Polygenic Score (PGS) ID: PGS001276

Predicted Trait
Reported Trait Retinal disorders in diseases classified elsewhere (time-to-event)
Mapped Trait(s) retinopathy (EFO_0003839)
Additional Trait Information https://biobankengine.stanford.edu/RIVAS_HG19/snpnet/HC881
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_HC881
Development Method
Name snpnet
Parameters NR
Variants
Original Genome Build GRCh37
Number of Variants 185
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
—
[
  • 1,507 cases
  • , 268,197 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
PPM008878 PSS004692|
African Ancestry|
6,497 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: TTE retinal disorders in diseases classified elsewhere — AUROC: 0.69535 [0.65164, 0.73906] R²: 0.04898
Incremental AUROC (full-covars): -0.01537
PGS R2 (no covariates): 0.00048
PGS AUROC (no covariates): 0.47863 [0.42888, 0.52839]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM008879 PSS004693|
East Asian Ancestry|
1,704 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: TTE retinal disorders in diseases classified elsewhere — AUROC: 0.78112 [0.63575, 0.92649] R²: 0.09795
Incremental AUROC (full-covars): -0.03107
PGS R2 (no covariates): 0.00124
PGS AUROC (no covariates): 0.45159 [0.20305, 0.70013]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM008880 PSS004694|
European Ancestry|
24,905 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: TTE retinal disorders in diseases classified elsewhere — AUROC: 0.70588 [0.66187, 0.7499] R²: 0.04864
Incremental AUROC (full-covars): 0.02939
PGS R2 (no covariates): 0.01461
PGS AUROC (no covariates): 0.60872 [0.55828, 0.65917]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM008881 PSS004695|
South Asian Ancestry|
7,831 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: TTE retinal disorders in diseases classified elsewhere — AUROC: 0.73414 [0.70226, 0.76602] R²: 0.08369
Incremental AUROC (full-covars): -7e-05
PGS R2 (no covariates): 0.00183
PGS AUROC (no covariates): 0.53682 [0.49711, 0.57653]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM008882 PSS004696|
European Ancestry|
67,425 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: TTE retinal disorders in diseases classified elsewhere — AUROC: 0.67399 [0.64743, 0.70056] R²: 0.03213
Incremental AUROC (full-covars): 0.02207
PGS R2 (no covariates): 0.00817
PGS AUROC (no covariates): 0.57664 [0.54625, 0.60704]		 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
PSS004692 — —
[
  • 129 cases
  • , 6,368 controls
]
 — African unspecified — UKB —
PSS004693 — —
[
  • 9 cases
  • , 1,695 controls
]
 — East Asian — UKB —
PSS004694 — —
[
  • 121 cases
  • , 24,784 controls
]
 — European non-white British ancestry UKB —
PSS004695 — —
[
  • 204 cases
  • , 7,627 controls
]
 — South Asian — UKB —
PSS004696 — —
[
  • 363 cases
  • , 67,062 controls
]
 — European white British ancestry UKB Testing cohort (heldout set)