Polygenic Score (PGS) ID: PGS003554

Predicted Trait
Reported Trait Vitamin D
Mapped Trait(s) vitamin D measurement (EFO_0004631)
Released in PGS Catalog: April 12, 2023
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Score Details

Score Construction
PGS Name cont-decay-log_vitaminD
Development Method
Name LDpred2-auto
Parameters vec_p_init = seq_log(1e-4, 0.9, length.out = 10), burn_in = 100, num_iter = 500, report_step = 5
Variants
Original Genome Build GRCh37
Number of Variants 979,739
Effect Weight Type beta
PGS Source
PGS Catalog Publication (PGP) ID PGP000457
Citation (link to publication) Ding Y et al. bioRxiv (2022) Preprint
Ancestry Distribution
Score Development/Training
European: 100%
338,072 individuals (100%)
PGS Evaluation
European: 44.4%
African: 22.2%
East Asian: 11.1%
Greater Middle Eastern: 11.1%
South Asian: 11.1%
9 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
— 338,072 individuals,
0.47 % Male samples
 European UKB — Mean = 56.8 years
Sd = 8.0 years		 — white British —

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
PPM017482 PSS010920|
European Ancestry|
18,261 individuals
 PGP000457 |
Ding Y et al. bioRxiv (2022)
|Pre		 Reported Trait: Vitamin D — — partial-R2: 0.05 sex, age, deprivation index, PC1-16 —
PPM017566 PSS010836|
European Ancestry|
3,767 individuals
 PGP000457 |
Ding Y et al. bioRxiv (2022)
|Pre		 Reported Trait: Vitamin D — — partial-R2: 0.03 sex, age, deprivation index, PC1-16 —
PPM017650 PSS010668|
European Ancestry|
5,901 individuals
 PGP000457 |
Ding Y et al. bioRxiv (2022)
|Pre		 Reported Trait: Vitamin D — — partial-R2: 0.05 sex, age, deprivation index, PC1-16 —
PPM017734 PSS010584|
Greater Middle Eastern Ancestry|
1,009 individuals
 PGP000457 |
Ding Y et al. bioRxiv (2022)
|Pre		 Reported Trait: Vitamin D — — partial-R2: 0.04 sex, age, deprivation index, PC1-16 —
PPM017818 PSS010248|
European Ancestry|
2,125 individuals
 PGP000457 |
Ding Y et al. bioRxiv (2022)
|Pre		 Reported Trait: Vitamin D — — partial-R2: 0.03 sex, age, deprivation index, PC1-16 —
PPM017902 PSS010500|
South Asian Ancestry|
5,140 individuals
 PGP000457 |
Ding Y et al. bioRxiv (2022)
|Pre		 Reported Trait: Vitamin D — — partial-R2: 0.01 sex, age, deprivation index, PC1-16 —
PPM017986 PSS010416|
East Asian Ancestry|
1,651 individuals
 PGP000457 |
Ding Y et al. bioRxiv (2022)
|Pre		 Reported Trait: Vitamin D — — partial-R2: 0.01 sex, age, deprivation index, PC1-16 —
PPM018154 PSS010752|
African Ancestry|
3,541 individuals
 PGP000457 |
Ding Y et al. bioRxiv (2022)
|Pre		 Reported Trait: Vitamin D — — partial-R2: 0.0 sex, age, deprivation index, PC1-16 —
PPM018070 PSS010332|
African Ancestry|
2,254 individuals
 PGP000457 |
Ding Y et al. bioRxiv (2022)
|Pre		 Reported Trait: Vitamin D — — partial-R2: 0.01 sex, age, deprivation index, PC1-16 —

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
PSS010752 — — 3,541 individuals,
46.0 % Male samples
 Mean = 51.9 years
Sd = 8.1 years		 African unspecified Nigerian UKB —
PSS010500 — — 5,140 individuals,
55.0 % Male samples
 Mean = 53.5 years
Sd = 8.5 years		 South Asian Indian UKB —
PSS010920 — — 18,261 individuals,
47.0 % Male samples
 Mean = 56.8 years
Sd = 8.0 years		 European white British UKB —
PSS010248 — — 2,125 individuals,
46.0 % Male samples
 Mean = 58.1 years
Sd = 7.1 years		 European Ashkenazi UKB —
PSS010668 — — 5,901 individuals,
46.0 % Male samples
 Mean = 54.4 years
Sd = 8.4 years		 European Italian UKB —
PSS010416 — — 1,651 individuals,
33.0 % Male samples
 Mean = 52.4 years
Sd = 7.8 years		 East Asian Chinese UKB —
PSS010836 — — 3,767 individuals,
39.0 % Male samples
 Mean = 54.2 years
Sd = 7.6 years		 European Polish UKB —
PSS010584 — — 1,009 individuals,
61.0 % Male samples
 Mean = 52.1 years
Sd = 8.0 years		 Greater Middle Eastern (Middle Eastern, North African or Persian) Iranian UKB —
PSS010332 — — 2,254 individuals,
36.0 % Male samples
 Mean = 52.5 years
Sd = 8.1 years		 African American or Afro-Caribbean Caribbean UKB —