 0.04851]
Incremental R2 (full-covars): 0.00185
PGS R2 (no covariates): 0.03716 [0.02894, 0.04538]		 age, sex, UKB array type, Genotype PCs —
PPM007344 PSS007150|
European Ancestry|
64,433 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
|Ext.		 Reported Trait: Gamma glutamyltransferase — — R²: 0.03846 [0.03562, 0.04131]
Incremental R2 (full-covars): 0.00223
PGS R2 (no covariates): 0.05018 [0.04697, 0.05339]		 age, sex, UKB array type, Genotype PCs —

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
PSS000689 — — 6,015 individuals — African unspecified — UKB —
PSS000690 — — 1,081 individuals — East Asian — UKB —
PSS000691 — — 23,560 individuals — European Non-British White UKB —
PSS000692 — — 7,336 individuals — South Asian — UKB —
PSS000693 — — 63,756 individuals — European
(British)		 — UKB —
PSS007146 — — 6,097 individuals — African unspecified — UKB —
PSS007147 — — 1,614 individuals — East Asian — UKB —
PSS007148 — — 23,750 individuals — European non-white British ancestry UKB —
PSS007149 — — 7,426 individuals — South Asian — UKB —
PSS007150 — — 64,433 individuals — European white British ancestry UKB Testing cohort (heldout set)