Trait: vitamin supplement exposure measurement

Experimental Factor Ontology (EFO) Information
Identifier EFO_0009116
Description Quantification of some aspect of the consumption of dietry vitamin supplements.
Trait category
Other measurement
Synonym vitamin use exposure measurement
Mapped term PMID:29535761

Associated Polygenic Score(s)

Filter PGS by Participant Ancestry
Individuals included in:
G - Source of Variant Associations (GWAS)
D - Score Development/Training
E - PGS Evaluation
List of ancestries includes:
Display options:
Ancestry legend
Multi-ancestry (including European)
Multi-ancestry (excluding European)
African
East Asian
South Asian
Additional Asian Ancestries
European
Greater Middle Eastern
Hispanic or Latin American
Additional Diverse Ancestries
Not Reported
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)
PGS001044
(GBE_BIN_FC2006179)
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Glucosamine intake vitamin supplement exposure measurement 324
-
 https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS001044/ScoringFiles/PGS001044.txt.gz
PGS001045
(GBE_BIN_FC6006155)
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Vitamin B9 intake vitamin supplement exposure measurement 5
-
 https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS001045/ScoringFiles/PGS001045.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
PPM007978 PGS001044
(GBE_BIN_FC2006179)
 PSS003864|
African Ancestry|
6,334 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Glucosamine — AUROC: 0.65622 [0.63608, 0.67636] R²: 0.06346
Incremental AUROC (full-covars): 0.00075
PGS R2 (no covariates): 0.00077
PGS AUROC (no covariates): 0.51768 [0.49687, 0.53848]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM007979 PGS001044
(GBE_BIN_FC2006179)
 PSS003865|
East Asian Ancestry|
1,651 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Glucosamine — AUROC: 0.68295 [0.65155, 0.71435] R²: 0.10514
Incremental AUROC (full-covars): -1e-05
PGS R2 (no covariates): 0.00024
PGS AUROC (no covariates): 0.50873 [0.47479, 0.54268]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM007980 PGS001044
(GBE_BIN_FC2006179)
 PSS003866|
European Ancestry|
24,820 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Glucosamine — AUROC: 0.63822 [0.62937, 0.64707] R²: 0.05449
Incremental AUROC (full-covars): 0.00027
PGS R2 (no covariates): 0.00015
PGS AUROC (no covariates): 0.50748 [0.49816, 0.51681]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM007981 PGS001044
(GBE_BIN_FC2006179)
 PSS003867|
South Asian Ancestry|
7,537 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Glucosamine — AUROC: 0.68783 [0.66995, 0.70572] R²: 0.08959
Incremental AUROC (full-covars): -3e-05
PGS R2 (no covariates): 0.00049
PGS AUROC (no covariates): 0.51694 [0.49696, 0.53692]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM007982 PGS001044
(GBE_BIN_FC2006179)
 PSS003868|
European Ancestry|
67,317 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Glucosamine — AUROC: 0.62303 [0.61791, 0.62815] R²: 0.04569
Incremental AUROC (full-covars): 0.00058
PGS R2 (no covariates): 0.00054
PGS AUROC (no covariates): 0.51206 [0.50661, 0.51751]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM007983 PGS001045
(GBE_BIN_FC6006155)
 PSS003999|
African Ancestry|
3,802 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Vitamin B9 vs no supplement — AUROC: 0.68475 [0.6556, 0.71389] R²: 0.07709
Incremental AUROC (full-covars): 0.00076
PGS R2 (no covariates): 0.00131
PGS AUROC (no covariates): 0.51314 [0.47991, 0.54637]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM007984 PGS001045
(GBE_BIN_FC6006155)
 PSS004000|
East Asian Ancestry|
1,075 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Vitamin B9 vs no supplement — AUROC: 0.66251 [0.57516, 0.74987] R²: 0.04224
Incremental AUROC (full-covars): -0.0024
PGS R2 (no covariates): 0.0034
PGS AUROC (no covariates): 0.46196 [0.35805, 0.56587]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM007985 PGS001045
(GBE_BIN_FC6006155)
 PSS004001|
European Ancestry|
16,782 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Vitamin B9 vs no supplement — AUROC: 0.63092 [0.61318, 0.64866] R²: 0.0323
Incremental AUROC (full-covars): 0.00015
PGS R2 (no covariates): 0.00013
PGS AUROC (no covariates): 0.50968 [0.49066, 0.5287]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM007986 PGS001045
(GBE_BIN_FC6006155)
 PSS004002|
South Asian Ancestry|
5,037 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Vitamin B9 vs no supplement — AUROC: 0.68137 [0.6527, 0.71004] R²: 0.0652
Incremental AUROC (full-covars): 0.0012
PGS R2 (no covariates): 0.00092
PGS AUROC (no covariates): 0.50692 [0.47257, 0.54128]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM007987 PGS001045
(GBE_BIN_FC6006155)
 PSS004003|
European Ancestry|
48,662 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Vitamin B9 vs no supplement — AUROC: 0.59438 [0.58013, 0.60863] R²: 0.01363
Incremental AUROC (full-covars): 0.00464
PGS R2 (no covariates): 0.00209
PGS AUROC (no covariates): 0.52811 [0.5127, 0.54352]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method

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
PSS003868 — —
[
  • 13,703 cases
  • , 53,614 controls
]
 — European white British ancestry UKB Testing cohort (heldout set)
PSS003999 — —
[
  • 327 cases
  • , 3,475 controls
]
 — African unspecified — UKB —
PSS004000 — —
[
  • 34 cases
  • , 1,041 controls
]
 — East Asian — UKB —
PSS004001 — —
[
  • 922 cases
  • , 15,860 controls
]
 — European non-white British ancestry UKB —
PSS004002 — —
[
  • 311 cases
  • , 4,726 controls
]
 — South Asian — UKB —
PSS004003 — —
[
  • 1,485 cases
  • , 47,177 controls
]
 — European white British ancestry UKB Testing cohort (heldout set)
PSS003864 — —
[
  • 842 cases
  • , 5,492 controls
]
 — African unspecified — UKB —
PSS003865 — —
[
  • 334 cases
  • , 1,317 controls
]
 — East Asian — UKB —
PSS003866 — —
[
  • 4,457 cases
  • , 20,363 controls
]
 — European non-white British ancestry UKB —
PSS003867 — —
[
  • 926 cases
  • , 6,611 controls
]
 — South Asian — UKB —