Polygenic Score (PGS) ID: PGS001322

Predicted Trait
Reported Trait Glaucoma
Mapped Trait(s) glaucoma (MONDO_0005041)
Additional Trait Information https://biobankengine.stanford.edu/RIVAS_HG19/snpnet/HC276
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_HC276
Development Method
Name snpnet
Parameters NR
Variants
Original Genome Build GRCh37
Number of Variants 655
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
—
[
  • 5,792 cases
  • , 263,912 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
PPM009102 PSS004408|
African Ancestry|
6,497 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Glaucoma — AUROC: 0.73888 [0.70843, 0.76932] R²: 0.0999
Incremental AUROC (full-covars): -0.00815
PGS R2 (no covariates): 0.00019
PGS AUROC (no covariates): 0.48469 [0.45088, 0.5185]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM009103 PSS004409|
East Asian Ancestry|
1,704 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Glaucoma — AUROC: 0.70681 [0.61243, 0.80118] R²: 0.05552
Incremental AUROC (full-covars): -0.01374
PGS R2 (no covariates): 0.00272
PGS AUROC (no covariates): 0.45399 [0.34399, 0.564]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM009104 PSS004410|
European Ancestry|
24,905 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Glaucoma — AUROC: 0.73317 [0.71252, 0.75382] R²: 0.0763
Incremental AUROC (full-covars): 0.01834
PGS R2 (no covariates): 0.01238
PGS AUROC (no covariates): 0.59932 [0.57386, 0.62477]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM009105 PSS004411|
South Asian Ancestry|
7,831 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Glaucoma — AUROC: 0.74918 [0.71835, 0.78] R²: 0.09545
Incremental AUROC (full-covars): 0.01096
PGS R2 (no covariates): 0.01142
PGS AUROC (no covariates): 0.59951 [0.56169, 0.63734]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM009106 PSS004412|
European Ancestry|
67,425 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Glaucoma — AUROC: 0.7048 [0.69206, 0.71754] R²: 0.0589
Incremental AUROC (full-covars): 0.02562
PGS R2 (no covariates): 0.015
PGS AUROC (no covariates): 0.60261 [0.58762, 0.6176]		 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
PSS004412 — —
[
  • 1,327 cases
  • , 66,098 controls
]
 — European white British ancestry UKB Testing cohort (heldout set)
PSS004408 — —
[
  • 265 cases
  • , 6,232 controls
]
 — African unspecified — UKB —
PSS004409 — —
[
  • 28 cases
  • , 1,676 controls
]
 — East Asian — UKB —
PSS004410 — —
[
  • 477 cases
  • , 24,428 controls
]
 — European non-white British ancestry UKB —
PSS004411 — —
[
  • 218 cases
  • , 7,613 controls
]
 — South Asian — UKB —