Polygenic Score (PGS) ID: PGS001381

Predicted Trait
Reported Trait Corneal hysteresis (R)
Mapped Trait(s) corneal hysteresis (EFO_0010066)
Additional Trait Information https://biobankengine.stanford.edu/RIVAS_HG19/snpnet/INI5256
Released in PGS Catalog: Nov. 25, 2021
Download Score FTP directory
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_INI5256
Development Method
Name snpnet
Parameters NR
Variants
Original Genome Build GRCh37
Number of Variants 2,500
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
PPM007190 PSS007446|
African Ancestry|
3,254 individuals
PGP000244 |
Tanigawa Y et al. medRxiv (2021)
|Pre
Reported Trait: Corneal hysteresis (R) : 0.01474 [0.00893, 0.02056]
Incremental R2 (full-covars): 0.00536
PGS R2 (no covariates): 0.0069 [0.00289, 0.01091]
age, sex, UKB array type, Genotype PCs
PPM007191 PSS007447|
East Asian Ancestry|
590 individuals
PGP000244 |
Tanigawa Y et al. medRxiv (2021)
|Pre
Reported Trait: Corneal hysteresis (R) : 0.04046 [0.02217, 0.05875]
Incremental R2 (full-covars): 0.01724
PGS R2 (no covariates): 0.0202 [0.007, 0.03339]
age, sex, UKB array type, Genotype PCs
PPM007192 PSS007448|
European Ancestry|
7,821 individuals
PGP000244 |
Tanigawa Y et al. medRxiv (2021)
|Pre
Reported Trait: Corneal hysteresis (R) : 0.05427 [0.0488, 0.05974]
Incremental R2 (full-covars): 0.03632
PGS R2 (no covariates): 0.03841 [0.03373, 0.04309]
age, sex, UKB array type, Genotype PCs
PPM007193 PSS007449|
South Asian Ancestry|
3,610 individuals
PGP000244 |
Tanigawa Y et al. medRxiv (2021)
|Pre
Reported Trait: Corneal hysteresis (R) : 0.01868 [0.01274, 0.02462]
Incremental R2 (full-covars): 0.01038
PGS R2 (no covariates): 0.01133 [0.00667, 0.01599]
age, sex, UKB array type, Genotype PCs
PPM007194 PSS007450|
European Ancestry|
16,290 individuals
PGP000244 |
Tanigawa Y et al. medRxiv (2021)
|Pre
Reported Trait: Corneal hysteresis (R) : 0.05727 [0.05386, 0.06067]
Incremental R2 (full-covars): 0.03743
PGS R2 (no covariates): 0.03774 [0.03492, 0.04056]
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
PSS007446 3,254 individuals African unspecified UKB
PSS007447 590 individuals East Asian UKB
PSS007448 7,821 individuals European non-white British ancestry UKB
PSS007449 3,610 individuals South Asian UKB
PSS007450 16,290 individuals European white British ancestry UKB Testing cohort (heldout set)