PGS Publication: PGP000201

Publication Information (EuropePMC)
Title Genetic analysis in European ancestry individuals identifies 517 loci associated with liver enzymes.
PubMed ID 33972514(Europe PMC)
doi 10.1038/s41467-021-22338-2
Publication Date May 10, 2021
Journal Nat Commun
Author(s) Pazoki R, Vujkovic M, Elliott J, Evangelou E, Gill D, Ghanbari M, van der Most PJ, Pinto RC, Wielscher M, Farlik M, Zuber V, de Knegt RJ, Snieder H, Uitterlinden AG, Lifelines Cohort Study, Lynch JA, Jiang X, Said S, Kaplan DE, Lee KM, Serper M, Carr RM, Tsao PS, Atkinson SR, Dehghan A, Tzoulaki I, Ikram MA, Herzig KH, Järvelin MR, Alizadeh BZ, O'Donnell CJ, Saleheen D, Voight BF, Chang KM, Thursz MR, Elliott P, VA Million Veteran Program.
Released in PGS Catalog: July 29, 2021

Associated Polygenic Score(s)

Filter PGS by Participant Ancestry
Individuals included in:
G - Source of Variant Associations (GWAS)
D - Score Development/Training
E - PGS Evaluation
List of ancestries includes:
Display options:
Ancestry legend
Multi-ancestry (including European)
Multi-ancestry (excluding European)
African
East Asian
South Asian
Additional Asian Ancestries
European
Greater Middle Eastern
Hispanic or Latin American
Additional Diverse Ancestries
Not Reported

PGS Developed By This Publication

Polygenic Score ID & Name PGS Publication ID (PGP) Reported Trait Mapped Trait(s) (Ontology) Number of Variants Ancestry distribution
GWAS
Dev
Eval
 Scoring File (FTP Link)
PGS000817
(GRS200_GGT)
 PGP000201 |
Pazoki R et al. Nat Commun (2021)
 Gamma-glutamyl transferase serum gamma-glutamyl transferase measurement 200
https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000817/ScoringFiles/PGS000817.txt.gz
PGS000816
(GRS150_ALT)
 PGP000201 |
Pazoki R et al. Nat Commun (2021)
 Alanine transaminase serum alanine aminotransferase measurement 150
https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000816/ScoringFiles/PGS000816.txt.gz
PGS000815
(GRS290_ALP)
 PGP000201 |
Pazoki R et al. Nat Commun (2021)
 Alkaline phosphatase alkaline phosphatase measurement 290
https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000815/ScoringFiles/PGS000815.txt.gz

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) 		Evaluated Score 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
PPM002176 PGS000816
(GRS150_ALT)
 PSS001062|
European Ancestry|
3,620 individuals
 PGP000201 |
Pazoki R et al. Nat Commun (2021)
 Reported Trait: Serum alanine transaminase level OR: 1.72 [1.36, 2.07] — — — —
PPM002177 PGS000817
(GRS200_GGT)
 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] — — — —
PPM002172 PGS000815
(GRS290_ALP)
 PSS001060|
European Ancestry|
331 individuals
 PGP000201 |
Pazoki R et al. Nat Commun (2021)
 Reported Trait: Serum alkaline phosphatase level β: 2.07 [1.49, 2.66] — — — Unit of measurement = U/L in alkaline phosphatase
PPM002173 PGS000816
(GRS150_ALT)
 PSS001060|
European Ancestry|
331 individuals
 PGP000201 |
Pazoki R et al. Nat Commun (2021)
 Reported Trait: Serum alanine transaminase level β: 3.09 [2.02, 4.17] — — — Unit of measurement = U/L in alanine transaminase
PPM002174 PGS000817
(GRS200_GGT)
 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
PPM002175 PGS000815
(GRS290_ALP)
 PSS001062|
European Ancestry|
3,620 individuals
 PGP000201 |
Pazoki R et al. Nat Commun (2021)
 Reported Trait: Serum alkaline phosphatase level OR: 1.88 [1.67, 2.09] — — — —

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
PSS001060 Serum concentrations of alanine transaminase (ALT) and alkaline phosphatase (ALP), 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. — 331 individuals — European — Airwave —
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 —