Polygenic Score (PGS) ID: PGS001045

Predicted Trait
Reported Trait Vitamin B9 intake
Mapped Trait(s) vitamin supplement exposure measurement (EFO_0009116)
Additional Trait Information https://biobankengine.stanford.edu/RIVAS_HG19/snpnet/BIN_FC6006155
Released in PGS Catalog: Oct. 21, 2021
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Score Details

Score Construction
PGS Name GBE_BIN_FC6006155
Development Method
Name snpnet
Parameters NR
Variants
Original Genome Build GRCh37
Number of Variants 5
Effect Weight Type NR
PGS Source
PGS Catalog Publication (PGP) ID PGP000244
Citation (link to publication) Tanigawa Y et al. PLoS Genet (2022)
Ancestry Distribution
Score Development/Training
European: 100%
194,699 individuals (100%)
PGS Evaluation
European: 40%
African: 20%
East Asian: 20%
South Asian: 20%
5 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
—
[
  • 5,999 cases
  • , 188,700 controls
]
 European UKB — — — white British ancestry —

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
PPM007983 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 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 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 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 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
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)