Polygenic Score (PGS) ID: PGS001410

Predicted Trait
Reported Trait Intra-ocular pressure, corneal-compensated (R)
Mapped Trait(s) intraocular pressure measurement (EFO_0004695)
Additional Trait Information https://biobankengine.stanford.edu/RIVAS_HG19/snpnet/INI5254
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_INI5254
Development Method
Name snpnet
Parameters NR
Variants
Original Genome Build GRCh37
Number of Variants 1,563
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%
65,229 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
65,229 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
PPM007185 PSS007436|
African Ancestry|
3,254 individuals
PGP000244 |
Tanigawa Y et al. medRxiv (2021)
|Pre
Reported Trait: Intra-ocular pressure, corneal-compensated (R) : 0.03133 [0.023, 0.03967]
Incremental R2 (full-covars): 0.00371
PGS R2 (no covariates): 0.00454 [0.00128, 0.0078]
age, sex, UKB array type, Genotype PCs
PPM007186 PSS007437|
East Asian Ancestry|
590 individuals
PGP000244 |
Tanigawa Y et al. medRxiv (2021)
|Pre
Reported Trait: Intra-ocular pressure, corneal-compensated (R) : 0.03676 [0.01926, 0.05426]
Incremental R2 (full-covars): 0.00553
PGS R2 (no covariates): 0.00565 [-0.00143, 0.01274]
age, sex, UKB array type, Genotype PCs
PPM007187 PSS007438|
European Ancestry|
7,821 individuals
PGP000244 |
Tanigawa Y et al. medRxiv (2021)
|Pre
Reported Trait: Intra-ocular pressure, corneal-compensated (R) : 0.02457 [0.02077, 0.02837]
Incremental R2 (full-covars): 0.00774
PGS R2 (no covariates): 0.0075 [0.00536, 0.00963]
age, sex, UKB array type, Genotype PCs
PPM007188 PSS007439|
South Asian Ancestry|
3,610 individuals
PGP000244 |
Tanigawa Y et al. medRxiv (2021)
|Pre
Reported Trait: Intra-ocular pressure, corneal-compensated (R) : 0.02885 [0.02155, 0.03616]
Incremental R2 (full-covars): 0.01476
PGS R2 (no covariates): 0.01471 [0.00942, 0.02]
age, sex, UKB array type, Genotype PCs
PPM007189 PSS007440|
European Ancestry|
16,290 individuals
PGP000244 |
Tanigawa Y et al. medRxiv (2021)
|Pre
Reported Trait: Intra-ocular pressure, corneal-compensated (R) : 0.037 [0.0342, 0.03979]
Incremental R2 (full-covars): 0.01657
PGS R2 (no covariates): 0.01663 [0.01471, 0.01854]
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
PSS007436 3,254 individuals African unspecified UKB
PSS007437 590 individuals East Asian UKB
PSS007438 7,821 individuals European non-white British ancestry UKB
PSS007439 3,610 individuals South Asian UKB
PSS007440 16,290 individuals European white British ancestry UKB Testing cohort (heldout set)