Polygenic Score (PGS) ID: PGS002200

Predicted Trait
Reported Trait Vitamin D
Mapped Trait(s) vitamin D level (OBA_1000968)
Additional Trait Information biological measures
Released in PGS Catalog: Jan. 10, 2022
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Score Details

Score Construction
PGS Name portability-ldpred2_log_vitaminD
Development Method
Name LDpred2 (bigsnpr)
Parameters LDpred2-auto using HapMap3 variants
Variants
Original Genome Build GRCh37
Number of Variants 567,735
Effect Weight Type beta
PGS Source
PGS Catalog Publication (PGP) ID PGP000263
Citation (link to publication) Privé F et al. Am J Hum Genet (2022)
Ancestry Distribution
Score Development/Training
European: 100%
391,124 individuals (100%)
PGS Evaluation
European: 37.5%
African: 25%
East Asian: 12.5%
Greater Middle Eastern: 12.5%
South Asian: 12.5%
8 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
— 391,124 individuals European UKB — — — UK (+ Ireland) —

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
PPM012447 PSS009470|
European Ancestry|
18,172 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Vitamin D — — Partial Correlation (partial-r): 0.2228 [0.2089, 0.2365] sex, age, birth date, deprivation index, 16 PCs —
PPM012448 PSS009244|
European Ancestry|
3,778 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Vitamin D — — Partial Correlation (partial-r): 0.174 [0.1428, 0.2048] sex, age, birth date, deprivation index, 16 PCs —
PPM012449 PSS008798|
European Ancestry|
6,046 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Vitamin D — — Partial Correlation (partial-r): 0.2231 [0.199, 0.247] sex, age, birth date, deprivation index, 16 PCs —
PPM012450 PSS008572|
Greater Middle Eastern Ancestry|
1,036 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Vitamin D — — Partial Correlation (partial-r): 0.1892 [0.1292, 0.2478] sex, age, birth date, deprivation index, 16 PCs —
PPM012452 PSS008127|
East Asian Ancestry|
1,662 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Vitamin D — — Partial Correlation (partial-r): 0.084 [0.0358, 0.1319] sex, age, birth date, deprivation index, 16 PCs —
PPM012453 PSS007914|
African Ancestry|
2,266 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Vitamin D — — Partial Correlation (partial-r): 0.0669 [0.0256, 0.1079] sex, age, birth date, deprivation index, 16 PCs —
PPM012454 PSS009018|
African Ancestry|
3,569 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Vitamin D — — Partial Correlation (partial-r): 0.0423 [0.0094, 0.0751] sex, age, birth date, deprivation index, 16 PCs —
PPM012451 PSS008350|
South Asian Ancestry|
5,186 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Vitamin D — — Partial Correlation (partial-r): 0.0828 [0.0557, 0.1098] sex, age, birth date, deprivation index, 16 PCs —

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
PSS008572 — — 1,036 individuals — Greater Middle Eastern (Middle Eastern, North African or Persian) Iran (Middle East) UKB —
PSS007914 — — 2,266 individuals — African American or Afro-Caribbean Carribean UKB —
PSS008350 — — 5,186 individuals — South Asian India (South Asia) UKB —
PSS009018 — — 3,569 individuals — African unspecified Nigeria (West Africa) UKB —
PSS008798 — — 6,046 individuals — European Italy (South Europe) UKB —
PSS009244 — — 3,778 individuals — European Poland (NE Europe) UKB —
PSS009470 — — 18,172 individuals — European UK (+ Ireland) UKB —
PSS008127 — — 1,662 individuals — East Asian China (East Asia) UKB —