Polygenic Score (PGS) ID: PGS000702

Predicted Trait
Reported Trait Vitamin D [nmol/L]
Mapped Trait(s) vitamin D measurement (EFO_0004631)
Released in PGS Catalog: Feb. 3, 2021
Download Score FTP directory
Terms and Licenses
Creative Commons Attribution 4.0 International (CC BY 4.0)

Score Details

Score Construction
PGS Name snpnet.Vitamin_D
Development Method
Name snpnet
Parameters 1,080,968 variants as input (directly genotyped variants, imputed HLA allelotypes, and CNVs)
Variants
Original Genome Build hg19
Number of Variants 8,012
Effect Weight Type beta
PGS Source
PGS Catalog Publication (PGP) ID PGP000128
Citation (link to publication) Sinnott-Armstrong N et al. Nat Genet (2021)
Ancestry Distribution
Score Development/Training
European: 100%
255,256 individuals (100%)
PGS Evaluation
European: 41.7%
African: 16.7%
East Asian: 16.7%
South Asian: 16.7%
Greater Middle Eastern: 8.3%
12 Sample Sets

Development Samples

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
223,327 individuals European
(British)		 UKB — — — — Training
31,929 individuals European
(British)		 UKB — — — — Validation

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
PPM001430 PSS000787|
African Ancestry|
5,845 individuals
 PGP000128 |
Sinnott-Armstrong N et al. Nat Genet (2021)
 Reported Trait: Vitamin D [nmol/L] — — R²: 0.09201
Spearman's ρ: 0.055		 Age, sex, PCs(1-40) —
PPM001465 PSS000788|
East Asian Ancestry|
1,055 individuals
 PGP000128 |
Sinnott-Armstrong N et al. Nat Genet (2021)
 Reported Trait: Vitamin D [nmol/L] — — R²: 0.11925
Spearman's ρ: 0.095		 Age, sex, PCs(1-40) —
PPM001500 PSS000789|
European Ancestry|
22,617 individuals
 PGP000128 |
Sinnott-Armstrong N et al. Nat Genet (2021)
 Reported Trait: Vitamin D [nmol/L] — — R²: 0.21171
Spearman's ρ: 0.211		 Age, sex, PCs(1-40) —
PPM001535 PSS000790|
South Asian Ancestry|
6,425 individuals
 PGP000128 |
Sinnott-Armstrong N et al. Nat Genet (2021)
 Reported Trait: Vitamin D [nmol/L] — — R²: 0.07695
Spearman's ρ: 0.08		 Age, sex, PCs(1-40) —
PPM001570 PSS000791|
European Ancestry|
60,998 individuals
 PGP000128 |
Sinnott-Armstrong N et al. Nat Genet (2021)
 Reported Trait: Vitamin D [nmol/L] — — R²: 0.22856
Spearman's ρ: 0.226		 Age, sex, PCs(1-40) —
PPM001586 PSS000803|
European Ancestry|
2,058 individuals
 PGP000128 |
Sinnott-Armstrong N et al. Nat Genet (2021)
 Reported Trait: Vitamin D [nmol/L] — — Spearman's ρ: 0.137 Age, sex —
PPM007435 PSS007216|
African Ancestry|
5,926 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
|Ext.		 Reported Trait: Vitamin D — — R²: 0.04539 [0.0355, 0.05527]
Incremental R2 (full-covars): 0.00047
PGS R2 (no covariates): 0.00322 [0.00047, 0.00597]		 age, sex, UKB array type, Genotype PCs —
PPM007436 PSS007217|
East Asian Ancestry|
1,570 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
|Ext.		 Reported Trait: Vitamin D — — R²: 0.05891 [0.03726, 0.08055]
Incremental R2 (full-covars): 0.00078
PGS R2 (no covariates): 0.00411 [-0.00194, 0.01016]		 age, sex, UKB array type, Genotype PCs —
PPM007437 PSS007218|
European Ancestry|
22,820 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
|Ext.		 Reported Trait: Vitamin D — — R²: 0.01597 [0.01288, 0.01905]
Incremental R2 (full-covars): 0.0019
PGS R2 (no covariates): 0.04772 [0.04255, 0.05289]		 age, sex, UKB array type, Genotype PCs —
PPM007438 PSS007219|
South Asian Ancestry|
6,507 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
|Ext.		 Reported Trait: Vitamin D — — R²: 0.05098 [0.04149, 0.06047]
Incremental R2 (full-covars): 0.00081
PGS R2 (no covariates): 0.00364 [0.00098, 0.00631]		 age, sex, UKB array type, Genotype PCs —
PPM007439 PSS007220|
European Ancestry|
61,724 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
|Ext.		 Reported Trait: Vitamin D — — R²: 0.01125 [0.00967, 0.01283]
Incremental R2 (full-covars): 0.00186
PGS R2 (no covariates): 0.0483 [0.04514, 0.05145]		 age, sex, UKB array type, Genotype PCs —
PPM022175 PSS011828|
Greater Middle Eastern Ancestry|
5,885 individuals
 PGP000682 |
Hendi NN et al. Front Nutr (2023)
|Ext.		 Reported Trait: Vitamin D deficiency OR: 0.0935 [0.042, 0.2071] AUROC: 0.68 — — —
PPM022176 PSS011828|
Greater Middle Eastern Ancestry|
5,885 individuals
 PGP000682 |
Hendi NN et al. Front Nutr (2023)
|Ext.		 Reported Trait: Vitamin D insufficiency and deficiency OR: 0.0832 [0.0259, 0.2646] AUROC: 0.6385 — — —

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
PSS011828 — — 5,885 individuals,
43.6 % Male samples
 Mean = 40.0 years Greater Middle Eastern (Middle Eastern, North African or Persian)
(Qatari)		 — QBB —
PSS000787 — — 5,845 individuals — African unspecified — UKB —
PSS000788 — — 1,055 individuals — East Asian — UKB —
PSS000789 — — 22,617 individuals — European Non-British White UKB —
PSS000790 — — 6,425 individuals — South Asian — UKB —
PSS000791 — — 60,998 individuals — European
(British)		 — UKB —
PSS007216 — — 5,926 individuals — African unspecified — UKB —
PSS007217 — — 1,570 individuals — East Asian — UKB —
PSS007218 — — 22,820 individuals — European non-white British ancestry UKB —
PSS007219 — — 6,507 individuals — South Asian — UKB —
PSS007220 — — 61,724 individuals — European white British ancestry UKB Testing cohort (heldout set)
PSS000803 — — 2,058 individuals — European Participants self-identifying as white MESA —