Polygenic Score (PGS) ID: PGS001321

Predicted Trait
Reported Trait Eye problems/disorders (Glaucoma)
Mapped Trait(s) glaucoma (MONDO_0005041)
Additional Trait Information https://biobankengine.stanford.edu/RIVAS_HG19/snpnet/BIN_FC2006148
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_BIN_FC2006148
Development Method
Name snpnet
Parameters NR
Variants
Original Genome Build GRCh37
Number of Variants 1,103
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%
90,517 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
—
[
  • 4,384 cases
  • , 86,133 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
PPM009097 PSS003849|
African Ancestry|
3,341 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Eye problems/disorders Glaucoma — AUROC: 0.75589 [0.72234, 0.78943] R²: 0.13943
Incremental AUROC (full-covars): -0.01209
PGS R2 (no covariates): 1e-05
PGS AUROC (no covariates): 0.49958 [0.46126, 0.5379]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM009098 PSS003850|
East Asian Ancestry|
715 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Eye problems/disorders Glaucoma — AUROC: 0.71808 [0.61808, 0.81809] R²: 0.09844
Incremental AUROC (full-covars): -0.01728
PGS R2 (no covariates): 0.00057
PGS AUROC (no covariates): 0.5191 [0.40156, 0.63664]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM009099 PSS003851|
European Ancestry|
9,888 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Eye problems/disorders Glaucoma — AUROC: 0.75377 [0.72896, 0.77858] R²: 0.11288
Incremental AUROC (full-covars): 0.01096
PGS R2 (no covariates): 0.01038
PGS AUROC (no covariates): 0.57925 [0.54955, 0.60894]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM009100 PSS003852|
South Asian Ancestry|
3,441 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Eye problems/disorders Glaucoma — AUROC: 0.7617 [0.72794, 0.79547] R²: 0.1335
Incremental AUROC (full-covars): 0.00638
PGS R2 (no covariates): 0.01082
PGS AUROC (no covariates): 0.57361 [0.5321, 0.61512]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM009101 PSS003853|
European Ancestry|
22,623 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Eye problems/disorders Glaucoma — AUROC: 0.72434 [0.70924, 0.73944] R²: 0.09306
Incremental AUROC (full-covars): 0.02225
PGS R2 (no covariates): 0.0194
PGS AUROC (no covariates): 0.60001 [0.58198, 0.61804]		 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
PSS003849 — —
[
  • 217 cases
  • , 3,124 controls
]
 — African unspecified — UKB —
PSS003850 — —
[
  • 23 cases
  • , 692 controls
]
 — East Asian — UKB —
PSS003851 — —
[
  • 373 cases
  • , 9,515 controls
]
 — European non-white British ancestry UKB —
PSS003852 — —
[
  • 178 cases
  • , 3,263 controls
]
 — South Asian — UKB —
PSS003853 — —
[
  • 1,054 cases
  • , 21,569 controls
]
 — European white British ancestry UKB Testing cohort (heldout set)