Polygenic Score (PGS) ID: PGS004712

Predicted Trait
Reported Trait Alkaline phosphatase
Mapped Trait(s) alkaline phosphatase measurement (EFO_0004533)
Released in PGS Catalog: March 28, 2024
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Score Details

Score Construction
PGS Name ALP_PRSmix_sas
Development Method
Name PRSmix
Parameters power=0.95; p=0.05
Variants
Original Genome Build hg38
Number of Variants 1,704,295
Effect Weight Type beta
PGS Source
PGS Catalog Publication (PGP) ID PGP000604
Citation (link to publication) Truong B et al. Cell Genom (2024)
Ancestry Distribution
Score Development/Training
South Asian: 100%
27,182 individuals (100%)
PGS Evaluation
South Asian: 100%
1 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
— 27,182 individuals South Asian G&H — — — — —

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
PPM020937 PSS011456|
South Asian Ancestry|
6,795 individuals
 PGP000604 |
Truong B et al. Cell Genom (2024)
 Reported Trait: Alkaline phosphatase — — Incremental R2 (Full model versus model with only covariates): 0.077 [0.065, 0.09] age, sex, PC1, PC2, PC3, PC4, PC5, PC6, PC7, PC8, PC9, PC10 Incremental R2 (Full model versus model with only covariates)

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
PSS011456 — — 6,795 individuals — South Asian — G&H —