Polygenic Score (PGS) ID: PGS001029

Predicted Trait
Reported Trait Other disorders of cornea (time-to-event)
Mapped Trait(s) corneal disease (EFO_0009464)
Additional Trait Information https://biobankengine.stanford.edu/RIVAS_HG19/snpnet/HC866
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_HC866
Development Method
Name snpnet
Parameters NR
Variants
Original Genome Build GRCh37
Number of Variants 22
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: 40%
African: 20%
East Asian: 20%
South Asian: 20%
5 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
—
[
  • 1,190 cases
  • , 268,514 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
PPM007908 PSS004662|
African Ancestry|
6,497 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: TTE other disorders of cornea — AUROC: 0.71052 [0.62918, 0.79186] R²: 0.05427
Incremental AUROC (full-covars): 0.0031
PGS R2 (no covariates): 0.00332
PGS AUROC (no covariates): 0.54756 [0.45415, 0.64098]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM007909 PSS004663|
East Asian Ancestry|
1,704 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: TTE other disorders of cornea — AUROC: 0.48912 [0.0043, 0.97395] R²: 0.00203
Incremental AUROC (full-covars): 0.0
PGS R2 (no covariates): 0.00633
PGS AUROC (no covariates): 0.40016 [0.0, 0.86755]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM007910 PSS004664|
European Ancestry|
24,905 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: TTE other disorders of cornea — AUROC: 0.63469 [0.57721, 0.69216] PGS R2 (no covariates): 0.01229
R²: 0.01902
Incremental AUROC (full-covars): 0.04837
PGS AUROC (no covariates): 0.59818 [0.5417, 0.65467]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM007911 PSS004665|
South Asian Ancestry|
7,831 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: TTE other disorders of cornea — AUROC: 0.62122 [0.5586, 0.68385] R²: 0.02027
Incremental AUROC (full-covars): -0.01924
PGS R2 (no covariates): 0.00532
PGS AUROC (no covariates): 0.44761 [0.382, 0.51322]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM007912 PSS004666|
European Ancestry|
67,425 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: TTE other disorders of cornea — AUROC: 0.60075 [0.56985, 0.63165] R²: 0.01227
Incremental AUROC (full-covars): 0.02429
PGS R2 (no covariates): 0.00807
PGS AUROC (no covariates): 0.58115 [0.55051, 0.61178]		 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
PSS004662 — —
[
  • 34 cases
  • , 6,463 controls
]
 — African unspecified — UKB —
PSS004663 — —
[
  • 3 cases
  • , 1,701 controls
]
 — East Asian — UKB —
PSS004664 — —
[
  • 104 cases
  • , 24,801 controls
]
 — European non-white British ancestry UKB —
PSS004665 — —
[
  • 61 cases
  • , 7,770 controls
]
 — South Asian — UKB —
PSS004666 — —
[
  • 353 cases
  • , 67,072 controls
]
 — European white British ancestry UKB Testing cohort (heldout set)