Polygenic Score (PGS) ID: PGS000815

Predicted Trait
Reported Trait Alkaline phosphatase
Mapped Trait(s) alkaline phosphatase measurement (EFO_0004533)
Released in PGS Catalog: July 29, 2021
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Score Details

Score Construction
PGS Name GRS290_ALP
Development Method
Name Variants associated with alkaline phosphatase levels.
Parameters p < 1e-9
Variants
Original Genome Build GRCh37
Number of Variants 290
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%
437,438 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: GCST90013406
Europe PMC: 33972514
 437,438 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
PPM002172 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
PPM002175 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 —
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 —