Polygenic Score (PGS) ID: PGS002574

Predicted Trait
Reported Trait Vitamin D
Mapped Trait(s) vitamin D measurement (EFO_0004631)
Released in PGS Catalog: June 9, 2022
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Score Details

Score Construction
PGS Name biochemistry_VitaminD.P+T.1e-06
Development Method
Name Pruning and Thresholding (P+T)
Parameters p < 1e-06
Variants
Original Genome Build GRCh37
Number of Variants 1,677
Effect Weight Type beta
PGS Source
PGS Catalog Publication (PGP) ID PGP000332
Citation (link to publication) Weissbrod O et al. Nat Genet (2022)
Ancestry Distribution
Source of Variant
Associations (GWAS)
European: 100%
307,287 individuals (100%)
PGS Evaluation
African: 25%
East Asian: 25%
European: 25%
South Asian: 25%
4 Sample Sets

Development Samples

Source of Variant Associations (GWAS)
Study Identifiers Sample Numbers Sample Ancestry Cohort(s)
— 307,287 individuals European UKB

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
PPM013996 PSS009863|
African Ancestry|
5,876 individuals
 PGP000332 |
Weissbrod O et al. Nat Genet (2022)
 Reported Trait: Vitamin D — — Incremental R2 (full model vs. covariates alone): 0.0031 age, sex, age*sex, assessment center, genotyping array, 10 PCs —
PPM014045 PSS009864|
East Asian Ancestry|
855 individuals
 PGP000332 |
Weissbrod O et al. Nat Genet (2022)
 Reported Trait: Vitamin D — — Incremental R2 (full model vs. covariates alone): 0.0039 age, sex, age*sex, assessment center, genotyping array, 10 PCs —
PPM014094 PSS009865|
European Ancestry|
39,443 individuals
 PGP000332 |
Weissbrod O et al. Nat Genet (2022)
 Reported Trait: Vitamin D — — Incremental R2 (full model vs. covariates alone): 0.0321 age, sex, age*sex, assessment center, genotyping array, 10 PCs —
PPM014143 PSS009866|
South Asian Ancestry|
6,746 individuals
 PGP000332 |
Weissbrod O et al. Nat Genet (2022)
 Reported Trait: Vitamin D — — Incremental R2 (full model vs. covariates alone): 0.0062 age, sex, age*sex, assessment center, genotyping array, 10 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
PSS009863 — — 5,876 individuals — African unspecified — UKB —
PSS009864 — — 855 individuals — East Asian — UKB —
PSS009865 — — 39,443 individuals — European Non-British European UKB —
PSS009866 — — 6,746 individuals — South Asian — UKB —