Polygenic Score (PGS) ID: PGS003190

Predicted Trait
Reported Trait Vitamin D
Mapped Trait(s) vitamin D measurement (EFO_0004631)
Additional Trait Information Vitamin D (quantile); Quantitative
Released in PGS Catalog: Nov. 23, 2022
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Terms and Licenses
PGS obtained from the Catalog should be cited appropriately, and used in accordance with any licensing restrictions set by the authors. See EBI Terms of Use (https://www.ebi.ac.uk/about/terms-of-use/) for additional details.

Score Details

Score Construction
PGS Name ExPRSweb_VitD_30890-irnt_PT_MGI_20211120
Development Method
Name Pruning and Thresholding (P+T)
Parameters LD Clumping (using Plink to calculate LD, MAF >= 1%, r^2 <= 0.1) & P-value threshold <=... 5.00e-06Show more
Variants
Original Genome Build GRCh37
Number of Variants 495
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%
329,247 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)
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Study Identifiers
Sample Numbers
Sample Ancestry
Cohort(s)
329,247 individualsEuropeanUKB
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Score Development/Training
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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 individualsEuropeanMGI25-Hydroxyvitamin D, Total (LOINC: 1989-3); Quantitative————
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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.

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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
PPM016101PSS010018|
European Ancestry|
6,926 individuals
PGP000393 |
Ma Y et al. Am J Hum Genet (2022)
Reported Trait: Vitamin Dβ: 1.44 (0.107)—R²: 0.0251SEX,AGE,Batch,PC1,PC2,PC3,PC4—
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Evaluated Samples

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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
PSS01001825-Hydroxyvitamin D, Total (LOINC: 1989-3); Quantitative—6,926 individuals—European—MGI—
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