| Predicted Trait | |
| Reported Trait | Vitamin B12 deficiency induced anemia (time-to-event) |
| Mapped Trait(s) | |
| Additional Trait Information | https://biobankengine.stanford.edu/RIVAS_HG19/snpnet/HC608 |
| Score Construction | |
| PGS Name | GBE_HC608 |
| Development Method | |
| Name | snpnet |
| Parameters | NR |
| Variants | |
| Original Genome Build | GRCh37 |
| Number of Variants | 121 |
| 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% 269,704 individuals (100%) |
| PGS Evaluation | European: 50% African: 25% South Asian: 25% 4 Sample Sets |
Study Identifiers
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Sample Numbers
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Sample Ancestry
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Cohort(s)
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Phenotype Definitions & Methods
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Age of Study Participants
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Participant Follow-up Time
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Additional Ancestry Description
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Additional Sample/Cohort Information
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|---|---|---|---|---|---|---|---|---|
| — | [
| European | UKB | — | — | — | white British ancestry | — |
PGS Performance Metric ID (PPM) |
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 |
|---|---|---|---|---|---|---|---|---|
| PPM009020 | 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 | 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 | 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 | 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
|
Participant Follow-up Time
|
Sample Numbers
|
Age of Study Participants
|
Sample Ancestry
|
Additional Ancestry Description
|
Cohort(s)
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Additional Sample/Cohort Information
|
|---|---|---|---|---|---|---|---|---|
| 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) |