Polygenic Score (PGS) ID: PGS001323

Predicted Trait
Reported Trait Glaucoma (time-to-event)
Mapped Trait(s) glaucoma (MONDO_0005041)
Additional Trait Information https://biobankengine.stanford.edu/RIVAS_HG19/snpnet/HC882
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_HC882
Development Method
Name snpnet
Parameters NR
Variants
Original Genome Build GRCh37
Number of Variants 2,066
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
—
[
  • 8,086 cases
  • , 261,618 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
PPM009107 PSS004697|
African Ancestry|
6,497 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: TTE glaucoma — AUROC: 0.72181 [0.69233, 0.75129] R²: 0.0918
Incremental AUROC (full-covars): -0.00164
PGS R2 (no covariates): 0.00184
PGS AUROC (no covariates): 0.53284 [0.50004, 0.56563]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM009108 PSS004698|
East Asian Ancestry|
1,704 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: TTE glaucoma — AUROC: 0.70826 [0.61816, 0.79836] R²: 0.06483
Incremental AUROC (full-covars): 0.01999
PGS R2 (no covariates): 0.00405
PGS AUROC (no covariates): 0.54496 [0.43191, 0.65802]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM009109 PSS004699|
European Ancestry|
24,905 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: TTE glaucoma — AUROC: 0.72679 [0.7079, 0.74569] R²: 0.07732
Incremental AUROC (full-covars): 0.0269
PGS R2 (no covariates): 0.01761
PGS AUROC (no covariates): 0.60838 [0.58579, 0.63096]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM009110 PSS004700|
South Asian Ancestry|
7,831 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: TTE glaucoma — AUROC: 0.73399 [0.70517, 0.76282] R²: 0.08727
Incremental AUROC (full-covars): 0.00993
PGS R2 (no covariates): 0.00928
PGS AUROC (no covariates): 0.57629 [0.54141, 0.61116]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM009111 PSS004701|
European Ancestry|
67,425 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: TTE glaucoma — AUROC: 0.70422 [0.69334, 0.7151] R²: 0.06469
Incremental AUROC (full-covars): 0.0364
PGS R2 (no covariates): 0.02201
PGS AUROC (no covariates): 0.61994 [0.60732, 0.63256]		 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
PSS004700 — —
[
  • 261 cases
  • , 7,570 controls
]
 — South Asian — UKB —
PSS004701 — —
[
  • 1,890 cases
  • , 65,535 controls
]
 — European white British ancestry UKB Testing cohort (heldout set)
PSS004697 — —
[
  • 307 cases
  • , 6,190 controls
]
 — African unspecified — UKB —
PSS004698 — —
[
  • 34 cases
  • , 1,670 controls
]
 — East Asian — UKB —
PSS004699 — —
[
  • 637 cases
  • , 24,268 controls
]
 — European non-white British ancestry UKB —