Polygenic Score (PGS) ID: PGS001319

Predicted Trait
Reported Trait Other metabolic disorders (time-to-event)
Mapped Trait(s) metabolic disease (EFO_0000589)
Additional Trait Information https://biobankengine.stanford.edu/RIVAS_HG19/snpnet/HC708
Released in PGS Catalog: Oct. 21, 2021
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Terms and Licenses
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_HC708
Development Method
Name snpnet
Parameters NR
Variants
Original Genome Build GRCh37
Number of Variants 2
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
—
[
  • 531 cases
  • , 269,173 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
PPM009088 PSS004610|
African Ancestry|
6,497 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: TTE other metabolic disorders — AUROC: 0.77406 [0.68678, 0.86135] R²: 0.06649
Incremental AUROC (full-covars): -0.00199
PGS R2 (no covariates): 0.00603
PGS AUROC (no covariates): 0.44259 [0.3516, 0.53358]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM009089 PSS004611|
European Ancestry|
24,905 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: TTE other metabolic disorders — AUROC: 0.70958 [0.62744, 0.79171] R²: 0.04504
Incremental AUROC (full-covars): 0.02495
PGS R2 (no covariates): 0.01479
PGS AUROC (no covariates): 0.54987 [0.46099, 0.63876]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM009090 PSS004612|
South Asian Ancestry|
7,831 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: TTE other metabolic disorders — AUROC: 0.64684 [0.54842, 0.74526] R²: 0.02913
Incremental AUROC (full-covars): -0.00029
PGS R2 (no covariates): 0.00067
PGS AUROC (no covariates): 0.52382 [0.42834, 0.61931]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM009091 PSS004613|
European Ancestry|
67,425 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: TTE other metabolic disorders — AUROC: 0.60186 [0.54294, 0.66079] R²: 0.02952
Incremental AUROC (full-covars): 0.09428
PGS R2 (no covariates): 0.05151
PGS AUROC (no covariates): 0.62356 [0.56795, 0.67918]		 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
PSS004612 — —
[
  • 26 cases
  • , 7,805 controls
]
 — South Asian — UKB —
PSS004613 — —
[
  • 112 cases
  • , 67,313 controls
]
 — European white British ancestry UKB Testing cohort (heldout set)
PSS004610 — —
[
  • 17 cases
  • , 6,480 controls
]
 — African unspecified — UKB —
PSS004611 — —
[
  • 41 cases
  • , 24,864 controls
]
 — European non-white British ancestry UKB —