Trait: folic acid measurement

Experimental Factor Ontology (EFO) Information
Identifier EFO_0005111
Description A measurement of the folic acid in a biological sample
Trait category
Other measurement
Synonyms 2 synonyms
  • folate measurement
  • vitamin B9 measurement
Mapped terms 2 mapped terms
  • NCIt:C74676
  • SNOMEDCT:104660009

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)
PGS001153
(GBE_BIN_FC18006155)
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Folic acid or folate (Vitamin B9) folic acid measurement 5
-
 https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS001153/ScoringFiles/PGS001153.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
PPM008487 PGS001153
(GBE_BIN_FC18006155)
 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 PGS001153
(GBE_BIN_FC18006155)
 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 PGS001153
(GBE_BIN_FC18006155)
 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 PGS001153
(GBE_BIN_FC18006155)
 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 PGS001153
(GBE_BIN_FC18006155)
 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 —