Polygenic Score (PGS) ID: PGS001383

Predicted Trait
Reported Trait Corneal resistance factor (R)
Mapped Trait(s) corneal resistance factor (EFO_0010067)
Additional Trait Information https://biobankengine.stanford.edu/RIVAS_HG19/snpnet/INI5257
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_INI5257
Development Method
Name snpnet
Parameters NR
Variants
Original Genome Build GRCh37
Number of Variants 3,941
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%
19,939 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
19,939 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
PPM007195 PSS007451|
African Ancestry|
1,002 individuals
PGP000244 |
Tanigawa Y et al. medRxiv (2021)
|Pre
Reported Trait: Corneal resistance factor (R) : 0.02531 [0.01192, 0.03869]
Incremental R2 (full-covars): 0.01226
PGS R2 (no covariates): 0.0127 [0.0031, 0.02231]
age, sex, UKB array type, Genotype PCs
PPM007196 PSS007452|
East Asian Ancestry|
161 individuals
PGP000244 |
Tanigawa Y et al. medRxiv (2021)
|Pre
Reported Trait: Corneal resistance factor (R) : 0.19696 [0.13534, 0.25858]
Incremental R2 (full-covars): 0.02804
PGS R2 (no covariates): 0.02639 [-0.00095, 0.05374]
age, sex, UKB array type, Genotype PCs
PPM007197 PSS007453|
European Ancestry|
2,380 individuals
PGP000244 |
Tanigawa Y et al. medRxiv (2021)
|Pre
Reported Trait: Corneal resistance factor (R) : 0.05219 [0.04244, 0.06193]
Incremental R2 (full-covars): 0.04314
PGS R2 (no covariates): 0.0443 [0.03524, 0.05336]
age, sex, UKB array type, Genotype PCs
PPM007198 PSS007454|
South Asian Ancestry|
1,090 individuals
PGP000244 |
Tanigawa Y et al. medRxiv (2021)
|Pre
Reported Trait: Corneal resistance factor (R) : 0.03596 [0.02131, 0.05061]
Incremental R2 (full-covars): 0.02434
PGS R2 (no covariates): 0.02524 [0.01283, 0.03765]
age, sex, UKB array type, Genotype PCs
PPM007199 PSS007455|
European Ancestry|
5,012 individuals
PGP000244 |
Tanigawa Y et al. medRxiv (2021)
|Pre
Reported Trait: Corneal resistance factor (R) : 0.07286 [0.06607, 0.07966]
Incremental R2 (full-covars): 0.06589
PGS R2 (no covariates): 0.06647 [0.05993, 0.073]
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
PSS007452 161 individuals East Asian UKB
PSS007453 2,380 individuals European non-white British ancestry UKB
PSS007454 1,090 individuals South Asian UKB
PSS007455 5,012 individuals European white British ancestry UKB Testing cohort (heldout set)
PSS007451 1,002 individuals African unspecified UKB