Polygenic Score (PGS) ID: PGS001275

Predicted Trait
Reported Trait Other retinal disorders (time-to-event)
Mapped Trait(s) retinopathy (EFO_0003839)
Additional Trait Information https://biobankengine.stanford.edu/RIVAS_HG19/snpnet/HC880
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_HC880
Development Method
Name snpnet
Parameters NR
Variants
Original Genome Build GRCh37
Number of Variants 6
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
—
[
  • 6,174 cases
  • , 263,530 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
PPM008873 PSS004687|
African Ancestry|
6,497 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: TTE other retinal disorders — AUROC: 0.70701 [0.6592, 0.75482] R²: 0.06654
Incremental AUROC (full-covars): -0.00077
PGS R2 (no covariates): 0.00011
PGS AUROC (no covariates): 0.50886 [0.45807, 0.55965]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM008874 PSS004688|
East Asian Ancestry|
1,704 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: TTE other retinal disorders — AUROC: 0.76408 [0.70187, 0.8263] R²: 0.11034
Incremental AUROC (full-covars): 0.00238
PGS R2 (no covariates): 0.00124
PGS AUROC (no covariates): 0.54196 [0.45417, 0.62976]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM008875 PSS004689|
European Ancestry|
24,905 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: TTE other retinal disorders — AUROC: 0.68838 [0.66508, 0.71167] R²: 0.04946
Incremental AUROC (full-covars): 0.00295
PGS R2 (no covariates): 0.00217
PGS AUROC (no covariates): 0.53609 [0.50994, 0.56223]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM008876 PSS004690|
South Asian Ancestry|
7,831 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: TTE other retinal disorders — AUROC: 0.73994 [0.71282, 0.76707] R²: 0.09449
Incremental AUROC (full-covars): 0.00101
PGS R2 (no covariates): 0.00053
PGS AUROC (no covariates): 0.51345 [0.47882, 0.54808]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM008877 PSS004691|
European Ancestry|
67,425 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: TTE other retinal disorders — AUROC: 0.67575 [0.6628, 0.6887] R²: 0.04416
Incremental AUROC (full-covars): 0.00229
PGS R2 (no covariates): 0.00203
PGS AUROC (no covariates): 0.53038 [0.51532, 0.54545]		 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
PSS004687 — —
[
  • 125 cases
  • , 6,372 controls
]
 — African unspecified — UKB —
PSS004688 — —
[
  • 43 cases
  • , 1,661 controls
]
 — East Asian — UKB —
PSS004689 — —
[
  • 490 cases
  • , 24,415 controls
]
 — European non-white British ancestry UKB —
PSS004690 — —
[
  • 284 cases
  • , 7,547 controls
]
 — South Asian — UKB —
PSS004691 — —
[
  • 1,549 cases
  • , 65,876 controls
]
 — European white British ancestry UKB Testing cohort (heldout set)