Experimental Factor Ontology (EFO) Information | |
Identifier | EFO_0000734 |
Description | A disease characterized by low serum levels of vitamin B12, either inherited or acquired. [PMID: 168... 46473]Show more |
Trait category |
Metabolic disorder
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Synonyms |
20 synonyms
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Mapped terms |
15 mapped terms
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Polygenic Score ID & Name
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PGS Publication ID (PGP)
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Reported Trait
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Mapped Trait(s) (Ontology)
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Number of Variants
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Ancestry distribution GWAS Dev Eval |
Scoring File (FTP Link)
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PGS001305 (GBE_HC608) | PGP000244 | Tanigawa Y et al. PLoS Genet (2022) | Vitamin B12 deficiency induced anemia (time-to-event) | vitamin B12 deficiency, anemia | 121 | - | https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS001305/ScoringFiles/PGS001305.txt.gz |
PGS Performance Metric ID (PPM) |
Evaluated Score
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PGS Sample Set ID (PSS) |
Performance Source
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Trait
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PGS Effect Sizes (per SD change) |
Classification Metrics
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Other Metrics
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Covariates Included in the Model
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PGS Performance: Other Relevant Information |
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PPM009020 | PGS001305 (GBE_HC608) | PSS004536| African Ancestry| 6,497 individuals | PGP000244 | Tanigawa Y et al. PLoS Genet (2022) | Reported Trait: TTE vitamin b12 deficiency anaemia | — | AUROC: 0.66063 [0.54547, 0.77579] | R²: 0.02699 Incremental AUROC (full-covars): 0.01762 PGS R2 (no covariates): 0.00536 PGS AUROC (no covariates): 0.5839 [0.43974, 0.72805] | age, sex, UKB array type, Genotype PCs | Full Model & PGS R2 is estimated using Nagelkerke's method |
PPM009021 | PGS001305 (GBE_HC608) | PSS004538| European Ancestry| 24,905 individuals | PGP000244 | Tanigawa Y et al. PLoS Genet (2022) | Reported Trait: TTE vitamin b12 deficiency anaemia | — | AUROC: 0.65118 [0.60827, 0.69409] | R²: 0.02729 Incremental AUROC (full-covars): 0.02555 PGS R2 (no covariates): 0.00865 PGS AUROC (no covariates): 0.59612 [0.5552, 0.63704] | age, sex, UKB array type, Genotype PCs | Full Model & PGS R2 is estimated using Nagelkerke's method |
PPM009022 | PGS001305 (GBE_HC608) | PSS004539| South Asian Ancestry| 7,831 individuals | PGP000244 | Tanigawa Y et al. PLoS Genet (2022) | Reported Trait: TTE vitamin b12 deficiency anaemia | — | AUROC: 0.72387 [0.6834, 0.76434] | R²: 0.06747 Incremental AUROC (full-covars): 0.01252 PGS R2 (no covariates): 0.00966 PGS AUROC (no covariates): 0.57469 [0.52685, 0.62252] | age, sex, UKB array type, Genotype PCs | Full Model & PGS R2 is estimated using Nagelkerke's method |
PPM009023 | PGS001305 (GBE_HC608) | PSS004540| European Ancestry| 67,425 individuals | PGP000244 | Tanigawa Y et al. PLoS Genet (2022) | Reported Trait: TTE vitamin b12 deficiency anaemia | — | AUROC: 0.64482 [0.61972, 0.66993] | R²: 0.02374 Incremental AUROC (full-covars): 0.02212 PGS R2 (no covariates): 0.0068 PGS AUROC (no covariates): 0.57972 [0.55331, 0.60612] | age, sex, UKB array type, Genotype PCs | Full Model & PGS R2 is estimated using Nagelkerke's method |
PGS Sample Set ID (PSS) |
Phenotype Definitions and Methods
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Participant Follow-up Time
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Sample Numbers
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Age of Study Participants
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Sample Ancestry
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Additional Ancestry Description
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Cohort(s)
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Additional Sample/Cohort Information
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PSS004536 | — | — | [
| — | African unspecified | — | UKB | — |
PSS004538 | — | — | [
| — | European | non-white British ancestry | UKB | — |
PSS004539 | — | — | [
| — | South Asian | — | UKB | — |
PSS004540 | — | — | [
| — | European | white British ancestry | UKB | Testing cohort (heldout set) |