Polygenic Score (PGS) ID: PGS001305

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
Released in PGS Catalog: Oct. 21, 2021
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PGS obtained from the Catalog should be cited appropriately, and used in accordance with any licensing restrictions set by the authors. See EBI Terms of Use (https://www.ebi.ac.uk/about/terms-of-use/) for additional details.

Score Details

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

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
—
[
  • 1,723 cases
  • , 267,981 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
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

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
PSS004540 — —
[
  • 447 cases
  • , 66,978 controls
]
 — European white British ancestry UKB Testing cohort (heldout set)
PSS004536 — —
[
  • 19 cases
  • , 6,478 controls
]
 — African unspecified — UKB —
PSS004538 — —
[
  • 160 cases
  • , 24,745 controls
]
 — European non-white British ancestry UKB —
PSS004539 — —
[
  • 138 cases
  • , 7,693 controls
]
 — South Asian — UKB —