Polygenic Score (PGS) ID: PGS001303

Predicted Trait
Reported Trait Other cataract (time-to-event)
Mapped Trait(s) cataract (EFO_0001059)
Additional Trait Information https://biobankengine.stanford.edu/RIVAS_HG19/snpnet/HC872
Released in PGS Catalog: Oct. 21, 2021
Download Score FTP directory
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_HC872
Development Method
Name snpnet
Parameters NR
Variants
Original Genome Build GRCh37
Number of Variants 480
Effect Weight Type NR
PGS Source
PGS Catalog Publication (PGP) ID PGP000244
Citation (link to publication) Tanigawa Y et al. medRxiv (2021) Preprint
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
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
[
  • 16,426 cases
  • , 253,278 controls
]
European white British ancestry UKB

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
PPM009010 PSS004677|
African Ancestry|
6,497 individuals
PGP000244 |
Tanigawa Y et al. medRxiv (2021)
|Pre
Reported Trait: TTE other cataract AUROC: 0.81396 [0.7961, 0.83182] : 0.23163
Incremental AUROC (full-covars): 5e-05
PGS R2 (no covariates): 0.00013
PGS AUROC (no covariates): 0.50326 [0.47798, 0.52854]
age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM009011 PSS004678|
East Asian Ancestry|
1,704 individuals
PGP000244 |
Tanigawa Y et al. medRxiv (2021)
|Pre
Reported Trait: TTE other cataract AUROC: 0.81597 [0.77997, 0.85198] : 0.21513
Incremental AUROC (full-covars): 0.00031
PGS R2 (no covariates): 0.00012
PGS AUROC (no covariates): 0.50879 [0.45096, 0.56661]
age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM009012 PSS004679|
European Ancestry|
24,905 individuals
PGP000244 |
Tanigawa Y et al. medRxiv (2021)
|Pre
Reported Trait: TTE other cataract AUROC: 0.75268 [0.74071, 0.76465] : 0.12486
Incremental AUROC (full-covars): 0.00345
PGS R2 (no covariates): 0.00455
PGS AUROC (no covariates): 0.5485 [0.53327, 0.56373]
age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM009013 PSS004680|
South Asian Ancestry|
7,831 individuals
PGP000244 |
Tanigawa Y et al. medRxiv (2021)
|Pre
Reported Trait: TTE other cataract AUROC: 0.79821 [0.78425, 0.81216] : 0.23261
Incremental AUROC (full-covars): 0.00152
PGS R2 (no covariates): 0.00238
PGS AUROC (no covariates): 0.52897 [0.51011, 0.54783]
age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM009014 PSS004681|
European Ancestry|
67,425 individuals
PGP000244 |
Tanigawa Y et al. medRxiv (2021)
|Pre
Reported Trait: TTE other cataract AUROC: 0.72387 [0.71653, 0.73121] : 0.09993
Incremental AUROC (full-covars): 0.00356
PGS R2 (no covariates): 0.0043
PGS AUROC (no covariates): 0.54593 [0.53685, 0.555]
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
PSS004677
[
  • 561 cases
  • , 5,936 controls
]
African unspecified UKB
PSS004678
[
  • 115 cases
  • , 1,589 controls
]
East Asian UKB
PSS004679
[
  • 1,448 cases
  • , 23,457 controls
]
European non-white British ancestry UKB
PSS004680
[
  • 986 cases
  • , 6,845 controls
]
South Asian UKB
PSS004681
[
  • 4,189 cases
  • , 63,236 controls
]
European white British ancestry UKB Testing cohort (heldout set)