Polygenic Score (PGS) ID: PGS003179

Predicted Trait
Reported Trait Vitamin D
Mapped Trait(s) vitamin D measurement (EFO_0004631)
Additional Trait Information Vitamin D; Quantitative
Released in PGS Catalog: Nov. 23, 2022
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Score Details

Score Construction
PGS Name ExPRSweb_VitD_100021-raw_LASSOSUM_MGI_20211120
Development Method
Name lassosum
Parameters Lassosum 0.4.4 (MAF >= 1%; autosomal variants only)s=1;Lambda=0.001
Variants
Original Genome Build GRCh37
Number of Variants 310,479
Effect Weight Type beta
PGS Source
PGS Catalog Publication (PGP) ID PGP000393
Citation (link to publication) Ma Y et al. Am J Hum Genet (2022)
Ancestry Distribution
Source of Variant
Associations (GWAS)
European: 100%
51,453 individuals (100%)
Score Development/Training
European: 100%
6,928 individuals (100%)
PGS Evaluation
European: 100%
1 Sample Sets

Development Samples

Source of Variant Associations (GWAS)
Study Identifiers Sample Numbers Sample Ancestry Cohort(s)
51,453 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
— 6,928 individuals European MGI 25-Hydroxyvitamin D, Total (LOINC: 1989-3); Quantitative — — — —

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
PPM016083 PSS010018|
European Ancestry|
6,926 individuals
 PGP000393 |
Ma Y et al. Am J Hum Genet (2022)
 Reported Trait: Vitamin D β: 0.171 (0.109) — R²: 0.00034 SEX,AGE,Batch,PC1,PC2,PC3,PC4 —

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
PSS010018 25-Hydroxyvitamin D, Total (LOINC: 1989-3); Quantitative — 6,926 individuals — European — MGI —