Polygenic Score (PGS) ID: PGS001302

Predicted Trait
Reported Trait Cataract
Mapped Trait(s) cataract (MONDO_0005129)
Additional Trait Information https://biobankengine.stanford.edu/RIVAS_HG19/snpnet/HC25
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_HC25
Development Method
Name snpnet
Parameters NR
Variants
Original Genome Build GRCh37
Number of Variants 1,214
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: 16.7%
East Asian: 16.7%
South Asian: 16.7%
6 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
—
[
  • 20,429 cases
  • , 249,275 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
PPM009005 PSS004379|
African Ancestry|
6,497 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Cataract — AUROC: 0.81842 [0.80148, 0.83536] R²: 0.25176
Incremental AUROC (full-covars): -0.00057
PGS R2 (no covariates): 0.00041
PGS AUROC (no covariates): 0.51203 [0.48858, 0.53548]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM009006 PSS004380|
East Asian Ancestry|
1,704 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Cataract — AUROC: 0.81531 [0.78353, 0.84709] R²: 0.22081
Incremental AUROC (full-covars): 0.00025
PGS R2 (no covariates): 0.00037
PGS AUROC (no covariates): 0.48894 [0.43818, 0.53971]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM009007 PSS004381|
European Ancestry|
24,905 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Cataract — AUROC: 0.76448 [0.75374, 0.77523] R²: 0.14636
Incremental AUROC (full-covars): 0.00517
PGS R2 (no covariates): 0.00768
PGS AUROC (no covariates): 0.56031 [0.5466, 0.57402]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM009008 PSS004382|
South Asian Ancestry|
7,831 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Cataract — AUROC: 0.81674 [0.80411, 0.82937] R²: 0.28207
Incremental AUROC (full-covars): 0.0031
PGS R2 (no covariates): 0.00627
PGS AUROC (no covariates): 0.54731 [0.52945, 0.56518]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM009009 PSS004383|
European Ancestry|
67,425 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Cataract — AUROC: 0.73692 [0.73039, 0.74345] R²: 0.12068
Incremental AUROC (full-covars): 0.00566
PGS R2 (no covariates): 0.00657
PGS AUROC (no covariates): 0.55468 [0.5465, 0.56286]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM018448 PSS010980|
European Ancestry|
4,797 individuals
 PGP000467 |
Farré X et al. Genes (Basel) (2023)
|Ext.		 Reported Trait: Eye colour β: 0.11584 — R²: 0.01115 — —
PPM018449 PSS010980|
European Ancestry|
4,797 individuals
 PGP000467 |
Farré X et al. Genes (Basel) (2023)
|Ext.		 Reported Trait: Sunscreen in exterior β: -0.03314 — R²: 0.0383 — —
PPM018450 PSS010980|
European Ancestry|
4,797 individuals
 PGP000467 |
Farré X et al. Genes (Basel) (2023)
|Ext.		 Reported Trait: Phototype score β: 0.70812 — R²: 0.03441 — —
PPM018451 PSS010980|
European Ancestry|
4,797 individuals
 PGP000467 |
Farré X et al. Genes (Basel) (2023)
|Ext.		 Reported Trait: Fitzpatrick scale β: 0.04334 — R²: 0.03185 — —

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
PSS004380 — —
[
  • 140 cases
  • , 1,564 controls
]
 — East Asian — UKB —
PSS004381 — —
[
  • 1,738 cases
  • , 23,167 controls
]
 — European non-white British ancestry UKB —
PSS004382 — —
[
  • 1,165 cases
  • , 6,666 controls
]
 — South Asian — UKB —
PSS004383 — —
[
  • 5,153 cases
  • , 62,272 controls
]
 — European white British ancestry UKB Testing cohort (heldout set)
PSS010980 — — 4,797 individuals — European — NR GCAT
PSS004379 — —
[
  • 637 cases
  • , 5,860 controls
]
 — African unspecified — UKB —