Polygenic Score (PGS) ID: PGS001153

Predicted Trait
Reported Trait Folic acid or folate (Vitamin B9)
Mapped Trait(s) folic acid measurement (EFO_0005111)
Additional Trait Information https://biobankengine.stanford.edu/RIVAS_HG19/snpnet/BIN_FC18006155
Released in PGS Catalog: Oct. 21, 2021
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Score Details

Score Construction
PGS Name GBE_BIN_FC18006155
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%
268,716 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
  • , 262,717 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
PPM008487 PSS003800|
African Ancestry|
6,313 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Folic acid or folate (Vitamin B9) — AUROC: 0.6634 [0.63271, 0.69409] R²: 0.0478
Incremental AUROC (full-covars): 0.00087
PGS R2 (no covariates): 0.00159
PGS AUROC (no covariates): 0.51941 [0.48659, 0.55223]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM008488 PSS003801|
East Asian Ancestry|
1,640 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Folic acid or folate (Vitamin B9) — AUROC: 0.63752 [0.54728, 0.72776] R²: 0.0289
Incremental AUROC (full-covars): -0.00046
PGS R2 (no covariates): 0.00218
PGS AUROC (no covariates): 0.46506 [0.36185, 0.56827]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM008489 PSS003802|
European Ancestry|
24,779 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Folic acid or folate (Vitamin B9) — AUROC: 0.60494 [0.58719, 0.6227] R²: 0.01823
Incremental AUROC (full-covars): 0.00018
PGS R2 (no covariates): 0.0001
PGS AUROC (no covariates): 0.50901 [0.49019, 0.52784]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM008490 PSS003803|
South Asian Ancestry|
7,500 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Folic acid or folate (Vitamin B9) — AUROC: 0.6488 [0.61837, 0.67924] R²: 0.0382
Incremental AUROC (full-covars): 0.00089
PGS R2 (no covariates): 0.00065
PGS AUROC (no covariates): 0.5068 [0.47267, 0.54094]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM008491 PSS003804|
European Ancestry|
67,194 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Folic acid or folate (Vitamin B9) — AUROC: 0.57772 [0.56344, 0.59201] R²: 0.00847
Incremental AUROC (full-covars): 0.00471
PGS R2 (no covariates): 0.00169
PGS AUROC (no covariates): 0.526 [0.51065, 0.54135]		 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
PSS003804 — —
[
  • 1,485 cases
  • , 65,709 controls
]
 — European white British ancestry UKB Testing cohort (heldout set)
PSS003800 — —
[
  • 327 cases
  • , 5,986 controls
]
 — African unspecified — UKB —
PSS003801 — —
[
  • 34 cases
  • , 1,606 controls
]
 — East Asian — UKB —
PSS003802 — —
[
  • 922 cases
  • , 23,857 controls
]
 — European non-white British ancestry UKB —
PSS003803 — —
[
  • 311 cases
  • , 7,189 controls
]
 — South Asian — UKB —