Polygenic Score (PGS) ID: PGS000882

Predicted Trait
Reported Trait 25-hydroxyvitamin D
Mapped Trait(s) vitamin D measurement (EFO_0004631)
Released in PGS Catalog: Aug. 26, 2021
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Score Details

Score Construction
PGS Name 25OHD_SBayesR_PGS
Development Method
Name SBayesR
Parameters pi 0.01, hsq 0.5, chain-length 25000, burn-in 5000
Variants
Original Genome Build hg19
Number of Variants 1,094,650
Effect Weight Type NR
PGS Source
PGS Catalog Publication (PGP) ID PGP000228
Citation (link to publication) Revez JA et al. Nat Commun (2020)
Ancestry Distribution
Source of Variant
Associations (GWAS)
European: 100%
417,580 individuals (100%)
PGS Evaluation
European: 66.7%
Greater Middle Eastern: 33.3%
3 Sample Sets

Development Samples

Source of Variant Associations (GWAS)
Study Identifiers Sample Numbers Sample Ancestry Cohort(s)
GWAS Catalog: GCST90000614
Europe PMC: 32242144
 417,580 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
PPM002526 PSS001141|
European Ancestry|
1,632 individuals
 PGP000228 |
Revez JA et al. Nat Commun (2020)
 Reported Trait: 25-hydroxyvitamin D levels β: 0.269 (0.02) — R²: 0.096 sex, assessment month, supplement intake (ever), PCs(1-5) —
PPM002527 PSS001142|
European Ancestry|
1,632 individuals
 PGP000228 |
Revez JA et al. Nat Commun (2020)
 Reported Trait: 25-hydroxyvitamin D levels β: 0.24 (0.024) — R²: 0.0554 — —
PPM020900 PSS011443|
Greater Middle Eastern Ancestry|
194 individuals
 PGP000600 |
Hendi NN et al. Nutrients (2023)
|Ext.		 Reported Trait: Vitamin D deficiency OR: 1.6 [1.3, 13.7] AUROC: 0.644 — Age, sex, 4 PCs Only 41,736 of 1,094,650 variants available in cohort

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
PSS011443 — — 194 individuals Mean = 71.13 years
Sd = 4.82 years		 Greater Middle Eastern (Middle Eastern, North African or Persian)
(Lebanese)		 — NR —
PSS001141 — — 1,632 individuals — European — QIMR —
PSS001142 — — 1,632 individuals — European — UKB —