Polygenic Score (PGS) ID: PGS001792

Predicted Trait
Reported Trait Primary open-angle glaucoma
Mapped Trait(s) glaucoma (EFO_0000516)
Released in PGS Catalog: Sept. 8, 2022
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Terms and Licenses
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Score Details

Score Construction
PGS Name 1kgeur_gbmi_leaveUKBBout_POAG_pst_eff_a1_b0.5_phiauto
Development Method
Name PRS-CS-auto
Parameters effective sample size and other defualt parameters
Variants
Original Genome Build GRCh37
Number of Variants 911,402
Effect Weight Type beta
PGS Source
PGS Catalog Publication (PGP) ID PGP000262
Citation (link to publication) Wang Y et al. medRxiv (2021) Preprint
Ancestry Distribution
Source of Variant
Associations (GWAS)
European: 71.9%
East Asian: 25.3%
African: 1.9%
Additional Diverse Ancestries: 0.9%
1,066,654 individuals (100%)
PGS Evaluation
Additional Asian Ancestries: 50%
European: 50%
2 Sample Sets

Development Samples

Source of Variant Associations (GWAS)
Study Identifiers Sample Numbers Sample Ancestry Cohort(s)
[
  • 404 cases
  • , 20,066 controls
]
African unspecified NR
[
  • 243 cases
  • , 9,103 controls
]
Native American BioMe
[
  • 9,715 cases
  • , 260,245 controls
]
East Asian BioMe, UCLA
[
  • 14,863 cases
  • , 752,015 controls
]
European BBJ, TWB, UCLA

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
PPM009305 PSS007704|
Additional Asian Ancestries|
7,787 individuals
PGP000262 |
Wang Y et al. medRxiv (2021)
|Pre
Reported Trait: Primary open-angle glaucoma AUROC: 0.856 Nagelkerke's R2 (covariates regressed out): 0.02991 sex,age,age2,age*sex,age^2*sex, 20PCs
PPM009296 PSS007715|
European Ancestry|
347,396 individuals
PGP000262 |
Wang Y et al. medRxiv (2021)
|Pre
Reported Trait: Primary open-angle glaucoma AUROC: 0.777 Nagelkerke's R2 (covariates regressed out): 0.03209 sex,age,age2,age*sex,age^2*sex, 20PCs

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
PSS007704
[
  • 49 cases
  • , 7,737 controls
]
Asian unspecified Central and South Asian UKB
PSS007715
[
  • 1,266 cases
  • , 346,129 controls
]
European UKB