Polygenic Score (PGS) ID: PGS001409

Predicted Trait
Reported Trait Intra-ocular pressure, corneal-compensated (L)
Mapped Trait(s) intraocular pressure measurement (EFO_0004695)
Additional Trait Information https://biobankengine.stanford.edu/RIVAS_HG19/snpnet/INI5262
Released in PGS Catalog: Nov. 25, 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_INI5262
Development Method
Name snpnet
Parameters NR
Variants
Original Genome Build GRCh37
Number of Variants 1,166
Effect Weight Type NR
PGS Source
PGS Catalog Publication (PGP) ID PGP000244
Citation (link to publication) Tanigawa Y et al. medRxiv (2021) Preprint
Ancestry Distribution
Score Development/Training
European: 100%
65,123 individuals (100%)
PGS Evaluation
European: 40%
African: 20%
East Asian: 20%
South Asian: 20%
5 Sample Sets

Development Samples

Score Development/Training
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
65,123 individuals European white British ancestry UKB Training + validation cohort (train_val)

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
PPM007200 PSS007456|
African Ancestry|
3,212 individuals
PGP000244 |
Tanigawa Y et al. medRxiv (2021)
|Pre
Reported Trait: Intra-ocular pressure, corneal-compensated (L) : 0.03733 [0.02829, 0.04637]
Incremental R2 (full-covars): -0.00441
PGS R2 (no covariates): 0.00031 [-0.00055, 0.00117]
age, sex, UKB array type, Genotype PCs
PPM007201 PSS007457|
East Asian Ancestry|
583 individuals
PGP000244 |
Tanigawa Y et al. medRxiv (2021)
|Pre
Reported Trait: Intra-ocular pressure, corneal-compensated (L) : 0.02837 [0.01286, 0.04387]
Incremental R2 (full-covars): -0.00286
PGS R2 (no covariates): 0.00142 [-0.00215, 0.00498]
age, sex, UKB array type, Genotype PCs
PPM007202 PSS007458|
European Ancestry|
7,806 individuals
PGP000244 |
Tanigawa Y et al. medRxiv (2021)
|Pre
Reported Trait: Intra-ocular pressure, corneal-compensated (L) : 0.0336 [0.0292, 0.038]
Incremental R2 (full-covars): 0.00913
PGS R2 (no covariates): 0.00923 [0.00687, 0.01159]
age, sex, UKB array type, Genotype PCs
PPM007203 PSS007459|
South Asian Ancestry|
3,565 individuals
PGP000244 |
Tanigawa Y et al. medRxiv (2021)
|Pre
Reported Trait: Intra-ocular pressure, corneal-compensated (L) : 0.03369 [0.02583, 0.04154]
Incremental R2 (full-covars): 0.01088
PGS R2 (no covariates): 0.01113 [0.00651, 0.01575]
age, sex, UKB array type, Genotype PCs
PPM007204 PSS007460|
European Ancestry|
16,274 individuals
PGP000244 |
Tanigawa Y et al. medRxiv (2021)
|Pre
Reported Trait: Intra-ocular pressure, corneal-compensated (L) : 0.03668 [0.03389, 0.03946]
Incremental R2 (full-covars): 0.01496
PGS R2 (no covariates): 0.01568 [0.01382, 0.01754]
age, sex, UKB array type, Genotype PCs

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
PSS007456 3,212 individuals African unspecified UKB
PSS007457 583 individuals East Asian UKB
PSS007458 7,806 individuals European non-white British ancestry UKB
PSS007459 3,565 individuals South Asian UKB
PSS007460 16,274 individuals European white British ancestry UKB Testing cohort (heldout set)