Polygenic Score (PGS) ID: PGS002672

Predicted Trait
Reported Trait Vitamin D
Mapped Trait(s) vitamin D level (OBA_1000968)
Released in PGS Catalog: June 9, 2022
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Score Details

Score Construction
PGS Name biochemistry_VitaminD.PolyFun-pred
Development Method
Name PolyFun-pred
Parameters NR
Variants
Original Genome Build GRCh37
Number of Variants 330,506
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
PPM014388 PSS009863|
African Ancestry|
5,876 individuals
 PGP000332 |
Weissbrod O et al. Nat Genet (2022)
 Reported Trait: Vitamin D — — Incremental R2 (full model when combined with BOLT-LMM vs. covariates alone): 0.0073 age, sex, age*sex, assessment center, genotyping array, 10 PCs See biochemistry_VitaminD.mixweights file at http://data.broadinstitute.org/alkesgroup/polypred_results for combination weights
PPM014437 PSS009864|
East Asian Ancestry|
855 individuals
 PGP000332 |
Weissbrod O et al. Nat Genet (2022)
 Reported Trait: Vitamin D — — Incremental R2 (full model when combined with BOLT-LMM vs. covariates alone): 0.0049 age, sex, age*sex, assessment center, genotyping array, 10 PCs See biochemistry_VitaminD.mixweights file at http://data.broadinstitute.org/alkesgroup/polypred_results for combination weights
PPM014486 PSS009865|
European Ancestry|
39,443 individuals
 PGP000332 |
Weissbrod O et al. Nat Genet (2022)
 Reported Trait: Vitamin D — — Incremental R2 (full model when combined with BOLT-LMM vs. covariates alone): 0.0591 age, sex, age*sex, assessment center, genotyping array, 10 PCs See biochemistry_VitaminD.mixweights file at http://data.broadinstitute.org/alkesgroup/polypred_results for combination weights
PPM014535 PSS009866|
South Asian Ancestry|
6,746 individuals
 PGP000332 |
Weissbrod O et al. Nat Genet (2022)
 Reported Trait: Vitamin D — — Incremental R2 (full model when combined with BOLT-LMM vs. covariates alone): 0.0134 age, sex, age*sex, assessment center, genotyping array, 10 PCs See biochemistry_VitaminD.mixweights file at http://data.broadinstitute.org/alkesgroup/polypred_results for combination weights

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 —