Polygenic Score (PGS) ID: PGS001797

Predicted Trait
Reported Trait Primary open-angle glaucoma
Mapped Trait(s) open-angle glaucoma (EFO_0004190)
Released in PGS Catalog: Sept. 8, 2022
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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 1kgeur_gbmi_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 885,417
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: 78.9%
East Asian: 18.1%
African: 1.8%
Additional Asian Ancestries: 0.6%
Additional Diverse Ancestries: 0.6%
1,487,447 individuals (100%)
PGS Evaluation
European: 100%
1 Sample Sets

Development Samples

Source of Variant Associations (GWAS)
Study Identifiers Sample Numbers Sample Ancestry Cohort(s)
[
  • 483 cases
  • , 26,323 controls
]
African unspecified UKB
[
  • 243 cases
  • , 9,103 controls
]
Native American BioMe
[
  • 9,715 cases
  • , 260,245 controls
]
East Asian BioMe, UCLA
[
  • 16,355 cases
  • , 1,156,550 controls
]
European BBJ, TWB, UCLA
[
  • 52 cases
  • , 8,378 controls
]
Asian unspecified 9 cohorts
  • BioVU
  • ,CCPM
  • ,EB
  • ,FinnGen
  • ,HUNT
  • ,MGBB
  • ,MGI
  • ,UCLA
  • ,UKB

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
PPM009313 PSS007695|
European Ancestry|
7,128 individuals
PGP000262 |
Wang Y et al. medRxiv (2021)
|Pre
Reported Trait: Primary open-angle glaucoma AUROC: 0.749 Nagelkerke's R2 (covariates regressed out): 0.03148 sex,age, 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
PSS007695
[
  • 224 cases
  • , 6,903 controls
]
European CanPath