PGS Publication: PGP000228

Publication Information (EuropePMC)
Title Genome-wide association study identifies 143 loci associated with 25 hydroxyvitamin D concentration.
PubMed ID 32242144(Europe PMC)
doi 10.1038/s41467-020-15421-7
Publication Date April 2, 2020
Journal Nat Commun
Author(s) Revez JA, Lin T, Qiao Z, Xue A, Holtz Y, Zhu Z, Zeng J, Wang H, Sidorenko J, Kemper KE, Vinkhuyzen AAE, Frater J, Eyles D, Burne THJ, Mitchell B, Martin NG, Zhu G, Visscher PM, Yang J, Wray NR, McGrath JJ.
Released in PGS Catalog: Aug. 26, 2021

Associated Polygenic Score(s)

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Individuals included in:
G - Source of Variant Associations (GWAS)
D - Score Development/Training
E - PGS Evaluation
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PGS Developed By This Publication

Polygenic Score ID & Name PGS Publication ID (PGP) Reported Trait Mapped Trait(s) (Ontology) Number of Variants Ancestry distribution
GWAS
Dev
Eval
 Scoring File (FTP Link)
PGS000882
(25OHD_SBayesR_PGS)
 PGP000228 |
Revez JA et al. Nat Commun (2020)
 25-hydroxyvitamin D vitamin D measurement 1,094,650
-
 https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000882/ScoringFiles/PGS000882.txt.gz

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) 		Evaluated Score 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
PPM002526 PGS000882
(25OHD_SBayesR_PGS)
 PSS001141|
European Ancestry|
1,632 individuals
 PGP000228 |
Revez JA et al. Nat Commun (2020)
 Reported Trait: 25-hydroxyvitamin D levels β: 0.269 (0.02) — R²: 0.096 sex, assessment month, supplement intake (ever), PCs(1-5) —
PPM002527 PGS000882
(25OHD_SBayesR_PGS)
 PSS001142|
European Ancestry|
1,632 individuals
 PGP000228 |
Revez JA et al. Nat Commun (2020)
 Reported Trait: 25-hydroxyvitamin D levels β: 0.24 (0.024) — R²: 0.0554 — —

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
PSS001141 — — 1,632 individuals — European — QIMR —
PSS001142 — — 1,632 individuals — European — UKB —